The impact of overdiagnosis on the selection of efficient lung cancer screening strategies.

PubMed

Han, Summer S; Ten Haaf, Kevin; Hazelton, William D; Munshi, Vidit N; Jeon, Jihyoun; Erdogan, Saadet A; Johanson, Colden; McMahon, Pamela M; Meza, Rafael; Kong, Chung Yin; Feuer, Eric J; de Koning, Harry J; Plevritis, Sylvia K

2017-06-01

The U.S. Preventive Services Task Force (USPSTF) recently updated their national lung screening guidelines and recommended low-dose computed tomography (LDCT) for lung cancer (LC) screening through age 80. However, the risk of overdiagnosis among older populations is a concern. Using four comparative models from the Cancer Intervention and Surveillance Modeling Network, we evaluate the overdiagnosis of the screening program recommended by USPSTF in the U.S. 1950 birth cohort. We estimate the number of LC deaths averted by screening (D) per overdiagnosed case (O), yielding the ratio D/O, to quantify the trade-off between the harms and benefits of LDCT. We analyze 576 hypothetical screening strategies that vary by age, smoking, and screening frequency and evaluate efficient screening strategies that maximize the D/O ratio and other metrics including D and life-years gained (LYG) per overdiagnosed case. The estimated D/O ratio for the USPSTF screening program is 2.85 (model range: 1.5-4.5) in the 1950 birth cohort, implying LDCT can prevent ∼3 LC deaths per overdiagnosed case. This D/O ratio increases by 22% when the program stops screening at an earlier age 75 instead of 80. Efficiency frontier analysis shows that while the most efficient screening strategies that maximize the mortality reduction (D) irrespective of overdiagnosis screen through age 80, screening strategies that stop at age 75 versus 80 produce greater efficiency in increasing life-years gained per overdiagnosed case. Given the risk of overdiagnosis with LC screening, the stopping age of screening merits further consideration when balancing benefits and harms. © 2017 UICC.

Circling motion and screen edges as an alternative input method for on-screen target manipulation.

PubMed

Ka, Hyun W; Simpson, Richard C

2017-04-01

To investigate a new alternative interaction method, called circling interface, for manipulating on-screen objects. To specify a target, the user makes a circling motion around the target. To specify a desired pointing command with the circling interface, each edge of the screen is used. The user selects a command before circling the target. To evaluate the circling interface, we conducted an experiment with 16 participants, comparing the performance on pointing tasks with different combinations of selection method (circling interface, physical mouse and dwelling interface) and input device (normal computer mouse, head pointer and joystick mouse emulator). A circling interface is compatible with many types of pointing devices, not requiring physical activation of mouse buttons, and is more efficient than dwell-clicking. Across all common pointing operations, the circling interface had a tendency to produce faster performance with a head-mounted mouse emulator than with a joystick mouse. The performance accuracy of the circling interface outperformed the dwelling interface. It was demonstrated that the circling interface has the potential as another alternative pointing method for selecting and manipulating objects in a graphical user interface. Implications for Rehabilitation A circling interface will improve clinical practice by providing an alternative pointing method that does not require physically activating mouse buttons and is more efficient than dwell-clicking. The Circling interface can also work with AAC devices.

Efficient screening of environmental isolates for Saccharomyces cerevisiae strains that are suitable for brewing.

PubMed

Fujihara, Hidehiko; Hino, Mika; Takashita, Hideharu; Kajiwara, Yasuhiro; Okamoto, Keiko; Furukawa, Kensuke

2014-01-01

We developed an efficient screening method for Saccharomyces cerevisiae strains from environmental isolates. MultiPlex PCR was performed targeting four brewing S. cerevisiae genes (SSU1, AWA1, BIO6, and FLO1). At least three genes among the four were amplified from all S. cerevisiae strains. The use of this method allowed us to successfully obtain S. cerevisiae strains.

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.

An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings

NASA Astrophysics Data System (ADS)

Maffucci, Irene; Hu, Xiao; Fumagalli, Valentina; Contini, Alessandro

2018-03-01

Nwat-MMGBSA is a variant of MM-PB/GBSA based on the inclusion of a number of explicit water molecules that are the closest to the ligand in each frame of a molecular dynamics trajectory. This method demonstrated improved correlations between calculated and experimental binding energies in both protein-protein interactions and ligand-receptor complexes, in comparison to the standard MM-GBSA. A protocol optimization, aimed to maximize efficacy and efficiency, is discussed here considering penicillopepsin, HIV1-protease, and BCL-XL as test cases. Calculations were performed in triplicates on both classic HPC environments and on standard workstations equipped by a GPU card, evidencing no statistical differences in the results. No relevant differences in correlation to experiments were also observed when performing Nwat-MMGBSA calculations on 4 ns or 1 ns long trajectories. A fully automatic workflow for structure-based virtual screening, performing from library set-up to docking and Nwat-MMGBSA rescoring, has then been developed. The protocol has been tested against no rescoring or standard MM-GBSA rescoring within a retrospective virtual screening of inhibitors of AmpC β-lactamase and of the Rac1-Tiam1 protein-protein interaction. In both cases, Nwat-MMGBSA rescoring provided a statistically significant increase in the ROC AUCs of between 20% and 30%, compared to docking scoring or to standard MM-GBSA rescoring.

Efficient high-throughput biological process characterization: Definitive screening design with the ambr250 bioreactor system.

PubMed

Tai, Mitchell; Ly, Amanda; Leung, Inne; Nayar, Gautam

2015-01-01

The burgeoning pipeline for new biologic drugs has increased the need for high-throughput process characterization to efficiently use process development resources. Breakthroughs in highly automated and parallelized upstream process development have led to technologies such as the 250-mL automated mini bioreactor (ambr250™) system. Furthermore, developments in modern design of experiments (DoE) have promoted the use of definitive screening design (DSD) as an efficient method to combine factor screening and characterization. Here we utilize the 24-bioreactor ambr250™ system with 10-factor DSD to demonstrate a systematic experimental workflow to efficiently characterize an Escherichia coli (E. coli) fermentation process for recombinant protein production. The generated process model is further validated by laboratory-scale experiments and shows how the strategy is useful for quality by design (QbD) approaches to control strategies for late-stage characterization. © 2015 American Institute of Chemical Engineers.

High-efficiency screen-printed belt co-fired solar cells on cast multicrystalline silicon

NASA Astrophysics Data System (ADS)

Upadhyaya, Ajay; Sheoran, Manav; Rohatgi, Ajeet

2005-01-01

High-efficiency 4cm2 untextured screen-printed solar cells were achieved on cast multicrystalline silicon. These cells were fabricated using a simple manufacturable process involving POCl3 diffusion for emitter, PECVD SiNx:H deposition for a single-layer antireflection coating and rapid co-firing of Ag grid, Al backcontact, and Al-BSF in a belt furnace. An optimized process sequence contributed to effective impurity gettering and defect passivation, resulting in high average bulk lifetimes in the range of 100-250 μs after the cell processing. The contact firing contributed to good ohmic contacts with low series resistance of <1Ωcm2, low backsurface recombination velocity of <500cm/s, and high fill factors of ˜0.78. These parameters resulted in 16.9% and 16.8% efficient untextured screen-printed cells with a single layer AR coating on heat exchanger method (HEM) and Baysix mc-Si. The identical process applied to the untextured float zone wafers gave an efficiency of 17.2%. The same optimized co-firing cycle, when applied to HEM mc-Si wafers with starting lifetimes varying over a wide range of 4-70 μs, resulted in cell efficiencies in the range of 16.5%-17%.

Visual detection technique for efficient screening and isolation of Salmonella based on a novel enrichment assay using chromatography membrane.

PubMed

Tang, F; Xiong, Y; Zhang, H; Wu, K; Xiang, Y; Shao, J-B; Ai, H-W; Xiang, Y-P; Zheng, X-L; Lv, J-R; Sun, H; Bao, L-S; Zhang, Z; Hu, H-B; Zhang, J-Y; Chen, L; Lu, J; Liu, W-Y; Mei, H; Ma, Y; Xu, C-F; Fang, A-Y; Gu, M; Xu, C-Y; Chen, Y; Chen, Z; Sun, Z-Y

2016-03-01

To detect Salmonella more efficiently and isolate strains more easily, a novel and simple detection method that uses an enrichment assay and two chromogenic reactions on a chromatography membrane was developed. Grade 3 chromatography paper is used as functionalized solid phase support (SPS), which contains specially optimized medium. One reaction for screening is based on the sulfate-reducing capacity of Salmonella. Hydrogen sulfide (H2S) generated by Salmonella reacts with ammonium ferric citrate to produce black colored ferrous sulfide. Another reaction is based on Salmonella C8 esterase that is unique for Enterobacteriaceae except Serratia and interacts with 4-methylumbelliferyl caprylate (MUCAP) to produce fluorescent umbelliferone, which is visible under ultraviolet light. A very low detection limit (10(1) CFU ml(-1)) for Salmonella was achieved on the background of 10(5) CFU ml(-1) Escherichia coli. More importantly, testing with more than 1,000 anal samples indicated that our method has a high positive detection rate and is relatively low cost, compared with the traditional culture-based method. It took only 1 day for the preliminary screening and 2 days to efficiently isolate the Salmonella cells, indicating that the new assay is specific, rapid, and simple for Salmonella detection. In contrast to the traditional culture-based method, this method can be easily used to screen and isolate targeted strains with the naked eye. The results of quantitative and comparative experiments showed that the visual detection technique is an efficient alternative method for the screening of Salmonella spp. in many applications of large-sized samples related to public health surveillance.

Evaluation of hydrate-screening methods.

PubMed

Cui, Yong; Yao, Erica

2008-07-01

The purpose of this work is to evaluate the effectiveness and reliability of several common hydrate-screening techniques, and to provide guidelines for designing hydrate-screening programs for new drug candidates. Ten hydrate-forming compounds were selected as model compounds and six hydrate-screening approaches were applied to these compounds in an effort to generate their hydrate forms. The results prove that no screening approach is universally effective in finding hydrates for small organic compounds. Rather, a combination of different methods should be used to improve screening reliability. Among the approaches tested, the dynamic water vapor sorption/desorption isotherm (DVI) method and storage under high humidity (HH) yielded 60-70% success ratios, the lowest among all techniques studied. The risk of false negatives arises in particular for nonhygroscopic compounds. On the other hand, both slurry in water (Slurry) and temperature cycling of aqueous suspension (TCS) showed high success rates (90%) with some exceptions. The mixed solvent systems (MSS) procedure also achieved high success rates (90%), and was found to be more suitable for water-insoluble compounds. For water-soluble compounds, MSS may not be the best approach because recrystallization is difficult in solutions with high water activity. Finally, vapor diffusion (VD) yielded a reasonably high success ratio in finding hydrates (80%). However, this method suffers from experimental difficulty and unreliable results for either highly water-soluble or water-insoluble compounds. This study indicates that a reliable hydrate-screening strategy should take into consideration the solubility and hygroscopicity of the compounds studied. A combination of the Slurry or TCS method with the MSS procedure could provide a screening strategy with reasonable reliability.

High-throughput screening with nanoimprinting 3D culture for efficient drug development by mimicking the tumor environment.

PubMed

Yoshii, Yukie; Furukawa, Takako; Waki, Atsuo; Okuyama, Hiroaki; Inoue, Masahiro; Itoh, Manabu; Zhang, Ming-Rong; Wakizaka, Hidekatsu; Sogawa, Chizuru; Kiyono, Yasushi; Yoshii, Hiroshi; Fujibayashi, Yasuhisa; Saga, Tsuneo

2015-05-01

Anti-cancer drug development typically utilizes high-throughput screening with two-dimensional (2D) cell culture. However, 2D culture induces cellular characteristics different from tumors in vivo, resulting in inefficient drug development. Here, we report an innovative high-throughput screening system using nanoimprinting 3D culture to simulate in vivo conditions, thereby facilitating efficient drug development. We demonstrated that cell line-based nanoimprinting 3D screening can more efficiently select drugs that effectively inhibit cancer growth in vivo as compared to 2D culture. Metabolic responses after treatment were assessed using positron emission tomography (PET) probes, and revealed similar characteristics between the 3D spheroids and in vivo tumors. Further, we developed an advanced method to adopt cancer cells from patient tumor tissues for high-throughput drug screening with nanoimprinting 3D culture, which we termed Cancer tissue-Originated Uniformed Spheroid Assay (COUSA). This system identified drugs that were effective in xenografts of the original patient tumors. Nanoimprinting 3D spheroids showed low permeability and formation of hypoxic regions inside, similar to in vivo tumors. Collectively, the nanoimprinting 3D culture provides easy-handling high-throughput drug screening system, which allows for efficient drug development by mimicking the tumor environment. The COUSA system could be a useful platform for drug development with patient cancer cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

The accuracy and efficiency of electronic screening for recruitment into a clinical trial on COPD.

PubMed

Schmickl, Christopher N; Li, Man; Li, Guangxi; Wetzstein, Marnie M; Herasevich, Vitaly; Gajic, Ognjen; Benzo, Roberto P

2011-10-01

Participant recruitment is an important process in successful conduct of randomized controlled trials. To facilitate enrollment into a National Institutes of Health-sponsored clinical trial involving patients with chronic obstructive pulmonary disease (COPD), we developed and prospectively validated an automated electronic screening tool based on boolean free-text search of admission notes in electronic medical records. During a 2-week validation period, all patients admitted to prespecified general medical services were screened for eligibility by both the electronic screening tool and a COPD nurse. Group discussion was the gold standard for confirmation of true-positive results. Compared with the gold standard, electronic screening yielded 100% sensitivity, 92% specificity, 100% negative predictive value, and 72% positive predictive value. Compared with traditional manual screening, electronic screening demonstrated time-saving potential of 76%. Thus, the electronic screening tool accurately identifies potential study subjects and improves efficiency of patient accrual for a clinical trial on COPD. This method may be expanded into other institutional and clinical settings. Copyright © 2011 Elsevier Ltd. All rights reserved.

LANL seismic screening method for existing buildings

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 andmore » 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.« less

Efficient screening method for determination of polycyclic aromatic hydrocarbons (PAHs) in airborne particles. Application in real samples of Santiago-Chile metropolitan urban area

NASA Astrophysics Data System (ADS)

Romero, Rodrigo; Sienra, Rosario; Richter, Pablo

A rapid analytical approach for determination of polycyclic aromatic hydrocarbons (PAHs) present in real samples of particulate matter (PM10 filters) was investigated, based on the use of water under sub critical conditions, and the subsequent determination by GC-MS (SIM). The method avoids the use of large volumes of organic solvents as dichloromethane, toluene or other unhealthy liquid organic mixtures which are normally used in time-consuming conventional sample preparation methods. By using leaching times <1 h, the method allows determination of PAHs in the range of ng/m 3 (detection limits between 0.05 and 0.2 ng/m 3 for 1458 m 3 of sampled air) with a precision expressed as RSD between 5.6% and 11.2%. The main idea behind this approach is to raise the temperature and pressure of water inside a miniaturized laboratory-made extraction unit and to decrease its dielectric constant from 80 to nearly 20. This effect allows an increase in the solubility of low polarity hydrocarbons such as PAHs. In this way, an extraction step of a few minutes can be sufficient for a quantitative extraction of airborne particles collected in high volume PM10 samplers. Parameters such as: extraction flow, static or dynamic extraction times and water volume were optimized by using a standard reference material. Technical details are given and a comparison using real samples is made between the conventional Soxhlet extraction method and the proposed approach. The proposed approach can be used as a quantitative method to characterize low molecular PAHs and simultaneously as a screening method for high molecular weight PAHs, because the recoveries are not quantitative for molecular weights over 202. In the specific case of the Santiago metropolitan area, due to the frequent occurrence of particulate matter during high pollution episodes, this approach was applied as an efficient short-time screening method for urban PAHs. Application of this screening method is recommended especially

Achieving shared efficiencies through cooperative implementation : commercial vehicle electronic screening

DOT National Transportation Integrated Search

1999-01-01

This brochure discusses how electronic screening of commercial vehicles can aid both state agencies and motor carriers. Benefits include: enhancing enforcement, increasing operations efficiency reducing pollution levels, promoting economic viability ...

Achieving shared efficiencies through cooperative implementation : commercial vehicle electronic screening

DOT National Transportation Integrated Search

1999-01-01

This brochure discusses how electronic screening of commercial vehicles can aid both state agencies and motor carriers. Benefits include: enhancing enforcement, increasing operations efficiency reducing pollution levels, promotes economic viability a...

42 CFR 455.452 - Other State screening methods.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 4 2013-10-01 2013-10-01 false Other State screening methods. 455.452 Section 455....452 Other State screening methods. Nothing in this subpart must restrict the State Medicaid agency from establishing provider screening methods in addition to or more stringent than those required by...

42 CFR 455.452 - Other State screening methods.

Code of Federal Regulations, 2011 CFR

2011-10-01

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

A Digital PCR-Based Method for Efficient and Highly Specific Screening of Genome Edited Cells

PubMed Central

Berman, Jennifer R.; Postovit, Lynne-Marie

2016-01-01

The rapid adoption of gene editing tools such as CRISPRs and TALENs for research and eventually therapeutics necessitates assays that can rapidly detect and quantitate the desired alterations. Currently, the most commonly used assay employs “mismatch nucleases” T7E1 or “Surveyor” that recognize and cleave heteroduplexed DNA amplicons containing mismatched base-pairs. However, this assay is prone to false positives due to cancer-associated mutations and/or SNPs and requires large amounts of starting material. Here we describe a powerful alternative wherein droplet digital PCR (ddPCR) can be used to decipher homozygous from heterozygous mutations with superior levels of both precision and sensitivity. We use this assay to detect knockout inducing alterations to stem cell associated proteins, NODAL and SFRP1, generated using either TALENs or an “all-in-one” CRISPR/Cas plasmid that we have modified for one-step cloning and blue/white screening of transformants. Moreover, we highlight how ddPCR can be used to assess the efficiency of varying TALEN-based strategies. Collectively, this work highlights how ddPCR-based screening can be paired with CRISPR and TALEN technologies to enable sensitive, specific, and streamlined approaches to gene editing and validation. PMID:27089539

Efficient screening for COPD using three steps: a cross-sectional study in Mexico City.

PubMed

Franco-Marina, Francisco; Fernandez-Plata, Rosario; Torre-Bouscoulet, Luis; García-Sancho, Cecilia; Sanchez-Gallen, Elisa; Martinez, David; Perez-Padilla, Rogelio

2014-05-20

Underdiagnosis of chronic obstructive pulmonary disease (COPD) in primary care can be improved by a more efficient screening strategy. To evaluate a three-step method of screening for COPD consisting of an initial short questionnaire followed by measurement of forced expiratory volume in 1s/forced expiratory volume in 6s (FEV1/FEV6) using an inexpensive pocket spirometer in those with high risk, and diagnostic quality spirometry in those with a low FEV1/FEV6. We analysed two related Mexico City cross-sectional samples. The 2003 Mexico City PLATINO survey (n=542) was used to develop a short questionnaire to determine the risk of COPD and a 2010 survey (n=737) additionally used a pocket spirometer. The discriminatory power of the two instruments was assessed with receiver operator characteristic (ROC) curves using three COPD definitions. The developed COPD scale included two variables from a simple questionnaire and, in ROC analysis, an area under the curve (AUC) between 0.64 and 0.77 was found to detect COPD. The pocket spirometer had an AUC between 0.85 and 0.88 to detect COPD. Using the COPD scale as a first screening step excluded 35-48% of the total population from further testing at the cost of not detecting 8-18% of those with COPD. Using the pocket spirometer and sending those with a FEV1/FEV6<0.80 for diagnostic quality spirometry is very efficient, and substantially improved the positive predictive value at the cost of not detecting one-third of COPD cases. A three-step screening strategy for COPD substantially reduces the need for spirometry testing when only a COPD scale is used for screening.

Screening of groundwater remedial alternatives for brownfield sites: a comprehensive method integrated MCDA with numerical simulation.

PubMed

Li, Wei; Zhang, Min; Wang, Mingyu; Han, Zhantao; Liu, Jiankai; Chen, Zhezhou; Liu, Bo; Yan, Yan; Liu, Zhu

2018-06-01

Brownfield sites pollution and remediation is an urgent environmental issue worldwide. The screening and assessment of remedial alternatives is especially complex owing to its multiple criteria that involves technique, economy, and policy. To help the decision-makers selecting the remedial alternatives efficiently, the criteria framework conducted by the U.S. EPA is improved and a comprehensive method that integrates multiple criteria decision analysis (MCDA) with numerical simulation is conducted in this paper. The criteria framework is modified and classified into three categories: qualitative, semi-quantitative, and quantitative criteria, MCDA method, AHP-PROMETHEE (analytical hierarchy process-preference ranking organization method for enrichment evaluation) is used to determine the priority ranking of the remedial alternatives and the solute transport simulation is conducted to assess the remedial efficiency. A case study was present to demonstrate the screening method in a brownfield site in Cangzhou, northern China. The results show that the systematic method provides a reliable way to quantify the priority of the remedial alternatives.

An efficient and rapid transgenic pollen screening and detection method using flow cytometry.

PubMed

Moon, Hong S; Eda, Shigetoshi; Saxton, Arnold M; Ow, David W; Stewart, C Neal

2011-01-01

Assaying for transgenic pollen, a major vector of transgene flow, provides valuable information and essential data for the study of gene flow and assessing the effectiveness of transgene containment. Most studies have employed microscopic screening methods or progeny analyses to estimate the frequency of transgenic pollen. However, these methods are time-consuming and laborious when large numbers of pollen grains must be analyzed to look for rare transgenic pollen grains. Thus, there is an urgent need for the development of a simple, rapid, and high throughput analysis method for transgenic pollen analysis. In this study, our objective was to determine the accuracy of using flow cytometry technology for transgenic pollen quantification in practical application where transgenic pollen is not frequent. A suspension of non-transgenic tobacco pollen was spiked with a known amount of verified transgenic tobacco pollen synthesizing low or high amounts of green fluorescent protein (GFP). The flow cytometric method detected approximately 75% and 100% of pollen grains synthesizing low and high amounts of GFP, respectively. The method is rapid, as it is able to count 5000 pollen grains per minute-long run. Our data indicate that this flow cytometric method is useful to study gene flow and assessment of transgene containment.

Optical efficiency of solar concentrators by a reverse optical path method.

PubMed

Parretta, A; Antonini, A; Milan, E; Stefancich, M; Martinelli, G; Armani, M

2008-09-15

A method for the optical characterization of a solar concentrator, based on the reverse illumination by a Lambertian source and measurement of intensity of light projected on a far screen, has been developed. It is shown that the projected light intensity is simply correlated to the angle-resolved efficiency of a concentrator, conventionally obtained by a direct illumination procedure. The method has been applied by simulating simple reflective nonimaging and Fresnel lens concentrators.

Hierarchical screening for multiple mental disorders.

PubMed

Batterham, Philip J; Calear, Alison L; Sunderland, Matthew; Carragher, Natacha; Christensen, Helen; Mackinnon, Andrew J

2013-10-01

There is a need for brief, accurate screening when assessing multiple mental disorders. Two-stage hierarchical screening, consisting of brief pre-screening followed by a battery of disorder-specific scales for those who meet diagnostic criteria, may increase the efficiency of screening without sacrificing precision. This study tested whether more efficient screening could be gained using two-stage hierarchical screening than by administering multiple separate tests. Two Australian adult samples (N=1990) with high rates of psychopathology were recruited using Facebook advertising to examine four methods of hierarchical screening for four mental disorders: major depressive disorder, generalised anxiety disorder, panic disorder and social phobia. Using K6 scores to determine whether full screening was required did not increase screening efficiency. However, pre-screening based on two decision tree approaches or item gating led to considerable reductions in the mean number of items presented per disorder screened, with estimated item reductions of up to 54%. The sensitivity of these hierarchical methods approached 100% relative to the full screening battery. Further testing of the hierarchical screening approach based on clinical criteria and in other samples is warranted. The results demonstrate that a two-phase hierarchical approach to screening multiple mental disorders leads to considerable increases efficiency gains without reducing accuracy. Screening programs should take advantage of prescreeners based on gating items or decision trees to reduce the burden on respondents. © 2013 Elsevier B.V. All rights reserved.

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

PubMed

Lee, Seong-Hun

2014-11-01

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

[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.

Evaluation of Nurses' Acceptance of Screen Display Methods with Temporarily Non-Display for Privacy Protection.

PubMed

Niimi, Yukari; Ota, Katsumasa; Ikegami, Chikako

2018-01-01

The purpose of this study was to explore nurses' acceptance of a screen display method that temporarily hides patient information for privacy protection. Using a questionnaire, we asked nurses to evaluate the display method from the viewpoints of safety and efficiency with respect to 22 personal information items. The nurses were favorably interested in introducing the display method into their hospital system; however, their acceptance varied.

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

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

Invert biopanning: A novel method for efficient and rapid isolation of scFvs by phage display technology.

PubMed

Rahbarnia, Leila; Farajnia, Safar; Babaei, Hossein; Majidi, Jafar; Veisi, Kamal; Tanomand, Asghar; Akbari, Bahman

2016-11-01

Phage display is a prominent screening technique for development of novel high affinity antibodies against almost any antigen. However, removing false positive clones in screening process remains a challenge. The aim of this study was to develop an efficient and rapid method for isolation of high affinity scFvs by removing NSBs without losing rare specific clones. Therefore, a novel two rounds strategy called invert biopanning was developed for isolating high affinity scFvs against EGFRvIII antigen from human scFv library. The efficiency of invert biopanning method (procedure III) was analyzed by comparing with results of conventional biopanning methods (procedures I and II). According to the results of polyclonal ELISA, the second round of procedure III displayed highest binding affinity against EGFRvIII peptide accompanied by lowest NSB comparing to other two procedures. Several positive clones were identified among output phages of procedure III by monoclonal phage ELISA which displayed high affinity to EGFRvIII antigen. In conclusion, results of our study indicate that invert biopanning is an efficient method for avoiding NSBs and conservation of rare specific clones during screening of a scFv phage library. Novel anti EGFRvIII scFv isolated could be a promising candidate for potential use in treatment of EGFRvIII expressing cancers. Copyright © 2016 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

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

Screen printed silver top electrode for efficient inverted organic solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Junwoo; Duraisamy, Navaneethan; Lee, Taik-Min

2015-10-15

Highlights: • Screen printing of silver pattern. • X-ray diffraction pattern confirmed the face centered cubic structure of silver. • Uniform surface morphology of silver pattern with sheet resistance of 0.06 Ω/sq. • The power conversion efficiency of fabricated solar cell is found to be 2.58%. - Abstract: The present work is mainly focused on replacement of the vacuum process for top electrode fabrication in organic solar cells. Silver top electrode deposited through solution based screen printing on pre-deposited polymeric thin film. The solution based printing technology provides uniform top electrode without damaging the underlying organic layers. The surface crystallinitymore » and surface morphology of silver top electrode are examined through X-ray diffraction, field-emission scanning electron microscope and atomic force microscope. The purity of silver is examined through X-ray energy dispersive spectroscopy. The top electrode exhibits face centered cubic structure with homogeneous morphology. The sheet resistance of top electrode is found to be 0.06 Ω/sq and an average pattern thickness of ∼15 μm. The power conversion efficiency is 2.58%. Our work demonstrates that the solution based screen printing is a significant role in the replacement of vacuum process for the fabrication of top electrode in organic solar cells.« less

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…

Efficient exploration of chemical space by fragment-based screening.

PubMed

Hall, Richard J; Mortenson, Paul N; Murray, Christopher W

2014-01-01

Screening methods seek to sample a vast chemical space in order to identify starting points for further chemical optimisation. Fragment based drug discovery exploits the superior sampling of chemical space that can be achieved when the molecular weight is restricted. Here we show that commercially available fragment space is still relatively poorly sampled and argue for highly sensitive screening methods to allow the detection of smaller fragments. We analyse the properties of our fragment library versus the properties of X-ray hits derived from the library. We particularly consider properties related to the degree of planarity of the fragments. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evaluation of a standard test method for screening fuels in soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

1996-12-31

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

The Efficiency of Different Salts to Screen Charge Interactions in Proteins: A Hofmeister Effect?

PubMed Central

Perez-Jimenez, Raul; Godoy-Ruiz, Raquel; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

2004-01-01

Understanding the screening by salts of charge-charge interactions in proteins is important for at least two reasons: a), screening by intracellular salt concentration may modulate the stability and interactions of proteins in vivo; and b), the in vitro experimental estimation of the contributions from charge-charge interactions to molecular processes involving proteins is generally carried out on the basis of the salt effect on process energetics, under the assumption that these interactions are screened out by moderate salt concentrations. Here, we explore experimentally the extent to which the screening efficiency depends on the nature of the salt. To this end, we have carried out an energetic characterization of the effect of NaCl (a nondenaturing salt), guanidinium chloride (a denaturing salt), and guanidinium thiocyanate (a stronger denaturant) on the stability of the wild-type form and a T14K variant of Escherichia coli thioredoxin. Our results suggest that the efficiency of different salts to screen charge-charge interactions correlates with their denaturing strength and with the position of the constituent ions in the Hofmeister rankings. This result appears consistent with the plausible relation of the Hofmeister rankings with the extent of solute accumulation/exclusion from protein surfaces. PMID:15041679

Automation to improve efficiency of field expedient injury prediction screening.

PubMed

Teyhen, Deydre S; Shaffer, Scott W; Umlauf, Jon A; Akerman, Raymond J; Canada, John B; Butler, Robert J; Goffar, Stephen L; Walker, Michael J; Kiesel, Kyle B; Plisky, Phillip J

2012-07-01

Musculoskeletal injuries are a primary source of disability in the U.S. Military. Physical training and sports-related activities account for up to 90% of all injuries, and 80% of these injuries are considered overuse in nature. As a result, there is a need to develop an evidence-based musculoskeletal screen that can assist with injury prevention. The purpose of this study was to assess the capability of an automated system to improve the efficiency of field expedient tests that may help predict injury risk and provide corrective strategies for deficits identified. The field expedient tests include survey questions and measures of movement quality, balance, trunk stability, power, mobility, and foot structure and mobility. Data entry for these tests was automated using handheld computers, barcode scanning, and netbook computers. An automated algorithm for injury risk stratification and mitigation techniques was run on a server computer. Without automation support, subjects were assessed in 84.5 ± 9.1 minutes per subject compared with 66.8 ± 6.1 minutes per subject with automation and 47.1 ± 5.2 minutes per subject with automation and process improvement measures (p < 0.001). The average time to manually enter the data was 22.2 ± 7.4 minutes per subject. An additional 11.5 ± 2.5 minutes per subject was required to manually assign an intervention strategy. Automation of this injury prevention screening protocol using handheld devices and netbook computers allowed for real-time data entry and enhanced the efficiency of injury screening, risk stratification, and prescription of a risk mitigation strategy.

The Cost-Effectiveness of High-Risk Lung Cancer Screening and Drivers of Program Efficiency.

PubMed

Cressman, Sonya; Peacock, Stuart J; Tammemägi, Martin C; Evans, William K; Leighl, Natasha B; Goffin, John R; Tremblay, Alain; Liu, Geoffrey; Manos, Daria; MacEachern, Paul; Bhatia, Rick; Puksa, Serge; Nicholas, Garth; McWilliams, Annette; Mayo, John R; Yee, John; English, John C; Pataky, Reka; McPherson, Emily; Atkar-Khattra, Sukhinder; Johnston, Michael R; Schmidt, Heidi; Shepherd, Frances A; Soghrati, Kam; Amjadi, Kayvan; Burrowes, Paul; Couture, Christian; Sekhon, Harmanjatinder S; Yasufuku, Kazuhiro; Goss, Glenwood; Ionescu, Diana N; Hwang, David M; Martel, Simon; Sin, Don D; Tan, Wan C; Urbanski, Stefan; Xu, Zhaolin; Tsao, Ming-Sound; Lam, Stephen

2017-08-01

Lung cancer risk prediction models have the potential to make programs more affordable; however, the economic evidence is limited. Participants in the National Lung Cancer Screening Trial (NLST) were retrospectively identified with the risk prediction tool developed from the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. The high-risk subgroup was assessed for lung cancer incidence and demographic characteristics compared with those in the low-risk subgroup and the Pan-Canadian Early Detection of Lung Cancer Study (PanCan), which is an observational study that was high-risk-selected in Canada. A comparison of high-risk screening versus standard care was made with a decision-analytic model using data from the NLST with Canadian cost data from screening and treatment in the PanCan study. Probabilistic and deterministic sensitivity analyses were undertaken to assess uncertainty and identify drivers of program efficiency. Use of the risk prediction tool developed from the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial with a threshold set at 2% over 6 years would have reduced the number of individuals who needed to be screened in the NLST by 81%. High-risk screening participants in the NLST had more adverse demographic characteristics than their counterparts in the PanCan study. High-risk screening would cost $20,724 (in 2015 Canadian dollars) per quality-adjusted life-year gained and would be considered cost-effective at a willingness-to-pay threshold of $100,000 in Canadian dollars per quality-adjusted life-year gained with a probability of 0.62. Cost-effectiveness was driven primarily by non-lung cancer outcomes. Higher noncurative drug costs or current costs for immunotherapy and targeted therapies in the United States would render lung cancer screening a cost-saving intervention. Non-lung cancer outcomes drive screening efficiency in diverse, tobacco-exposed populations. Use of risk selection can reduce the budget impact, and

Rational Methods for the Selection of Diverse Screening Compounds

PubMed Central

Huggins, David J.; Venkitaraman, Ashok R.; Spring, David R.

2016-01-01

Traditionally a pursuit of large pharmaceutical companies, high-throughput screening assays are becoming increasingly common within academic and government laboratories. This shift has been instrumental in enabling projects that have not been commercially viable, such as chemical probe discovery and screening against high risk targets. Once an assay has been prepared and validated, it must be fed with screening compounds. Crafting a successful collection of small molecules for screening poses a significant challenge. An optimized collection will minimize false positives whilst maximizing hit rates of compounds that are amenable to lead generation and optimization. Without due consideration of the relevant protein targets and the downstream screening assays, compound filtering and selection can fail to explore the great extent of chemical diversity and eschew valuable novelty. Herein, we discuss the different factors to be considered and methods that may be employed when assembling a structurally diverse compound screening collection. Rational methods for selecting diverse chemical libraries are essential for their effective use in high-throughput screens. PMID:21261294

Virtual screening and rational drug design method using structure generation system based on 3D-QSAR and docking.

PubMed

Chen, H F; Dong, X C; Zen, B S; Gao, K; Yuan, S G; Panaye, A; Doucet, J P; Fan, B T

2003-08-01

An efficient virtual and rational drug design method is presented. It combines virtual bioactive compound generation with 3D-QSAR model and docking. Using this method, it is possible to generate a lot of highly diverse molecules and find virtual active lead compounds. The method was validated by the study of a set of anti-tumor drugs. With the constraints of pharmacophore obtained by DISCO implemented in SYBYL 6.8, 97 virtual bioactive compounds were generated, and their anti-tumor activities were predicted by CoMFA. Eight structures with high activity were selected and screened by the 3D-QSAR model. The most active generated structure was further investigated by modifying its structure in order to increase the activity. A comparative docking study with telomeric receptor was carried out, and the results showed that the generated structures could form more stable complexes with receptor than the reference compound selected from experimental data. This investigation showed that the proposed method was a feasible way for rational drug design with high screening efficiency.

Maximally efficient two-stage screening: Determining intellectual disability in Taiwanese military conscripts

PubMed Central

Chien, Chia-Chang; Huang, Shu-Fen; Lung, For-Wey

2009-01-01

Objective: The purpose of this study was to apply a two-stage screening method for the large-scale intelligence screening of military conscripts. Methods: We collected 99 conscripted soldiers whose educational levels were senior high school level or lower to be the participants. Every participant was required to take the Wisconsin Card Sorting Test (WCST) and the Wechsler Adult Intelligence Scale-Revised (WAIS-R) assessments. Results: Logistic regression analysis showed the conceptual level responses (CLR) index of the WCST was the most significant index for determining intellectual disability (ID; FIQ ≤ 84). We used the receiver operating characteristic curve to determine the optimum cut-off point of CLR. The optimum one cut-off point of CLR was 66; the two cut-off points were 49 and 66. Comparing the two-stage window screening with the two-stage positive screening, the area under the curve and the positive predictive value increased. Moreover, the cost of the two-stage window screening decreased by 59%. Conclusion: The two-stage window screening is more accurate and economical than the two-stage positive screening. Our results provide an example for the use of two-stage screening and the possibility of the WCST to replace WAIS-R in large-scale screenings for ID in the future. PMID:21197345

Cost-effectiveness analysis of colorectal cancer screening methods in Iran.

PubMed

Allameh, Zahra; Davari, Majid; Emami, Mohammad Hasan

2011-03-01

Screening can prevent colorectal cancer from becoming advanced by early detection of precancerous lesions. Cost-effectiveness analysis of colorectal cancer screening methods is highly necessary due to increased prevalence, decreased age at onset and the limited budget in Iran. Methods of screening currently available in Iran were selected. A systematic search revealed the sensitivity and specificity of each method. For this study, a model for a 20 year screening period of a population of 100,000 apparently healthy persons of ages 45-65 years in Isfahan Province was used. The cost-effectiveness of each method and the ratio of cost-effectiveness were calculated based on this model. The most and the least effective methods were CT colonography and fecal occult blood test, respectively. The highest and lowest expenditures in the governmental sector were related to fecal occult blood test and flexible sigmoidoscopy and in the private sector, to CT colonography and fecal occult blood test, respectively. The cost per cancer detected in 20 years of screening in the governmental sector was 0.28, 0.22 and 0.42 billion Rials, respectively for screening by colonoscopy, flexible sigmoidoscopy and fecal occult blood test. In the private sector, these were 1.54 (colonoscopy), 1.68 (flexible sigmoidoscopy), and 1.60 (fecal occult blood test) billion and 2.58 billion Rials for CT colonography, respectively. Although CT colonography is the most effective method, it needs a budget of 2.58 billion Rials for each screened patient. If costs in the governmental sector are considered, flexible sigmoidoscopy would be the most cost-effective method for screening the 45 - 65-year-old population in Iran.

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.

Breast cancer screening (BCS) chart: a basic and preliminary model for making screening mammography more productive and efficient.

PubMed

Poorolajal, Jalal; Akbari, Mohammad Esmaeil; Ziaee, Fatane; Karami, Manoochehr; Ghoncheh, Mahshid

2017-05-15

The breast cancer screening (BCS) chart is suggested as a basic and preliminary tool to improve efficiency of screening mammography. We conducted this case-control study in 2016 and enrolled 1422 women aged 30-75 years, including 506 women with breast cancer (cases) and 916 women without breast cancer (controls). We developed the BCS chart using a multiple logistic regression analysis. We combined the risks of breast cancer to predict the individual risk of breast cancer. Then, we stratified and colored the predicted risk probabilities as follows: <05% (green), 05-09% (yellow), 10-14% (orange), 15-19% (red), 20-24% (brown) and ≥25% (black). The BCS chart provides the risk probability of breast cancer, based on age, body mass index, late menopause, having a benign breast disease and a positive family history of breast cancer among the first-degree or the second/third-degree relatives. According to this chart, an individual can be classified in a category of low risk (green), medium risk (yellow and orange), high risk (red and brown) and very high risk (black) for breast cancer. This chart is a flexible and easy to use tool that can detect high-risk subjects and make the screening program more efficient and productive. © The Author 2017. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Electroformed screens with uniform hole size

NASA Technical Reports Server (NTRS)

Schaer, G. R.

1968-01-01

Efficient method electroforms fine-mesh nickel screens, or plagues, with uniform hole size and accurate spacing between holes. An electroformed nickel mandrel has nonconducting silicone rubber projections that duplicate the desired hole size and shape in the finished nickel screen.

Advancement of Analysis Method for Electromagnetic Screening Effect of Mountain Tunnel

NASA Astrophysics Data System (ADS)

Okutani, Tamio; Nakamura, Nobuyuki; Terada, Natsuki; Fukuda, Mitsuyoshi; Tate, Yutaka; Inada, Satoshi; Itoh, Hidenori; Wakao, Shinji

In this paper we report advancement of an analysis method for electromagnetic screening effect of mountain tunnel with a multiple conductor circuit model. On A.C. electrified railways it is a great issue to manage the influence of electromagnetic induction caused by feeding circuits. Tunnels are said to have a screening effect to reduce the electromagnetic induction because a large amount of steel is used in the tunnels. But recently the screening effect is less expected because New Austrian Tunneling Method (NATM), in which the amount of steel used is less than in conventional methods, is adopted as the standard tunneling method for constructing mountain tunnels. So we measured and analyzed the actual screening effect of mountain tunnels constructed with NATM. In the process of the analysis we have advanced a method to analyze the screening effect more precisely. In this method we can adequately model tunnel structure as a part of multiple conductor circuit.

A simple and efficient method to visualize and quantify the efficiency of chromosomal mutations from genome editing

PubMed Central

Fu, Liezhen; Wen, Luan; Luu, Nga; Shi, Yun-Bo

2016-01-01

Genome editing with designer nucleases such as TALEN and CRISPR/Cas enzymes has broad applications. Delivery of these designer nucleases into organisms induces various genetic mutations including deletions, insertions and nucleotide substitutions. Characterizing those mutations is critical for evaluating the efficacy and specificity of targeted genome editing. While a number of methods have been developed to identify the mutations, none other than sequencing allows the identification of the most desired mutations, i.e., out-of-frame insertions/deletions that disrupt genes. Here we report a simple and efficient method to visualize and quantify the efficiency of genomic mutations induced by genome-editing. Our approach is based on the expression of a two-color fusion protein in a vector that allows the insertion of the edited region in the genome in between the two color moieties. We show that our approach not only easily identifies developing animals with desired mutations but also efficiently quantifies the mutation rate in vivo. Furthermore, by using LacZα and GFP as the color moieties, our approach can even eliminate the need for a fluorescent microscope, allowing the analysis with simple bright field visualization. Such an approach will greatly simplify the screen for effective genome-editing enzymes and identify the desired mutant cells/animals. PMID:27748423

Advantages of Crystallographic Fragment Screening: Functional and Mechanistic Insights from a Powerful Platform for Efficient Drug Discovery

PubMed Central

Patel, Disha; Bauman, Joseph D.; Arnold, Eddy

2015-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this “chemical interrogation” of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. PMID:25117499

Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery.

PubMed

Patel, Disha; Bauman, Joseph D; Arnold, Eddy

2014-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. Copyright © 2014. Published by Elsevier Ltd.

Equity and practice issues in colorectal cancer screening: Mixed-methods study.

PubMed

Buchman, Sandy; Rozmovits, Linda; Glazier, Richard H

2016-04-01

To investigate overall colorectal cancer (CRC) screening rates, patterns in the use of types of CRC screening, and sociodemographic characteristics associated with CRC screening; and to gain insight into physicians' perceptions about and use of fecal occult blood testing [FOBT] and colonoscopy for patients at average risk of CRC. Mixed-methods study using cross-sectional administrative data on patient sociodemographic characteristics and semistructured telephone interviews with physicians. Toronto, Ont. Patients aged 50 to 74 years and physicians in family health teams in the Toronto Central Local Health Integration Network. Rates of CRC screening by type; sociodemographic characteristics associated with CRC screening; thematic analysis using constant comparative method for semistructured interviews. Ontario administrative data on CRC screening showed lower overall screening rates among those who were younger, male patients, those who had lower income, and recent immigrants. Colonoscopy rates were especially low among those with lower income and those who were recent immigrants. Semistructured interviews revealed that physician opinions about CRC screening for average-risk patients were divided: one group of physicians accepted the evidence and recommendations for FOBT and the other group of physicians strongly supported colonoscopy for these patients, believing that the FOBT was an inferior screening method. Physicians identified specialist recommendations and patient expectations as factors that influenced their decisions regarding CRC screening type. There was considerable variation in CRC screening by sociodemographic characteristics. A key theme that emerged from the interviews was that physicians were divided in their preference for FOBT or colonoscopy; factors that influenced physician preference included the health care system, recommendations by other specialists, and patient characteristics. Providing an informed choice of screening method to patients

Parallel production and verification of protein products using a novel high-throughput screening method.

PubMed

Tegel, Hanna; Yderland, Louise; Boström, Tove; Eriksson, Cecilia; Ukkonen, Kaisa; Vasala, Antti; Neubauer, Peter; Ottosson, Jenny; Hober, Sophia

2011-08-01

Protein production and analysis in a parallel fashion is today applied in laboratories worldwide and there is a great need to improve the techniques and systems used for this purpose. In order to save time and money, a fast and reliable screening method for analysis of protein production and also verification of the protein product is desired. Here, a micro-scale protocol for the parallel production and screening of 96 proteins in plate format is described. Protein capture was achieved using immobilized metal affinity chromatography and the product was verified using matrix-assisted laser desorption ionization time-of-flight MS. In order to obtain sufficiently high cell densities and product yield in the small-volume cultivations, the EnBase® cultivation technology was applied, which enables cultivation in as small volumes as 150 μL. Here, the efficiency of the method is demonstrated by producing 96 human, recombinant proteins, both in micro-scale and using a standard full-scale protocol and comparing the results in regard to both protein identity and sample purity. The results obtained are highly comparable to those acquired through employing standard full-scale purification protocols, thus validating this method as a successful initial screening step before protein production at a larger scale. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Eliciting women's cervical screening preferences: a mixed methods systematic review protocol.

PubMed

Wood, Brianne; Van Katwyk, Susan Rogers; El-Khatib, Ziad; McFaul, Susan; Taljaard, Monica; Wright, Erica; Graham, Ian D; Little, Julian

2016-08-11

With the accumulation of evidence regarding potential harms of cancer screening in recent years, researchers, policy-makers, and the public are becoming more critical of population-based cancer screening. Consequently, a high-quality cancer screening program should consider individuals' values and preferences when determining recommendations. In cervical cancer screening, offering women autonomy is considered a "person-centered" approach to health care services; however, it may impact the effectiveness of the program should women choose to not participate. As part of a larger project to investigate women's cervical screening preferences and correlates of these preferences, this systematic review will capture quantitative and qualitative investigations of women's cervical screening preferences and the methods used to elicit them. This mixed methods synthesis will use a thematic analysis approach to synthesize qualitative, quantitative, and mixed methods evidence. This protocol describes the methods that will be used in this investigation. A search strategy has been developed with a health librarian and peer reviewed using PRESS. Based on this strategy, five databases and the gray literature will be searched for studies that meet the inclusion criteria. The quality of the included individual studies will be examined using the Mixed Methods Appraisal Tool. Three reviewers will extract data from the primary studies on the tools or instruments used to elicit women's preferences regarding cervical cancer screening, theoretical frameworks used, outcomes measured, the outstanding themes from quantitative and qualitative evidence, and the identified preferences for cervical cancer screening. We will describe the relationships between study results and the study population, "intervention" (e.g., tool or instrument), and context. We will follow the PRISMA reporting guideline. We will compare findings across studies and between study methods (e.g., qualitative versus

From molecular engineering to process engineering: development of high-throughput screening methods in enzyme directed evolution.

PubMed

Ye, Lidan; Yang, Chengcheng; Yu, Hongwei

2018-01-01

With increasing concerns in sustainable development, biocatalysis has been recognized as a competitive alternative to traditional chemical routes in the past decades. As nature's biocatalysts, enzymes are able to catalyze a broad range of chemical transformations, not only with mild reaction conditions but also with high activity and selectivity. However, the insufficient activity or enantioselectivity of natural enzymes toward non-natural substrates limits their industrial application, while directed evolution provides a potent solution to this problem, thanks to its independence on detailed knowledge about the relationship between sequence, structure, and mechanism/function of the enzymes. A proper high-throughput screening (HTS) method is the key to successful and efficient directed evolution. In recent years, huge varieties of HTS methods have been developed for rapid evaluation of mutant libraries, ranging from in vitro screening to in vivo selection, from indicator addition to multi-enzyme system construction, and from plate screening to computation- or machine-assisted screening. Recently, there is a tendency to integrate directed evolution with metabolic engineering in biosynthesis, using metabolites as HTS indicators, which implies that directed evolution has transformed from molecular engineering to process engineering. This paper aims to provide an overview of HTS methods categorized based on the reaction principles or types by summarizing related studies published in recent years including the work from our group, to discuss assay design strategies and typical examples of HTS methods, and to share our understanding on HTS method development for directed evolution of enzymes involved in specific catalytic reactions or metabolic pathways.

Diagnostic methods for platelet bacteria screening: current status and developments.

PubMed

Störmer, Melanie; Vollmer, Tanja

2014-02-01

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

Diagnostic Methods for Platelet Bacteria Screening: Current Status and Developments

PubMed Central

Störmer, Melanie; Vollmer, Tanja

2014-01-01

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

4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening

PubMed Central

2011-01-01

Background The performance of 3D-based virtual screening similarity functions is affected by the applied conformations of compounds. Therefore, the results of 3D approaches are often less robust than 2D approaches. The application of 3D methods on multiple conformer data sets normally reduces this weakness, but entails a significant computational overhead. Therefore, we developed a special conformational space encoding by means of Gaussian mixture models and a similarity function that operates on these models. The application of a model-based encoding allows an efficient comparison of the conformational space of compounds. Results Comparisons of our 4D flexible atom-pair approach with over 15 state-of-the-art 2D- and 3D-based virtual screening similarity functions on the 40 data sets of the Directory of Useful Decoys show a robust performance of our approach. Even 3D-based approaches that operate on multiple conformers yield inferior results. The 4D flexible atom-pair method achieves an averaged AUC value of 0.78 on the filtered Directory of Useful Decoys data sets. The best 2D- and 3D-based approaches of this study yield an AUC value of 0.74 and 0.72, respectively. As a result, the 4D flexible atom-pair approach achieves an average rank of 1.25 with respect to 15 other state-of-the-art similarity functions and four different evaluation metrics. Conclusions Our 4D method yields a robust performance on 40 pharmaceutically relevant targets. The conformational space encoding enables an efficient comparison of the conformational space. Therefore, the weakness of the 3D-based approaches on single conformations is circumvented. With over 100,000 similarity calculations on a single desktop CPU, the utilization of the 4D flexible atom-pair in real-world applications is feasible. PMID:21733172

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

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-30

... Screening and Testing Methods AGENCY: Consumer Product Safety Commission. ACTION: Notice. SUMMARY: The... symposium on phthalates screening and testing methods. The symposium will be held at the CPSC's National... submit comments, identified by Docket No. CPSC-2012-0008, by any of the following methods: Electronic...

High throughput screening of active pharmaceutical ingredients by UPLC.

PubMed

Al-Sayah, Mohammad A; Rizos, Panagiota; Antonucci, Vincent; Wu, Naijun

2008-07-01

Ultra performance LC (UPLC) was evaluated as an efficient screening approach to facilitate method development for drug candidates. Three stationary phases were screened: C-18, phenyl, and Shield RP 18 with column dimensions of 150 mm x 2.1 mm, 1.7 microm, which should theoretically generate 35,000 plates or 175% of the typical column plate count of a conventional 250 mm x 4.6 mm, 5 microm particle column. Thirteen different active pharmaceutical ingredients (APIs) were screened using this column set with a standardized mobile-phase gradient. The UPLC method selectivity results were compared to those obtained for these compounds via methods developed through laborious trial and error screening experiments using numerous conventional HPLC mobile and stationary phases. Peak capacity was compared for columns packed with 5 microm particles and columns packed with 1.7 microm particles. The impurities screened by UPLC were confirmed by LC/MS. The results demonstrate that simple, high efficiency UPLC gradients are a feasible and productive alternative to more conventional multiparametric chromatographic screening approaches for many compounds in the early stages of drug development.

[Staged oncological screening with TG test].

PubMed

Bakhlaev, I E; Ageenko, A I; Rolik, I S

2006-01-01

The authors present their analysis of screening methods used for early diagnostics of cancer of various localization and for detection of high-risk individuals. They offer a program of step-by-step screening that makes it possible to cover more population with prophylactic examination and to reduce the need for special examination methods. TG-test is a universal and the most informative blastomatous process indicator at any stage, including the preclinical one. The practical screening results double the revealing rate of oncopathology and allow for three-fold reduction in the diagnostic costs compared with standard methods of cancer diagnostics. The medical efficiency of the oncological screening is high; in one third of the examined patients a tumor is diagnosed at the preclinical stage.

An integrated high resolution mass spectrometric data acquisition method for rapid screening of saponins in Panax notoginseng (Sanqi).

PubMed

Lai, Chang-Jiang-Sheng; Tan, Ting; Zeng, Su-Ling; Qi, Lian-Wen; Liu, Xin-Guang; Dong, Xin; Li, Ping; Liu, E-Hu

2015-05-10

The aim of this study was to develop a convenient method without pretreatments for nontarget discovery of interested compounds. The segment and exposure strategy, coupled with two mass spectrometer data acquisition methods was firstly proposed for screening the saponins in extract of Panax notoginseng (Sanqi) via high-performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry (HPLC-QTOF/MS). By gradually removing certain major or moderate interference compounds, the developed segment and exposure strategy could significantly improve the detection efficiency for trace compounds. Moreover, the newly developed five-point screening approach based on a modified mass defect filter strategy and the visual isotopic ion technique was verified to be efficient and reliable in picking out the interested precursor ions. In total, 234 ginsenosides including 67 potential new ones were characterized or tentatively identified from the extract of Sanqi. Particularly, some unusual compounds containing the branched glycosyl group or new substituted acyl groups were firstly reported. The proposed integrated strategy held a strong promise for analyses of the complex mixtures. Copyright © 2015 Elsevier B.V. All rights reserved.

The novel measuring method for screening and assessing chromium content in clothes and shoes materials

NASA Astrophysics Data System (ADS)

Salerno-Kochan, R.

2017-10-01

The aim of this paper is to propose the bioindicative measuring method for screening and assessing the safety of textile and leather materials in relation to chemical threats. This method is based on toxicological assay in which Tetrahymena pyriformis, unicellular organism belonging to protozoans, is used as a test organism. For the realization of the research goal the sensitivity threshold of test organisms to chromium(VI) solutions was identified. The changes in cell development of test organisms in chromium solutions were registered by colorimetric measurements in the presence of alamarBlue® cell viability reagent. Empirical data enabled to fit logistic curves on the base of which the level of chromium toxicity was estimated. In the second step, harmfulness of aqueous extracts obtained from textile and leather samples containing chromium in relation to test organisms was evaluated. The performed research confirmed the high efficiency of the proposed method in screening and assessing chromium content in clothes and shoes materials and showed possibilities of using it in safety assessment of products with regard to chemical risks.

Evaluation of Dried Urine Spot Method to Screen Cotinine among Tobacco Dependents: An Exploratory Study.

PubMed

Jain, Raka; Quraishi, Rizwana; Verma, Arpita

2017-01-01

Assessment of cotinine, a metabolite of nicotine in body fluids, is an important approach for validating the self-report among tobacco users. Adaptation of assays on dried urine spots (DUSs) has advantages of ease of collection, transportation, minimal invasiveness, and requirement of small volume. The aim of the present study was to develop an efficient method for testing cotinine in DUSs and evaluating its clinical applicability. This involved optimization of conditions for detection, recovery, and stability of cotinine from dried urine, spotted on filter paper. Enzyme-linked immunosorbent assay was used for screening, whereas confirmation was done by gas chromatography. For clinical applicability, urine samples of tobacco users were tested. Water was found to be a suitable extracting solvent as compared to carbonate-bicarbonate buffer (pH 9.2) and saline. Screening was achieved by two punches taken from a 20 μl (diameter 1.3 cm) spotted urine samples, and confirmation was achieved by five complete circles each of 20 μl sample volume. The recovery was found to be 97% in water. Limit of detection for the method was found to be 100 ng/ml. No signs of significant degradation were found under all storage conditions. All the urine samples of tobacco users were found to be positive by a conventional method as well as DUSs, and the method proved to be efficient. DUS samples are a useful alternative for biological monitoring of recent nicotine use, especially in developing countries where sample logistics could be an important concern.

Projection screen having reduced ambient light scattering

DOEpatents

Sweatt, William C [Albuquerque, NM

2010-05-11

An apparatus and method for improving the contrast between incident projected light and ambient light reflected from a projection screen are described. The efficiency of the projection screen for reflection of the projected light remains high, while permitting the projection screen to be utilized in a brightly lighted room. Light power requirements from the projection system utilized may be reduced.

Rapid automated method for screening of enteric pathogens from stool specimens.

PubMed Central

Villasante, P A; Agulla, A; Merino, F J; Pérez, T; Ladrón de Guevara, C; Velasco, A C

1987-01-01

A total of 800 colonies suggestive of Salmonella, Shigella, or Yersinia species isolated on stool differential agar media were inoculated onto both conventional biochemical test media (triple sugar iron agar, urea agar, and phenylalanine agar) and Entero Pathogen Screen cards of the AutoMicrobic system (Vitek Systems, Inc., Hazelwood, Mo.). Based on the conventional tests, the AutoMicrobic system method yielded the following results: 587 true-negatives, 185 true-positives, 2 false-negatives, and 26 false-positives (sensitivity, 99%; specificity, 96%). Both true-positive and true-negative results were achieved considerably earlier than false results (P less than 0.001). The Entero Pathogen Screen card method is a fast, easy, and sensitive method for screening for Salmonella, Shigella, or Yersinia species. The impossibility of screening for oxidase-positive pathogens is a minor disadvantage of this method. PMID:3553230

Quantitative methylene blue decolourisation assays as rapid screening tools for assessing the efficiency of catalytic reactions.

PubMed

Kruid, Jan; Fogel, Ronen; Limson, Janice Leigh

2017-05-01

Identifying the most efficient oxidation process to achieve maximum removal of a target pollutant compound forms the subject of much research. There exists a need to develop rapid screening tools to support research in this area. In this work we report on the development of a quantitative assay as a means for identifying catalysts capable of decolourising methylene blue through the generation of oxidising species from hydrogen peroxide. Here, a previously described methylene blue test strip method was repurposed as a quantitative, aqueous-based spectrophotometric assay. From amongst a selection of metal salts and metallophthalocyanine complexes, monitoring of the decolourisation of the cationic dye methylene blue (via Fenton-like and non-Fenton oxidation reactions) by the assay identified the following to be suitable oxidation catalysts: CuSO 4 (a Fenton-like catalyst), iron(II)phthalocyanine (a non-Fenton oxidation catalyst), as well as manganese(II) phthalocyanine. The applicability of the method was examined for the removal of bisphenol A (BPA), as measured by HPLC, during parallel oxidation experiments. The order of catalytic activity was identified as FePc > MnPc > CuSO 4 for both BPA and MB. The quantitative MB decolourisation assay may offer a rapid method for screening a wide range of potential catalysts for oxidation processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diagnostic methods of TSH in thyroid screening tests.

PubMed

Matyjaszek-Matuszek, Beata; Pyzik, Aleksandra; Nowakowski, Andrzej; Jarosz, Mirosław J

2013-01-01

Reliable and quick thyreologic diagnostics, as well as verification of the effectiveness of the therapy undertaken, is of great importance for the state of health of society. The measurement of plasma TSH is the commonly accepted and most sensitive screening test for primary thyroid disorders, which are the most frequent diseases related to the endocrine glands. At present, the available methods for the determination of TSH are characterized by high sensitivity ≤0.01 µIU/ml and lack of cross-reactivity. However, many drugs and substances, as well as pathological conditions, may affect the TSH level. evaluation of contemporary laboratory methods for the determination of TSH and the principles of interpretation of screening tests. In many countries, the TSH test is the only test performed in the diagnostics of thyroid function; nevertheless, it seems that for genuine and objective assessment of thyroid status the TSH level, together with FT4 level, should be absolutely determined, which allows the differentiation and assessment of the intensity of thyroid function disorders and foresee its consequences. The interpretation of TSH results in screening tests is different in such population groups as: children aged under 14, pregnant women, the elderly, and patients with non-thyroidal illnesses. From among currently used laboratory methods for determination of TSH levels, third generation non-isotopic methods are most frequently recommended, especially the method of immunochemiluminescence.

Screening-Level Ecological Risk Assessment Methods, Revision 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mirenda, Richard J.

2012-08-16

This document provides guidance for screening-level assessments of potential adverse impacts to ecological resources from release of environmental contaminants at the Los Alamos National Laboratory (LANL or the Laboratory). The methods presented are based on two objectives, namely: to provide a basis for reaching consensus with regulators, managers, and other interested parties on how to conduct screening-level ecological risk investigations at the Laboratory; and to provide guidance for ecological risk assessors under the Environmental Programs (EP) Directorate. This guidance promotes consistency, rigor, and defensibility in ecological screening investigations and in reporting those investigation results. The purpose of the screening assessmentmore » is to provide information to the risk managers so informed riskmanagement decisions can be made. This document provides examples of recommendations and possible risk-management strategies.« less

Restriction digest screening facilitates efficient detection of site-directed mutations introduced by CRISPR in C. albicans UME6

PubMed Central

Evans, Ben A.; Smith, Olivia L.; Pickerill, Ethan S.; York, Mary K.; Buenconsejo, Kristen J.P.; Chambers, Antonio E.

2018-01-01

Introduction of point mutations to a gene of interest is a powerful tool when determining protein function. CRISPR-mediated genome editing allows for more efficient transfer of a desired mutation into a wide range of model organisms. Traditionally, PCR amplification and DNA sequencing is used to determine if isolates contain the intended mutation. However, mutation efficiency is highly variable, potentially making sequencing costly and time consuming. To more efficiently screen for correct transformants, we have identified restriction enzymes sites that encode for two identical amino acids or one or two stop codons. We used CRISPR to introduce these restriction sites directly upstream of the Candida albicans UME6 Zn2+-binding domain, a known regulator of C. albicans filamentation. While repair templates coding for different restriction sites were not equally successful at introducing mutations, restriction digest screening enabled us to rapidly identify isolates with the intended mutation in a cost-efficient manner. In addition, mutated isolates have clear defects in filamentation and virulence compared to wild type C. albicans. Our data suggest restriction digestion screening efficiently identifies point mutations introduced by CRISPR and streamlines the process of identifying residues important for a phenotype of interest. PMID:29892505

Restriction digest screening facilitates efficient detection of site-directed mutations introduced by CRISPR in C. albicans UME6.

PubMed

Evans, Ben A; Smith, Olivia L; Pickerill, Ethan S; York, Mary K; Buenconsejo, Kristen J P; Chambers, Antonio E; Bernstein, Douglas A

2018-01-01

Introduction of point mutations to a gene of interest is a powerful tool when determining protein function. CRISPR-mediated genome editing allows for more efficient transfer of a desired mutation into a wide range of model organisms. Traditionally, PCR amplification and DNA sequencing is used to determine if isolates contain the intended mutation. However, mutation efficiency is highly variable, potentially making sequencing costly and time consuming. To more efficiently screen for correct transformants, we have identified restriction enzymes sites that encode for two identical amino acids or one or two stop codons. We used CRISPR to introduce these restriction sites directly upstream of the Candida albicans UME6 Zn 2+ -binding domain, a known regulator of C. albicans filamentation. While repair templates coding for different restriction sites were not equally successful at introducing mutations, restriction digest screening enabled us to rapidly identify isolates with the intended mutation in a cost-efficient manner. In addition, mutated isolates have clear defects in filamentation and virulence compared to wild type C. albicans . Our data suggest restriction digestion screening efficiently identifies point mutations introduced by CRISPR and streamlines the process of identifying residues important for a phenotype of interest.

Maximally efficient two-stage screening: Determining intellectual disability in Taiwanese military conscripts.

PubMed

Chien, Chia-Chang; Huang, Shu-Fen; Lung, For-Wey

2009-01-27

The purpose of this study was to apply a two-stage screening method for the large-scale intelligence screening of military conscripts. We collected 99 conscripted soldiers whose educational levels were senior high school level or lower to be the participants. Every participant was required to take the Wisconsin Card Sorting Test (WCST) and the Wechsler Adult Intelligence Scale-Revised (WAIS-R) assessments. Logistic regression analysis showed the conceptual level responses (CLR) index of the WCST was the most significant index for determining intellectual disability (ID; FIQ ≤ 84). We used the receiver operating characteristic curve to determine the optimum cut-off point of CLR. The optimum one cut-off point of CLR was 66; the two cut-off points were 49 and 66. Comparing the two-stage window screening with the two-stage positive screening, the area under the curve and the positive predictive value increased. Moreover, the cost of the two-stage window screening decreased by 59%. The two-stage window screening is more accurate and economical than the two-stage positive screening. Our results provide an example for the use of two-stage screening and the possibility of the WCST to replace WAIS-R in large-scale screenings for ID in the future.

An efficient platform for genetic selection and screening of gene switches in Escherichia coli

PubMed Central

Muranaka, Norihito; Sharma, Vandana; Nomura, Yoko; Yokobayashi, Yohei

2009-01-01

Engineered gene switches and circuits that can sense various biochemical and physical signals, perform computation, and produce predictable outputs are expected to greatly advance our ability to program complex cellular behaviors. However, rational design of gene switches and circuits that function in living cells is challenging due to the complex intracellular milieu. Consequently, most successful designs of gene switches and circuits have relied, to some extent, on high-throughput screening and/or selection from combinatorial libraries of gene switch and circuit variants. In this study, we describe a generic and efficient platform for selection and screening of gene switches and circuits in Escherichia coli from large libraries. The single-gene dual selection marker tetA was translationally fused to green fluorescent protein (gfpuv) via a flexible peptide linker and used as a dual selection and screening marker for laboratory evolution of gene switches. Single-cycle (sequential positive and negative selections) enrichment efficiencies of >7000 were observed in mock selections of model libraries containing functional riboswitches in liquid culture. The technique was applied to optimize various parameters affecting the selection outcome, and to isolate novel thiamine pyrophosphate riboswitches from a complex library. Artificial riboswitches with excellent characteristics were isolated that exhibit up to 58-fold activation as measured by fluorescent reporter gene assay. PMID:19190095

Shape-Based Virtual Screening with Volumetric Aligned Molecular Shapes

PubMed Central

Koes, David Ryan; Camacho, Carlos J.

2014-01-01

Shape-based virtual screening is an established and effective method for identifying small molecules that are similar in shape and function to a reference ligand. We describe a new method of shape-based virtual screening, volumetric aligned molecular shapes (VAMS). VAMS uses efficient data structures to encode and search molecular shapes. We demonstrate that VAMS is an effective method for shape-based virtual screening and that it can be successfully used as a pre-filter to accelerate more computationally demanding search algorithms. Unique to VAMS is a novel minimum/maximum shape constraint query for precisely specifying the desired molecular shape. Shape constraint searches in VAMS are particularly efficient and millions of shapes can be searched in a fraction of a second. We compare the performance of VAMS with two other shape-based virtual screening algorithms a benchmark of 102 protein targets consisting of more than 32 million molecular shapes and find that VAMS provides a competitive trade-off between run-time performance and virtual screening performance. PMID:25049193

Modified microplate method for rapid and efficient estimation of siderophore produced by bacteria.

PubMed

Arora, Naveen Kumar; Verma, Maya

2017-12-01

In this study, siderophore production by various bacteria amongst the plant-growth-promoting rhizobacteria was quantified by a rapid and efficient method. In total, 23 siderophore-producing bacterial isolates/strains were taken to estimate their siderophore-producing ability by the standard method (chrome azurol sulphonate assay) as well as 96 well microplate method. Production of siderophore was estimated in percent siderophore unit by both the methods. It was observed that data obtained by both methods correlated positively with each other proving the correctness of microplate method. By the modified microplate method, siderophore production by several bacterial strains can be estimated both qualitatively and quantitatively at one go, saving time, chemicals, making it very less tedious, and also being cheaper in comparison with the method currently in use. The modified microtiter plate method as proposed here makes it far easier to screen the plant-growth-promoting character of plant-associated bacteria.

Improvement of screening methods for silicon planar semiconductor devices

NASA Technical Reports Server (NTRS)

Berger, W. M.

1972-01-01

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

Three screening methods for cognitive dysfunction using the Mini-Mental State Examination and Korean Dementia Screening Questionnaire.

PubMed

Choi, Seong Hye; Park, Moon Ho

2016-02-01

To screen for and determine cognitive dysfunction, cognitive tests and/or informant reports are commonly used. However, these cognitive tests and informant reports are not always available. The present study investigated three screening methods using the Mini-Mental State Examination (MMSE) as the cognitive test, and the Korean dementia screening questionnaire (KDSQ) as the informant report. Participants were recruited from the Korea Clinical Research Center for Dementia of South Korea, and included 2861 patients with Alzheimer's disease (dementia), 3519 patients with mild cognitive impairment and 1375 controls with no cognitive dysfunction. Three screening methods were tested: (i) MMSE alone (MMSE(cut-off) ); (ii) a conventional combination of MMSE and KDSQ (MMSE+KDSQ(cut-off) ); and (iii) a decision tree with MMSE and KDSQ (MMSE+KDSQ(decision tree) ). For discriminating any cognitive dysfunction from controls, MMSE+KDSQ(cut-off) had the highest area under the receiver operating characteristic curve (0.784). For discriminating dementia from controls, MMSE+KDSQ(cut-off) had the highest area under the receiver operating characteristic curve (0.899). For discriminating mild cognitive impairment from controls, MMSE(cut-off) had the highest area under the receiver operating characteristic curve (0.683). MMSE+KDSQ(decision tree) showed the highest sensitivity for all discriminations. For overall classification accuracy, MMSE+KDSQ(decision tree) had the highest value (70.0%). These three methods had different advantageous properties for screening and staging cognitive dysfunction. As there might be different availability across clinical settings, these three methods can be selected and used according to situational needs. © 2015 Japan Geriatrics Society.

Fragment Screening and HIV Therapeutics

PubMed Central

Bauman, Joseph D.; Patel, Disha; Arnold, Eddy

2013-01-01

Fragment screening has proven to be a powerful alternative to traditional methods for drug discovery. Biophysical methods, such as X-ray crystallography, NMR spectroscopy, and surface plasmon resonance, are used to screen a diverse library of small molecule compounds. Although compounds identified via this approach have relatively weak affinity, they provide a good platform for lead development and are highly efficient binders with respect to their size. Fragment screening has been utilized for a wide-range of targets, including HIV-1 proteins. Here, we review the fragment screening studies targeting HIV-1 proteins using X-ray crystallography or surface plasmon resonance. These studies have successfully detected binding of novel fragments to either previously established or new sites on HIV-1 protease and reverse transcriptase. In addition, fragment screening against HIV-1 reverse transcriptase has been used as a tool to better understand the complex nature of ligand binding to a flexible target. PMID:21972022

Experimental cocrystal screening and solution based scale-up cocrystallization methods.

PubMed

Malamatari, Maria; Ross, Steven A; Douroumis, Dennis; Velaga, Sitaram P

2017-08-01

Cocrystals are crystalline single phase materials composed of two or more different molecular and/or ionic compounds generally in a stoichiometric ratio which are neither solvates nor simple salts. If one of the components is an active pharmaceutical ingredient (API), the term pharmaceutical cocrystal is often used. There is a growing interest among drug development scientists in exploring cocrystals, as means to address physicochemical, biopharmaceutical and mechanical properties and expand solid form diversity of the API. Conventionally, coformers are selected based on crystal engineering principles, and the equimolar mixtures of API and coformers are subjected to solution-based crystallization that are commonly employed in polymorph and salt screening. However, the availability of new knowledge on cocrystal phase behaviour in solid state and solutions has spurred the development and implementation of more rational experimental cocrystal screening as well as scale-up methods. This review aims to provide overview of commonly employed solid form screening techniques in drug development with an emphasis on cocrystal screening methodologies. The latest developments in understanding and the use of cocrystal phase diagrams in both screening and solution based scale-up methods are also presented. Final section is devoted to reviewing the state of the art research covering solution based scale-up cocrystallization process for different cocrystals besides more recent continuous crystallization methods. Copyright © 2017 Elsevier B.V. All rights reserved.

Terbium-sensitized luminescence screening method for fluoroquinolones in beef serum

USDA-ARS?s Scientific Manuscript database

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...

A deep learning method for early screening of lung cancer

NASA Astrophysics Data System (ADS)

Zhang, Kunpeng; Jiang, Huiqin; Ma, Ling; Gao, Jianbo; Yang, Xiaopeng

2018-04-01

Lung cancer is the leading cause of cancer-related deaths among men. In this paper, we propose a pulmonary nodule detection method for early screening of lung cancer based on the improved AlexNet model. In order to maintain the same image quality as the existing B/S architecture PACS system, we convert the original CT image into JPEG format image by analyzing the DICOM file firstly. Secondly, in view of the large size and complex background of CT chest images, we design the convolution neural network on basis of AlexNet model and sparse convolution structure. At last we train our models on the software named DIGITS which is provided by NVIDIA. The main contribution of this paper is to apply the convolutional neural network for the early screening of lung cancer and improve the screening accuracy by combining the AlexNet model with the sparse convolution structure. We make a series of experiments on the chest CT images using the proposed method, of which the sensitivity and specificity indicates that the method presented in this paper can effectively improve the accuracy of early screening of lung cancer and it has certain clinical significance at the same time.

Time-resolved luminescence screening method for enrofloxacin in beef serum

USDA-ARS?s Scientific Manuscript database

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 ...

Chemical screening method for the rapid identification of microbial sources of marine invertebrate-associated metabolites.

PubMed

Berrue, Fabrice; Withers, Sydnor T; Haltli, Brad; Withers, Jo; Kerr, Russell G

2011-03-21

Marine invertebrates have proven to be a rich source of secondary metabolites. The growing recognition that marine microorganisms associated with invertebrate hosts are involved in the biosynthesis of secondary metabolites offers new alternatives for the discovery and development of marine natural products. However, the discovery of microorganisms producing secondary metabolites previously attributed to an invertebrate host poses a significant challenge. This study describes an efficient chemical screening method utilizing a 96-well plate-based bacterial cultivation strategy to identify and isolate microbial producers of marine invertebrate-associated metabolites.

A new method to address verification bias in studies of clinical screening tests: cervical cancer screening assays as an example.

PubMed

Xue, Xiaonan; Kim, Mimi Y; Castle, Philip E; Strickler, Howard D

2014-03-01

Studies to evaluate clinical screening tests often face the problem that the "gold standard" diagnostic approach is costly and/or invasive. It is therefore common to verify only a subset of negative screening tests using the gold standard method. However, undersampling the screen negatives can lead to substantial overestimation of the sensitivity and underestimation of the specificity of the diagnostic test. Our objective was to develop a simple and accurate statistical method to address this "verification bias." We developed a weighted generalized estimating equation approach to estimate, in a single model, the accuracy (eg, sensitivity/specificity) of multiple assays and simultaneously compare results between assays while addressing verification bias. This approach can be implemented using standard statistical software. Simulations were conducted to assess the proposed method. An example is provided using a cervical cancer screening trial that compared the accuracy of human papillomavirus and Pap tests, with histologic data as the gold standard. The proposed approach performed well in estimating and comparing the accuracy of multiple assays in the presence of verification bias. The proposed approach is an easy to apply and accurate method for addressing verification bias in studies of multiple screening methods. Copyright © 2014 Elsevier Inc. All rights reserved.

A time-efficient algorithm for implementing the Catmull-Clark subdivision method

NASA Astrophysics Data System (ADS)

Ioannou, G.; Savva, A.; Stylianou, V.

2015-10-01

Splines are the most popular methods in Figure Modeling and CAGD (Computer Aided Geometric Design) in generating smooth surfaces from a number of control points. The control points define the shape of a figure and splines calculate the required number of points which when displayed on a computer screen the result is a smooth surface. However, spline methods are based on a rectangular topological structure of points, i.e., a two-dimensional table of vertices, and thus cannot generate complex figures, such as the human and animal bodies that their complex structure does not allow them to be defined by a regular rectangular grid. On the other hand surface subdivision methods, which are derived by splines, generate surfaces which are defined by an arbitrary topology of control points. This is the reason that during the last fifteen years subdivision methods have taken the lead over regular spline methods in all areas of modeling in both industry and research. The cost of executing computer software developed to read control points and calculate the surface is run-time, due to the fact that the surface-structure required for handling arbitrary topological grids is very complicate. There are many software programs that have been developed related to the implementation of subdivision surfaces however, not many algorithms are documented in the literature, to support developers for writing efficient code. This paper aims to assist programmers by presenting a time-efficient algorithm for implementing subdivision splines. The Catmull-Clark which is the most popular of the subdivision methods has been employed to illustrate the algorithm.

Reverse screening methods to search for the protein targets of chemopreventive compounds

NASA Astrophysics Data System (ADS)

Huang, Hongbin; Zhang, Guigui; Zhou, Yuquan; Lin, Chenru; Chen, Suling; Lin, Yutong; Mai, Shangkang; Huang, Zunnan

2018-05-01

This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and

Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds.

PubMed

Huang, Hongbin; Zhang, Guigui; Zhou, Yuquan; Lin, Chenru; Chen, Suling; Lin, Yutong; Mai, Shangkang; Huang, Zunnan

2018-01-01

This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget, and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn

Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds

PubMed Central

Huang, Hongbin; Zhang, Guigui; Zhou, Yuquan; Lin, Chenru; Chen, Suling; Lin, Yutong; Mai, Shangkang; Huang, Zunnan

2018-01-01

This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget, and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn

The evolving role of new imaging methods in breast screening.

PubMed

Houssami, Nehmat; Ciatto, Stefano

2011-09-01

The potential to avert breast cancer deaths through screening means that efforts continue to identify methods which may enhance early detection. While the role of most new imaging technologies remains in adjunct screening or in the work-up of mammography-detected abnormalities, some of the new breast imaging tests (such as MRI) have roles in screening groups of women defined by increased cancer risk. This paper highlights the evidence and the current role of new breast imaging technologies in screening, focusing on those that have broader application in population screening, including digital mammography, breast ultrasound in women with dense breasts, and computer-aided detection. It highlights that evidence on new imaging in screening comes mostly from non-randomised studies that have quantified test detection capability as adjunct to mammography, or have compared measures of screening performance for new technologies with that of conventional mammography. Two RCTs have provided high-quality evidence on the equivalence of digital and conventional mammography and on outcomes of screen-reading complemented by CAD. Many of these imaging technologies enhance cancer detection but also increase recall and false positives in screening. Copyright © 2011 Elsevier Inc. All rights reserved.

A Screening Method for Assessing Cumulative Impacts

PubMed Central

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

2012-01-01

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

A screening method for biotinidase deficiency in newborns.

PubMed

Heard, G S; Secor McVoy, J R; Wolf, B

1984-01-01

We describe a method for neonatal screening for biotinidase (EC 3.5.1.12) deficiency. Biotinidase activity is assessed colorimetrically from dried samples of whole blood spotted on the same filter papers as used in the neonatal screening for phenylketonuria. After the reaction, samples from normal infants are characteristically purple, whereas those from affected individuals are straw-colored. To confirm the deficiency, the enzyme is quantitatively assayed in additional blood spots or serum. A pilot study has been initiated with samples obtained by the Commonwealth of Virginia for phenylketonuria testing.

Plate-based diversity subset screening: an efficient paradigm for high throughput screening of a large screening file.

PubMed

Bell, Andrew S; Bradley, Joseph; Everett, Jeremy R; Knight, Michelle; Loesel, Jens; Mathias, John; McLoughlin, David; Mills, James; Sharp, Robert E; Williams, Christine; Wood, Terence P

2013-05-01

The screening files of many large companies, including Pfizer, have grown considerably due to internal chemistry efforts, company mergers and acquisitions, external contracted synthesis, or compound purchase schemes. In order to screen the targets of interest in a cost-effective fashion, we devised an easy-to-assemble, plate-based diversity subset (PBDS) that represents almost the entire computed chemical space of the screening file whilst comprising only a fraction of the plates in the collection. In order to create this file, we developed new design principles for the quality assessment of screening plates: the Rule of 40 (Ro40) and a plate selection process that insured excellent coverage of both library chemistry and legacy chemistry space. This paper describes the rationale, design, construction, and performance of the PBDS, that has evolved into the standard paradigm for singleton (one compound per well) high-throughput screening in Pfizer since its introduction in 2006.

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.

Probe molecules (PrM) approach in adverse outcome pathway (AOP) based high throughput screening (HTS): in vivo discovery for developing in vitro target methods

EPA Science Inventory

Efficient and accurate adverse outcome pathway (AOP) based high-throughput screening (HTS) methods use a systems biology based approach to computationally model in vitro cellular and molecular data for rapid chemical prioritization; however, not all HTS assays are grounded by rel...

Compound Transfer by Acoustic Droplet Ejection Promotes Quality and Efficiency in Ultra-High-Throughput Screening Campaigns.

PubMed

Dawes, Timothy D; Turincio, Rebecca; Jones, Steven W; Rodriguez, Richard A; Gadiagellan, Dhireshan; Thana, Peter; Clark, Kevin R; Gustafson, Amy E; Orren, Linda; Liimatta, Marya; Gross, Daniel P; Maurer, Till; Beresini, Maureen H

2016-02-01

Acoustic droplet ejection (ADE) as a means of transferring library compounds has had a dramatic impact on the way in which high-throughput screening campaigns are conducted in many laboratories. Two Labcyte Echo ADE liquid handlers form the core of the compound transfer operation in our 1536-well based ultra-high-throughput screening (uHTS) system. Use of these instruments has promoted flexibility in compound formatting in addition to minimizing waste and eliminating compound carryover. We describe the use of ADE for the generation of assay-ready plates for primary screening as well as for follow-up dose-response evaluations. Custom software has enabled us to harness the information generated by the ADE instrumentation. Compound transfer via ADE also contributes to the screening process outside of the uHTS system. A second fully automated ADE-based system has been used to augment the capacity of the uHTS system as well as to permit efficient use of previously picked compound aliquots for secondary assay evaluations. Essential to the utility of ADE in the high-throughput screening process is the high quality of the resulting data. Examples of data generated at various stages of high-throughput screening campaigns are provided. Advantages and disadvantages of the use of ADE in high-throughput screening are discussed. © 2015 Society for Laboratory Automation and Screening.

Simulation optimization of PSA-threshold based prostate cancer screening policies

PubMed Central

Zhang, Jingyu; Denton, Brian T.; Shah, Nilay D.; Inman, Brant A.

2013-01-01

We describe a simulation optimization method to design PSA screening policies based on expected quality adjusted life years (QALYs). Our method integrates a simulation model in a genetic algorithm which uses a probabilistic method for selection of the best policy. We present computational results about the efficiency of our algorithm. The best policy generated by our algorithm is compared to previously recommended screening policies. Using the policies determined by our model, we present evidence that patients should be screened more aggressively but for a shorter length of time than previously published guidelines recommend. PMID:22302420

[Screening methods for mild cognitive impairment in primary care].

PubMed

Freire Pérez, Alberto

2017-06-01

Diagnosis of mild cognitive impairment (MCI) is always clinical and screening methods only indicate that the patient has a higher risk of this condition. In MCI, there is a slight decline in some cognitive abilities that does not affect activities of daily living and therefore does not produce social or occupational disability. The definitive diagnosis of MCI requires a considerable time investment that is very rarely possible to provide in primary care (PC) consultations. Hence the need for PC physicians to employ rapid and simple screening methods (brief cognitive assessment -BCA-) that allow objective identification of patients likely to have MCI in a few minutes. This article reviews the BCA tools that can truly be applied in less than 10 minutes. The phototest is a brief screening tool that is easy to use and interpret by physicians and is well accepted by patients. Consequently, it is one of the most useful tests in PC for screening of both MCI and dementia. In addition to BCA, instrumental activities of daily living scales should also be applied to differentiate MCI from dementia. Copyright © 2017 Sociedad Española de Geriatría y Gerontología. Publicado por Elsevier España, S.L.U. All rights reserved.

Anthropometric methods for obesity screening in schoolchildren: the Ouro Preto Study.

PubMed

Cándido, A P C; Alosta, J P S; Oliveira, C T; Freitas, R N; Freitas, S N; Machado-Coelho, G L L

2012-01-01

Childhood obesity is increasing dramatically in last decades. To evaluate the usefulness of body mass index (BMI), skinfold thickness (ST), waist circumference (WC), and foot-to-foot bioelectrical impedance (BIA-FF) for screening for obesity in mixed-race population, using the tetrapolar bioelectrical impedance (BIA-T) technique as reference method. A cross-sectional-based population study was performed in the city of Ouro Preto, Brazil, in 2006. Schoolchildren aged 6-15 years (n = 788) was randomly selected according to age and sex stratified by the proportion of students in each schools of the city. Nonparametric receiver operating characteristic (ROC) analysis was used to define the sensitivity and specificity for each method studied using the tetrapolar method as reference. The BMI and the BIA-FF were the most suitable for adiposity screening in pre-pubertal and pubertal stages because they present a better balance between sensitivity and specificity, and smaller misclassification. For post-pubertal boys, the BF-ST-D was the best body fat assessment method. The results suggest that BIA-FF and BMI are choice methods for obesity screening in mixed population and that the method choice for body fat screening must be done according to sexual maturity of boys and girls. The present study demonstrates the need to perform studies in wider mixed-race population to determine anthropometric parameters and to examine the predictive ability of methods and cut-offs here elucidated in the development of obesity.

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.

Immobilized OBOC combinatorial bead array to facilitate multiplicative screening.

PubMed

Xiao, Wenwu; Bononi, Fernanda C; Townsend, Jared; Li, Yuanpei; Liu, Ruiwu; Lam, Kit S

2013-07-01

One-bead-one-compound (OBOC) combinatorial library screening has been broadly utilized for the last two decades to identify small molecules, peptides or peptidomimetics targeting variable screening probes such as cell surface receptors, bacteria, protein kinases, phosphatases, proteases etc. In previous screening methods, library beads were suspended in solution and screened against one single probe. Only the positive beads were tracked and isolated for additional screens and finally selected for chemical decoding. During this process, the remaining negative beads were not tracked and discarded. Here we report a novel bead immobilization method such that a bead library array can be conveniently prepared and screened in its entirety, sequentially many times with a series of distinct probes. This method not only allows us to increase the screening efficiency but also permits us to determine the binding profile of each and every library bead against a large number of target receptors. As proof of concept, we serially screened a random OBOC disulfide containing cyclic heptapeptide library with three water soluble dyes as model probes: malachite green, bromocresol purple and indigo carmine. This multiplicative screening approach resulted in a rapid determination of the binding profile of each and every bead respective to each of the three dyes. Beads that interacted with malachite green only, bromocresol purple only, or both indigo carmine and bromocresol purple were isolated, and their peptide sequences were determined with microsequencer. Ultimately, the novel OBOC multiplicative screening approach could play a key role in the enhancement of existing on-bead assays such as whole cell binding, bacteria binding, protein binding, posttranslational modifications etc. with increased efficiency, capacity, and specificity.

An efficient screen for peroxisome-deficient mutants of Pichia pastoris.

PubMed Central

Liu, H; Tan, X; Veenhuis, M; McCollum, D; Cregg, J M

1992-01-01

We describe a rapid and efficient screen for peroxisome-deficient (per) mutants in the yeast Pichia pastoris. The screen relies on the unusual ability of P. pastoris to grow on two carbon sources, methanol and oleic acid, both of which absolutely require peroxisomes to be metabolized. A collection of 280 methanol utilization-defective (Mut-) P. pastoris mutants was isolated, organized into 46 complementation groups, and tested for those that were also oleate-utilization defective (Out-) but still capable of growth on ethanol and glucose. Mutants in 10 groups met this phenotypic description, and 8 of these were observed by electron microscopy to be peroxisome deficient (Per-). In each per mutant, Mut-, Out-, and Per- phenotypes were tightly linked and therefore were most likely due to a mutation at a single locus. Subcellular fractionation experiments indicated that the peroxisomal marker enzyme catalase was mislocalized to the cytosol in both methanol- and oleate-induced cultures of the mutants. In contrast, alcohol oxidase, a peroxisomal methanol utilization pathway enzyme, was virtually absent from per mutant cells. The relative ease of per mutant isolation in P. pastoris, in conjunction with well-developed procedures for its molecular and genetic manipulation, makes this organism an attractive system for studies on peroxisome biogenesis. Images PMID:1629154

76 FR 21673 - Alternative Efficiency Determination Methods and Alternate Rating Methods

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-18

... EERE-2011-BP-TP-00024] RIN 1904-AC46 Alternative Efficiency Determination Methods and Alternate Rating Methods AGENCY: Office of Energy Efficiency and Renewable Energy, Department of Energy. ACTION: Notice of... and data related to the use of computer simulations, mathematical methods, and other alternative...

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. Copyright © 2017 Elsevier B.V. All rights reserved.

A simple and sensitive high-throughput GFP screening in woody and herbaceous plants.

PubMed

Hily, Jean-Michel; Liu, Zongrang

2009-03-01

Green fluorescent protein (GFP) has been used widely as a powerful bioluminescent reporter, but its visualization by existing methods in tissues or whole plants and its utilization for high-throughput screening remains challenging in many species. Here, we report a fluorescence image analyzer-based method for GFP detection and its utility for high-throughput screening of transformed plants. Of three detection methods tested, the Typhoon fluorescence scanner was able to detect GFP fluorescence in all Arabidopsis thaliana tissues and apple leaves, while regular fluorescence microscopy detected it only in Arabidopsis flowers and siliques but barely in the leaves of either Arabidopsis or apple. The hand-held UV illumination method failed in all tissues of both species. Additionally, the Typhoon imager was able to detect GFP fluorescence in both green and non-green tissues of Arabidopsis seedlings as well as in imbibed seeds, qualifying it as a high-throughput screening tool, which was further demonstrated by screening the seedlings of primary transformed T(0) seeds. Of the 30,000 germinating Arabidopsis seedlings screened, at least 69 GFP-positive lines were identified, accounting for an approximately 0.23% transformation efficiency. About 14,000 seedlings grown in 16 Petri plates could be screened within an hour, making the screening process significantly more efficient and robust than any other existing high-throughput screening method for transgenic plants.

Using Decision-Analytic Modeling to Isolate Interventions That Are Feasible, Efficient and Optimal: An Application from the Norwegian Cervical Cancer Screening Program.

PubMed

Pedersen, Kine; Sørbye, Sveinung Wergeland; Burger, Emily Annika; Lönnberg, Stefan; Kristiansen, Ivar Sønbø

2015-12-01

Decision makers often need to simultaneously consider multiple criteria or outcomes when deciding whether to adopt new health interventions. Using decision analysis within the context of cervical cancer screening in Norway, we aimed to aid decision makers in identifying a subset of relevant strategies that are simultaneously efficient, feasible, and optimal. We developed an age-stratified probabilistic decision tree model following a cohort of women attending primary screening through one screening round. We enumerated detected precancers (i.e., cervical intraepithelial neoplasia of grade 2 or more severe (CIN2+)), colposcopies performed, and monetary costs associated with 10 alternative triage algorithms for women with abnormal cytology results. As efficiency metrics, we calculated incremental cost-effectiveness, and harm-benefit, ratios, defined as the additional costs, or the additional number of colposcopies, per additional CIN2+ detected. We estimated capacity requirements and uncertainty surrounding which strategy is optimal according to the decision rule, involving willingness to pay (monetary or resources consumed per added benefit). For ages 25 to 33 years, we eliminated four strategies that did not fall on either efficiency frontier, while one strategy was efficient with respect to both efficiency metrics. Compared with current practice in Norway, two strategies detected more precancers at lower monetary costs, but some required more colposcopies. Similar results were found for women aged 34 to 69 years. Improving the effectiveness and efficiency of cervical cancer screening may necessitate additional resources. Although efficient and feasible, both society and individuals must specify their willingness to accept the additional resources and perceived harms required to increase effectiveness before a strategy can be considered optimal. Copyright © 2015. Published by Elsevier Inc.

Randomized Comparison of 3 Methods to Screen for Domestic Violence in Family Practice

PubMed Central

Chen, Ping-Hsin; Rovi, Sue; Washington, Judy; Jacobs, Abbie; Vega, Marielos; Pan, Ko-Yu; Johnson, Mark S.

2007-01-01

PURPOSE We undertook a study to compare 3 ways of administering brief domestic violence screening questionnaires: self-administered questionnaire, medical staff interview, and physician interview. METHODS We conducted a randomized trial of 3 screening protocols for domestic violence in 4 urban family medicine practices with mostly minority patients. We randomly assigned 523 female patients, aged 18 years or older and currently involved with a partner, to 1 of 3 screening protocols. Each included 2 brief screening tools: HITS and WAST-Short. Outcome measures were domestic violence disclosure, patient and clinician comfort with the screening, and time spent screening. RESULTS Overall prevalence of domestic violence was 14%. Most patients (93.4%) and clinicians (84.5%) were comfortable with the screening questions and method of administering them. Average time spent screening was 4.4 minutes. Disclosure rates, patient and clinician comfort with screening, and time spent screening were similar among the 3 protocols. In addition, WAST-Short was validated in this sample of minority women by comparison with HITS and with the 8-item WAST. CONCLUSIONS Domestic violence is common, and we found that most patients and clinicians are comfortable with domestic violence screening in urban family medicine settings. Patient self-administered domestic violence screening is as effective as clinician interview in terms of disclosure, comfort, and time spent screening. PMID:17893385

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...

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.

Spectroscopic and Spectrometric Methods Used for the Screening of Certain Herbal Food Supplements Suspected of Adulteration

PubMed Central

Mateescu, Cristina; Popescu, Anca Mihaela; Radu, Gabriel Lucian; Onisei, Tatiana; Raducanu, Adina Elena

2017-01-01

Purpose: This study was carried out in order to find a reliable method for the fast detection of adulterated herbal food supplements with sexual enhancement claims. As some herbal products are advertised as "all natural", their "efficiency" is often increased by addition of active pharmaceutical ingredients such as PDE-5 inhibitors, which can be a real health threat for the consumer. Methodes: Adulterants, potentially present in 50 herbal food supplements with sexual improvement claims, were detected using 2 spectroscopic methods - Raman and Fourier Transform Infrared - known for reliability, reproductibility, and an easy sample preparation. GC-MS technique was used to confirm the potential adulterants spectra. Results: About 22% (11 out of 50 samples) of herbal food supplements with sexual enhancement claims analyzed by spectroscopic and spectrometric methods proved to be "enriched" with active pharmaceutical compounds such as: sildenafil and two of its analogues, tadalafil and phenolphthalein. The occurence of phenolphthalein could be the reason for the non-relevant results obtained by FTIR method in some samples. 91% of the adulterated herbal food supplements were originating from China. Conclusion: The results of this screening highlighted the necessity for an accurate analysis of all alleged herbal aphrodisiacs on the Romanian market. This is a first such a screening analysis carried out on herbal food supplements with sexual enhancement claims. PMID:28761827

Spectroscopic and Spectrometric Methods Used for the Screening of Certain Herbal Food Supplements Suspected of Adulteration.

PubMed

Mateescu, Cristina; Popescu, Anca Mihaela; Radu, Gabriel Lucian; Onisei, Tatiana; Raducanu, Adina Elena

2017-06-01

Purpose: This study was carried out in order to find a reliable method for the fast detection of adulterated herbal food supplements with sexual enhancement claims. As some herbal products are advertised as "all natural", their "efficiency" is often increased by addition of active pharmaceutical ingredients such as PDE-5 inhibitors, which can be a real health threat for the consumer. Methodes: Adulterants, potentially present in 50 herbal food supplements with sexual improvement claims, were detected using 2 spectroscopic methods - Raman and Fourier Transform Infrared - known for reliability, reproductibility, and an easy sample preparation. GC-MS technique was used to confirm the potential adulterants spectra. Results: About 22% (11 out of 50 samples) of herbal food supplements with sexual enhancement claims analyzed by spectroscopic and spectrometric methods proved to be "enriched" with active pharmaceutical compounds such as: sildenafil and two of its analogues, tadalafil and phenolphthalein. The occurence of phenolphthalein could be the reason for the non-relevant results obtained by FTIR method in some samples. 91% of the adulterated herbal food supplements were originating from China. Conclusion: The results of this screening highlighted the necessity for an accurate analysis of all alleged herbal aphrodisiacs on the Romanian market. This is a first such a screening analysis carried out on herbal food supplements with sexual enhancement claims.

Toward cost-efficient sampling methods

NASA Astrophysics Data System (ADS)

Luo, Peng; Li, Yongli; Wu, Chong; Zhang, Guijie

2015-09-01

The sampling method has been paid much attention in the field of complex network in general and statistical physics in particular. This paper proposes two new sampling methods based on the idea that a small part of vertices with high node degree could possess the most structure information of a complex network. The two proposed sampling methods are efficient in sampling high degree nodes so that they would be useful even if the sampling rate is low, which means cost-efficient. The first new sampling method is developed on the basis of the widely used stratified random sampling (SRS) method and the second one improves the famous snowball sampling (SBS) method. In order to demonstrate the validity and accuracy of two new sampling methods, we compare them with the existing sampling methods in three commonly used simulation networks that are scale-free network, random network, small-world network, and also in two real networks. The experimental results illustrate that the two proposed sampling methods perform much better than the existing sampling methods in terms of achieving the true network structure characteristics reflected by clustering coefficient, Bonacich centrality and average path length, especially when the sampling rate is low.

Development of an Excel-based laboratory information management system for improving workflow efficiencies in early ADME screening.

PubMed

Lu, Xinyan

2016-01-01

There is a clear requirement for enhancing laboratory information management during early absorption, distribution, metabolism and excretion (ADME) screening. The application of a commercial laboratory information management system (LIMS) is limited by complexity, insufficient flexibility, high costs and extended timelines. An improved custom in-house LIMS for ADME screening was developed using Excel. All Excel templates were generated through macros and formulae, and information flow was streamlined as much as possible. This system has been successfully applied in task generation, process control and data management, with a reduction in both labor time and human error rates. An Excel-based LIMS can provide a simple, flexible and cost/time-saving solution for improving workflow efficiencies in early ADME screening.

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.

ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis.

PubMed

Trümbach, Dietrich; Pfeiffer, Susanne; Poppe, Manuel; Scherb, Hagen; Doll, Sebastian; Wurst, Wolfgang; Schick, Joel A

2017-11-25

As CRISPR/Cas9 mediated screens with pooled guide libraries in somatic cells become increasingly established, an unmet need for rapid and accurate companion informatics tools has emerged. We have developed a lightweight and efficient software to easily manipulate large raw next generation sequencing datasets derived from such screens into informative relational context with graphical support. The advantages of the software entitled ENCoRE (Easy NGS-to-Gene CRISPR REsults) include a simple graphical workflow, platform independence, local and fast multithreaded processing, data pre-processing and gene mapping with custom library import. We demonstrate the capabilities of ENCoRE to interrogate results from a pooled CRISPR cellular viability screen following Tumor Necrosis Factor-alpha challenge. The results not only identified stereotypical players in extrinsic apoptotic signaling but two as yet uncharacterized members of the extrinsic apoptotic cascade, Smg7 and Ces2a. We further validated and characterized cell lines containing mutations in these genes against a panel of cell death stimuli and involvement in p53 signaling. In summary, this software enables bench scientists with sensitive data or without access to informatic cores to rapidly interpret results from large scale experiments resulting from pooled CRISPR/Cas9 library screens.

Nutrigenetic screening strains of the mulberry silkworm, Bombyx mori, for nutritional efficiency.

PubMed

Ramesha, Chinnaswamy; Lakshmi, Hothur; Kumari, Savarapu Sugnana; Anuradha, Chevva M; Kumar, Chitta Suresh

2012-01-01

The activity of sericulture is declining due the reduction of mulberry production area in sericulture practicing countries lead to adverse effects on silkworm rearing and cocoon production. Screening for nutrigenetic traits in silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) is an essential prerequisite for better understanding and development of nutritionally efficient breeds/hybrids, which show less food consumption with higher efficiency conversion. The aim of this study was to identify nutritionally efficient polyvoltine silkworm strains using the germplasm breeds RMW(2), RMW(3), RMW(4), RMG(3), RMG(1), RMG(4), RMG(5), RMG(6) and APM(1) as the control. The 1(st) day of 5(th) stage silkworm larvae of polyvoltine strains were subjected to standard gravimetric analysis until spinning for three consecutive generations covering 3 different seasons on 19 nutrigenetic traits. Highly significant (p ≤ 0.001) differences were found among all nutrigenetic traits of polyvoltine silkworm strains in the experimental groups. The nutritionally efficient polvoltine silkworm strains were resulted by utilizing nutrition consumption index and efficiency of conversion of ingesta/cocoon traits as the index. Higher nutritional efficiency conversions were found in the polyvoltine silkworm strains on efficiency of conversion of ingesta to cocoon and shell than control. Comparatively smaller consumption index, respiration, metabolic rate with superior relative growth rate, and quantum of food ingesta and digesta requisite per gram of cocoon and shell were found; the lowest amount was in new polyvoltine strains compared to the control. Furthermore, based on the overall nutrigenetic traits utilized as index or 'biomarkers', three polyvoltine silkworm strains (RMG(4), RMW(2), and RMW(3)) were identified as having the potential for nutrition efficiency conversion. The data from the present study advances our knowledge for the development of nutritionally efficient silkworm breeds

Nutrigenetic screening strains of the mulberry silkworm, Bombyx mori, for nutritional efficiency.

PubMed

Chinnaswamy, Ramesha; Lakshmi, Hothur; Kumari, Savarapu S; Anuradha, Chebba M; Kumar, Chitta S

2012-01-01

The activity of sericulture is declining due the reduction of mulberry production area in sericulture practicing countries lead to adverse effects on silkworm rearing and cocoon production. Screening for nutrigenetic traits in silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) is an essential prerequisite for better understanding and development of nutritionally efficient breeds/hybrids, which show less food consumption with higher efficiency conversion. The aim of this study was to identify nutritionally efficient polyvoltine silkworm strains using the germplasm breeds RMW(2), RMW(3), RMW(4), RMG(3), RMG(1), RMG(4), RMG(5), RMG(6) and APM(1) as the control. The 1(st) day of 5(th) stage silkworm larvae of polyvoltine strains were subjected to standard gravimetric analysis until spinning for three consecutive generations covering three different seasons on 19 nutrigenetic traits. Highly significant (p ≤ 0.001) differences were found among all nutrigenetic traits of polyvoltine silkworm strains in the experimental groups. The nutritionally efficient polvoltine silkworm strains were resulted by utilizing nutrition consumption index and efficiency of conversion of ingesta/cocoon traits as the index. Higher nutritional efficiency conversions were found in the polyvoltine silkworm strains on efficiency of conversion of ingesta to cocoon and shell than control. Comparatively smaller consumption index, respiration, metabolic rate with superior relative growth rate, and quantum of food ingesta and digesta requisite per gram of cocoon and shell were shown; the lowest amount was in new polyvoltine strains compared to the control. Furthermore, based on the overall nutrigenetic traits utilized as index or 'biomarkers', three polyvoltine silkworm strains (RMG(4), RMW(2), and RMW(3)) were identified as having the potential for nutrition efficiency conversion. The data from the present study advances our knowledge for the development of nutritionally efficient silkworm breeds

Nutrigenetic Screening Strains of the Mulberry Silkworm, Bombyx mori, for Nutritional Efficiency

PubMed Central

Chinnaswamy, Ramesha; Lakshmi, Hothur; Kumari, Savarapu S.; Anuradha, Chebba M.; Kumar, Chitta S.

2012-01-01

The activity of sericulture is declining due the reduction of mulberry production area in sericulture practicing countries lead to adverse effects on silkworm rearing and cocoon production. Screening for nutrigenetic traits in silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) is an essential prerequisite for better understanding and development of nutritionally efficient breeds/hybrids, which show less food consumption with higher efficiency conversion. The aim of this study was to identify nutritionally efficient polyvoltine silkworm strains using the germplasm breeds RMW2, RMW3, RMW4, RMG3, RMG1, RMG4, RMG5, RMG6 and APM1 as the control. The 1st day of 5th stage silkworm larvae of polyvoltine strains were subjected to standard gravimetric analysis until spinning for three consecutive generations covering three different seasons on 19 nutrigenetic traits. Highly significant (p ≤ 0.001) differences were found among all nutrigenetic traits of polyvoltine silkworm strains in the experimental groups. The nutritionally efficient polvoltine silkworm strains were resulted by utilizing nutrition consumption index and efficiency of conversion of ingesta/cocoon traits as the index. Higher nutritional efficiency conversions were found in the polyvoltine silkworm strains on efficiency of conversion of ingesta to cocoon and shell than control. Comparatively smaller consumption index, respiration, metabolic rate with superior relative growth rate, and quantum of food ingesta and digesta requisite per gram of cocoon and shell were shown; the lowest amount was in new polyvoltine strains compared to the control. Furthermore, based on the overall nutrigenetic traits utilized as index or ‘biomarkers’, three polyvoltine silkworm strains (RMG4, RMW2, and RMW3) were identified as having the potential for nutrition efficiency conversion. The data from the present study advances our knowledge for the development of nutritionally efficient silkworm breeds/hybrids and their

Nutrigenetic Screening Strains of the Mulberry Silkworm, Bombyx mori, for Nutritional Efficiency

PubMed Central

Ramesha, Chinnaswamy; Lakshmi, Hothur; Kumari, Savarapu Sugnana; Anuradha, Chevva M.; Kumar, Chitta Suresh

2012-01-01

The activity of sericulture is declining due the reduction of mulberry production area in sericulture practicing countries lead to adverse effects on silkworm rearing and cocoon production. Screening for nutrigenetic traits in silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) is an essential prerequisite for better understanding and development of nutritionally efficient breeds/hybrids, which show less food consumption with higher efficiency conversion. The aim of this study was to identify nutritionally efficient polyvoltine silkworm strains using the germplasm breeds RMW2, RMW3, RMW4, RMG3, RMG1, RMG4, RMG5, RMG6 and APM1 as the control. The 1st day of 5th stage silkworm larvae of polyvoltine strains were subjected to standard gravimetric analysis until spinning for three consecutive generations covering 3 different seasons on 19 nutrigenetic traits. Highly significant (p ≤ 0.001) differences were found among all nutrigenetic traits of polyvoltine silkworm strains in the experimental groups. The nutritionally efficient polvoltine silkworm strains were resulted by utilizing nutrition consumption index and efficiency of conversion of ingesta/cocoon traits as the index. Higher nutritional efficiency conversions were found in the polyvoltine silkworm strains on efficiency of conversion of ingesta to cocoon and shell than control. Comparatively smaller consumption index, respiration, metabolic rate with superior relative growth rate, and quantum of food ingesta and digesta requisite per gram of cocoon and shell were found; the lowest amount was in new polyvoltine strains compared to the control. Furthermore, based on the overall nutrigenetic traits utilized as index or ‘biomarkers’, three polyvoltine silkworm strains (RMG4, RMW2, and RMW3) were identified as having the potential for nutrition efficiency conversion. The data from the present study advances our knowledge for the development of nutritionally efficient silkworm breeds/hybrids and their effective

Screening of pollution control and clean-up materials for river chemical spills using the multiple case-based reasoning method with a difference-driven revision strategy.

PubMed

Liu, Rentao; Jiang, Jiping; Guo, Liang; Shi, Bin; Liu, Jie; Du, Zhaolin; Wang, Peng

2016-06-01

In-depth filtering of emergency disposal technology (EDT) and materials has been required in the process of environmental pollution emergency disposal. However, an urgent problem that must be solved is how to quickly and accurately select the most appropriate materials for treating a pollution event from the existing spill control and clean-up materials (SCCM). To meet this need, the following objectives were addressed in this study. First, the material base and a case base for environment pollution emergency disposal were established to build a foundation and provide material for SCCM screening. Second, the multiple case-based reasoning model method with a difference-driven revision strategy (DDRS-MCBR) was applied to improve the original dual case-based reasoning model method system, and screening and decision-making was performed for SCCM using this model. Third, an actual environmental pollution accident from 2012 was used as a case study to verify the material base, case base, and screening model. The results demonstrated that the DDRS-MCBR method was fast, efficient, and practical. The DDRS-MCBR method changes the passive situation in which the choice of SCCM screening depends only on the subjective experience of the decision maker and offers a new approach to screening SCCM.

Fluorophore Absorption Size Exclusion Chromatography (FA-SEC): An Alternative Method for High-Throughput Detergent Screening of Membrane Proteins.

PubMed

Lin, Sung-Yao; Sun, Xing-Han; Hsiao, Yu-Hsuan; Chang, Shao-En; Li, Guan-Syun; Hu, Nien-Jen

2016-01-01

Membrane proteins play key roles in many fundamental functions in cells including ATP synthesis, ion and molecule transporter, cell signalling and enzymatic reactions, accounting for ~30% genes of whole genomes. However, the hydrophobic nature of membrane proteins frequently hampers the progress of structure determination. Detergent screening is the critical step in obtaining stable detergent-solubilized membrane proteins and well-diffracting protein crystals. Fluorescence Detection Size Exclusion Chromatography (FSEC) has been developed to monitor the extraction efficiency and monodispersity of membrane proteins in detergent micelles. By tracing the FSEC profiles of GFP-fused membrane proteins, this method significantly enhances the throughput of detergent screening. However, current methods to acquire FSEC profiles require either an in-line fluorescence detector with the SEC equipment or an off-line spectrofluorometer microplate reader. Here, we introduce an alternative method detecting the absorption of GFP (FA-SEC) at 485 nm, thus making this methodology possible on conventional SEC equipment through the in-line absorbance spectrometer. The results demonstrate that absorption is in great correlation with fluorescence of GFP. The comparably weaker absorption signal can be improved by using a longer path-length flow cell. The FA-SEC profiles were congruent with the ones plotted by FSEC, suggesting FA-SEC could be a comparable and economical setup for detergent screening of membrane proteins.

Recruitment methods employed in the prostate, lung, colorectal, and ovarian cancer screening trial

PubMed Central

Gren, Lisa; Broski, Karen; Childs, Jeffery; Cordes, Jill; Engelhard, Deborah; Gahagan, Betsy; Gamito, Eduard; Gardner, Vivien; Geisser, Mindy; Higgins, Darlene; Jenkins, Victoria; Lamerato, Lois; Lappe, Karen; Lowery, Heidi; McGuire, Colleen; Miedzinski, Mollie; Ogden, Sheryl; Tenorio, Sally; Watt, Gavin; Wohlers, Bonita; Marcus, Pamela

2015-01-01

Background The Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO) is a US National Cancer Institute (NCI)-funded randomized controlled trial designed to evaluate whether certain screening tests reduce mortality from prostate, lung, colorectal, and ovarian cancer. To obtain adequate statistical power, it was necessary to enroll over 150,000 healthy volunteers. Recruitment began in 1993 and ended in 2001. Purpose Our goal is to evaluate the success of recruitment methods employed by the 10 PLCO screening centers. We also provide estimates of recruitment yield and cost for our most successful strategy, direct mail. Methods Each screening center selected its own methods of recruitment. Methods changed throughout the recruitment period as needed. For this manuscript, representatives from each screening center provided information on methods utilized and their success. Results In the United States between 1993 and 2001, ten screening centers enrolled 154,934 study participants. Based on participant self-report, an estimated 95% of individuals were recruited by direct mail. Overall, enrollment yield for direct mail was 1.0%. Individual center enrollment yield ranged from 0.7% to 3.8%. Cost per enrolled participant was $9.64–35.38 for direct mail, excluding personnel costs. Limitations Numeric data on recruitment processes were not kept consistently at individual screening centers. Numeric data in this manuscript are based on the experiences of 5 of the 10 centers. Conclusions Direct mail, using rosters of names and addresses from profit and not-for-profit (including government) organizations, was the most successful and most often used recruitment method. Other recruitment strategies, such as community outreach and use of mass media, can be an important adjunct to direct mail in recruiting minority populations. PMID:19254935

Establishment of an efficient genetic transformation method in Dunaliella tertiolecta mediated by Agrobacterium tumefaciens.

PubMed

Norzagaray-Valenzuela, Claudia D; Germán-Báez, Lourdes J; Valdez-Flores, Marco A; Hernández-Verdugo, Sergio; Shelton, Luke M; Valdez-Ortiz, Angel

2018-05-16

Microalgae are photosynthetic microorganisms widely used for the production of highly valued compounds, and recently they have been shown to be promising as a system for the heterologous expression of proteins. Several transformation methods have been successfully developed, from which the Agrobacterium tumefaciens-mediated method remains the most promising. However, microalgae transformation efficiency by A. tumefaciens is shown to vary depending on several transformation conditions. The present study aimed to establish an efficient genetic transformation system in the green microalgae Dunaliella tertiolecta using the A. tumefaciens method. The parameters assessed were the infection medium, the concentration of the A. tumefaciens and co-culture time. As a preliminary screening, the expression of the gusA gene and the viability of transformed cells were evaluated and used to calculate a novel parameter called Transformation Efficiency Index (TEI). The statistical analysis of TEI values showed five treatments with the highest gusA gene expression. To ensure stable transformation, transformed colonies were cultured on selective medium using hygromycin B and the DNA of resistant colonies were extracted after five subcultures and molecularly analyzed by PCR. Results revealed that treatments which use solid infection medium, A. tumefaciens OD 600  = 0.5 and co-culture times of 72 h exhibited the highest percentage of stable gusA expression. Overall, this study established an efficient, optimized A. tumefaciens-mediated genetic transformation of D. tertiolecta, which represents a relatively easy procedure with no expensive equipment required. This simple and efficient protocol opens the possibility for further genetic manipulation of this commercially-important microalgae for biotechnological applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Taguchi's technique: an effective method for improving X-ray medical radiographic screen performance.

PubMed

Vlachogiannis, J G

2003-01-01

Taguchi's technique is a helpful tool to achieve experimental optimization of a large number of decision variables with a small number of off-line experiments. The technique appears to be an ideal tool for improving the performance of X-ray medical radiographic screens under a noise source. Currently there are very many guides available for improving the efficiency of X-ray medical radiographic screens. These guides can be refined using a second-stage parameter optimization. based on Taguchi's technique, selecting the optimum levels of controllable X-ray radiographic screen factors. A real example of the proposed technique is presented giving certain performance criteria. The present research proposes the reinforcement of X-ray radiography by Taguchi's technique as a novel hardware mechanism.

Fragment-based lead generation: identification of seed fragments by a highly efficient fragment screening technology

NASA Astrophysics Data System (ADS)

Neumann, Lars; Ritscher, Allegra; Müller, Gerhard; Hafenbradl, Doris

2009-08-01

For the detection of the precise and unambiguous binding of fragments to a specific binding site on the target protein, we have developed a novel reporter displacement binding assay technology. The application of this technology for the fragment screening as well as the fragment evolution process with a specific modelling based design strategy is demonstrated for inhibitors of the protein kinase p38alpha. In a fragment screening approach seed fragments were identified which were then used to build compounds from the deep-pocket towards the hinge binding area of the protein kinase p38alpha based on a modelling approach. BIRB796 was used as a blueprint for the alignment of the fragments. The fragment evolution of these deep-pocket binding fragments towards the fully optimized inhibitor BIRB796 included the modulation of the residence time as well as the affinity. The goal of our study was to evaluate the robustness and efficiency of our novel fragment screening technology at high fragment concentrations, compare the screening data with biochemical activity data and to demonstrate the evolution of the hit fragments with fast kinetics, into slow kinetic inhibitors in an in silico approach.

Challenges for Detecting Valproic Acid in a Nontargeted Urine Drug Screening Method.

PubMed

Pope, Jeffrey D; Black, Marion J; Drummer, Olaf H; Schneider, Hans G

2017-08-01

Valproic acid (VPA) is a widely prescribed medicine, and acute toxicity is possible. As such, it should be included in any nontargeted urine drug screening method. In many published liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) methods, VPA is usually measured using a pseudo-multiple reaction monitoring (MRM) transition. We investigate a simple ultra-high-performance liquid chromatography-quadrupole time-of-flight (QTof) approach to detect the presence of VPA with more confidence. Three commercially sourced VPA metabolites were characterized and added to a nontargeted high-resolution MS urine drug screening method. All analyses were performed on a Waters Xevo G2-XS LC-QTof in negative electrospray ionization mode. The mass detector was operated in MS mode, and data were processed with UNIFI software. Sixty-eight patient urine samples, which were previously identified by a well-established gas chromatography-MS method as containing VPA, were analyzed on the Waters Xevo G2-XS LC-QTof, to validate this approach. VPA metabolite standards were characterized, and their detection data were added to the broad drug screening library. VPA metabolites were readily detectable in the urine of patients taking VPA. The inclusion of characterized VPA metabolites provides a simple and reliable method enabling the detection of VPA in nontargeted urine drug screening.

Electronic Properties, Screening, and Efficient Carrier Transport in NaSbS 2

DOE PAGES

Sun, Jifeng; Singh, David J.

2017-02-13

NaSbS 2 is a semiconductor that was recently shown to have remarkable efficacy as a solar absorber indicating efficient charge collection even in material containing defects. We report first-principles calculations of properties that show (1) an indirect gap only slightly smaller than the direct gap, which may impede the recombination of photoexcited carriers, (2) highly anisotropic electronic and optical properties reflecting a layered crystal structure, (3) a pushed-up valence-band maximum due to repulsion from the Sb 5s states, and (4) cross-gap hybridization between the S p—derived valence bands and the Sb 5p states. This latter feature leads to enhanced Bornmore » effective charges that can provide local screening and, therefore, defect tolerance. Finally, these features are discussed in relation to the performance of the compound as a semiconductor with efficient charge collection.« less

A Triangulation Method for Identifying Hydrostratigraphic Locations of Well Screens

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

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. Copyright 1999 Academic Press.

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.

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

Screening natural antioxidants in peanut shell using DPPH-HPLC-DAD-TOF/MS methods.

PubMed

Qiu, Jiying; Chen, Leilei; Zhu, Qingjun; Wang, Daijie; Wang, Wenliang; Sun, Xin; Liu, Xiaoyong; Du, Fangling

2012-12-15

Peanut shell, a byproduct in oil production, is rich in natural antioxidants. Here, a rapid and efficient method using DPPH-HPLC-DAD-TOF/MS was used for the first time to screen antioxidants in peanut shell. The method is based on the hypothesis that upon reaction with 1, 1-diphenyl-2-picrylhydrazyl (DPPH), the peak areas of compounds with potential antioxidant activities in the HPLC chromatogram will be significantly reduced or disappeared, and the identity confirmation could be achieved by HPLC-DAD-TOF/MS technique. With this method, three compounds possessing potential antioxidant activities were found abundantly in the methanolic extract of peanut shell. They were identified as 5,7-dihydroxychromone, eriodictyol, and luteolin. The contents of these compounds were 0.59, 0.92, and 2.36 mg/g, respectively, and luteolin possessed the strongest radical scavenging capacity. DPPH-HPLC-DAD-TOF/MS assay facilitated rapid identification and determination of natural antioxidants in peanut shell, which may be helpful for value-added utilization of peanut processing byproducts. Copyright © 2012 Elsevier Ltd. All rights reserved.

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...

An Efficient New Device to Release Eggs From Heterodera glycines.

PubMed

Faghihi, J; Ferris, J M

2000-12-01

A new apparatus to release eggs from cysts of soybean cyst nematode (Heterodera glycines) is described and its efficiency evaluated. A rubber stopper was mounted on a bolt, and cysts were ground against a 60-mesh screen. Eggs and second-stage juveniles were washed into a series of screens nested underneath the apparatus. This method was fast and efficient, and had no ill effect on prepared inoculum.

Fragment-based screening in tandem with phenotypic screening provides novel antiparasitic hits.

PubMed

Blaazer, Antoni R; Orrling, Kristina M; Shanmugham, Anitha; Jansen, Chimed; Maes, Louis; Edink, Ewald; Sterk, Geert Jan; Siderius, Marco; England, Paul; Bailey, David; de Esch, Iwan J P; Leurs, Rob

2015-01-01

Methods to discover biologically active small molecules include target-based and phenotypic screening approaches. One of the main difficulties in drug discovery is elucidating and exploiting the relationship between drug activity at the protein target and disease modification, a phenotypic endpoint. Fragment-based drug discovery is a target-based approach that typically involves the screening of a relatively small number of fragment-like (molecular weight <300) molecules that efficiently cover chemical space. Here, we report a fragment screening on TbrPDEB1, an essential cyclic nucleotide phosphodiesterase (PDE) from Trypanosoma brucei, and human PDE4D, an off-target, in a workflow in which fragment hits and a series of close analogs are subsequently screened for antiparasitic activity in a phenotypic panel. The phenotypic panel contained T. brucei, Trypanosoma cruzi, Leishmania infantum, and Plasmodium falciparum, the causative agents of human African trypanosomiasis (sleeping sickness), Chagas disease, leishmaniasis, and malaria, respectively, as well as MRC-5 human lung cells. This hybrid screening workflow has resulted in the discovery of various benzhydryl ethers with antiprotozoal activity and low toxicity, representing interesting starting points for further antiparasitic optimization. © 2014 Society for Laboratory Automation and Screening.

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test.

PubMed

Zhang, Qingyang

2018-05-16

Differential co-expression analysis, as a complement of differential expression analysis, offers significant insights into the changes in molecular mechanism of different phenotypes. A prevailing approach to detecting differentially co-expressed genes is to compare Pearson's correlation coefficients in two phenotypes. However, due to the limitations of Pearson's correlation measure, this approach lacks the power to detect nonlinear changes in gene co-expression which is common in gene regulatory networks. In this work, a new nonparametric procedure is proposed to search differentially co-expressed gene pairs in different phenotypes from large-scale data. Our computational pipeline consisted of two main steps, a screening step and a testing step. The screening step is to reduce the search space by filtering out all the independent gene pairs using distance correlation measure. In the testing step, we compare the gene co-expression patterns in different phenotypes by a recently developed edge-count test. Both steps are distribution-free and targeting nonlinear relations. We illustrate the promise of the new approach by analyzing the Cancer Genome Atlas data and the METABRIC data for breast cancer subtypes. Compared with some existing methods, the new method is more powerful in detecting nonlinear type of differential co-expressions. The distance correlation screening can greatly improve computational efficiency, facilitating its application to large data sets.

Gastric cancer screening of a high-risk population in Japan using serum pepsinogen and barium digital radiography.

PubMed

Ohata, Hiroshi; Oka, Masashi; Yanaoka, Kimihiko; Shimizu, Yasuhito; Mukoubayashi, Chizu; Mugitani, Kouichi; Iwane, Masataka; Nakamura, Hideya; Tamai, Hideyuki; Arii, Kenji; Nakata, Hiroya; Yoshimura, Noriko; Takeshita, Tetsuya; Miki, Kazumasa; Mohara, Osamu; Ichinose, Masao

2005-10-01

With the aim of developing more efficient gastric cancer screening programs for use in Japan, we studied a new screening program that combines serum pepsinogen (PG) testing and barium digital radiography (DR). A total of 17 647 middle-aged male subjects underwent workplace screening over a 7-year period using a combination of PG testing and DR. This program's effectiveness, as well as other characteristics of the program, was analyzed. Forty-nine cases of gastric cancer were detected (comprising 88% early cancer cases). The detection rate was 0.28%, and the positive predictive value was 0.85%. The PG test detected 63.3% of cases, DR detected 69.4% of cases, and both tests were positive in 32.7% of cancer cases. The two methods were almost equally effective, and were considerably more effective than conventional screening using photofluorography. Each screening method detected a distinct gastric cancer subgroup; the PG test efficiently detected asymptomatic small early cancer with intestinal type histology, while DR was efficient at detecting cancers with depressed or ulcerated morphology and diffuse type histology. The cost for the detection of a single cancer was much less than that for conventional screening. In fact, it is possible to further reduce the cost of detecting a single cancer to a cost comparable to that of surgically resecting a single gastric cancer. Thus, it is probable that a highly efficient gastric cancer screening system can be implemented by combining the two screening methods. Such a screening program would be beneficial in a population at high risk for gastric cancer.

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.

[Computerized monitoring for integrated cervical screening. Rationale, methods and indicators of participation].

PubMed

Bucchi, L; Pierri, C; Caprara, L; Cortecchia, S; De Lillo, M; Bondi, A

2003-02-01

This paper presents a computerised system for the monitoring of integrated cervical screening, i.e. the integration of spontaneous Pap smear practice into organised screening. The general characteristics of the system are described, including background and rationale (integrated cervical screening in European countries, impact of integration on monitoring, decentralised organization of screening and levels of monitoring), general methods (definitions, sections, software description, and setting of application), and indicators of participation (distribution by time interval since previous Pap smear, distribution by screening sector--organised screening centres vs public and private clinical settings--, distribution by time interval between the last two Pap smears, and movement of women between the two screening sectors). Also, the paper reports the results of the application of these indicators in the general database of the Pathology Department of Imola Health District in northern Italy.

Efficient method of evaluation for Gaussian Hartree-Fock exchange operator for Gau-PBE functional

NASA Astrophysics Data System (ADS)

Song, Jong-Won; Hirao, Kimihiko

2015-07-01

We previously developed an efficient screened hybrid functional called Gaussian-Perdew-Burke-Ernzerhof (Gau-PBE) [Song et al., J. Chem. Phys. 135, 071103 (2011)] for large molecules and extended systems, which is characterized by the usage of a Gaussian function as a modified Coulomb potential for the Hartree-Fock (HF) exchange. We found that the adoption of a Gaussian HF exchange operator considerably decreases the calculation time cost of periodic systems while improving the reproducibility of the bandgaps of semiconductors. We present a distance-based screening scheme here that is tailored for the Gaussian HF exchange integral that utilizes multipole expansion for the Gaussian two-electron integrals. We found a new multipole screening scheme helps to save the time cost for the HF exchange integration by efficiently decreasing the number of integrals of, specifically, the near field region without incurring substantial changes in total energy. In our assessment on the periodic systems of seven semiconductors, the Gau-PBE hybrid functional with a new screening scheme has 1.56 times the time cost of a pure functional while the previous Gau-PBE was 1.84 times and HSE06 was 3.34 times.

Efficient method of evaluation for Gaussian Hartree-Fock exchange operator for Gau-PBE functional

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Jong-Won; Hirao, Kimihiko, E-mail: hirao@riken.jp

2015-07-14

We previously developed an efficient screened hybrid functional called Gaussian-Perdew–Burke–Ernzerhof (Gau-PBE) [Song et al., J. Chem. Phys. 135, 071103 (2011)] for large molecules and extended systems, which is characterized by the usage of a Gaussian function as a modified Coulomb potential for the Hartree-Fock (HF) exchange. We found that the adoption of a Gaussian HF exchange operator considerably decreases the calculation time cost of periodic systems while improving the reproducibility of the bandgaps of semiconductors. We present a distance-based screening scheme here that is tailored for the Gaussian HF exchange integral that utilizes multipole expansion for the Gaussian two-electron integrals.more » We found a new multipole screening scheme helps to save the time cost for the HF exchange integration by efficiently decreasing the number of integrals of, specifically, the near field region without incurring substantial changes in total energy. In our assessment on the periodic systems of seven semiconductors, the Gau-PBE hybrid functional with a new screening scheme has 1.56 times the time cost of a pure functional while the previous Gau-PBE was 1.84 times and HSE06 was 3.34 times.« less

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...

Establishment of cocrystal cocktail grinding method for rational screening of pharmaceutical cocrystals.

PubMed

Yamamoto, Katsuhiko; Tsutsumi, Shunichirou; Ikeda, Yukihiro

2012-11-01

Cocrystals (CCs) used in the pharmaceutical industry are defined as complex crystals formed by reaction between an API and a cocrystal former (CCF); unlike salts, CCs do not show proton transfer. Recently, pharmaceutical CCs have been used to improve the drug-likeness of APIs, such as solubility and stability. Grinding is more effective for CC synthesis than crystallization from solution because in the former case, the API can predominantly interact with the CCF without being affected by solvents. However, this method is tedious because the API is ground with only one CCF at a time. We developed a cocktail cocrystal grinding (CCG) method, in which a mixture of CCFs having the same functional group was used. No false negatives/positives were observed in CCG when carbamazepine was used as the model compound. This method could be used to obtain CCs of piroxicam and spironolactone. False negatives were observed for only one compound from among three model compounds, indicating that CCG facilitates efficient CC detection and that it has higher throughput than does the conventional method. Further, CCG is fast and suitable for rational CC screening, and it helps identify the partial structure of CCFs that forms synthons with an API. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

[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.

Directed differentiation of embryonic stem cells using a bead-based combinatorial screening method.

PubMed

Tarunina, Marina; Hernandez, Diana; Johnson, Christopher J; Rybtsov, Stanislav; Ramathas, Vidya; Jeyakumar, Mylvaganam; Watson, Thomas; Hook, Lilian; Medvinsky, Alexander; Mason, Chris; Choo, Yen

2014-01-01

We have developed a rapid, bead-based combinatorial screening method to determine optimal combinations of variables that direct stem cell differentiation to produce known or novel cell types having pre-determined characteristics. Here we describe three experiments comprising stepwise exposure of mouse or human embryonic cells to 10,000 combinations of serum-free differentiation media, through which we discovered multiple novel, efficient and robust protocols to generate a number of specific hematopoietic and neural lineages. We further demonstrate that the technology can be used to optimize existing protocols in order to substitute costly growth factors with bioactive small molecules and/or increase cell yield, and to identify in vitro conditions for the production of rare developmental intermediates such as an embryonic lymphoid progenitor cell that has not previously been reported.

Directed Differentiation of Embryonic Stem Cells Using a Bead-Based Combinatorial Screening Method

PubMed Central

Tarunina, Marina; Hernandez, Diana; Johnson, Christopher J.; Rybtsov, Stanislav; Ramathas, Vidya; Jeyakumar, Mylvaganam; Watson, Thomas; Hook, Lilian; Medvinsky, Alexander; Mason, Chris; Choo, Yen

2014-01-01

We have developed a rapid, bead-based combinatorial screening method to determine optimal combinations of variables that direct stem cell differentiation to produce known or novel cell types having pre-determined characteristics. Here we describe three experiments comprising stepwise exposure of mouse or human embryonic cells to 10,000 combinations of serum-free differentiation media, through which we discovered multiple novel, efficient and robust protocols to generate a number of specific hematopoietic and neural lineages. We further demonstrate that the technology can be used to optimize existing protocols in order to substitute costly growth factors with bioactive small molecules and/or increase cell yield, and to identify in vitro conditions for the production of rare developmental intermediates such as an embryonic lymphoid progenitor cell that has not previously been reported. PMID:25251366

An Efficient New Device to Release Eggs From Heterodera glycines

PubMed Central

Faghihi, J.; Ferris, J. M.

2000-01-01

A new apparatus to release eggs from cysts of soybean cyst nematode (Heterodera glycines) is described and its efficiency evaluated. A rubber stopper was mounted on a bolt, and cysts were ground against a 60-mesh screen. Eggs and second-stage juveniles were washed into a series of screens nested underneath the apparatus. This method was fast and efficient, and had no ill effect on prepared inoculum. PMID:19270996

Shaping a screening file for maximal lead discovery efficiency and effectiveness: elimination of molecular redundancy.

PubMed

Bakken, Gregory A; Bell, Andrew S; Boehm, Markus; Everett, Jeremy R; Gonzales, Rosalia; Hepworth, David; Klug-McLeod, Jacquelyn L; Lanfear, Jeremy; Loesel, Jens; Mathias, John; Wood, Terence P

2012-11-26

High Throughput Screening (HTS) is a successful strategy for finding hits and leads that have the opportunity to be converted into drugs. In this paper we highlight novel computational methods used to select compounds to build a new screening file at Pfizer and the analytical methods we used to assess their quality. We also introduce the novel concept of molecular redundancy to help decide on the density of compounds required in any region of chemical space in order to be confident of running successful HTS campaigns.

The role of affordances in children's learning performance and efficiency when using virtual manipulative mathematics touch-screen apps

NASA Astrophysics Data System (ADS)

Moyer-Packenham, Patricia S.; Bullock, Emma K.; Shumway, Jessica F.; Tucker, Stephen I.; Watts, Christina M.; Westenskow, Arla; Anderson-Pence, Katie L.; Maahs-Fladung, Cathy; Boyer-Thurgood, Jennifer; Gulkilik, Hilal; Jordan, Kerry

2016-03-01

This paper focuses on understanding the role that affordances played in children's learning performance and efficiency during clinical interviews of their interactions with mathematics apps on touch-screen devices. One hundred children, ages 3 to 8, each used six different virtual manipulative mathematics apps during 30-40-min interviews. The study used a convergent mixed methods design, in which quantitative and qualitative data were collected concurrently to answer the research questions (Creswell and Plano Clark 2011). Videos were used to capture each child's interactions with the virtual manipulative mathematics apps, document learning performance and efficiency, and record children's interactions with the affordances within the apps. Quantitized video data answered the research question on differences in children's learning performance and efficiency between pre- and post-assessments. A Wilcoxon matched pairs signed-rank test was used to explore these data. Qualitative video data was used to identify affordance access by children when using each app, identifying 95 potential helping and hindering affordances among the 18 apps. The results showed that there were changes in children's learning performance and efficiency when children accessed a helping or a hindering affordance. Helping affordances were more likely to be accessed by children who progressed between the pre- and post-assessments, and the same affordances had helping and hindering effects for different children. These results have important implications for the design of virtual manipulative mathematics learning apps.

DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0.

PubMed

Jiang, Xiaohui; Kumar, Kamal; Hu, Xin; Wallqvist, Anders; Reifman, Jaques

2008-09-08

Small-molecule docking is an important tool in studying receptor-ligand interactions and in identifying potential drug candidates. Previously, we developed a software tool (DOVIS) to perform large-scale virtual screening of small molecules in parallel on Linux clusters, using AutoDock 3.05 as the docking engine. DOVIS enables the seamless screening of millions of compounds on high-performance computing platforms. In this paper, we report significant advances in the software implementation of DOVIS 2.0, including enhanced screening capability, improved file system efficiency, and extended usability. To keep DOVIS up-to-date, we upgraded the software's docking engine to the more accurate AutoDock 4.0 code. We developed a new parallelization scheme to improve runtime efficiency and modified the AutoDock code to reduce excessive file operations during large-scale virtual screening jobs. We also implemented an algorithm to output docked ligands in an industry standard format, sd-file format, which can be easily interfaced with other modeling programs. Finally, we constructed a wrapper-script interface to enable automatic rescoring of docked ligands by arbitrarily selected third-party scoring programs. The significance of the new DOVIS 2.0 software compared with the previous version lies in its improved performance and usability. The new version makes the computation highly efficient by automating load balancing, significantly reducing excessive file operations by more than 95%, providing outputs that conform to industry standard sd-file format, and providing a general wrapper-script interface for rescoring of docked ligands. The new DOVIS 2.0 package is freely available to the public under the GNU General Public License.

Coformer screening using thermal analysis based on binary phase diagrams.

PubMed

Yamashita, Hiroyuki; Hirakura, Yutaka; Yuda, Masamichi; Terada, Katsuhide

2014-08-01

The advent of cocrystals has demonstrated a growing need for efficient and comprehensive coformer screening in search of better development forms, including salt forms. Here, we investigated a coformer screening system for salts and cocrystals based on binary phase diagrams using thermal analysis and examined the effectiveness of the method. Indomethacin and tenoxicam were used as models of active pharmaceutical ingredients (APIs). Physical mixtures of an API and 42 kinds of coformers were analyzed using Differential Scanning Calorimetry (DSC) and X-ray DSC. We also conducted coformer screening using a conventional slurry method and compared these results with those from the thermal analysis method and previous studies. Compared with the slurry method, the thermal analysis method was a high-performance screening system, particularly for APIs with low solubility and/or propensity to form solvates. However, this method faced hurdles for screening coformers combined with an API in the presence of kinetic hindrance for salt or cocrystal formation during heating or if there is degradation near the metastable eutectic temperature. The thermal analysis and slurry methods are considered complementary to each other for coformer screening. Feasibility of the thermal analysis method in drug discovery practice is ensured given its small scale and high throughput.

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

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.

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.

Nontargeted Screening Method for Illegal Additives Based on Ultrahigh-Performance Liquid Chromatography-High-Resolution Mass Spectrometry.

PubMed

Fu, Yanqing; Zhou, Zhihui; Kong, Hongwei; Lu, Xin; Zhao, Xinjie; Chen, Yihui; Chen, Jia; Wu, Zeming; Xu, Zhiliang; Zhao, Chunxia; Xu, Guowang

2016-09-06

Identification of illegal additives in complex matrixes is important in the food safety field. In this study a nontargeted screening strategy was developed to find illegal additives based on ultrahigh-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS). First, an analytical method for possible illegal additives in complex matrixes was established including fast sample pretreatment, accurate UHPLC separation, and HRMS detection. Second, efficient data processing and differential analysis workflow were suggested and applied to find potential risk compounds. Third, structure elucidation of risk compounds was performed by (1) searching online databases [Metlin and the Human Metabolome Database (HMDB)] and an in-house database which was established at the above-defined conditions of UHPLC-HRMS analysis and contains information on retention time, mass spectra (MS), and tandem mass spectra (MS/MS) of 475 illegal additives, (2) analyzing fragment ions, and (3) referring to fragmentation rules. Fish was taken as an example to show the usefulness of the nontargeted screening strategy, and six additives were found in suspected fish samples. Quantitative analysis was further carried out to determine the contents of these compounds. The satisfactory application of this strategy in fish samples means that it can also be used in the screening of illegal additives in other kinds of food samples.

A Systematic Evaluation of Field-Based Screening Methods for the Assessment of Anterior Cruciate Ligament (ACL) Injury Risk.

PubMed

Fox, Aaron S; Bonacci, Jason; McLean, Scott G; Spittle, Michael; Saunders, Natalie

2016-05-01

Laboratory-based measures provide an accurate method to identify risk factors for anterior cruciate ligament (ACL) injury; however, these methods are generally prohibitive to the wider community. Screening methods that can be completed in a field or clinical setting may be more applicable for wider community use. Examination of field-based screening methods for ACL injury risk can aid in identifying the most applicable method(s) for use in these settings. The objective of this systematic review was to evaluate and compare field-based screening methods for ACL injury risk to determine their efficacy of use in wider community settings. An electronic database search was conducted on the SPORTDiscus™, MEDLINE, AMED and CINAHL databases (January 1990-July 2015) using a combination of relevant keywords. A secondary search of the same databases, using relevant keywords from identified screening methods, was also undertaken. Studies identified as potentially relevant were independently examined by two reviewers for inclusion. Where consensus could not be reached, a third reviewer was consulted. Original research articles that examined screening methods for ACL injury risk that could be undertaken outside of a laboratory setting were included for review. Two reviewers independently assessed the quality of included studies. Included studies were categorized according to the screening method they examined. A description of each screening method, and data pertaining to the ability to prospectively identify ACL injuries, validity and reliability, recommendations for identifying 'at-risk' athletes, equipment and training required to complete screening, time taken to screen athletes, and applicability of the screening method across sports and athletes were extracted from relevant studies. Of 1077 citations from the initial search, a total of 25 articles were identified as potentially relevant, with 12 meeting all inclusion/exclusion criteria. From the secondary search, eight

FIELD SCREENING METHODS FOR HAZARDOUS WASTES AND TOXIC CHEMICALS

EPA Science Inventory

The purpose of this document is to present the technical papers that were presented at the Second International Symposium on Field Screening Methods for Hazardous Wastes and Toxic Chemicals. ixty platform presentations were made and included in one of ten sessions: hemical sensor...

Newborn screening for cystic fibrosis in Wisconsin: comparison of biochemical and molecular methods.

PubMed

Gregg, R G; Simantel, A; Farrell, P M; Koscik, R; Kosorok, M R; Laxova, A; Laessig, R; Hoffman, G; Hassemer, D; Mischler, E H; Splaingard, M

1997-06-01

To evaluate neonatal screening for cystic fibrosis (CF), including study of the screening procedures and characteristics of false-positive infants, over the past 10 years in Wisconsin. An important objective evolving from the original design has been to compare use of a single-tier immunoreactive trypsinogen (IRT) screening method with that of a two-tier method using IRT and analyses of samples for the most common cystic fibrosis transmembrane regulator (CFTR) (DeltaF508) mutation. We also examined the benefit of including up to 10 additional CFTR mutations in the screening protocol. From 1985 to 1994, using either the IRT or IRT/DNA protocol, 220 862 and 104 308 neonates, respectively, were screened for CF. For the IRT protocol, neonates with an IRT >/=180 ng/mL were considered positive, and the standard sweat chloride test was administered to determine CF status. For the IRT/DNA protocol, samples from the original dried-blood specimen on the Guthrie card of neonates with an IRT >/=110 ng/mL were tested for the presence of the DeltaF508 CFTR allele, and if the DNA test revealed one or two DeltaF508 alleles, a sweat test was obtained. Both screening procedures had very high specificity. The sensitivity tended to be higher with the IRT/DNA protocol, but the differences were not statistically significant. The positive predictive value of the IRT/DNA screening protocol was 15.2% compared with 6.4% if the same samples had been screened by the IRT method. Assessment of the false-positive IRT/DNA population revealed that the two-tier method eliminates the disproportionate number of infants with low Apgar scores and also the high prevalence of African-Americans identified previously in our study of newborns with high IRT levels. We found that 55% of DNA-positive CF infants were homozygous for DeltaF508 and 40% had one DeltaF508 allele. Adding analyses for 10 more CFTR mutations has only a small effect on the sensitivity but is likely to add significantly to the cost of

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. Copyright © 2014 Elsevier B.V. All rights reserved.

Hydrophobic and porous cellulose nanofibrous screen for efficient particulate matter (PM2.5) blocking

NASA Astrophysics Data System (ADS)

Chen, Liping; Guo, Yi; Peng, Xinsheng

2017-10-01

Particulate matter (PM2.5) pollution in air seriously affects public health. However, both bulk thickness and the accumulation of PM particles typically lead to a quick decline in the air permeability and large pressure drops of the conventional air clean membranes. In this work, we choose cellulose nanofibers (CNFs, a low cost, biodegradable and sustainable material) to form a hydrophobic and porous CNF thin layer on a stainless steel screen (300 mesh with pore size of 48 µm) through a simple filtration-assisted gelation process and subsequent polydimethylsiloxane modification. The prepared hydrophobic CNFs/stainless steel screen demonstrates highly efficient PM2.5 blocking based on size-sieving effect, fast air permeability and long-term durability under natural ventilation conditions in the relative humidity range from 45% to 93%. This technique holds great potential for indoor PM2.5 blocking under natural ventilation conditions.

Rapid screening of guar gum using portable Raman spectral identification methods.

PubMed

Srivastava, Hirsch K; Wolfgang, Steven; Rodriguez, Jason D

2016-01-25

Guar gum is a well-known inactive ingredient (excipient) used in a variety of oral pharmaceutical dosage forms as a thickener and stabilizer of suspensions and as a binder of powders. It is also widely used as a food ingredient in which case alternatives with similar properties, including chemically similar gums, are readily available. Recent supply shortages and price fluctuations have caused guar gum to come under increasing scrutiny for possible adulteration by substitution of cheaper alternatives. One way that the U.S. FDA is attempting to screen pharmaceutical ingredients at risk for adulteration or substitution is through field-deployable spectroscopic screening. Here we report a comprehensive approach to evaluate two field-deployable Raman methods--spectral correlation and principal component analysis--to differentiate guar gum from other gums. We report a comparison of the sensitivity of the spectroscopic screening methods with current compendial identification tests. The ability of the spectroscopic methods to perform unambiguous identification of guar gum compared to other gums makes them an enhanced surveillance alternative to the current compendial identification tests, which are largely subjective in nature. Our findings indicate that Raman spectral identification methods perform better than compendial identification methods and are able to distinguish guar gum from other gums with 100% accuracy for samples tested by spectral correlation and principal component analysis. Published by Elsevier B.V.

Multiplex and label-free screening of foodborne pathogens using surface plasmon resonance imaging

USDA-ARS?s Scientific Manuscript database

In order to protect outbreaks caused by foodborne pathogens, more rapid and efficient methods are needed for pathogen screening from food samples. Surface plasmon resonance imaging (SPRi) is an emerging optical technique, which allows for label-free screening of multiple targets simultaneously with ...

An efficient visualization method for analyzing biometric data

NASA Astrophysics Data System (ADS)

Rahmes, Mark; McGonagle, Mike; Yates, J. Harlan; Henning, Ronda; Hackett, Jay

2013-05-01

We introduce a novel application for biometric data analysis. This technology can be used as part of a unique and systematic approach designed to augment existing processing chains. Our system provides image quality control and analysis capabilities. We show how analysis and efficient visualization are used as part of an automated process. The goal of this system is to provide a unified platform for the analysis of biometric images that reduce manual effort and increase the likelihood of a match being brought to an examiner's attention from either a manual or lights-out application. We discuss the functionality of FeatureSCOPE™ which provides an efficient tool for feature analysis and quality control of biometric extracted features. Biometric databases must be checked for accuracy for a large volume of data attributes. Our solution accelerates review of features by a factor of up to 100 times. Review of qualitative results and cost reduction is shown by using efficient parallel visual review for quality control. Our process automatically sorts and filters features for examination, and packs these into a condensed view. An analyst can then rapidly page through screens of features and flag and annotate outliers as necessary.

Adolescent substance use screening in primary care: validity of computer self-administered vs. clinician-administered screening

PubMed Central

Harris, Sion Kim; Knight, John R; Van Hook, Shari; Sherritt, Lon; Brooks, Traci; Kulig, John W; Nordt, Christina; Saitz, Richard

2015-01-01

Background Computer self-administration may help busy pediatricians’ offices increase adolescent substance use screening rates efficiently and effectively, if proven to yield valid responses. The CRAFFT screening protocol for adolescents has demonstrated validity as an interview, but a computer self-entry approach needs validity testing. The aim of this study was to evaluate the criterion validity and time efficiency of a computerized adolescent substance use screening protocol implemented by self-administration or clinician-administration. Methods 12- to 17-year-old patients coming for routine care at three primary care clinics completed the computerized screen by both self-administration and clinician-administration during their visit. To account for order effects, we randomly assigned participants to self-administer the screen either before or after seeing their clinician. Both were conducted using a tablet computer and included identical items (any past-12-month use of tobacco, alcohol, drugs; past-3-months frequency of each; and six CRAFFT items). The criterion measure for substance use was the Timeline Follow-Back, and for alcohol/drug use disorder, the Adolescent Diagnostic Interview, both conducted by confidential research assistant-interview after the visit. Tobacco dependence risk was assessed with the self-administered Hooked on Nicotine Checklist (HONC). Analyses accounted for the multi-site cluster sampling design. Results Among 136 participants, mean age was 15.0±1.5 yrs, 54% were girls, 53% were Black or Hispanic, and 67% had ≥3 prior visits with their clinician. Twenty-seven percent reported any substance use (including tobacco) in the past 12 months, 7% met criteria for an alcohol or cannabis use disorder, and 4% were HONC-positive. Sensitivity/specificity of the screener were high for detecting past-12-month use or disorder and did not differ between computer and clinician. Mean completion time was 49 seconds (95%CI 44-54) for computer and 74

Comparative Evaluation of Preliminary Screening Methods for Colorectal Cancer in a Mass Program.

PubMed

Ye, Ding; Huang, Qiuchi; Li, Qilong; Jiang, Xiyi; Mamat, Mayila; Tang, Mengling; Wang, Jianbing; Chen, Kun

2017-09-01

The fecal immunochemical test (FIT) has been widely used in preliminary screening for colorectal cancer (CRC). The high-risk factor questionnaire (HRFQ) and quantitative risk-assessment method (QRAM) are recommended for estimating the risk of CRC qualitatively and quantitatively in China. We aimed to prospectively compare the diagnostic values of CRC preliminary screening methods to identify which method is preferable as a screening strategy. Individuals aged 40-74 years old were enrolled in a mass CRC screening program from January 1, 2007 to December 31, 2014, in Jiashan County, Zhejiang Province, China. FIT of two stool specimens at 1-week intervals was performed by laboratory personnel and face-to-face interviews were conducted by trained investigators. Screening data in the program were linked to a CRC surveillance and registry system, and CRC cases reported in the system were regarded as true patients. A total of 96,043 subjects were included. The sensitivity and specificity of FIT for detecting CRC cases were 75.49% (95% CI 69.84-80.39) and 90.36% (95% CI 90.17-90.54), respectively. QRAM was more sensitive (p < 0.001) and less specific (p < 0.001) than HRFQ. The sensitivity and specificity of FIT along with HRFQ were 86.56% (95% CI 81.81-90.22) and 81.37% (95% CI 81.12-81.62), and those of FIT along with QRAM were 88.93% (95% CI 84.47-92.23) and 73.95% (95% CI 73.67-74.23). Our findings suggest that CRC preliminary screening with FIT and QRAM in parallel has high sensitivity and satisfactory specificity, and is a useful strategy in mass screening programs.

Computational efficiency for the surface renewal method

NASA Astrophysics Data System (ADS)

Kelley, Jason; Higgins, Chad

2018-04-01

Measuring surface fluxes using the surface renewal (SR) method requires programmatic algorithms for tabulation, algebraic calculation, and data quality control. A number of different methods have been published describing automated calibration of SR parameters. Because the SR method utilizes high-frequency (10 Hz+) measurements, some steps in the flux calculation are computationally expensive, especially when automating SR to perform many iterations of these calculations. Several new algorithms were written that perform the required calculations more efficiently and rapidly, and that tested for sensitivity to length of flux averaging period, ability to measure over a large range of lag timescales, and overall computational efficiency. These algorithms utilize signal processing techniques and algebraic simplifications that demonstrate simple modifications that dramatically improve computational efficiency. The results here complement efforts by other authors to standardize a robust and accurate computational SR method. Increased speed of computation time grants flexibility to implementing the SR method, opening new avenues for SR to be used in research, for applied monitoring, and in novel field deployments.

Screening Systems and Decision Making at the Preschool Level: Application of a Comprehensive Validity Framework

ERIC Educational Resources Information Center

Kettler, Ryan J.; Feeney-Kettler, Kelly A.

2011-01-01

Universal screening is designed to be an efficient method for identifying preschool students with mental health problems, but prior to use, screening systems must be evaluated to determine their appropriateness within a specific setting. In this article, an evidence-based validity framework is applied to four screening systems for identifying…

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.

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.

The impact of socioeconomic factors on the efficiency of voluntary toxoplasmosis screening during pregnancy: a population-based study.

PubMed

Lange, A E; Thyrian, J R; Wetzka, S; Flessa, S; Hoffmann, W; Zygmunt, M; Fusch, C; Lode, H N; Heckmann, M

2016-07-29

Congenital toxoplasmosis is associated with severe complications. German state health insurance covers rubella, but not toxoplasmosis, immunity screening. We analysed the effect of socioeconomic factors on the efficiency of private toxoplasmosis screening during pregnancy. Toxoplasmosis and rubella screening data (n = 5402 mothers) were collected within the population-based Survey of Neonates in Pomerania (SNiP). At the first-trimester screening, 34.4 % (88.1 %) of expecting mothers were immune to toxoplasmosis (rubella). Susceptibility for toxoplasmosis (rubella) was observed in 39.6 % (8.9 %) and 25.8 % (2.95 %) were not tested. Data on a 2(nd) screening were available in a subgroup of women with negative immunity showing less than 45 % participation rate. Active toxoplasmosis (no rubella) infection was observed in 0.3 % (n = 17) of pregnant women. A multiple logistic regression model (AIC = 719.67; AUC = 0.725) revealed that the likelihood of participating in a second toxoplasmosis screening increased among women with a good level of education and a steady partnership and decreased with paternal unemployment and the absence of breastfeeding. The highest probability of non-participation in toxoplasmosis screening was found among women with temporal burden and family responsibilities. A cost-benefit analysis showed that covering general screening for toxoplasmosis with health insurance saved costs. Toxoplasmosis carried a substantial risk of infection during pregnancy. Although increased socioeconomic status was positively associated with the participation in toxoplasmosis screening, this was not the case when pregnant women had strong temporal burden and family responsibilities. This data supports the need for toxoplasmosis screening among pregnant women as a general healthcare benefit covered by insurance.

Barriers to Breast and Cervical Cancer Screening in Singapore: a Mixed Methods Analysis.

PubMed

Malhotra, Chetna; Bilger, Marcel; Liu, Joy; Finkelstein, Eric

2016-01-01

In order to increase breast and cervical cancer screening uptake in Singapore, women's perceived barriers to screening need to be identified and overcome. Using data from both focus groups and surveys, we aimed to assess perceived barriers and motivations for breast and cervical cancer screening. We conducted 8 focus groups with 64 women, using thematic analysis to identify overarching themes related to women's attitudes towards screening. Based on recurring themes from focus groups, several hypotheses regarding potential barriers and motivations to screen were generated and tested through a national survey of 801 women aged 25-64. Focus group participants had misconceptions related to screening, believing that the procedures were painful. Cost was an issue, as well as efficacy and fatalism. By identifying barriers to and motivators for screening through a mixed-method design that has both nuance and external validity, this study offers valuable suggestions to policymakers to improve breast and cervical cancer screening uptake in Singapore.

Comprehensive Urine Drug Screen by Gas Chromatography/Mass Spectrometry (GC/MS).

PubMed

Ramoo, Bheemraj; Funke, Melissa; Frazee, Clint; Garg, Uttam

2016-01-01

Drug screening is an essential component of clinical toxicology laboratory service. Some laboratories use only automated chemistry analyzers for limited screening of drugs of abuse and few other drugs. Other laboratories use a combination of various techniques such as immunoassays, colorimetric tests, and mass spectrometry to provide more detailed comprehensive drug screening. Mass spectrometry, gas or liquid, can screen for hundreds of drugs and is often considered the gold standard for comprehensive drug screening. We describe an efficient and rapid gas chromatography/mass spectrometry (GC/MS) method for comprehensive drug screening in urine which utilizes a liquid-liquid extraction, sample concentration, and analysis by GC/MS.

A Systematic Protein Refolding Screen Method using the DGR Approach Reveals that Time and Secondary TSA are Essential Variables.

PubMed

Wang, Yuanze; van Oosterwijk, Niels; Ali, Ameena M; Adawy, Alaa; Anindya, Atsarina L; Dömling, Alexander S S; Groves, Matthew R

2017-08-24

Refolding of proteins derived from inclusion bodies is very promising as it can provide a reliable source of target proteins of high purity. However, inclusion body-based protein production is often limited by the lack of techniques for the detection of correctly refolded protein. Thus, the selection of the refolding conditions is mostly achieved using trial and error approaches and is thus a time-consuming process. In this study, we use the latest developments in the differential scanning fluorimetry guided refolding approach as an analytical method to detect correctly refolded protein. We describe a systematic buffer screen that contains a 96-well primary pH-refolding screen in conjunction with a secondary additive screen. Our research demonstrates that this approach could be applied for determining refolding conditions for several proteins. In addition, it revealed which "helper" molecules, such as arginine and additives are essential. Four different proteins: HA-RBD, MDM2, IL-17A and PD-L1 were used to validate our refolding approach. Our systematic protocol evaluates the impact of the "helper" molecules, the pH, buffer system and time on the protein refolding process in a high-throughput fashion. Finally, we demonstrate that refolding time and a secondary thermal shift assay buffer screen are critical factors for improving refolding efficiency.

Methods comparison for microsatellite marker development: Different isolation methods, different yield efficiency

NASA Astrophysics Data System (ADS)

Zhan, Aibin; Bao, Zhenmin; Hu, Xiaoli; Lu, Wei; Hu, Jingjie

2009-06-01

Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology, quantitative genetics and genomics. Therefore, it is extremely necessary to select several versatile, low-cost, efficient and time- and labor-saving methods to develop a large panel of microsatellite markers. In this study, we used Zhikong scallop ( Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency, while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time- and cost-saving, it is difficult to obtain a large number of microsatellite markers, mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study, we recommend two methods, microsatellite-enriched library construction method and FIASCO-colony hybridization method, for large-scale microsatellite marker development. Both methods were derived from the microsatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.

Screening methods for post-stroke visual impairment: a systematic review.

PubMed

Hanna, Kerry Louise; Hepworth, Lauren Rachel; Rowe, Fiona

2017-12-01

assess all potential post-stroke visual impairments. The current tools screen for only a number of potential stroke-related impairments, which means many visual defects may be missed. The sensitivity of those which screen for all impairments is significantly lowered when patients are unable to report their visual symptoms. Future research is required to develop a tool capable of assessing stroke patients which encompasses all potential visual deficits and can also be easily performed by both the patients and administered by health care professionals in order to ensure all stroke survivors with visual impairment are accurately identified and managed. Implications for Rehabilitation Over 65% of stroke survivors will suffer from a visual impairment, whereas 45% of stroke units do not assess vision. Visual impairment significantly reduces the quality of life, such as being unable to return to work, driving and depression. This review outlines the available screening methods to accurately identify stroke survivors with visual impairments. Identifying visual impairment after stroke can aid general rehabilitation and thus, improve the quality of life for these patients.

A screening mammography program. Staying alive and making it work.

PubMed

Monsees, B S; Destouet, J M

1992-01-01

The success of a mammography screening program requires thorough planning. A dependably high volume and a streamlined efficient operation are essential to survival of the program. Factors that warrant consideration prior to designing such a program include the following: Distinction between screening and diagnostic mammography examinations. Selection of a site that will meet the needs of the community and yet provide a consistently high volume. Low examination cost for screening mammography coupled with a detailed financial analysis and reappraisal on an ongoing basis. A customized marketing program that incorporates methods to increase awareness, compliance, and utilization by women and referring physicians. Well-trained, efficient, and dedicated personnel. An operation that is designed for rapid throughput and expeditious patient flow. An efficient plan for film handling, interpretation, reporting, and storage. Timely communication of examination results. A reliable mechanism for follow-up evaluation and outcome data collection. Establishment of a consistent and reliable quality assurance program and the production of high quality mammograms.

Virtual screening of mandelate racemase mutants with enhanced activity based on binding energy in the transition state.

PubMed

Gu, Jiali; Liu, Min; Guo, Fei; Xie, Wenping; Lu, Wenqiang; Ye, Lidan; Chen, Zhirong; Yuan, Shenfeng; Yu, Hongwei

2014-02-05

Mandelate racemase (MR) is a promising candidate for the dynamic kinetic resolution of racemates. However, the poor activity of MR towards most of its non-natural substrates limits its widespread application. In this work, a virtual screening method based on the binding energy in the transition state was established to assist in the screening of MR mutants with enhanced catalytic efficiency. Using R-3-chloromandelic acid as a model substrate, a total of 53 mutants were constructed based on rational design in the two rounds of screening. The number of mutants for experimental validation was brought down to 17 by the virtual screening method, among which 14 variants turned out to possess improved catalytic efficiency. The variant V26I/Y54V showed 5.2-fold higher catalytic efficiency (k(cat)/K(m)) towards R-3-chloromandelic acid than that observed for the wild-type enzyme. Using this strategy, mutants were successfully obtained for two other substrates, R-mandelamide and R-2-naphthylglycolate (V26I and V29L, respectively), both with a 2-fold improvement in catalytic efficiency. These results demonstrated that this method could effectively predict the trend of mutational effects on catalysis. Analysis from the energetic and structural assays indicated that the enhanced interactions between the active sites and the substrate in the transition state led to improved catalytic efficiency. It was concluded that this virtual screening method based on the binding energy in the transition state was beneficial in enzyme rational redesign and helped to better understand the catalytic properties of the enzyme. Copyright © 2013 Elsevier Inc. All rights reserved.

Efficient integration method for fictitious domain approaches

NASA Astrophysics Data System (ADS)

Duczek, Sascha; Gabbert, Ulrich

2015-10-01

In the current article, we present an efficient and accurate numerical method for the integration of the system matrices in fictitious domain approaches such as the finite cell method (FCM). In the framework of the FCM, the physical domain is embedded in a geometrically larger domain of simple shape which is discretized using a regular Cartesian grid of cells. Therefore, a spacetree-based adaptive quadrature technique is normally deployed to resolve the geometry of the structure. Depending on the complexity of the structure under investigation this method accounts for most of the computational effort. To reduce the computational costs for computing the system matrices an efficient quadrature scheme based on the divergence theorem (Gauß-Ostrogradsky theorem) is proposed. Using this theorem the dimension of the integral is reduced by one, i.e. instead of solving the integral for the whole domain only its contour needs to be considered. In the current paper, we present the general principles of the integration method and its implementation. The results to several two-dimensional benchmark problems highlight its properties. The efficiency of the proposed method is compared to conventional spacetree-based integration techniques.

Strategies for the screening of antibiotic residues in eggs: comparison of the validation of the classical microbiological method with an immunobiosensor method.

PubMed

Gaudin, Valérie; Rault, Annie; Hedou, Celine; Soumet, Christophe; Verdon, Eric

2017-09-01

Efficient screening methods are needed to control antibiotic residues in eggs. A microbiological kit (Explorer® 2.0 test (Zeu Inmunotech, Spain)) and an immunobiosensor kit (Microarray II (AM® II) on Evidence Investigator™ system (Randox, UK)) have been evaluated and validated for screening of antibiotic residues in eggs, according to the European decision EC/2002/657 and to the European guideline for the validation of screening methods. The e-reader™ system, a new automatic incubator/reading system, was coupled to the Explorer 2.0 test. The AM II kit can detect residues of six different families of antibiotics in different matrices including eggs. For both tests, a different liquid/liquid extraction of eggs had to be developed. Specificities of the Explorer 2.0 and AM II kit were equal to 8% and 0% respectively. The detection capabilities were determined for 19 antibiotics, with representatives from different families, for Explorer 2.0 and 12 antibiotics for the AM II kit. For the nine antibiotics having a maximum residue limit (MRL) in eggs, the detection capabilities CCβ of Explorer 2.0 were below the MRL for four antibiotics, equal to the MRL for two antibiotics and between 1 and 1.5 MRLs for the three remaining antibiotics (tetracyclines). For the antibiotics from other families, the detection capabilities were low for beta-lactams and sulfonamides and satisfactory for dihydrostreptomycin (DHS) and fluoroquinolones, which are usually difficult to detect with microbiological tests. The CCβ values of the AM II kit were much lower than the respective MRLs for three detected antibiotics (tetracycline, oxytetracycline, tylosin). Concerning the nine other antibiotics, the detection capabilities determined were low. The highest CCβ was obtained for streptomycin (100 µg kg -1 ).

An Efficient and Rapid Method to Monitor the Oxidative Degradation of Protein Pharmaceuticals: Probing Tyrosine Oxidation with Fluorogenic Derivatization.

PubMed

Bommana, Rupesh; Mozziconacci, Olivier; John Wang, Y; Schöneich, Christian

2017-07-01

The loss of potency of protein therapeutics can be linked to the oxidation of specific amino acid residues leading to a great variety of oxidative modifications. The comprehensive identification of these oxidative modifications requires high-resolution mass spectrometry analysis, which requires time and expensive resources. Here, we propose a fluorogenic derivatization method of oxidized Tyr and Phe yielding benzoxazole derivatives, as an orthogonal technique for the rapid screening of protein oxidation. Four model proteins, IgG1, human growth hormone (hGH), insulin and bovine serum albumin (BSA) were exposed to oxidation via peroxyl radicals and metal-catalyzed reactions and efficiently screened by fluorogenic derivatization of Tyr and Phe oxidation products. Complementary LC-MS analysis was done to identify the extent of methionine oxidation in oxidized proteins. The Fluorogenic derivatization technique can easily be adapted to a 96-well plate, in which several protein formulations can be screened in short time. Representatively for hGH, we show that the formation of benzoxazole parallels the oxidation of Met to methionine sulfoxide which enables estimation of Met oxidation by just recording the fluorescence. Our rapid fluorescence based screening allows for the fast comparison of the stability of multiple formulations.

[Selection of a melanine concentrating hormone receptor-1 (MCHR1) antagonists' focused library and its biological screening with AequoScreen].

PubMed

Flachner, Beáta; Hajdú, István; Dobi, Krisztina; Lorincz, Zsolt; Cseh, Sándor; Dormán, György

2013-01-01

Target focused libraries can be rapidly selected by 2D virtual screening methods from multimillion compounds' repositories if structures of active compounds are available. In the present study a multi-step virtual and in vitro screening cascade is reported to select Melanin Concentrating Hormone Receptor-1 (MCHR1) antagonists. The 2D similarity search combined with physicochemical parameter filtering is suitable for selecting candidates from multimillion compounds' repository. The seeds of the first round virtual screening were collected from the literature and commercial databases, while the seeds of the second round were the hits of the first round. In vitro screening underlined the efficiency of our approach, as in the second screening round the hit rate (8.6 %) significantly improved compared to the first round (1.9%), reaching the antagonist activity even below 10 nM.

The Role of Affordances in Children's Learning Performance and Efficiency When Using Virtual Manipulative Mathematics Touch-Screen Apps

ERIC Educational Resources Information Center

Moyer-Packenham, Patricia S.; Bullock, Emma K.; Shumway, Jessica F.; Tucker, Stephen I.; Watts, Christina M.; Westenskow, Arla; Anderson-Pence, Katie L.; Maahs-Fladung, Cathy; Boyer-Thurgood, Jennifer; Gulkilik, Hilal; Jordan, Kerry

2016-01-01

This paper focuses on understanding the role that affordances played in children's learning performance and efficiency during clinical interviews of their interactions with mathematics apps on touch-screen devices. One hundred children, ages 3 to 8, each used six different virtual manipulative mathematics apps during 30-40-min interviews. The…

Parameterised post-Newtonian expansion in screened regions

NASA Astrophysics Data System (ADS)

McManus, Ryan; Lombriser, Lucas; Peñarrubia, Jorge

2017-12-01

The parameterised post-Newtonian (PPN) formalism has enabled stringent tests of static weak-field gravity in a theory-independent manner. Here we incorporate screening mechanisms of modified gravity theories into the framework by introducing an effective gravitational coupling and defining the PPN parameters as functions of position. To determine these functions we develop a general method for efficiently performing the post-Newtonian expansion in screened regimes. For illustration, we derive all the PPN functions for a cubic galileon and a chameleon model. We also analyse the Shapiro time delay effect for these two models and find no deviations from General Relativity insofar as the signal path and the perturbing mass reside in a screened region of space.

Modulation of molecular hybridization and charge screening in a carbon nanotube network channel using the electrical pulse method.

PubMed

Woo, Jun-Myung; Kim, Seok Hyang; Chun, Honnggu; Kim, Sung Jae; Ahn, Jinhong; Park, Young June

2013-09-21

In this paper, we investigate the effect of electrical pulse bias on DNA hybridization events in a biosensor platform, using a Carbon Nanotube Network (CNN) and Gold Nano Particles (GNP) as an electrical channel. The scheme provides both hybridization rate enhancement of bio molecules, and electrical measurement in a transient state to avoid the charge screening effect, thereby significantly improving the sensitivity. As an example, the probe DNA molecules oscillate with pulse trains, resulting in the enhancement of DNA hybridization efficiency, and accordingly of the sensor performances in Tris-EDTA (TE) buffer solution, by as much as over three times, compared to the non-biasing conditions. More importantly, a wide dynamic range of 10(6) (target-DNA concentration from 5 pM to 5 μM) is achieved in human serum. In addition, the pulse biasing method enables one to obtain the conductance change, before the ions within the Electrical Double Layer (EDL) are redistributed, to avoid the charge screening effect, leading to an additional sensitivity enhancement.

Comprehensive Cancer Screening among Unmarried Women Aged 40–75 Years: Results from the Cancer Screening Project for Women

PubMed Central

Rogers, Michelle L.; Armstrong, Gene F.; Rakowski, William; Bowen, Deborah J.; Hughes, Tonda; McGarry, Kelly A.

2009-01-01

Abstract Objectives We explored self-reported rates of individual on-schedule breast, cervical, and colorectal cancer screenings, as well as an aggregate measure of comprehensive screenings, among unmarried women aged 40–75 years. We compared women who partner with women (WPW) or with women and men (WPWM) to women who partner exclusively with men (WPM). We also compared barriers to on-schedule cancer screenings between WPW/WPWM and WPM. Methods Comparable targeted and respondent-driven sampling methods were used to enroll 213 WPW/WPWM and 417 WPM (n = 630). Logistic regression models were computed to determine if partner gender was associated with each measure of on-schedule screening after controlling for demographic characteristics, health behaviors, and cancer-related experiences. Results Overall, 74.3% of women reported on-schedule breast screening, 78.3% reported on-schedule cervical screening, 66.5% reported on-schedule colorectal screening, and 56.7% reported being on-schedule for comprehensive screening. Partner gender was not associated with any of the measures of on-schedule screening in multivariable analyses. However, women who reported ever putting off, avoiding, or changing the place of screenings because of sexual orientation were less likely to be on-schedule for comprehensive screening. Women who reported barriers associated with taking time from work and body image concerns were also less likely to be on-schedule for comprehensive screening. Conclusions Barriers to cancer screening were comparable across types of examinations as well as between WPW/WPWM and WPM. Developing health promotion programs for unmarried women that address concomitant detection and prevention behaviors may improve the efficiency and effectiveness of healthcare delivery and ultimately assist in reducing multiple disease risks. PMID:19361311

A rapid, efficient and sensitive plate assay for detection and screening of l-asparaginase-producing microorganisms.

PubMed

Mahajan, Richi V; Saran, Saurabh; Saxena, Rajendra K; Srivastava, Ayush K

2013-04-01

l-Asparaginase-producing microbes are conventionally screened on phenol red l-asparagine-containing plates. However, sometimes the contrast of the zone obtained (between yellow and pink) is not very sharp and distinct. In the present investigation, an improved method for screening of the microorganisms producing extracellular l-asparaginase is reported wherein bromothymol blue (BTB) is incorporated as pH indicator in l-asparagine-containing medium instead of phenol red. Plates containing BTB at acidic pH are yellow and turn dark blue at alkaline pH. Thus, a dense dark blue zone is formed around microbial colonies producing l-asparaginase, differentiating between enzyme producers and non-producers. The present method is more sensitive and accurate than the conventional method for screening of both fungi and bacteria producing extracellular l-asparaginase. Furthermore, BTB gives a transient green colour at neutral pH (7.0) and dark blue colour at higher pH 8.0-9.0, indicating the potency of the microorganism for l-asparaginase production. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Novel method for high-throughput colony PCR screening in nanoliter-reactors

PubMed Central

Walser, Marcel; Pellaux, Rene; Meyer, Andreas; Bechtold, Matthias; Vanderschuren, Herve; Reinhardt, Richard; Magyar, Joseph; Panke, Sven; Held, Martin

2009-01-01

We introduce a technology for the rapid identification and sequencing of conserved DNA elements employing a novel suspension array based on nanoliter (nl)-reactors made from alginate. The reactors have a volume of 35 nl and serve as reaction compartments during monoseptic growth of microbial library clones, colony lysis, thermocycling and screening for sequence motifs via semi-quantitative fluorescence analyses. nl-Reactors were kept in suspension during all high-throughput steps which allowed performing the protocol in a highly space-effective fashion and at negligible expenses of consumables and reagents. As a first application, 11 high-quality microsatellites for polymorphism studies in cassava were isolated and sequenced out of a library of 20 000 clones in 2 days. The technology is widely scalable and we envision that throughputs for nl-reactor based screenings can be increased up to 100 000 and more samples per day thereby efficiently complementing protocols based on established deep-sequencing technologies. PMID:19282448

Comparison of three noninvasive methods for hemoglobin screening of blood donors.

PubMed

Ardin, Sergey; Störmer, Melanie; Radojska, Stela; Oustianskaia, Larissa; Hahn, Moritz; Gathof, Birgit S

2015-02-01

To prevent phlebotomy of anemic individuals and to ensure hemoglobin (Hb) content of the blood units, Hb screening of blood donors before donation is essential. Hb values are mostly evaluated by measurement of capillary blood obtained from fingerstick. Rapid noninvasive methods have recently become available and may be preferred by donors and staff. The aim of this study was to evaluate for the first time all different noninvasive methods for Hb screening. Blood donors were screened for Hb levels in three different trials using three different noninvasive methods (Haemospect [MBR Optical Systems GmbH & Co. KG], NBM 200 [LMB Technology GmbH], Pronto-7 [Masimo Europe Ltd]) in comparison to the established fingerstick method (CompoLab Hb [Fresenius Kabi GmbH]) and to levels obtained from venous samples on a cell counter (Sysmex [Sysmex Europe GmbH]) as reference. The usability of the noninvasive methods was assessed with an especially developed survey. Technical failures occurred by using the Pronto-7 due to nail polish, skin color, or ambient light. The NBM 200 also showed a high sensitivity to ambient light and noticeably lower Hb levels for women than obtained from the Sysmex. The statistical analysis showed the following bias and standard deviation of differences of all methods in comparison to the venous results: Haemospect, -0.22 ± 1.24; NBM, 200 -0.12 ± 1.14; Pronto-7, -0.50 ± 0.99; and CompoLab Hb, -0.53 ± 0.81. Noninvasive Hb tests represent an attractive alternative by eliminating pain and reducing risks of blood contamination. The main problem for generating reliable results seems to be preanalytical variability in sampling. Despite the sensitivity to environmental stress, all methods are suitable for Hb measurement. © 2014 AABB.

A fast boosting-based screening method for large-scale association study in complex traits with genetic heterogeneity.

PubMed

Wang, Lu-Yong; Fasulo, D

2006-01-01

Genome-wide association study for complex diseases will generate massive amount of single nucleotide polymorphisms (SNPs) data. Univariate statistical test (i.e. Fisher exact test) was used to single out non-associated SNPs. However, the disease-susceptible SNPs may have little marginal effects in population and are unlikely to retain after the univariate tests. Also, model-based methods are impractical for large-scale dataset. Moreover, genetic heterogeneity makes the traditional methods harder to identify the genetic causes of diseases. A more recent random forest method provides a more robust method for screening the SNPs in thousands scale. However, for more large-scale data, i.e., Affymetrix Human Mapping 100K GeneChip data, a faster screening method is required to screening SNPs in whole-genome large scale association analysis with genetic heterogeneity. We propose a boosting-based method for rapid screening in large-scale analysis of complex traits in the presence of genetic heterogeneity. It provides a relatively fast and fairly good tool for screening and limiting the candidate SNPs for further more complex computational modeling task.

Fragment screening of cyclin G-associated kinase by weak affinity chromatography.

PubMed

Meiby, Elinor; Knapp, Stefan; Elkins, Jonathan M; Ohlson, Sten

2012-11-01

Fragment-based drug discovery (FBDD) has become a new strategy for drug discovery where lead compounds are evolved from small molecules. These fragments form low affinity interactions (dissociation constant (K(D)) = mM - μM) with protein targets, which require fragment screening methods of sufficient sensitivity. Weak affinity chromatography (WAC) is a promising new technology for fragment screening based on selective retention of fragments by a drug target. Kinases are a major pharmaceutical target, and FBDD has been successfully applied to several of these targets. In this work, we have demonstrated the potential to use WAC in combination with mass spectrometry (MS) detection for fragment screening of a kinase target-cyclin G-associated kinase (GAK). One hundred seventy fragments were selected for WAC screening by virtual screening of a commercial fragment library against the ATP-binding site of five different proteins. GAK protein was immobilized on a capillary HPLC column, and compound binding was characterized by frontal affinity chromatography. Compounds were screened in sets of 13 or 14, in combination with MS detection for enhanced throughput. Seventy-eight fragments (46 %) with K(D) < 200 μM were detected, including a few highly efficient GAK binders (K(D) of 2 μM; ligand efficiency = 0.51). Of special interest is that chiral screening by WAC may be possible, as two stereoisomeric fragments, which both contained one chiral center, demonstrated twin peaks. This ability, in combination with the robustness, sensitivity, and simplicity of WAC makes it a new method for fragment screening of considerable potential.

The acute social defeat stress and nest-building test paradigm: A potential new method to screen drugs for depressive-like symptoms.

PubMed

Otabi, Hikari; Goto, Tatsuhiko; Okayama, Tsuyoshi; Kohari, Daisuke; Toyoda, Atsushi

2017-02-01

Psychosocial stress can cause mental conditions such as depression in humans. To develop drug therapies for the treatment of depression, it is necessary to use animal models of depression to screen drug candidates that exhibit anti-depressive effects. Unfortunately, the present methods of drug screening for antidepressants, the forced-swim test and tail-suspension test, are limiting factors in drug discovery because they are not based on the constructive validity of objective phenotypes in depression. Previously, we discovered that the onset of nest building is severely delayed in mice exposed to subchronic mild social defeat stress (sCSDS). Therefore, a novel paradigm combining acute social defeat stress (ASDS) and the nest-building test (SNB) were established for the efficient screening of drugs for depressive-like symptoms. Since ASDS severely delayed the nest-building process as shown in chronically social defeated mice, we sought to rescue the delayed nest-building behavior in ASDS mice. Injecting a specific serotonin 2a receptor antagonist (SR-46349B), the nest-building deficit exhibited by ASDS mice was partially rescued. On the other hand, a selective serotonin reuptake inhibitor (fluoxetine) did not rescue the nest-building deficit in ASDS mice. Therefore, we conclude that the SNB paradigm is an another potential behavioral method for screening drugs for depressive-like symptoms including attention deficit, anxiety, low locomotion, and decreased motivation. Copyright © 2016 Elsevier B.V. All rights reserved.

Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP).

PubMed

Hoskins, Roger A; Stapleton, Mark; George, Reed A; Yu, Charles; Wan, Kenneth H; Carlson, Joseph W; Celniker, Susan E

2005-12-02

cDNA cloning is a central technology in molecular biology. cDNA sequences are used to determine mRNA transcript structures, including splice junctions, open reading frames (ORFs) and 5'- and 3'-untranslated regions (UTRs). cDNA clones are valuable reagents for functional studies of genes and proteins. Expressed Sequence Tag (EST) sequencing is the method of choice for recovering cDNAs representing many of the transcripts encoded in a eukaryotic genome. However, EST sequencing samples a cDNA library at random, and it recovers transcripts with low expression levels inefficiently. We describe a PCR-based method for directed screening of plasmid cDNA libraries. We demonstrate its utility in a screen of libraries used in our Drosophila EST projects for 153 transcription factor genes that were not represented by full-length cDNA clones in our Drosophila Gene Collection. We recovered high-quality, full-length cDNAs for 72 genes and variously compromised clones for an additional 32 genes. The method can be used at any scale, from the isolation of cDNA clones for a particular gene of interest, to the improvement of large gene collections in model organisms and the human. Finally, we discuss the relative merits of directed cDNA library screening and RT-PCR approaches.

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

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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach

NASA Astrophysics Data System (ADS)

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D.; Duvenaud, David; MacLaurin, Dougal; Blood-Forsythe, Martin A.; Chae, Hyun Sik; Einzinger, Markus; Ha, Dong-Gwang; Wu, Tony; Markopoulos, Georgios; Jeon, Soonok; Kang, Hosuk; Miyazaki, Hiroshi; Numata, Masaki; Kim, Sunghan; Huang, Wenliang; Hong, Seong Ik; Baldo, Marc; Adams, Ryan P.; Aspuru-Guzik, Alán

2016-10-01

Virtual screening is becoming a ground-breaking tool for molecular discovery due to the exponential growth of available computer time and constant improvement of simulation and machine learning techniques. We report an integrated organic functional material design process that incorporates theoretical insight, quantum chemistry, cheminformatics, machine learning, industrial expertise, organic synthesis, molecular characterization, device fabrication and optoelectronic testing. After exploring a search space of 1.6 million molecules and screening over 400,000 of them using time-dependent density functional theory, we identified thousands of promising novel organic light-emitting diode molecules across the visible spectrum. Our team collaboratively selected the best candidates from this set. The experimentally determined external quantum efficiencies for these synthesized candidates were as large as 22%.

Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach.

PubMed

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D; Duvenaud, David; Maclaurin, Dougal; Blood-Forsythe, Martin A; Chae, Hyun Sik; Einzinger, Markus; Ha, Dong-Gwang; Wu, Tony; Markopoulos, Georgios; Jeon, Soonok; Kang, Hosuk; Miyazaki, Hiroshi; Numata, Masaki; Kim, Sunghan; Huang, Wenliang; Hong, Seong Ik; Baldo, Marc; Adams, Ryan P; Aspuru-Guzik, Alán

2016-10-01

Virtual screening is becoming a ground-breaking tool for molecular discovery due to the exponential growth of available computer time and constant improvement of simulation and machine learning techniques. We report an integrated organic functional material design process that incorporates theoretical insight, quantum chemistry, cheminformatics, machine learning, industrial expertise, organic synthesis, molecular characterization, device fabrication and optoelectronic testing. After exploring a search space of 1.6 million molecules and screening over 400,000 of them using time-dependent density functional theory, we identified thousands of promising novel organic light-emitting diode molecules across the visible spectrum. Our team collaboratively selected the best candidates from this set. The experimentally determined external quantum efficiencies for these synthesized candidates were as large as 22%.

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. Copyright © 2013 Elsevier B.V. All rights reserved.

Preventing Sudden Death: Cardiovascular Screening of Young Athletes.

ERIC Educational Resources Information Center

Ades, Philip A.

1992-01-01

Efficiently and inexpensively identifying athletes at risk for exercise-related sudden death is difficult. The article discusses types of cardiac disorders and outlines a practical screening method that features a cardiac history questionnaire designed to identify symptomatic athletes and those with a family history of congenital heart disease.…

Evaluation of Thermoelectric Devices by the Slope-Efficiency Method

DTIC Science & Technology

2016-09-01

ARL-TR-7837 ● SEP 2016 US Army Research Laboratory Evaluation of Thermoelectric Devices by the Slope-Efficiency Method by...Evaluation of Thermoelectric Devices by the Slope-Efficiency Method by Patrick J Taylor Sensors and Electron Devices Directorate, ARL Jay R...

Comparative analysis of quantitative efficiency evaluation methods for transportation networks.

PubMed

He, Yuxin; Qin, Jin; Hong, Jian

2017-01-01

An effective evaluation of transportation network efficiency could offer guidance for the optimal control of urban traffic. Based on the introduction and related mathematical analysis of three quantitative evaluation methods for transportation network efficiency, this paper compares the information measured by them, including network structure, traffic demand, travel choice behavior and other factors which affect network efficiency. Accordingly, the applicability of various evaluation methods is discussed. Through analyzing different transportation network examples it is obtained that Q-H method could reflect the influence of network structure, traffic demand and user route choice behavior on transportation network efficiency well. In addition, the transportation network efficiency measured by this method and Braess's Paradox can be explained with each other, which indicates a better evaluation of the real operation condition of transportation network. Through the analysis of the network efficiency calculated by Q-H method, it can also be drawn that a specific appropriate demand is existed to a given transportation network. Meanwhile, under the fixed demand, both the critical network structure that guarantees the stability and the basic operation of the network and a specific network structure contributing to the largest value of the transportation network efficiency can be identified.

EPA’s Travel Efficiency Method (TEAM) AMPO Presentation

EPA Pesticide Factsheets

Presentation describes EPA’s Travel Efficiency Assessment Method (TEAM) assessing potential travel efficiency strategies for reducing travel activity and emissions, includes reduction estimates in Vehicle Miles Traveled in four different geographic areas.

Efficiency of personal dosimetry methods in vascular interventional radiology.

PubMed

Bacchim Neto, Fernando Antonio; Alves, Allan Felipe Fattori; Mascarenhas, Yvone Maria; Giacomini, Guilherme; Maués, Nadine Helena Pelegrino Bastos; Nicolucci, Patrícia; de Freitas, Carlos Clayton Macedo; Alvarez, Matheus; Pina, Diana Rodrigues de

2017-05-01

The aim of the present study was to determine the efficiency of six methods for calculate the effective dose (E) that is received by health professionals during vascular interventional procedures. We evaluated the efficiency of six methods that are currently used to estimate professionals' E, based on national and international recommendations for interventional radiology. Equivalent doses on the head, neck, chest, abdomen, feet, and hands of seven professionals were monitored during 50 vascular interventional radiology procedures. Professionals' E was calculated for each procedure according to six methods that are commonly employed internationally. To determine the best method, a more efficient E calculation method was used to determine the reference value (reference E) for comparison. The highest equivalent dose were found for the hands (0.34±0.93mSv). The two methods that are described by Brazilian regulations overestimated E by approximately 100% and 200%. The more efficient method was the one that is recommended by the United States National Council on Radiological Protection and Measurements (NCRP). The mean and median differences of this method relative to reference E were close to 0%, and its standard deviation was the lowest among the six methods. The present study showed that the most precise method was the one that is recommended by the NCRP, which uses two dosimeters (one over and one under protective aprons). The use of methods that employ at least two dosimeters are more efficient and provide better information regarding estimates of E and doses for shielded and unshielded regions. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Localization of interictal epileptic spikes with MEG: optimization of an automated beamformer screening method (SAMepi) in a diverse epilepsy population

PubMed Central

Scott, Jonathan M.; Robinson, Stephen E.; Holroyd, Tom; Coppola, Richard; Sato, Susumu; Inati, Sara K.

2016-01-01

OBJECTIVE To describe and optimize an automated beamforming technique followed by identification of locations with excess kurtosis (g2) for efficient detection and localization of interictal spikes in medically refractory epilepsy patients. METHODS Synthetic Aperture Magnetometry with g2 averaged over a sliding time window (SAMepi) was performed in 7 focal epilepsy patients and 5 healthy volunteers. The effect of varied window lengths on detection of spiking activity was evaluated. RESULTS Sliding window lengths of 0.5–10 seconds performed similarly, with 0.5 and 1 second windows detecting spiking activity in one of the 3 virtual sensor locations with highest kurtosis. These locations were concordant with the region of eventual surgical resection in these 7 patients who remained seizure free at one year. Average g2 values increased with increasing sliding window length in all subjects. In healthy volunteers kurtosis values stabilized in datasets longer than two minutes. CONCLUSIONS SAMepi using g2 averaged over 1 second sliding time windows in datasets of at least 2 minutes duration reliably identified interictal spiking and the presumed seizure focus in these 7 patients. Screening the 5 locations with highest kurtosis values for spiking activity is an efficient and accurate technique for localizing interictal activity using MEG. SIGNIFICANCE SAMepi should be applied using the parameter values and procedure described for optimal detection and localization of interictal spikes. Use of this screening procedure could significantly improve the efficiency of MEG analysis if clinically validated. PMID:27760068

SELEX-Based Screening of Exosome-Tropic RNA.

PubMed

Yamashita, Takuma; Shinotsuka, Haruka; Takahashi, Yuki; Kato, Kana; Nishikawa, Makiya; Takakura, Yoshinobu

2017-01-01

Cell-derived nanosized vesicles or exosomes are expected to become delivery carriers for functional RNAs, such as small interfering RNA (siRNA). A method to efficiently load functional RNAs into exosomes is required for the development of exosome-based delivery carriers of functional RNAs. However, there is no method to find exosome-tropic exogenous RNA sequences. In this study, we used a systematic evolution of ligands by exponential enrichment (SELEX) method to screen exosome-tropic RNAs that can be used to load functional RNAs into exosomes by conjugation. Pooled single stranded 80-base RNAs, each of which contains a randomized 40-base sequence, were transfected into B16-BL6 murine melanoma cells and exosomes were collected from the cells. RNAs extracted from the exosomes were subjected to next round of SELEX. Cloning and sequencing of RNAs in SELEX-screened RNA pools showed that 29 of 56 clones had a typical RNA sequence. The sequence found by SELEX was enriched in exosomes after transfection to B16-BL6 cells. The results show that the SELEX-based method can be used for screening of exosome-tropic RNAs.

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.

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.

An automatic on-line 2,2-diphenyl-1-picrylhydrazyl-high performance liquid chromatography method for high-throughput screening of antioxidants from natural products.

PubMed

Lu, Yanzhen; Wu, Nan; Fang, Yingtong; Shaheen, Nusrat; Wei, Yun

2017-10-27

Many natural products are rich in antioxidants which play an important role in preventing or postponing a variety of diseases, such as cardiovascular and inflammatory disease, diabetes as well as breast cancer. In this paper, an automatic on-line 2,2-diphenyl-1-picrylhydrazyl-high performance liquid chromatography (DPPH-HPLC) method was established for antioxidants screening with nine standards including organic acids (4-hydroxyphenylacetic acid, p-coumaric acid, ferulic acid, and benzoic acid), alkaloids (coptisine and berberine), and flavonoids (quercitrin, astragalin, and quercetin). The optimal concentration of DPPH was determined, and six potential antioxidants including 4-hydroxyphenylacetic acid, p-coumaric acid, ferulic acid, quercitrin, astragalin, and quercetin, and three non-antioxidants including benzoic acid, coptisine, and berberine, were successfully screened out and validated by conventional DPPH radical scavenging activity assay. The established method has been applied to the crude samples of Saccharum officinarum rinds, Coptis chinensis powders, and Malus pumila leaves, consecutively. Two potential antioxidant compounds from Saccharum officinarum rinds and five potential antioxidant compounds from Malus pumila eaves were rapidly screened out. Then these seven potential antioxidants were purified and identified as p-coumaric acid, ferulic acid, phloridzin, isoquercitrin, quercetin-3-xyloside, quercetin-3-arabinoside, and quercetin-3-rhamnoside using countercurrent chromatography combined with mass spectrometry and their antioxidant activities were further evaluated by conventional DPPH radical scavenging assay. The activity result was in accordance with that of the established method. This established method is cheap and automatic, and could be used as an efficient tool for high-throughput antioxidant screening from various complex natural products. Copyright © 2017 Elsevier B.V. All rights reserved.

A novel accelerated oxidative stability screening method for pharmaceutical solids.

PubMed

Zhu, Donghua Alan; Zhang, Geoff G Z; George, Karen L S T; Zhou, Deliang

2011-08-01

Despite the fact that oxidation is the second most frequent degradation pathway for pharmaceuticals, means of evaluating the oxidative stability of pharmaceutical solids, especially effective stress testing, are still lacking. This paper describes a novel experimental method for peroxide-mediated oxidative stress testing on pharmaceutical solids. The method utilizes urea-hydrogen peroxide, a molecular complex that undergoes solid-state decomposition and releases hydrogen peroxide vapor at elevated temperatures (e.g., 30°C), as a source of peroxide. The experimental setting for this method is simple, convenient, and can be operated routinely in most laboratories. The fundamental parameter of the system, that is, hydrogen peroxide vapor pressure, was determined using a modified spectrophotometric method. The feasibility and utility of the proposed method in solid form selection have been demonstrated using various solid forms of ephedrine. No degradation was detected for ephedrine hydrochloride after exposure to the hydrogen peroxide vapor for 2 weeks, whereas both anhydrate and hemihydrate free base forms degraded rapidly under the test conditions. In addition, both the anhydrate and the hemihydrate free base degraded faster when exposed to hydrogen peroxide vapor at 30°C under dry condition than at 30°C/75% relative humidity (RH). A new degradation product was also observed under the drier condition. The proposed method provides more relevant screening conditions for solid dosage forms, and is useful in selecting optimal solid form(s), determining potential degradation products, and formulation screening during development. Copyright © 2011 Wiley-Liss, Inc.

Use of machine learning to improve autism screening and diagnostic instruments: effectiveness, efficiency, and multi-instrument fusion

PubMed Central

Bone, Daniel; Bishop, Somer; Black, Matthew P.; Goodwin, Matthew S.; Lord, Catherine; Narayanan, Shrikanth S.

2016-01-01

Background Machine learning (ML) provides novel opportunities for human behavior research and clinical translation, yet its application can have noted pitfalls (Bone et al., 2015). In this work, we fastidiously utilize ML to derive autism spectrum disorder (ASD) instrument algorithms in an attempt to improve upon widely-used ASD screening and diagnostic tools. Methods The data consisted of Autism Diagnostic Interview-Revised (ADI-R) and Social Responsiveness Scale (SRS) scores for 1,264 verbal individuals with ASD and 462 verbal individuals with non-ASD developmental or psychiatric disorders (DD), split at age 10. Algorithms were created via a robust ML classifier, support vector machine (SVM), while targeting best-estimate clinical diagnosis of ASD vs. non-ASD. Parameter settings were tuned in multiple levels of cross-validation. Results The created algorithms were more effective (higher performing) than current algorithms, were tunable (sensitivity and specificity can be differentially weighted), and were more efficient (achieving near-peak performance with five or fewer codes). Results from ML-based fusion of ADI-R and SRS are reported. We present a screener algorithm for below (above) age 10 that reached 89.2% (86.7%) sensitivity and 59.0% (53.4%) specificity with only five behavioral codes. Conclusions ML is useful for creating robust, customizable instrument algorithms. In a unique dataset comprised of controls with other difficulties, our findings highlight limitations of current caregiver-report instruments and indicate possible avenues for improving ASD screening and diagnostic tools. PMID:27090613

Comparative analysis of quantitative efficiency evaluation methods for transportation networks

PubMed Central

He, Yuxin; Hong, Jian

2017-01-01

An effective evaluation of transportation network efficiency could offer guidance for the optimal control of urban traffic. Based on the introduction and related mathematical analysis of three quantitative evaluation methods for transportation network efficiency, this paper compares the information measured by them, including network structure, traffic demand, travel choice behavior and other factors which affect network efficiency. Accordingly, the applicability of various evaluation methods is discussed. Through analyzing different transportation network examples it is obtained that Q-H method could reflect the influence of network structure, traffic demand and user route choice behavior on transportation network efficiency well. In addition, the transportation network efficiency measured by this method and Braess’s Paradox can be explained with each other, which indicates a better evaluation of the real operation condition of transportation network. Through the analysis of the network efficiency calculated by Q-H method, it can also be drawn that a specific appropriate demand is existed to a given transportation network. Meanwhile, under the fixed demand, both the critical network structure that guarantees the stability and the basic operation of the network and a specific network structure contributing to the largest value of the transportation network efficiency can be identified. PMID:28399165

Plate-based diversity subset screening generation 2: an improved paradigm for high-throughput screening of large compound files.

PubMed

Bell, Andrew S; Bradley, Joseph; Everett, Jeremy R; Loesel, Jens; McLoughlin, David; Mills, James; Peakman, Marie-Claire; Sharp, Robert E; Williams, Christine; Zhu, Hongyao

2016-11-01

High-throughput screening (HTS) is an effective method for lead and probe discovery that is widely used in industry and academia to identify novel chemical matter and to initiate the drug discovery process. However, HTS can be time consuming and costly and the use of subsets as an efficient alternative to screening entire compound collections has been investigated. Subsets may be selected on the basis of chemical diversity, molecular properties, biological activity diversity or biological target focus. Previously, we described a novel form of subset screening: plate-based diversity subset (PBDS) screening, in which the screening subset is constructed by plate selection (rather than individual compound cherry-picking), using algorithms that select for compound quality and chemical diversity on a plate basis. In this paper, we describe a second-generation approach to the construction of an updated subset: PBDS2, using both plate and individual compound selection, that has an improved coverage of the chemical space of the screening file, whilst only selecting the same number of plates for screening. We describe the validation of PBDS2 and its successful use in hit and lead discovery. PBDS2 screening became the default mode of singleton (one compound per well) HTS for lead discovery in Pfizer.

New screening methods for donor eye-bank eyes.

PubMed

Terry, M A; Ousley, P J

1999-07-01

Current methods of screening donor eyes for corneal transplantation are not always effective in excluding corneas with abnormal topography. We used the Orbscan to determine whether corneal-thickness maps could be used as a technique for donor tissue screening. Forty eye-bank eyes were measured with the Orbscan, and a corneal-thickness map was generated. Average central pachymetry measurements from each map were compared with the thinnest midperipheral thickness reading. Two eyes from a donor who had photorefractive keratectomy (PRK) and two eyes from a donor with keratoconus were then compared with the normal donor eye results. The average difference between the thinnest midperipheral pachymetry and the central pachymetry in the control group was 0.040 +/- 0.026 mm. The eyes from the donor with PRK showed larger disparities between the central and midperipheral thicknesses because of the thinned central cornea, with differences of 0.154 mm in the right eye and 0.106 mm in the left eye. The eyes from the donor with keratoconus had midperipheral corneas that were thinner than the center, indicating eccentric, ectatic cones. The differences in thickness between the center and midperiphery in the eyes from the donor with PRK and the donor with keratoconus differed from the control group by >2 SD. Diseases or surgery that affect the relationship between the central and midperipheral corneal thickness may be screened through Orbscan pachymetry mapping with comparison with a normal range.

Establishment of A431 cell membrane chromatography-RPLC method for screening target components from Radix Caulophylli.

PubMed

Hou, Xiaofang; Wang, Sicen; Hou, Jingjing; He, Langchong

2011-03-01

We describe here an analytical method of A431 cell membrane chromatography (A431/CMC) (CMC, cell membrane chromatography) combined with RPLC for recognition, separation, and identification of target components from traditional Chinese medicines (TCMs) Radix Caulophylli. The A431 cells with high expressed epidermal growth factor receptor (EGFR) were used to prepare the stationary phase in the CMC model. Retention fractions on the A431-CMC model were collected using an automated fraction collection and injection module (FC/I). Each fraction was analyzed by RPLC under the optimized conditions. Gefitinib and erlotinib were used as standard compounds to investigate the suitability and reliability of the A431 cell membrane chromatography-RPLC method prior to screening target component from Radix Caulophylli total alkaloids. The results indicated that caulophine and taspine were the target component acting on the epidermal growth factor receptor. This method could be an efficient way in drug discovery using natural medicinal herbs as a source of novel compounds. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Benefits of an Android Based Tablet Application in Primary Screening for Eye Diseases in a Rural Population, India.

PubMed

Imtiaz, Sayed Ahmed; Krishnaiah, Sannapaneni; Yadav, Sunil Kumar; Bharath, Balasubramaniam; Ramani, Ramanathan V

2017-04-01

To investigate the effectiveness, efficiency and cost gains in collecting patient eye health information from remote rural villages of India by trained field investigators through an Android Based Tablet Application namely 'Sankara Electronic Remote Vision Information System (SERVIS)". During January and March 2016, a population based cross-sectional study was conducted in three Indian states employing SERVIS and manual method. The SERVIS application has a 48-items survey instrument programed into the application. Data on 281 individuals were collected for each of these methods as part of screening. The demographic details of individuals between both screening methods were comparable (P>0.05). The mean time (in minutes) to screen an individual by SERVIS was significantly less when compared to manual method (6.57±1.46 versus 11.93±1.53) (P<0.0001). The efficiency of SERVIS in screening was significantly evident as 26% (n = 73) of the patients screened have been referred to campsite and 69.8% (n = 51) of those referred were visited the campsite for a detailed eye examination by an ophthalmologist. The cost of screening through SERVIS is significantly less when compared to manual method; INR 7,633 (USD 113.9) Versus INR 24,780 (USD 370). SERVIS is an effective and efficient tool in terms of patients' referral conversion to the camp site leading to timely detection of potential blinding eye conditions and their appropriate treatment. This ensures timely prevention of avoidable blindness and visual impairment. In addition, the storage and access of eye health epidemiological quality data is helpful to plan appropriate blindness prevention initiatives in rural India.

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…

A new approach for the screening of carotid lesions: a 'fast-track' method with the use of new generation hand-held ultrasound devices.

PubMed

Aboyans, V; Lacroix, P; Jeannicot, A; Guilloux, J; Bertin, F; Laskar, M

2004-09-01

We assessed the usefulness of fast-track neck sonography with a new-generation hand-held ultrasound scanner in the detection of > or =60% carotid stenosis. Patients with a past history of atherosclerotic disease or presence of risk factors were enrolled. All had fast-track carotid screening with a hand-held ultrasound scanner. Initial assessment was performed with our quick imaging protocol. A second examiner performed a conventional complete carotid duplex as gold-standard. We enrolled 197 consecutive patients with a mean age of 67 years (range 35-94). A carotid stenosis >60% was detected in 13 cases (6%). The sensitivity, specificity, positive and negative predictive value of fast-track sonography was 100%, 64%, 17% and 100%, respectively. Concomitant power Doppler imaging during the fast-track method did not improve accuracy. The use of a fast-track method with a hand-held ultrasound device can reduce the number of unnecessary carotid Duplex and enhance the screening efficiency without missing significant carotid stenoses.

Condorcet and borda count fusion method for ligand-based virtual screening.

PubMed

Ahmed, Ali; Saeed, Faisal; Salim, Naomie; Abdo, Ammar

2014-01-01

It is known that any individual similarity measure will not always give the best recall of active molecule structure for all types of activity classes. Recently, the effectiveness of ligand-based virtual screening approaches can be enhanced by using data fusion. Data fusion can be implemented using two different approaches: group fusion and similarity fusion. Similarity fusion involves searching using multiple similarity measures. The similarity scores, or ranking, for each similarity measure are combined to obtain the final ranking of the compounds in the database. The Condorcet fusion method was examined. This approach combines the outputs of similarity searches from eleven association and distance similarity coefficients, and then the winner measure for each class of molecules, based on Condorcet fusion, was chosen to be the best method of searching. The recall of retrieved active molecules at top 5% and significant test are used to evaluate our proposed method. 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 experiments with the standard two data sets show that the use of Condorcet fusion provides a very simple way of improving the ligand-based virtual screening, especially when the active molecules being sought have a lowest degree of structural heterogeneity. However, the effectiveness of the Condorcet fusion was increased slightly when structural sets of high diversity activities were being sought.

Condorcet and borda count fusion method for ligand-based virtual screening

PubMed Central

2014-01-01

Background It is known that any individual similarity measure will not always give the best recall of active molecule structure for all types of activity classes. Recently, the effectiveness of ligand-based virtual screening approaches can be enhanced by using data fusion. Data fusion can be implemented using two different approaches: group fusion and similarity fusion. Similarity fusion involves searching using multiple similarity measures. The similarity scores, or ranking, for each similarity measure are combined to obtain the final ranking of the compounds in the database. Results The Condorcet fusion method was examined. This approach combines the outputs of similarity searches from eleven association and distance similarity coefficients, and then the winner measure for each class of molecules, based on Condorcet fusion, was chosen to be the best method of searching. The recall of retrieved active molecules at top 5% and significant test are used to evaluate our proposed method. 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. Conclusions Simulated virtual screening experiments with the standard two data sets show that the use of Condorcet fusion provides a very simple way of improving the ligand-based virtual screening, especially when the active molecules being sought have a lowest degree of structural heterogeneity. However, the effectiveness of the Condorcet fusion was increased slightly when structural sets of high diversity activities were being sought. PMID:24883114

Hidden drivers of low-dose pharmaceutical pollutant mixtures revealed by the novel GSA-QHTS screening method

PubMed Central

Rodea-Palomares, Ismael; Gonzalez-Pleiter, Miguel; Gonzalo, Soledad; Rosal, Roberto; Leganes, Francisco; Sabater, Sergi; Casellas, Maria; Muñoz-Carpena, Rafael; Fernández-Piñas, Francisca

2016-01-01

The ecological impacts of emerging pollutants such as pharmaceuticals are not well understood. The lack of experimental approaches for the identification of pollutant effects in realistic settings (that is, low doses, complex mixtures, and variable environmental conditions) supports the widespread perception that these effects are often unpredictable. To address this, we developed a novel screening method (GSA-QHTS) that couples the computational power of global sensitivity analysis (GSA) with the experimental efficiency of quantitative high-throughput screening (QHTS). We present a case study where GSA-QHTS allowed for the identification of the main pharmaceutical pollutants (and their interactions), driving biological effects of low-dose complex mixtures at the microbial population level. The QHTS experiments involved the integrated analysis of nearly 2700 observations from an array of 180 unique low-dose mixtures, representing the most complex and data-rich experimental mixture effect assessment of main pharmaceutical pollutants to date. An ecological scaling-up experiment confirmed that this subset of pollutants also affects typical freshwater microbial community assemblages. Contrary to our expectations and challenging established scientific opinion, the bioactivity of the mixtures was not predicted by the null mixture models, and the main drivers that were identified by GSA-QHTS were overlooked by the current effect assessment scheme. Our results suggest that current chemical effect assessment methods overlook a substantial number of ecologically dangerous chemical pollutants and introduce a new operational framework for their systematic identification. PMID:27617294

Development and validation of real-time PCR screening methods for detection of cry1A.105 and cry2Ab2 genes in genetically modified organisms.

PubMed

Dinon, Andréia Z; Prins, Theo W; van Dijk, Jeroen P; Arisi, Ana Carolina M; Scholtens, Ingrid M J; Kok, Esther J

2011-05-01

Primers and probes were developed for the element-specific detection of cry1A.105 and cry2Ab2 genes, based on their DNA sequence as present in GM maize MON89034. Cry genes are present in many genetically modified (GM) plants and they are important targets for developing GMO element-specific detection methods. Element-specific methods can be of use to screen for the presence of GMOs in food and feed supply chains. Moreover, a combination of GMO elements may indicate the potential presence of unapproved GMOs (UGMs). Primer-probe combinations were evaluated in terms of specificity, efficiency and limit of detection. Except for specificity, the complete experiment was performed in 9 PCR runs, on 9 different days and by testing 8 DNA concentrations. The results showed a high specificity and efficiency for cry1A.105 and cry2Ab2 detection. The limit of detection was between 0.05 and 0.01 ng DNA per PCR reaction for both assays. These data confirm the applicability of these new primer-probe combinations for element detection that can contribute to the screening for GM and UGM crops in food and feed samples.

Pharmacy diabetes care program: analysis of two screening methods for undiagnosed type 2 diabetes in Australian community pharmacy.

PubMed

Krass, I; Mitchell, B; Clarke, P; Brillant, M; Dienaar, R; Hughes, J; Lau, P; Peterson, G; Stewart, K; Taylor, S; Wilkinson, J; Armour, C

2007-03-01

To compare the efficacy and cost-effectiveness of two methods of screening for undiagnosed type 2 diabetes in Australian community pharmacy. A random sample of 30 pharmacies were allocated into two groups: (i) tick test only (TTO); or (ii) sequential screening (SS) method. Both methods used the same initial risk assessment for type 2 diabetes. Subjects with one or more risk factors in the TTO group were offered a referral to their general practitioner (GP). Under the SS method, patients with risk factors were offered a capillary blood glucose test and those identified as being at risk referred to a GP. The effectiveness and cost-effectiveness of these approaches was assessed. A total of 1286 people were screened over a period of 3 months. The rate of diagnosis of diabetes was significantly higher for SS compared with the TTO method (1.7% versus 0.2%; p=0.008). The SS method resulted in fewer referrals to the GP and a higher uptake of referrals than the TTO method and so was the more cost-effective screening method. SS is the superior method from a cost and efficacy perspective. It should be considered as the preferred option for screening by community based pharmacists in Australia.

[Effects, safety and cost-benefit analysis of Down syndrome screening in first trimester].

PubMed

Shengmou, Lin; Min, Chen; Chenhong, Wang; Shengli, Li; Jiansheng, Xie; Hui, Yuan; Dinghao, Lin; Xiaoxia, Wu; Wei, Wang; Hongyun, Zhang; Haiyan, Tang

2014-05-01

To investigate the effects, safety and cost-benefit analysis of Down syndrome screening in first trimester. From January 2009 to December 2012, 43 729 pregnant women undergoing 3 methods of Down syndrome traditional screening strategies in Shenzhen Maternity and Child Healthcare Hospital were studied retrospectively, including in 17 502 cases in pregnancy associated plasma protein A (PAPP-A) and free β-hCG measured biochemistry screening, 14 080 cases in nuchal translucency (NT) screening and 12 147 cases in combined screening, meanwhile, 7 389 cases on non-invasive fetal trisomy test (NIFTY) were performed in Huada Gene Research Institute(BGI). The effects and safety of four screening strategies were assessed throughout a decision tree. The economical characters of each screening strategy were compared by cost-effectiveness analysis as well as cost-benefit analysis. (1) The effects of four strategies are: NIFTY > combined screening > NT screening > biochemistry screening. (2) The safety of four strategies are: NIFTY > combined screening > NT screening > biochemistry screening. (3) Cost-effectiveness analysis and cost-benefit analysis:the biochemistry screening has lowest cost-effectiveness ratio (CER) and highest cost-benefit ratio (CBR), which performed a better economical efficiency. The incremental CER of three traditional screening strategies are all less than the economical burden of Down syndrome.NIFTY has highest CER and negative net present value (NPV), NPV would be positive and CBR would be more than 1 if the price of NIFTY reduce to 1 434 Yuan. Combined screening possess best screening efficiency, while biochemistry screening was demonstrated more economical in traditional screening.NIFTY is the future of Down syndrome screening.

TU-EF-204-08: Dose Efficiency of Added Beam-Shaping Filter with Varied Attenuation Levels in Lung-Cancer Screening CT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, C; Yu, L; Vrieze, T

Purpose: Added filtration such as tin filter has the potential to improve dose efficiency of x-ray beam in lung-cancer screening CT. However, dose efficiency with added beam filtration is highly dependent on patient attenuation level. In this phantom study, we evaluated the image quality at different tube voltages with and without added tin filter when attenuation level varies. Methods: A 30 x 20 cm anthropomorphic thorax phantom with three added extension rings were used to simulate small (S), medium (M), large (L), and extra-large (XL) adult patients. These phantoms were scanned on a 192-slice CT scanner (Force, Siemens) at 100more » and 120kV without tin filtration, and 100 and 150 kV with tin filtration (100Sn and 150Sn), at multiple dose levels at each kV. Images were reconstructed using iterative reconstruction (ADMIRE, Siemens). Radiation dose was measured with a 0.6 cc ion chamber in the middle and peripheral areas of the phantom. Image quality was assessed using mean image noise at uniform areas in the central region and lung. Radiation dose that is required for each kV to match the noise in a routine lung-cancer CT screening technique (120kV, 25 quality reference mAs) was calculated. Results: At each of the four phantom sizes, 100Sn had the lowest noise in both soft tissue and lung. Compared with 120 kV, 100Sn saved 39%–60% dose for the same noise, depending on phantom size. For the XL phantom (50 by 40 cm), 150Sn provided images with the least beam-hardening artifact in peripheral region. Conclusion: For thoracic CT, added tin filtration can provide considerable dose reduction compared with 120 kV. 100Sn provides better dose efficiencies for all phantom sizes, while 150Sn provides better image quality in peripheral region for extra-large patients. Drs.Joel G. Fletcher and Cynthia H. McCollough receive research support from Siemens Healthcare.« less

User-composable Electronic Health Record Improves Efficiency of Clinician Data Viewing for Patient Case Appraisal: A Mixed-Methods Study

PubMed Central

Senathirajah, Yalini; Kaufman, David; Bakken, Suzanne

2016-01-01

Background: Challenges in the design of electronic health records (EHRs) include designing usable systems that must meet the complex, rapidly changing, and high-stakes information needs of clinicians. The ability to move and assemble elements together on the same page has significant human-computer interaction (HCI) and efficiency advantages, and can mitigate the problems of negotiating multiple fixed screens and the associated cognitive burdens. Objective: We compare MedWISE—a novel EHR that supports user-composable displays—with a conventional EHR in terms of the number of repeat views of data elements for patient case appraisal. Design and Methods: The study used mixed-methods for examination of clinical data viewing in four patient cases. The study compared use of an experimental user-composable EHR with use of a conventional EHR, for case appraisal. Eleven clinicians used a user-composable EHR in a case appraisal task in the laboratory setting. This was compared with log file analysis of the same patient cases in the conventional EHR. We investigated the number of repeat views of the same clinical information during a session and across these two contexts, and compared them using Fisher’s exact test. Results: There was a significant difference (p<.0001) in proportion of cases with repeat data element viewing between the user-composable EHR (14.6 percent) and conventional EHR (72.6 percent). Discussion and Conclusion: Users of conventional EHRs repeatedly viewed the same information elements in the same session, as revealed by log files. Our findings are consistent with the hypothesis that conventional systems require that the user view many screens and remember information between screens, causing the user to forget information and to have to access the information a second time. Other mechanisms (such as reduction in navigation over a population of users due to interface sharing, and information selection) may also contribute to increased efficiency in

20180312 - Evaluating the applicability of read-across tools and high throughput screening data for food relevant chemicals (SOT)

EPA Science Inventory

Alternative toxicity assessment methods to characterize the hazards of chemical substances have been proposed to reduce animal testing and screen thousands of chemicals in an efficient manner. Resources to accomplish these goals include utilizing large in vitro chemical screening...

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. Copyright © 2016. Published by Elsevier B.V.

[Cost-effectiveness analysis on colorectal cancer screening program].

PubMed

Huang, Q C; Ye, D; Jiang, X Y; Li, Q L; Yao, K Y; Wang, J B; Jin, M J; Chen, K

2017-01-10

Objective: To evaluate the cost-effectiveness of colorectal cancer screening program in different age groups from the view of health economics. Methods: The screening compliance rates, detection rates in different age groups were calculated by using the data from colorectal cancer screening program in Jiashan county, Zhejiang province. The differences in indicator among age groups were analyzed with χ (2) test or trend χ (2) test. The ratios of cost to the number of case were calculated according to cost statistics. Results: The detection rates of immunochemical fecal occult blood test (iFOBT) positivity, advanced adenoma and colorectal cancer and early stage cancer increased with age, while the early diagnosis rates were negatively associated with age. After exclusion the younger counterpart, the cost-effectiveness of individuals aged >50 years could be reduced by 15 %- 30 % . Conclusion: From health economic perspective, it is beneficial to start colorectal cancer screening at age of 50 years to improve the efficiency of the screening.

Constraint factor graph cut-based active contour method for automated cellular image segmentation in RNAi screening.

PubMed

Chen, C; Li, H; Zhou, X; Wong, S T C

2008-05-01

Image-based, high throughput genome-wide RNA interference (RNAi) experiments are increasingly carried out to facilitate the understanding of gene functions in intricate biological processes. Automated screening of such experiments generates a large number of images with great variations in image quality, which makes manual analysis unreasonably time-consuming. Therefore, effective techniques for automatic image analysis are urgently needed, in which segmentation is one of the most important steps. This paper proposes a fully automatic method for cells segmentation in genome-wide RNAi screening images. The method consists of two steps: nuclei and cytoplasm segmentation. Nuclei are extracted and labelled to initialize cytoplasm segmentation. Since the quality of RNAi image is rather poor, a novel scale-adaptive steerable filter is designed to enhance the image in order to extract long and thin protrusions on the spiky cells. Then, constraint factor GCBAC method and morphological algorithms are combined to be an integrated method to segment tight clustered cells. Compared with the results obtained by using seeded watershed and the ground truth, that is, manual labelling results by experts in RNAi screening data, our method achieves higher accuracy. Compared with active contour methods, our method consumes much less time. The positive results indicate that the proposed method can be applied in automatic image analysis of multi-channel image screening data.

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

EPA Science Inventory

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

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.

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 ...

Barrier screens: a method to sample blood-fed and host-seeking exophilic mosquitoes

PubMed Central

2013-01-01

Background Determining the proportion of blood meals on humans by outdoor-feeding and resting mosquitoes is challenging. This is largely due to the difficulty of finding an adequate and unbiased sample of resting, engorged mosquitoes to enable the identification of host blood meal sources. This is particularly difficult in the south-west Pacific countries of Indonesia, the Solomon Islands and Papua New Guinea where thick vegetation constitutes the primary resting sites for the exophilic mosquitoes that are the primary malaria and filariasis vectors. Methods Barrier screens of shade-cloth netting attached to bamboo poles were constructed between villages and likely areas where mosquitoes might seek blood meals or rest. Flying mosquitoes, obstructed by the barrier screens, would temporarily stop and could then be captured by aspiration at hourly intervals throughout the night. Results In the three countries where this method was evaluated, blood-fed females of Anopheles farauti, Anopheles bancroftii, Anopheles longirostris, Anopheles sundaicus, Anopheles vagus, Anopheles kochi, Anopheles annularis, Anopheles tessellatus, Culex vishnui, Culex quinquefasciatus and Mansonia spp were collected while resting on the barrier screens. In addition, female Anopheles punctulatus and Armigeres spp as well as male An. farauti, Cx. vishnui, Cx. quinquefasciatus and Aedes species were similarly captured. Conclusions Building barrier screens as temporary resting sites in areas where mosquitoes were likely to fly was an extremely time-effective method for collecting an unbiased representative sample of engorged mosquitoes for determining the human blood index. PMID:23379959

Determination of a Screening Metric for High Diversity DNA Libraries.

PubMed

Guido, Nicholas J; Handerson, Steven; Joseph, Elaine M; Leake, Devin; Kung, Li A

2016-01-01

The fields of antibody engineering, enzyme optimization and pathway construction rely increasingly on screening complex variant DNA libraries. These highly diverse libraries allow researchers to sample a maximized sequence space; and therefore, more rapidly identify proteins with significantly improved activity. The current state of the art in synthetic biology allows for libraries with billions of variants, pushing the limits of researchers' ability to qualify libraries for screening by measuring the traditional quality metrics of fidelity and diversity of variants. Instead, when screening variant libraries, researchers typically use a generic, and often insufficient, oversampling rate based on a common rule-of-thumb. We have developed methods to calculate a library-specific oversampling metric, based on fidelity, diversity, and representation of variants, which informs researchers, prior to screening the library, of the amount of oversampling required to ensure that the desired fraction of variant molecules will be sampled. To derive this oversampling metric, we developed a novel alignment tool to efficiently measure frequency counts of individual nucleotide variant positions using next-generation sequencing data. Next, we apply a method based on the "coupon collector" probability theory to construct a curve of upper bound estimates of the sampling size required for any desired variant coverage. The calculated oversampling metric will guide researchers to maximize their efficiency in using highly variant libraries.

An efficient method for computation of the manipulator inertia matrix

NASA Technical Reports Server (NTRS)

Fijany, Amir; Bejczy, Antal K.

1989-01-01

An efficient method of computation of the manipulator inertia matrix is presented. Using spatial notations, the method leads to the definition of the composite rigid-body spatial inertia, which is a spatial representation of the notion of augmented body. The previously proposed methods, the physical interpretations leading to their derivation, and their redundancies are analyzed. The proposed method achieves a greater efficiency by eliminating the redundancy in the intrinsic equations as well as by a better choice of coordinate frame for their projection. In this case, removing the redundancy leads to greater efficiency of the computation in both serial and parallel senses.

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 bottlemore » 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.« less

Structural and optical characterization of NiSe film grown by screen-printing method

NASA Astrophysics Data System (ADS)

Sharma, Kapil; Sharma, D. K.; Dwivedi, D. K.; Kumar, Vipin

2018-05-01

In present investigation NiSe films were grown by economical screen-printing method. Optimum conditions for growing good quality screen-printed films were found. The films were characterized for their structural and optical properties. The polycrystalline nature of films with hexagonal structure was confirmed through XRD analysis. Direct type of optical band gap of 1.75 eV for the NiSe film was confirmed by optical characterization.

Division of methods for counting helminths' eggs and the problem of efficiency of these methods.

PubMed

Jaromin-Gleń, Katarzyna; Kłapeć, Teresa; Łagód, Grzegorz; Karamon, Jacek; Malicki, Jacek; Skowrońska, Agata; Bieganowski, Andrzej

2017-03-21

From the sanitary and epidemiological aspects, information concerning the developmental forms of intestinal parasites, especially the eggs of helminths present in our environment in: water, soil, sandpits, sewage sludge, crops watered with wastewater are very important. The methods described in the relevant literature may be classified in various ways, primarily according to the methodology of the preparation of samples from environmental matrices prepared for analysis, and the sole methods of counting and chambers/instruments used for this purpose. In addition, there is a possibility to perform the classification of the research methods analyzed from the aspect of the method and time of identification of the individuals counted, or the necessity for staining them. Standard methods for identification of helminths' eggs from environmental matrices are usually characterized by low efficiency, i.e. from 30% to approximately 80%. The efficiency of the method applied may be measured in a dual way, either by using the method of internal standard or the 'Split/Spike' method. While measuring simultaneously in an examined object the efficiency of the method and the number of eggs, the 'actual' number of eggs may be calculated by multiplying the obtained value of the discovered eggs of helminths by inverse efficiency.

Conditional screening for ultra-high dimensional covariates with survival outcomes

PubMed Central

Hong, Hyokyoung G.; Li, Yi

2017-01-01

Identifying important biomarkers that are predictive for cancer patients’ prognosis is key in gaining better insights into the biological influences on the disease and has become a critical component of precision medicine. The emergence of large-scale biomedical survival studies, which typically involve excessive number of biomarkers, has brought high demand in designing efficient screening tools for selecting predictive biomarkers. The vast amount of biomarkers defies any existing variable selection methods via regularization. The recently developed variable screening methods, though powerful in many practical setting, fail to incorporate prior information on the importance of each biomarker and are less powerful in detecting marginally weak while jointly important signals. We propose a new conditional screening method for survival outcome data by computing the marginal contribution of each biomarker given priorily known biological information. This is based on the premise that some biomarkers are known to be associated with disease outcomes a priori. Our method possesses sure screening properties and a vanishing false selection rate. The utility of the proposal is further confirmed with extensive simulation studies and analysis of a diffuse large B-cell lymphoma dataset. We are pleased to dedicate this work to Jack Kalbfleisch, who has made instrumental contributions to the development of modern methods of analyzing survival data. PMID:27933468

iScreen: Image-Based High-Content RNAi Screening Analysis Tools.

PubMed

Zhong, Rui; Dong, Xiaonan; Levine, Beth; Xie, Yang; Xiao, Guanghua

2015-09-01

High-throughput RNA interference (RNAi) screening has opened up a path to investigating functional genomics in a genome-wide pattern. However, such studies are often restricted to assays that have a single readout format. Recently, advanced image technologies have been coupled with high-throughput RNAi screening to develop high-content screening, in which one or more cell image(s), instead of a single readout, were generated from each well. This image-based high-content screening technology has led to genome-wide functional annotation in a wider spectrum of biological research studies, as well as in drug and target discovery, so that complex cellular phenotypes can be measured in a multiparametric format. Despite these advances, data analysis and visualization tools are still largely lacking for these types of experiments. Therefore, we developed iScreen (image-Based High-content RNAi Screening Analysis Tool), an R package for the statistical modeling and visualization of image-based high-content RNAi screening. Two case studies were used to demonstrate the capability and efficiency of the iScreen package. iScreen is available for download on CRAN (http://cran.cnr.berkeley.edu/web/packages/iScreen/index.html). The user manual is also available as a supplementary document. © 2014 Society for Laboratory Automation and Screening.

Screening for colorectal cancer.

PubMed

Ross, C C

1988-12-01

Efforts to decrease the number of deaths from colorectal cancer have focused on screening techniques, since no etiologic agent has been identified. Current screening regimens are designed to detect colorectal cancer in a large population in a cost-efficient manner and to minimize the risks associated with work-ups for false-positive tests. A two-part screening questionnaire for colorectal cancer helps identify patients who are at moderate risk for this cancer.

Risk Profiling May Improve Lung Cancer Screening

Cancer.gov

A new modeling study suggests that individualized, risk-based selection of ever-smokers for lung cancer screening may prevent more lung cancer deaths and improve the effectiveness and efficiency of screening compared with current screening recommendations

Design method of high-efficient 
LED headlamp lens.

PubMed

Chen, Fei; Wang, Kai; Qin, Zong; Wu, Dan; Luo, Xiaobing; Liu, Sheng

2010-09-27

Low optical efficiency of light-emitting diode (LED) based headlamp is one of the most important issues to obstruct applications of LEDs in headlamp. An effective high-efficient LED headlamp freeform lens design method is introduced in this paper. A low-beam lens and a high-beam lens for LED headlamp are designed according to this method. Monte Carlo ray tracing simulation results demonstrate that the LED headlamp with these two lenses can fully comply with the ECE regulation without any other lens or reflector. Moreover, optical efficiencies of both these two lenses are more than 88% in theory.

Microfluidic Devices for Drug Delivery Systems and Drug Screening

PubMed Central

Kompella, Uday B.; Damiati, Safa A.

2018-01-01

Microfluidic devices present unique advantages for the development of efficient drug carrier particles, cell-free protein synthesis systems, and rapid techniques for direct drug screening. Compared to bulk methods, by efficiently controlling the geometries of the fabricated chip and the flow rates of multiphase fluids, microfluidic technology enables the generation of highly stable, uniform, monodispersed particles with higher encapsulation efficiency. Since the existing preclinical models are inefficient drug screens for predicting clinical outcomes, microfluidic platforms might offer a more rapid and cost-effective alternative. Compared to 2D cell culture systems and in vivo animal models, microfluidic 3D platforms mimic the in vivo cell systems in a simple, inexpensive manner, which allows high throughput and multiplexed drug screening at the cell, organ, and whole-body levels. In this review, the generation of appropriate drug or gene carriers including different particle types using different configurations of microfluidic devices is highlighted. Additionally, this paper discusses the emergence of fabricated microfluidic cell-free protein synthesis systems for potential use at point of care as well as cell-, organ-, and human-on-a-chip models as smart, sensitive, and reproducible platforms, allowing the investigation of the effects of drugs under conditions imitating the biological system. PMID:29462948

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. 2013 by John Wiley & Sons, Inc.

Isotonic Regression Based-Method in Quantitative High-Throughput Screenings for Genotoxicity

PubMed Central

Fujii, Yosuke; Narita, Takeo; Tice, Raymond Richard; Takeda, Shunich

2015-01-01

Quantitative high-throughput screenings (qHTSs) for genotoxicity are conducted as part of comprehensive toxicology screening projects. The most widely used method is to compare the dose-response data of a wild-type and DNA repair gene knockout mutants, using model-fitting to the Hill equation (HE). However, this method performs poorly when the observed viability does not fit the equation well, as frequently happens in qHTS. More capable methods must be developed for qHTS where large data variations are unavoidable. In this study, we applied an isotonic regression (IR) method and compared its performance with HE under multiple data conditions. When dose-response data were suitable to draw HE curves with upper and lower asymptotes and experimental random errors were small, HE was better than IR, but when random errors were big, there was no difference between HE and IR. However, when the drawn curves did not have two asymptotes, IR showed better performance (p < 0.05, exact paired Wilcoxon test) with higher specificity (65% in HE vs. 96% in IR). In summary, IR performed similarly to HE when dose-response data were optimal, whereas IR clearly performed better in suboptimal conditions. These findings indicate that IR would be useful in qHTS for comparing dose-response data. PMID:26673567

A novel tandem mass spectrometry method for first-line screening of mainly beta-thalassemia from dried blood spots.

PubMed

Yu, Chaowen; Huang, Shuodan; Wang, Ming; Zhang, Juan; Liu, Hao; Yuan, Zhaojian; Wang, Xingbin; He, Xiaoyan; Wang, Jie; Zou, Lin

2017-02-10

Traditional methods for thalassemia screening are time-consuming and easily affected by cell hemolysis or hemoglobin degradation in stored blood samples. Tandem mass spectrometry (MS/MS) proved to be an effective technology for sickle cell disorders (SCD) screening. Here, we developed a novel MS/MS method for β-thalassemia screening from dried blood spots (DBS). Stable isotopic-labeled peptides were used as internal standards for quantification and calculation of the α:β-globin ratios. We used the α:β-globin ratio cutoffs to differentiate between normal individuals and patients with thalassemia. About 781 patients and 300 normal individuals were analyzed. The α:β-globin ratios showed significant difference between normal and β-thalassemia patients (P<0.01), particularly when the disease was homozygous or double heterozygous with another α- or β-thalassemia mutation. In the parallel study, all cases screened for suspected thalassemia from six hundred DBS samples by using this MS/MS method were successfully confirmed by genotyping. The intra-assay and inter-assay CVs of the ratios ranged from 2.4% to 3.9% and 4.7% to 7.1%, and there was no significant sample carryover or matrix effect for this MS/MS method. Combined with SCD screening, this MS/MS method could be used as a first-line screening assay for both structural and expression abnormalities of human hemoglobin. Traditional methods for thalassemia screening were depending on the structural integrity of tetramers and could be affected by hemolysis and degradation of whole blood samples, especially when stored. We used proteospecific peptides produced by the tryptic digestion of each globin to evaluate the production ratio between α- and β-globin chains, which turned out to be quite stable even when stored for more than two months. Though most of the peptides were specific to α-globin or β-globin, we only chose four most informative peptides and its stable isotopic-labeled peptides as internal

Convenient, sensitive and high-throughput method for screening botanic origin.

PubMed

Yuan, Yuan; Jiang, Chao; Liu, Libing; Yu, Shulin; Cui, Zhanhu; Chen, Min; Lin, Shufang; Wang, Shu; Huang, Luqi

2014-06-23

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.

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.

A new screening method for amphetamine and methamphetamine using dansyl chloride derivatization and cartridge fluorescence.

PubMed

Yamada, H; Ikeda-Wada, S; Oguri, K

1998-07-01

A new screening method for amphetamines was developed. It consists of derivatization with dansyl chloride, extraction of the derivative using a Sep-Pak C18 or a Bond Elut C18, solid phase extraction columns, and visualization of the fluorescence of the cartridge. A control test using drug-free urine showed no fluorescence. Amphetamine, methamphetamine and the methylenedioxy derivatives exhibited strong fluorescence, while related compounds, such as N-ethylamphetamine and fenetylline, were negative or weakly positive. The disadvantage of the present method is that it is a multi-step procedure and 20-30 min is required for screening. However, since it has a different specificity from the widely used immunochemical technique, it is suggested to be a useful screen for amphetamines.

Screening of a new cadmium hyperaccumulator, Galinsoga parviflora, from winter farmland weeds using the artificially high soil cadmium concentration method.

PubMed

Lin, Lijin; Jin, Qian; Liu, Yingjie; Ning, Bo; Liao, Ming'an; Luo, Li

2014-11-01

A new method, the artificially high soil cadmium (Cd) concentration method, was used to screen for Cd hyperaccumulators among winter farmland weeds. Galinsoga parviflora was the most promising remedial plant among 5 Cd accumulators or hyperaccumulators. In Cd concentration gradient experiments, as soil Cd concentration increased, root and shoot biomass decreased, and their Cd contents increased. In additional concentration gradient experiments, superoxide dismutase and peroxidase activities increased with soil Cd concentrations up to 75 mg kg(-1) , while expression of their isoenzymes strengthened. Catalase (CAT) activity declined and CAT isoenzyme expression weakened at soil Cd concentrations less than 50 mg kg(-1) . The maxima of Cd contents in shoots and roots were 137.63 mg kg(-1) and 105.70 mg kg(-1) , respectively, at 100 mg kg(-1) Cd in soil. The root and shoot bioconcentration factors exceeded 1.0, as did the translocation factor. In a field experiment, total extraction of Cd by shoots was 1.35 mg m(-2) to 1.43 mg m(-2) at soil Cd levels of 2.04 mg kg(-1) to 2.89 mg kg(-1) . Therefore, the artificially high soil Cd concentration method was effective for screening Cd hyperaccumulators. Galinsoga parviflora is a Cd hyperaccumulator that could be used to efficiently remediate Cd-contaminated farmland soil. © 2014 SETAC.

A mutant screening method by critical annealing temperature-PCR for site-directed mutagenesis.

PubMed

Liu, Ying; Wu, Ting; Song, Jian; Chen, Xuelian; Zhang, Yu; Wan, Yu

2013-03-11

Distinguishing desired mutants from parental templates and undesired mutants is a problem not well solved in Quikchange™ mutagenesis. Although Dpn I digestion can eliminate methylated parental (WT) DNA, the efficiency is not satisfying due to the existence of hemi-methylated DNA in the PCR products, which is resistant to Dpn I. The present study designed a novel critical annealing temperature (T(c))-PCR to replace Dpn I digestion for more perfect mutant distinguishing, in which part-overlapping primers containing mutation(s) were used to reduce initial concentration of template DNA in mutagenic PCR. A T(c)-PCR with the same mutagenic primers was performed without Dpn I digestion. The T(c) for each pair of the primers was identified by gradient PCR. The relationship between PCR-identified T(c) and T(m) of the primers was analyzed and modeled with correlation and regression. Gradient PCR identified a T(c) for each of 14 tested mutagenic primers, which could discriminate mismatched parental molecules and undesired mutants from desired mutants. The PCR-identified T(c) was correlated to the primer's T(m) (r = 0.804, P<0.0001). Thus, in practical applications, the T(c) can be easily calculated with a regression equation, T(c)= 48.81 + 0.253*T(m). The new protocol introduced a novel T(c)-PCR method for mutant screening which can more efficiently and accurately select against parental molecules and undesired mutations in mutagenic sequence segments.

New Method of Screening Young Children for Defects in Visual Acuity*

PubMed Central

Withnell, Allan; Wilson, H. E.

1968-01-01

The methods used at present for screening young children's vision have disadvantages, such as that the child's intelligence can affect the result. In a new method three white cards are used; these are printed with one, two, or three black blocks arranged so that if a child can correctly state the number of blocks at 6 metres the visual acuity is at least 6/9. When tested on 186 children the new method gave better results than conventional tests; eight children with defective vision were picked up only by the new method and none were missed. PMID:5681052

New method of screening young children for defects in visual acuity.

PubMed

Withnell, A; Wilson, H E

1968-10-19

The methods used at present for screening young children's vision have disadvantages, such as that the child's intelligence can affect the result. In a new method three white cards are used; these are printed with one, two, or three black blocks arranged so that if a child can correctly state the number of blocks at 6 metres the visual acuity is at least 6/9. When tested on 186 children the new method gave better results than conventional tests; eight children with defective vision were picked up only by the new method and none were missed.

Large-scale virtual screening on public cloud resources with Apache Spark.

PubMed

Capuccini, Marco; Ahmed, Laeeq; Schaal, Wesley; Laure, Erwin; Spjuth, Ola

2017-01-01

Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally expensive, however it constitutes a trivially parallelizable task. Most of the available parallel implementations are based on message passing interface, relying on low failure rate hardware and fast network connection. Google's MapReduce revolutionized large-scale analysis, enabling the processing of massive datasets on commodity hardware and cloud resources, providing transparent scalability and fault tolerance at the software level. Open source implementations of MapReduce include Apache Hadoop and the more recent Apache Spark. We developed a method to run existing docking-based screening software on distributed cloud resources, utilizing the MapReduce approach. We benchmarked our method, which is implemented in Apache Spark, docking a publicly available target receptor against [Formula: see text]2.2 M compounds. The performance experiments show a good parallel efficiency (87%) when running in a public cloud environment. Our method enables parallel Structure-based virtual screening on public cloud resources or commodity computer clusters. The degree of scalability that we achieve allows for trying out our method on relatively small libraries first and then to scale to larger libraries. Our implementation is named Spark-VS and it is freely available as open source from GitHub (https://github.com/mcapuccini/spark-vs).Graphical abstract.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Michael; Haeri, Hossein; Reynolds, Arlis

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

Computationally inexpensive identification of noninformative model parameters by sequential screening

NASA Astrophysics Data System (ADS)

Cuntz, Matthias; Mai, Juliane; Zink, Matthias; Thober, Stephan; Kumar, Rohini; Schäfer, David; Schrön, Martin; Craven, John; Rakovec, Oldrich; Spieler, Diana; Prykhodko, Vladyslav; Dalmasso, Giovanni; Musuuza, Jude; Langenberg, Ben; Attinger, Sabine; Samaniego, Luis

2015-08-01

Environmental models tend to require increasing computational time and resources as physical process descriptions are improved or new descriptions are incorporated. Many-query applications such as sensitivity analysis or model calibration usually require a large number of model evaluations leading to high computational demand. This often limits the feasibility of rigorous analyses. Here we present a fully automated sequential screening method that selects only informative parameters for a given model output. The method requires a number of model evaluations that is approximately 10 times the number of model parameters. It was tested using the mesoscale hydrologic model mHM in three hydrologically unique European river catchments. It identified around 20 informative parameters out of 52, with different informative parameters in each catchment. The screening method was evaluated with subsequent analyses using all 52 as well as only the informative parameters. Subsequent Sobol's global sensitivity analysis led to almost identical results yet required 40% fewer model evaluations after screening. mHM was calibrated with all and with only informative parameters in the three catchments. Model performances for daily discharge were equally high in both cases with Nash-Sutcliffe efficiencies above 0.82. Calibration using only the informative parameters needed just one third of the number of model evaluations. The universality of the sequential screening method was demonstrated using several general test functions from the literature. We therefore recommend the use of the computationally inexpensive sequential screening method prior to rigorous analyses on complex environmental models.

Computationally inexpensive identification of noninformative model parameters by sequential screening

NASA Astrophysics Data System (ADS)

Mai, Juliane; Cuntz, Matthias; Zink, Matthias; Thober, Stephan; Kumar, Rohini; Schäfer, David; Schrön, Martin; Craven, John; Rakovec, Oldrich; Spieler, Diana; Prykhodko, Vladyslav; Dalmasso, Giovanni; Musuuza, Jude; Langenberg, Ben; Attinger, Sabine; Samaniego, Luis

2016-04-01

Environmental models tend to require increasing computational time and resources as physical process descriptions are improved or new descriptions are incorporated. Many-query applications such as sensitivity analysis or model calibration usually require a large number of model evaluations leading to high computational demand. This often limits the feasibility of rigorous analyses. Here we present a fully automated sequential screening method that selects only informative parameters for a given model output. The method requires a number of model evaluations that is approximately 10 times the number of model parameters. It was tested using the mesoscale hydrologic model mHM in three hydrologically unique European river catchments. It identified around 20 informative parameters out of 52, with different informative parameters in each catchment. The screening method was evaluated with subsequent analyses using all 52 as well as only the informative parameters. Subsequent Sobol's global sensitivity analysis led to almost identical results yet required 40% fewer model evaluations after screening. mHM was calibrated with all and with only informative parameters in the three catchments. Model performances for daily discharge were equally high in both cases with Nash-Sutcliffe efficiencies above 0.82. Calibration using only the informative parameters needed just one third of the number of model evaluations. The universality of the sequential screening method was demonstrated using several general test functions from the literature. We therefore recommend the use of the computationally inexpensive sequential screening method prior to rigorous analyses on complex environmental models.

An efficient unstructured WENO method for supersonic reactive flows

NASA Astrophysics Data System (ADS)

Zhao, Wen-Geng; Zheng, Hong-Wei; Liu, Feng-Jun; Shi, Xiao-Tian; Gao, Jun; Hu, Ning; Lv, Meng; Chen, Si-Cong; Zhao, Hong-Da

2018-03-01

An efficient high-order numerical method for supersonic reactive flows is proposed in this article. The reactive source term and convection term are solved separately by splitting scheme. In the reaction step, an adaptive time-step method is presented, which can improve the efficiency greatly. In the convection step, a third-order accurate weighted essentially non-oscillatory (WENO) method is adopted to reconstruct the solution in the unstructured grids. Numerical results show that our new method can capture the correct propagation speed of the detonation wave exactly even in coarse grids, while high order accuracy can be achieved in the smooth region. In addition, the proposed adaptive splitting method can reduce the computational cost greatly compared with the traditional splitting method.

Allergic sensitization: screening methods

PubMed Central

2014-01-01

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

Radiologic findings of screen-detected cancers in an organized population-based screening mammography program in Turkey

PubMed Central

Kayhan, Arda; Arıbal, Erkin; Şahin, Cennet; Taşçı, Ömür Can; Gürdal, Sibel Özkan; Öztürk, Enis; Hatipoğlu, Hayat Halide; Özaydın, Nilüfer; Cabioğlu, Neslihan; Özçınar, Beyza; Özmen, Vahit

2016-01-01

PURPOSE Bahçeşehir Breast Cancer Screening Program is a population based organized screening program in Turkey, where asymptomatic women aged 40–69 years are screened biannually. In this prospective study, we aimed to determine the mammographic findings of screen-detected cancers and discuss the efficacy of breast cancer screening in a developing country. METHODS A total of 6912 women were screened in three rounds. The radiologic findings were grouped as mass, focal asymmetry, calcification, and architectural distortion. Masses were classified according to shape, border, and density. Calcifications were grouped according to morphology and distribution. Cancers were grouped according to the clinical stage. RESULTS Seventy cancers were detected with an incidence of 4.8/1000. Two cancers were detected in other centers and three were not visualized mammographically. Mammographic presentations of the remaining 65 cancers were mass (47.7%, n=31), calcification (30.8%, n=20), focal asymmetry (16.9%, n=11), architectural distortion (3.1%, n=2), and skin thickening (1.5%, n=1). The numbers of stage 0, 1, 2, 3, and 4 cancers were 13 (20.0%), 34 (52.3%), 14 (21.5%), 3 (4.6%), and 1 (1.5%), respectively. The numbers of interval and missed cancers were 5 (7.4%) and 7 (10.3%), respectively. CONCLUSION A high incidence of early breast cancer has been detected. The incidence of missed and interval cancers did not show major differences from western screening trials. We believe that this study will pioneer implementation of efficient population-based mammographic screenings in developing countries. PMID:27705880

Screening and large-scale expression of membrane proteins in mammalian cells for structural studies.

PubMed

Goehring, April; Lee, Chia-Hsueh; Wang, Kevin H; Michel, Jennifer Carlisle; Claxton, Derek P; Baconguis, Isabelle; Althoff, Thorsten; Fischer, Suzanne; Garcia, K Christopher; Gouaux, Eric

2014-11-01

Structural, biochemical and biophysical studies of eukaryotic membrane proteins are often hampered by difficulties in overexpression of the candidate molecule. Baculovirus transduction of mammalian cells (BacMam), although a powerful method to heterologously express membrane proteins, can be cumbersome for screening and expression of multiple constructs. We therefore developed plasmid Eric Gouaux (pEG) BacMam, a vector optimized for use in screening assays, as well as for efficient production of baculovirus and robust expression of the target protein. In this protocol, we show how to use small-scale transient transfection and fluorescence-detection size-exclusion chromatography (FSEC) experiments using a GFP-His8-tagged candidate protein to screen for monodispersity and expression level. Once promising candidates are identified, we describe how to generate baculovirus, transduce HEK293S GnTI(-) (N-acetylglucosaminyltransferase I-negative) cells in suspension culture and overexpress the candidate protein. We have used these methods to prepare pure samples of chicken acid-sensing ion channel 1a (cASIC1) and Caenorhabditis elegans glutamate-gated chloride channel (GluCl) for X-ray crystallography, demonstrating how to rapidly and efficiently screen hundreds of constructs and accomplish large-scale expression in 4-6 weeks.

Methods of Efficient Study Habits and Physics Learning

NASA Astrophysics Data System (ADS)

Zettili, Nouredine

2010-02-01

We want to discuss the methods of efficient study habits and how they can be used by students to help them improve learning physics. In particular, we deal with the most efficient techniques needed to help students improve their study skills. We focus on topics such as the skills of how to develop long term memory, how to improve concentration power, how to take class notes, how to prepare for and take exams, how to study scientific subjects such as physics. We argue that the students who conscientiously use the methods of efficient study habits achieve higher results than those students who do not; moreover, a student equipped with the proper study skills will spend much less time to learn a subject than a student who has no good study habits. The underlying issue here is not the quantity of time allocated to the study efforts by the students, but the efficiency and quality of actions so that the student can function at peak efficiency. These ideas were developed as part of Project IMPACTSEED (IMproving Physics And Chemistry Teaching in SEcondary Education), an outreach grant funded by the Alabama Commission on Higher Education. This project is motivated by a major pressing local need: A large number of high school physics teachers teach out of field. )

vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available.

PubMed

Chaput, Ludovic; Martinez-Sanz, Juan; Quiniou, Eric; Rigolet, Pascal; Saettel, Nicolas; Mouawad, Liliane

2016-01-01

In drug design, one may be confronted to the problem of finding hits for targets for which no small inhibiting molecules are known and only low-throughput experiments are available (like ITC or NMR studies), two common difficulties encountered in a typical academic setting. Using a virtual screening strategy like docking can alleviate some of the problems and save a considerable amount of time by selecting only top-ranking molecules, but only if the method is very efficient, i.e. when a good proportion of actives are found in the 1-10 % best ranked molecules. The use of several programs (in our study, Gold, Surflex, FlexX and Glide were considered) shows a divergence of the results, which presents a difficulty in guiding the experiments. To overcome this divergence and increase the yield of the virtual screening, we created the standard deviation consensus (SDC) and variable SDC (vSDC) methods, consisting of the intersection of molecule sets from several virtual screening programs, based on the standard deviations of their ranking distributions. SDC allowed us to find hits for two new protein targets by testing only 9 and 11 small molecules from a chemical library of circa 15,000 compounds. Furthermore, vSDC, when applied to the 102 proteins of the DUD-E benchmarking database, succeeded in finding more hits than any of the four isolated programs for 13-60 % of the targets. In addition, when only 10 molecules of each of the 102 chemical libraries were considered, vSDC performed better in the number of hits found, with an improvement of 6-24 % over the 10 best-ranked molecules given by the individual docking programs.Graphical abstractIn drug design, for a given target and a given chemical library, the results obtained with different virtual screening programs are divergent. So how to rationally guide the experimental tests, especially when only a few number of experiments can be made? The variable Standard Deviation Consensus (vSDC) method was developed to

A Computationally Efficient Method for Polyphonic Pitch Estimation

NASA Astrophysics Data System (ADS)

Zhou, Ruohua; Reiss, Joshua D.; Mattavelli, Marco; Zoia, Giorgio

2009-12-01

This paper presents a computationally efficient method for polyphonic pitch estimation. The method employs the Fast Resonator Time-Frequency Image (RTFI) as the basic time-frequency analysis tool. The approach is composed of two main stages. First, a preliminary pitch estimation is obtained by means of a simple peak-picking procedure in the pitch energy spectrum. Such spectrum is calculated from the original RTFI energy spectrum according to harmonic grouping principles. Then the incorrect estimations are removed according to spectral irregularity and knowledge of the harmonic structures of the music notes played on commonly used music instruments. The new approach is compared with a variety of other frame-based polyphonic pitch estimation methods, and results demonstrate the high performance and computational efficiency of the approach.

A small-bolt method for screening tree protectants against bark beetles (coleoptera: curculionidae)

Treesearch

B.L. Strom; L.M. Roton

2009-01-01

A simple, small-bolt method was developed and refi ned for evaluating and screening treatments being considered as prophylactics against bark beetles (Coleoptera: Curculionidae: Scolytinae). Using this method, 4 insecticide products (3 active ingredients) were evaluated against the southern pine beetle, Dendroctonus frontalis Zimmermann, intermittently during a period...

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.

Methods for detection of ataxia telangiectasia mutations

DOEpatents

Gatti, Richard A.

2005-10-04

The present invention is directed to a method of screening large, complex, polyexonic eukaryotic genes such as the ATM gene for mutations and polymorphisms by an improved version of single strand conformation polymorphism (SSCP) electrophoresis that allows electrophoresis of two or three amplified segments in a single lane. The present invention also is directed to new mutations and polymorphisms in the ATM gene that are useful in performing more accurate screening of human DNA samples for mutations and in distinguishing mutations from polymorphisms, thereby improving the efficiency of automated screening methods.

Highly efficient preparation of sphingoid bases from glucosylceramides by chemoenzymatic method[S

PubMed Central

Gowda, Siddabasave Gowda B.; Usuki, Seigo; Hammam, Mostafa A. S.; Murai, Yuta; Igarashi, Yasuyuki; Monde, Kenji

2016-01-01

Sphingoid base derivatives have attracted increasing attention as promising chemotherapeutic candidates against lifestyle diseases such as diabetes and cancer. Natural sphingoid bases can be a potential resource instead of those derived by time-consuming total organic synthesis. In particular, glucosylceramides (GlcCers) in food plants are enriched sources of sphingoid bases, differing from those of animals. Several chemical methodologies to transform GlcCers to sphingoid bases have already investigated; however, these conventional methods using acid or alkaline hydrolysis are not efficient due to poor reaction yield, producing complex by-products and resulting in separation problems. In this study, an extremely efficient and practical chemoenzymatic transformation method has been developed using microwave-enhanced butanolysis of GlcCers and a large amount of readily available almond β-glucosidase for its deglycosylation reaction of lysoGlcCers. The method is superior to conventional acid/base hydrolysis methods in its rapidity and its reaction cleanness (no isomerization, no rearrangement) with excellent overall yield. PMID:26667669

Economic evaluation of Chagas disease screening in Spain.

PubMed

Imaz-Iglesia, Iñaki; Miguel, Lucía García-San; Ayala-Morillas, L Eduardo; García-Pérez, Lidia; González-Enríquez, Jesús; Blasco-Hernández, Teresa; Martín-Águeda, María Belén; Sarría-Santamera, Antonio

2015-08-01

Although Spain is the European country with the highest Chagas disease burden, the country does not have a national control program of the disease. The purpose of this study is to evaluate the efficiency of several strategies for Chagas disease screening among Latin American residents living in Spain. The following screening strategies were evaluated: (1) non-screening; (2) screening of the Latin American pregnant women and their newborns; (3) screening also the relatives of the positive pregnant women; (4) screening also the relatives of the negative pregnant women. A cost-utility analysis was carried out to compare the four strategies from two perspectives, the societal and the Spanish National Health System (SNHS). A decision tree representing the clinical evolution of Chagas disease throughout patient's life was built. The strategies were compared through the incremental cost-utility ratio, using euros as cost measurement and quality-adjusted life years as utility measurement. A sensitivity analysis was performed to test the model parameters and their influence on the results. We found the "Non-screening" as the most expensive and less effective of the evaluated strategies, from both the societal and the SNHS perspectives. Among the screening evaluated strategies the most efficient was, from both perspectives, to extent the antenatal screening of the Latin American pregnant women and their newborns up to the relatives of the positive women. Several parameters influenced significantly on the sensitivity analyses, particularly the chronic treatment efficacy or the prevalence of Chagas disease. In conclusion, for the general Latin American immigrants living in Spain the most efficient would be to screen the Latin American mothers, their newborns and the close relatives of the mothers with a positive serology. However for higher prevalence immigrant population the most efficient intervention would be to extend the program to the close relatives of the negative

Overview of a workshop on screening methods for detecting potential (anti-) estrogenic/androgenic chemicals in wildlife

USGS Publications Warehouse

Ankley, Gerald T.; Mihaich, Ellen; Stahl, Ralph G.; Tillitt, Donald E.; Colborn, Theo; McMaster, Suzzanne; Miller, Ron; Bantle, John; Campbell, Pamela; Denslow, Nancy; Dickerson, Richard L.; Folmar, Leroy C.; Fry, Michael; Giesy, John P.; Gray, L. Earl; Guiney, Patrick; Hutchinson, Thomas; Kennedy, Sean W.; Kramer, Vincent; LeBlanc, Gerald A.; Mayes, Monte; Nimrod, Alison; Patino, Reynaldo; Peterson, Richard; Purdy, Richard; Ringer, Robert; Thomas, Peter C.; Touart, Les; Van Der Kraak, Glen; Zacharewski, Tim

1998-01-01

The U.S. Congress has passed legislation requiring the U.S. Environmental Protection Agency (U.S. EPA) to develop, validate, and implement screening tests for identifying potential endocrine-disrupting chemicals within 3 years. To aid in the identification of methods suitable for this purpose, the U.S. EPA, the Chemical Manufacturers Association, and the World Wildlife Fund sponsored several workshops, including the present one, which dealt with wildlife species. This workshop was convened with 30 international scientists representing multiple disciplines in March 1997 in Kansas City, Missouri, USA. Participants at the meeting identified methods in terms of their ability to indicate (anti-) estrogenic/androgenic effects, particularly in the context of developmental and reproductive processes. Data derived from structure-activity relationship models and in vitro test systems, although useful in certain contexts, cannot at present replace in vivo tests as the sole basis for screening. A consensus was reached that existing mammalian test methods (e.g., with rats or mice) generally are suitable as screens for assessing potential (anti-) estrogenic/ androgenic effects in mammalian wildlife. However, due to factors such as among-class variation in receptor structure and endocrine function, it is uncertain if these mammalian assays would be of broad utility as screens for other classes of vertebrate wildlife. Existing full and partial life-cycle tests with some avian and fish species could successfully identify chemicals causing endocrine disruption; however, these long-term tests are not suitable for routine screening. However, a number of short-term tests with species from these two classes exist that could serve as effective screening tools for chemicals inducing (anti-) estrogenic/androgenic effects. Existing methods suitable for identifying chemicals with these mechanisms of action in reptiles and amphibians are limited, but in the future, tests with species from

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

PubMed Central

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

2006-01-01

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

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.

NMR screening in fragment-based drug design: a practical guide.

PubMed

Kim, Hai-Young; Wyss, Daniel F

2015-01-01

Fragment-based drug design (FBDD) comprises both fragment-based screening (FBS) to find hits and elaboration of these hits to lead compounds. Typical fragment hits have lower molecular weight (<300-350 Da) and lower initial potency but higher ligand efficiency when compared to those from high-throughput screening. NMR spectroscopy has been widely used for FBDD since it identifies and localizes the binding site of weakly interacting hits on the target protein. Here we describe ligand-based NMR methods for hit identification from fragment libraries and for functional cross-validation of primary hits.

Development of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line.

PubMed

Dehler, Carola E; Boudinot, Pierre; Martin, Samuel A M; Collet, Bertrand

2016-08-01

CRISPR/Cas9 system has been used widely in animals and plants to direct mutagenesis. To date, no such method exists for fish somatic cell lines. We describe an efficient procedure for genome editing in the Chinook salmon Oncorhynchus tshawytscha CHSE. This cell line was genetically modified to firstly overexpress a monomeric form of EGFP (cell line CHSE-E Geneticin resistant) and additionally to overexpress nCas9n, a nuclear version of Cas9 (cell line CHSE-EC, Hygromycin and Geneticin resistant). A pre-validated sgRNA was produced in vitro and used to transfect CHSE-EC cells. The EGFP gene was disrupted in 34.6 % of cells, as estimated by FACS and microscopy. The targeted locus was characterised by PCR amplification, cloning and sequencing of PCR products; inactivation of the EGFP gene by deletions in the expected site was validated in 25 % of clones. This method opens perspectives for functional genomic studies compatible with high-throughput screening.

Direct metallization local Al-back surface field for high efficiency screen printed crystalline silicon solar cells.

PubMed

Lee, Jonghwan; Park, Cheolmin; Dao, Vinh Ai; Lee, Youn-Jung; Ryu, Kyungyul; Choi, Gyuho; Kim, Bonggi; Ju, Minkyu; Jeong, Chaehwan; Yi, Junsin

2013-11-01

In this paper, we present a detailed study on the local back contact (LBC) formation of rear-surface-passivated silicon solar cells, where both the LBC opening and metallization are realized by one-step alloying of a dot of fine pattern screen-printed aluminum paste with the silicon substrate. Based on energy dispersive spectrometer (EDS) and scanning electron microscopy (SEM) characterizations, we suggest that the aluminum distribution and the silicon concentration determine the local-back-surface-field (Al-p+) layer thickness, resistivity of the Al-p+ and hence the quality of the Al-p+ formation. The highest penetration of silicon concentration of 78.17% in aluminum resulted in the formation of a 5 microm-deep Al-p+ layer, and the minimum LBC resistivity of 0.92 x 10-6 omega cm2. The degradation of the rear-surface passivation due to high temperature of the LBC formation process can be fully recovered by forming gas annealing (FGA) at temperature and hydrogen content of 450 degrees C and 15%, respectively. The application of the optimized LBC of rear-surface-passivated by a dot of fine pattern screen(-) printed aluminum paste resulted in efficiency of up to 19.98% for the p-type czochralski (CZ) silicon wafers with 10.24 cm2 cell size at 649 mV open circuit voltage. By FGA for rear-surface passivation recovery, efficiencies up to 20.35% with a V(OC) of 662 mV, FF of 82%, and J(SC) of 37.5 mA/cm2 were demonstrated.

Semiautomated TaqMan PCR screening of GMO labelled samples for (unauthorised) GMOs.

PubMed

Scholtens, Ingrid M J; Molenaar, Bonnie; van Hoof, Richard A; Zaaijer, Stephanie; Prins, Theo W; Kok, Esther J

2017-06-01

In most countries, systems are in place to analyse food products for the potential presence of genetically modified organisms (GMOs), to enforce labelling requirements and to screen for the potential presence of unauthorised GMOs. With the growing number of GMOs on the world market, a larger diversity of methods is required for informative analyses. In this paper, the specificity of an extended screening set consisting of 32 screening methods to identify different crop species (endogenous genes) and GMO elements was verified against 59 different GMO reference materials. In addition, a cost- and time-efficient strategy for DNA isolation, screening and identification is presented. A module for semiautomated analysis of the screening results and planning of subsequent event-specific tests for identification has been developed. The Excel-based module contains information on the experimentally verified specificity of the element methods and of the EU authorisation status of the GMO events. If a detected GMO element cannot be explained by any of the events as identified in the same sample, this may indicate the presence of an unknown unauthorised GMO that may not yet have been assessed for its safety for humans, animals or the environment.

Web-Based Versus Conventional Training for Medical Students on Infant Gross Motor Screening.

PubMed

Pusponegoro, Hardiono D; Soebadi, Amanda; Surya, Raymond

2015-12-01

Early detection of developmental abnormalities is important for early intervention. A simple screening method is needed for use by general practitioners, as is an effective and efficient training method. This study aims to evaluate the effectiveness, acceptability, and usability of Web-based training for medical students on a simple gross motor screening method in infants. Fifth-year medical students at University of Indonesia in Jakarta were randomized into two groups. A Web-based training group received online video modules, discussions, and assessments (at www.schoology.com ). A conventional training group received a 1-day live training using the same module. Both groups completed identical pre- and posttests and the User Satisfaction Questionnaire (USQ). The Web-based group also completed the System Usability Scale (SUS). The module was based on a gross motor screening method used in the World Health Organization Multicentre Growth Reference Study. There were 39 and 32 subjects in the Web-based and conventional groups, respectively. Mean pretest versus posttest scores (correct answers out of 20) were 9.05 versus 16.95 (p=0.0001) in the Web-based group and 9.31 versus 16.88 (p=0.0001) in the conventional group. Mean difference between pre- and posttest scores did not differ significantly between the Web-based and conventional groups (mean [standard deviation], 7.56 [3.252] versus 7.90 [5.170]; p=0.741]. Both training methods were acceptable based on USQ scores. Based on SUS scores, the Web-based training had good usability. Web-based training is an effective, efficient, and acceptable training method for medical students on simple infant gross motor screening and is as effective as conventional training.

Structuring in complex plasma for nonlinearly screened dust particles

NASA Astrophysics Data System (ADS)

Tsytovich, Vadim; Gusein-zade, Namik

2014-03-01

An explanation is proposed for the recently discovered effect of spontaneous dusty plasma structuring (and the appearance of compact dust structures) under conditions of nonlinear dust screening. Physical processes are considered that make homogenous dusty plasma universally unstable and lead to the appearance of structures. It is shown for the first time that the efficiency of structuring increases substantially in the presence of plasma flows caused by the charging of nonlinearly screened dust grains. General results are obtained for arbitrary nonlinear screening, and special attention is paid to the model of nonlinear screening often used since 1964. The growth rate of structuring instability is derived. It is shown that, in the case of nonlinear screening, the structuring has a threshold determined by the friction of grains against the neutral gas. The theoretically obtained threshold agrees with recent experimental observations. The dispersion relation for dusty plasma structuring is shown to be similar to the dispersion relation for gravitational instability with an effective gravitational constant. The effective dust attraction caused by this instability is shown to be collective, and the dependence of the effective gravitational constant on the dust-to-ion density ratio is found explicitly for the first time. It is demonstrated that the proposed method of calculation of dust attraction by using the effective gravitational constant is the most efficient and straightforward. Understanding of the role of nonlinear screening gives deeper physical grounds for the theoretical interpretation of the observed phenomenon of dust crystal formation in complex plasmas.

Adaptive Gaussian mixture models for pre-screening in GPR data

NASA Astrophysics Data System (ADS)

Torrione, Peter; Morton, Kenneth, Jr.; Besaw, Lance E.

2011-06-01

Due to the large amount of data generated by vehicle-mounted ground penetrating radar (GPR) antennae arrays, advanced feature extraction and classification can only be performed on a small subset of data during real-time operation. As a result, most GPR based landmine detection systems implement "pre-screening" algorithms to processes all of the data generated by the antennae array and identify locations with anomalous signatures for more advanced processing. These pre-screening algorithms must be computationally efficient and obtain high probability of detection, but can permit a false alarm rate which might be higher than the total system requirements. Many approaches to prescreening have previously been proposed, including linear prediction coefficients, the LMS algorithm, and CFAR-based approaches. Similar pre-screening techniques have also been developed in the field of video processing to identify anomalous behavior or anomalous objects. One such algorithm, an online k-means approximation to an adaptive Gaussian mixture model (GMM), is particularly well-suited to application for pre-screening in GPR data due to its computational efficiency, non-linear nature, and relevance of the logic underlying the algorithm to GPR processing. In this work we explore the application of an adaptive GMM-based approach for anomaly detection from the video processing literature to pre-screening in GPR data. Results with the ARA Nemesis landmine detection system demonstrate significant pre-screening performance improvements compared to alternative approaches, and indicate that the proposed algorithm is a complimentary technique to existing methods.

[Application of precursor ion scanning method in rapid screening of illegally added phosphodiesterase-5 inhibitors and their unknown derivatives in Chinese traditional patent medicines and health foods].

PubMed

Sun, Jing; Cao, Ling; Feng, Youlong; Tan, Li

2014-11-01

The compounds with similar structure often have similar pharmacological activities. So it is a trend for illegal addition that new derivatives of effective drugs are synthesized to avoid the statutory test. This bring challenges to crack down on illegal addition behavior, however, modified derivatives usually have similar product ions, which allow for precursor ion scanning. In this work, precursor ion scanning mode of a triple quadrupole mass spectrometer was first applied to screen illegally added drugs in complex matrix such as Chinese traditional patent medicines and healthy foods. Phosphodiesterase-5 inhibitors were used as experimental examples. Through the analysis of the structure and mass spectrum characteristics of the compounds, phosphodiesterase-5 inhibitors were classified, and their common product ions were screened by full scan of product ions of typical compounds. Then high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method with precursor ion scanning mode was established based on the optimization of MS parameters. The effect of mass parameters and the choice of fragment ions were also studied. The method was applied to determine actual samples and further refined. The results demonstrated that this method can meet the need of rapid screening of unknown derivatives of phosphodiesterase-5 inhibitors in complex matrix, and prevent unknown derivatives undetected. This method shows advantages in sensitivity, specificity and efficiency, and is worth to be further investigated.

To expand coverage, or increase frequency: Quantifying the tradeoffs between equity and efficiency facing cervical cancer screening programs in low‐resource settings

PubMed Central

Tsu, Vivien; Jeronimo, Jose; Mvundura, Mercy; Lee, Kyueun; Kim, Jane J.

2017-01-01

Cervical cancer is a leading cause of cancer death worldwide, with 85% of the disease burden residing in less developed regions. To inform evidence‐based decision‐making as cervical cancer screening programs are planned, implemented, and scaled in low‐ and middle‐income countries, we used cost and test performance data from the START‐UP demonstration project in Uganda and a microsimulation model of HPV infection and cervical carcinogenesis to quantify the health benefits, distributional equity, cost‐effectiveness, and financial impact of either (1) improving access to cervical cancer screening or (2) increasing the number of lifetime screening opportunities for women who already have access. We found that when baseline screening coverage was low (i.e., 30%), expanding coverage of screening once in a lifetime to 50% can yield comparable reductions in cancer risk to screening two or three times in a lifetime at 30% coverage, lead to greater reductions in health disparities, and cost 150 international dollars (I$) per year of life saved (YLS). At higher baseline screening coverage levels (i.e., 70%), screening three times in a lifetime yielded greater health benefits than expanding screening once in a lifetime to 90% coverage, and would have a cost‐effectiveness ratio (I$590 per YLS) below Uganda's per capita GDP. Given very low baseline coverage at present, we conclude that a policy focus on increasing access for previously unscreened women appears to be more compatible with improving both equity and efficiency than a focus on increasing frequency for a small subset of women. PMID:27925175

Screening of a Brassica napus bacterial artificial chromosome library using highly parallel single nucleotide polymorphism assays

PubMed Central

2013-01-01

Background Efficient screening of bacterial artificial chromosome (BAC) libraries with polymerase chain reaction (PCR)-based markers is feasible provided that a multidimensional pooling strategy is implemented. Single nucleotide polymorphisms (SNPs) can be screened in multiplexed format, therefore this marker type lends itself particularly well for medium- to high-throughput applications. Combining the power of multiplex-PCR assays with a multidimensional pooling system may prove to be especially challenging in a polyploid genome. In polyploid genomes two classes of SNPs need to be distinguished, polymorphisms between accessions (intragenomic SNPs) and those differentiating between homoeologous genomes (intergenomic SNPs). We have assessed whether the highly parallel Illumina GoldenGate® Genotyping Assay is suitable for the screening of a BAC library of the polyploid Brassica napus genome. Results A multidimensional screening platform was developed for a Brassica napus BAC library which is composed of almost 83,000 clones. Intragenomic and intergenomic SNPs were included in Illumina’s GoldenGate® Genotyping Assay and both SNP classes were used successfully for screening of the multidimensional BAC pools of the Brassica napus library. An optimized scoring method is proposed which is especially valuable for SNP calling of intergenomic SNPs. Validation of the genotyping results by independent methods revealed a success of approximately 80% for the multiplex PCR-based screening regardless of whether intra- or intergenomic SNPs were evaluated. Conclusions Illumina’s GoldenGate® Genotyping Assay can be efficiently used for screening of multidimensional Brassica napus BAC pools. SNP calling was specifically tailored for the evaluation of BAC pool screening data. The developed scoring method can be implemented independently of plant reference samples. It is demonstrated that intergenomic SNPs represent a powerful tool for BAC library screening of a polyploid genome

Non invasive diagnostic methods for better screening of peripheral arterial disease.

PubMed

Nirala, Neelamshobha; Periyasamy, R; Kumar, Awanish

2018-05-16

Peripheral arterial disease (PAD) is a common circulatory problem in which narrowed arteries reduce blood flow to extremities usually legs. It does not receive enough blood flow to keep up with demand. This causes symptoms, most notably leg pain while walking which is known as claudication. It is a common manifestation of type II Diabetes, but the relationship between other vascular diseases and lower limb (LL)-PAD has been poorly understood and investigated. When assessing a patient with clinically LLPAD, two questions are in order to establish a diagnosis: one is non-invasive testing and other is invasive. Invasive methods are painful and get so bad that some people need to have a leg surgery. People with Diabetes are at increased risk for amputation and it is used only when the damage is very severe. Diagnosis of LLPAD begins with a physical examination, patient history, certain questionnaire and non invasive mode of diagnosis is started for the screening of patients. Clinicians check for weak pulses in the legs and then decide for further diagnosis. Paper discusses the prevalence of LLPAD worldwide and in India along with the clinical effectiveness and limitations of these methods in case of Diabetes. The focus of this review is to discuss only those non invasive methods which are widely used for screening of LLPAD like Ankle brachial index (ABI), Toe brachial Index (TBI), and use of photoplethysmogram (PPG) specially in case of Diabetic patients. Also, this paper gives an overview of the work done using ABI, TBI, and PPG for detection of LLPAD. These tests are not painful and could be performed in a cost-effective manner to avoid delays in screening/diagnosis and also reduce costs. Copyright © 2018. Published by Elsevier Inc.

Screening College Students for Hypercholesterolemia.

ERIC Educational Resources Information Center

Faigel, Harris C.

1992-01-01

Describes one college's mandatory mass cholesterol screening for new students. Each year, over 30 beginning students with unknown hypercholesterolemia were detected. The program suggests that mass screening efficiently and economically identifies students who would benefit from cholesterol reduction, a modifiable risk in coronary artery disease.…

Efficient forced vibration reanalysis method for rotating electric machines

NASA Astrophysics Data System (ADS)

Saito, Akira; Suzuki, Hiromitsu; Kuroishi, Masakatsu; Nakai, Hideo

2015-01-01

Rotating electric machines are subject to forced vibration by magnetic force excitation with wide-band frequency spectrum that are dependent on the operating conditions. Therefore, when designing the electric machines, it is inevitable to compute the vibration response of the machines at various operating conditions efficiently and accurately. This paper presents an efficient frequency-domain vibration analysis method for the electric machines. The method enables the efficient re-analysis of the vibration response of electric machines at various operating conditions without the necessity to re-compute the harmonic response by finite element analyses. Theoretical background of the proposed method is provided, which is based on the modal reduction of the magnetic force excitation by a set of amplitude-modulated standing-waves. The method is applied to the forced response vibration of the interior permanent magnet motor at a fixed operating condition. The results computed by the proposed method agree very well with those computed by the conventional harmonic response analysis by the FEA. The proposed method is then applied to the spin-up test condition to demonstrate its applicability to various operating conditions. It is observed that the proposed method can successfully be applied to the spin-up test conditions, and the measured dominant frequency peaks in the frequency response can be well captured by the proposed approach.

Who Gets the Job? First-Generation College Students' Perceptions of Employer Screening Methods

ERIC Educational Resources Information Center

Parks-Yancy, Rochelle; Cooley, Delonia

2018-01-01

What are first-generation college students' (FGCS) perspectives of employment screening methods? The authors investigate which methods FGCS believe are likely to cause an employer to extend a job offer and which methods yield the best pool of job applicants. Survey data were collected from undergraduate business majors. They were analyzed using…

Applying operations research to optimize a novel population management system for cancer screening

PubMed Central

Zai, Adrian H; Kim, Seokjin; Kamis, Arnold; Hung, Ken; Ronquillo, Jeremiah G; Chueh, Henry C; Atlas, Steven J

2014-01-01

Objective To optimize a new visit-independent, population-based cancer screening system (TopCare) by using operations research techniques to simulate changes in patient outreach staffing levels (delegates, navigators), modifications to user workflow within the information technology (IT) system, and changes in cancer screening recommendations. Materials and methods TopCare was modeled as a multiserver, multiphase queueing system. Simulation experiments implemented the queueing network model following a next-event time-advance mechanism, in which systematic adjustments were made to staffing levels, IT workflow settings, and cancer screening frequency in order to assess their impact on overdue screenings per patient. Results TopCare reduced the average number of overdue screenings per patient from 1.17 at inception to 0.86 during simulation to 0.23 at steady state. Increases in the workforce improved the effectiveness of TopCare. In particular, increasing the delegate or navigator staff level by one person improved screening completion rates by 1.3% or 12.2%, respectively. In contrast, changes in the amount of time a patient entry stays on delegate and navigator lists had little impact on overdue screenings. Finally, lengthening the screening interval increased efficiency within TopCare by decreasing overdue screenings at the patient level, resulting in a smaller number of overdue patients needing delegates for screening and a higher fraction of screenings completed by delegates. Conclusions Simulating the impact of changes in staffing, system parameters, and clinical inputs on the effectiveness and efficiency of care can inform the allocation of limited resources in population management. PMID:24043318

Video Tape Application to Higher Education: Pre-Employment Screening. Final Report.

ERIC Educational Resources Information Center

Millet, June E.; Smith, Lawrence H.

Significant needs and additional pressures have been imposed on those persons involved in faculty selection activities on college campuses today. The combination of greater numbers of highly qualified candidates and restricted interview budgets suggests the need for more efficient and less costly methods of employment screening. In addition,…

Assessing Regional Emissions Reductions from Travel Efficiency: Applying the Travel Efficiency Assessment Method

EPA Pesticide Factsheets

This presentation from the 2016 TRB Summer Conference on Transportation Planning and Air Quality summarizes the application of the Travel Efficiency Assessment Method (TEAM) which analyzed selected transportation emission reduction strategies in three case

Robust high-throughput batch screening method in 384-well format with optical in-line resin quantification.

PubMed

Kittelmann, Jörg; Ottens, Marcel; Hubbuch, Jürgen

2015-04-15

High-throughput batch screening technologies have become an important tool in downstream process development. Although continuative miniaturization saves time and sample consumption, there is yet no screening process described in the 384-well microplate format. Several processes are established in the 96-well dimension to investigate protein-adsorbent interactions, utilizing between 6.8 and 50 μL resin per well. However, as sample consumption scales with resin volumes and throughput scales with experiments per microplate, they are limited in costs and saved time. In this work, a new method for in-well resin quantification by optical means, applicable in the 384-well format, and resin volumes as small as 0.1 μL is introduced. A HTS batch isotherm process is described, utilizing this new method in combination with optical sample volume quantification for screening of isotherm parameters in 384-well microplates. Results are qualified by confidence bounds determined by bootstrap analysis and a comprehensive Monte Carlo study of error propagation. This new approach opens the door to a variety of screening processes in the 384-well format on HTS stations, higher quality screening data and an increase in throughput. Copyright © 2015 Elsevier B.V. All rights reserved.

The effectiveness of scoliosis screening programs: methods for systematic review and expert panel recommendations formulation

PubMed Central

2013-01-01

Background Literature on scoliosis screening is vast, however because of the observational nature of available data and methodological flaws, data interpretation is often complex, leading to incomplete and sometimes, somewhat misleading conclusions. The need to propose a set of methods for critical appraisal of the literature about scoliosis screening, a comprehensive summary and rating of the available evidence appeared essential. Methods To address these gaps, the study aims were: i) To propose a framework for the assessment of published studies on scoliosis screening effectiveness; ii) To suggest specific questions to be answered on screening effectiveness instead of trying to reach a global position for or against the programs; iii) To contextualize the knowledge through expert panel consultation and meaningful recommendations. The general methodological approach proceeds through the following steps: Elaboration of the conceptual framework; Formulation of the review questions; Identification of the criteria for the review; Selection of the studies; Critical assessment of the studies; Results synthesis; Formulation and grading of recommendations in response to the questions. This plan follows at best GRADE Group (Grades of Recommendation, Assessment, Development and Evaluation) requirements for systematic reviews, assessing quality of evidence and grading the strength of recommendations. Conclusions In this article, the methods developed in support of this work are presented since they may be of some interest for similar reviews in scoliosis and orthopaedic fields. PMID:23883346

CORALINA: a universal method for the generation of gRNA libraries for CRISPR-based screening.

PubMed

Köferle, Anna; Worf, Karolina; Breunig, Christopher; Baumann, Valentin; Herrero, Javier; Wiesbeck, Maximilian; Hutter, Lukas H; Götz, Magdalena; Fuchs, Christiane; Beck, Stephan; Stricker, Stefan H

2016-11-14

The bacterial CRISPR system is fast becoming the most popular genetic and epigenetic engineering tool due to its universal applicability and adaptability. The desire to deploy CRISPR-based methods in a large variety of species and contexts has created an urgent need for the development of easy, time- and cost-effective methods enabling large-scale screening approaches. Here we describe CORALINA (comprehensive gRNA library generation through controlled nuclease activity), a method for the generation of comprehensive gRNA libraries for CRISPR-based screens. CORALINA gRNA libraries can be derived from any source of DNA without the need of complex oligonucleotide synthesis. We show the utility of CORALINA for human and mouse genomic DNA, its reproducibility in covering the most relevant genomic features including regulatory, coding and non-coding sequences and confirm the functionality of CORALINA generated gRNAs. The simplicity and cost-effectiveness make CORALINA suitable for any experimental system. The unprecedented sequence complexities obtainable with CORALINA libraries are a necessary pre-requisite for less biased large scale genomic and epigenomic screens.

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. Copyright © 2016 Elsevier B.V. All rights reserved.

Microelectroporation device for genomic screening

DOEpatents

Perroud, Thomas D.; Renzi, Ronald F.; Negrete, Oscar; Claudnic, Mark R.

2014-09-09

We have developed an microelectroporation device that combines microarrays of oligonucleotides, microfluidic channels, and electroporation for cell transfection and high-throughput screening applications (e.g. RNA interference screens). Microarrays allow the deposition of thousands of different oligonucleotides in microscopic spots. Microfluidic channels and microwells enable efficient loading of cells into the device and prevent cross-contamination between different oligonucleotides spots. Electroporation allows optimal transfection of nucleic acids into cells (especially hard-to-transfect cells such as primary cells) by minimizing cell death while maximizing transfection efficiency. This invention has the advantage of a higher throughput and lower cost, while preventing cross-contamination compared to conventional screening technologies. Moreover, this device does not require bulky robotic liquid handling equipment and is inherently safer given that it is a closed system.

77 FR 31756 - Energy Conservation Program: Alternative Efficiency Determination Methods and Alternative Rating...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-30

...-AC46 Energy Conservation Program: Alternative Efficiency Determination Methods and Alternative Rating Methods: Public Meeting AGENCY: Office of Energy Efficiency and Renewable Energy, Department of Energy... regulations authorizing the use of alternative methods of determining energy efficiency or energy consumption...

["Allergic Progression": importance of Phadiatop and RAST fx5 as screening measures for childhood atopy].

PubMed

Molkhou, P

1999-04-01

Since discovery of IgE in 1967, which was a real revolution in allergy field, new biological methods as Phadiatop for inhalant allergens and RAST fx5 for food allergens, have been used routinely. Both methods are very useful for reliable and cost efficient atopy screening.

Biological optimization systems for enhancing photosynthetic efficiency and methods of use

DOEpatents

Hunt, Ryan W.; Chinnasamy, Senthil; Das, Keshav C.; de Mattos, Erico Rolim

2012-11-06

Biological optimization systems for enhancing photosynthetic efficiency and methods of use. Specifically, methods for enhancing photosynthetic efficiency including applying pulsed light to a photosynthetic organism, using a chlorophyll fluorescence feedback control system to determine one or more photosynthetic efficiency parameters, and adjusting one or more of the photosynthetic efficiency parameters to drive the photosynthesis by the delivery of an amount of light to optimize light absorption of the photosynthetic organism while providing enough dark time between light pulses to prevent oversaturation of the chlorophyll reaction centers are disclosed.

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.

A Sector Capacity Assessment Method Based on Airspace Utilization Efficiency

NASA Astrophysics Data System (ADS)

Zhang, Jianping; Zhang, Ping; Li, Zhen; Zou, Xiang

2018-02-01

Sector capacity is one of the core factors affecting the safety and the efficiency of the air traffic system. Most of previous sector capacity assessment methods only considered the air traffic controller’s (ATCO’s) workload. These methods are not only limited which only concern about the safety, but also not accurate enough. In this paper, we employ the integrated quantitative index system proposed in one of our previous literatures. We use the principal component analysis (PCA) to find out the principal indicators among the indicators so as to calculate the airspace utilization efficiency. In addition, we use a series of fitting functions to test and define the correlation between the dense of air traffic flow and the airspace utilization efficiency. The sector capacity is then decided as the value of the dense of air traffic flow corresponding to the maximum airspace utilization efficiency. We also use the same series of fitting functions to test the correlation between the dese of air traffic flow and the ATCOs’ workload. We examine our method with a large amount of empirical operating data of Chengdu Controlling Center and obtain a reliable sector capacity value. Experiment results also show superiority of our method against those only consider the ATCO’s workload in terms of better correlation between the airspace utilization efficiency and the dense of air traffic flow.

Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

PubMed

Yachie, Nozomu; Petsalaki, Evangelia; Mellor, Joseph C; Weile, Jochen; Jacob, Yves; Verby, Marta; Ozturk, Sedide B; Li, Siyang; Cote, Atina G; Mosca, Roberto; Knapp, Jennifer J; Ko, Minjeong; Yu, Analyn; Gebbia, Marinella; Sahni, Nidhi; Yi, Song; Tyagi, Tanya; Sheykhkarimli, Dayag; Roth, Jonathan F; Wong, Cassandra; Musa, Louai; Snider, Jamie; Liu, Yi-Chun; Yu, Haiyuan; Braun, Pascal; Stagljar, Igor; Hao, Tong; Calderwood, Michael A; Pelletier, Laurence; Aloy, Patrick; Hill, David E; Vidal, Marc; Roth, Frederick P

2016-04-22

High-throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome-scale interaction mapping. Here, we report Barcode Fusion Genetics-Yeast Two-Hybrid (BFG-Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG-Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein-pair barcodes that can be quantified via next-generation sequencing. We applied BFG-Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG-Y2H increases the efficiency of protein matrix screening, with quality that is on par with state-of-the-art Y2H methods. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

CRISPR-Cas9-Edited Site Sequencing (CRES-Seq): An Efficient and High-Throughput Method for the Selection of CRISPR-Cas9-Edited Clones.

PubMed

Veeranagouda, Yaligara; Debono-Lagneaux, Delphine; Fournet, Hamida; Thill, Gilbert; Didier, Michel

2018-01-16

The emergence of clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) gene editing systems has enabled the creation of specific mutants at low cost, in a short time and with high efficiency, in eukaryotic cells. Since a CRISPR-Cas9 system typically creates an array of mutations in targeted sites, a successful gene editing project requires careful selection of edited clones. This process can be very challenging, especially when working with multiallelic genes and/or polyploid cells (such as cancer and plants cells). Here we described a next-generation sequencing method called CRISPR-Cas9 Edited Site Sequencing (CRES-Seq) for the efficient and high-throughput screening of CRISPR-Cas9-edited clones. CRES-Seq facilitates the precise genotyping up to 96 CRISPR-Cas9-edited sites (CRES) in a single MiniSeq (Illumina) run with an approximate sequencing cost of $6/clone. CRES-Seq is particularly useful when multiple genes are simultaneously targeted by CRISPR-Cas9, and also for screening of clones generated from multiallelic genes/polyploid cells. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.

Ultra-high-throughput screening method for the directed evolution of glucose oxidase.

PubMed

Ostafe, Raluca; Prodanovic, Radivoje; Nazor, Jovana; Fischer, Rainer

2014-03-20

Glucose oxidase (GOx) is used in many industrial processes that could benefit from improved versions of the enzyme. Some improvements like higher activity under physiological conditions and thermal stability could be useful for GOx applications in biosensors and biofuel cells. Directed evolution is one of the currently available methods to engineer improved GOx variants. Here, we describe an ultra-high-throughput screening system for sorting the best enzyme variants generated by directed evolution that incorporates several methodological refinements: flow cytometry, in vitro compartmentalization, yeast surface display, fluorescent labeling of the expressed enzyme, delivery of glucose substrate to the reaction mixture through the oil phase, and covalent labeling of the cells with fluorescein-tyramide. The method enables quantitative screening of gene libraries to identify clones with improved activity and it also allows cells to be selected based not only on the overall activity but also on the specific activity of the enzyme. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microengineering methods for cell-based microarrays and high-throughput drug-screening applications.

PubMed

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

2011-09-01

Screening for effective therapeutic agents from millions of drug candidates is costly, time consuming, and often faces concerns due to the 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 has 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 great potential to provide repeatable 3D cell-based constructs with high temporal, spatial control and versatility.

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

Screening for prodromal Parkinson's disease in the general community: a sleep-based approach.

PubMed

Postuma, Ronald B; Pelletier, Amelie; Berg, Daniela; Gagnon, Jean-Francois; Escudier, Frédérique; Montplaisir, Jacques

2016-05-01

Neuroprotective therapy for Parkinson's disease (PD) is most likely to be effective if provided in its prodromal stages. However, identifying prodromal PD is difficult because PD is relatively uncommon, and most markers are nonspecific. Rapid eye movement (REM) sleep behavior disorder (RBD) is by far the strongest clinical marker of prodromal PD, but most patients do not seek out medical attention. Developing an efficient way of diagnosing RBD from the general community may be the most practical method to detect prodromal PD. We developed a screening strategy that began with a newspaper advertisement containing a single-question screen for RBD. All screen-positive subjects underwent an interview based on the Innsbruck RBD inventory aimed to optimize the positive predictive value. Those who passed both screens underwent confirmatory polysomnography. The proportion of screened RBD patients who met the International Parkinson and Movement Disorder Society (MDS) criteria for prodromal PD was assessed. A broad array of clinical markers of neurodegeneration was compared between newspaper-screened RBD patients and 130 RBD patients clinically referred to the sleep center. Of 111 RBD-screen-positive participants, 40 (36%) passed the secondary screen, and 29 underwent full polysomnography. Of these 29 patients, 19 were ultimately proven to have RBD (PPV = 66%), 12 (63%) of whom met the criteria for prodromal PD. Compared to patients referred to the sleep center, newspaper-screened patients had similar age, sex, olfaction, autonomic function, and color vision. However, motor and cognitive assessments were slightly better in newspaper-screened patients. A multistep screening approach using RBD screening questionnaires and telephone follow-up can efficiently identify prodromal PD in the general community. Copyright © 2016 Elsevier B.V. All rights reserved.

Screening and large-scale expression of membrane proteins in mammalian cells for structural studies

PubMed Central

Goehring, April; Lee, Chia-Hsueh; Wang, Kevin H.; Michel, Jennifer Carlisle; Claxton, Derek P.; Baconguis, Isabelle; Althoff, Thorsten; Fischer, Suzanne; Garcia, K. Christopher; Gouaux, Eric

2014-01-01

Structural, biochemical and biophysical studies of eukaryotic membrane proteins are often hampered by difficulties in over-expression of the candidate molecule. Baculovirus transduction of mammalian cells (BacMam), although a powerful method to heterologously express membrane proteins, can be cumbersome for screening and expression of multiple constructs. We therefore developed plasmid Eric Gouaux (pEG) BacMam, a vector optimized for use in screening assays, as well as for efficient production of baculovirus and robust expression of the target protein. In this protocol we show how to use small-scale transient transfection and fluorescence-detection, size-exclusion chromatography (FSEC) experiments using a GFP-His8 tagged candidate protein to screen for monodispersity and expression level. Once promising candidates are identified, we describe how to generate baculovirus, transduce HEK293S GnTI− (N-acetylglucosaminyltransferase I-negative) cells in suspension culture, and over-express the candidate protein. We have used these methods to prepare pure samples of chicken acid-sensing ion channel 1a (cASIC1) and Caenorhabditis elegans glutamate-gated chloride channel (GluCl), for X-ray crystallography, demonstrating how to rapidly and efficiently screen hundreds of constructs and accomplish large-scale expression in 4-6 weeks. PMID:25299155

Efficient Methods of Estimating Switchgrass Biomass Supplies

USDA-ARS?s Scientific Manuscript database

Switchgrass (Panicum virgatum L.) is being developed as a biofuel feedstock for the United States. Efficient and accurate methods to estimate switchgrass biomass feedstock supply within a production area will be required by biorefineries. Our main objective was to determine the effectiveness of in...

Efficient Training of Supervised Spiking Neural Network via Accurate Synaptic-Efficiency Adjustment Method.

PubMed

Xie, Xiurui; Qu, Hong; Yi, Zhang; Kurths, Jurgen

2017-06-01

The spiking neural network (SNN) is the third generation of neural networks and performs remarkably well in cognitive tasks, such as pattern recognition. The temporal neural encode mechanism found in biological hippocampus enables SNN to possess more powerful computation capability than networks with other encoding schemes. However, this temporal encoding approach requires neurons to process information serially on time, which reduces learning efficiency significantly. To keep the powerful computation capability of the temporal encoding mechanism and to overcome its low efficiency in the training of SNNs, a new training algorithm, the accurate synaptic-efficiency adjustment method is proposed in this paper. Inspired by the selective attention mechanism of the primate visual system, our algorithm selects only the target spike time as attention areas, and ignores voltage states of the untarget ones, resulting in a significant reduction of training time. Besides, our algorithm employs a cost function based on the voltage difference between the potential of the output neuron and the firing threshold of the SNN, instead of the traditional precise firing time distance. A normalized spike-timing-dependent-plasticity learning window is applied to assigning this error to different synapses for instructing their training. Comprehensive simulations are conducted to investigate the learning properties of our algorithm, with input neurons emitting both single spike and multiple spikes. Simulation results indicate that our algorithm possesses higher learning performance than the existing other methods and achieves the state-of-the-art efficiency in the training of SNN.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ravindra, M.K.; Banon, H.

1992-07-01

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ravindra, M.K.; Banon, H.

1992-07-01

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

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. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

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

Danish method study on cervical screening in women offered HPV vaccination as girls (Trial23): a study protocol.

PubMed

Thamsborg, Lise Holst; Andersen, Berit; Larsen, Lise Grupe; Christensen, Jette; Johansen, Tonje; Hariri, Jalil; Christiansen, Sanne; Rygaard, Carsten; Lynge, Elsebeth

2018-05-26

The first birth cohorts of women offered human papillomavirus (HPV) vaccination as girls are now entering cervical screening. However, there is no international consensus on how to screen HPV vaccinated women. These women are better protected against cervical cancer and could therefore be offered less intensive screening. Primary HPV testing is more sensitive than cytology, allowing for a longer screening interval. The aim of Trial23 is to investigate if primary HPV testing with cytology triage of HPV positive samples is a reasonable screening scheme for women offered HPV vaccination as girls. Trial23 is a method study embedded in the existing cervical screening programme in four out of five Danish regions. Without affecting the screening programme, women born in 1994 are randomised to present screening with liquid-based cytology every third year (present programme arm) or present screening plus an HPV test (HPV arm). The study started 1 February 2017 and will run over three screening rounds corresponding to 7-8 years. The primary endpoint is cervical intraepithelial neoplasia grade 3 or above. The trial is undertaken as a non-inferiority study including intention-to-treat and per-protocol analyses. The potential effect of primary HPV screening with a 6-year interval will be calculated from the observed data. The study protocol has been submitted to the ethical committee and deemed a method study. All women are screened according to routine guidelines. The study will contribute new evidence on the future screening of HPV vaccinated birth cohorts of women. All results will be published in open-access journal. NCT03049553; Pre-results. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Taking transgenic rice drought screening to the field.

PubMed

Gaudin, Amélie C M; Henry, Amelia; Sparks, Adam H; Slamet-Loedin, Inez H

2013-01-01

Numerous transgenes have been reported to increase rice drought resistance, mostly in small-scale experiments under vegetative-stage drought stress, but few studies have included grain yield or field evaluations. Different definitions of drought resistance are currently in use for field-based and laboratory evaluations of transgenics, the former emphasizing plant responses that may not be linked to yield under drought. Although those fundamental studies use efficient protocols to uncover and validate gene functions, screening conditions differ greatly from field drought environments where the onset of drought stress symptoms is slow (2-3 weeks). Simplified screening methods, including severely stressed survival studies, are therefore not likely to identify transgenic events with better yield performance under drought in the target environment. As biosafety regulations are becoming established to allow field trials in some rice-producing countries, there is a need to develop relevant screening procedures that scale from preliminary event selection to greenhouse and field trials. Multilocation testing in a range of drought environments may reveal that different transgenes are necessary for different types of drought-prone field conditions. We describe here a pipeline to improve the selection efficiency and reproducibility of results across drought treatments and test the potential of transgenic rice for the development of drought-resistant material for agricultural purposes.

Comparison of Instructional Methods for Screening, Brief Intervention, and Referral to Treatment for Substance Use in Nursing Education.

PubMed

Knopf-Amelung, Sarah; Gotham, Heather; Kuofie, Araba; Young, Pamela; Manney Stinson, Ronalda; Lynn, Jolene; Barker, Kendra; Hildreth, Jessica

Most nursing programs lack curriculum on substance use. This project evaluated 3 didactic instructional methods for teaching baccalaureate nursing students about screening, brief intervention, and referral to treatment for substance use. In-person, asynchronous narrated slides and interactive online instructional methods were all effective in developing students' competency; however, active learning methods (in-person and interactive online course) were more effective in changing students' attitudes about their role in screening and intervening for drug use.

A web-based screening and accrual strategy for a cancer prevention clinical trial in healthy smokers.

PubMed

Mohebati, Arash; Knutson, Allison; Zhou, Xi Kathy; Smith, Judith J; Brown, Powel H; Dannenberg, Andrew J; Szabo, Eva

2012-09-01

Screening and recruitment of qualified subjects for clinical trials is an essential component of translational research, and it can be quite challenging if the most efficient recruitment method is not utilized. In this report, we describe a successful web-based screening and accrual method used in a randomized prospective chemoprevention clinical trial with urinary biomarker endpoints. The targeted study population was a group of at-risk healthy current smokers with no evidence of lung disease. Craigslist was used as the sole recruitment modality for this study. All interested subjects were directed to a pre-screening website, in which subject questionnaire responses were linked to the study coordinator's secure e-mail account. Of the 429 initial inquiries, 189 individuals were initially eligible based on the questionnaire response. One hundred twenty-two people were telephone-screened, of whom 98 subjects were consented, 84 were randomized and 77 subjects completed the study successfully. Utilizing this single web-based advertising strategy, accrual for the trial was completed 7 months prior to the projected date. Craigslist is a cost effective and efficient web-based resource that can be utilized in accruing subjects to some chemoprevention trials. Published by Elsevier Inc.

A web-based screening and accrual strategy for a cancer prevention clinical trial in healthy smokers

PubMed Central

Mohebati, Arash; Knutson, Allison; Zhou, Xi Kathy; Smith, Judith J.; Brown, Powel H.; Dannenberg, Andrew J.; Szabo, Eva

2012-01-01

Screening and recruitment of qualified subjects for clinical trials is an essential component of translational research, and it can be quite challenging if the most efficient recruitment method is not utilized. In this report, we describe a successful web-based screening and accrual method used in a randomized prospective chemoprevention clinical trial with urinary biomarker endpoints. The targeted study population was a group of at-risk healthy current smokers with no evidence of lung disease. Craigslist was used as the sole recruitment modality for this study. All interested subjects were directed to a pre-screening website, in which subject questionnaire responses were linked to the study coordinator's secure e-mail account. Of the 429 initial inquiries, 189 individuals were initially eligible based on the questionnaire response. One hundred twenty-two people were telephone-screened, of whom 98 subjects were consented, 84 were randomized and 77 subjects completed the study successfully. Utilizing this single web-based advertising strategy, accrual for the trial was completed 7 months prior to the projected date. Craigslist is a cost effective and efficient web-based resource that can be utilized in accruing subjects to some chemoprevention trials. PMID:22771576

Efficient Sporulation of Saccharomyces cerevisiae in a 96 Multiwell Format.

PubMed

Paulissen, Scott M; Huang, Linda S

2016-09-17

During times of nutritional stress, Saccharomyces cerevisiae undergoes gametogenesis, known as sporulation. Diploid yeast cells that are starved for nitrogen and carbon will initiate the sporulation process. The process of sporulation includes meiosis followed by spore formation, where the haploid nuclei are packaged into environmentally resistant spores. We have developed methods for the efficient sporulation of budding yeast in 96 multiwell plates, to increase the throughput of screening yeast cells for sporulation phenotypes. These methods are compatible with screening with yeast containing plasmids requiring nutritional selection, when appropriate minimal media is used, or with screening yeast with genomic alterations, when a rich presporulation regimen is used. We find that for this method, aeration during sporulation is critical for spore formation, and have devised techniques to ensure sufficient aeration that are compatible with the 96 multiwell plate format. Although these methods do not achieve the typical ~80% level of sporulation that can be achieved in large-volume flask based experiments, these methods will reliably achieve about 50-60% level of sporulation in small-volume multiwell plates.

Cost and effectiveness comparison of two methods for screening potential blood donors for anaemia in Vietnam.

PubMed

Tyrrell, A; Worrall, E; Que, T N; Bates, I

2011-06-01

To compare the cost and effectiveness of Copper Sulphate (CS) and HemoCue (HC) methods for screening blood donors for anaemia. Robust information from developing countries about cost and effectiveness of anaemia screening methods for blood donors is scarce. In such countries there are widespread shortages of blood, so the most cost-effective method should maximise blood supply without compromising donor safety. Economic data (e.g. staff time, equipment and buildings) were collected from direct observation of procedures and purchase data from Hanoi's Central Blood Bank administrative department. A framework for comparing the cost and effectiveness of anaemia screening methods was developed and a cost per effective (i.e. usable and accurate) test was generated for each method. Samples from 100 potential donors from the Hanoi Central Blood Bank (static) and 198 from two mobile units were tested. The mean probability of an ineffective anaemia test was 0·1 (0·05-0·2). The average cost of an HC test was $0·75 (static $0·61 and mobile $0·89) and a CS test was $0·31 (static $0·17 and mobile $0·45). The difference between static and mobile units was predominantly due to transport costs; the difference between the two methods was predominantly due to the HC microcuvettes. In this setting the CS yields greater value for money than the HC method for screening blood donors. The relative cost and effectiveness of CS and HC may be different in places with higher staff turnover, lower test accuracy, higher anaemia prevalence or lower workload than in Vietnam. © 2010 Liverpool School of Tropical Medicine. Transfusion Medicine © 2010 British Blood Transfusion Society.

Prediction of Phase Behavior of Spray-Dried Amorphous Solid Dispersions: Assessment of Thermodynamic Models, Standard Screening Methods and a Novel Atomization Screening Device with Regard to Prediction Accuracy

PubMed Central

Chavez, Pierre-François; Meeus, Joke; Robin, Florent; Schubert, Martin Alexander; Somville, Pascal

2018-01-01

The evaluation of drug–polymer miscibility in the early phase of drug development is essential to ensure successful amorphous solid dispersion (ASD) manufacturing. This work investigates the comparison of thermodynamic models, conventional experimental screening methods (solvent casting, quench cooling), and a novel atomization screening device based on their ability to predict drug–polymer miscibility, solid state properties (Tg value and width), and adequate polymer selection during the development of spray-dried amorphous solid dispersions (SDASDs). Binary ASDs of four drugs and seven polymers were produced at 20:80, 40:60, 60:40, and 80:20 (w/w). Samples were systematically analyzed using modulated differential scanning calorimetry (mDSC) and X-ray powder diffraction (XRPD). Principal component analysis (PCA) was used to qualitatively assess the predictability of screening methods with regards to SDASD development. Poor correlation was found between theoretical models and experimentally-obtained results. Additionally, the limited ability of usual screening methods to predict the miscibility of SDASDs did not guarantee the appropriate selection of lead excipient for the manufacturing of robust SDASDs. Contrary to standard approaches, our novel screening device allowed the selection of optimal polymer and drug loading and established insight into the final properties and performance of SDASDs at an early stage, therefore enabling the optimization of the scaled-up late-stage development. PMID:29518936

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

2017-05-01

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. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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

USDA-ARS?s Scientific Manuscript database

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...

An Evaluation of the Efficiency of Different Hygienisation Methods

NASA Astrophysics Data System (ADS)

Zrubková, M.

2017-10-01

The aim of this study is to evaluate the efficiency of hygienisation by pasteurisation, temperature-phased anaerobic digestion and sludge liming. A summary of the legislation concerning sludge treatment, disposal and recycling is included. The hygienisation methods are compared not only in terms of hygienisation efficiency but a comparison of other criteria is also included.

An efficient early phase 2 procedure to screen medications for efficacy in smoking cessation.

PubMed

Perkins, Kenneth A; Lerman, Caryn

2014-01-01

Initial screening of new medications for potential efficacy (i.e., Food and Drug Administration (FDA) early phase 2), such as in aiding smoking cessation, should be efficient in identifying which drugs do, or do not, warrant more extensive (and expensive) clinical testing. This focused review outlines our research on development, evaluation, and validation of an efficient crossover procedure for sensitivity in detecting medication efficacy for smoking cessation. First-line FDA-approved medications of nicotine patch, varenicline, and bupropion were tested as model drugs, in three separate placebo-controlled studies. We also tested specificity of our procedure in identifying a drug that lacks efficacy, using modafinil. This crossover procedure showed sensitivity (increased days of abstinence) during week-long "practice" quit attempts with each of the active cessation medications (positive controls) versus placebo, but not with modafinil (negative control) versus placebo, as hypothesized. Sensitivity to medication efficacy signal was observed only in smokers high in intrinsic quit motivation (i.e., already preparing to quit soon) and not smokers low in intrinsic quit motivation, even if monetarily reinforced for abstinence (i.e., given extrinsic motivation). A crossover procedure requiring less time and fewer subjects than formal trials may provide an efficient strategy for a go/no-go decision whether to advance to subsequent phase 2 randomized clinical trials with a novel drug. Future research is needed to replicate our results and evaluate this procedure with novel compounds, identify factors that may limit its utility, and evaluate its applicability to testing efficacy of compounds for treating other forms of addiction.

Direct Measurements of Smartphone Screen-Time: Relationships with Demographics and Sleep

PubMed Central

Christensen, Matthew A.; Bettencourt, Laura; Kaye, Leanne; Moturu, Sai T.; Nguyen, Kaylin T.; Olgin, Jeffrey E.; Pletcher, Mark J.; Marcus, Gregory M.

2016-01-01

Background Smartphones are increasingly integrated into everyday life, but frequency of use has not yet been objectively measured and compared to demographics, health information, and in particular, sleep quality. Aims The aim of this study was to characterize smartphone use by measuring screen-time directly, determine factors that are associated with increased screen-time, and to test the hypothesis that increased screen-time is associated with poor sleep. Methods We performed a cross-sectional analysis in a subset of 653 participants enrolled in the Health eHeart Study, an internet-based longitudinal cohort study open to any interested adult (≥ 18 years). Smartphone screen-time (the number of minutes in each hour the screen was on) was measured continuously via smartphone application. For each participant, total and average screen-time were computed over 30-day windows. Average screen-time specifically during self-reported bedtime hours and sleeping period was also computed. Demographics, medical information, and sleep habits (Pittsburgh Sleep Quality Index–PSQI) were obtained by survey. Linear regression was used to obtain effect estimates. Results Total screen-time over 30 days was a median 38.4 hours (IQR 21.4 to 61.3) and average screen-time over 30 days was a median 3.7 minutes per hour (IQR 2.2 to 5.5). Younger age, self-reported race/ethnicity of Black and "Other" were associated with longer average screen-time after adjustment for potential confounders. Longer average screen-time was associated with shorter sleep duration and worse sleep-efficiency. Longer average screen-times during bedtime and the sleeping period were associated with poor sleep quality, decreased sleep efficiency, and longer sleep onset latency. Conclusions These findings on actual smartphone screen-time build upon prior work based on self-report and confirm that adults spend a substantial amount of time using their smartphones. Screen-time differs across age and race, but is

Efficiency and flexibility using implicit methods within atmosphere dycores

NASA Astrophysics Data System (ADS)

Evans, K. J.; Archibald, R.; Norman, M. R.; Gardner, D. J.; Woodward, C. S.; Worley, P.; Taylor, M.

2016-12-01

A suite of explicit and implicit methods are evaluated for a range of configurations of the shallow water dynamical core within the spectral-element Community Atmosphere Model (CAM-SE) to explore their relative computational performance. The configurations are designed to explore the attributes of each method under different but relevant model usage scenarios including varied spectral order within an element, static regional refinement, and scaling to large problem sizes. The limitations and benefits of using explicit versus implicit, with different discretizations and parameters, are discussed in light of trade-offs such as MPI communication, memory, and inherent efficiency bottlenecks. For the regionally refined shallow water configurations, the implicit BDF2 method is about the same efficiency as an explicit Runge-Kutta method, without including a preconditioner. Performance of the implicit methods with the residual function executed on a GPU is also presented; there is speed up for the residual relative to a CPU, but overwhelming transfer costs motivate moving more of the solver to the device. Given the performance behavior of implicit methods within the shallow water dynamical core, the recommendation for future work using implicit solvers is conditional based on scale separation and the stiffness of the problem. The strong growth of linear iterations with increasing resolution or time step size is the main bottleneck to computational efficiency. Within the hydrostatic dynamical core, of CAM-SE, we present results utilizing approximate block factorization preconditioners implemented using the Trilinos library of solvers. They reduce the cost of linear system solves and improve parallel scalability. We provide a summary of the remaining efficiency considerations within the preconditioner and utilization of the GPU, as well as a discussion about the benefits of a time stepping method that provides converged and stable solutions for a much wider range of time

Comparison of different screening methods for blood pressure disorders in children and adolescents.

PubMed

Mourato, Felipe Alves; Lima Filho, José Luiz; Mattos, Sandra da Silva

2015-01-01

To compare different methods of screening for blood pressure disorders in children and adolescents. A database with 17,083 medical records of patients from a pediatric cardiology clinic was used. After analyzing the inclusion and exclusion criteria, 5,650 were selected. These were divided into two age groups: between 5 and 13 years and between 13 and 18 years. The blood pressure measurement was classified as normal, pre-hypertensive, or hypertensive, consistent with recent guidelines and the selected screening methods. Sensitivity, specificity, and accuracy were then calculated according to gender and age range. The formulas proposed by Somu and Ardissino's table showed low sensitivity in identifying pre-hypertension in all age groups, whereas the table proposed by Kaelber showed the best results. The ratio between blood pressure and height showed low specificity in the younger age group, but showed good performance in adolescents. Screening tools used for the assessment of blood pressure disorders in children and adolescents may be useful to decrease the current rate of underdiagnosis of this condition. The table proposed by Kaelber showed the best results; however, the ratio between BP and height demonstrated specific advantages, as it does not require tables. Copyright © 2014 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Nutrient supplements boost yeast transformation efficiency

PubMed Central

Yu, Sheng-Chun; Dawson, Alexander; Henderson, Alyssa C.; Lockyer, Eloise J.; Read, Emily; Sritharan, Gayathri; Ryan, Marjah; Sgroi, Mara; Ngou, Pok M.; Woodruff, Rosie; Zhang, Ruifeng; Ren Teen Chia, Travis; Liu, Yu; Xiang, Yiyu; Spanu, Pietro D.

2016-01-01

Efficiency of yeast transformation is determined by the rate of yeast endocytosis. The aim of this study was to investigate the effect of introducing amino acids and other nutrients (inositol, adenine, or p-aminobenzoic acid) in the transformation medium to develop a highly efficient yeast transformation protocol. The target of rapamycin complex 1 (TORC1) kinase signalling complex influences the rate of yeast endocytosis. TORC signaling is induced by amino acids in the media. Here, we found that increasing the concentration of amino acids and other nutrients in the growth media lead to an increase yeast transformation efficiency up to 107 CFU per μg plasmid DNA and per 108 cells with a 13.8 kb plasmid DNA. This is over 130 times that of current published methods. This improvement may facilitate more efficient experimentation in which transformation efficiency is critical, such as yeast two-hybrid screening. PMID:27760994

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. Copyright © 2016 Elsevier B.V. All rights reserved.

Factors Associated with Recruitment and Screening in the Treatment for Adolescents with Depression Study (TADS)

ERIC Educational Resources Information Center

May, Diane E.; Hallin, Mary J.; Kratochvil, Christopher J.; Puumala, Susan E.; Smith, Lynette S.; Reinecke, Mark A.; Silva, Susan G.; Weller, Elizabeth B.; Vitiello, Benedetto; Breland-Noble, Alfiee; March, John S.

2007-01-01

Objective: To examine factors associated with eligibility and randomization and consider the efficiency of recruitment methods. Method: Adolescents, ages 12 to 17 years, were telephone screened (N = 2,804) followed by in-person evaluation (N = 1,088) for the Treatment for Adolescents With Depression Study. Separate logistic regression models,…

An efficient multilevel optimization method for engineering design

NASA Technical Reports Server (NTRS)

Vanderplaats, G. N.; Yang, Y. J.; Kim, D. S.

1988-01-01

An efficient multilevel deisgn optimization technique is presented. The proposed method is based on the concept of providing linearized information between the system level and subsystem level optimization tasks. The advantages of the method are that it does not require optimum sensitivities, nonlinear equality constraints are not needed, and the method is relatively easy to use. The disadvantage is that the coupling between subsystems is not dealt with in a precise mathematical manner.

A deep learning and novelty detection framework for rapid phenotyping in high-content screening

PubMed Central

Sommer, Christoph; Hoefler, Rudolf; Samwer, Matthias; Gerlich, Daniel W.

2017-01-01

Supervised machine learning is a powerful and widely used method for analyzing high-content screening data. Despite its accuracy, efficiency, and versatility, supervised machine learning has drawbacks, most notably its dependence on a priori knowledge of expected phenotypes and time-consuming classifier training. We provide a solution to these limitations with CellCognition Explorer, a generic novelty detection and deep learning framework. Application to several large-scale screening data sets on nuclear and mitotic cell morphologies demonstrates that CellCognition Explorer enables discovery of rare phenotypes without user training, which has broad implications for improved assay development in high-content screening. PMID:28954863

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.

Screening of antagonistic bacteria for biological control of nursery wilt of black pepper (Piper nigrum).

PubMed

Anith, K N; Radhakrishnan, N V; Manomohandas, T P

2003-01-01

Bacterial antagonists of Phytophthora capsici were isolated from underground shoot portions of rooted cuttings of black pepper. Initially isolates were screened by dual culture on potato dextrose agar and carrot agar. Further, a screening was done on black pepper shoots for supression of lesion caused by the pathogen. Most of the antagonists showed varying levels of antagonism in the dual culture and the shoot assay. Isolate PN-026, showing the highest suppression of lesion development in the shoot assay was found to be the most efficient antagonist in reducing Phytophthora capsici induced nursery wilt of black pepper. This screening involving the host, pathogen, and the antagonist, performed on black pepper shoot (the planting material for this vegetatively propagated crop), could be used as a rapid and reliable method for the isolation of efficient bacterial antagonists of P. capsici.

Method for assessing in-service motor efficiency and in-service motor/load efficiency

DOEpatents

Kueck, John D.; Otaduy, Pedro J.

1997-01-01

A method and apparatus for assessing the efficiency of an in-service motor. The operating characteristics of the in-service motor are remotely measured. The operating characteristics are then applied to an equivalent circuit for electrical motors. Finally the equivalent circuit is evaluated to determine the performance characteristics of said in-service motor. Based upon the evaluation an individual is able to determine the rotor speed, power output, efficiency, and toque of the in-service motor. Additionally, an individual is able to confirm the calculations by comparing measured values with values obtained as a result of the motor equivalent circuit evaluation.

User-composable Electronic Health Record Improves Efficiency of Clinician Data Viewing for Patient Case Appraisal: A Mixed-Methods Study.

PubMed

Senathirajah, Yalini; Kaufman, David; Bakken, Suzanne

2016-01-01

Challenges in the design of electronic health records (EHRs) include designing usable systems that must meet the complex, rapidly changing, and high-stakes information needs of clinicians. The ability to move and assemble elements together on the same page has significant human-computer interaction (HCI) and efficiency advantages, and can mitigate the problems of negotiating multiple fixed screens and the associated cognitive burdens. We compare MedWISE-a novel EHR that supports user-composable displays-with a conventional EHR in terms of the number of repeat views of data elements for patient case appraisal. The study used mixed-methods for examination of clinical data viewing in four patient cases. The study compared use of an experimental user-composable EHR with use of a conventional EHR, for case appraisal. Eleven clinicians used a user-composable EHR in a case appraisal task in the laboratory setting. This was compared with log file analysis of the same patient cases in the conventional EHR. We investigated the number of repeat views of the same clinical information during a session and across these two contexts, and compared them using Fisher's exact test. There was a significant difference (p<.0001) in proportion of cases with repeat data element viewing between the user-composable EHR (14.6 percent) and conventional EHR (72.6 percent). Users of conventional EHRs repeatedly viewed the same information elements in the same session, as revealed by log files. Our findings are consistent with the hypothesis that conventional systems require that the user view many screens and remember information between screens, causing the user to forget information and to have to access the information a second time. Other mechanisms (such as reduction in navigation over a population of users due to interface sharing, and information selection) may also contribute to increased efficiency in the experimental system. Systems that allow a composable approach that enables the

Screening efficiency of the self-report version of the Multidimensional Anxiety Scale for Children in a highly comorbid inpatient sample.

PubMed

Skarphedinsson, Gudmundur; Villabø, Marianne A; Lauth, Bertrand

2015-01-01

The Multidimensional Anxiety Scale for Children (MASC) is a widely used self-report questionnaire for the assessment of anxiety symptoms in children and adolescents with well documented predictive validity of the total score and subscales in internalizing and mixed clinical samples. However, no data exist on the screening efficiency in an inpatient sample of adolescents. To examine the psychometric properties and screening efficiency of the MASC in a high comorbid inpatient sample. The current study used receiver operating characteristic (ROC) analyses to investigate the predictive value of the MASC total and subscale scores for the Schedule for Affective Disorders and Schizophrenia for School-age children-Present and Lifetime version (K-SADS-PL), DSM-IV diagnoses of generalized anxiety disorder (GAD), separation anxiety disorder (SAD) and social phobia (SoP) in a highly comorbid inpatient sample of adolescents (11-18 years). The MASC total score predicted any anxiety disorder (AD) and GAD moderately well. Physical symptoms predicted GAD moderately well. Social anxiety and separation anxiety/panic did not predict SoP or SAD, respectively. Physical symptoms and harm avoidance also predicted the presence of major depressive disorder. The findings support the utility of the MASC total score to predict the presence of any AD and GAD. However, the utility of the social anxiety and separation anxiety/panic subscales showed limited utility to predict the presence of SAD and SoP, respectively. The MASC has probably a more limited function in screening for AD among a highly comorbid inpatient sample of severely affected adolescents. Our results should be interpreted in the light of a small, mixed sample of inpatient adolescents.

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.

Efficient parameter estimation in longitudinal data analysis using a hybrid GEE method.

PubMed

Leung, Denis H Y; Wang, You-Gan; Zhu, Min

2009-07-01

The method of generalized estimating equations (GEEs) provides consistent estimates of the regression parameters in a marginal regression model for longitudinal data, even when the working correlation model is misspecified (Liang and Zeger, 1986). However, the efficiency of a GEE estimate can be seriously affected by the choice of the working correlation model. This study addresses this problem by proposing a hybrid method that combines multiple GEEs based on different working correlation models, using the empirical likelihood method (Qin and Lawless, 1994). Analyses show that this hybrid method is more efficient than a GEE using a misspecified working correlation model. Furthermore, if one of the working correlation structures correctly models the within-subject correlations, then this hybrid method provides the most efficient parameter estimates. In simulations, the hybrid method's finite-sample performance is superior to a GEE under any of the commonly used working correlation models and is almost fully efficient in all scenarios studied. The hybrid method is illustrated using data from a longitudinal study of the respiratory infection rates in 275 Indonesian children.

CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus.

PubMed

Bhattacharya, Dipankan; Marfo, Chris A; Li, Davis; Lane, Maura; Khokha, Mustafa K

2015-12-15

Congenital malformations are the major cause of infant mortality in the US and Europe. Due to rapid advances in human genomics, we can now efficiently identify sequence variants that may cause disease in these patients. However, establishing disease causality remains a challenge. Additionally, in the case of congenital heart disease, many of the identified candidate genes are either novel to embryonic development or have no known function. Therefore, there is a pressing need to develop inexpensive and efficient technologies to screen these candidate genes for disease phenocopy in model systems and to perform functional studies to uncover their role in development. For this purpose, we sought to test F0 CRISPR based gene editing as a loss of function strategy for disease phenocopy in the frog model organism, Xenopus tropicalis. We demonstrate that the CRISPR/Cas9 system can efficiently modify both alleles in the F0 generation within a few hours post fertilization, recapitulating even early disease phenotypes that are highly similar to knockdowns from morpholino oligos (MOs) in nearly all cases tested. We find that injecting Cas9 protein is dramatically more efficacious and less toxic than cas9 mRNA. We conclude that CRISPR based F0 gene modification in X. tropicalis is efficient and cost effective and readily recapitulates disease and MO phenotypes. Copyright © 2015 Elsevier Inc. All rights reserved.

Using quality improvement methods to optimize resources and maximize productivity in an anesthesia screening and consultation clinic.

PubMed

Varughese, Anna M; Hagerman, Nancy; Townsend, Mari E

2013-07-01

The anesthesia preoperative screening and evaluation of a patient prior to surgery is a critical element in the safe and effective delivery of anesthesia care. In this era of increased focus on cost containment, many anesthesia practices are looking for ways to maximize productivity while maintaining the quality of the preoperative evaluation process by harnessing and optimizing all available resources. We sought to develop a Nurse Practitioner-assisted Preoperative Anesthesia Screening process using quality improvement methods with the goal of maintaining the quality of the screening process, while at the same time redirecting anesthesiologists time for the provision of nonoperating room (OR) anesthesia. The Nurse practitioner (NP) time (approximately 10 h per week) directed to this project was gained as a result of an earlier resource utilization improvement project within the Department of Anesthesia. The goal of this improvement project was to increase the proportion of patient anesthesia screens conducted by NPs to 50% within 6 months. After discussion with key stakeholders of the process, a multidisciplinary improvement team identified a set of operational factors (key drivers) believed to be important to the success of the preoperative anesthesia screening process. These included the development of dedicated NP time for daily screening, NP competency and confidence with the screening process, effective mentoring by anesthesiologists, standardization of screening process, and communication with stakeholders of the process, that is, surgeons. These key drivers focused on the development of several interventions such as (i) NP education in the preoperative anesthesia screening for consultation process by a series of didactic lectures conducted by anesthesiologists, and NP's shadowing an anesthesiologist during the screening process, (ii) Anesthesiologist mentoring and assessment of NP screenings using the dual screening process whereby both anesthesiologists

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,…

Anti-pulmonary fibrotic activity of salvianolic acid B was screened by a novel method based on the cyto-biophysical properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Miao; Zheng, Mingjing; Xu, Hanying

Various methods have been used to evaluate anti-fibrotic activity of drugs. However, most of them are complicated, labor-intensive and lack of efficiency. This study was intended to develop a rapid method for anti-fibrotic drugs screening based on biophysical properties. A549 cells in vitro were stimulated with transforming growth factor-β1 (TGF-β1), and fibrogenesis was confirmed by conventional immunological assays. Meanwhile, the alterations of cyto-biophysical properties including morphology, roughness and stiffness were measured utilizing atomic force microscopy (AFM). It was found that fibrogenesis was accompanied with changes of cellular biophysical properties. TGF-β1-stimulated A549 cells became remarkably longer, rougher and stiffer than the control.more » Then, the effect of N-acetyl-L-cysteine (NAC) as a positive drug on ameliorating fibrogenesis in TGF-β1-stimulated A549 cells was verified respectively by immunological and biophysical markers. The result of Principal Component Analysis showed that stiffness was a leading index among all biophysical markers during fibrogenesis. Salvianolic acid B (SalB), a natural anti-oxidant, was detected by AFM to protect TGF-β1-stimulated A549 cells against stiffening. Then, SalB treatment was provided in preventive mode on a rat model of bleomycin (BLM) -induced pulmonary fibrosis. The results showed that SalB treatment significantly ameliorated BLM-induced histological alterations, blocked collagen accumulations and reduced α-SMA expression in lung tissues. All these results revealed the anti-pulmonary fibrotic activity of SalB. Detection of cyto-biophysical properties were therefore recommended as a rapid method for anti-pulmonary fibrotic drugs screening. - Highlights: • Fibrogenesis was accompanied with the changes of cyto-biophysical properties. • Cyto-biophysical properties could be markers for anti-fibrotic drugs screening. • Stiffness is a leading index among all biophysical markers. • Sal

IspE Inhibitors Identified by a Combination of In Silico and In Vitro High-Throughput Screening

PubMed Central

Tidten-Luksch, Naomi; Grimaldi, Raffaella; Torrie, Leah S.; Frearson, Julie A.; Hunter, William N.; Brenk, Ruth

2012-01-01

CDP-ME kinase (IspE) contributes to the non-mevalonate or deoxy-xylulose phosphate (DOXP) pathway for isoprenoid precursor biosynthesis found in many species of bacteria and apicomplexan parasites. IspE has been shown to be essential by genetic methods and since it is absent from humans it constitutes a promising target for antimicrobial drug development. Using in silico screening directed against the substrate binding site and in vitro high-throughput screening directed against both, the substrate and co-factor binding sites, non-substrate-like IspE inhibitors have been discovered and structure-activity relationships were derived. The best inhibitors in each series have high ligand efficiencies and favourable physico-chemical properties rendering them promising starting points for drug discovery. Putative binding modes of the ligands were suggested which are consistent with established structure-activity relationships. The applied screening methods were complementary in discovering hit compounds, and a comparison of both approaches highlights their strengths and weaknesses. It is noteworthy that compounds identified by virtual screening methods provided the controls for the biochemical screens. PMID:22563402

A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders

PubMed Central

Cui, Naiwen; Zhang, Huidan; Schneider, Nils; Tao, Ye; Asahara, Haruichi; Sun, Zhiyi; Cai, Yamei; Koehler, Stephan A.; de Greef, Tom F. A.; Abbaspourrad, Alireza; Weitz, David A.; Chong, Shaorong

2016-01-01

Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (103–106). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution. PMID:26940078

Screening and identification of aerobic denitrifiers

NASA Astrophysics Data System (ADS)

Shao, K.; Deng, H. M.; Chen, Y. T.; Zhou, H. J.; Yan, G. X.

2016-08-01

With the standards of the effluent quality more stringent, it becomes a quite serious problem for municipalities and industries to remove nitrogen from wastewater. Bioremediation is a potential method for the removal of nitrogen and other pollutants because of its high efficiency and low cost. Seven predominant aerobic denitrifiers were screened and characterized from the activated sludge in the CAST unit. Some of these strains removed 87% nitrate nitrogen at least. Based on their phenotypic and phylogenetic characteristics, the isolates were identified as the genera of Ralstonia, Achromobacter, Aeromonas and Enterobacter.

Screening for increased cardiometabolic risk in primary care: a systematic review

PubMed Central

den Engelsen, Corine; Koekkoek, Paula S; Godefrooij, Merijn B; Spigt, Mark G; Rutten, Guy E

2014-01-01

Background Many programmes to detect and prevent cardiovascular disease (CVD) have been performed, but the optimal strategy is not yet clear. Aim To present a systematic review of cardiometabolic screening programmes performed among apparently healthy people (not yet known to have CVD, diabetes, or cardiometabolic risk factors) and mixed populations (apparently healthy people and people diagnosed with risk factor or disease) to define the optimal screening strategy. Design and setting Systematic review of studies performed in primary care in Western countries. Method MEDLINE, Embase, and CINAHL databases were searched for studies screening for increased cardiometabolic risk. Exclusion criteria were studies designed to assess prevalence of risk factors without follow-up or treatment; without involving a GP; when fewer than two risk factors were considered as the primary outcome; and studies constrained to ethnic minorities. Results The search strategy yielded 11 445 hits; 26 met the inclusion criteria. Five studies (1995–2012) were conducted in apparently healthy populations: three used a stepwise method. Response rates varied from 24% to 79%. Twenty-one studies (1967–2012) were performed in mixed populations; one used a stepwise method. Response rates varied from 50% to 75%. Prevalence rates could not be compared because of heterogeneity of used thresholds and eligible populations. Observed time trends were a shift from mixed to apparently healthy populations, increasing use of risk scores, and increasing use of stepwise screening methods. Conclusion The optimal screening strategy in primary care is likely stepwise, in apparently healthy people, with the use of risk scores. Increasing public awareness and actively involving GPs might facilitate screening efficiency and uptake. PMID:25267047

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...

Feeding methods and efficiencies of selected frugivorous birds

USGS Publications Warehouse

Foster, M.S.

1987-01-01

I report on handling methods and efficiencies of 26 species of Paraguayan birds freeding on fruits of Allophyllus edulis (Sapindaceae). A bird may swallow fruits whole (Type I: pluck and swallow feeders), hold a fruit and cut the pulp from the seed with the edge of the bill, swallowing the pulp but not the seed (Type II: cut or mash feeders), or take bites of pulp from a fruit that hangs from the tree or that is held and manipulated against a branch (Type III: push and bite feeders). In terms of absolute amount of pulp obtained from a fruit, and amount obtained per unit time. Type I species are far more efficient than Type II and III species. Bill morphology influences feeding methods but is not the only important factor. Diet breadth does not appear to be significant. Consideration of feeding efficiency relative to the needs of the birds indicates that these species need to spend relatively little time feeding to meet their estimated energetic needs, and that handling time has a relatively trivial effect on the time/energy budges of the bird species observed.

A review on EEG-based methods for screening and diagnosing alcohol use disorder.

PubMed

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

2018-04-01

The screening test for alcohol use disorder (AUD) patients has been of subjective nature and could be misleading in particular cases such as a misreporting the actual quantity of alcohol intake. Although the neuroimaging modality such as electroencephalography (EEG) has shown promising research results in achieving objectivity during the screening and diagnosis of AUD patients. However, the translation of these findings for clinical applications has been largely understudied and hence less clear. This study advocates the use of EEG as a diagnostic and screening tool for AUD patients that may help the clinicians during clinical decision making. In this context, a comprehensive review on EEG-based methods is provided including related electrophysiological techniques reported in the literature. More specifically, the EEG abnormalities associated with the conditions of AUD patients are summarized. The aim is to explore the potentials of objective techniques involving quantities/features derived from resting EEG, event-related potentials or event-related oscillations data.

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. Copyright © 2015

A fully automated primary screening system for the discovery of therapeutic antibodies directly from B cells.

PubMed

Tickle, Simon; Howells, Louise; O'Dowd, Victoria; Starkie, Dale; Whale, Kevin; Saunders, Mark; Lee, David; Lightwood, Daniel

2015-04-01

For a therapeutic antibody to succeed, it must meet a range of potency, stability, and specificity criteria. Many of these characteristics are conferred by the amino acid sequence of the heavy and light chain variable regions and, for this reason, can be screened for during antibody selection. However, it is important to consider that antibodies satisfying all these criteria may be of low frequency in an immunized animal; for this reason, it is essential to have a mechanism that allows for efficient sampling of the immune repertoire. UCB's core antibody discovery platform combines high-throughput B cell culture screening and the identification and isolation of single, antigen-specific IgG-secreting B cells through a proprietary technique called the "fluorescent foci" method. Using state-of-the-art automation to facilitate primary screening, extremely efficient interrogation of the natural antibody repertoire is made possible; more than 1 billion immune B cells can now be screened to provide a useful starting point from which to identify the rare therapeutic antibody. This article will describe the design, construction, and commissioning of a bespoke automated screening platform and two examples of how it was used to screen for antibodies against two targets. © 2014 Society for Laboratory Automation and Screening.

A simple, fast and cheap non-SPE screening method for antibacterial residue analysis in milk and liver using liquid chromatography-tandem mass spectrometry.

PubMed

Martins, Magda Targa; Melo, Jéssica; Barreto, Fabiano; Hoff, Rodrigo Barcellos; Jank, Louise; Bittencourt, Michele Soares; Arsand, Juliana Bazzan; Schapoval, Elfrides Eva Scherman

2014-11-01

In routine laboratory work, screening methods for multiclass analysis can process a large number of samples in a short time. The main challenge is to develop a methodology to detect as many different classes of residues as possible, combined with speed and low cost. An efficient technique for the analysis of multiclass antibacterial residues (fluoroquinolones, tetracyclines, sulfonamides and trimethoprim) was developed based on simple, environment-friendly extraction for bovine milk, cattle and poultry liver. Acidified ethanol was used as an extracting solvent for milk samples. Liver samples were treated using EDTA-washed sand for cell disruption, methanol:water and acidified acetonitrile as extracting solvent. A total of 24 antibacterial residues were detected and confirmed using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), at levels between 10, 25 and 50% of the maximum residue limit (MRL). For liver samples a metabolite (sulfaquinoxaline-OH) was also monitored. A validation procedure was conducted for screening purposes in accordance with European Union requirements (2002/657/EC). The detection capability (CCβ) false compliant rate was less than 5% at the lowest level for each residue. Specificity and ruggedness were also discussed. Incurred and routine samples were analyzed and the method was successfully applied. The results proved that this method can be an important tool in routine analysis, since it is very fast and reliable. Copyright © 2014. Published by Elsevier B.V.

High-efficiency solar cell and method for fabrication

DOEpatents

Hou, Hong Q.; Reinhardt, Kitt C.

1999-01-01

A high-efficiency 3- or 4-junction solar cell is disclosed with a theoretical AM0 energy conversion efficiency of about 40%. The solar cell includes p-n junctions formed from indium gallium arsenide nitride (InGaAsN), gallium arsenide (GaAs) and indium gallium aluminum phosphide (InGaAlP) separated by n-p tunnel junctions. An optional germanium (Ge) p-n junction can be formed in the substrate upon which the other p-n junctions are grown. The bandgap energies for each p-n junction are tailored to provide substantially equal short-circuit currents for each p-n junction, thereby eliminating current bottlenecks and improving the overall energy conversion efficiency of the solar cell. Additionally, the use of an InGaAsN p-n junction overcomes super-bandgap energy losses that are present in conventional multi-junction solar cells. A method is also disclosed for fabricating the high-efficiency 3- or 4-junction solar cell by metal-organic chemical vapor deposition (MOCVD).

Tuberculosis screening among Bolivian sex workers and their children.

PubMed

Chiang, Silvia S; Paulus, Jessica K; Huang, Chi-Cheng; Newby, P K; Castellón Quiroga, Dora; Boynton-Jarrett, Renée; Antkowiak, Lara

2015-06-01

Bolivian sex workers were more likely than other employed women to report tuberculosis screening only if they reported HIV screening. Of all women with household tuberculosis exposure, <40% reported screening for themselves or their children. Coupling tuberculosis screening with sex workers' mandatory HIV screenings may be a cost-efficient disease-control strategy. Copyright © 2014 Ministry of Health, Saudi Arabia. Published by Elsevier Ltd. All rights reserved.

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

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.

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.

Efficient Parallel Formulations of Hierarchical Methods and Their Applications

NASA Astrophysics Data System (ADS)

Grama, Ananth Y.

1996-01-01

Hierarchical methods such as the Fast Multipole Method (FMM) and Barnes-Hut (BH) are used for rapid evaluation of potential (gravitational, electrostatic) fields in particle systems. They are also used for solving integral equations using boundary element methods. The linear systems arising from these methods are dense and are solved iteratively. Hierarchical methods reduce the complexity of the core matrix-vector product from O(n^2) to O(n log n) and the memory requirement from O(n^2) to O(n). We have developed highly scalable parallel formulations of a hybrid FMM/BH method that are capable of handling arbitrarily irregular distributions. We apply these formulations to astrophysical simulations of Plummer and Gaussian galaxies. We have used our parallel formulations to solve the integral form of the Laplace equation. We show that our parallel hierarchical mat-vecs yield high efficiency and overall performance even on relatively small problems. A problem containing approximately 200K nodes takes under a second to compute on 256 processors and yet yields over 85% efficiency. The efficiency and raw performance is expected to increase for bigger problems. For the 200K node problem, our code delivers about 5 GFLOPS of performance on a 256 processor T3D. This is impressive considering the fact that the problem has floating point divides and roots, and very little locality resulting in poor cache performance. A dense matrix-vector product of the same dimensions would require about 0.5 TeraBytes of memory and about 770 TeraFLOPS of computing speed. Clearly, if the loss in accuracy resulting from the use of hierarchical methods is acceptable, our code yields significant savings in time and memory. We also study the convergence of a GMRES solver built around this mat-vec. We accelerate the convergence of the solver using three preconditioning techniques: diagonal scaling, block-diagonal preconditioning, and inner-outer preconditioning. We study the performance and parallel

Frailty screening methods for predicting outcome of a comprehensive geriatric assessment in elderly patients with cancer: a systematic review.

PubMed

Hamaker, Marije E; Jonker, Judith M; de Rooij, Sophia E; Vos, Alinda G; Smorenburg, Carolien H; van Munster, Barbara C

2012-10-01

Comprehensive geriatric assessment (CGA) is done to detect vulnerability in elderly patients with cancer so that treatment can be adjusted accordingly; however, this process is time-consuming and pre-screening is often used to identify fit patients who are able to receive standard treatment versus those in whom a full CGA should be done. We aimed to assess which of the frailty screening methods available show the best sensitivity and specificity for predicting the presence of impairments on CGA in elderly patients with cancer. We did a systematic search of Medline and Embase, and a hand-search of conference abstracts, for studies on the association between frailty screening outcome and results of CGA in elderly patients with cancer. Our search identified 4440 reports, of which 22 publications from 14 studies, were included in this Review. Seven different frailty screening methods were assessed. The median sensitivity and specificity of each screening method for predicting frailty on CGA were as follows: Vulnerable Elders Survey-13 (VES-13), 68% and 78%; Geriatric 8 (G8), 87% and 61%; Triage Risk Screening Tool (TRST 1+; patient considered frail if one or more impairments present), 92% and 47%, Groningen Frailty Index (GFI) 57% and 86%, Fried frailty criteria 31% and 91%, Barber 59% and 79%, and abbreviated CGA (aCGA) 51% and 97%. However, even in case of the highest sensitivity, the negative predictive value was only roughly 60%. G8 and TRST 1+ had the highest sensitivity for frailty, but both had poor specificity and negative predictive value. These findings suggest that, for now, it might be beneficial for all elderly patients with cancer to receive a complete geriatric assessment, since available frailty screening methods have insufficient discriminative power to select patients for further assessment. Copyright © 2012 Elsevier Ltd. All rights reserved.

Development of a fast and efficient method for hepatitis A virus concentration from green onion.

PubMed

Zheng, Yan; Hu, Yuan

2017-11-01

Hepatitis A virus (HAV) can cause serious liver disease and even death. HAV outbreaks are associated with the consumption of raw or minimally processed produce, making it a major public health concern. Infections have occurred despite the fact that effective HAV vaccine has been available. Development of a rapid and sensitive HAV detection method is necessary for an investigation of an HAV outbreak. Detection of HAV is complicated by the lack of a reliable culture method. In addition, due to the low infectious dose of HAV, these methods must be very sensitive. Current methods rely on efficient sample preparation and concentration steps followed by sensitive molecular detection techniques. Using green onions which was involved in most recent HAV outbreaks as a representative produce, a method of capturing virus particles was developed using carboxyl-derivatized magnetic beads in this study. Carboxyl beads, like antibody-coated beads or cationic beads, detect HAV at a level as low as 100 pfu/25g of green onions. RNA from virus concentrated in this manner can be released by heat-shock (98°C 5min) for molecular detection without sacrificing sensitivity. Bypassing the RNA extraction procedure saves time and removes multiple manipulation steps, which makes large scale HAV screening possible. In addition, the inclusion of beef extract and pectinase rather than NP40 in the elution buffer improved the HAV liberation from the food matrix over current methods by nearly 10 fold. The method proposed in this study provides a promising tool to improve food risk assessment and protect public health. Published by Elsevier B.V.

A screening method to distinguish syndromic from sporadic spinal extradural arachnoid cyst.

PubMed

Ogura, Yoji; Yabuki, Shoji; Fujibayashi, Shunsuke; Okada, Eijiro; Iwanami, Akio; Watanabe, Kota; Nakamura, Masaya; Matsumoto, Morio; Ishii, Ken; Ikegawa, Shiro

2018-05-01

Spinal extradural arachnoid cyst (SEDAC) is a cystic lesion that protrudes into the epidural space from a small dural defect. Early diagnosis of SEDAC is important because its expansion causes neurological damage. Two types of SEDAC, syndromic and sporadic, are present. Syndromic SEDAC is inherited as a part of lymphedema-distichiasis syndrome caused by mutations in the FOXC2 gene; however, it is often mistaken as sporadic because of low penetrance. It is not reasonable to conduct a genetic testing for all SEDAC patients and their family members. The aim of this study is to establish an effective screening method to distinguish syndromic SEDAC from sporadic SEDAC. We performed a retrospective review of medical records and imaging studies of 29 subjects who were diagnosed with SEDAC. Clinical features, family history and magnetic resonance imaging (MRI) were analyzed. Mutations in FOXC2 were examined by Sanger-sequencing of the entire coding region of the genes. SEDAC having a mutation in FOXC2 gene was defined with syndromic SEDAC. Eleven subjects had a heterozygous mutation in FOXC2. They were all familial and hence syndromic SEDAC. Only one proband had known family history of SEDAC at diagnosis. MRI findings and physical examinations, especially eye and leg examinations, were quite useful to screen syndromic SEDAC. Physical examination often showed accompanying lymphedema and distichiasis in syndromic SEDAC. Syndromic SEDAC tended to have multiple cysts out of the thoracolumbar area. We established an effective screening method based on physical examinations and MRI findings. Copyright © 2018 The Japanese Orthopaedic Association. Published by Elsevier B.V. All rights reserved.

Chip-based generation of carbon nanodots via electrochemical oxidation of screen printed carbon electrodes and the applications for efficient cell imaging and electrochemiluminescence enhancement

NASA Astrophysics Data System (ADS)

Xu, Yuanhong; Liu, Jingquan; Zhang, Jizhen; Zong, Xidan; Jia, Xiaofang; Li, Dan; Wang, Erkang

2015-05-01

A portable lab-on-a-chip methodology to generate ionic liquid-functionalized carbon nanodots (CNDs) was developed via electrochemical oxidation of screen printed carbon electrodes. The CNDs can be successfully applied for efficient cell imaging and solid-state electrochemiluminescence sensor fabrication on the paper-based chips.A portable lab-on-a-chip methodology to generate ionic liquid-functionalized carbon nanodots (CNDs) was developed via electrochemical oxidation of screen printed carbon electrodes. The CNDs can be successfully applied for efficient cell imaging and solid-state electrochemiluminescence sensor fabrication on the paper-based chips. Electronic supplementary information (ESI) available: Experimental section; Fig. S1. XPS spectra of the as-prepared CNDs after being dialyzed for 72 hours; Fig. S2. LSCM images showing time-dependent fluorescence signals of HeLa cells treated by the as-prepared CNDs; Tripropylamine analysis using the Nafion/CNDs modified ECL sensor. See DOI: 10.1039/c5nr01765c

Just-in-Time Compound Pooling Increases Primary Screening Capacity without Compromising Screening Quality.

PubMed

Elkin, L L; Harden, D G; Saldanha, S; Ferguson, H; Cheney, D L; Pieniazek, S N; Maloney, D P; Zewinski, J; O'Connell, J; Banks, M

2015-06-01

Compound pooling, or multiplexing more than one compound per well during primary high-throughput screening (HTS), is a controversial approach with a long history of limited success. Many issues with this approach likely arise from long-term storage of library plates containing complex mixtures of compounds at high concentrations. Due to the historical difficulties with using multiplexed library plates, primary HTS often uses a one-compound-one-well approach. However, as compound collections grow, innovative strategies are required to increase the capacity of primary screening campaigns. Toward this goal, we have developed a novel compound pooling method that increases screening capacity without compromising data quality. This method circumvents issues related to the long-term storage of complex compound mixtures by using acoustic dispensing to enable "just-in-time" compound pooling directly in the assay well immediately prior to assay. Using this method, we can pool two compounds per well, effectively doubling the capacity of a primary screen. Here, we present data from pilot studies using just-in-time pooling, as well as data from a large >2-million-compound screen using this approach. These data suggest that, for many targets, this method can be used to vastly increase screening capacity without significant reduction in the ability to detect screening hits. © 2015 Society for Laboratory Automation and Screening.

Comparison of real-time PCR with disk diffusion, agar screen and E-test methods for detection of methicillin-resistant Staphylococcus aureus.

PubMed

Shariati, Laleh; Validi, Majid; Tabatabaiefar, Mohammad Amin; Karimi, Ali; Nafisi, Mohammad Reza

2010-12-01

Methicillin-resistant Staphylococcus aureus (MRSA) is a nosocomial pathogen. Our main objective was to compare oxacillin disk test, oxacillin E-test, and oxacillin agar screen for detection of methicillin resistance in S. aureus, using real-time PCR for mecA as the "gold standard" comparison assay. 196 S. aureus isolates were identified out of 284 Staphylococcus isolates. These isolates were screened for MRSA with several methods: disk diffusion, agar screen (6.0 μg/ml), oxacillin E-test, and real-time PCR for detection of mecA gene. Of the 196 S. aureus isolates tested, 96 isolates (49%) were mecA-positive and 100 isolates (51%) mecA-negative. All methods tested had a statistically significant agreement with real-time PCR. E-test was 100% sensitive and specific for mecA presence. The sensitivity and specificity of oxacillin agar screen method were 98 and 99%, respectively and sensitivity and specificity of oxacillin disk diffusion method were 95 and 93%, respectively. In the present study, oxacillin E-test is proposed as the best phenotypic method. For economic reasons, the oxacillin agar screen method (6.0 μg/ml), which is suitable for the detection of MRSA, is recommended due to its accuracy and low cost.

Methodology for a randomised controlled trial of preschool vision screening. A new approach with the 'ALSPAC' project.

PubMed

Williams, C; Harrad, R A; Harvey, I; Frankel, S; Golding, J

1996-06-01

We present the methodology of a population-based Randomised Controlled Trial, comparing an intensive programme of primary preschool vision screening by orthoptists with the usual non-specialist screening. The aims of the trial are to compare the effectiveness and costs of intensive orthoptic screening with non-specialist measures. The orthoptic screening programme will be evaluated both as a composite package and in terms of the screening value of the individual tests at specific ages. This trial is nested within a large population-based longitudinal study. Additional demographic and developmental data on the children in the trial are therefore available. The results of the trial will be used to help clarify which methods of preschool ophthalmic population screening are best in terms of disease detection and cost efficiency.

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

PubMed

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

2013-09-01

A simple and rapid screening method was developed for the detection of citrinin in fungal cultures using Coconut Cream Agar (CCA) described previously for detecting aflatoxin and ochratoxin A. Fifteen isolates of Penicillium citrinum were inoculated onto CCA and incubated at 25 and 30°C for 10 days. All isolates produced a distinct yellow green fluorescence on CCA when the reverse side of the agar plates were viewed under long wavelength UV light. Detection was optimal at 25°C after four to 5 days of incubation. Isolates positive by the CCA method also tested positive for citrinin production by the TLC agar plug method after growth on CCA, Czapek yeast extract agar and yeast extract sucrose agar. Control cultures were negative by both methods, indicating that the CCA Petri dish method was suitable for screening cultures for citrinin production. © 2013 The Society for Applied Microbiology.

Salicylic and jasmonic acid pathways are necessary for defence against Dickeya solani as revealed by a novel method for Blackleg disease screening of in vitro grown potato.

PubMed

Burra, D D; Mühlenbock, P; Andreasson, E

2015-09-01

Potato is major crop ensuring food security in Europe, and blackleg disease is increasingly causing losses in yield and during storage. Recently, one blackleg pathogen, Dickeya solani has been shown to be spreading in Northern Europe that causes aggressive disease development. Currently, identification of tolerant commercial potato varieties has been unsuccessful; this is confounded by the complicated etiology of the disease and a strong environmental influence on disease development. There is currently a lack of efficient testing systems. Here, we describe a system for quantification of blackleg symptoms on shoots of sterile in vitro potato plants, which saves time and space compared to greenhouse and existing field assays. We found no evidence for differences in infection between the described in vitro-based screening method and existing greenhouse assays. This system facilitates efficient screening of blackleg disease response of potato plants independent of other microorganisms and variable environmental conditions. We therefore used the in vitro screening method to increase understanding of plant mechanisms involved in blackleg disease development by analysing disease response of hormone- related (salicylic and jasmonic acid) transgenic potato plants. We show that both jasmonic (JA) and salicylic (SA) acid pathways regulate tolerance to blackleg disease in potato, a result unlike previous findings in Arabidopsis defence response to necrotrophic bacteria. We confirm this by showing induction of a SA marker, pathogenesis-related protein 1 (StPR1), and a JA marker, lipoxygenase (StLOX), in Dickeya solani infected in vitro potato plants. We also observed that tubers of transgenic potato plants were more susceptible to soft rot compared to wild type, suggesting a role for SA and JA pathways in general tolerance to Dickeya. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

Influence relevance voting: an accurate and interpretable virtual high throughput screening method.

PubMed

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

2009-04-01

Given activity training data from high-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 nonlinearly combining the influences of a chemical's neighbors in the training set. Influences are decomposed, also nonlinearly, 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 data sets, 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.

Improving Electronic Sensor Reliability by Robust Outlier Screening

PubMed Central

Moreno-Lizaranzu, Manuel J.; Cuesta, Federico

2013-01-01

Electronic sensors are widely used in different application areas, and in some of them, such as automotive or medical equipment, they must perform with an extremely low defect rate. Increasing reliability is paramount. Outlier detection algorithms are a key component in screening latent defects and decreasing the number of customer quality incidents (CQIs). This paper focuses on new spatial algorithms (Good Die in a Bad Cluster with Statistical Bins (GDBC SB) and Bad Bin in a Bad Cluster (BBBC)) and an advanced outlier screening method, called Robust Dynamic Part Averaging Testing (RDPAT), as well as two practical improvements, which significantly enhance existing algorithms. Those methods have been used in production in Freescale® Semiconductor probe factories around the world for several years. Moreover, a study was conducted with production data of 289,080 dice with 26 CQIs to determine and compare the efficiency and effectiveness of all these algorithms in identifying CQIs. PMID:24113682

Improving electronic sensor reliability by robust outlier screening.

PubMed

Moreno-Lizaranzu, Manuel J; Cuesta, Federico

2013-10-09

Electronic sensors are widely used in different application areas, and in some of them, such as automotive or medical equipment, they must perform with an extremely low defect rate. Increasing reliability is paramount. Outlier detection algorithms are a key component in screening latent defects and decreasing the number of customer quality incidents (CQIs). This paper focuses on new spatial algorithms (Good Die in a Bad Cluster with Statistical Bins (GDBC SB) and Bad Bin in a Bad Cluster (BBBC)) and an advanced outlier screening method, called Robust Dynamic Part Averaging Testing (RDPAT), as well as two practical improvements, which significantly enhance existing algorithms. Those methods have been used in production in Freescale® Semiconductor probe factories around the world for several years. Moreover, a study was conducted with production data of 289,080 dice with 26 CQIs to determine and compare the efficiency and effectiveness of all these algorithms in identifying CQIs.

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

Flexible methods for segmentation evaluation: results from CT-based luggage screening.

PubMed

Karimi, Seemeen; Jiang, Xiaoqian; Cosman, Pamela; Martz, Harry

2014-01-01

Imaging systems used in aviation security include segmentation algorithms in an automatic threat recognition pipeline. The segmentation algorithms evolve in response to emerging threats and changing performance requirements. Analysis of segmentation algorithms' behavior, including the nature of errors and feature recovery, facilitates their development. However, evaluation methods from the literature provide limited characterization of the segmentation algorithms. To develop segmentation evaluation methods that measure systematic errors such as oversegmentation and undersegmentation, outliers, and overall errors. The methods must measure feature recovery and allow us to prioritize segments. We developed two complementary evaluation methods using statistical techniques and information theory. We also created a semi-automatic method to define ground truth from 3D images. We applied our methods to evaluate five segmentation algorithms developed for CT luggage screening. We validated our methods with synthetic problems and an observer evaluation. Both methods selected the same best segmentation algorithm. Human evaluation confirmed the findings. The measurement of systematic errors and prioritization helped in understanding the behavior of each segmentation algorithm. Our evaluation methods allow us to measure and explain the accuracy of segmentation algorithms.

Effect of screens in wide-angle diffusers

NASA Technical Reports Server (NTRS)

Schubauer, G B; Spangenberg, W G

1949-01-01

An experimental investigation at low airspeeds was made of the filling effect observed when a screen or similar resistance is placed across a diffuser. The filling effect is found to be real in that screens can prevent separation or restore separated flow in diffusers even of extreme divergence and to depend principally on screen location and pressure-drop coefficient of the screen. Results are given for three different diffusers of circular cross section with a variety of screen arrangements. Effects of single screens and multiple screens are shown. The mechanics of the filling effect is explained, and possible efficiencies are discussed. Results of arrangements of multiple screens in wide-angle diffusers are given to show a possible application to damping screens as used in wind tunnels to reduce turbulence. (author)

Efficient method for assessing channel instability near bridges

USGS Publications Warehouse

Robinson, Bret A.; Thompson, R.E.

1993-01-01

Efficient methods for data collection and processing are required to complete channel-instability assessments at 5,600 bridge sites in Indiana at an affordable cost and within a reasonable time frame while maintaining the quality of the assessments. To provide this needed efficiency and quality control, a data-collection form was developed that specifies the data to be collected and the order of data collection. This form represents a modification of previous forms that grouped variables according to type rather than by order of collection. Assessments completed during two field seasons showed that greater efficiency was achieved by using a fill-in-the-blank form that organizes the data to be recorded in a specified order: in the vehicle, from the roadway, in the upstream channel, under the bridge, and in the downstream channel.

Smart Screening System (S3) In Taconite Processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daryoush Allaei; Ryan Wartman; David Tarnowski

2006-03-01

The conventional screening machines used in processing plants have had undesirable high noise and vibration levels. They also have had unsatisfactorily low screening efficiency, high energy consumption, high maintenance cost, low productivity, and poor worker safety. These conventional vibrating machines have been used in almost every processing plant. Most of the current material separation technology uses heavy and inefficient electric motors with an unbalanced rotating mass to generate the shaking. In addition to being excessively noisy, inefficient, and high-maintenance, these vibrating machines are often the bottleneck in the entire process. Furthermore, these motors, along with the vibrating machines and supportingmore » structure, shake other machines and structures in the vicinity. The latter increases maintenance costs while reducing worker health and safety. The conventional vibrating fine screens at taconite processing plants have had the same problems as those listed above. This has resulted in lower screening efficiency, higher energy and maintenance cost, and lower productivity and workers safety concerns. The focus of this work is on the design of a high performance screening machine suitable for taconite processing plants. SmartScreens{trademark} technology uses miniaturized motors, based on smart materials, to generate the shaking. The underlying technologies are Energy Flow Control{trademark} and Vibration Control by Confinement{trademark}. These concepts are used to direct energy flow and confine energy efficiently and effectively to the screen function. The SmartScreens{trademark} technology addresses problems related to noise and vibration, screening efficiency, productivity, and maintenance cost and worker safety. Successful development of SmartScreens{trademark} technology will bring drastic changes to the screening and physical separation industry. The final designs for key components of the SmartScreens{trademark} have been developed. The

Mammogram screening in Chile: Using mixed methods to implement health policy planning at the primary care level

PubMed Central

Puschel, Klaus; Thompson, Beti

2011-01-01

Summary Breast cancer has the highest incidence of all cancers among women in Chile. In 2005, a national health program progressively introduced free mammography screening for women aged 50 and older; however, three years later the rates of compliance with mammographic screening was only 12% in Santiago, the capital city of Chile. This implementation article combines the findings of two previous studies that applied qualitative and quantitative methods to improve mammography screening in an area of Santiago. Socio-cultural and accessibility factors were identified as barriers and facilitators during the qualitative phase of the study and then applied to the design of a quantitative randomized clinical trial. After six months of intervention, 6% of women in the standard care group, 51.8% in the low intensity intervention group, and 70.1% in the high intensity intervention group had undergone a screening mammogram. This review discusses how the utilization of mixed methods research can contribute to the improvement of the implementation of health policies in local communities. PMID:21334897

Development of a small-molecule screening method for inhibitors of cellular response to myostatin and activin A.

PubMed

Cash, Jennifer N; Angerman, Elizabeth B; Kirby, R Jason; Merck, Lisa; Seibel, William L; Wortman, Matthew D; Papoian, Ruben; Nelson, Sandra; Thompson, Thomas B

2013-08-01

Myostatin, a member of the transforming growth factor (TGF)-β family of secreted ligands, is a strong negative regulator of muscle growth. As such, therapeutic inhibitors of myostatin are actively being investigated for their potential in the treatment of muscle-wasting diseases such as muscular dystrophy and sarcopenia. Here, we sought to develop a high-throughput screening (HTS) method for small-molecule inhibitors that target myostatin. We created a HEK293 stable cell line that expresses the (CAGA)12-luciferase reporter construct and robustly responds to signaling of certain classes of TGF-β family ligands. After optimization and miniaturization of the assay to a 384-well format, we successfully screened a library of compounds for inhibition of myostatin and the closely related activin A. Selection of some of the tested compounds was directed by in silico screening against myostatin, which led to an enrichment of target hits as compared with random selection. Altogether, we present an HTS method that will be useful for screening potential inhibitors of not only myostatin but also many other ligands of the TGF-β family.

Development of a novel and highly efficient method of isolating bacteriophages from water.