Chromatin Landscapes of Retroviral and Transposon Integration Profiles

PubMed Central

Badhai, Jitendra; Rust, Alistair G.; Rad, Roland; Hilkens, John; Berns, Anton; van Lohuizen, Maarten; Wessels, Lodewyk F. A.; de Ridder, Jeroen

2014-01-01

The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of to unselected integrations in the mouse genome for the Sleeping Beauty (SB) and piggyBac (PB) transposons, and the Mouse Mammary Tumor Virus (MMTV). We analyzed (epi)genomic features to generate bias maps at both local and genome-wide scales. MMTV showed a remarkably uniform distribution of integrations across the genome. More distinct preferences were observed for the two transposons, with PB showing remarkable resemblance to bias profiles of the Murine Leukemia Virus. Furthermore, we present a model where target site selection is directed at multiple scales. At a large scale, target site selection is similar across systems, and defined by domain-oriented features, namely expression of proximal genes, proximity to CpG islands and to genic features, chromatin compaction and replication timing. Notable differences between the systems are mainly observed at smaller scales, and are directed by a diverse range of features. To study the effect of these biases on integration sites occupied under selective pressure, we turned to insertional mutagenesis (IM) screens. In IM screens, putative cancer genes are identified by finding frequently targeted genomic regions, or Common Integration Sites (CISs). Within three recently completed IM screens, we identified 7%–33% putative false positive CISs, which are likely not the result of the oncogenic selection process. Moreover, results indicate that PB, compared to SB, is more suited to tag oncogenes. PMID:24721906

New Synthesis and Tritium Labeling of a Selective Ligand for Studying High-affinity γ-Hydroxybutyrate (GHB) Binding Sites

PubMed Central

Vogensen, Stine B.; Marek, Aleš; Bay, Tina; Wellendorph, Petrine; Kehler, Jan; Bundgaard, Christoffer; Frølund, Bente; Pedersen, Martin H.F.; Clausen, Rasmus P.

2013-01-01

3-Hydroxycyclopent-1-enecarboxylic acid (HOCPCA, 1) is a potent ligand for the high-affinity GHB binding sites in the CNS. An improved synthesis of 1 together with a very efficient synthesis of [3H]-1 is described. The radiosynthesis employs in situ generated lithium trimethoxyborotritide. Screening of 1 against different CNS targets establishes a high selectivity and we demonstrate in vivo brain penetration. In vitro characterization of [3H]-1 binding shows high specificity to the high-affinity GHB binding sites. PMID:24053696

Evolving artificial metalloenzymes via random mutagenesis

NASA Astrophysics Data System (ADS)

Yang, Hao; Swartz, Alan M.; Park, Hyun June; Srivastava, Poonam; Ellis-Guardiola, Ken; Upp, David M.; Lee, Gihoon; Belsare, Ketaki; Gu, Yifan; Zhang, Chen; Moellering, Raymond E.; Lewis, Jared C.

2018-03-01

Random mutagenesis has the potential to optimize the efficiency and selectivity of protein catalysts without requiring detailed knowledge of protein structure; however, introducing synthetic metal cofactors complicates the expression and screening of enzyme libraries, and activity arising from free cofactor must be eliminated. Here we report an efficient platform to create and screen libraries of artificial metalloenzymes (ArMs) via random mutagenesis, which we use to evolve highly selective dirhodium cyclopropanases. Error-prone PCR and combinatorial codon mutagenesis enabled multiplexed analysis of random mutations, including at sites distal to the putative ArM active site that are difficult to identify using targeted mutagenesis approaches. Variants that exhibited significantly improved selectivity for each of the cyclopropane product enantiomers were identified, and higher activity than previously reported ArM cyclopropanases obtained via targeted mutagenesis was also observed. This improved selectivity carried over to other dirhodium-catalysed transformations, including N-H, S-H and Si-H insertion, demonstrating that ArMs evolved for one reaction can serve as starting points to evolve catalysts for others.

Graphic products used in the evaluation of traditional and emerging remote sensing technologies for the detection of fugitive contamination at selected superfund hazardous waste sites

USGS Publications Warehouse

Slonecker, E. Terrence; Fisher, Gary B.

2011-01-01

This report presents the overhead imagery and field sampling results used to prepare U.S. Geological Survey Open-File Report 2011-1050, 'Evaluation of Traditional and Emerging Remote Sensing Technologies for the Detection of Fugitive Contamination at Selected Superfund Hazardous Waste Sites'. These graphic products were used in the evaluation of remote sensing technology in postclosure monitoring of hazardous waste sites and represent an ongoing research effort. Soil sampling results presented here were accomplished with field portable x-ray fluoresence (XRF) technology and are used as screening tools only representing the current conditions of metals and other contaminants at selected Superfund hazardous waste sites.

Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge

NASA Astrophysics Data System (ADS)

Kumar, Ashutosh; Zhang, Kam Y. J.

2012-05-01

SAMPL3 fragment based virtual screening challenge provides a valuable opportunity for researchers to test their programs, methods and screening protocols in a blind testing environment. We participated in SAMPL3 challenge and evaluated our virtual fragment screening protocol, which involves RosettaLigand as the core component by screening a 500 fragments Maybridge library against bovine pancreatic trypsin. Our study reaffirmed that the real test for any virtual screening approach would be in a blind testing environment. The analyses presented in this paper also showed that virtual screening performance can be improved, if a set of known active compounds is available and parameters and methods that yield better enrichment are selected. Our study also highlighted that to achieve accurate orientation and conformation of ligands within a binding site, selecting an appropriate method to calculate partial charges is important. Another finding is that using multiple receptor ensembles in docking does not always yield better enrichment than individual receptors. On the basis of our results and retrospective analyses from SAMPL3 fragment screening challenge we anticipate that chances of success in a fragment screening process could be increased significantly with careful selection of receptor structures, protein flexibility, sufficient conformational sampling within binding pocket and accurate assignment of ligand and protein partial charges.

A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore

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

Miller, J. Richard; Dunham, Steve; Mochalkin, Igor

2009-06-25

As the need for novel antibiotic classes to combat bacterial drug resistance increases, the paucity of leads resulting from target-based antibacterial screening of pharmaceutical compound libraries is of major concern. One explanation for this lack of success is that antibacterial screening efforts have not leveraged the eukaryotic bias resulting from more extensive chemistry efforts targeting eukaryotic gene families such as G protein-coupled receptors and protein kinases. Consistent with a focus on antibacterial target space resembling these eukaryotic targets, we used whole-cell screening to identify a series of antibacterial pyridopyrimidines derived from a protein kinase inhibitor pharmacophore. In bacteria, the pyridopyrimidinesmore » target the ATP-binding site of biotin carboxylase (BC), which catalyzes the first enzymatic step of fatty acid biosynthesis. These inhibitors are effective in vitro and in vivo against fastidious Gram-negative pathogens including Haemophilus influenzae. Although the BC active site has architectural similarity to those of eukaryotic protein kinases, inhibitor binding to the BC ATP-binding site is distinct from the protein kinase-binding mode, such that the inhibitors are selective for bacterial BC. In summary, we have discovered a promising class of potent antibacterials with a previously undescribed mechanism of action. In consideration of the eukaryotic bias of pharmaceutical libraries, our findings also suggest that pursuit of a novel inhibitor leads for antibacterial targets with active-site structural similarity to known human targets will likely be more fruitful than the traditional focus on unique bacterial target space, particularly when structure-based and computational methodologies are applied to ensure bacterial selectivity.« less

Assignment of sockeye salmon (Oncorhynchus nerka) to spawning sites using DNA markers.

PubMed

Corley-Smith, Graham E; Wennerberg, Liv; Schembri, Joy A; Lim, Chinten J; Cooper, Karen L; Brandhorst, Bruce P

2005-01-01

Randomly amplified polymorphic DNA (RAPD) markers were used to assign individual adult sockeye salmon to their spawning sites using a genotype assignment test. Six primers were selected for use by screening bulked DNA samples for markers missing in fish from one or more of 5 sites in British Columbia or Alaska. Of 73 markers scored, 54 showed variation between or within sites among the sampled fish. Thirty-seven of the variable markers were not detected in any fish from one or more sites; 18 variable markers were detected in all fish from one or more other sites. Thus 25% of markers scored were found in all fish of some sites and in no fish of some other sites. An assignment test placed all 70 fish tested into their correct populations. Principal coordinate analysis of genetic variation produced clusters of fish corresponding to each sampling site. No sex-specific RAPD markers were detected among more than 1300 screened.

Environmental concern-based site screening of carbon dioxide geological storage in China.

PubMed

Cai, Bofeng; Li, Qi; Liu, Guizhen; Liu, Lancui; Jin, Taotao; Shi, Hui

2017-08-08

Environmental impacts and risks related to carbon dioxide (CO 2 ) capture and storage (CCS) projects may have direct effects on the decision-making process during CCS site selection. This paper proposes a novel method of environmental optimization for CCS site selection using China's ecological red line approach. Moreover, this paper established a GIS based spatial analysis model of environmental optimization during CCS site selection by a large database. The comprehensive data coverage of environmental elements and fine 1 km spatial resolution were used in the database. The quartile method was used for value assignment for specific indicators including the prohibited index and restricted index. The screening results show that areas classified as having high environmental suitability (classes III and IV) in China account for 620,800 km 2 and 156,600 km 2 , respectively, and are mainly distributed in Inner Mongolia, Qinghai and Xinjiang. The environmental suitability class IV areas of Bayingol Mongolian Autonomous Prefecture, Hotan Prefecture, Aksu Prefecture, Hulunbuir, Xilingol League and other prefecture-level regions not only cover large land areas, but also form a continuous area in the three provincial-level administrative units. This study may benefit the national macro-strategic deployment and implementation of CCS spatial layout and environmental management in China.

Multidimensional Programming Methods for Energy Facility Siting: Alternative Approaches

NASA Technical Reports Server (NTRS)

Solomon, B. D.; Haynes, K. E.

1982-01-01

The use of multidimensional optimization methods in solving power plant siting problems, which are characterized by several conflicting, noncommensurable objectives is addressed. After a discussion of data requirements and exclusionary site screening methods for bounding the decision space, classes of multiobjective and goal programming models are discussed in the context of finite site selection. Advantages and limitations of these approaches are highlighted and the linkage of multidimensional methods with the subjective, behavioral components of the power plant siting process is emphasized.

An analysis of the costs of implementing the National Newborn Hearing Screening Programme in England.

PubMed

Uus, K; Bamford, J; Taylor, R

2006-01-01

The primary aim of this analysis was to prospectively assess the full economic costs associated with implementing Newborn Hearing Screening Programme (NHSP) based on a two-stage screen, transient evoked otoacoustic emissions followed, if there is no clear response, by automated auditory brainstem response. Economic data were also collected from the Infant Distraction Test Screening (IDTS) service performed by health visitors at around eight months of age, which was being phased out. A comparison of costs and outcomes associated with NHSP and IDTS was conducted. 20 NHSP sites were invited to provide detailed cost data on NHSP implementation and 14 of these sites were selected to provide costs on the IDTS service that was being supplanted. There was marked variability in the costs. Given the higher yield of NHSP sites, the average cost per case detected across NHSP sites (31,410 pounds/case) was approximately half that of IDTS sites (69,919 pounds/case). Including family costs, the average total cost per case of NHSP (34,826 pounds/case) was almost a quarter of IDTS (117,942 pounds/case). Family costs and cost per case associated with NHSP are considerably less than that with IDTS. These findings support the policy of implementation of NHSP and the phasing out of the IDTS.

Synergism of virtual screening and medicinal chemistry: identification and optimization of allosteric antagonists of metabotropic glutamate receptor 1.

PubMed

Noeske, Tobias; Trifanova, Dina; Kauss, Valerjans; Renner, Steffen; Parsons, Christopher G; Schneider, Gisbert; Weil, Tanja

2009-08-01

We report the identification of novel potent and selective metabotropic glutamate receptor 1 (mGluR1) antagonists by virtual screening and subsequent hit optimization. For ligand-based virtual screening, molecules were represented by a topological pharmacophore descriptor (CATS-2D) and clustered by a self-organizing map (SOM). The most promising compounds were tested in mGluR1 functional and binding assays. We identified a potent chemotype exhibiting selective antagonistic activity at mGluR1 (functional IC(50)=0.74+/-0.29 microM). Hit optimization yielded lead structure 16 with an affinity of K(i)=0.024+/-0.001 microM and greater than 1000-fold selectivity for mGluR1 versus mGluR5. Homology-based receptor modelling suggests a binding site compatible with previously reported mutation studies. Our study demonstrates the usefulness of ligand-based virtual screening for scaffold-hopping and rapid lead structure identification in early drug discovery projects.

Selecting Patients for Intra-arterial Therapy in the Context of a Clinical Trial for Neuroprotection

PubMed Central

Lyden, Patrick; Weymer, Sara; Coffey, Chris; Cudkowicz, Merit; Berg, Samantha; O’Brien, Sarah; Fisher, Marc; Haley, E. Clarke; Khatri, Pooja; Saver, Jeff; Levine, Steven; Levy, Howard; Rymer, Marilyn; Wechsler, Lawrence; Jadhav, Ashutosh; McNeil, Elizabeth; Waddy, Salina; Pryor, Kent

2016-01-01

Background and Purpose The advent of intra-arterial neurothrombectomy (IAT) for acute ischemic stroke opens a potentially transformative opportunity to improve neuroprotection studies. Combining a putative neuroprotectant with recanalization could produce more powerful trials but could introduce heterogeneity and adverse event possibilities. We sought to demonstrate feasibility of IAT in neuroprotectant trials by defining IAT selection criteria for an ongoing neuroprotectant clinical trial. Methods The study drug, 3K3A-APC, is a pleiotropic cytoprotectant and may reduce thrombolysis associated hemorrhage. The NeuroNEXT trial NN104 (RHAPSODY) is designed to establish a maximally tolerated dose of 3K3A-APC. Each trial site provided their IAT selection criteria. An expert panel reviewed site criteria and published evidence. Finally, the trial leadership designed IAT selection criteria. Results Derived selection criteria reflected consistency among the sites and comparability to published IAT trials. A protocol amendment allowing IAT (and relaxed age, NIHSS, and time limits) in the RHAPSODY trial was implemented on June 15, 2015. Recruitment before and after the amendment improved from 8 enrolled patients (601 screened, 1.3%) to 51 patients (821 screened, 6.2%), OR [95%CL] of 4.9 [2.3,10.4], p<0.001). Gross recruitment was 0.11 patients/site/month vs. 0.43 patients/site/month, respectively, before and after the amendment. Conclusions It is feasible to include IAT in a neuroprotectant trial for acute ischemic stroke. Criteria are presented for including such patients in a manner that is consistent with published evidence for IAT while still preserving the ability to test the role of the putative neuroprotectant. Clinical Trial Registration Clinical Trial Registration-URL: http://www.clinicaltrials.gov. Unique identifier: NCT02222714. PMID:27803392

Selecting Patients for Intra-Arterial Therapy in the Context of a Clinical Trial for Neuroprotection.

PubMed

Lyden, Patrick; Weymer, Sara; Coffey, Chris; Cudkowicz, Merit; Berg, Samantha; O'Brien, Sarah; Fisher, Marc; Haley, E Clarke; Khatri, Pooja; Saver, Jeff; Levine, Steven; Levy, Howard; Rymer, Marilyn; Wechsler, Lawrence; Jadhav, Ashutosh; McNeil, Elizabeth; Waddy, Salina; Pryor, Kent

2016-12-01

The advent of intra-arterial neurothrombectomy (IAT) for acute ischemic stroke opens a potentially transformative opportunity to improve neuroprotection studies. Combining a putative neuroprotectant with recanalization could produce more powerful trials but could introduce heterogeneity and adverse event possibilities. We sought to demonstrate feasibility of IAT in neuroprotectant trials by defining IAT selection criteria for an ongoing neuroprotectant clinical trial. The study drug, 3K3A-APC, is a pleiotropic cytoprotectant and may reduce thrombolysis-associated hemorrhage. The NeuroNEXT trial NN104 (RHAPSODY) is designed to establish a maximally tolerated dose of 3K3A-APC. Each trial site provided their IAT selection criteria. An expert panel reviewed site criteria and published evidence. Finally, the trial leadership designed IAT selection criteria. Derived selection criteria reflected consistency among the sites and comparability to published IAT trials. A protocol amendment allowing IAT (and relaxed age, National Institutes of Health Stroke Scale, and time limits) in the RHAPSODY trial was implemented on June 15, 2015. Recruitment before and after the amendment improved from 8 enrolled patients (601 screened, 1.3%) to 51 patients (821 screened, 6.2%; odds ratio [95% confidence limit] of 4.9 [2.3-10.4]; P<0.001). Gross recruitment was 0.11 patients per site month versus 0.43 patients per site per month, respectively, before and after the amendment. It is feasible to include IAT in a neuroprotectant trial for acute ischemic stroke. Criteria are presented for including such patients in a manner that is consistent with published evidence for IAT while still preserving the ability to test the role of the putative neuroprotectant. URL: http://www.clinicaltrials.gov. Unique identifier: NCT02222714. © 2016 American Heart Association, Inc.

Selection-dependent and Independent Generation of CRISPR/Cas9-mediated Gene Knockouts in Mammalian Cells.

PubMed

Sternburg, Erin L; Dias, Kristen C; Karginov, Fedor V

2017-06-16

The CRISPR/Cas9 genome engineering system has revolutionized biology by allowing for precise genome editing with little effort. Guided by a single guide RNA (sgRNA) that confers specificity, the Cas9 protein cleaves both DNA strands at the targeted locus. The DNA break can trigger either non-homologous end joining (NHEJ) or homology directed repair (HDR). NHEJ can introduce small deletions or insertions which lead to frame-shift mutations, while HDR allows for larger and more precise perturbations. Here, we present protocols for generating knockout cell lines by coupling established CRISPR/Cas9 methods with two options for downstream selection/screening. The NHEJ approach uses a single sgRNA cut site and selection-independent screening, where protein production is assessed by dot immunoblot in a high-throughput manner. The HDR approach uses two sgRNA cut sites that span the gene of interest. Together with a provided HDR template, this method can achieve deletion of tens of kb, aided by the inserted selectable resistance marker. The appropriate applications and advantages of each method are discussed.

A new technique for the rapid screening and selection of large pieces of tissue for ultrastructural evaluation.

PubMed

Dalley, B K; Seliger, W G

1980-05-01

A simple and rapid technique is described for the screening of Epon embedded organ slices for the location, isolation, and removal of small specific sites for ultrastructural study with the transmission electron microscope. This procedure consists of perfusion fixation followed by making 1 to 21/2 mm thick slices of relatively large pieces of the organs, control of the degree and evenness of the osmium staining by addition of 3% sodium iodate, and infiltration with a fluorescent dye prior to embedment in Epon. Tissue slices are embedded in wafer-shaped blocks, generally with several slices in one "wafer", and are examined in a controlled manner using a rapid form of serial surface polishing. Each level of the polished wafer is examined using an epi-illuminated fluorescence microscope, and selected sites are chosen at each level for ultrastructural study. Methods are also described for marking each selected site using a conventional slide marker, and for the removal of the selected site in the form of a small disc of Epon, after which the Epon wafer can be further serially polished and the examination continued. Areas to be thin-sectioned are removed using a core drill mounted on a model-maker's drill press. The technique is simple, does not require the destruction of remaining tissues to evaluate more critically a single small site, allows for the easy maintenance of tissue orientation, and the most time-consuming portions of the technique can be quickly taught to a person with no previous histological training.

Effective virtual screening protocol for CYP2C9 ligands using a screening site constructed from flurbiprofen and S-warfarin pockets

NASA Astrophysics Data System (ADS)

Polgár, Tímea; Menyhárd, Dóra K.; Keserű, György M.

2007-09-01

An effective virtual screening protocol was developed against an extended active site of CYP2C9, which was derived from X-ray structures complexed with flubiprofen and S-warfarin. Virtual screening has been effectively supported by our structure-based pharmacophore model. Importance of hot residues identified by mutation data and structural analysis was first estimated in an enrichment study. Key role of Arg108 and Phe114 in ligand binding was also underlined. Our screening protocol successfully identified 76% of known CYP2C9 ligands in the top 1% of the ranked database resulting 76-fold enrichment relative to random situation. Relevance of the protocol was further confirmed in selectivity studies, when 89% of CYP2C9 ligands were retrieved from a mixture of CYP2C9 and CYP2C8 ligands, while only 22% of CYP2C8 ligands were found applying the structure-based pharmacophore constraints. Moderate discrimination of CYP2C9 ligands from CYP2C18 and CYP2C19 ligands could also be achieved extending the application domain of our virtual screening protocol for the entire CYP2C family. Our findings further demonstrate the existence of an active site comprising of at least two binding pockets and strengthens the need of involvement of protein flexibility in virtual screening.

Enrichment assessment of multiple virtual screening strategies for Toll-like receptor 8 agonists based on a maximal unbiased benchmarking data set.

PubMed

Pei, Fen; Jin, Hongwei; Zhou, Xin; Xia, Jie; Sun, Lidan; Liu, Zhenming; Zhang, Liangren

2015-11-01

Toll-like receptor 8 agonists, which activate adaptive immune responses by inducing robust production of T-helper 1-polarizing cytokines, are promising candidates for vaccine adjuvants. As the binding site of toll-like receptor 8 is large and highly flexible, virtual screening by individual method has inevitable limitations; thus, a comprehensive comparison of different methods may provide insights into seeking effective strategy for the discovery of novel toll-like receptor 8 agonists. In this study, the performance of knowledge-based pharmacophore, shape-based 3D screening, and combined strategies was assessed against a maximum unbiased benchmarking data set containing 13 actives and 1302 decoys specialized for toll-like receptor 8 agonists. Prior structure-activity relationship knowledge was involved in knowledge-based pharmacophore generation, and a set of antagonists was innovatively used to verify the selectivity of the selected knowledge-based pharmacophore. The benchmarking data set was generated from our recently developed 'mubd-decoymaker' protocol. The enrichment assessment demonstrated a considerable performance through our selected three-layer virtual screening strategy: knowledge-based pharmacophore (Phar1) screening, shape-based 3D similarity search (Q4_combo), and then a Gold docking screening. This virtual screening strategy could be further employed to perform large-scale database screening and to discover novel toll-like receptor 8 agonists. © 2015 John Wiley & Sons A/S.

Residency application screening tools: A survey of academic medical centers.

PubMed

Hillebrand, Kristen; Leinum, Corey J; Desai, Sonya; Pettit, Natasha N; Fuller, Patrick D

2015-06-01

The current use and content of screening tools utilized by ASHP-accredited pharmacy residency programs were assessed. A survey consisting of 19 questions assessing residency programs and the screening of pharmacy residency program applicants was e-mailed to residency directors of 362 pharmacy residency programs at 105 University HealthSystem Consortium (UHC)-member institutions. Questions gathered general program demographic information, data related to applicant growth from residency years 2010-11 to 2011-12, and information about the residency screening processes currently used. Responses were received from 73 residency program sites (69.5%) of the 105 UHC-member institutions to whom the e-mail was sent. Many sites used screening tools to calculate applicants' scores and then determined which candidates to invite for an onsite interview based on applicants' scores and group discussion. Seventy-eight percent (n = 57) of the 73 responding institutions reported the use of a screening tool or rubric to select applicants to invite for onsite interviews. The most common method of evaluation was individual applicant review before meeting as a group to discuss candidate selection. The most important factor for determining which residency candidate to interview was the overall impression based on the candidate's curriculum vitae (CV) and letters of recommendation. Most residency programs in UHC-member hospitals used a screening tool to determine which applicants to invite for an onsite interview. The most important factor for determining which residency candidate to interview was the overall impression based on the candidate's CV and letters of recommendation. Copyright © 2015 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

Identification of potential glutaminyl cyclase inhibitors from lead-like libraries by in silico and in vitro fragment-based screening.

PubMed

Szaszkó, Mária; Hajdú, István; Flachner, Beáta; Dobi, Krisztina; Magyar, Csaba; Simon, István; Lőrincz, Zsolt; Kapui, Zoltán; Pázmány, Tamás; Cseh, Sándor; Dormán, György

2017-02-01

A glutaminyl cyclase (QC) fragment library was in silico selected by disconnection of the structure of known QC inhibitors and by lead-like 2D virtual screening of the same set. The resulting fragment library (204 compounds) was acquired from commercial suppliers and pre-screened by differential scanning fluorimetry followed by functional in vitro assays. In this way, 10 fragment hits were identified ([Formula: see text]5 % hit rate, best inhibitory activity: 16 [Formula: see text]). The in vitro hits were then docked to the active site of QC, and the best scoring compounds were analyzed for binding interactions. Two fragments bound to different regions in a complementary manner, and thus, linking those fragments offered a rational strategy to generate novel QC inhibitors. Based on the structure of the virtual linked fragment, a 77-membered QC target focused library was selected from vendor databases and docked to the active site of QC. A PubChem search confirmed that the best scoring analogues are novel, potential QC inhibitors.

Analytical methods for characterization of explosives-contaminated sites on U.S. Army installations

NASA Astrophysics Data System (ADS)

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

1995-10-01

The U.S. Army manufactures munitions at facilities throughout the United States. Many of these facilities are contaminated with residues of explosives from production, disposal of off- specification, and out-of-data munitions. The first step in remediating these sites is careful characterization. Currently sites are being characterized using a combination of on-site field screening and off-site laboratory analysis. Most of the contamination is associated with TNT (2,4,6-trinitrotoluene) and RDX (hexahydro-1,3,5-tri-nitro-1,3,5-triazine) and their manufacturing impurities and environmental transformation products. Both colorimetric and enzyme immunoassay-based field screening methods have been used successfully for on-site characterization. These methods have similar detection capabilities but differ in their selectivity. Although field screening is very cost-effective, laboratory analysis is still required to fully characterize a site. Laboratory analysis for explosives residues in the United States is generally conducted using high-performance liquid chromatography equipped with a UV detector. Air-dried soils are extracted with acetonitrile in an ultrasonic bath. Water is analyzed directly if detection limits in the range of 10 - 20 (mu) g/L are acceptable, or preconcentrated using either salting-out solvent extraction with acetonitrile or solid phase extraction.

Improving site selection in clinical studies: a standardised, objective, multistep method and first experience results.

PubMed

Hurtado-Chong, Anahí; Joeris, Alexander; Hess, Denise; Blauth, Michael

2017-07-12

A considerable number of clinical studies experience delays, which result in increased duration and costs. In multicentre studies, patient recruitment is among the leading causes of delays. Poor site selection can result in low recruitment and bad data quality. Site selection is therefore crucial for study quality and completion, but currently no specific guidelines are available. Selection of sites adequate to participate in a prospective multicentre cohort study was performed through an open call using a newly developed objective multistep approach. The method is based on use of a network, definition of objective criteria and a systematic screening process. Out of 266 interested sites, 24 were shortlisted and finally 12 sites were selected to participate in the study. The steps in the process included an open call through a network, use of selection questionnaires tailored to the study, evaluation of responses using objective criteria and scripted telephone interviews. At each step, the number of candidate sites was quickly reduced leaving only the most promising candidates. Recruitment and quality of data went according to expectations in spite of the contracting problems faced with some sites. The results of our first experience with a standardised and objective method of site selection are encouraging. The site selection method described here can serve as a guideline for other researchers performing multicentre studies. ClinicalTrials.gov: NCT02297581. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Prospective CO 2 saline resource estimation methodology: Refinement of existing US-DOE-NETL methods based on data availability

DOE PAGES

Goodman, Angela; Sanguinito, Sean; Levine, Jonathan S.

2016-09-28

Carbon storage resource estimation in subsurface saline formations plays an important role in establishing the scale of carbon capture and storage activities for governmental policy and commercial project decision-making. Prospective CO 2 resource estimation of large regions or subregions, such as a basin, occurs at the initial screening stages of a project using only limited publicly available geophysical data, i.e. prior to project-specific site selection data generation. As the scale of investigation is narrowed and selected areas and formations are identified, prospective CO 2 resource estimation can be refined and uncertainty narrowed when site-specific geophysical data are available. Here, wemore » refine the United States Department of Energy – National Energy Technology Laboratory (US-DOE-NETL) methodology as the scale of investigation is narrowed from very large regional assessments down to selected areas and formations that may be developed for commercial storage. In addition, we present a new notation that explicitly identifies differences between data availability and data sources used for geologic parameters and efficiency factors as the scale of investigation is narrowed. This CO 2 resource estimation method is available for screening formations in a tool called CO 2-SCREEN.« less

Prospective CO 2 saline resource estimation methodology: Refinement of existing US-DOE-NETL methods based on data availability

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

Goodman, Angela; Sanguinito, Sean; Levine, Jonathan S.

Carbon storage resource estimation in subsurface saline formations plays an important role in establishing the scale of carbon capture and storage activities for governmental policy and commercial project decision-making. Prospective CO 2 resource estimation of large regions or subregions, such as a basin, occurs at the initial screening stages of a project using only limited publicly available geophysical data, i.e. prior to project-specific site selection data generation. As the scale of investigation is narrowed and selected areas and formations are identified, prospective CO 2 resource estimation can be refined and uncertainty narrowed when site-specific geophysical data are available. Here, wemore » refine the United States Department of Energy – National Energy Technology Laboratory (US-DOE-NETL) methodology as the scale of investigation is narrowed from very large regional assessments down to selected areas and formations that may be developed for commercial storage. In addition, we present a new notation that explicitly identifies differences between data availability and data sources used for geologic parameters and efficiency factors as the scale of investigation is narrowed. This CO 2 resource estimation method is available for screening formations in a tool called CO 2-SCREEN.« less

Pursuing Excellence: The Power of Selection Science to Provide Meaningful Data and Enhance Efficiency in Selecting Surgical Trainees.

PubMed

Gardner, Aimee K; Dunkin, Brian J

2018-05-01

As current screening methods for selecting surgical trainees are receiving increasing scrutiny, development of a more efficient and effective selection system is needed. We describe the process of creating an evidence-based selection system and examine its impact on screening efficiency, faculty perceptions, and improving representation of underrepresented minorities. The program partnered with an expert in organizational science to identify fellowship position requirements and associated competencies. Situational judgment tests, personality profiles, structured interviews, and technical skills assessments were used to measure these competencies. The situational judgment test and personality profiles were administered online and used to identify candidates to invite for on-site structured interviews and skills testing. A final rank list was created based on all data points and their respective importance. All faculty completed follow-up surveys regarding their perceptions of the process. Candidate demographic and experience data were pulled from the application website. Fifty-five of 72 applicants met eligibility requirements and were invited to take the online assessment, with 50 (91%) completing it. Average time to complete was 42 ± 12 minutes. Eighteen applicants (35%) were invited for on-site structured interviews and skills testing-a greater than 50% reduction in number of invites compared to prior years. Time estimates reveal that the process will result in a time savings of 68% for future iterations, compared to traditional methodologies. Fellowship faculty (N = 5) agreed on the value and efficiency of the process. Underrepresented minority candidates increased from an initial 70% to 92% being invited for an interview and ranked using the new screening tools. Applying selection science to the process of choosing surgical trainees is feasible, efficient, and well-received by faculty for making selection decisions.

Evaluation of Cervicography Screening for Cervical Cancer in a High Risk Population

DTIC Science & Technology

2000-02-16

Higher sensitivity was associated with younger age , premenopausal status, the presence of metaplasia. the absence of cervicovaginal atrophy, and improved...recommended for postmenopausal women and/or women ages 50 and older. iv EVALUATION OF CERVICOGRAPHY SCREENING FOR CERVICAL CANCER IN A HIGH-RISK POPULATION...Institute. The Guanacaste site was selected because of its consistently high age -adjusted rates of cervical cancer despite existing Papanicolaou

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.

Eucalyptus Energy Farm: feasibility study and demonstration. Phase 1: site and species selection

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

Mariani, E.O.; Wood, W.A.; Kouchoukos, P.C.

1978-06-01

The results of investigations to determine the feasibility for establishing ''Eucalyptus Energy Farms'' as a potential source of biomass derived energy are presented. Included in this report are: the results of an extensive literature search and numerous field interviews (both domestically and internationally) to identify those Eucalyptus species most suitable for use within the United States; a description of the site selection criteria, site selection process, and identification of potential sites for use in testing the Eucalyptus Energy Farm concept; a description of the Eucalyptus species selection criteria, species selection process, and an identification of the specific species recommended formore » testing at specific sites; preliminary engineering designs for each of the proposed plantation sites; and environmental impact considerations related to Eucalyptus growing. It is concluded that although the Eucalyptus are extremely temperature sensitive and the geographic areas which appear suitable for their planting (within the United States) are principally confined to western and central California and the warmest regions of the southeastern United States, each of the areas contain large amounts of marginal land which could be converted into Eucalyptus based biomass plantations. Suitable sites, which are representative of the larger marginal land areas, are immediately available for use in establishing Eucalyptus screening test sites. Furthermore, there are not significant environmental conditions which would preclude the establishment of these initial test sites. It is therefore recommended that efforts be initiated to obtain selected provenances of Eucalyptus seeds (of the designated species) for further field testing and data collection within the United States, and that actual site selection be initiated.« less

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.

A Phenotypic Screen for Functional Mutants of Human Adenosine Deaminase Acting on RNA 1.

PubMed

Wang, Yuru; Havel, Jocelyn; Beal, Peter A

2015-11-20

Adenosine deaminases acting on RNA (ADARs) are RNA-editing enzymes responsible for the conversion of adenosine to inosine at specific locations in cellular RNAs. ADAR1 and ADAR2 are two members of the family that have been shown to be catalytically active. Earlier, we reported a phenotypic screen for the study of human ADAR2 using budding yeast S. cerevisiae as the host system. While this screen has been successfully applied to the study of ADAR2, it failed with ADAR1. Here, we report a new reporter that uses a novel editing substrate and is suitable for the study of ADAR1. We screened plasmid libraries with randomized codons for two important residues in human ADAR1 (G1007 and E1008). The screening results combined with in vitro deamination assays led to the identification of mutants that are more active than the wild type protein. Furthermore, a screen of the ADAR1 E1008X library with a reporter construct bearing an A•G mismatch at the editing site suggests one role for the residue at position 1008 is to sense the identity of the base pairing partner for the editing site adenosine. This work has provided a starting point for future in vitro evolution studies of ADAR1 and led to new insight into ADAR's editing site selectivity.

Community-based screening for obstetric fistula in Nigeria: a novel approach

PubMed Central

2014-01-01

Background Obstetric fistula continues to have devastating effects on the physical, social, and economic lives of thousands of women in many low-resource settings. Governments require credible estimates of the backlog of existing cases requiring care to effectively plan for the treatment of fistula cases. Our study aims to quantify the backlog of obstetric fistula cases within two states via community-based screenings and to assess the questions in the Demographic Health Survey (DHS) fistula module. Methods The screening sites, all lower level health facilities, were selected based on their geographic coverage, prior relationships with the communities and availability of fistula surgery facilities in the state. This cross-sectional study included women who presented for fistula screenings at study facilities based on their perceived fistula-like symptoms. Research assistants administered the pre-screening questionnaire. Nurse-midwives then conducted a medical exam. Univariate and bivariate analyses are presented. Results A total of 268 women attended the screenings. Based on the pre-screening interview, the backlog of fistula cases reported was 75 (28% of women screened). The backlog identified after the medical exam was 26 fistula cases (29.5% of women screened) in Kebbi State sites and 12 cases in Cross River State sites (6.7%). Verification assessment showed that the DHS questionnaire had 92% sensitivity, 83% specificity with 47% positive predictive value and 98% negative predictive value for identifying women afflicted by fistula among women who came for the screenings. Conclusions This methodology, involving effective, locally appropriate messaging and community outreach followed up with medical examination by nurse-midwives at lower level facilities, is challenging, but represents a promising approach to identify the backlog of women needing surgery and to link them with surgical facilities. PMID:24456506

Structure-Guided Screening for Functionally Selective D2 Dopamine Receptor Ligands from a Virtual Chemical Library.

PubMed

Männel, Barbara; Jaiteh, Mariama; Zeifman, Alexey; Randakova, Alena; Möller, Dorothee; Hübner, Harald; Gmeiner, Peter; Carlsson, Jens

2017-10-20

Functionally selective ligands stabilize conformations of G protein-coupled receptors (GPCRs) that induce a preference for signaling via a subset of the intracellular pathways activated by the endogenous agonists. The possibility to fine-tune the functional activity of a receptor provides opportunities to develop drugs that selectively signal via pathways associated with a therapeutic effect and avoid those causing side effects. Animal studies have indicated that ligands displaying functional selectivity at the D 2 dopamine receptor (D 2 R) could be safer and more efficacious drugs against neuropsychiatric diseases. In this work, computational design of functionally selective D 2 R ligands was explored using structure-based virtual screening. Molecular docking of known functionally selective ligands to a D 2 R homology model indicated that such compounds were anchored by interactions with the orthosteric site and extended into a common secondary pocket. A tailored virtual library with close to 13 000 compounds bearing 2,3-dichlorophenylpiperazine, a privileged orthosteric scaffold, connected to diverse chemical moieties via a linker was docked to the D 2 R model. Eighteen top-ranked compounds that occupied both the orthosteric and allosteric site were synthesized, leading to the discovery of 16 partial agonists. A majority of the ligands had comparable maximum effects in the G protein and β-arrestin recruitment assays, but a subset displayed preference for a single pathway. In particular, compound 4 stimulated β-arrestin recruitment (EC 50 = 320 nM, E max = 16%) but had no detectable G protein signaling. The use of structure-based screening and virtual libraries to discover GPCR ligands with tailored functional properties will be discussed.

Screening of extremotolerant fungi for the bioremediation of hydrocarbon contaminated sites

NASA Astrophysics Data System (ADS)

Poyntner, Caroline; Blasi, Barbara; Prenafeta, Francesc; Sterflinger, Katja

2015-04-01

Bioremediation can be used to treat contaminated sites, by taking advantage of microorganisms which have the potential to degrade a wide range of contaminants. While research has been focused mainly on bacteria, the knowledge on other microorganisms, especially fungal communities, is still limited. However, the use of fungi may have advantages compared to bacteria. Extremophile fungi like the black yeasts can withstand high levels of environmental stress (e.g. range of pH, water availability and temperature, presence of toxic chemicals). Therefore they might be applicable in situations, where bacterial communities show limited performance. In order to identify fungi which are good candidates for bioremediation application, a selection of 163 fungal strains, mostly from the group of the black yeasts, was tested for their capability to degrade three different pollutants: hexadecane, toluene, and polychlorinated biphenyl 126, which were used as model compounds for aliphatic hydrocarbons, aromatic hydrocarbons and polychlorinated biphenyls. These chemicals are frequently found in sites contaminated by oil, gas and coal. The screening was based on a two-step selection approach. As a first step, a high throughput method was developed to screen the relatively large amount of fungal strains regarding their tolerance to the contaminants. A microtiter plate based method was developed for monitoring fungal growth in the presence of the selected contaminants photometrically with a Tecan reader. Twenty five strains out of 163, being species of the genera Cladophilaophora, Scedosporium and Exophiala, showed the ability to grow on at least 2 hydrocarbons, and are therefore the most promising candidates for further tests. In a second step, degradation of the contaminants was investigated in more detail for a subset of the screened fungi. This was done by closing the carbon balance in sealed liquid cultures in which the selected pollutant was introduce as the sole source of carbon and energy. Substrate depletion and CO2 accumulation in the headspace were monitored chromatographically. In the course of these experiments, two strains showed a good capacity to grow on toluene. In summary, the presented screening method can be used to identify potential candidates for the fungal degradation of contaminants. Further research is necessary to investigate the potential use of the identified fungal strains for remediation purposes.

Philippine Wind Farm Analysis and Site Selection Analysis, 1 January 2000 - 31 December 2000

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

Conover, K.

2001-12-01

The U.S. Department of Energy (DOE), through the National Renewable Energy Laboratory (NREL), has been working in partnership with the U.S. Agency for International Development (USAID) in an ongoing process to quantify the Philippine wind energy potential and foster wind farm development. As part of that process, NREL retained Global Energy Concepts, LLC (GEC) to review and update the policy needs as well as develop a site-screening process applicable for the Philippines. GEC worked closely with the Philippines National Power Corporation (NPC) in completing this work. This report provides the results of the policy needs and site selection analyses conductedmore » by GEC.« less

Selective staining of proteins with hydrophobic surface sites on a native electrophoretic gel.

PubMed

Bertsch, Martina; Kassner, Richard J

2003-01-01

Chemical proteomics aims to characterize all of the proteins in the proteome with respect to their function, which is associated with their interaction with other molecules. We propose the identification of a subproteomic library of expressed proteins whose native structures are typified by the presence of hydrophobic surface sites, which are often involved in interactions with small molecules, membrane lipids, and other proteins, pertaining to their functions. We demonstrate that soluble globular proteins with hydrophobic surface sites can be detected selectively by staining on an electrophoretic gel run under nondenaturing conditions. The application of these staining techniques may help elucidate new catalytic, transport, and regulatory functionalities in complex proteomic screenings.

Combinatorially Screened Peptide as Targeted Covalent Binder: Alteration of Bait-Conjugated Peptide to Reactive Modifier.

PubMed

Uematsu, Shuta; Tabuchi, Yudai; Ito, Yuji; Taki, Masumi

2018-06-01

A peptide-type covalent binder for a target protein was obtained by combinatorial screening of fluoroprobe-conjugated peptide libraries on bacteriophage T7. The solvatochromic fluoroprobe works as a bait during the affinity selection process of phage display. To obtain the targeted covalent binder, the bait in the selected consensus peptide was altered into a reactive warhead possessing a sulfonyl fluoride. The reaction efficiency and site/position specificity of the covalent conjugation between the binder and the target protein were evaluated by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and rationalized by a protein-ligand docking simulation.

Human recombinant beta-secretase immobilized enzyme reactor for fast hits' selection and characterization from a virtual screening library.

PubMed

De Simone, Angela; Mancini, Francesca; Cosconati, Sandro; Marinelli, Luciana; La Pietra, Valeria; Novellino, Ettore; Andrisano, Vincenza

2013-01-25

In the present work, a human recombinant BACE1 immobilized enzyme reactor (hrBACE1-IMER) has been applied for the sensitive fast screening of 38 compounds selected through a virtual screening approach. HrBACE1-IMER was inserted into a liquid chromatograph coupled with a fluorescent detector. A fluorogenic peptide substrate (M-2420), containing the β-secretase site of the Swedish mutation of APP, was injected and cleaved in the on-line HPLC-hrBACE1-IMER system, giving rise to the fluorescent product. The compounds of the library were tested for their ability to inhibit BACE1 in the immobilized format and to reduce the area related to the chromatographic peak of the fluorescent enzymatic product. The results were validated in solution by using two different FRET methods. Due to the efficient virtual screening methodology, more than fifty percent of the selected compounds showed a measurable inhibitory activity. One of the most active compound (a bis-indanone derivative) was characterized in terms of IC(50) and K(i) determination on the hrBACE1-IMER. Thus, the hrBACE1-IMER has been confirmed as a valid tool for the throughput screening of different chemical entities with potency lower than 30μM for the fast hits' selection and for mode of action determination. Copyright © 2012 Elsevier B.V. All rights reserved.

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

Venteris, Erik R.; McBride, Robert; Coleman, Andre M.

Locating sites for new algae cultivation facilities is a complex task. The climate must support high growth rates, and cultivation ponds require appropriate land and water resources as well as key utility and transportation infrastructure. We employ our spatiotemporal Biomass Assessment Tool (BAT) to select promising locations based on the open-pond cultivation of Arthrospira sp. and a strain of the order Desmidiales. 64,000 potential sites across the southern United States were evaluated. We progressively apply a range of screening criteria and track their impact on the number of selected sites, geographic location, and biomass productivity. Both strains demonstrate maximum productivitymore » along the Gulf of Mexico coast, with the highest values on the Florida peninsula. In contrast, sites meeting all selection criteria for Arthrospira were located along the southern coast of Texas and for Desmidiales were located in Louisiana and southern Arkansas. Site selection was driven mainly by the lack of oil pipeline access in Florida and elevated groundwater salinity in southern Texas. The requirement for low salinity freshwater (<400 mg L-1) constrained Desmidiales locations; siting flexibility is greater for salt-tolerant species such as Arthrospira. Combined siting factors can result in significant departures from regions of maximum productivity but are within the expected range of site-specific process improvements.« less

Identifying and collecting pertinent medical records for centralized abstraction in a multi-center randomized clinical trial: the model used by the American College of Radiology arm of the National Lung Screening Trial.

PubMed

Gareen, Ilana F; Sicks, JoRean D; Jain, Amanda Adams; Moline, Denise; Coffman-Kadish, Nancy

2013-01-01

In clinical trials and epidemiologic studies, information on medical care utilization and health outcomes is often obtained from medical records. For multi-center studies, this information may be gathered by personnel at individual sites or by staff at a central coordinating center. We describe the process used to develop a HIPAA-compliant centralized process to collect medical record information for a large multi-center cancer screening trial. The framework used to select, request, and track medical records incorporated a participant questionnaire with unique identifiers for each medical provider. De-identified information from the questionnaires was sent to the coordinating center indexed by these identifiers. The central coordinating center selected specific medical providers for abstraction and notified sites using these identifiers. The site personnel then linked the identifiers with medical provider information. Staff at the sites collected medical records and provided them for central abstraction. Medical records were successfully obtained and abstracted to ascertain information on outcomes and health care utilization in a study with over 18,000 study participants. Collection of records required for outcomes related to positive screening examinations and lung cancer diagnosis exceeded 90%. Collection of records for all aims was 87.32%. We designed a successful centralized medical record abstraction process that may be generalized to other research settings, including observational studies. The coordinating center received no identifying data. The process satisfied requirements imposed by the Health Insurance Portability and Accountability Act and concerns of site institutional review boards with respect to protected health information. Copyright © 2012 Elsevier Inc. All rights reserved.

Identifying and collecting pertinent medical records for centralized abstraction in a multi-center randomized clinical trial: The model used by the American College of Radiology arm of the National Lung Screening Trial

PubMed Central

Gareen, Ilana F.; Sicks, JoRean; Adams, Amanda; Moline, Denise; Coffman-Kadish, Nancy

2012-01-01

Background In clinical trials and epidemiologic studies, information on medical care utilization and health outcomes is often obtained from medical records. For multi-center studies, this information may be gathered by personnel at individual sites or by staff at a central coordinating center. We describe the process used to develop a HIPAA-compliant centralized process to collect medical record information for a large multi-center cancer screening trial. Methods The framework used to select, request, and track medical records incorporated a participant questionnaire with unique identifiers for each medical provider. De-identified information from the questionnaires was sent to the coordinating center indexed by these identifiers. The central coordinating center selected specific medical providers for abstraction and notified sites using these identifiers. The site personnel then linked the identifiers with medical provider information. Staff at the sites collected medical records and provided them for central abstraction. Results Medical records were successfully obtained and abstracted to ascertain information on outcomes and health care utilization in a study with over 18,000 study participants. Collection of records required for outcomes related to positive screening examinations and lung cancer diagnosis exceeded 90%. Collection of records for all aims was 87.32%. Conclusions We designed a successful centralized medical record abstraction process that may be generalized to other research settings, including observational studies. The coordinating center received no identifying data. The process satisfied requirements imposed by the Health Insurance Portability and Accountability Act and concerns of site institutional review boards with respect to protected health information. PMID:22982342

Optimization of protease-inhibitor interactions by randomizing adventitious contacts

PubMed Central

Komiyama, Tomoko; VanderLugt, Bryan; Fugère, Martin; Day, Robert; Kaufman, Randal J.; Fuller, Robert S.

2003-01-01

Polypeptide protease inhibitors are often found to inhibit targets with which they did not coevolve, as in the case of high-affinity inhibition of bacterial subtilisin by the leech inhibitor eglin c. Two kinds of contacts exist in such complexes: (i) reactive site loop-active site contacts and (ii) interactions outside of these that form the broader enzyme-inhibitor interface. We hypothesized that the second class of “adventitious” contacts could be optimized to generate significant increases in affinity for a target enzyme or discrimination of an inhibitor for closely related target proteases. We began with a modified eglin c, Arg-42–Arg-45–eglin, in which the reactive site loop had been optimized for subtilisin-related processing proteases of the Kex2/furin family. We randomized 10 potential adventitious contact residues and screened for inhibition of soluble human furin. Substitutions at one of these sites, Y49, were also screened against yeast Kex2 and human PC7. These screens identified not only variants that exhibited increased affinity (up to 20-fold), but also species that exhibited enhanced selectivity, that is, increased discrimination between the target enzymes (up to 41-fold for furin versus PC7 and 20-fold for PC7 versus furin). One variant, Asp-49–Arg-42–Arg-45–eglin, exhibited a Ki of 310 pM for furin and blocked furin-dependent processing of von Willebrand factor in COS-1 cells when added to the culture medium of the cells. The exploitation of adventitious contact sites may provide a versatile technique for developing potent, selective inhibitors for newly discovered proteases and could in principle be applied to optimize numerous protein–protein interactions. PMID:12832612

Corrective Action Decision Document for Corrective Action Unit 340: Pesticide Release sites, Nevada Test Site, Nevada

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

DOE /NV

This Corrective Action Decision Document has been prepared for Corrective Action Unit 340, the NTS Pesticide Release Sites, in accordance with the Federal Facility Agreement and Consent Order of 1996 (FFACO, 1996). Corrective Action Unit 340 is located at the Nevada Test Site, Nevada, and is comprised of the following Corrective Action Sites: 23-21-01, Area 23 Quonset Hut 800 Pesticide Release Ditch; 23-18-03, Area 23 Skid Huts Pesticide Storage; and 15-18-02, Area 15 Quonset Hut 15-11 Pesticide Storage. The purpose of this Corrective Action Decision Document is to identify and provide a rationale for the selection of a recommended correctivemore » action alternative for each Corrective Action Site. The scope of this Corrective Action Decision Document consists of the following tasks: Develop corrective action objectives; Identify corrective action alternative screening criteria; Develop corrective action alternatives; Perform detailed and comparative evaluations of the corrective action alternatives in relation to the corrective action objectives and screening criteria; and Recommend and justify a preferred corrective action alternative for each Corrective Action Site.« less

Site characterization report for the basalt waste isolation project. Volume II

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

None

1982-11-01

The reference location for a repository in basalt for the terminal storage of nuclear wastes on the Hanford Site and the candidate horizons within this reference repository location have been identified and the preliminary characterization work in support of the site screening process has been completed. Fifteen technical questions regarding the qualification of the site were identified to be addressed during the detailed site characterization phase of the US Department of Energy-National Waste Terminal Storage Program site selection process. Resolution of these questions will be provided in the final site characterization progress report, currently planned to be issued in 1987,more » and in the safety analysis report to be submitted with the License Application. The additional information needed to resolve these questions and the plans for obtaining the information have been identified. This Site Characterization Report documents the results of the site screening process, the preliminary site characterization data, the technical issues that need to be addressed, and the plans for resolving these issues. Volume 2 contains chapters 6 through 12: geochemistry; surface hydrology; climatology, meteorology, and air quality; environmental, land-use, and socioeconomic characteristics; repository design; waste package; and performance assessment.« less

Fragment-Linking Approach Using (19)F NMR Spectroscopy To Obtain Highly Potent and Selective Inhibitors of β-Secretase.

PubMed

Jordan, John B; Whittington, Douglas A; Bartberger, Michael D; Sickmier, E Allen; Chen, Kui; Cheng, Yuan; Judd, Ted

2016-04-28

Fragment-based drug discovery (FBDD) has become a widely used tool in small-molecule drug discovery efforts. One of the most commonly used biophysical methods in detecting weak binding of fragments is nuclear magnetic resonance (NMR) spectroscopy. In particular, FBDD performed with (19)F NMR-based methods has been shown to provide several advantages over (1)H NMR using traditional magnetization-transfer and/or two-dimensional methods. Here, we demonstrate the utility and power of (19)F-based fragment screening by detailing the identification of a second-site fragment through (19)F NMR screening that binds to a specific pocket of the aspartic acid protease, β-secretase (BACE-1). The identification of this second-site fragment allowed the undertaking of a fragment-linking approach, which ultimately yielded a molecule exhibiting a more than 360-fold increase in potency while maintaining reasonable ligand efficiency and gaining much improved selectivity over cathepsin-D (CatD). X-ray crystallographic studies of the molecules demonstrated that the linked fragments exhibited binding modes consistent with those predicted from the targeted screening approach, through-space NMR data, and molecular modeling.

Quantification of map similarity to magnetic pre-screening for heavy metal pollution assessment in top soil

NASA Astrophysics Data System (ADS)

Cao, L.; Appel, E.; Roesler, W.; Ojha, G.

2013-12-01

From numerous published results, the link between magnetic concentration and heavy metal (HM) concentrations is well established. However, bivariate correlation analysis does not imply causality, and if there are extreme values, which often appear in magnetic data, they can lead to seemingly excellent correlation. It seems clear that site selection for chemical sampling based on magnetic pre-screening can deliver a superior result for outlining HM pollution, but this conclusion has only been drawn from qualitative evaluation so far. In this study, we use map similarity comparison techniques to demonstrate the usefulness of a combined magnetic-chemical approach quantitatively. We chose available data around the 'Schwarze Pumpe', a large coal burning power plant complex located in eastern Germany. The site of 'Schwarze Pumpe' is suitable for a demonstration study as soil in its surrounding is heavy fly-ash polluted, the magnetic natural background is very low, and magnetic investigations can be done in undisturbed forest soil. Magnetic susceptibility (MS) of top soil was measured by a Bartington MS2D surface sensor at 180 locations and by a SM400 downhole device in ~0.5m deep vertical sections at 90 locations. Cores from the 90 downhole sites were also studied for HM analysis. From these results 85 sites could be used to determine a spatial distribution map of HM contents reflecting the 'True' situation of pollution. Different sets comprising 30 sites were chosen by arbitrarily selection from the above 85 sample sites (we refer to four such maps here: S1-4). Additionally, we determined a 'Targeted' map from 30 sites selected on the basis of the pre-screening MS results. The map comparison process is as follows: (1) categorization of all absolute values into five classes by the Natural Breaks classification method; (2) use Delaunay triangulation for connecting the sample locations in the x-y plane; (3) determination of a distribution map of triangular planes with classified values as the Z coordinate; (4) calculation of normal vectors for each individual triangular plane; (5)transformation to the TINs into raster data assigning the same normal vectors to all grid-points which are inside the same TIN; (6) calculation of the root-mean-square of angles between normal vectors of two maps at the same grid points. Additionally, we applied the kappa statistics method to assess map similarities, and moreover developed a Fuzzy set approach. Combining both methods using indices of Khisto, Klocation, Kappa, Kfuzzy obtains a broad comparison system, which allows determining the degree of similarity and also the spatial distribution of similarity between two maps. The results indicate that the similarity between the 'Targeted' and 'True' distribution map is higher than that between 'S1-4' and the 'True' map. It manifests that magnetic pre-screening can provide a reliable basis for targeted selection of chemical sampling sites demonstrating the superior efficiency of a combined magnetic-chemical site assessment in comparison to a traditional chemical-only approach.

Health, Safety, and Environmental Screening and Ranking Frameworkfor Geologic CO2 Storage Site Selection

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

Oldenburg, Curtis M.

2006-03-15

This report describes a screening and ranking framework(SRF) developed to evaluate potential geologic carbon dioxide (CO2)storage sites on the basis of health, safety, and environmental (HSE)risk arising from possible CO2 leakage. The approach is based on theassumption that HSE risk due to CO2 leakage is dependent on three basiccharacteristics of a geologic CO2 storage site: (1) the potential forprimary containment by the target formation, (2) the potential forsecondary containment if the primary formation leaks, and (3) thepotential for attenuation and dispersion of leaking CO2 if the primaryformation leaks and secondary containment fails. The framework isimplemented in a spreadsheet in whichmore » users enter numerical scoresrepresenting expert opinions or general information available frompublished materials along with estimates of uncertainty to evaluate thethree basic characteristics in order to screen and rank candidate sites.Application of the framework to the Rio Vista Gas Field, Ventura OilField, and Mammoth Mountain demonstrates the approach. Refinements andextensions are possible through the use of more detailed data or modelresults in place of property proxies. Revisions and extensions to improvethe approach are anticipated in the near future as it is used and testedby colleagues and collaborators.« less

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. Published by Elsevier B.V.

Evaluation of Suitability of Selected Set of Department of Defense Military Bases and Department of Energy Facilities for Siting a Small Modular Reactor

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

Poore III, Willis P; Belles, Randy; Mays, Gary T

This report summarizes the approach that ORNL developed for screening a sample set of US Department of Defense (DOD) military base sites and DOE sites for possible powering with an SMR; the methodology employed, including spatial modeling; and initial results for several sample sites. The objective in conducting this type of siting evaluation is demonstrate the capability to characterize specific DOD and DOE sites to identify any particular issues associated with powering the sites with an SMR using OR-SAGE; it is not intended to be a definitive assessment per se as to the absolute suitability of any particular site.

Straightforward hit identification approach in fragment-based discovery of bromodomain-containing protein 4 (BRD4) inhibitors.

PubMed

Borysko, Petro; Moroz, Yurii S; Vasylchenko, Oleksandr V; Hurmach, Vasyl V; Starodubtseva, Anastasia; Stefanishena, Natalia; Nesteruk, Kateryna; Zozulya, Sergey; Kondratov, Ivan S; Grygorenko, Oleksandr O

2018-05-09

A combination approach of a fragment screening and "SAR by catalog" was used for the discovery of bromodomain-containing protein 4 (BRD4) inhibitors. Initial screening of 3695-fragment library against bromodomain 1 of BRD4 using thermal shift assay (TSA), followed by initial hit validation, resulted in 73 fragment hits, which were used to construct a follow-up library selected from available screening collection. Additionally, analogs of inactive fragments, as well as a set of randomly selected compounds were also prepared (3 × 3200 compounds in total). Screening of the resulting sets using TSA, followed by re-testing at several concentrations, counter-screen, and TR-FRET assay resulted in 18 confirmed hits. Compounds derived from the initial fragment set showed better hit rate as compared to the other two sets. Finally, building dose-response curves revealed three compounds with IC 50  = 1.9-7.4 μM. For these compounds, binding sites and conformations in the BRD4 (4UYD) have been determined by docking. Copyright © 2018 Elsevier Ltd. All rights reserved.

Ultrasonographic nerve enlargement of the median and ulnar nerves and the cervical nerve roots in patients with demyelinating Charcot-Marie-Tooth disease: distinction from patients with chronic inflammatory demyelinating polyneuropathy.

PubMed

Sugimoto, Takamichi; Ochi, Kazuhide; Hosomi, Naohisa; Takahashi, Tetsuya; Ueno, Hiroki; Nakamura, Takeshi; Nagano, Yoshito; Maruyama, Hirofumi; Kohriyama, Tatsuo; Matsumoto, Masayasu

2013-10-01

Demyelinating Charcot-Marie-Tooth disease (CMT) and chronic inflammatory demyelinating polyneuropathy (CIDP) are both demyelinating polyneuropathies. The differences in nerve enlargement degree and pattern at multiple evaluation sites/levels are not well known. We investigated the differences in nerve enlargement degree and the distribution pattern of nerve enlargement in patients with demyelinating CMT and CIDP, and verified the appropriate combination of sites/levels to differentiate between these diseases. Ten patients (aged 23-84 years, three females) with demyelinating CMT and 16 patients (aged 30-85 years, five females) with CIDP were evaluated in this study. The nerve sizes were measured at 24 predetermined sites/levels from the median and ulnar nerves and the cervical nerve roots (CNR) using ultrasonography. The evaluation sites/levels were classified into three regions: distal, intermediate and cervical. The number of sites/levels that exhibited nerve enlargement (enlargement site number, ESN) in each region was determined from the 24 sites/levels and from the selected eight screening sites/levels, respectively. The cross-sectional areas of the peripheral nerves were markedly larger at all evaluation sites in patients with demyelinating CMT than in patients with CIDP (p < 0.01). However, the nerve sizes of CNR were not significantly different between patients with either disease. When we evaluated ESN of four selected sites for screening from the intermediate region, the sensitivity and specificity to distinguish between demyelinating CMT and CIDP were 0.90 and 0.94, respectively, with the cut-off value set at four. Nerve ultrasonography is useful to detect nerve enlargement and can clarify morphological differences in nerves between patients with demyelinating CMT and CIDP.

A randomized controlled Alzheimer's disease prevention trial's evolution into an exposure trial: the PREADViSE Trial.

PubMed

Kryscio, R J; Abner, E L; Schmitt, F A; Goodman, P J; Mendiondo, M; Caban-Holt, A; Dennis, B C; Mathews, M; Klein, E A; Crowley, J J

2013-01-01

To summarize the ongoing prevention of Alzheimer's disease (AD) by vitamin E and selenium (PREADViSE) trial as an ancillary study to SELECT (a large prostate cancer prevention trial) and to present the blinded results of the first year as an exposure study. PREADViSE was designed as a double blind randomized controlled trial (RCT). SELECT terminated after median of 5.5 years of exposure to supplements due to a futility analysis. Both trials then converted into an exposure study. In the randomized component PREADViSE enrolled 7,547 men age 62 or older (60 if African American). Once the trial terminated 4,246 of these men volunteered for the exposure study. Demographics were similar for both groups with exposure volunteers having baseline mean age 67.3 ± 5.2 years, 15.3 ± 2.4 years of education, 9.8% African Americans, and 22.0% reporting a family history of dementia. In the RCT men were randomly assigned to either daily doses of 400 IU of vitamin E or placebo and 200 µg of selenium or placebo using a 2x2 factorial structure. In the RCT, participants completed the memory impairment screen (MIS), and if they failed, underwent a longer screening (based on an expanded Consortium to Establish a Registry in AD [CERAD] battery). CERAD failure resulted in visits to their clinician for medical examination with records of these examinations forwarded to the PREADViSE center for further review. In the exposure study, men are contacted by telephone and complete the telephone version of the memory impairment screen (MIS-T) screen. If they fail the MIS-T, a modified telephone interview of cognitive status (TICS-M) exam is given. A failed TICS-M exam also leads to a visit to their clinician for an in-depth examination and forwarding of records for a centralized consensus diagnosis by expert clinicians. A subgroup of the men who pass the MIS-T also take the TICS-M exam for validation purposes. While this ancillary trial was open to all 427 SELECT clinical sites, only 130 (30.0%) of the sites chose to participate in PREADViSE. Staff turnover at the sites presented challenges when training persons unfamiliar with cognitive testing procedures to conduct the memory screens. In the RCT few participants (1.6%) failed the MIS screen and among those who passed this screen a significant practice effect was encountered. In the exposure study 3,581 men were reached by phone in year 1, 15.7% could not be reached after 5 calls, and of those contacted 6.0% refused the screen even after consenting to the procedures at their clinical site. Most notable is that the failure rate for the MIS-T increased fourfold to 7.2%. Of the 257 men who took the TICS-M, 84.0% failed and were asked to contact their physicians for a more detailed memory assessment, and approximately half of these had some form of dementia or cognitive impairment. Several of these dementia cases are not AD. Partnering with SELECT led to an AD prevention trial conducted at a very reasonable cost by taking advantage of the experience and efficient clinical trial management found in a cancer cooperative group (Southwest Oncology Group or SWOG). Once unblinded, the RCT and exposure study data have the potential to yield new information on long term exposure to antioxidant supplements under controlled conditions.

A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase.

PubMed

Nagatoishi, Satoru; Yamaguchi, Sou; Katoh, Etsuko; Kajita, Keita; Yokotagawa, Takane; Kanai, Satoru; Furuya, Toshio; Tsumoto, Kouhei

2018-05-01

19 F NMR has recently emerged as an efficient, sensitive tool for analyzing protein binding to small molecules, and surface plasmon resonance (SPR) is also a popular tool for this purpose. Herein a combination of 19 F NMR and SPR was used to find novel binders to the ATP-binding pocket of MAP kinase extracellular regulated kinase 2 (ERK2) by fragment screening with an original fluorinated-fragment library. The 19 F NMR screening yielded a high primary hit rate of binders to the ERK2 ATP-binding pocket compared with the rate for the SPR screening. Hit compounds were evaluated and categorized according to their ability to bind to different binding sites in the ATP-binding pocket. The binding manner was characterized by using isothermal titration calorimetry and docking simulation. Combining 19 F NMR with other biophysical methods allows the identification of multiple types of hit compounds, thereby increasing opportunities for drug design using preferred fragments. Copyright © 2018 Elsevier Ltd. All rights reserved.

A multi-model approach to nucleic acid-based drug development.

PubMed

Gautherot, Isabelle; Sodoyer, Regís

2004-01-01

With the advent of functional genomics and the shift of interest towards sequence-based therapeutics, the past decades have witnessed intense research efforts on nucleic acid-mediated gene regulation technologies. Today, RNA interference is emerging as a groundbreaking discovery, holding promise for development of genetic modulators of unprecedented potency. Twenty-five years after the discovery of antisense RNA and ribozymes, gene control therapeutics are still facing developmental difficulties, with only one US FDA-approved antisense drug currently available in the clinic. Limited predictability of target site selection models is recognized as one major stumbling block that is shared by all of the so-called complementary technologies, slowing the progress towards a commercial product. Currently employed in vitro systems for target site selection include RNAse H-based mapping, antisense oligonucleotide microarrays, and functional screening approaches using libraries of catalysts with randomized target-binding arms to identify optimal ribozyme/DNAzyme cleavage sites. Individually, each strategy has its drawbacks from a drug development perspective. Utilization of message-modulating sequences as therapeutic agents requires that their action on a given target transcript meets criteria of potency and selectivity in the natural physiological environment. In addition to sequence-dependent characteristics, other factors will influence annealing reactions and duplex stability, as well as nucleic acid-mediated catalysis. Parallel consideration of physiological selection systems thus appears essential for screening for nucleic acid compounds proposed for therapeutic applications. Cellular message-targeting studies face issues relating to efficient nucleic acid delivery and appropriate analysis of response. For reliability and simplicity, prokaryotic systems can provide a rapid and cost-effective means of studying message targeting under pseudo-cellular conditions, but such approaches also have limitations. To streamline nucleic acid drug discovery, we propose a multi-model strategy integrating high-throughput-adapted bacterial screening, followed by reporter-based and/or natural cellular models and potentially also in vitro assays for characterization of the most promising candidate sequences, before final in vivo testing.

EFFECTS OF THE VARIATION OF SELECT SAMPLING PARAMETERS ON SOIL VAPOR CONCENTRATIONS

EPA Science Inventory

Currently soil vapor surveys are commonly used as a screening technique to delineate subsurface volatile organic compound (VOC) contaminant plumes and to provide information for vapor intrusion and contaminated site evaluations. To improve our understanding of the fate and transp...

Optimal design of stormwater basins with bio-sorption activated media (BAM) in karst environments - phase I : site screening and selection.

DOT National Transportation Integrated Search

2015-12-01

Anthropogenic activities within the Silver Springs springshed over recent decades may have contributed : to elevated nutrient concentrations in stormwater runoff and groundwater, leading to the eutrophication : of Silver Springs. To remove the nutrie...

Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.

PubMed

Huschmann, Franziska U; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S; Mueller, Uwe

2016-05-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.

Structures of endothiapepsin–fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library

PubMed Central

Huschmann, Franziska U.; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S.; Mueller, Uwe

2016-01-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein–ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin–fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity. PMID:27139825

Combinatorial evolution of site- and enantioselective catalysts for polyene epoxidation

NASA Astrophysics Data System (ADS)

Lichtor, Phillip A.; Miller, Scott J.

2012-12-01

Selectivity in the catalytic functionalization of complex molecules is a major challenge in chemical synthesis. The problem is magnified when there are several possible stereochemical outcomes and when similar functional groups occur repeatedly within the same molecule. Selective polyene oxidation provides an archetypical example of this challenge. Historically, enzymatic catalysis has provided the only precedents. Although non-enzymatic catalysts that meet some of these challenges became known, a comprehensive solution has remained elusive. Here, we describe low molecular weight peptide-based catalysts, discovered through a combinatorial synthesis and screening protocol, that exhibit site- and enantioselective oxidation of certain positions of various isoprenols. This diversity-based approach, which exhibits features reminiscent of the directed evolution of enzymes, delivers catalysts that compare favourably to the state-of-the-art for the asymmetric oxidation of these compounds. Moreover, the approach culminated in catalysts that exhibit alternative-site selectivity in comparison to oxidation catalysts previously described.

Identification of DNA primase inhibitors via a combined fragment-based and virtual screening

NASA Astrophysics Data System (ADS)

Ilic, Stefan; Akabayov, Sabine R.; Arthanari, Haribabu; Wagner, Gerhard; Richardson, Charles C.; Akabayov, Barak

2016-11-01

The structural differences between bacterial and human primases render the former an excellent target for drug design. Here we describe a technique for selecting small molecule inhibitors of the activity of T7 DNA primase, an ideal model for bacterial primases due to their common structural and functional features. Using NMR screening, fragment molecules that bind T7 primase were identified and then exploited in virtual filtration to select larger molecules from the ZINC database. The molecules were docked to the primase active site using the available primase crystal structure and ranked based on their predicted binding energies to identify the best candidates for functional and structural investigations. Biochemical assays revealed that some of the molecules inhibit T7 primase-dependent DNA replication. The binding mechanism was delineated via NMR spectroscopy. Our approach, which combines fragment based and virtual screening, is rapid and cost effective and can be applied to other targets.

Mycorrhizae of poplars

Treesearch

R. C. Schultz; J. G. Isebrands; P. P. Kormanik

1983-01-01

Poplar hybrids, being screened for short-rotation intensive culture, can form ecto-, endo-, or ectendo-mycorrhizae or may be autotrophic. Different sections of the genus Populus tend to be selective in the type of mycorrhizae formed. Knowledge of which types are formed influences the kinds of propagule production, site preparation, and herbicide...

A Potent and Site-Selective Agonist of TRPA1.

PubMed

Takaya, Junichiro; Mio, Kazuhiro; Shiraishi, Takuya; Kurokawa, Tatsuki; Otsuka, Shinya; Mori, Yasuo; Uesugi, Motonari

2015-12-23

TRPA1 is a member of the transient receptor potential (TRP) cation channel family that is expressed primarily on sensory neurons. This chemosensor is activated through covalent modification of multiple cysteine residues with a wide range of reactive compounds including allyl isothiocyanate (AITC), a spicy component of wasabi. The present study reports on potent and selective agonists of TRPA1, discovered through screening 1657 electrophilic molecules. In an effort to validate the mode of action of hit molecules, we noted a new TRPA1-selective agonist, JT010 (molecule 1), which opens the TRPA1 channel by covalently and site-selectively binding to Cys621 (EC50 = 0.65 nM). The results suggest that a single modification of Cys621 is sufficient to open the TRPA1 channel. The TRPA1-selective probe described herein might be useful for further mechanistic studies of TRPA1 activation.

Identification of new allosteric sites and modulators of AChE through computational and experimental tools.

PubMed

Roca, Carlos; Requena, Carlos; Sebastián-Pérez, Víctor; Malhotra, Sony; Radoux, Chris; Pérez, Concepción; Martinez, Ana; Antonio Páez, Juan; Blundell, Tom L; Campillo, Nuria E

2018-12-01

Allosteric sites on proteins are targeted for designing more selective inhibitors of enzyme activity and to discover new functions. Acetylcholinesterase (AChE), which is most widely known for the hydrolysis of the neurotransmitter acetylcholine, has a peripheral allosteric subsite responsible for amyloidosis in Alzheimer's disease through interaction with amyloid β-peptide. However, AChE plays other non-hydrolytic functions. Here, we identify and characterise using computational tools two new allosteric sites in AChE, which have allowed us to identify allosteric inhibitors by virtual screening guided by structure-based and fragment hotspot strategies. The identified compounds were also screened for in vitro inhibition of AChE and three were observed to be active. Further experimental (kinetic) and computational (molecular dynamics) studies have been performed to verify the allosteric activity. These new compounds may be valuable pharmacological tools in the study of non-cholinergic functions of AChE.

Screening and ranking framework (SRF) for geologic CO2 storagesite selection on the basis of HSE risk

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

Oldenburg, Curtis M.

2006-11-27

A screening and ranking framework (SRF) has been developedto evaluate potential geologic carbon dioxide (CO2) storage sites on thebasis of health, safety, and environmental (HSE) risk arising from CO2leakage. The approach is based on the assumption that CO2 leakage risk isdependent on three basic characteristics of a geologic CO2 storage site:(1) the potential for primary containment by the target formation; (2)the potential for secondary containment if the primary formation leaks;and (3) the potential for attenuation and dispersion of leaking CO2 ifthe primary formation leaks and secondary containment fails. Theframework is implemented in a spreadsheet in which users enter numericalscores representingmore » expert opinions or published information along withestimates of uncertainty. Applications to three sites in Californiademonstrate the approach. Refinements and extensions are possible throughthe use of more detailed data or model results in place of propertyproxies.« less

In silico strategies for the selection of chelating compounds with potential application in metal-promoted neurodegenerative diseases

NASA Astrophysics Data System (ADS)

Rodríguez-Rodríguez, Cristina; Rimola, Albert; Alí-Torres, Jorge; Sodupe, Mariona; González-Duarte, Pilar

2011-01-01

The development of new strategies to find commercial molecules with promising biochemical features is a main target in the field of biomedicine chemistry. In this work we present an in silico-based protocol that allows identifying commercial compounds with suitable metal coordinating and pharmacokinetic properties to act as metal-ion chelators in metal-promoted neurodegenerative diseases (MpND). Selection of the chelating ligands is done by combining quantum chemical calculations with the search of commercial compounds on different databases via virtual screening. Starting from different designed molecular frameworks, which mainly constitute the binding site, the virtual screening on databases facilitates the identification of different commercial molecules that enclose such scaffolds and, by imposing a set of chemical and pharmacokinetic filters, obey some drug-like requirements mandatory to deal with MpND. The quantum mechanical calculations are useful to gauge the chelating properties of the selected candidate molecules by determining the structure of metal complexes and evaluating their stability constants. With the proposed strategy, commercial compounds containing N and S donor atoms in the binding sites and capable to cross the BBB have been identified and their chelating properties analyzed.

Hydrologic and chemical data from an experiment to examine temporal variability in water samples from screened wells on Cape Cod, Massachusetts

USGS Publications Warehouse

Reilly, Thomas E.

1994-01-01

An experiment was designed to evaluate the changing chemical composition of the water pumped from a well screened in a physically and chemically heterogenous aquifer. Well F453-63, at the U.S. Geological Survey Toxic-Substances Hydrology research site located on Cape Cod, Massachusetts, was selected because it was known that the screen penetrated both the oxic and anoxic zones of the sewage plume from the Otis Air Base sewage-disposal sand beds. The experiment was conducted on August 12, 1992. Well F453-63 was sampled over time as it was pumped continuously, and three multilevel samplers were used to document the vertical distribution of selected chemicals in the ground water in the immediate vicinity of the well. All water samples obtained during the experiment were analyzed in the field for specific conductance and pH. The samples were subsequently analyzed for concentrations of ferrous iron (Fe+2), boron, calcium, chloride, iron (Fe total), phosphorus, potassium, magnesium, manganese, sodium, zinc, and nitrogen species, including nitrous oxide, ammonium, nitrite and nitrate. The results of these chemical analyses along with appropriate physical measurements of the site and aquifer material are documented in this data report.

Canada's Deep Geological Repository for Used Nuclear Fuel - Geo-scientific Site Evaluation Process - 13117

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

Blyth, Alec; Ben Belfadhel, Mahrez; Hirschorn, Sarah

2013-07-01

The Nuclear Waste Management Organization (NWMO) is responsible for implementing Adaptive Phased Management (APM), the approach selected by the Government of Canada for long-term management of used nuclear fuel generated by Canadian nuclear reactors. The ultimate objective of APM is the centralized containment and isolation of Canada's used nuclear fuel in a Deep Geological Repository in a suitable rock formation at a depth of approximately 500 meters (m) (1,640 feet [ft]). In May 2010, the NWMO published a nine-step site selection process that serves as the road map to decision-making on the location for the deep geological repository. The safetymore » and appropriateness of any potential site will be assessed against a number of factors, both technical and social in nature. The selected site will be one that can be demonstrated to be able to safely contain and isolate used nuclear fuel, protecting humans and the environment over the very long term. The geo-scientific suitability of potential candidate sites will be assessed in a stepwise manner following a progressive and thorough site evaluation process that addresses a series of geo-scientific factors revolving around five safety functions. The geo-scientific site evaluation process includes: Initial Screenings; Preliminary Assessments; and Detailed Site Evaluations. As of November 2012, 22 communities have entered the site selection process (three in northern Saskatchewan and 18 in northwestern and southwestern Ontario). (authors)« less

Results of the Analyses of Screening Surface and Well Water Samples from Decatur, Alabama for Selected Perfluorinated Compounds

EPA Science Inventory

EPA has conducted testing of agricultural sites in Alabama where sewage sludge was applied from a local wastewater treatment plant that receives wastewater from numerous industrial sources, including facilities that manufacture and use perfluorooctanoic acid (PFOA) and other perf...

Optimal design of stormwater basins with bio-sorption activated media (BAM) in karst environments - phase I : site screening and selection, [summary].

DOT National Transportation Integrated Search

2015-11-01

Nutrient content is a concern in Floridas aquifers and springs sources of drinking water, : recreation, and the states natural beauty. In recent years, the nitrogen content of Floridas : aquifer springs has risen. This increase in nutrie...

Enterobacteriaceae and related organisms recovered from biofilms in a commercial shell egg processing facility.

USDA-ARS?s Scientific Manuscript database

During six visits, biofilms from egg contact and non-contact surfaces in a commercial shell egg processing facility were sampled. Thirty-five different sample sites were selected: Pre-wash and wash tanks (lids, screens, tank interiors, nozzle guards), post-wash spindles, blower filters, belts (far...

Health, Safety, and Environmental Screening and Ranking Frameworkfor Geologic CO2 Storage Site Selection

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

Oldenburg, Curtis M.

2005-09-19

This report describes a screening and ranking framework(SRF) developed to evaluate potential geologic carbon dioxide (CO2) storage sites on the basis of health, safety, and environmental (HSE) risk arising from possible CO2 leakage. The approach is based on the assumption that HSE risk due to CO2 leakage is dependent on three basic characteristics of a geologic CO2 storage site: (1) the potential for primary containment by the target formation; (2) the potential for secondary containment if the primary formation leaks; and (3) the potential for attenuation and dispersion of leaking CO2 if the primary formation leaks and secondary containment fails.more » The framework is implemented in a spreadsheet in which users enter numerical scores representing expert opinions or general information available from published materials along with estimates of uncertainty to evaluate the three basic characteristics in order to screen and rank candidate sites. Application of the framework to the Rio Visa Gas Field, Ventura Oil Field, and Mammoth Mountain demonstrates the approach. Refinements and extensions are possible through the use of more detailed data or model results in place of property proxies. Revisions and extensions to improve the approach are anticipated in the near future as it is used and tested by colleagues and collaborators.« less

Identification of fecal input sites in spring water by selection and genotyping of multiresistant Escherichia coli.

PubMed

Wicki, Melanie; Karabulut, Fatma; Auckenthaler, Adrian; Felleisen, Richard; Tanner, Marcel; Baumgartner, Andreas

2011-12-01

The localization of fecal input sites is important for water quality management. For this purpose, we have developed a new approach based on a three-step procedure, including a preparatory phase, the screening of multiresistant bacteria using selective agar plates, and a typing phase where selected Escherichia coli isolates are characterized by antibiotic resistance profiles and molecular fingerprinting techniques (pulsed-field gel electrophoresis [PFGE]). These two well-known source tracking methods were combined in order to reduce cost and effort. This approach was successfully applied under field conditions in a study area located in the north-western part of Switzerland. E. coli isolates from spring water and surface water samples collected in this area were screened with selective agar plates. In this way, 21 different groups, each consisting of strains with the same pattern of antibiotic resistance, were found. Of these, four groups were further analyzed using PFGE. Strains with identical PFGE profiles were detected repeatedly, demonstrating the suitability of this method for the localization of fecal input sites over an extended period of time. Identical PFGE patterns of strains detected in water from two different springs were also found in the stream flowing through the study area. These results demonstrated the applicability of the new approach for the examination of incidents of fecal contamination in drinking water. The advantages of the described approach over genotyping methods currently being used to identify sources of fecal contaminants are a reduction in time, costs, and the effort required. Identical isolates could be identified without the construction of large libraries.

Phage diabody repertoires for selection of large numbers of bispecific antibody fragments.

PubMed

McGuinness, B T; Walter, G; FitzGerald, K; Schuler, P; Mahoney, W; Duncan, A R; Hoogenboom, H R

1996-09-01

Methods for the generation of large numbers of different bispecific antibodies are presented. Cloning strategies are detailed to create repertoires of bispecific diabody molecules with variability on one or both of the antigen binding sites. This diabody format, when combined with the power of phage display technology, allows the generation and analysis of thousands of different bispecific molecules. Selection for binding presumably also selects for more stable diabodies. Phage diabody libraries enable screening or selection of the best combination bispecific molecule with regards to affinity of binding, epitope recognition and pairing before manufacture of the best candidate.

Pharmacophore Based Virtual Screening Approach to Identify Selective PDE4B Inhibitors

PubMed Central

Gaurav, Anand; Gautam, Vertika

2017-01-01

Phosphodiesterase 4 (PDE4) has been established as a promising target in asthma and chronic obstructive pulmonary disease. PDE4B subtype selective inhibitors are known to reduce the dose limiting adverse effect associated with non-selective PDE4B inhibitors. This makes the development of PDE4B subtype selective inhibitors a desirable research goal. To achieve this goal, ligand based pharmacophore modeling approach is employed. Separate pharmacophore hypotheses for PDE4B and PDE4D inhibitors were generated using HypoGen algorithm and 106 PDE4 inhibitors from literature having thiopyrano [3,2-d] Pyrimidines, 2-arylpyrimidines, and triazines skeleton. Suitable training and test sets were created using the molecules as per the guidelines available for HypoGen program. Training set was used for hypothesis development while test set was used for validation purpose. Fisher validation was also used to test the significance of the developed hypothesis. The validated pharmacophore hypotheses for PDE4B and PDE4D inhibitors were used in sequential virtual screening of zinc database of drug like molecules to identify selective PDE4B inhibitors. The hits were screened for their estimated activity and fit value. The top hit was subjected to docking into the active sites of PDE4B and PDE4D to confirm its selectivity for PDE4B. The hits are proposed to be evaluated further using in-vitro assays. PMID:29201082

Maize aflatoxin accumulation segregates with early maturing selections from an S2 breeding cross population.

PubMed

Henry, W Brien

2013-01-15

Maize breeders continue to seek new sources of aflatoxin resistance, but most lines identified as resistance sources are late maturing. The vast difference in flowering time makes it hard to cross these lines with proprietary commercial lines that mature much earlier and often subjects the reproductive phase of these resistant lines to the hottest and driest portion of the summer, making silking, pollination and grain fill challenging. Two hundred crosses from the GEM Project were screened for aflatoxin accumulation at Mississippi State in 2008, and a subset of these lines were screened again in 2009. The breeding cross UR13085:S99g99u was identified as a potential source of aflatoxin resistance, and maturity-based selections were made from an S2 breeding population from this same germplasm source: UR13085:S99g99u-B-B. The earliest maturing selections performed poorly for aflatoxin accumulation, but later maturing selections were identified with favorable levels of aflatoxin accumulation. These selections, while designated as "late" within this study, matured earlier than most aflatoxin resistant lines presently available to breeders. Two selections from this study, designated S5_L7 and S5_L8, are potential sources of aflatoxin resistance and will be advanced for line development and additional aflatoxin screening over more site years and environments.

DC-Analyzer-facilitated combinatorial strategy for rapid directed evolution of functional enzymes with multiple mutagenesis sites.

PubMed

Wang, Xiong; Zheng, Kai; Zheng, Huayu; Nie, Hongli; Yang, Zujun; Tang, Lixia

2014-12-20

Iterative saturation mutagenesis (ISM) has been shown to be a powerful method for directed evolution. In this study, the approach was modified (termed M-ISM) by combining the single-site saturation mutagenesis method with a DC-Analyzer-facilitated combinatorial strategy, aiming to evolve novel biocatalysts efficiently in the case where multiple sites are targeted simultaneously. Initially, all target sites were explored individually by constructing single-site saturation mutagenesis libraries. Next, the top two to four variants in each library were selected and combined using the DC-Analyzer-facilitated combinatorial strategy. In addition to site-saturation mutagenesis, iterative saturation mutagenesis also needed to be performed. The advantages of M-ISM over ISM were that the screening effort is greatly reduced, and the entire M-ISM procedure was less time-consuming. The M-ISM strategy was successfully applied to the randomization of halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) when five interesting sites were targeted simultaneously. After screening 900 clones in total, six positive mutants were obtained. These mutants exhibited 4.0- to 9.3-fold higher k(cat) values than did the wild-type HheC toward 1,3-dichloro-2-propanol. However, with the ISM strategy, the best hit showed a 5.9-fold higher k(cat) value toward 1,3-DCP than the wild-type HheC, which was obtained after screening 4000 clones from four rounds of mutagenesis. Therefore, M-ISM could serve as a simple and efficient version of ISM for the randomization of target genes with multiple positions of interest.

A screen for immunity genes evolving under positive selection in Drosophila.

PubMed

Jiggins, F M; Kim, K W

2007-05-01

Genes involved in the immune system tend to have higher rates of adaptive evolution than other genes in the genome, probably because they are coevolving with pathogens. We have screened a sample of Drosophila genes to identify those evolving under positive selection. First, we identified rapidly evolving immunity genes by comparing 140 loci in Drosophila erecta and D. yakuba. Secondly, we resequenced 23 of the fastest evolving genes from the independent species pair D. melanogaster and D. simulans, and identified those under positive selection using a McDonald-Kreitman test. There was strong evidence of adaptive evolution in two serine proteases (persephone and spirit) and a homolog of the Anopheles serpin SRPN6, and weaker evidence in another serine protease and the death domain protein dFADD. These results add to mounting evidence that immune signalling pathway molecules often evolve rapidly, possibly because they are sites of host-parasite coevolution.

Follow-up and timeliness after an abnormal cancer screening among underserved, urban women in a patient navigation program

PubMed Central

Markossian, Talar W.; Darnell, Julie S.; Calhoun, Elizabeth A.

2012-01-01

Background We evaluated the efficacy of a Chicago-based cancer patient navigation program developed to increase the proportion of patients reaching diagnostic resolution and reduce the time from abnormal screening test to definitive diagnostic resolution. Methods Women with an abnormal breast (n=352) or cervical (n=545) cancer screening test were recruited for the quasi-experimental study. Navigation subjects originated from five federally qualified health center sites and one safety net hospital. Records-based concurrent control subjects were selected from 20 sites. Control sites had similar characteristics to the navigated sites in terms of patient volume, racial/ethnic composition, and payor mix. Mixed-effects logistic regression and Cox proportional hazard regression analyses were conducted to compare navigation and control patients reaching diagnostic resolution by 60 days and time to resolution, adjusting for demographic covariates and site. Results Compared to controls, the breast navigation group had shorter time to diagnostic resolution (aHR=1.65, CI=1.20–2.28) and the cervical navigation group had shorter time to diagnostic resolution for those who resolved after 30 days (aHR= 2.31, CI=1.75–3.06), with no difference before 30 days (aHR= 1.42, CI=0.83–2.43). Variables significantly associated with longer time to resolution for breast cancer screening abnormalities were being older, never partnered, abnormal mammogram and BI-RADS 3, and being younger and Black for cervical abnormalities. Conclusions Patient navigation reduces time from abnormal cancer finding to definitive diagnosis in underserved women. Impact Results support efforts to use patient navigation as a strategy to reduce cancer disparities among socioeconomically disadvantaged women. PMID:23045544

Follow-up and timeliness after an abnormal cancer screening among underserved, urban women in a patient navigation program.

PubMed

Markossian, Talar W; Darnell, Julie S; Calhoun, Elizabeth A

2012-10-01

We evaluated the efficacy of a Chicago-based cancer patient navigation program developed to increase the proportion of patients reaching diagnostic resolution and reduce the time from abnormal screening test to definitive diagnostic resolution. Women with an abnormal breast (n = 352) or cervical (n = 545) cancer screening test were recruited for the quasi-experimental study. Navigation subjects originated from five federally qualified health center sites and one safety net hospital. Records-based concurrent control subjects were selected from 20 sites. Control sites had similar characteristics to the navigated sites in terms of patient volume, racial/ethnic composition, and payor mix. Mixed-effects logistic regression and Cox proportional hazard regression analyses were conducted to compare navigation and control patients reaching diagnostic resolution by 60 days and time to resolution, adjusting for demographic covariates and site. Compared with controls, the breast navigation group had shorter time to diagnostic resolution (aHR = 1.65, CI = 1.20-2.28) and the cervical navigation group had shorter time to diagnostic resolution for those who resolved after 30 days (aHR = 2.31, CI = 1.75-3.06), with no difference before 30 days (aHR = 1.42, CI = 0.83-2.43). Variables significantly associated with longer time to resolution for breast cancer screening abnormalities were being older, never partnered, abnormal mammogram and BI-RADS 3, and being younger and Black for cervical abnormalities. Patient navigation reduces time from abnormal cancer finding to definitive diagnosis in underserved women. Results support efforts to use patient navigation as a strategy to reduce cancer disparities among socioeconomically disadvantaged women. 2012 AACR

Environmental site description for a Uranium Atomic Vapor Laser Isotope Separation (U-AVLIS) production plant at the Paducah Gaseous Diffusion Plant site

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

Marmer, G.J.; Dunn, C.P.; Moeller, K.L.

Uranium enrichment in the United States has utilized a diffusion process to preferentially enrich the U-235 isotope in the uranium product. The U-AVLIS process is based on electrostatic extraction of photoionized U-235 atoms from an atomic vapor stream created by electron-beam vaporization of uranium metal alloy. The U-235 atoms are ionized when precisely tuned laser light -- of appropriate power, spectral, and temporal characteristics -- illuminates the uranium vapor and selectively photoionizes the U-235 isotope. A programmatic document for use in screening DOE site to locate a U-AVLIS production plant was developed and implemented in two parts. The first partmore » consisted of a series of screening analyses, based on exclusionary and other criteria, that identified a reasonable number of candidate sites. These sites were subjected to a more rigorous and detailed comparative analysis for the purpose of developing a short list of reasonable alternative sites for later environmental examination. This environmental site description (ESD) provides a detailed description of the PGDP site and vicinity suitable for use in an environmental impact statement (EIS). The report is based on existing literature, data collected at the site, and information collected by Argonne National Laboratory (ANL) staff during a site visit. 65 refs., 15 tabs.« less

Screening for contaminants of emerging concern in Northern Colorado Plateau Network waters: 2015 surface-water data

USGS Publications Warehouse

Weissinger, R; Battaglin, William A.; Bradley, Paul M.

2016-01-01

Patterns of detections at other sampling locations will be explored in future reports. This is an interim report. Limited sampling will continue in 2016 at selected sites in coordination with the USGS. A final report is expected upon completion of the USGS project in 2017.

MODELS AND METHODS FOR PETROLEUM HYDROCARBON RISK ASSESSMENT: ONSITE, LUSTRISK, AND HSSM

EPA Science Inventory

U.S. EPA has developed three tiers of models for analysis of fuel releases from underground storage tank (UST) systems: 1) OnSite; 2) LUSTRisk, and 3) the Hydrocarbon Spill Screening Model (HSSM). The tiered approach to modeling allows users to select a model based upon the amoun...

Targeting SDF-1/CXCL12 with a ligand that prevents activation of CXCR4 through structure based drug design

PubMed Central

Veldkamp, Christopher T.; Ziarek, Joshua J.; Peterson, Francis C.; Chen, Yu; Volkman, Brian F.

2010-01-01

CXCL12 is an attractive target for clinical therapy because of its involvement in autoimmune diseases, cancer growth, metastasis, and neovascularization. Tyrosine sulfation at three positions in the CXCR4 N-terminus is crucial for specific, high-affinity CXCL12 binding. An NMR structure of the complex between the CXCL12 dimer and a sulfotyrosine-containing CXCR4 fragment enabled high-throughput in silico screening for inhibitors of the chemokine-receptor interface. A total of 1.4 million compounds from the ZINC database were docked into a cleft on the CXCL12 surface normally occupied by sulfotyrosine 21 (sY21), and five were selected for experimental screening. NMR titrations with CXCL12 revealed that four compounds occupy the sY21 site, one of which binds with a Kd of 64 µM. This compound selectively inhibits SDF1-induced CXCR4 signaling in THP1 cells. Our results suggest that sulfotyrosine recognition sites can be targeted for the development of novel chemokine inhibitors. PMID:20459090

Using the QCM Biosensor-Based T7 Phage Display Combined with Bioinformatics Analysis for Target Identification of Bioactive Small Molecule.

PubMed

Takakusagi, Yoichi; Takakusagi, Kaori; Sugawara, Fumio; Sakaguchi, Kengo

2018-01-01

Identification of target proteins that directly bind to bioactive small molecule is of great interest in terms of clarifying the mode of action of the small molecule as well as elucidating the biological phenomena at the molecular level. Of the experimental technologies available, T7 phage display allows comprehensive screening of small molecule-recognizing amino acid sequence from the peptide libraries displayed on the T7 phage capsid. Here, we describe the T7 phage display strategy that is combined with quartz-crystal microbalance (QCM) biosensor for affinity selection platform and bioinformatics analysis for small molecule-recognizing short peptides. This method dramatically enhances efficacy and throughput of the screening for small molecule-recognizing amino acid sequences without repeated rounds of selection. Subsequent execution of bioinformatics programs allows combinatorial and comprehensive target protein discovery of small molecules with its binding site, regardless of protein sample insolubility, instability, or inaccessibility of the fixed small molecules to internally located binding site on larger target proteins when conventional proteomics approaches are used.

Costs and effectiveness of the fast track intervention for antisocial behavior.

PubMed

Foster, E Michael

2010-09-01

Antisocial behavior is enormously costly to the youth involved, their families, victims, taxpayers and other members of society. These costs are generated by school failure, delinquency and involvement in the juvenile justice system, drug use, health services and other services. For prevention programs to be cost effective, they must reduce these costly behaviors and outcomes. The Fast Track intervention is a 10-year, multi-component prevention program targeting antisocial behavior. The intervention identified children at school entry and provided intervention services over a 10-year period. This study examined the intervention's impact on outcomes affecting societal costs using data through late adolescence. The intervention is being evaluated through a multi-cohort, multi-site, multi-year randomized control trial of program participants and comparable children and youth in similar schools, and that study provides the data for these analyses. Schools within four sites (Durham, NC; Nashville, TN; Seattle, WA; and rural central Pennsylvania) were selected as high-risk based on crime and poverty statistics of the neighborhoods they served. Within each site, schools were divided into multiple sets matched for demographics (size, percentage free/reduced lunch, ethnic composition); one set within each pair was randomly assigned to the intervention and one to the control condition. Within participating schools, high-risk children were identified using a multiple-gating procedure. For each of three annual cohorts, all kindergarteners (9,594 total) in 54 schools were screened for classroom conduct problems by teachers. Those children scoring in the top 40% within cohort and site were then solicited for the next stage of screening for home behavior problems by the parents, and 91% agreed (n = 3,274). The teacher and parent screening scores were then standardized within site and combined into a sum score. These summed scores represented a total severity-of-risk screen score. Children were selected for inclusion into the study based on this screen score, moving from the highest score downward until desired sample sizes were reached within sites, cohorts, and conditions. The intervention lacked both the breadth and depth of effects on costly outcomes to demonstrate cost-effectiveness or even effectiveness. The outcomes examined here reflect effects observed during measurement windows that are not complete for every outcome. Data are lacking on some potential outcomes, such as the use of mental health services before year 7. The most intensive psychosocial intervention ever fielded did not produce meaningful and consistent effects on costly outcomes. The lack of effects through high school suggests that the intervention will not become cost-effective as participants progress through adulthood. Future research should consider alternative approaches to prevention youth violence.

Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors

NASA Astrophysics Data System (ADS)

Kalid, Ori; Toledo Warshaviak, Dora; Shechter, Sharon; Sherman, Woody; Shacham, Sharon

2012-11-01

We present the Consensus Induced Fit Docking (cIFD) approach for adapting a protein binding site to accommodate multiple diverse ligands for virtual screening. This novel approach results in a single binding site structure that can bind diverse chemotypes and is thus highly useful for efficient structure-based virtual screening. We first describe the cIFD method and its validation on three targets that were previously shown to be challenging for docking programs (COX-2, estrogen receptor, and HIV reverse transcriptase). We then demonstrate the application of cIFD to the challenging discovery of irreversible Crm1 inhibitors. We report the identification of 33 novel Crm1 inhibitors, which resulted from the testing of 402 purchased compounds selected from a screening set containing 261,680 compounds. This corresponds to a hit rate of 8.2 %. The novel Crm1 inhibitors reveal diverse chemical structures, validating the utility of the cIFD method in a real-world drug discovery project. This approach offers a pragmatic way to implicitly account for protein flexibility without the additional computational costs of ensemble docking or including full protein flexibility during virtual screening.

Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking.

PubMed

Strecker, Claas; Meyer, Bernd

2018-05-29

Protein flexibility poses a major challenge to docking of potential ligands in that the binding site can adopt different shapes. Docking algorithms usually keep the protein rigid and only allow the ligand to be treated as flexible. However, a wrong assessment of the shape of the binding pocket can prevent a ligand from adapting a correct pose. Ensemble docking is a simple yet promising method to solve this problem: Ligands are docked into multiple structures, and the results are subsequently merged. Selection of protein structures is a significant factor for this approach. In this work we perform a comprehensive and comparative study evaluating the impact of structure selection on ensemble docking. We perform ensemble docking with several crystal structures and with structures derived from molecular dynamics simulations of renin, an attractive target for antihypertensive drugs. Here, 500 ns of MD simulations revealed binding site shapes not found in any available crystal structure. We evaluate the importance of structure selection for ensemble docking by comparing binding pose prediction, ability to rank actives above nonactives (screening utility), and scoring accuracy. As a result, for ensemble definition k-means clustering appears to be better suited than hierarchical clustering with average linkage. The best performing ensemble consists of four crystal structures and is able to reproduce the native ligand poses better than any individual crystal structure. Moreover this ensemble outperforms 88% of all individual crystal structures in terms of screening utility as well as scoring accuracy. Similarly, ensembles of MD-derived structures perform on average better than 75% of any individual crystal structure in terms of scoring accuracy at all inspected ensembles sizes.

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.

Molecular Quantum Similarity, Chemical Reactivity and Database Screening of 3D Pharmacophores of the Protein Kinases A, B and G from Mycobacterium tuberculosis.

PubMed

Morales-Bayuelo, Alejandro

2017-06-21

Mycobacterium tuberculosis remains one of the world's most devastating pathogens. For this reason, we developed a study involving 3D pharmacophore searching, selectivity analysis and database screening for a series of anti-tuberculosis compounds, associated with the protein kinases A, B, and G. This theoretical study is expected to shed some light onto some molecular aspects that could contribute to the knowledge of the molecular mechanics behind interactions of these compounds, with anti-tuberculosis activity. Using the Molecular Quantum Similarity field and reactivity descriptors supported in the Density Functional Theory, it was possible to measure the quantification of the steric and electrostatic effects through the Overlap and Coulomb quantitative convergence (alpha and beta) scales. In addition, an analysis of reactivity indices using global and local descriptors was developed, identifying the binding sites and selectivity on these anti-tuberculosis compounds in the active sites. Finally, the reported pharmacophores to PKn A, B and G, were used to carry out database screening, using a database with anti-tuberculosis drugs from the Kelly Chibale research group (http://www.kellychibaleresearch.uct.ac.za/), to find the compounds with affinity for the specific protein targets associated with PKn A, B and G. In this regard, this hybrid methodology (Molecular Mechanic/Quantum Chemistry) shows new insights into drug design that may be useful in the tuberculosis treatment today.

A Learning Collaborative Approach to Improve Primary Care STI Screening.

PubMed

McKee, M Diane; Alderman, Elizabeth; York, Deborah V; Blank, Arthur E; Briggs, Rahil D; Hoidal, Kelsey E S; Kus, Christopher; Lechuga, Claudia; Mann, Marie; Meissner, Paul; Patel, Nisha; Racine, Andrew D

2017-10-01

The Bronx Ongoing Pediatric Screening (BOPS) project sought to improve screening for sexual activity and sexually transmitted infections (gonorrhea and chlamydia [GCC] and HIV) in a primary care network, employing a modified learning collaborative, real-time clinical data feedback to practices, improvement coaching, and a pay-for-quality monetary incentive. Outcomes are compared for 11 BOPS-participating sites and 10 non-participating sites. The quarterly median rate for documenting sexual activity status increased from 55% to 88% (BOPS sites) and from 13% to 74% (non-BOPS sites). GCC screening of sexually active youth increased at BOPS and non-BOPS sites. Screening at non-health care maintenance visits improved more at BOPS than non-BOPS sites. Data from nonparticipating sites suggests that introduction of an adolescent EMR template or other factors improved screening rates regardless of BOPS participation; BOPS activities appear to promote additional improvement of screening during non-health maintenance visits.

A comprehensive study of Superfund program benefits in the Denver and Tampa Bay metropolitan areas

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

Held, K.; Casper, B.; Siddhanti, S.K.

1995-12-31

The purpose of the study is to evaluate the benefits of the Superfund program in selected geographic areas. The study demonstrates how the cleanup of Superfund sites has improved the overall quality of life of those in the affected communities. The study presents findings on the benefits of Superfund cleanup activity in the Denver, Colorado and Tampa Bay, Florida metropolitan areas. Denver and Tampa Bay were chosen from several areas that the EPA evaluated and screened during the initial phase of the study. These locations were chosen because of a substantial presence of Superfund activities, making it possible to assessmore » the efficacy of the program. Several features make this study unique in terms of its overall goal. The study examines a broad range of benefit categories related to human health, environmental, and socioeconomic effects of Superfund cleanup activities. The study is also designed to assess benefits due to completed, current, and future planned activity at Superfund sites. This assessment covers Federal remedial activities at National Priorities List (NPL) sites, as well as relevant Federal removal actions in the study areas. These benefits are investigated from an area-wide perspective, as opposed to site-by-site, to determine Superfund`s overall effect on the communities in each area. The study consists of two major phases: Phase 1: Screening and ranking 16 prospective geographic areas and selecting Denver and Tampa Bay as the most appropriate areas for in-depth analysis; and Phase 2: Developing methodologies for assessing benefits, collecting relevant data, and analyzing the benefits from Superfund cleanup activity.« less

Virtual screening of potential inhibitors from TCM for the CPSF30 binding site on the NS1A protein of influenza A virus.

PubMed

Ai, Haixin; Zhang, Li; Chang, Alan K; Wei, Hongyun; Che, Yuchen; Liu, Hongsheng

2014-03-01

Inhibition of CPSF30 function by the effector domain of influenza A virus of non-structural protein 1 (NS1A) protein plays a critical role in the suppression of host key antiviral response. The CPSF30-binding site of NS1A appears to be a very attractive target for the development of new drugs against influenza A virus. In this study, structure-based molecular docking was utilized to screen more than 30,000 compounds from a Traditional Chinese Medicine (TCM) database. Four drug-like compounds were selected as potential inhibitors for the CPSF30-binding site of NS1A. Docking conformation analysis results showed that these potential inhibitors could bind to the CPSF30-binding site with strong hydrophobic interactions and weak hydrogen bonds. Molecular dynamics simulations and MM-PBSA calculations suggested that two of the inhibitors, compounds 32056 and 31674, could stably bind to the CPSF30-binding site with high binding free energy. These two compounds could be modified to achieve higher binding affinity, so that they may be used as potential leads in the development of new anti-influenza drugs.

Screening of metal-organic frameworks for carbon dioxide capture from flue gas using a combined experimental and modeling approach.

PubMed

Yazaydin, A Ozgür; Snurr, Randall Q; Park, Tae-Hong; Koh, Kyoungmoo; Liu, Jian; Levan, M Douglas; Benin, Annabelle I; Jakubczak, Paulina; Lanuza, Mary; Galloway, Douglas B; Low, John J; Willis, Richard R

2009-12-30

A diverse collection of 14 metal-organic frameworks (MOFs) was screened for CO(2) capture from flue gas using a combined experimental and modeling approach. Adsorption measurements are reported for the screened MOFs at room temperature up to 1 bar. These data are used to validate a generalized strategy for molecular modeling of CO(2) and other small molecules in MOFs. MOFs possessing a high density of open metal sites are found to adsorb significant amounts of CO(2) even at low pressure. An excellent correlation is found between the heat of adsorption and the amount of CO(2) adsorbed below 1 bar. Molecular modeling can aid in selection of adsorbents for CO(2) capture from flue gas by screening a large number of MOFs.

10 CFR 960.3-2-1 - Site screening for potentially acceptable sites.

Code of Federal Regulations, 2010 CFR

2010-01-01

... POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-1 Site screening for... first repository, the process shall begin with site-screening activities that consider large land masses... repositories, the Secretary shall first identify the State within which the site is located in a decision-basis...

Mosquito-borne arbovirus surveillance at selected sites in diverse ecological zones of Kenya; 2007 – 2012

PubMed Central

2013-01-01

Background Increased frequency of arbovirus outbreaks in East Africa necessitated the determination of distribution of risk by entomologic arbovirus surveillance. A systematic vector surveillance programme spanning 5 years and covering 11 sites representing seven of the eight provinces in Kenya and located in diverse ecological zones was carried out. Methods Mosquitoes were sampled bi-annually during the wet seasons and screened for arboviruses. Mosquitoes were identified to species, pooled by species, collection date and site and screened for arboviruses by isolation in cell culture and/or RT-PCR screening and sequencing. Results Over 450,000 mosquitoes in 15,890 pools were screened with 83 viruses being detected/isolated that include members of the alphavirus, flavivirus and orthobunyavirus genera many of which are known to be of significant public health importance in the East African region. These include West Nile, Ndumu, Sindbis, Bunyamwera, Pongola and Usutu viruses detected from diverse sites. Ngari virus, which was associated with hemorrhagic fever in northern Kenya in 1997/98 was isolated from a pool of Anopheles funestus sampled from Tana-delta and from Aedes mcintoshi from Garissa. Insect only flaviviruses previously undescribed in Kenya were also isolated in the coastal site of Rabai. A flavivirus most closely related to the Chaoyang virus, a new virus recently identified in China and two isolates closely related to Quang Binh virus previously unreported in Kenya were also detected. Conclusion Active transmission of arboviruses of public health significance continues in various parts of the country with possible undetermined human impact. Arbovirus activity was highest in the pastoralist dominated semi-arid to arid zones sites of the country where 49% of the viruses were isolated suggesting a role of animals as amplifiers and indicating the need for improved arbovirus disease diagnosis among pastoral communities. PMID:23663381

Evaluation of chemical data from selected sites in the Surface-Water Ambient Monitoring Program (SWAMP) in Florida

USGS Publications Warehouse

Katz, B.G.; Collins, J.J.

1998-01-01

A cooperative study between the Florida Department of Environmental Protection (FDEP) and the U.S. Geological Survey was conducted to assess the integrity of selected water-quality data collected at 150 sites in the FDEP Surface-Water Ambient Monitoring Program (SWAMP) in Florida. The assessment included determining the consistency of the water-quality data collected statewide, including commonality of monitoring procedures and analytes, screening of the gross validity of a chemical analysis, and quality assurance and quality control (QA/QC) procedures. Four tests were used to screen data at selected SWAMP sites to estimate the gross validity of selected chemical data: (1) the ratio of dissolved solids (in milligrams per liter) to specific conductance (in microsiemens per centimeter); (2) the ratio of total cations (in milliequivalents per liter) multiplied by 100 to specific conductance (in microsiemens per centimeter); (3) the ratio of total anions (in milliequivalents per liter) multiplied by 100 to specific conductance (in microsiemens per centimeter); and (4) the ionic charge-balance error. Although the results of the four screening tests indicate that the chemical data generally are quite reliable, the extremely small number of samples (less than 5 percent of the total number of samples) with sufficient chemical information to run the tests may not provide a representative indication of the analytical accuracy of all laboratories in the program. In addition to the four screening tests, unusually low or high values were flagged for field and laboratory pH (less than 4.0 and greater than 9.0) and specific conductance (less than 10 and greater than 10,000 microsiemens per centimeter). The numbers of flagged data were less than 1 percent of the 19,937 water samples with pH values and less than 0.6 percent of the 16,553 water samples with specific conductance values. Thirty-four agencies responded to a detailed questionnaire that was sent to more than 60 agencies involved in the collection and analysis of surface-water-quality data for SWAMP. The purpose of the survey was to evaluate quality assurance methods and consistency of methods statewide. Information was compiled and summarized on monitoring network design, data review and upload procedures, laboratory and field sampling methods, and data practices. Currently, most agencies that responded to the survey follow FDEP-approved QA/QC protocol for sampling and have quality assurance practices for recording and reporting data. Also, most agencies responded that calibration procedures were followed in the laboratory for analysis of data, but no responses were given about the specific procedures. Approximately 50 percent of the respondents indicated that laboratory analysis methods have changed over time. With so many laboratories involved in analyzing samples for SWAMP, it is difficult to compare water quality from one site to another due to different reporting conventions for chemical constituents and different analytical methods over time. Most agencies responded that calibration methods are followed in the field, but no specific details were provided. Grab samples are the most common method of collection. Other data screening procedures are necessary to further evaluate the validity of chemical data collected at SWAMP sites. High variability in the concentration of targeted constituents may signal analytical problems, but more likely changes in concentration are related to hydrologic conditions. This underscores the need for accurate measurements of discharge, lake stage, tidal stage at the time of sampling so that changes in constituent concentrations can be properly evaluated and fluxes (loads) of nutrients or metals, for example, can be calculated and compared over time.

Chlamydia screening interventions from community pharmacies: a systematic review.

PubMed

Gudka, Sajni; Afuwape, Folasade E; Wong, Bessie; Yow, Xuan Li; Anderson, Claire; Clifford, Rhonda M

2013-07-01

Chlamydia (Chlamydia trachomatis) is the most commonly notified sexually transmissible infection in Australia. Increasing the number of people aged 16-25 years being tested for chlamydia has become a key objective. The strategy recommends that chlamydia screening sites should be easy to access. Community pharmacies are conveniently located and easily accessible. This review aimed to determine the different types of pharmacy-based chlamydia screening interventions, describe their uptake rates, and understand issues around the acceptability of and barriers to testing. Seven electronic databases were searched for peer-reviewed articles published up to 30 October 2011 for studies that reported chlamydia screening interventions from community pharmacies, or had qualitative evidence on acceptability or barriers linked with interventions. Of the 163 publications identified, 12 met the inclusion criteria. Nine reported chlamydia screening interventions in a pharmacy setting, whereas three focussed on perspectives on chlamydia screening. Pharmacists could offer a chlamydia test to consumers attending the pharmacy for a sexual health-related consultation, or consumers could request a chlamydia test as part of a population-based intervention. Participating consumers said pharmacies were accessible and convenient, and pharmacists were competent when offering a chlamydia test. Pharmacists reported selectively offering tests to women they thought would be most at risk, undermining the principles of opportunistic interventions. Chlamydia screening from community pharmacies is feasible, and can provide an accessible, convenient venue to get a test. Professional implementation support, alongside resources, education and training programs, and incentives may overcome the issue of pharmacists selectively offering the test.

In silico approaches to predict the potential of milk protein-derived peptides as dipeptidyl peptidase IV (DPP-IV) inhibitors.

PubMed

Nongonierma, Alice B; Mooney, Catherine; Shields, Denis C; FitzGerald, Richard J

2014-07-01

Molecular docking of a library of all 8000 possible tripeptides to the active site of DPP-IV was used to determine their binding potential. A number of tripeptides were selected for experimental testing, however, there was no direct correlation between the Vina score and their in vitro DPP-IV inhibitory properties. While Trp-Trp-Trp, the peptide with the best docking score, was a moderate DPP-IV inhibitor (IC50 216μM), Lineweaver and Burk analysis revealed its action to be non-competitive. This suggested that it may not bind to the active site of DPP-IV as assumed in the docking prediction. Furthermore, there was no significant link between DPP-IV inhibition and the physicochemical properties of the peptides (molecular mass, hydrophobicity, hydrophobic moment (μH), isoelectric point (pI) and charge). LIGPLOTs indicated that competitive inhibitory peptides were predicted to have both hydrophobic and hydrogen bond interactions with the active site of DPP-IV. DPP-IV inhibitory peptides generally had a hydrophobic or aromatic amino acid at the N-terminus, preferentially a Trp for non-competitive inhibitors and a broader range of residues for competitive inhibitors (Ile, Leu, Val, Phe, Trp or Tyr). Two of the potent DPP-IV inhibitors, Ile-Pro-Ile and Trp-Pro (IC50 values of 3.5 and 44.2μM, respectively), were predicted to be gastrointestinally/intestinally stable. This work highlights the needs to test the assumptions (i.e. competitive binding) of any integrated strategy of computational and experimental screening, in optimizing screening. Future strategies targeting allosteric mechanisms may need to rely more on structure-activity relationship modeling, rather than on docking, in computationally selecting peptides for screening. Copyright © 2014 Elsevier Inc. All rights reserved.

Developing Hypothetical Inhibition Mechanism of Novel Urea Transporter B Inhibitor

NASA Astrophysics Data System (ADS)

Li, Min; Tou, Weng Ieong; Zhou, Hong; Li, Fei; Ren, Huiwen; Chen, Calvin Yu-Chian; Yang, Baoxue

2014-07-01

Urea transporter B (UT-B) is a membrane channel protein that specifically transports urea. UT-B null mouse exhibited urea selective urine concentrating ability deficiency, which suggests the potential clinical applications of the UT-B inhibitors as novel diuretics. Primary high-throughput virtual screening (HTVS) of 50000 small-molecular drug-like compounds identified 2319 hit compounds. These 2319 compounds were screened by high-throughput screening using an erythrocyte osmotic lysis assay. Based on the pharmacological data, putative UT-B binding sites were identified by structure-based drug design and validated by ligand-based and QSAR model. Additionally, UT-B structural and functional characteristics under inhibitors treated and untreated conditions were simulated by molecular dynamics (MD). As the result, we identified four classes of compounds with UT-B inhibitory activity and predicted a human UT-B model, based on which computative binding sites were identified and validated. A novel potential mechanism of UT-B inhibitory activity was discovered by comparing UT-B from different species. Results suggest residue PHE198 in rat and mouse UT-B might block the inhibitor migration pathway. Inhibitory mechanisms of UT-B inhibitors and the functions of key residues in UT-B were proposed. The binding site analysis provides a structural basis for lead identification and optimization of UT-B inhibitors.

Dual-Screened Vertical Circulation Wells for Groundwater Lowering in Unconfined Aquifers.

PubMed

Jin, Yulan; Holzbecher, Ekkehard; Sauter, Martin

2016-01-01

A new type of vertical circulation well (VCW) is used for groundwater dewatering at construction sites. This type of VCW consists of an abstraction screen in the upper part and an injection screen in the lower part of a borehole, whereby drawdown is achieved without net withdrawal of groundwater from the aquifer. The objective of this study is to evaluate the operation of such wells including the identification of relevant factors and parameters based on field data of a test site and comprehensive numerical simulations. The numerical model is able to delineate the drawdown of groundwater table, defined as free-surface, by coupling the arbitrary Lagrangian-Eulerian algorithm with the groundwater flow equation. Model validation is achieved by comparing the field observations with the model results. Eventually, the influences of selected well operation and aquifer parameters on drawdown and on the groundwater flow field are investigated by means of parameter sensitivity analysis. The results show that the drawdown is proportional to the flow rate, inversely proportional to the aquifer conductivity, and almost independent of the aquifer anisotropy in the direct vicinity of the well. The position of the abstraction screen has a stronger effect on drawdown than the position of the injection screen. The streamline pattern depends strongly on the separation length of the screens and on the aquifer anisotropy, but not on the flow rate and the horizontal hydraulic conductivity. © 2015, National Ground Water Association.

Recruitment of African Americans into prostate cancer screening.

PubMed

Weinrich, S P; Boyd, M D; Bradford, D; Mossa, M S; Weinrich, M

1998-01-01

Both incidence and mortality rates for prostate cancer are significantly higher in African American men than in white men. This report identifies community sites for the optimal recruitment of African American men into prostate cancer screening. A descriptive study was conducted, providing an educational program to 1369 African American men, 1264 of whom completed a survey on demographic data, prostate cancer knowledge, and prostate cancer screening history. The programs were offered at six different types of community sites, including various work sites, churches, housing projects, National Association for Advancement of Colored Persons (NAACP) sites, barber shops, and a state fairground. Free prostate cancer screening was offered to all participants. The advertised mass screening site (state fairground), the most common method used nationally to recruit African American men for cancer screening, was the least effective site, with only 16 men completing the survey. Of the 1264 men completing the survey at all community sites, 597 men (47%) did so at work sites and 438 (35%) did so at churches. Per site, the largest percentage of men who had never been screened was at work sites (n = 276, 46%) and NAACP sites (n = 22, 33.8%). The highest percentage of men who obtained free screening were at the state fairground (14 of 16), churches (256 of 438), and work sites (336 of 597). The most prostate cancers were detected at the housing projects, where 3 of 38 (7.9%) men who were screened received diagnoses of prostate cancer. To reduce prostate mortality rates in African American men, healthcare providers need to make a concerted effort to increase prostate cancer education and screening in this population. To be effective, recruitment of African American men must move from a provider/health site orientation to a consumer/community orientation. These findings indicate that recruitment strategies are more successful if efforts are based in the community or where a large number of African American men live and/or work. Because a history of screening has been shown to be a predictor for current participation, programs need to target men who have not had previous screening ever or within the last year. In addition, the large percentage of men recruited at work sites who had not been screened previously indicates an opportunity for collaboration with healthcare professionals in employee health programs. Efforts to increase participation in prostate cancer screening will be enhanced significantly by eliciting the active involvement of community leaders.

Detecting Coevolution in and among Protein Domains

PubMed Central

Yeang, Chen-Hsiang; Haussler, David

2007-01-01

Correlated changes of nucleic or amino acids have provided strong information about the structures and interactions of molecules. Despite the rich literature in coevolutionary sequence analysis, previous methods often have to trade off between generality, simplicity, phylogenetic information, and specific knowledge about interactions. Furthermore, despite the evidence of coevolution in selected protein families, a comprehensive screening of coevolution among all protein domains is still lacking. We propose an augmented continuous-time Markov process model for sequence coevolution. The model can handle different types of interactions, incorporate phylogenetic information and sequence substitution, has only one extra free parameter, and requires no knowledge about interaction rules. We employ this model to large-scale screenings on the entire protein domain database (Pfam). Strikingly, with 0.1 trillion tests executed, the majority of the inferred coevolving protein domains are functionally related, and the coevolving amino acid residues are spatially coupled. Moreover, many of the coevolving positions are located at functionally important sites of proteins/protein complexes, such as the subunit linkers of superoxide dismutase, the tRNA binding sites of ribosomes, the DNA binding region of RNA polymerase, and the active and ligand binding sites of various enzymes. The results suggest sequence coevolution manifests structural and functional constraints of proteins. The intricate relations between sequence coevolution and various selective constraints are worth pursuing at a deeper level. PMID:17983264

Phage display: concept, innovations, applications and future.

PubMed

Pande, Jyoti; Szewczyk, Magdalena M; Grover, Ashok K

2010-01-01

Phage display is the technology that allows expression of exogenous (poly)peptides on the surface of phage particles. The concept is simple in principle: a library of phage particles expressing a wide diversity of peptides is used to select those that bind the desired target. The filamentous phage M13 is the most commonly used vector to create random peptide display libraries. Several methods including recombinant techniques have been developed to increase the diversity of the library. On the other extreme, libraries with various biases can be created for specific purposes. For instance, when the sequence of the peptide that binds the target is known, its affinity and selectivity can be increased by screening libraries created with limited mutagenesis of the peptide. Phage libraries are screened for binding to synthetic or native targets. The initial screening of library by basic biopanning has been extended to column chromatography including negative screening and competition between selected phage clones to identify high affinity ligands with greater target specificity. The rapid isolation of specific ligands by phage display is advantageous in many applications including selection of inhibitors for the active and allosteric sites of the enzymes, receptor agonists and antagonists, and G-protein binding modulatory peptides. Phage display has been used in epitope mapping and analysis of protein-protein interactions. The specific ligands isolated from phage libraries can be used in therapeutic target validation, drug design and vaccine development. Phage display can also be used in conjunction with other methods. The past innovations and those to come promise a bright future for this field. Copyright © 2010 Elsevier Inc. All rights reserved.

Inventory Data Package for Hanford Assessments

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

Kincaid, Charles T.; Eslinger, Paul W.; Aaberg, Rosanne L.

2006-06-01

This document presents the basis for a compilation of inventory for radioactive contaminants of interest by year for all potentially impactive waste sites on the Hanford Site for which inventory data exist in records or could be reasonably estimated. This document also includes discussions of the historical, current, and reasonably foreseeable (1944 to 2070) future radioactive waste and waste sites; the inventories of radionuclides that may have a potential for environmental impacts; a description of the method(s) for estimating inventories where records are inadequate; a description of the screening method(s) used to select those sites and contaminants that might makemore » a substantial contribution to impacts; a listing of the remedial actions and their completion dates for waste sites; and tables showing the best estimate inventories available for Hanford assessments.« less

Identification of ER Proteins Involved in the Functional Organisation of the Early Secretory Pathway in Drosophila Cells by a Targeted RNAi Screen

PubMed Central

Kondylis, Vangelis; Tang, Yang; Fuchs, Florian; Boutros, Michael; Rabouille, Catherine

2011-01-01

Background In Drosophila, the early secretory apparatus comprises discrete paired Golgi stacks in close proximity to exit sites from the endoplasmic reticulum (tER sites), thus forming tER-Golgi units. Although many components involved in secretion have been identified, the structural components sustaining its organisation are less known. Here we set out to identify novel ER resident proteins involved in the of tER-Golgi unit organisation. Results To do so, we designed a novel screening strategy combining a bioinformatics pre-selection with an RNAi screen. We first selected 156 proteins exhibiting known or related ER retention/retrieval signals from a list of proteins predicted to have a signal sequence. We then performed a microscopy-based primary and confirmation RNAi screen in Drosophila S2 cells directly scoring the organisation of the tER-Golgi units. We identified 49 hits, most of which leading to an increased number of smaller tER-Golgi units (MG for “more and smaller Golgi”) upon depletion. 16 of them were validated and characterised, showing that this phenotype was not due to an inhibition in secretion, a block in G2, or ER stress. Interestingly, the MG phenotype was often accompanied by an increase in the cell volume. Out of 6 proteins, 4 were localised to the ER. Conclusions This work has identified novel proteins involved in the organisation of the Drosophila early secretory pathway. It contributes to the effort of assigning protein functions to gene annotation in the secretory pathway, and analysis of the MG hits revealed an enrichment of ER proteins. These results suggest a link between ER localisation, aspects of cell metabolism and tER-Golgi structural organisation. PMID:21383842

Identification of ER proteins involved in the functional organisation of the early secretory pathway in Drosophila cells by a targeted RNAi screen.

PubMed

Kondylis, Vangelis; Tang, Yang; Fuchs, Florian; Boutros, Michael; Rabouille, Catherine

2011-02-23

In Drosophila, the early secretory apparatus comprises discrete paired Golgi stacks in close proximity to exit sites from the endoplasmic reticulum (tER sites), thus forming tER-Golgi units. Although many components involved in secretion have been identified, the structural components sustaining its organisation are less known. Here we set out to identify novel ER resident proteins involved in the of tER-Golgi unit organisation. To do so, we designed a novel screening strategy combining a bioinformatics pre-selection with an RNAi screen. We first selected 156 proteins exhibiting known or related ER retention/retrieval signals from a list of proteins predicted to have a signal sequence. We then performed a microscopy-based primary and confirmation RNAi screen in Drosophila S2 cells directly scoring the organisation of the tER-Golgi units. We identified 49 hits, most of which leading to an increased number of smaller tER-Golgi units (MG for "more and smaller Golgi") upon depletion. 16 of them were validated and characterised, showing that this phenotype was not due to an inhibition in secretion, a block in G2, or ER stress. Interestingly, the MG phenotype was often accompanied by an increase in the cell volume. Out of 6 proteins, 4 were localised to the ER. This work has identified novel proteins involved in the organisation of the Drosophila early secretory pathway. It contributes to the effort of assigning protein functions to gene annotation in the secretory pathway, and analysis of the MG hits revealed an enrichment of ER proteins. These results suggest a link between ER localisation, aspects of cell metabolism and tER-Golgi structural organisation.

Methodology and Estimates of Scour at Selected Bridge Sites in Alaska

USGS Publications Warehouse

Heinrichs, Thomas A.; Kennedy, Ben W.; Langley, Dustin E.; Burrows, Robert L.

2001-01-01

The U.S. Geological Survey estimated scour depths at 325 bridges in Alaska as part of a cooperative agreement with the Alaska Department of Transportation and Public Facilities. The department selected these sites from approximately 806 State-owned bridges as potentially susceptible to scour during extreme floods. Pier scour and contraction scour were computed for the selected bridges by using methods recommended by the Federal Highway Administration. The U.S. Geological Survey used a four-step procedure to estimate scour: (1) Compute magnitudes of the 100- and 500-year floods. (2) Determine cross-section geometry and hydraulic properties for each bridge site. (3) Compute the water-surface profile for the 100- and 500-year floods. (4) Compute contraction and pier scour. This procedure is unique because the cross sections were developed from existing data on file to make a quantitative estimate of scour. This screening method has the advantage of providing scour depths and bed elevations for comparison with bridge-foundation elevations without the time and expense of a field survey. Four examples of bridge-scour analyses are summarized in the appendix.

Offshore rectenna feasbility

NASA Technical Reports Server (NTRS)

Freeman, J. W.; Hervey, D.; Glaser, P.

1980-01-01

A preliminary study of the feasibility and cost of an offshore rectenna to serve the upper metropolitan east coast was performed. A candidate site at which to build a 5 GW rectenna was selected on the basis of proximity to load centers, avoidance of shipping lanes, sea floor terrain, and relocated conditions. Several types of support structures were selected for study based initially on the reference system rectenna concept of a wire mesh ground screen and dipoles each with its own rectifier and filter circuits. Possible secondary uses of an offshore rectenna were examined and are evaluated.

Spatial and temporal patterns of micropollutants upstream and downstream of 24 WWTPs across Switzerland

NASA Astrophysics Data System (ADS)

Spycher, Barbara; Deuber, Fabian; Kistler, David; Burdon, Frank; Reyes, Marta; Alder, Alfredo C.; Joss, Adriano; Eggen, Rik; Singer, Heinz; Stamm, Christian

2015-04-01

Treated wastewater is an important source of micropollutants in many streams. These chemicals consist of very diverse set of compounds that may vary in space and time. In order to improve our understanding of such spatio-temporal patterns of micropollutants in surface waters, we compared upstream and downstream locations at 24 sites across the Swiss Plateau and Jura (12 sites in the 2013 campaign, 12 sites during the 2014 campaign). Each site represents the most upstream treatment plant in the corresponding catchment. This survey is part of the interdisciplinary, Eawag-wide research project EcoImpact that aims at elucidating the ecological effects of micropollutants on stream ecosystems. In 2013, a broad analytical screening was applied to samples collected during winter (January) and summer conditions (June). Based in these results, the bi-monthly samples obtained in 2014 were analysed for a set of about 60 selected organic micropollutants and 10 heavy metals. The screening results demonstrate that generally pharmaceuticals, artificial sweeteners and corrosion inhibitors make up the largest part of the organic micropollutants. Pesticides including biocides and plant protection products are also regularly found but at lower concentrations. This presentation will analyse the variability of the micropollutant patterns across the different sites and how upstream conditions and the wastewater composition changes with season.

CARDIOVASCULAR SCREENING OF YOUNG ATHLETES: A REVIEW OF ECONOMIC EVALUATIONS.

PubMed

Gerkens, Sophie; Van Brabandt, Hans; Desomer, Anja; Leonard, Christian; Neyt, Mattias

2017-01-01

Some experts have promoted preparticipative cardiovascular screening programs for young athletes and have claimed that such programs were cost-effective without performing a critical analysis of studies supporting this statement. In this systematic review, a critical assessment of economic evaluations on these programs is performed to determine if they really provide value for money. A systematic review of economic evaluations was performed on December 24, 2014. Web sites of health technology assessment agencies, the Cochrane database of systematic review, the National Health Service Economic Evaluation Database of the Cochrane Library, EMBASE, Medline, Psychinfo, and EconLit were searched to retrieve (reviews of) economic evaluations. No language or time restrictions were imposed and predefined selection criteria were used. Selected studies were critically assessed applying a structured data extraction sheet. Five relevant economic evaluations were critically assessed. Results of these studies were mixed. However, those in favor of screening made (methodological) incorrect choices, of which the most important one was not taking into account a no-screening alternative as comparator. Compared with no screening, other strategies (history and physical examination or history and physical examination plus electrocardiogram) were not considered cost-effective. Results of primary economic evaluations should not be blindly copied without critical assessment. Economic evaluations in this field lack the support of robust evidence. Negative consequences of screening (false positive findings, overtreatment) should also be taken into account and may cause more harm than good. A mass screening of young athletes for cardiovascular diseases does not provide value for money and should be discouraged.

Improvements in osteoporosis testing and care are found following the wide scale implementation of the Ontario Fracture Clinic Screening Program: An interrupted time series analysis.

PubMed

Beaton, Dorcas E; Mamdani, Muhammad; Zheng, Hong; Jaglal, Susan; Cadarette, Suzanne M; Bogoch, Earl R; Sale, Joanna E M; Sujic, Rebeka; Jain, Ravi

2017-12-01

We evaluated a system-wide impact of a health intervention to improve treatment of osteoporosis after a fragility fracture. The intervention consisted of assigning a screening coordinator to selected fracture clinics to identify, educate, and follow up with fragility fracture patients and inform their physicians of the need to evaluate bone health. Thirty-seven hospitals in the province of Ontario (Canada) were assigned a screening coordinator. Twenty-three similar hospitals were control sites. All hospitals had orthopedic services and handled moderate-to-higher volumes of fracture patients. Administrative health data were used to evaluate the impact of the intervention.Fragility fracture patients (≥50 years; hip, humerus, forearm, spine, or pelvis fracture) were identified from administrative health records. Cases were fractures treated at 1 of the 37 hospitals assigned a coordinator. Controls were the same types of fractures at the control sites. Data were assembled for 20 quarters before and 10 quarters after the implementation (from January 2002 to March 2010). To test for a shift in trends, we employed an interrupted time series analysis-a study design used to evaluate the longitudinal effects of interventions, through regression modelling. The primary outcome measure was bone mineral density (BMD) testing. Osteoporosis medication initiation and persistence rates were secondary outcomes in a subset of patients ≥66 years of age.A total of 147,071 patients were used in the analysis. BMD testing rates increased from 17.0% pre-intervention to 20.9% post-intervention at intervention sites (P < .01) compared with no change at control sites (14.9% and 14.9%, P = .33). Medication initiation improved significantly at intervention sites (21.6-23.97%; P = .02) but not at control sites (17.5-18.5%; P = .27). Persistence with bisphosphonates decreased at all sites, from 59.9% to 56.4% at intervention sites (P = .02) and more so from 62.3% to 54.2% at control sites (P < .01) using 50% proportion of days covered (PDC 50).Significant improvements in BMD testing and treatment initiation were observed after the initiation of a coordinator-based screening program to improve osteoporosis management following fragility fracture.

Improvements in osteoporosis testing and care are found following the wide scale implementation of the Ontario Fracture Clinic Screening Program

PubMed Central

Beaton, Dorcas E.; Mamdani, Muhammad; Zheng, Hong; Jaglal, Susan; Cadarette, Suzanne M.; Bogoch, Earl R.; Sale, Joanna E. M.; Sujic, Rebeka; Jain, Ravi

2017-01-01

Abstract We evaluated a system-wide impact of a health intervention to improve treatment of osteoporosis after a fragility fracture. The intervention consisted of assigning a screening coordinator to selected fracture clinics to identify, educate, and follow up with fragility fracture patients and inform their physicians of the need to evaluate bone health. Thirty-seven hospitals in the province of Ontario (Canada) were assigned a screening coordinator. Twenty-three similar hospitals were control sites. All hospitals had orthopedic services and handled moderate-to-higher volumes of fracture patients. Administrative health data were used to evaluate the impact of the intervention. Fragility fracture patients (≥50 years; hip, humerus, forearm, spine, or pelvis fracture) were identified from administrative health records. Cases were fractures treated at 1 of the 37 hospitals assigned a coordinator. Controls were the same types of fractures at the control sites. Data were assembled for 20 quarters before and 10 quarters after the implementation (from January 2002 to March 2010). To test for a shift in trends, we employed an interrupted time series analysis—a study design used to evaluate the longitudinal effects of interventions, through regression modelling. The primary outcome measure was bone mineral density (BMD) testing. Osteoporosis medication initiation and persistence rates were secondary outcomes in a subset of patients ≥66 years of age. A total of 147,071 patients were used in the analysis. BMD testing rates increased from 17.0% pre-intervention to 20.9% post-intervention at intervention sites (P < .01) compared with no change at control sites (14.9% and 14.9%, P = .33). Medication initiation improved significantly at intervention sites (21.6–23.97%; P = .02) but not at control sites (17.5–18.5%; P = .27). Persistence with bisphosphonates decreased at all sites, from 59.9% to 56.4% at intervention sites (P = .02) and more so from 62.3% to 54.2% at control sites (P < .01) using 50% proportion of days covered (PDC 50). Significant improvements in BMD testing and treatment initiation were observed after the initiation of a coordinator-based screening program to improve osteoporosis management following fragility fracture. PMID:29310418

10 CFR 960.3-2-1 - Site screening for potentially acceptable sites.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Section 960.3-2-1 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-1 Site screening for... technical guidelines can exist in the same land unit, the DOE shall seek to evaluate the composite...

10 CFR 960.3-2-1 - Site screening for potentially acceptable sites.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Section 960.3-2-1 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-1 Site screening for... technical guidelines can exist in the same land unit, the DOE shall seek to evaluate the composite...

10 CFR 960.3-2-1 - Site screening for potentially acceptable sites.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Section 960.3-2-1 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-1 Site screening for... technical guidelines can exist in the same land unit, the DOE shall seek to evaluate the composite...

Docking and scoring in virtual screening for drug discovery: methods and applications.

PubMed

Kitchen, Douglas B; Decornez, Hélène; Furr, John R; Bajorath, Jürgen

2004-11-01

Computational approaches that 'dock' small molecules into the structures of macromolecular targets and 'score' their potential complementarity to binding sites are widely used in hit identification and lead optimization. Indeed, there are now a number of drugs whose development was heavily influenced by or based on structure-based design and screening strategies, such as HIV protease inhibitors. Nevertheless, there remain significant challenges in the application of these approaches, in particular in relation to current scoring schemes. Here, we review key concepts and specific features of small-molecule-protein docking methods, highlight selected applications and discuss recent advances that aim to address the acknowledged limitations of established approaches.

Unifying Screening Processes Within the PROSPR Consortium: A Conceptual Model for Breast, Cervical, and Colorectal Cancer Screening

PubMed Central

Kim, Jane J.; Schapira, Marilyn M.; Tosteson, Anna N. A.; Zauber, Ann G.; Geiger, Ann M.; Kamineni, Aruna; Weaver, Donald L.; Tiro, Jasmin A.

2015-01-01

General frameworks of the cancer screening process are available, but none directly compare the process in detail across different organ sites. This limits the ability of medical and public health professionals to develop and evaluate coordinated screening programs that apply resources and population management strategies available for one cancer site to other sites. We present a trans-organ conceptual model that incorporates a single screening episode for breast, cervical, and colorectal cancers into a unified framework based on clinical guidelines and protocols; the model concepts could be expanded to other organ sites. The model covers four types of care in the screening process: risk assessment, detection, diagnosis, and treatment. Interfaces between different provider teams (eg, primary care and specialty care), including communication and transfer of responsibility, may occur when transitioning between types of care. Our model highlights across each organ site similarities and differences in steps, interfaces, and transitions in the screening process and documents the conclusion of a screening episode. This model was developed within the National Cancer Institute–funded consortium Population-based Research Optimizing Screening through Personalized Regimens (PROSPR). PROSPR aims to optimize the screening process for breast, cervical, and colorectal cancer and includes seven research centers and a statistical coordinating center. Given current health care reform initiatives in the United States, this conceptual model can facilitate the development of comprehensive quality metrics for cancer screening and promote trans-organ comparative cancer screening research. PROSPR findings will support the design of interventions that improve screening outcomes across multiple cancer sites. PMID:25957378

Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge

NASA Astrophysics Data System (ADS)

Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Santos-Martins, Diogo; Olson, Arthur J.

2014-04-01

To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational structure-based drug discovery tools and strategies that are being developed to advance the goals of the newly created, multi-institution, NIH-funded center called the "HIV Interaction and Viral Evolution Center".

Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge.

PubMed

Perryman, Alexander L; Santiago, Daniel N; Forli, Stefano; Martins, Diogo Santos; Olson, Arthur J

2014-04-01

To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational structure-based drug discovery tools and strategies that are being developed to advance the goals of the newly created, multi-institution, NIH-funded center called the "HIV Interaction and Viral Evolution Center".

Application of virtual screening and molecular dynamics for the analysis of selectivity of inhibitors of HU proteins targeted to the DNA-recognition site

NASA Astrophysics Data System (ADS)

Talyzina, A. A.; Agapova, Yu. K.; Podshivalov, D. D.; Timofeev, V. I.; Sidorov-Biryukov, D. D.; Rakitina, T. V.

2017-11-01

DNA-Binding HU proteins are essential for the maintenance of genomic DNA supercoiling and compaction in prokaryotic cells and are promising pharmacological targets for the design of new antibacterial agents. The virtual screening for low-molecular-weight compounds capable of specifically interacting with the DNA-recognition loop of the HU protein from the mycoplasma Spiroplasma melliferum was performed. The ability of the initially selected ligands to form stable complexes with the protein target was assessed by molecular dynamics simulation. One compound, which forms an unstable complex, was eliminated by means of a combination of computational methods, resulting in a decrease in the number of compounds that will pass to the experimental test phase. This approach can be used to solve a wide range of problems related to the search for and validation of low-molecular-weight inhibitors specific for a particular protein target.

The Patroon Creek Contamination Migration Investigation

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

Dufek, K.; Zafran, A.; Moore, J.T.

2006-07-01

Shaw performed a Site Investigation (SI) for sediment within the Unnamed Tributary of the Patroon Creek, a section of the Patroon Creek, and the Three Mile Reservoir as part of the overall contract with the United States Army Corps of Engineers (USACE) to remediate the Colonie Formerly Utilized Sites Remedial Action Program (FUSRAP) Site. The Unnamed Tributary formerly flowed through the former Patroon Lake, which was located on the main site property and was used as a landfill for radiological and chemical wastes. The objective of the investigation was to determine the absence/presence of radioactive contamination within the three Areasmore » of Concern (AOC). In order to accomplish this objective, Shaw assembled a team to produce a Technical Memorandum that provided an in-depth understanding of the environmental conditions related to the Patroon Creek. Upon completion and analysis of the Technical Memorandum, a Conceptual Site Model (CSM) was constructed and a Technical Planning Program (TPP) was held to develop a Sediment Investigation Work Plan and Sediment Investigation Sampling and Analysis Plan. A total of 32 sample locations were analyzed using on-site direct gamma scans with a Pancake Geiger-Mueller (PGM) instrument for screening purposes and samples were analyzed at on-site and off-site laboratories. The highest interval from each core scan was selected for on-site analysis utilizing a High Purity Germanium (HPGe) detector. Eight of these samples were sent off-site for gamma/alpha spectroscopy confirmation. The data collected during the SI indicated that the U-238 cleanup criterion was exceeded in sediment samples collected from two locations within the Unnamed Tributary but not in downstream sections of Patroon Creek or Three Mile Reservoir. Future actions for impacted sediment in the Unnamed Tributary will be further evaluated. Concentrations of U-238 and Th-232 in all other off-site sediment samples collected from the Unnamed Tributary, Patroon Creek, and the Three Mile Reservoir indicate that no further action is required in these areas. The data was also compared to ecological screening criteria. None of the contaminants of concern (U-238, Th-232, and U-235) had concentrations exceeding the screening values. The evaluation indicates no adverse impacts to ecological receptors. (authors)« less

Infinium HumanMethylation450 BeadChip

Cancer.gov

The HumanMethylation450 BeadChip offers a unique combination of comprehensive, expert-selected coverage and high throughput at a low price, making it ideal for screening large sample populations such as those used in genome-wide association study cohorts. By providing quantitative methylation measurement at the single-CpG–site level for normal and FFPE samples, this assay offers powerful resolution for understanding epigenetic changes.

Screening for cardiac disease in potential recruits to the British Army.

PubMed

Cox, Andrew T; Cameron-Smith, M; Folkes, F; Sharma, S; Boos, C

2015-09-01

The British Army screens potential recruits for disease, including cardiovascular disease, at the pre-employment medical assessment in the Army Selection Centres. The epidemiology of cardiovascular disease in the Armed Forces coupled with the high physical demand placed on the cardiovascular system, often in remote locations make screening desirable. This is particularly pertinent as servicemen and women die from cardiovascular disease each year. To evaluate this particular screening system it is essential to understand the aim of the system, how it is designed and how screening systems in general are evaluated. The efficacy of a screening test is quantified using the measurements of sensitivity, specificity and likelihood ratios. These measurements are defined and the pitfalls associated with evaluating a screening system are described. The different screening tests used to identify cardiac disease and their individual strengths and weaknesses, are illustrated. Finally the article reviews the previous British Army recruit cardiac screening system, that used a stereotyped history and physical examination and the newer system that replaced it, which includes the incorporation of the 12-lead ECG and on site echocardiography in individuals revealing abnormalities on history, examination or ECG. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Influence of qualitative research on women's health screening guidelines.

PubMed

Abadir, Anna Maria; Lang, Ariella; Klein, Talia; Abenhaim, Haim Arie

2014-01-01

Considerable time and resources are allocated to carry out qualitative research. The purpose of our study was to evaluate the availability of qualitative research on women's health screening and assess its influence on screening practice guidelines in the United States, Canada, and the United Kingdom. Medline, CINHAL, and WEB of Science databases were used to identify the availability of qualitative research conducted in the past 15 years on 3 different women's health screening topics: cervical cancer screening, breast cancer screening, and prenatal first-trimester screening. Key national practice guidelines on women's health screening were selected using the National Guideline Clearinghouse web site. Bibliometric analysis was used to determine the frequency of qualitative references cited in the guidelines. A total of 272 qualitative research papers on women's health screening was identified: 109 on cervical cancer screening, 104 on breast cancer screening, and 59 on prenatal first-trimester screening. The qualitative studies focused on health care provider perspectives as well as ethical, ethnographic, psychological, and social issues surrounding screening. Fifteen national clinical practice guidelines on women's health screening were identified. A total of 943 references was cited, only 2 of which comprised of qualitative research cited by only 1 clinical practice guideline. Although there is considerable qualitative research that has been carried out on women's health screening, its incorporation into clinical practice guidelines is minimal. Further exploration of the disconnect between the two is important for enhancing knowledge translation of qualitative research within clinical practice. Copyright © 2014 Mosby, Inc. All rights reserved.

MX Siting Investigation. Prime Characterization Sites Central High Plains Candidate Siting Province.

DTIC Science & Technology

1979-02-15

information obtained from these studies , in combination with data obtained in the Screen- ing studies , has been used for geotechnical ranking (FN-TR-25). I...Plains Candi- date Siting Province (CSP), one of six provinces included in the geotechnical Characterization studies . The location of the sites within...remaining after Intermediate Screening were divided into CSPs based on similar geotechnical characteristics. Intermediate Screening studies (FN-TR-17

Endoscopy in screening for digestive cancer

PubMed Central

Lambert, René

2012-01-01

The aim of this study is to describe the role of endoscopy in detection and treatment of neoplastic lesions of the digestive mucosa in asymptomatic persons. Esophageal squamous cell cancer occurs in relation to nutritional deficiency and alcohol or tobacco consumption. Esophageal adenocarcinoma develops in Barrett’s esophagus, and stomach cancer in chronic gastric atrophy with Helicobacter pylori infection. Colorectal cancer is favoured by a high intake in calories, excess weight, low physical activity. In opportunistic or individual screening endoscopy is the primary detection procedure offered to an asymptomatic individual. In organized or mass screening proposed by National Health Authorities to a population, endoscopy is performed only in persons found positive to a filter selection test. The indications of primary upper gastrointestinal endoscopy and colonoscopy in opportunistic screening are increasingly developing over the world. Organized screening trials are proposed in some regions of China at high risk for esophageal cancer; the selection test is cytology of a balloon or sponge scrapping; they are proposed in Japan for stomach cancer with photofluorography as a selection test; and in Europe, America and Japan; for colorectal cancer with the fecal occult blood test as a selection test. Organized screening trials in a country require an evaluation: the benefit of the intervention assessed by its impact on incidence and on the 5 year survival for the concerned tumor site; in addition a number of bias interfering with the evaluation have to be controlled. Drawbacks of screening are in the morbidity of the diagnostic and treatment procedures and in overdetection of none clinically relevant lesions. The strategy of endoscopic screening applies to early cancer and to benign adenomatous precursors of adenocarcinoma. Diagnostic endoscopy is conducted in 2 steps: at first detection of an abnormal area through changes in relief, in color or in the course of superficial capillaries; then characterization of the morphology of the lesion according to the Paris classification and prediction of the risk of malignancy and depth of invasion, with the help of chromoscopy, magnification and image processing with neutrophil bactericidal index or FICE. Then treatment decision offers 3 options according to histologic prediction: abstention, endoscopic resection, surgery. The rigorous quality control of endoscopy will reduce the miss rate of lesions and the occurrence of interval cancer. PMID:23293721

A Randomized Controlled Trial of a Tailored Interactive Computer-Delivered Intervention to Promote Colorectal Cancer Screening: Sometimes More is Just the Same

PubMed Central

Bartholomew, Leona K.; McQueen, Amy; Bettencourt, Judy L.; Greisinger, Anthony; Coan, Sharon P.; Lairson, David; Chan, Wenyaw; Hawley, S. T.; Myers, R. E.

2012-01-01

Background There have been few studies of tailored interventions to promote colorectal cancer (CRC) screening. Purpose We conducted a randomized trial of a tailored, interactive intervention to increase CRC screening. Methods Patients 50–70 years completed a baseline survey, were randomized to one of three groups, and attended a wellness exam after being exposed to a tailored intervention about CRC screening (tailored group), a public web site about CRC screening (web site group), or no intervention (survey-only group). The primary outcome was completion of any recommended CRC screening by 6 months. Results There was no statistically significant difference in screening by 6 months: 30%, 31%, and 28% of the survey-only, web site, and tailored groups were screened. Exposure to the tailored intervention was associated with increased knowledge and CRC screening self-efficacy at 2 weeks and 6 months. Family history, prior screening, stage of change, and physician recommendation moderated the intervention effects. Conclusions A tailored intervention was not more effective at increasing screening than a public web site or only being surveyed. PMID:21271365

Multiple receptor-ligand based pharmacophore modeling and molecular docking to screen the selective inhibitors of matrix metalloproteinase-9 from natural products.

PubMed

Gao, Qi; Wang, Yijun; Hou, Jiaying; Yao, Qizheng; Zhang, Ji

2017-07-01

Matrix metalloproteinase-9 (MMP-9) is an attractive target for cancer therapy. In this study, the pharmacophore model of MMP-9 inhibitors is built based on the experimental binding structures of multiple receptor-ligand complexes. It is found that the pharmacophore model consists of six chemical features, including two hydrogen bond acceptors, one hydrogen bond donor, one ring aromatic regions, and two hydrophobic (HY) features. Among them, the two HY features are especially important because they can enter the S1' pocket of MMP-9 which determines the selectivity of MMP-9 inhibitors. The reliability of pharmacophore model is validated based on the two different decoy sets and relevant experimental data. The virtual screening, combining pharmacophore model with molecular docking, is performed to identify the selective MMP-9 inhibitors from a database of natural products. The four novel MMP-9 inhibitors of natural products, NP-000686, NP-001752, NP-014331, and NP-015905, are found; one of them, NP-000686, is used to perform the experiment of in vitro bioassay inhibiting MMP-9, and the IC 50 value was estimated to be only 13.4 µM, showing the strongly inhibitory activity of NP-000686 against MMP-9, which suggests that our screening results should be reliable. The binding modes of screened inhibitors with MMP-9 active sites were discussed. In addition, the ADMET properties and physicochemical properties of screened four compounds were assessed. The found MMP-9 inhibitors of natural products could serve as the lead compounds for designing the new MMP-9 inhibitors by carrying out structural modifications in the future.

Identification of two integration sites in favor of transgene expression in Trichoderma reesei.

PubMed

Qin, Lina; Jiang, Xianzhang; Dong, Zhiyang; Huang, Jianzhong; Chen, Xiuzhen

2018-01-01

The ascomycete fungus Trichoderma reesei was widely used as a biotechnological workhorse for production of cellulases and recombinant proteins due to its large capacity of protein secretion. Transgenesis by random integration of a gene of interest (GOI) into the genome of T. reesei can generate series of strains that express different levels of the indicated transgene. The insertion site of the GOI plays an important role in the ultimate production of the targeted proteins. However, so far no systematic studies have been made to identify transgene integration loci for optimal expression of the GOI in T. reesei . Currently, only the locus of exocellobiohydrolases I encoding gene ( cbh1) is widely used as a promising integration site to lead to high expression level of the GOI. No additional sites associated with efficient gene expression have been characterized. To search for gene integration sites that benefit for the secreted expression of GOI, the food-and-mouth disease virus 2A protein was applied for co-expression of an Aspergillus niger lipA gene and Discosoma sp. DsRed1 gene in T. reesei, by random integration of the expression cassette into the genome. We demonstrated that the fluorescent intensity of RFP (red fluorescent protein) inside of the cell was well correlated with the secreted lipase yields, based on which, we successfully developed a high-throughput screening method to screen strains with relatively higher secreted expression of the GOI (in this study, lipase). The copy number and the insertion sites of the transgene were investigated among the selected highly expressed strains. Eventually, in addition to cbh1 gene locus, two other genome insertion loci that efficiently facilitate gene expression in T. reesei were identified. We have successfully developed a high-throughput screening method to screen strains with optimal expression of the indicated secreted proteins in T. reesei . Moreover, we identified two optimal genome loci for transgene expression, which could provide new approach to modulate gene expression levels while retaining the indicated promoter and culture conditions.

Structural basis for ligand recognition at the benzodiazepine binding site of GABAA alpha 3 receptor, and pharmacophore-based virtual screening approach.

PubMed

Vijayan, R S K; Ghoshal, Nanda

2008-10-01

Given the heterogeneity of GABA(A) receptor, the pharmacological significance of identifying subtype selective modulators is increasingly being recognized. Thus, drugs selective for GABA(A) alpha(3) receptors are expected to display fewer side effects than the drugs presently in clinical use. Hence we carried out 3D QSAR (three-dimensional quantitative structure-activity relationship) studies on a series of novel GABA(A) alpha(3) subtype selective modulators to gain more insight into subtype affinity. To identify the 3D functional attributes required for subtype selectivity, a chemical feature-based pharmacophore, primarily based on selective ligands representing diverse structural classes was generated. The obtained pseudo receptor model of the benzodiazepine binding site revealed a binding mode akin to "Message-Address" concept. Scaffold hopping was carried out across multi-conformational May Bridge database for the identification of novel chemotypes. Further a focused data reduction approach was employed to choose a subset of enriched compounds based on "Drug likeness" and "Similarity-based" methods. These results taken together could provide impetus for rational design and optimization of more selective and high affinity leads with a potential to have decreased adverse effects.

Unifying screening processes within the PROSPR consortium: a conceptual model for breast, cervical, and colorectal cancer screening.

PubMed

Beaber, Elisabeth F; Kim, Jane J; Schapira, Marilyn M; Tosteson, Anna N A; Zauber, Ann G; Geiger, Ann M; Kamineni, Aruna; Weaver, Donald L; Tiro, Jasmin A

2015-06-01

General frameworks of the cancer screening process are available, but none directly compare the process in detail across different organ sites. This limits the ability of medical and public health professionals to develop and evaluate coordinated screening programs that apply resources and population management strategies available for one cancer site to other sites. We present a trans-organ conceptual model that incorporates a single screening episode for breast, cervical, and colorectal cancers into a unified framework based on clinical guidelines and protocols; the model concepts could be expanded to other organ sites. The model covers four types of care in the screening process: risk assessment, detection, diagnosis, and treatment. Interfaces between different provider teams (eg, primary care and specialty care), including communication and transfer of responsibility, may occur when transitioning between types of care. Our model highlights across each organ site similarities and differences in steps, interfaces, and transitions in the screening process and documents the conclusion of a screening episode. This model was developed within the National Cancer Institute-funded consortium Population-based Research Optimizing Screening through Personalized Regimens (PROSPR). PROSPR aims to optimize the screening process for breast, cervical, and colorectal cancer and includes seven research centers and a statistical coordinating center. Given current health care reform initiatives in the United States, this conceptual model can facilitate the development of comprehensive quality metrics for cancer screening and promote trans-organ comparative cancer screening research. PROSPR findings will support the design of interventions that improve screening outcomes across multiple cancer sites. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Using MCDA and GIS for hazardous waste landfill siting considering land scarcity for waste disposal.

PubMed

De Feo, Giovanni; De Gisi, Sabino

2014-11-01

The main aim of this study was to develop a procedure that minimizes the wasting of space for the siting of hazardous waste landfills as part of a solid waste management system. We wanted to tackle the shortage of land for waste disposal that is a serious and growing problem in most large urban regions. The procedure combines a multi-criteria decision analysis (MCDA) approach with a geographical information system (GIS). The GIS was utilised to obtain an initial screening in order to eliminate unsuitable areas, whereas the MCDA was developed to select the most suitable sites. The novelty of the proposed siting procedure is the introduction of a new screening phase before the macro-siting step aimed at producing a "land use map of potentially suitable areas" for the siting of solid waste facilities which simultaneously takes into consideration all plant types. The issue of obtaining sites evaluations of a specific facility was coupled with the issue of not wasting land appropriate to facilitate other types of waste management options. In the developed case study, the use of an innovative criteria weighting tool (the "Priority Scale") in combination with the Analytic Hierarchy Process was useful to easier define the priorities of the evaluation criteria in comparison with other classic methods such as the Paired Comparison Technique in combination with the Simple Additive Weighting method. Copyright © 2014 Elsevier Ltd. All rights reserved.

Screening for the Pesticides Atrazine, Chlorpyrifos, Diazinon, Metolachlor, and Simazine in Selected Michigan Streams, March-November 2005

USGS Publications Warehouse

Fogarty, Lisa R.; Duris, Joseph W.

2007-01-01

From March through November 2005, the U.S. Geological Survey, in cooperation with the Michigan Department of Environmental Quality (MDEQ), did a statewide screening to aid in understanding the occurrence and distribution of selected pesticides in Michigan streams. Stream-water samples were collected from 23 sites throughout Michigan. In all, 320 water samples were analyzed by use of rapid immunoassay methods for the herbicides atrazine, metolachlor, and simazine and the insecticides chlorpyrifos and diazinon. On one occasion (June, 2005), atrazine concentrations exceeded the Michigan water-quality value (7.3 micrograms per liter) at the Black River in St. Clair County. Neither chlorpyrifos nor diazinon was detected during April through September. MDEQ detected chlorpyrifos in streams throughout the state in November. Herbicide concentrations were highest in samples influenced by intensive agriculture; however, median herbicide concentrations were similar among agricultural and urban sites. Concentrations of herbicides were very low to undetected in undeveloped areas. Seasonal patterns were also evident during the sampling period. Increased concentrations generally occurred in late spring to early summer. At 11 sites, daily sampling was done every day for 5 days following a rainfall after herbicide application in the area. Substantial changes in concentrations of herbicides - greater than tenfold from the previous day - were observed during the daily sampling. No consistent relation was found between concentration and streamflow. Results of this study may be used to aid in the development of a more comprehensive pesticide monitoring study for the State of Michigan.

Fragment screening using capillary electrophoresis (CEfrag) for hit identification of heat shock protein 90 ATPase inhibitors.

PubMed

Austin, Carol; Pettit, Simon N; Magnolo, Sharon K; Sanvoisin, Jonathan; Chen, Wenjie; Wood, Stephen P; Freeman, Lauren D; Pengelly, Reuben J; Hughes, Dallas E

2012-08-01

CEfrag is a new fragment screening technology based on affinity capillary electrophoresis (ACE). Here we report on the development of a mobility shift competition assay using full-length human heat shock protein 90α (Hsp90α), radicicol as the competitor probe ligand, and successful screening of the Selcia fragment library. The CEfrag assay was able to detect weaker affinity (IC(50) >500 µM) fragments than were detected by a fluorescence polarization competition assay using FITC-labeled geldanamycin. The binding site of selected fragments was determined by co-crystallization with recombinant Hsp90α N-terminal domain and X-ray analysis. The results of this study confirm that CEfrag is a sensitive microscale technique enabling detection of fragments binding to the biological target in near-physiological solution.

Evaluating the adequacy of a reference site pool for ecological assessments in environmentally complex regions

USGS Publications Warehouse

Ode, Peter R.; Rehn, Andrew C.; Mazor, Raphael D.; Schiff, Kenneth C.; Stein, Eric D.; May, Jason; Brown, Larry R.; Herbst, David B.; Gillette, D.D.; Lunde, Kevin; Hawkins, Charles P.

2016-01-01

Many advances in the field of bioassessment have focused on approaches for objectively selecting the pool of reference sites used to establish expectations for healthy waterbodies, but little emphasis has been placed on ways to evaluate the suitability of the reference-site pool for its intended applications (e.g., compliance assessment vs ambient monitoring). These evaluations are critical because an inadequately evaluated reference pool may bias assessments in some settings. We present an approach for evaluating the adequacy of a reference-site pool for supporting biotic-index development in environmentally heterogeneous and pervasively altered regions. We followed common approaches for selecting sites with low levels of anthropogenic stress to screen 1985 candidate stream reaches to create a pool of 590 reference sites for assessing the biological integrity of streams in California, USA. We assessed the resulting pool of reference sites against 2 performance criteria. First, we evaluated how well the reference-site pool represented the range of natural gradients present in the entire population of streams as estimated by sites sampled through probabilistic surveys. Second, we evaluated the degree to which we were successful in rejecting sites influenced by anthropogenic stress by comparing biological metric scores at reference sites with the most vs fewest potential sources of stress. Using this approach, we established a reference-site pool with low levels of human-associated stress and broad coverage of environmental heterogeneity. This approach should be widely applicable and customizable to particular regional or programmatic needs.

Discovery of Novel New Delhi Metallo-β-Lactamases-1 Inhibitors by Multistep Virtual Screening

PubMed Central

Wang, Xuequan; Lu, Meiling; Shi, Yang; Ou, Yu; Cheng, Xiaodong

2015-01-01

The emergence of NDM-1 containing multi-antibiotic resistant "Superbugs" necessitates the needs of developing of novel NDM-1inhibitors. In this study, we report the discovery of novel NDM-1 inhibitors by multi-step virtual screening. From a 2,800,000 virtual drug-like compound library selected from the ZINC database, we generated a focused NDM-1 inhibitor library containing 298 compounds of which 44 chemical compounds were purchased and evaluated experimentally for their ability to inhibit NDM-1 in vitro. Three novel NDM-1 inhibitors with micromolar IC50 values were validated. The most potent inhibitor, VNI-41, inhibited NDM-1 with an IC50 of 29.6 ± 1.3 μM. Molecular dynamic simulation revealed that VNI-41 interacted extensively with the active site. In particular, the sulfonamide group of VNI-41 interacts directly with the metal ion Zn1 that is critical for the catalysis. These results demonstrate the feasibility of applying virtual screening methodologies in identifying novel inhibitors for NDM-1, a metallo-β-lactamase with a malleable active site and provide a mechanism base for rational design of NDM-1 inhibitors using sulfonamide as a functional scaffold. PMID:25734558

Assertions of Japanese Websites for and Against Cancer Screening: a Text Mining Analysis

PubMed

Okuhara, Tsuyoshi; Ishikawa, Hirono; Okada, Masahumi; Kato, Mio; Kiuchi, Takahiro

2017-04-01

Background: Cancer screening rates are lower in Japan than in Western countries such as the United States and the United Kingdom. While health professionals publish pro-cancer-screening messages online to encourage proactive seeking for screening, anti-screening activists use the same medium to warn readers against following guidelines. Contents of pro- and anti-cancer-screening sites may contribute to readers’ acceptance of one or the other position. We aimed to use a text-mining method to examine frequently appearing contents on sites for and against cancer screening. Methods: We conducted online searches in December 2016 using two major search engines in Japan (Google Japan and Yahoo! Japan). Targeted websites were classified as “pro”, “anti”, or “neutral” depending on their claims, with the author(s) classified as “health professional”, “mass media”, or “layperson”. Text-mining analyses were conducted, and statistical analysis was performed using the chi-square test. Results: Of the 169 websites analyzed, the top-three most frequently appearing content topics in pro sites were reducing mortality via cancer screening, benefits of early detection, and recommendations for obtaining detailed examination. The top three most frequent in anti-sites were harm from radiation exposure, non-efficacy of cancer screening, and lack of necessity of early detection. Anti-sites also frequently referred to a well-known Japanese radiologist, Makoto Kondo, who rejects the standard forms of cancer care. Conclusion: Our findings should enable authors of pro-cancer-screening sites to write to counter misleading anti-cancer-screening messages and facilitate dissemination of accurate information. Creative Commons Attribution License

A Chemogenomic Analysis of Ionization Constants - Implications for Drug Discovery

PubMed Central

Manallack, David T.; Prankerd, Richard J.; Nassta, Gemma C.; Ursu, Oleg; Oprea, Tudor I.; Chalmers, David K.

2013-01-01

Chemogenomics methods seek to characterize the interaction between drugs and biological systems and are an important guide for the selection of screening compounds. The acid/base character of drugs has a profound influence on their affinity for the receptor, on their absorption, distribution, metabolism, excretion and toxicity (ADMET) profile and the way the drug can be formulated. In particular, the charge state of a molecule greatly influences its lipophilicity and biopharmaceutical characteristics. This study investigates the acid/base profile of human small molecule drugs, chemogenomics datasets and screening compounds including a natural products set. We estimate the ionization constants (pKa values) of these compounds and determine the identity of the ionizable functional groups in each set. We find substantial differences in acid/base profiles of the chemogenomic classes. In many cases, these differences can be linked to the nature of the target binding site and the corresponding functional groups needed for recognition of the ligand. Clear differences are also observed between the acid/base characteristics of drugs and screening compounds. For example, the proportion of drugs containing a carboxylic acid was 20%, in stark contrast to a value of 2.4% for the screening set sample. The proportion of aliphatic amines was 27% for drugs and only 3.4% for screening compounds. This suggests that there is a mismatch between commercially available screening compounds and the compounds that are likely to interact with a given chemogenomic target family. Our analysis provides a guide for the selection of screening compounds to better target specific chemogenomic families with regard to the overall balance of acids, bases and pKa distributions. PMID:23303535

Evaluating cost and resource use associated with pulse oximetry screening for critical congenital heart disease: Empiric estimates and sources of variation.

PubMed

Reeder, Matthew R; Kim, Jaewhan; Nance, Amy; Krikov, Sergey; Feldkamp, Marcia L; Randall, Harper; Botto, Lorenzo D

2015-11-01

Newborn screening for critical congenital heart disease (CCHD) using pulse oximetry is being implemented in the United States and internationally; however, few data are available on the associated in-hospital costs and use of resources. Time and motion study in well-baby nurseries at two large urban hospitals in Utah using different approaches to pulse oximetry screening. Two observers recorded the time for each screening step together with provider and equipment characteristics. Structured questionnaire provided additional information on labor and equipment costs. Fifty-three CCHD screens were observed. At site A (n = 22), screening was mostly done by medical assistants (95%) using disposable probes (100%); at site B (n = 31), screening was mostly performed by certified nursing assistants (90%) using reusable probes (90%). Considering only first screens (n = 53), the median screen time was 8.6 min (range: 3.2-23.2), with no significant difference between sites. The overall cost ($ in 2014) of screening per baby was $24.52 at site A and $2.60 at site B. Nearly all the variation in cost (90%) was due to the cost of disposable probes; labor costs were similar between sites. CCHD screening by means of pulse oximetry is reasonably fast for most babies, leading to relative small labor costs with little variation by provider type. The main driver of costs is equipment: in a high throughput setting, reusable probes are currently associated with considerable cost saving compared with disposable probes. As programs expand to universal screening, improved and cheaper technologies could lead to considerable economies of scale. © 2015 Wiley Periodicals, Inc.

Discovery and Characterization of Non-ATP Site Inhibitors of the Mitogen Activated Protein (MAP) Kinases

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

Comess, Kenneth M.; Sun, Chaohong; Abad-Zapatero, Cele

Inhibition of protein kinases has validated therapeutic utility for cancer, with at least seven kinase inhibitor drugs on the market. Protein kinase inhibition also has significant potential for a variety of other diseases, including diabetes, pain, cognition, and chronic inflammatory and immunologic diseases. However, as the vast majority of current approaches to kinase inhibition target the highly conserved ATP-binding site, the use of kinase inhibitors in treating nononcology diseases may require great selectivity for the target kinase. As protein kinases are signal transducers that are involved in binding to a variety of other proteins, targeting alternative, less conserved sites onmore » the protein may provide an avenue for greater selectivity. Here we report an affinity-based, high-throughput screening technique that allows nonbiased interrogation of small molecule libraries for binding to all exposed sites on a protein surface. This approach was used to screen both the c-Jun N-terminal protein kinase Jnk-1 (involved in insulin signaling) and p38{alpha} (involved in the formation of TNF{alpha} and other cytokines). In addition to canonical ATP-site ligands, compounds were identified that bind to novel allosteric sites. The nature, biological relevance, and mode of binding of these ligands were extensively characterized using two-dimensional {sup 1}H/{sup 13}C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38{alpha} both belong to the MAP kinase family, and the allosteric ligands for both targets bind similarly on a ledge of the protein surface exposed by the MAP insertion present in the CMGC family of protein kinases and distant from the active site. Medicinal chemistry studies resulted in an improved Jnk-1 ligand able to increase adiponectin secretion in human adipocytes and increase insulin-induced protein kinase PKB phosphorylation in human hepatocytes, in similar fashion to Jnk-1 siRNA and to rosiglitazone treatment. Together, the data suggest that these new ligand series bind to a novel, allosteric, and physiologically relevant site and therefore represent a unique approach to identify kinase inhibitors.« less

Tutorial Guide: Computer-Aided Structural Modeling (CASM). Version 5.00

DTIC Science & Technology

1994-04-01

2-3 SITE-SPECIFIC DATA DIALOG WINDOW ................. 2-4 SAVING PROJECT DATA ....................... 2-7 PRINTING PROJECT CRITERIA DATA...you to the main CASM screen without saving changes. REGIONAL DATA DIALOG WINDOW The Regonal• Dtadlalg windtow contim ms0•twrmofogoik hronimdon.The...Information so that It will be Included In your hardcopy output. 3. Select OK to save your Regional Data entries. The Regional Data dalog window will disappear

Identification of Transthyretin Fibril Formation Inhibitors Using Structure-Based Virtual Screening.

PubMed

Ortore, Gabriella; Martinelli, Adriano

2017-08-22

Transthyretin (TTR) is the primary carrier for thyroxine (T 4 ) in cerebrospinal fluid and a secondary carrier in blood. TTR is a stable homotetramer, but certain factors, genetic or environmental, could promote its degradation to form amyloid fibrils. A docking study using crystal structures of wild-type TTR was planned; our aim was to design new ligands that are able to inhibit TTR fibril formation. The computational protocol was thought to overcome the multiple binding modes of the ligands induced by the peculiarity of the TTR binding site and by the pseudosymmetry of the site pockets, which generally weaken such structure-based studies. Two docking steps, one that is very fast and a subsequent step that is more accurate, were used to screen the Aldrich Market Select database. Five compounds were selected, and their activity toward inhibiting TTR fibril formation was assessed. Three compounds were observed to be actives, two of which have the same potency as the positive control, and the other was found to be a promising lead compound. These results validate a computational protocol that is able to archive information on the key interactions between database compounds and TTR, which is valuable for supporting further studies. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multimodal biopanning of T7 phage-displayed peptides reveals angiomotin as a potential receptor of the anti-angiogenic macrolide Roxithromycin.

PubMed

Takakusagi, Kaori; Takakusagi, Yoichi; Suzuki, Takahiro; Toizaki, Aya; Suzuki, Aiko; Kawakatsu, Yaichi; Watanabe, Madoka; Saito, Yukihiro; Fukuda, Ryushi; Nakazaki, Atsuo; Kobayashi, Susumu; Sakaguchi, Kengo; Sugawara, Fumio

2015-01-27

Roxithromycin (RXM) is a semi-synthetic fourteen-membered macrolide antibiotic that shows anti-angiogenic activity in solid tumors. In the present study, we conducted biopanning of T7 phage-displayed peptides either on a 96-well formatted microplate, a flow injection-type quartz-crystal microbalance (QCM) biosensor, or a cuvette-type QCM. RXM-selected peptides of different sequence, length and number were obtained from each mode of screening. Subsequent bioinformatics analysis of the RXM-selected peptides consistently gave positive scores for the extracellular domain (E458-T596) of angiomotin (Amot), indicating that this may comprise a binding region for RXM. Bead pull down assay and QCM analysis confirmed that RXM directly interacts with Amot via the screen-guided region, which also corresponds to the binding site for the endogenous anti-angiogenic inhibitor angiostatin (Anst). Thus, multimodal biopanning of T7PD revealed that RXM binds to the extracellular domain on Amot as a common binding site with Anst, leading to inhibition of angiogenesis-dependent tumor growth and metastasis. These data might explain the molecular basis underlying the mechanism of action for the anti-angiogenic activity of RXM. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

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.

10 CFR 960.3-2 - Siting process.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Siting process. 960.3-2 Section 960.3-2 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2 Siting process. The siting process begins with site screening...

10 CFR 960.3-2 - Siting process.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Siting process. 960.3-2 Section 960.3-2 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2 Siting process. The siting process begins with site screening...

10 CFR 960.3-2 - Siting process.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Siting process. 960.3-2 Section 960.3-2 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2 Siting process. The siting process begins with site screening...

10 CFR 960.3-2 - Siting process.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Siting process. 960.3-2 Section 960.3-2 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2 Siting process. The siting process begins with site screening...

Remedial investigation/feasibility study badger army ammunition plant Baraboo, Wisconsin. Volume 2. Feasibility study report

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

NONE

1994-08-01

This Feasibility Study (FS) report for the Badger Army Ammunition Plant (BAAP) in Baraboo, Wisconsin, was prepared by ABB Environmental Services, Inc. (ABB-ES) as a component of Task Order 1 of Contract DAAAl5-91-D-OOO8 with the U.S. Army Environmental Center (USAEC). This report uses the results presented in the Final Remedial Investigation (RI) report (ABB-ES, 1993a) to develop and screen alternatives for remediation of contaminated media at BAAP. The purpose of this FS report is to develop, screen, and evaluate site-specific remedial alternatives to mitigate the impact of site-derived chemicals and ultimately provide protection of human health and the environment. Preferredmore » alternatives for each site are included in this report. Based on previous environmental studies at BAAP, 11 potential hazardous waste sites were ranked according to potential contributions of hazardous chemicals to the environment. These sites were designated as Waste Management Areas because some of the sites contain multiple Solid Waste Management Units (SWMUs). The sites selected to undergo facility assessment and corrective actions are: the Propellant Burning Ground (including Landfill), Deterrent Burning Ground, existing Landfill, Settling Ponds and Spoils Disposal Area, Rocket Paste Area, Oleum Plant and Oleum Plant Pond, Nitroglycerine Pond, old Acid Area, new Acid Area, and Ballistics Pond. The USAEC added an 11th site, the Old Fuel Oil Tank, to the list in October 1989 after discovery of fuel-contaminated soils during excavation of a water line in the vicinity of the old fuel oil tank foundation.« less

Remedial investigation/feasibility study badger army ammunition plant Baraboo, Wisconsin. Volume 3. Feasibility study report (Final)

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

NONE

1994-08-01

This Feasibility Study (FS) report for the Badger Army Ammunition Plant (BAAP) in Baraboo, Wisconsin, was prepared by ABB Environmental Services, Inc. (ABB-ES) as a component of Task Order 1 of Contract DAAAl5-91-D-OOO8 with the U.S. Army Environmental Center (USAEC). This report uses the results presented in the Final Remedial Investigation (RI) report (ABB-ES, 1993a) to develop and screen alternatives for remediation of contaminated media at BAAP. The purpose of this FS report is to develop, screen, and evaluate site-specific remedial alternatives to mitigate the impact of site-derived chemicals and ultimately provide protection of human health and the environment. Preferredmore » alternatives for each site are included in this report. Based on previous environmental studies at BAAP, 11 potential hazardous waste sites were ranked according to potential contributions of hazardous chemicals to the environment. These sites were designated as Waste Management Areas because some of the sites contain multiple Solid Waste Management Units (SWMUs). The sites selected to undergo facility assessment and corrective actions are: the Propellant Burning Ground (including Landfill), Deterrent Burning Ground, existing Landfill, Settling Ponds and Spoils Disposal Area, Rocket Paste Area, Oleum Plant and Oleum Plant Pond, Nitroglycerine Pond, old Acid Area, new Acid Area, and Ballistics Pond. The USAEC added an 11th site, the Old Fuel Oil Tank, to the list in October 1989 after discovery of fuel-contaminated soils during excavation of a water line in the vicinity of the old fuel oil tank foundation.« less

Remedial investigation/feasibility study badger army ammunition plant Baraboo, Wisconsin. Volume 1. Feasibility study report

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

NONE

1994-08-01

This Feasibility Study (FS) report for the Badger Army Ammunition Plant (BAAP) in Baraboo, Wisconsin, was prepared by ABB Environmental Services, Inc. (ABB-ES) as a component of Task Order 1 of Contract DAAAl5-91-D-OOO8 with the U.S. Army Environmental Center (USAEC). This report uses the results presented in the Final Remedial Investigation (RI) report (ABB-ES, 1993a) to develop and screen alternatives for remediation of contaminated media at BAAP. The purpose of this FS report is to develop, screen, and evaluate site-specific remedial alternatives to mitigate the impact of site-derived chemicals and ultimately provide protection of human health and the environment. Preferredmore » alternatives for each site are included in this report. Based on previous environmental studies at BAAP, 11 potential hazardous waste sites were ranked according to potential contributions of hazardous chemicals to the environment. These sites were designated as Waste Management Areas because some of the sites contain multiple Solid Waste Management Units (SWMUs). The sites selected to undergo facility assessment and corrective actions are: the Propellant Burning Ground (including Landfill), Deterrent Burning Ground, existing Landfill, Settling Ponds and Spoils Disposal Area, Rocket Paste Area, Oleum Plant and Oleum Plant Pond, Nitroglycerine Pond, old Acid Area, new Acid Area, and Ballistics Pond. The USAEC added an 11th site, the Old Fuel Oil Tank, to the list in October 1989 after discovery of fuel-contaminated soils during excavation of a water line in the vicinity of the old fuel oil tank foundation.« less

Stringent and reproducible tetracycline-regulated transgene expression by site-specific insertion at chromosomal loci with pre-characterised induction characteristics

PubMed Central

Brough, Rachel; Papanastasiou, Antigoni M; Porter, Andrew CG

2007-01-01

Background The ability to regulate transgene expression has many applications, mostly concerning the analysis of gene function. Desirable induction characteristics, such as low un-induced expression, high induced expression and limited cellular heterogeneity, can be seriously impaired by chromosomal position effects at the site of transgene integration. Many clones may therefore need to be screened before one with optimal induction characteristics is identified. Furthermore, such screens must be repeated for each new transgene investigated, and comparisons between clones with different transgenes is complicated by their different integration sites. Results To circumvent these problems we have developed a "screen and insert" strategy in which clones carrying a transgene for a fluorescent reporter are first screened for those with optimal induction characteristics. Site-specific recombination (SSR) is then be used repeatedly to insert any new transgene at the reporter transgene locus of such clones so that optimal induction characteristics are conferred upon it. Here we have tested in a human fibrosarcoma cell line (HT1080) two of many possible implementations of this approach. Clones (e.g. Rht14-10) in which a GFP reporter gene is very stringently regulated by the tetracycline (tet) transactivator (tTA) protein were first identified flow-cytometrically. Transgenes encoding luciferase, I-SceI endonuclease or Rad52 were then inserted by SSR at a LoxP site adjacent to the GFP gene resulting stringent tet-regulated transgene expression. In clone Rht14-10, increases in expression from essentially background levels (+tet) to more than 104-fold above background (-tet) were reproducibly detected after Cre-mediated insertion of either the luciferase or the I-SceI transgenes. Conclusion Although previous methods have made use of SSR to integrate transgenes at defined sites, none has effectively combined this with a pre-selection step to identify integration sites that support optimal regulatory characteristics. Rht14-10 and similar HT1080-derived clones can now be used in conjunction with a convenient delivery vector (pIN2-neoMCS), in a simple 3-step protocol leading to stringent and reproducible transgene regulation. This approach will be particularly useful for transgenes whose products are very active at low concentrations and/or for comparisons of multiple related transgenes. PMID:17493262

Web-based screening and brief intervention for the spectrum of alcohol problems.

PubMed

Saitz, Richard; Helmuth, Eric D; Aromaa, Susan E; Guard, Anara; Belanger, Marc; Rosenbloom, David L

2004-11-01

Many persons who drink excessively remain unidentified and do not receive interventions. Screening and intervention using the World Wide Web could make such services more accessible and therefore more widely used. To evaluate the use of a novel alcohol screening and brief intervention Web site. A Web site was developed, posted, and its use was evaluated. We analyzed a sample of visitors who completed alcohol screening over a 14-month period to describe their alcohol use, and their use of portions of the Web site that provide information and referral resources. The Internet. Web site visitors, with a focus on visitors who completed an alcohol-screening questionnaire about their own drinking. Brief intervention via the Web site, consisting mainly of feedback, advice, and a menu of change options and referral information. Self-reported drinking amounts and alcohol screening test scores, and utilization of Web site components. Visitors completed online alcohol screening questionnaires at a rate of 50,711/year of 115,925 visitors/year. In a 14-month period, 39,842 adults completed the questionnaire about their own drinking habits; 66% were men, 90% reported drinking hazardous amounts (per occasion or typical weekly amounts), 88% reported binge (per occasion) drinking, and 55% reported typically exceeding weekly risky drinking limits. Most (65%) had alcohol screening test results (AUDIT > or = 8) consistent with alcohol abuse or dependence; similar proportions of women and men were hazardous drinkers. One-fifth of visitors visited portions of the Web site that provided additional information about alcohol use and referrals. Visitors with possible alcohol abuse or dependence were more likely than those without these disorders to visit a part of the Web site designed for those seeking additional help (33% vs. 8%, P < 0.0001). A well-publicized, easily accessible, research-based screening and intervention Web site can attract many users, most of whom are drinking excessively, and many of whom avail themselves of referral information after receiving individualized feedback.

Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.

PubMed

Kamboj, Atul; Hallwirth, Claus V; Alexander, Ian E; McCowage, Geoffrey B; Kramer, Belinda

2017-06-17

The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic. Ub-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/ .

Diabetes and cardiometabolic risk factors in Cambodia: Results from two screening studies.

PubMed

Wagner, Julie; Naranjo, Diana; Khun, Touch; Seng, Serey; Horn, Ien S; Suttiratana, Sakinah C; Keuky, Lim

2018-02-01

Despite growing attention to diabetes throughout Asia, data from Southeast Asia are limited. This article reports rates of diabetes, hypertension, and obesity in Cambodia. Two studies were conducted across different regions of Cambodia: (i) a 2012 screening study across urban, semi-urban, and rural areas that used point-of-care capillary glucose for determination of diabetes (n = 13 997); and (ii) a 2005 epidemiological study with random selection from two main urban areas that used oral glucose tolerance tests for determination of diabetes (n = 1863). Blood pressure and anthropometrics were also measured. In the screening study, rates of diabetes were significantly higher in urban than rural sites, with intermediate rates in semi-urban areas. There was a significant dose-response effect for urbanicity on overweight, obesity, and waist:hip ratio, with higher rates for urban versus semi-urban and for semi-urban versus rural locales. Rural sites had the lowest rates of hypertension, followed by urban and semi-urban sites. Among people who screened positive for diabetes, there was a dose-response effect for urbanicity on undiagnosed diabetes; rates of previously undiagnosed diabetes were lowest in urban (51%), followed by semi-urban (55%) and rural (67%) locales. Rural participants reported the highest rates of smoking and alcohol use. In the urban epidemiological study, prevalence rates of diabetes and impaired glucose tolerance were approximately 10%, indicating a prevalence of total glucose intolerance of approximately 20%. In Cambodia, diabetes rates are high among urban residents and undiagnosed diabetes is highest among rural residents. A country-wide public health response is urgently needed; as development continues, rates of diabetes are expected to rise. © 2017 Ruijin Hospital, Shanghai Jiaotong University School of Medicine and John Wiley & Sons Australia, Ltd.

Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families

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

Popovic, Ana; Hai, Tran; Tchigvintsev, Anatoly

Metagenomics has made accessible an enormous reserve of global biochemical diversity. In order to tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. Here, we validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalyticmore » residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.« less

Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families

DOE PAGES

Popovic, Ana; Hai, Tran; Tchigvintsev, Anatoly; ...

2017-03-08

Metagenomics has made accessible an enormous reserve of global biochemical diversity. In order to tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. Here, we validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalyticmore » residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.« less

Prevalence of Homelessness in the Emergency Department Setting.

PubMed

Feldman, Brett J; Calogero, Cristina G; Elsayed, Kareem S; Abbasi, Osman Z; Enyart, Joshua; Friel, Timothy J; Abunamous, Yasir H; Dusza, Stephen W; Greenberg, Marna Rayl

2017-04-01

According to the National Alliance to End Homelessness, the national rate of homelessness has been cited as 17.7 homeless people/10,000 people in the general population, and 24.8 homeless veterans/10,000 veterans in the general population. However, it is unknown what the prevalence of homelessness is in the emergency department (ED) setting. We set out to determine the prevalence of homelessness or at risk for homelessness in the ED setting. Using a five-question screening tool derived from the U.S. Department of Housing and Urban Development, Health and Human Services and the Veterans Administration definition for homelessness, we surveyed all patients meeting inclusion/exclusion criteria on scheduled shifts in one of three EDs in Northeastern Pennsylvania. To participate, subjects had to be a registered patient in the ED, be 18 years or older, speak English, have the capacity to answer survey questions, not be critically ill, be willing to participate, and not have taken the survey before. We selected two survey periods to represent seasonal variations. We included 4,395 subjects in the analysis. The mean age of those who screened positive for homelessness or at risk for homelessness was 43.1 (SD 16.6). Overall, 136 (3.1%) participants screened positive for at risk for homelessness and 309 (7.0%) screened positive for homelessness. A total of 103 subjects (9.8%) screened positive for homelessness or at risk for homelessness on weekends and 312 (10.3%) on weekdays (p=0.64). The proportion of those screening positive for homelessness or at risk for homelessness varied by site: 145 (7.5%) at the trauma center, 151(9.1%) at the suburban site, and 149 (18.7%) at the center city site, p<0.001.There was no statistical significance to the difference between the trauma center and the suburban site (p=.088), but there was statistical significance between both the suburban and the trauma center when compared to the center city site (both p<0.0001). The proportion of those screening positive for homelessness in the summer months (156, 7.5%) was similar to those in the winter months (153, 6.6%), p=0.23. In our study, the overall prevalence of homelessness or at risk for homelessness was 10.1 percent. This prevalence did not seem to vary between weekdays and weekends. Additionally, summer months had a prevalence that was as concerning as winter months. The prevalence does, however, seem to vary by institutional characteristics even in the same geographic region. Understanding the patterns of prevalence of homelessness is a step toward considering possible interventions to assist this vulnerable population.

Dual-tail arylsulfone-based benzenesulfonamides differently match the hydrophobic and hydrophilic halves of human carbonic anhydrases active sites: Selective inhibitors for the tumor-associated hCA IX isoform.

PubMed

Ibrahim, Hany S; Allam, Heba Abdelrasheed; Mahmoud, Walaa R; Bonardi, Alessandro; Nocentini, Alessio; Gratteri, Paola; Ibrahim, Eslam S; Abdel-Aziz, Hatem A; Supuran, Claudiu T

2018-05-25

The synthesis and characterization of two new sets of arylsulfonehydrazone benzenesulfonamides (4a-4i with phenyl tail and 4j-4q with tolyl tail) are reported. The compounds were designed according to a dual-tails approach to modulate the interactions of the ligands portions at the outer rim of both hydrophobic and hydrophilic active site halves of human isoforms of carbonic anhydrase (CA, EC 4.2.1.1). The synthesized sulfonamides were evaluated in vitro for their inhibitory activity against the following human (h) isoforms, hCA I, II, IV and IX. With the latter being a validated anticancer drug target and a marker of tumor hypoxia, attractive results arose from the Compounds' inhibitory screening in terms of potency and selectivity. Indeed, whereas the first subset of compounds 4a-4i exhibited great efficacy in inhibiting both the ubiquitous, off-target hCA II (K I s 9.5-172.0 nM) and hCA IX (K I s 7.5-131.5 nM), the second subset of tolyl-bearing derivatives 4j-4q were shown to possess a selective hCA IX inhibitory action over isoforms I, II and IV. The most selective compounds 4l and 4n were further screened for their in vitro cytotoxic activity against MCF-7 and MDA-MB-231 cancer cell lines under hypoxic conditions. The selective IX/II inhibitory trend of 4j-4q compared to those of compounds 4a-4i was unveiled by docking studies. Further exploration of these molecules could be useful for the development of novel antitumor agents with a selective CA inhibitory mechanism. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Zebrafish embryos as a screen for DNA methylation modifications after compound exposure

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

Bouwmeester, Manon C.; Ruiter, Sander; Lommelaars, Tobias

Modified epigenetic programming early in life is proposed to underlie the development of an adverse adult phenotype, known as the Developmental Origins of Health and Disease (DOHaD) concept. Several environmental contaminants have been implicated as modifying factors of the developing epigenome. This underlines the need to investigate this newly recognized toxicological risk and systematically screen for the epigenome modifying potential of compounds. In this study, we examined the applicability of the zebrafish embryo as a screening model for DNA methylation modifications. Embryos were exposed from 0 to 72 h post fertilization (hpf) to bisphenol-A (BPA), diethylstilbestrol, 17α-ethynylestradiol, nickel, cadmium, tributyltin,more » arsenite, perfluoroctanoic acid, valproic acid, flusilazole, 5-azacytidine (5AC) in subtoxic concentrations. Both global and site-specific methylation was examined. Global methylation was only affected by 5AC. Genome wide locus-specific analysis was performed for BPA exposed embryos using Digital Restriction Enzyme Analysis of Methylation (DREAM), which showed minimal wide scale effects on the genome, whereas potential informative markers were not confirmed by pyrosequencing. Site-specific methylation was examined in the promoter regions of three selected genes vasa, vtg1 and cyp19a2, of which vasa (ddx4) was the most responsive. This analysis distinguished estrogenic compounds from metals by direction and sensitivity of the effect compared to embryotoxicity. In conclusion, the zebrafish embryo is a potential screening tool to examine DNA methylation modifications after xenobiotic exposure. The next step is to examine the adult phenotype of exposed embryos and to analyze molecular mechanisms that potentially link epigenetic effects and altered phenotypes, to support the DOHaD hypothesis. - Highlights: • Compound induced effects on DNA methylation in zebrafish embryos • Global methylation not an informative biomarker • Minimal genome wide site specific changes as detected with DREAM • Compound/class specific effects suggested by pyrosequence of specific targets • Zebrafish embryo may be a screening model for epigenetic effects.« less

Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.

PubMed

Jeschek, Markus; Gerngross, Daniel; Panke, Sven

2016-03-31

Rational flux design in metabolic engineering approaches remains difficult since important pathway information is frequently not available. Therefore empirical methods are applied that randomly change absolute and relative pathway enzyme levels and subsequently screen for variants with improved performance. However, screening is often limited on the analytical side, generating a strong incentive to construct small but smart libraries. Here we introduce RedLibs (Reduced Libraries), an algorithm that allows for the rational design of smart combinatorial libraries for pathway optimization thereby minimizing the use of experimental resources. We demonstrate the utility of RedLibs for the design of ribosome-binding site libraries by in silico and in vivo screening with fluorescent proteins and perform a simple two-step optimization of the product selectivity in the branched multistep pathway for violacein biosynthesis, indicating a general applicability for the algorithm and the proposed heuristics. We expect that RedLibs will substantially simplify the refactoring of synthetic metabolic pathways.

Band-selective excited ultrahigh resolution PSYCHE-TOCSY: fast screening of organic molecules and complex mixtures.

PubMed

Kakita, Veera Mohana Rao; Vemulapalli, Sahithya Phani Babu; Bharatam, Jagadeesh

2016-04-01

Precise assignments of (1) H atomic sites and establishment of their through-bond COSY or TOCSY connectivity are crucial for molecular structural characterization by using (1) H NMR spectroscopy. However, this exercise is often hampered by signal overlap, primarily because of (1) H-(1) H scalar coupling multiplets, even at typical high magnetic fields. The recent developments in homodecoupling strategies for effectively suppressing the coupling multiplets into nice singlets (pure-shift), particularly, Morris's advanced broadband pure-shift yielded by chirp excitation (PSYCHE) decoupling and ultrahigh resolution PSYCHE-TOCSY schemes, have shown new possibilities for unambiguous structural elucidation of complex organic molecules. The superior broadband PSYCHE-TOCSY exhibits enhanced performance over the earlier TOCSY methods, which however warrants prolonged experimental times due to the requirement of large number of dwell increments along the indirect dimension. Herein, we present fast and band-selective analog of the broadband PSYCHE-TOCSY, which is useful for analyzing complex organic molecules that exhibit characteristic yet crowded spectral regions. The simple pulse scheme relies on band-selective excitation (BSE) followed by PSYCHE homodecoupling in the indirect dimension. The BSE-PSYCHE-TOCSY has been exemplified for Estradiol and a complex carbohydrate mixture comprised of six constituents of closely comparable molecular weights. The experimental times are greatly reduced viz., ~20 fold for Estradiol and ~10 fold for carbohydrate mixture, with respect to the broadband PSYCHE-TOCSY. Furthermore, unlike the earlier homonuclear band-selective decoupling, the BSE-PSYCHE-decoupling provides fully decoupled pure-shift spectra for all the individual chemical sites within the excited band. The BSE-PSYCHE-TOCSY is expected to have significant potential for quick screening of complex organic molecules and mixtures at ultrahigh resolution. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Molecular screening of compounds to the predicted Protein-Protein Interaction site of Rb1-E7 with p53- E6 in HPV

PubMed Central

Shaikh, Faraz; Sanehi, Parvish; Rawal, Rakesh

2012-01-01

Cervical cancer is malignant neoplasm of the cervix uteri or cervical area. Human Papillomaviruses (HPVs) which are heterogeneous groups of small double stranded DNA viruses are considered as the primary cause of cervical cancer, involved in 90% of all Cervical Cancers. Two early HPV genes, E6 and E7, are known to play crucial role in tumor formation. E6 binds with p53 and prevents its translocation and thereby inhibit the ability of p53 to activate or repress target genes. E7 binds to hypophosphorylated Rb and thereby induces cells to enter into premature S-phase by disrupting Rb-E2F complexes. The strategy of the research work was to target the site of interaction of Rb1 -E7 & p53-E6. A total of 88 compounds were selected for molecular screening, based on comprehensive literature survey for natural compounds with anti-cancer activity. Molecular docking analysis was carried out with Molegro Virtual Docker, to screen the 88 chosen compounds and rank them according to their binding affinity towards the site of interaction of the viral oncoproteins and human tumor suppressor proteins. The docking result revealed that Nicandrenone a member of Withanolides family of chemical compounds as the most likely molecule that can be used as a candidate drug against HPV induced cervical cancer. Abbreviations HPV - Human Papiloma Virus, HTSP - Human Tumor Suppressor Proteins, VOP - Viral oncoproteins. PMID:22829740

A Knock-in Reporter for a Novel AR-Targeted Therapy

DTIC Science & Technology

2016-05-01

of this research is to explore a possibility whether the CRISPR -Cas9 technology, an emerging genome-editing approach, could be applied to develop a...in this report that the CRISPR -Cas9 system could indeed mediate high-efficient insertion of a selection gene into a site immediately downstream of...inhibitory for AR expression. 15. SUBJECT TERMS Androgen receptor, high-throughput drug screening assay, reporter gene assay, CRISPR -Cas9, genome editing

Development of a Protocol and a Screening Tool for Selection of DNAPL Source Area Remediation

DTIC Science & Technology

2012-02-01

the different remedial time frames used in the modeling case studies. • Matrix Diffusion: Modeling results demonstrated that in fractured rock ...being used for the ISCO, EISB and SEAR fractured rock numerical simulations at the field scale. Figure 2-4 presents the distribution of intrinsic...sedimentary limestone, sandstone, and shale, igneous basalts and granites, and metamorphous rock . For the modeling sites, three general geologies are

A randomised trial of non-mydriatic ultra-wide field retinal imaging versus usual care to screen for diabetic eye disease: rationale and protocol for the Clearsight trial

PubMed Central

Mahon, Lewis W; Klar, Neil S; Schulz, David C; Gonder, John R; Hramiak, Irene M; Mahon, Jeffrey L

2017-01-01

Introduction Suboptimal screening for diabetic eye disease is a major cause of preventable vision loss. Screening barriers include mydriasis and the extra time patients need to attend dedicated eye screening appointments. In the Clearsight trial, we are testing whether screening by non-mydriatic ultra-wide field (NM UWF) imaging on the day patients attend their diabetes outpatient clinic visit improves detection of clinically important eye disease compared with usual screening. Methods and analysis Patients with diabetes due for a screening eye exam by the 2013 Canadian Diabetes Association (CDA) practice guidelines are being randomised to on-site screening by NM UWF imaging on the day of their clinic visit or to usual screening where, per CDA guidelines, they are encouraged to arrange an exam by an optometrist. The primary outcome is actionable eye disease (AED) based on a need for referral to ophthalmology and/or increased ocular surveillance. The primary analysis will use an intention-to-screen approach that compares the proportions of detected AED between on-site and usual screening groups under a superiority hypothesis in favour of on-site screening. With 740 randomised participants, the study will have 80% power to detect ≥5% absolute increase in the AED rate among on-site screening versus usual screening participants. This difference translates into a number-needed-to-screen by on-site screening of 20 to detect 1 additional person with AED. Ethics and dissemination The protocol was approved by the institutional review board of Western University. The findings of the trial will be disseminated directly to participants and through peer-reviewed publications and conference presentations. Trial registration number ClinicalTrials.Gov NCT02579837 (registered 16 October 2015). Protocol issue date 18 November 2015. PMID:28775182

Testing contamination risk assessment methods for toxic elements from mine waste sites

NASA Astrophysics Data System (ADS)

Abdaal, A.; Jordan, G.; Szilassi, P.; Kiss, J.; Detzky, G.

2012-04-01

Major incidents involving mine waste facilities and poor environmental management practices have left a legacy of thousands of contaminated sites like in the historic mining areas in the Carpathian Basin. Associated environmental risks have triggered the development of new EU environmental legislation to prevent and minimize the effects of such incidents. The Mine Waste Directive requires the risk-based inventory of all mine waste sites in Europe by May 2012. In order to address the mining problems a standard risk-based Pre-selection protocol has been developed by the EU Commission. This paper discusses the heavy metal contamination in acid mine drainage (AMD) for risk assessment (RA) along the Source-Pathway-Receptor chain using decision support methods which are intended to aid national and regional organizations in the inventory and assessment of potentially contaminated mine waste sites. Several recognized methods such as the European Environmental Agency (EEA) standard PRAMS model for soil contamination, US EPA-based AIMSS and Irish HMS-IRC models for RA of abandoned sites are reviewed, compared and tested for the mining waste environment. In total 145 ore mine waste sites have been selected for scientific testing using the EU Pre-selection protocol as a case study from Hungary. The proportion of uncertain to certain responses for a site and for the total number of sites may give an insight of specific and overall uncertainty in the data we use. The Pre-selection questions are efficiently linked to a GIS system as database inquiries using digital spatial data to directly generate answers. Key parameters such as distance to the nearest surface and ground water bodies, to settlements and protected areas are calculated and statistically evaluated using STATGRAPHICS® in order to calibrate the RA models. According to our scientific research results, of the 145 sites 11 sites are the most risky having foundation slope >20o, 57 sites are within distance <500m to the nearest surface water bodies, and 33 sites are within distance <680m to the nearest settlements. Moreover 25 sites lie directly above the 'poor status' ground water bodies and 91 sites are located in the protected Natura2000 sites (distance =0). Analysis of the total score of all sites was performed, resulting in six risk classes, as follows: <21 (class I, 4 sites), 21-31 (class II, 16 sites), 31-42 (class III, 27 sites), 42-54 (class II, 38 sites), 54-66 (class V, 40 sites) and >66 (class VI, 20 sites). The total risk scores and key parameters are provided in separate tables and GIS maps, in order to facilitate interpretation and comparison. Results of the Pre-selection protocol are consistent with those of the screening PRAMS model. KEY WORDS contamination risk assessment, Mine Waste Directive, Pre-selection Protocol, PRA.MS, AIMSS, abandoned mine sites, GIS

Marine Hydrokinetic Resource Assessment for Domestic Army, Air Force, and Coast Guard Facilities

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

Robichaud, Robi J; Ingram, Michael

NREL/DOE undertook a study for the US Army, Coast Guard and Air Force to investigate the potential for marine hydrokinetic (MHK) devices to meet the energy load at coastal bases in the future as MHK technology evolves. A wide range of data from tidal and wave, environmental, shipping, etc. databases were used to screen the DOD bases. A series of scoring algorithms were developed to facilitate site review to lead to eventual down select for more detailed, site specific bathymetric tidal resource evaluation. The Army's Camp Edwards, MA and the Coast Guard's Training Center Cape May, NJ (TRACEN Cape May)more » were selected and the Georgia Institute of Technology performed the analyses. An NREL/DOE MHK team visited the bases to further discuss with the base personnel MHK technology's potential for providing power to the bases in the future and frame the potential impact to existing power systems.« less

Supplement to MTI study on selective passenger screening in the mass transit rail environment.

DOT National Transportation Integrated Search

2010-01-01

This supplement updates and adds to MTIs 2007 report on Selective Screening of Rail Passengers (Jenkins and Butterworth MTI 06-07: Selective Screening of Rail Passengers). The report reviews current screening programs implemented (or planned) by n...

Back propagation artificial neural network for community Alzheimer's disease screening in China.

PubMed

Tang, Jun; Wu, Lei; Huang, Helang; Feng, Jiang; Yuan, Yefeng; Zhou, Yueping; Huang, Peng; Xu, Yan; Yu, Chao

2013-01-25

Alzheimer's disease patients diagnosed with the Chinese Classification of Mental Disorders diagnostic criteria were selected from the community through on-site sampling. Levels of macro and trace elements were measured in blood samples using an atomic absorption method, and neurotransmitters were measured using a radioimmunoassay method. SPSS 13.0 was used to establish a database, and a back propagation artificial neural network for Alzheimer's disease prediction was simulated using Clementine 12.0 software. With scores of activities of daily living, creatinine, 5-hydroxytryptamine, age, dopamine and aluminum as input variables, the results revealed that the area under the curve in our back propagation artificial neural network was 0.929 (95% confidence interval: 0.868-0.968), sensitivity was 90.00%, specificity was 95.00%, and accuracy was 92.50%. The findings indicated that the results of back propagation artificial neural network established based on the above six variables were satisfactory for screening and diagnosis of Alzheimer's disease in patients selected from the community.

Back propagation artificial neural network for community Alzheimer's disease screening in China★

PubMed Central

Tang, Jun; Wu, Lei; Huang, Helang; Feng, Jiang; Yuan, Yefeng; Zhou, Yueping; Huang, Peng; Xu, Yan; Yu, Chao

2013-01-01

Alzheimer's disease patients diagnosed with the Chinese Classification of Mental Disorders diagnostic criteria were selected from the community through on-site sampling. Levels of macro and trace elements were measured in blood samples using an atomic absorption method, and neurotransmitters were measured using a radioimmunoassay method. SPSS 13.0 was used to establish a database, and a back propagation artificial neural network for Alzheimer's disease prediction was simulated using Clementine 12.0 software. With scores of activities of daily living, creatinine, 5-hydroxytryptamine, age, dopamine and aluminum as input variables, the results revealed that the area under the curve in our back propagation artificial neural network was 0.929 (95% confidence interval: 0.868–0.968), sensitivity was 90.00%, specificity was 95.00%, and accuracy was 92.50%. The findings indicated that the results of back propagation artificial neural network established based on the above six variables were satisfactory for screening and diagnosis of Alzheimer's disease in patients selected from the community. PMID:25206598

Screening selectively harnessed environmental microbial communities for biodegradation of polycyclic aromatic hydrocarbons in moving bed biofilm reactors.

PubMed

Demeter, Marc A; Lemire, Joseph A; Mercer, Sean M; Turner, Raymond J

2017-03-01

Bacteria are often found tolerating polluted environments. Such bacteria may be exploited to bioremediate contaminants in controlled ex situ reactor systems. One potential strategic goal of such systems is to harness microbes directly from the environment such that they exhibit the capacity to markedly degrade organic pollutants of interest. Here, the use of biofilm cultivation techniques to inoculate and activate moving bed biofilm reactor (MBBR) systems for the degradation of polycyclic aromatic hydrocarbons (PAHs) was explored. Biofilms were cultivated from 4 different hydrocarbon contaminated sites using a minimal medium spiked with the 16 EPA identified PAHs. Overall, all 4 inoculant sources resulted in biofilm communities capable of tolerating the presence of PAHs, but only 2 of these exhibited enhanced PAH catabolic gene prevalence coupled with significant degradation of select PAH compounds. Comparisons between inoculant sources highlighted the dependence of this method on appropriate inoculant screening and biostimulation efforts. Copyright © 2016 Elsevier Ltd. All rights reserved.

Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65

PubMed Central

Huang, Xi-Ping; Karpiak, Joel; Kroeze, Wesley K.; Zhu, Hu; Chen, Xin; Moy, Sheryl S.; Saddoris, Kara A.; Nikolova, Viktoriya; Farrell, Martilias S.; Wang, Sheng; Mangano, Thomas J.; Deshpande, Deepak A.; Jiang, Alice; Penn, Raymond B.; Jin, Jian; Koller, Beverly H.; Kenakin, Terry; Shoichet, Brian K.; Roth, Bryan L.

2016-01-01

At least 120 non-olfactory G protein-coupled receptors in the human genome are ”orphans” for which endogenous ligands are unknown, and many have no selective ligands, hindering elucidation of their biological functions and clinical relevance. Among these is GPR68, a proton receptor that lacks small molecule modulators for probing its biology. Yeast-based screens against GPR68 identified the benzodiazepine drug lorazepam as a non-selective GPR68 positive allosteric modulator. Over 3000 GPR68 homology models were refined to recognize lorazepam in a putative allosteric site. Docking 3.1 million molecules predicted new GPR68 modulators many of which were confirmed in functional assays. One potent GPR68 modulator—ogerin– suppressed recall in fear conditioning in wild-type, but not in GPR68 knockout mice. The same approach led to the discovery of allosteric agonists and negative allosteric modulators for GPR65. Combining physical and structure-based screening may be broadly useful for ligand discovery for understudied and orphan GPCRs. PMID:26550826

Novel synthesis and structural characterization of a high-affinity paramagnetic kinase probe for the identification of non-ATP site binders by nuclear magnetic resonance.

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

Moy, Franklin J.; Lee, Arthur; Gavrin, Lori Krim

2010-07-23

To aid in the pursuit of selective kinase inhibitors, we have developed a unique ATP site binder tool for the detection of binders outside the ATP site by nuclear magnetic resonance (NMR). We report here the novel synthesis that led to this paramagnetic spin-labeled pyrazolopyrimidine probe (1), which exhibits nanomolar inhibitory activity against multiple kinases. We demonstrate the application of this probe by performing NMR binding experiments with Lck and Src kinases and utilize it to detect the binding of two compounds proximal to the ATP site. The complex structure of the probe with Lck is also presented, revealing howmore » the probe fits in the ATP site and the specific interactions it has with the protein. We believe that this spin-labeled probe is a valuable tool that holds broad applicability in a screen for non-ATP site binders.« less

Formulation and evaluation of floating tablet of H2-receptor antagonist.

PubMed

Kesarla, Rajesh S; Vora, Pratik Ashwinbhai; Sridhar, B K; Patel, Gunvant; Omri, Abdelwahab

2015-01-01

Conventional sustained dosage form of ranitidine hydrochloride (HCl) does not prevent frequent administration due to its degradation in colonic media and limited absorption in the upper part of GIT. Ranitidine HCl floating tablet was formulated with sublimation method to overcome the stated problem. Compatibility study for screening potential excipients was carried out using Fourier transform infrared spectroscopy (FT-IR) and differential scanning chromatography (DSC). Selected excipients were further evaluated for optimizing the formulation. Preliminary screening of binder, polymer and sublimating material was based on hardness and drug release, drug release with release kinetics and floating lag time with total floatation time, respectively. Selected excipients were subjected to 3(2) factorial design with polymer and sublimating material as independent factors. Matrix tablets were obtained by using 16/32" flat-faced beveled edges punches followed by sublimation. FT-IR and DSC indicated no significant incompatibility with selected excipients. Klucel-LF, POLYOX WSR N 60 K and l-menthol were selected as binder, polymer and sublimating material, respectively, for factorial design batches after preliminary screening. From the factorial design batches, optimum concentration to release the drug within 12 h was found to be 420 mg of POLYOX and 40 mg of l-menthol. Stability studies indicated the formulation as stable. Ranitidine HCl matrix floating tablets were formulated to release 90% of drug in stomach within 12 h. Hence, release of the drug could be sustained within narrow absorption site. Moreover, the dosage form was found to be floating within a fraction of second independent of the pH of media ensuring a robust formulation.

Primer for Using RE-Powering Data to Screen Sites for Renewable Energy Potential

EPA Pesticide Factsheets

This reference guide provides users with tips for using the RE-Powering Screening Dataset spreadsheet, which contains detailed site information on over 60,000 contaminated lands, landfills, and mine sites.

Application of Spatial Data Modeling and Geographical Information Systems (GIS) for Identification of Potential Siting Options for Various Electrical Generation Sources

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

Mays, Gary T; Belles, Randy; Blevins, Brandon R

2012-05-01

Oak Ridge National Laboratory (ORNL) initiated an internal National Electric Generation Siting Study, which is an ongoing multiphase study addressing several key questions related to our national electrical energy supply. This effort has led to the development of a tool, OR-SAGE (Oak Ridge Siting Analysis for power Generation Expansion), to support siting evaluations. The objective in developing OR-SAGE was to use industry-accepted approaches and/or develop appropriate criteria for screening sites and employ an array of Geographic Information Systems (GIS) data sources at ORNL to identify candidate areas for a power generation technology application. The initial phase of the study examinedmore » nuclear power generation. These early nuclear phase results were shared with staff from the Electric Power Research Institute (EPRI), which formed the genesis and support for an expansion of the work to several other power generation forms, including advanced coal with carbon capture and storage (CCS), solar, and compressed air energy storage (CAES). Wind generation was not included in this scope of work for EPRI. The OR-SAGE tool is essentially a dynamic visualization database. The results shown in this report represent a single static set of results using a specific set of input parameters. In this case, the GIS input parameters were optimized to support an economic study conducted by EPRI. A single set of individual results should not be construed as an ultimate energy solution, since US energy policy is very complex. However, the strength of the OR-SAGE tool is that numerous alternative scenarios can be quickly generated to provide additional insight into electrical generation or other GIS-based applications. The screening process divides the contiguous United States into 100 x 100 m (1-hectare) squares (cells), applying successive power generation-appropriate site selection and evaluation criteria (SSEC) to each cell. There are just under 700 million cells representing the contiguous United States. If a cell meets the requirements of each criterion, the cell is deemed a candidate area for siting a specific power generation form relative to a reference plant for that power type. Some SSEC parameters preclude siting a power plant because of an environmental, regulatory, or land-use constraint. Other SSEC assist in identifying less favorable areas, such as proximity to hazardous operations. All of the selected SSEC tend to recommend against sites. The focus of the ORNL electrical generation source siting study is on identifying candidate areas from which potential sites might be selected, stopping short of performing any detailed site evaluations or comparisons. This approach is designed to quickly screen for and characterize candidate areas. Critical assumptions supporting this work include the supply of cooling water to thermoelectric power generation; a methodology to provide an adequate siting footprint for typical power plant applications; a methodology to estimate thermoelectric plant capacity while accounting for available cooling water; and a methodology to account for future ({approx}2035) siting limitations as population increases and demands on freshwater sources change. OR-SAGE algorithms were built to account for these critical assumptions. Stream flow is the primary thermoelectric plant cooling source evaluated in this study. All cooling was assumed to be provided by a closed-cycle cooling (CCC) system requiring makeup water to account for evaporation and blowdown. Limited evaluations of shoreline cooling and the use of municipal processed water (gray) cooling were performed. Using a representative set of SSEC as input to the OR-SAGE tool and employing the accompanying critical assumptions, independent results for the various power generation sources studied were calculated.« less

Canada's Deep Geological Repository For Used Nuclear Fuel -The Geoscientific Site Evaluation Process

NASA Astrophysics Data System (ADS)

Hirschorn, S.; Ben Belfadhel, M.; Blyth, A.; DesRoches, A. J.; McKelvie, J. R. M.; Parmenter, A.; Sanchez-Rico Castejon, M.; Urrutia-Bustos, A.; Vorauer, A.

2014-12-01

The Nuclear Waste Management Organization (NWMO) is responsible for implementing Adaptive Phased Management, the approach selected by the Government of Canada for long-term management of used nuclear fuel generated by Canadian nuclear reactors. In May 2010, the NWMO published and initiated a nine-step site selection process to find an informed and willing community to host a deep geological repository for Canada's used nuclear fuel. The site selection process is designed to address a broad range of technical and social, economic and cultural factors. The suitability of candidate areas will be assessed in a stepwise manner over a period of many years and include three main steps: Initial Screenings; Preliminary Assessments; and Detailed Site Characterizations. The Preliminary Assessment is conducted in two phases. NWMO has completed Phase 1 preliminary assessments for the first eight communities that entered into this step. While the Phase 1 desktop geoscientific assessments showed that each of the eight communities contains general areas that have the potential to satisfy the geoscientific safety requirements for hosting a deep geological repository, the assessment identified varying degrees of geoscientific complexity and uncertainty between communities, reflecting their different geological settings and structural histories. Phase 2 activities will include a sequence of high-resolution airborne geophysical surveys and focused geological field mapping to ground-truth lithology and structural features, followed by limited deep borehole drilling and testing. These activities will further evaluate the site's ability to meet the safety functions that a site would need to ultimately satisfy in order to be considered suitable. This paper provides an update on the site evaluation process and describes the approach, methods and criteria that are being used to conduct the geoscientific Preliminary Assessments.

High-throughput Screening Identification of Poliovirus RNA-dependent RNA Polymerase Inhibitors

PubMed Central

Campagnola, Grace; Gong, Peng; Peersen, Olve B.

2011-01-01

Viral RNA-dependent RNA polymerase (RdRP) enzymes are essential for the replication of positive-strand RNA viruses and established targets for the development of selective antiviral therapeutics. In this work we have carried out a high-throughput screen of 154,267 compounds to identify poliovirus polymerase inhibitors using a fluorescence based RNA elongation assay. Screening and subsequent validation experiments using kinetic methods and RNA product analysis resulted in the identification of seven inhibitors that affect the RNA binding, initiation, or elongation activity of the polymerase. X-ray crystallography data show clear density for five of the compounds in the active site of the poliovirus polymerase elongation complex. The inhibitors occupy the NTP binding site by stacking on the priming nucleotide and interacting with the templating base, yet competition studies show fairly weak IC50 values in the low μM range. A comparison with nucleotide bound structures suggests that weak binding is likely due to the lack of a triphosphate group on the inhibitors. Consequently, the inhibitors are primarily effective at blocking polymerase initiation and do not effectively compete with NTP binding during processive elongation. These findings are discussed in the context of the polymerase elongation complex structure and allosteric control of the viral RdRP catalytic cycle. PMID:21722674

Exploring the selectivity of auto-inducer complex with LuxR using molecular docking, mutational studies and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Rajamanikandan, Sundaraj; Srinivasan, Pappu

2017-03-01

Bacteria communicate with one another using extracellular signaling molecules called auto-inducers (AHLs), a process termed as quorum sensing. The quorum sensing process allows bacteria to regulate various physiological activities. In this regard, quorum sensing master regulator LuxR from Vibrio harveyi represents an attractive therapeutic target for the development of novel anti-quorum sensing agents. Eventhough the binding of AHL complex with LuxR is evidenced in earlier reports, but their mode of binding is not clearly determined. Therefore, in the present work, molecular docking, in silico mutational studies, molecular dynamics simulations and free energy calculations were performed to understand the selectivity of AHL into the binding site of LuxR. The results revealed that Asn133 and Gln137 residues play a crucial role in recognizing AHL more effectively into the binding site of LuxR with good binding free energy. In addition to that, the carbonyl group presents in the lactone ring and amide group of AHL plays a vital role in the formation of hydrogen bond interactions with the protein. Further, structure based virtual screening was performed using ChemBridge database to screen potent lead molecules against LuxR. 4-benzyl-2-pyrrolidinone and N-[2(1-cyclohexen-1-yl) enthyl]-N'(2-ethoxyphenyl) were selected based on dock score, binding affinity and mode of interactions with the receptor. Furthermore, binding free energy, density functional theory and ADME prediction were performed to rank the lead molecules. Thus, the identified lead molecules can be used for the development of anti-quorum sensing drugs.

Is GPS telemetry location error screening beneficial?

USGS Publications Warehouse

Ironside, Kirsten E.; Mattson, David J.; Arundel, Terry; Hansen, Jered R.

2017-01-01

The accuracy of global positioning system (GPS) locations obtained from study animals tagged with GPS monitoring devices has been a concern as to the degree it influences assessments of movement patterns, space use, and resource selection estimates. Many methods have been proposed for screening data to retain the most accurate positions for analysis, based on dilution of precision (DOP) measures, and whether the position is a two dimensional or three dimensional fix. Here we further explore the utility of these measures, by testing a Telonics GEN3 GPS collar's positional accuracy across a wide range of environmental conditions. We found the relationship between location error and fix dimension and DOP metrics extremely weak (r2adj ∼ 0.01) in our study area. Environmental factors such as topographic exposure, canopy cover, and vegetation height explained more of the variance (r2adj = 15.08%). Our field testing covered sites where sky-view was so limited it affected GPS performance to the degree fix attempts failed frequently (fix success rates ranged 0.00–100.00% over 67 sites). Screening data using PDOP did not effectively reduce the location error in the remaining dataset. Removing two dimensional fixes reduced the mean location error by 10.95 meters, but also resulted in a 54.50% data reduction. Therefore screening data under the range of conditions sampled here would reduce information on animal movement with minor improvements in accuracy and potentially introduce bias towards more open terrain and vegetation.

EPA RE-Powering Screening Shapefile

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Center for Program Analysis (CPA) initiated the RE-Powering America??s Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

Virtual Screening Techniques to Probe the Antimalarial Activity of some Traditionally Used Phytochemicals.

PubMed

Shibi, Indira G; Aswathy, Lilly; Jisha, Radhakrishnan S; Masand, Vijay H; Gajbhiye, Jayant M

2016-01-01

Malaria parasites show resistance to most of the antimalarial drugs and hence developing antimalarials which can act on multitargets rather than a single target will be a promising strategy of drug design. Here we report a new approach by which virtual screening of 292 unique phytochemicals present in 72 traditionally important herbs is used for finding out inhibitors of plasmepsin-2 and falcipain-2 for antimalarial activity against P. falciparum. Initial screenings of the selected molecules by Random Forest algorithm model of Weka using the bioassay datasets AID 504850 and AID 2302 screened 120 out of the total 292 phytochemicals to be active against the targets. Toxtree scan cautioned 21 compounds to be either carcinogenic or mutagenic and were thus removed for further analysis. Out of the remaining 99 compounds, only 46 compounds offered drug-likeness as per the 'rule of five' criteria. Out of ten antimalarial drug targets, only two target proteins such as 3BPF and 3PNR of falcipain-2 and 1PFZ and 2BJU of plasmepsin-2 are selected as targets. The potential binding of the selected 46 compounds to the active sites of these four targets was analyzed using MOE software. The docked conformations and the interactions with the binding pocket residues of the target proteins were understood by 'Ligplot' analysis. It has been found that 8 compounds are dual inhibitors of falcipain-2 and plasmepsin-2, with the best binding energies. Compound 117 (6aR, 12aS)-12a-Hydroxy-9-methoxy-2,3-dimethylenedioxy-8-prenylrotenone (Usaratenoid C) present in the plant Millettia usaramensis showed maximum molecular docking score.

Association of Antioxidant Supplement Use and Dementia in the Prevention of Alzheimer's Disease by Vitamin E and Selenium Trial (PREADViSE).

PubMed

Kryscio, Richard J; Abner, Erin L; Caban-Holt, Allison; Lovell, Mark; Goodman, Phyllis; Darke, Amy K; Yee, Monica; Crowley, John; Schmitt, Frederick A

2017-05-01

Oxidative stress is an established dementia pathway, but it is unknown if the use of antioxidant supplements can prevent dementia. To determine if antioxidant supplements (vitamin E or selenium) used alone or in combination can prevent dementia in asymptomatic older men. The Prevention of Alzheimer's Disease by Vitamin E and Selenium (PREADViSE) trial began as a double-blind randomized clinical trial in May 2002, which transformed into a cohort study from September 2009 to May 2015. The PREADViSE trial was ancillary to the Selenium and Vitamin E Cancer Prevention Trial (SELECT), a randomized clinical trial of the same antioxidant supplements for preventing prostate cancer, which closed in 2009 owing to findings from a futility analysis. The PREADViSE trial recruited 7540 men, of whom 3786 continued into the cohort study. Participants were at least 60 years old at study entry and were enrolled at 130 SELECT sites, and Cox proportional hazards models were used in a modified intent-to-treat analysis to compare hazard rates among the study arms. Participants were randomized to vitamin E, selenium, vitamin E and selenium, or placebo. While taking study supplements, enrolled men visited their SELECT site and were evaluated for dementia using a 2-stage screen. During the cohort study, men were contacted by telephone and assessed using an enhanced 2-stage cognitive screen. In both phases, men were encouraged to visit their physician if the screen results indicated possible cognitive impairment. Dementia case ascertainment relied on a consensus review of the cognitive screens and medical records for men with suspected dementia who visited their physician for an evaluation or by review of all available information, including a functional assessment screen. The mean (SD) baseline age of the 7540 participants was 67.5 (5.3) years, with 3936 (52.2%) reporting a college education or better, 754 (10.0%) reporting black race, and 505 (6.7%) reporting Hispanic ethnicity. Dementia incidence (325 of 7338 men [4.4%]) was not different among the 4 study arms. A Cox model, which adjusted incidence for participant demographic information and baseline self-reported comorbidities, yielded hazard ratios of 0.88 (95% CI, 0.64-1.20) for vitamin E, 0.83 (0.60-1.13) for selenium, and 1.00 (0.75-1.35) for the combination compared with placebo. Neither supplement prevented dementia. To our knowledge, this is the first study to investigate the long-term association of antioxidant supplement use and dementia incidence among asymptomatic men.

Valuing Equal Protection in Aviation Security Screening.

PubMed

Nguyen, Kenneth D; Rosoff, Heather; John, Richard S

2017-12-01

The growing number of anti-terrorism policies has elevated public concerns about discrimination. Within the context of airport security screening, the current study examines how American travelers value the principle of equal protection by quantifying the "equity premium" that they are willing to sacrifice to avoid screening procedures that result in differential treatments. In addition, we applied the notion of procedural justice to explore the effect of alternative selective screening procedures on the value of equal protection. Two-hundred and twenty-two respondents were randomly assigned to one of three selective screening procedures: (1) randomly, (2) using behavioral indicators, or (3) based on demographic characteristics. They were asked to choose between airlines using either an equal or a discriminatory screening procedure. While the former requires all passengers to be screened in the same manner, the latter mandates all passengers undergo a quick primary screening and, in addition, some passengers are selected for a secondary screening based on a predetermined selection criterion. Equity premiums were quantified in terms of monetary cost, wait time, convenience, and safety compromise. Results show that equity premiums varied greatly across respondents, with many indicating little willingness to sacrifice to avoid inequitable screening, and a smaller minority willing to sacrifice anything to avoid the discriminatory screening. The selective screening manipulation was effective in that equity premiums were greater under selection by demographic characteristics compared to the other two procedures. © 2017 Society for Risk Analysis.

Estimation of Anticipated Performance Index and Air Pollution Tolerance Index and of vegetation around the marble industrial areas of Potwar region: bioindicators of plant pollution response.

PubMed

Noor, Mehwish Jamil; Sultana, Shazia; Fatima, Sonia; Ahmad, Mushtaq; Zafar, Muhammad; Sarfraz, Maliha; Balkhyour, Masour A; Safi, Sher Zaman; Ashraf, Muhammad Aqeel

2015-06-01

Mitigating industrial air pollution is a big challenge, in such scenario screening of plants as a bio monitor is extremely significant. It requires proper selection and screening of sensitive and tolerant plant species which are bio indicator and sink for air pollution. The present study was designed to evaluate the Air Pollution Tolerance Index (APTI) and Anticipated Performance Index (API) of the common flora. Fifteen common plant species from among trees, herb and shrubs i.e. Chenopodium album (Chenopodiaceae), Parthenium hysterophorus (Asteraceae), Amaranthus viridis (Amaranthaceae), Lantana camara (Verbenaceaea), Ziziphus nummulari (Rhamnaceae), Silibum merianum (Asteraceae), Cannabis sativa (Cannabinaceae), Calatropis procera (Asclepediaceae), Ricinus communis (Euphorbiaceae), Melia azadirachta (Meliaceae), Psidium guajava (Myrtaceae), Eucalyptus globules (Myrtaceae), Broussonetia papyrifera (Moraceae), Withania somnifera (Solanaceae) and Sapium sabiferum (Euphorbiaceae) were selected growing frequently in vicinity of Marble industries in Potwar region. APTI and API of selected plant species were analyzed by determining important biochemical parameter i.e. total chlorophyll, ascorbic acid, relative water content and pH etc. Furthermore the selected vegetation was studied for physiological, economic, morphological and biological characteristics. The soil of studied sites was analyzed. It was found that most the selected plant species are sensitive to air pollution. However B. papyrifera, E. globulus and R. communis shows the highest API and therefore recommended for plantation in marble dust pollution stress area.

A case study of risk assessment in contaminated site remediation in China

NASA Astrophysics Data System (ADS)

Ye, S.; Guo, J.; Wu, J.; Wang, J.; Chien, C.; Stahl, R.; Mack, E.; Grosso, N.

2013-12-01

A field site in Nanjing, China was selected for a case study of risk assessment in contaminated site remediation. This site is about 100m long and 100m wide. A chemical plant (1999-2010) at the site manufactured optical brightener PF, 2-Amino-4-methylphenol and 2-Nitro-4-methylphenol, totally three products. Soil and groundwater samples were collected and analyzed for PPL 126 (126 pollutants in the 'Priority Pollutants List' issued by US EPA). Values of the Dutch Standards were used as the screening criteria for soil and ground water. Low levels of ethylbenezene, chlorobenzene, 1,3-dichlorobenzene and 1,4- dichlorobenzene were detected in one soil sample. Concentrations above Dutch Target Value (DTV) of benzene, toluene, ethylbenzene, chlorobenzene, 1,2-dichlorobenzene, 1,3-dichlorobenzene, 1,4-dichlorobenzene, and/or 1,2,4-trichlorobenzene, phenol, and/or 2,4-dichlorophenol were exhibited in two groundwater samples. The ground water was especially highly impacted by bichlorobenzenes and trichlorobenzenes. The maximum concentration of impacts was 7.3 mg/L of 1,2,4-trichlorobenzene in groundwater which was 730 times higher than Dutch Intervention Values (DIV). Risk of soil and groundwater at this site was assessed according to the guidelines issued by Chinese MEP and US EPA, respectively. Finally, remedy techniques were selected according to the result of risk assessment and the characteristics of hydrogeology conditions and contaminants.

Developments in SPR Fragment Screening.

PubMed

Chavanieu, Alain; Pugnière, Martine

2016-01-01

Fragment-based approaches have played an increasing role alongside high-throughput screening in drug discovery for 15 years. The label-free biosensor technology based on surface plasmon resonance (SPR) is now sensitive and informative enough to serve during primary screens and validation steps. In this review, the authors discuss the role of SPR in fragment screening. After a brief description of the underlying principles of the technique and main device developments, they evaluate the advantages and adaptations of SPR for fragment-based drug discovery. SPR can also be applied to challenging targets such as membrane receptors and enzymes. The high-level of immobilization of the protein target and its stability are key points for a relevant screening that can be optimized using oriented immobilized proteins and regenerable sensors. Furthermore, to decrease the rate of false negatives, a selectivity test may be performed in parallel on the main target bearing the binding site mutated or blocked with a low-off-rate ligand. Fragment-based drug design, integrated in a rational workflow led by SPR, will thus have a predominant role for the next wave of drug discovery which could be greatly enhanced by new improvements in SPR devices.

Regulation of Mammary Stem Cell Quiescence via Post-Translational Modification of DeltaNp63alpha

DTIC Science & Technology

2014-02-01

mRNA expression in atopic dermatitis following narrow- band ultraviolet B phototherapy: results of a pilot study. J Dermatol Sci 44: 56– 58. 39. Lee...Change II site-directed mutagenesis kit ( Cat # 200523-5) with the following set of primers; sense primer 59-CGATGCTCTCGCTCCAGCACCCGC- CATCCCCTCC-39, and...Invitrogen, Cat #11668) according to manufacturers protocol. Kinome Screen The Silencer Select Human Kinase siRNA Library ( Cat - alog#4397918) from Ambion

Final Programmatic Environmental Assessment for Base-Wide Military Construction Planning at Kirtland Air Force Base, New Mexico

DTIC Science & Technology

2013-11-01

primarily of granite, metamorphic rock , and marine carbonate rocks that are approximately 57 million years old (Kirtland AFB 2012a). The dominant soils...erosion. Tijeras soils are commonly used as rangeland, but tracts can be divided for urban development and building. Rock outcrop – Orthids complex...health or the environment. Although six sites have been identified and meet the screening criteria, these same criteria may be used to select other

A new spatial multi-criteria decision support tool for site selection for implementation of managed aquifer recharge.

PubMed

Rahman, M Azizur; Rusteberg, Bernd; Gogu, R C; Lobo Ferreira, J P; Sauter, Martin

2012-05-30

This study reports the development of a new spatial multi-criteria decision analysis (SMCDA) software tool for selecting suitable sites for Managed Aquifer Recharge (MAR) systems. The new SMCDA software tool functions based on the combination of existing multi-criteria evaluation methods with modern decision analysis techniques. More specifically, non-compensatory screening, criteria standardization and weighting, and Analytical Hierarchy Process (AHP) have been combined with Weighted Linear Combination (WLC) and Ordered Weighted Averaging (OWA). This SMCDA tool may be implemented with a wide range of decision maker's preferences. The tool's user-friendly interface helps guide the decision maker through the sequential steps for site selection, those steps namely being constraint mapping, criteria hierarchy, criteria standardization and weighting, and criteria overlay. The tool offers some predetermined default criteria and standard methods to increase the trade-off between ease-of-use and efficiency. Integrated into ArcGIS, the tool has the advantage of using GIS tools for spatial analysis, and herein data may be processed and displayed. The tool is non-site specific, adaptive, and comprehensive, and may be applied to any type of site-selection problem. For demonstrating the robustness of the new tool, a case study was planned and executed at Algarve Region, Portugal. The efficiency of the SMCDA tool in the decision making process for selecting suitable sites for MAR was also demonstrated. Specific aspects of the tool such as built-in default criteria, explicit decision steps, and flexibility in choosing different options were key features, which benefited the study. The new SMCDA tool can be augmented by groundwater flow and transport modeling so as to achieve a more comprehensive approach to the selection process for the best locations of the MAR infiltration basins, as well as the locations of recovery wells and areas of groundwater protection. The new spatial multicriteria analysis tool has already been implemented within the GIS based Gabardine decision support system as an innovative MAR planning tool. Copyright © 2012 Elsevier Ltd. All rights reserved.

Experience with a proposed teleradiology system for digital mammography

NASA Astrophysics Data System (ADS)

Saulnier, Emilie T.; Mitchell, Robert J.; Abdel-Malek, Aiman A.; Dudding, Kathryn E.

1995-05-01

Teleradiology offers significant improvement in efficiency and effectiveness over current practices in traditional film/screen-based diagnosis. In the context of digital mammography, the increasing number of women who need to be screened for breast cancer, including those in remote rural regions, make the advantages of teleradiology especially attractive for digital mammography. At the same time, the size and resolution of digital mammograms are among the most challenging to support in a cost effective teleradiology system. This paper describes a teleradiology architecture developed for use with digital mammography by GE Corporate Research and Development in collaboration with Massachusetts General Hospital under National Cancer Institute (NCI/NIH) grant number R01 CA60246-01. Experience with a testbed prototype is described. The telemammography architecture is intended to consist of a main mammography diagnostic site serving several remote screening sites. As patient exams become available, they are forwarded by an image server to the diagnostic site over a WAN communications link. A radiologist at the diagnostic site views a patient exam as it arrives, interprets it, and then relays a report back to the technician at the remote site. A secondary future scenario consists of mobile units which forward images to a remote site, which then forwards them to the main diagnostic site. The testbed architecture is based on the Digital Imaging and Communications in Medicine (DICOM) standard, created by the American College of Radiology (ACR) and National Electrical Manufacturers Association (NEMA). A specification of vendor-independent data formats and data transfer services for digital medical images, DICOM specifies a protocol suite starting at the application layer downward, including the TCP/IP layers. The current DICOM definition does not provide an information element that is specifically tailored to mammography, so we have used the DICOM secondary capture data format for the mammography images. In conclusion, experience with the testbed is described, as is performance analysis related to selection of network components needed to extend this architecture to clinical evaluation. Recommendations are made as to the critical areas for future work.

Screening and assessment of solidification/stabilization amendments suitable for soils of lead-acid battery contaminated site.

PubMed

Zhang, Zhuo; Guo, Guanlin; Teng, Yanguo; Wang, Jinsheng; Rhee, Jae Seong; Wang, Sen; Li, Fasheng

2015-05-15

Lead exposure via ingestion of soil and dust generally occurs at lead-acid battery manufacturing and recycling sites. Screening solidification/stabilization (S/S) amendments suitable for lead contaminated soil in an abandoned lead-acid battery factory site was conducted based on its chemical forms and environmental risks. Twelve amendments were used to immobilize the Pb in soil and assess the solidification/stabilization efficiency by toxicity leaching tests. The results indicated that three amendments, KH₂PO₄ (KP), KH₂PO₄:oyster shell power=1:1 (by mass ratio; SPP), and KH₂PO₄:sintered magnesia=1:1 (by mass ratio; KPM) had higher remediation efficiencies that led to a 92% reduction in leachable Pb with the addition of 5% amendments, while the acid soluble fraction of Pb (AS-Pb) decreased by 41-46% and the residual fraction (RS-Pb) increased by 16-25%. The S/S costs of the three selected amendments KP, SPP, and KPM could be controlled to $22.3 per ton of soil when the Pb concentration in soil ranged from 2000 to 3000 mg/kg. The results of this study demonstrated that KP, SPP, and KPM can effectively decrease bioavailability of Pb. These findings could provide basis for decision-making of S/S remediation of lead-acid battery contaminated sites. Copyright © 2015 Elsevier B.V. All rights reserved.

Quality of prostate cancer screening information on the websites of nationally recognized cancer centers and health organizations.

PubMed

Manole, Bogdan-Alexandru; Wakefield, Daniel V; Dove, Austin P; Dulaney, Caleb R; Marcrom, Samuel R; Schwartz, David L; Farmer, Michael R

2017-12-24

The purpose of this study was to survey the accessibility and quality of prostate-specific antigen (PSA) screening information from National Cancer Institute (NCI) cancer center and public health organization Web sites. We surveyed the December 1, 2016, version of all 63 NCI-designated cancer center public Web sites and 5 major online clearinghouses from allied public/private organizations (cancer.gov, cancer.org, PCF.org, USPSTF.org, and CDC.gov). Web sites were analyzed according to a 50-item list of validated health care information quality measures. Web sites were graded by 2 blinded reviewers. Interrater agreement was confirmed by Cohen kappa coefficient. Ninety percent of Web sites addressed PSA screening. Cancer center sites covered 45% of topics surveyed, whereas organization Web sites addressed 70%. All organizational Web pages addressed the possibility of false-positive screening results; 41% of cancer center Web pages did not. Forty percent of cancer center Web pages also did not discuss next steps if a PSA test was positive. Only 6% of cancer center Web pages were rated by our reviewers as "superior" (eg, addressing >75% of the surveyed topics) versus 20% of organizational Web pages. Interrater agreement between our reviewers was high (kappa coefficient = 0.602). NCI-designated cancer center Web sites publish lower quality public information about PSA screening than sites run by major allied organizations. Nonetheless, information and communication deficiencies were observed across all surveyed sites. In an age of increasing patient consumerism, prospective prostate cancer patients would benefit from improved online PSA screening information from provider and advocacy organizations. Validated cancer patient Web educational standards remain an important, understudied priority. Copyright © 2018. Published by Elsevier Inc.

Plant-uptake of uranium: Hydroponic and soil system studies

USGS Publications Warehouse

Ramaswami, A.; Carr, P.; Burkhardt, M.

2001-01-01

Limited information is available on screening and selection of terrestrial plants for uptake and translocation of uranium from soil. This article evaluates the removal of uranium from water and soil by selected plants, comparing plant performance in hydroponic systems with that in two soil systems (a sandy-loam soil and an organic-rich soil). Plants selected for this study were Sunflower (Helianthus giganteus), Spring Vetch (Vicia sativa), Hairy Vetch (Vicia villosa), Juniper (Juniperus monosperma), Indian Mustard (Brassica juncea), and Bush Bean (Phaseolus nanus). Plant performance was evaluated both in terms of the percent uranium extracted from the three systems, as well as the biological absorption coefficient (BAC) that normalized uranium uptake to plant biomass. Study results indicate that uranium extraction efficiency decreased sharply across hydroponic, sandy and organic soil systems, indicating that soil organic matter sequestered uranium, rendering it largely unavailable for plant uptake. These results indicate that site-specific soils must be used to screen plants for uranium extraction capability; plant behavior in hydroponic systems does not correlate well with that in soil systems. One plant species, Juniper, exhibited consistent uranium extraction efficiencies and BACs in both sandy and organic soils, suggesting unique uranium extraction capabilities.

Preliminary selection and evaluation of the binding of aptamers against a Hantavirus antigen using fluorescence spectroscopy and modeling

NASA Astrophysics Data System (ADS)

Missailidis, Sotiris; de Oliveira, Renata Carvalho; Silva, Dilson; Cortez, Célia Martins; Guterres, Alexandro; Vicente, Luciana Helena Bassan; de Godoy, Daniela Tupy; Lemos, Elba

2015-12-01

In this study we have aimed to develop novel aptamers against the Hantavirus nucleoprotein N, a valid antigen already used in the Hantavirus reference laboratory of the Institute Oswaldo Cruz in Rio de Janeiro, Brazil. Such aptamers, if they are found to bind with high affinity and specificity for the selected hantavirus antigen, they could be translated into novel diagnostic assays with the ability to provide early detection for hantaviroses and their related disease syndromes. In a preliminary screening, we have managed to identify three aptamer species. We have analyzed a short and a long version of these aptamer using fluorescence spectroscopy and modelled their binding. We have identified Stern-Volmer constants for the selected aptamers, which have shown affinity for their target, with a different binding between the short and the long versions of them. Short aptamers have shown to have a higher Stern-Volmer constant and the ability to potentially bind to more than one binding site on the antigen. The information provided by the spectroscopic screening has been invaluable in allowing us to define candidates for further development into diagnostic assays.

Easier operation and similar power of 10 g monofilament test for screening diabetic peripheral neuropathy.

PubMed

Zhang, Qi; Yi, Na; Liu, Siying; Zheng, Hangping; Qiao, Xiaona; Xiong, Qian; Liu, Xiaoxia; Zhang, Shuo; Wen, Jie; Ye, Hongying; Zhou, Linuo; Li, Yiming; Hu, Renming; Lu, Bin

2018-01-01

Objective The 10 g Semmes-Weinstein monofilament evaluation (SWME) of 4 sites on each foot is recommended for distal symmetric polyneuropathy screening and diagnosis. A similar method has been proposed to diagnose 'high-risk' (for ulceration) feet, using 3 sites per foot. This study compared the effectiveness of SWME for testing 3, 4 and 10 sites per foot to identify patients with diabetic neuropathy. Methods We included 3497 subjects in a SWME of 10 sites; records from the 10-site SWME were used for a SWME of 3 and 4 sites. Neuropathy symptom scores and neuropathy deficit scores were evaluated to identify patients with diabetic peripheral neuropathy. Results The sensitivities of the 10 g SWME for 3, 4 and 10 sites were 17.8%, 19.0% and 22.4%, respectively. The Kappa coefficients for the SWME tests of 3, 4 and 10 sites were high (range: 0.78-0.93). Conclusions There were no significant differences in the effectiveness of 3-, 4- and 10-site SWME testing for diabetic peripheral neuropathy screening. SWME testing of 3 sites on each foot may be sufficient to screen for diabetic neuropathy.

In silico screening of small molecule libraries using the dengue virus envelope E protein has identified compounds with antiviral activity against multiple flaviviruses.

PubMed

Kampmann, Thorsten; Yennamalli, Ragothaman; Campbell, Phillipa; Stoermer, Martin J; Fairlie, David P; Kobe, Bostjan; Young, Paul R

2009-12-01

The flaviviruses comprise a large group of related viruses, many of which pose a significant global human health threat, most notably the dengue viruses (DENV), West Nile virus (WNV) and yellow fever virus (YFV). Flaviviruses enter host cells via fusion of the viral and cellular membranes, a process mediated by the major viral envelope protein E as it undergoes a low pH induced conformational change in the endosomal compartment of the host cell. This essential entry stage in the flavivirus life cycle provides an attractive target for the development of antiviral agents. We performed an in silico docking screen of the Maybridge chemical database within a previously described ligand binding pocket in the dengue E protein structure that is thought to play a key role in the conformational transitions that lead to membrane fusion. The biological activity of selected compounds identified from this screen revealed low micromolar antiviral potency against dengue virus for two of the compounds. Our results also provide the first evidence that compounds selected to bind to this ligand binding site on the flavivirus E protein abrogate fusion activity. Interestingly, one of these compounds also has antiviral activity against both WNV (kunjin strain) and YFV.

Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease.

PubMed

Li, Nan; Ainsworth, Richard I; Ding, Bo; Hou, Tingjun; Wang, Wei

2015-07-27

Human immunodeficiency virus (HIV) protease inhibitors (PIs) are important components of highly active anti-retroviral therapy (HAART) that block the catalytic site of HIV protease, thus preventing maturation of the HIV virion. However, with two decades of PI prescriptions in clinical practice, drug-resistant HIV mutants have now been found for all of the PI drugs. Therefore, the continuous development of new PI drugs is crucial both to combat the existing drug-resistant HIV strains and to provide treatments for future patients. Here we purpose an HIV PI drug design strategy to select candidate PIs with binding energy distributions dominated by interactions with conserved protease residues in both wild-type and various drug-resistant mutants. On the basis of this strategy, we have constructed a virtual screening pipeline including combinatorial library construction, combinatorial docking, MM/GBSA-based rescoring, and reranking on the basis of the binding energy distribution. We have tested our strategy on lopinavir by modifying its two functional groups. From an initial 751 689 candidate molecules, 18 candidate inhibitors were selected using the pipeline for experimental validation. IC50 measurements and drug resistance predictions successfully identified two ligands with both HIV protease inhibitor activity and an improved drug resistance profile on 2382 HIV mutants. This study provides a proof of concept for the integration of MM/GBSA energy analysis and drug resistance information at the stage of virtual screening and sheds light on future HIV drug design and the use of virtual screening to combat drug resistance.

Screening guide for rapid assessment of liquefaction hazard at highway bridge sites

DOT National Transportation Integrated Search

1998-06-16

As an aid to seismic hazard assessment, this report provides a "screening guide" for systematic evaluation of liquefactin hazard at bridge sites and a guide for prioritizing sites for further investigation or mitigation. The guide presents a systemat...

Evaluation of four rapid methods for hemoglobin screening of whole blood donors in mobile collection settings.

PubMed

Gómez-Simón, Antonia; Navarro-Núñez, Leyre; Pérez-Ceballos, Elena; Lozano, María L; Candela, María J; Cascales, Almudena; Martínez, Constantino; Corral, Javier; Vicente, Vicente; Rivera, José

2007-06-01

Predonation hemoglobin measurement is a problematic requirement in mobile donation settings, where accurate determination of venous hemoglobin by hematology analyzers is not available. We have evaluated hemoglobin screening in prospective donors by the semiquantitative copper sulphate test and by capillary blood samples analyzed by three portable photometers, HemoCue, STAT-Site MHgb, and the CompoLab HB system. Capillary blood samples were obtained from 380 donors and tested by the copper sulphate test and by at least one of the named portable photometers. Predonation venous hemoglobin was also determined in all donors using a Coulter Max-M analyzer. The three photometers provided acceptable reproducibility (CV below 5%), and displayed a significant correlation between the capillary blood samples and the venous hemoglobin (R2 0.5-0.8). HemoCue showed the best agreement with venous hemoglobin determination, followed by STAT-Site MHgb, and the CompoLab HB system. The copper sulphate test provided the highest rate of donors acceptance (83%) despite unacceptable hemoglobin levels, and the lowest rate for donor deferral (1%) despite acceptable hemoglobin levels. The percentage of donors correctly categorized for blood donation by the portable hemoglobinometers was 85%, 82%, and 76% for CompoLab HB system, HemoCue and STAT-Site, respectively. Our data suggest that hemoglobin determination remains a conflictive issue in donor selection in the mobile setting. Without appropriate performance control, capillary hemoglobin screening by either the copper sulphate method or by the novel portable hemoglobinometers could be inaccurate, thus potentially affecting both donor safety and the blood supply.

Binding-Site Assessment by Virtual Fragment Screening

PubMed Central

Huang, Niu; Jacobson, Matthew P.

2010-01-01

The accurate prediction of protein druggability (propensity to bind high-affinity drug-like small molecules) would greatly benefit the fields of chemical genomics and drug discovery. We have developed a novel approach to quantitatively assess protein druggability by computationally screening a fragment-like compound library. In analogy to NMR-based fragment screening, we dock ∼11000 fragments against a given binding site and compute a computational hit rate based on the fraction of molecules that exceed an empirically chosen score cutoff. We perform a large-scale evaluation of the approach on four datasets, totaling 152 binding sites. We demonstrate that computed hit rates correlate with hit rates measured experimentally in a previously published NMR-based screening method. Secondly, we show that the in silico fragment screening method can be used to distinguish known druggable and non-druggable targets, including both enzymes and protein-protein interaction sites. Finally, we explore the sensitivity of the results to different receptor conformations, including flexible protein-protein interaction sites. Besides its original aim to assess druggability of different protein targets, this method could be used to identifying druggable conformations of flexible binding site for lead discovery, and suggesting strategies for growing or joining initial fragment hits to obtain more potent inhibitors. PMID:20404926

Walla Walla River Basin Fish Screen Evaluations; Nursery Bridge Fishway, Garden City/Lowden II, and Little Walla Walla Sites, 2004 Annual Report.

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

Vucelick, J.; McMichael, G.

2004-11-01

Pacific Northwest National Laboratory evaluated the fish screens at the Nursery Bridge Fishway, the Garden City/Lowden II site west of Walla Walla, Washington, and the Little Walla Walla site in Milton-Freewater, Oregon, in the Walla Walla River Basin during 2004. The fish-screen facilities were examined to determine if they were being effectively operated and maintained to provide for safe fish passage. At the Nursery Bridge Fishway, the screens were evaluated specifically to determine whether the louvers that aid in controlling water flow from behind the screens could be adjusted so that the screens would meet fish-protection criteria. Data were collectedmore » to determine whether velocities in front of the screens met current National Oceanic and Atmospheric Administration's National Marine Fisheries Service (NOAA Fisheries) (formerly NMFS) criteria to promote safe and timely fish passage before and after changing the louver settings. The Little Walla Walla screens were evaluated to determine how a build-up of algae on the screens affected water velocities.« less

Modelling the Costs and Effects of Selective and Universal Hospital Admission Screening for Methicillin-Resistant Staphylococcus aureus

PubMed Central

Hubben, Gijs; Bootsma, Martin; Luteijn, Michiel; Glynn, Diarmuid; Bishai, David

2011-01-01

Background Screening at hospital admission for carriage of methicillin-resistant Staphylococcus aureus (MRSA) has been proposed as a strategy to reduce nosocomial infections. The objective of this study was to determine the long-term costs and health benefits of selective and universal screening for MRSA at hospital admission, using both PCR-based and chromogenic media-based tests in various settings. Methodology/Principal Findings A simulation model of MRSA transmission was used to determine costs and effects over 15 years from a US healthcare perspective. We compared admission screening together with isolation of identified carriers against a baseline policy without screening or isolation. Strategies included selective screening of high risk patients or universal admission screening, with PCR-based or chromogenic media-based tests, in medium (5%) or high nosocomial prevalence (15%) settings. The costs of screening and isolation per averted MRSA infection were lowest using selective chromogenic-based screening in high and medium prevalence settings, at $4,100 and $10,300, respectively. Replacing the chromogenic-based test with a PCR-based test costs $13,000 and $36,200 per additional infection averted, and subsequent extension to universal screening with PCR would cost $131,000 and $232,700 per additional infection averted, in high and medium prevalence settings respectively. Assuming $17,645 benefit per infection averted, the most cost-saving strategies in high and medium prevalence settings were selective screening with PCR and selective screening with chromogenic, respectively. Conclusions/Significance Admission screening costs $4,100–$21,200 per infection averted, depending on strategy and setting. Including financial benefits from averted infections, screening could well be cost saving. PMID:21483492

Evaluation of a novel virtual screening strategy using receptor decoy binding sites.

PubMed

Patel, Hershna; Kukol, Andreas

2016-08-23

Virtual screening is used in biomedical research to predict the binding affinity of a large set of small organic molecules to protein receptor targets. This report shows the development and evaluation of a novel yet straightforward attempt to improve this ranking in receptor-based molecular docking using a receptor-decoy strategy. This strategy includes defining a decoy binding site on the receptor and adjusting the ranking of the true binding-site virtual screen based on the decoy-site screen. The results show that by docking against a receptor-decoy site with Autodock Vina, improved Receiver Operator Characteristic Enrichment (ROCE) was achieved for 5 out of fifteen receptor targets investigated, when up to 15 % of a decoy site rank list was considered. No improved enrichment was seen for 7 targets, while for 3 targets the ROCE was reduced. The extent to which this strategy can effectively improve ligand prediction is dependent on the target receptor investigated.

Washington Phase II Fish Diversion Screen Evaluations in the Yakima and Touchet River Basins, 2005-2006 Annual Reports.

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

Chamness, Mickie; Abernethy, C.; Tunnicliffe, Cherylyn

2006-02-01

In 2005, Pacific Northwest National Laboratory (PNNL) researchers evaluated 25 Phase II fish screen sites in the Yakima and Touchet river basins. Pacific Northwest National Laboratory performs these evaluations for Bonneville Power Administration (BPA) to determine whether the fish screening devices meet National Marine Fisheries Service (NMFS) criteria to promote safe and timely fish passage. Evaluations consist of measuring velocities in front of the screens, using an underwater camera to look at the condition and environment in front of the screens, and noting the general condition and operation of the sites. Results of the evaluations in 2005 include the following:more » (1) Most approach velocities met the NMFS criterion of less than or equal to 0.4 fps. Less than 13% of all approach measurements exceeded the criterion, and these occurred at 10 of the sites. Flat-plate screens had more problems than drum screens with high approach velocities. (2) Bypass velocities generally were greater than sweep velocities, but sweep velocities often did not increase toward the bypass. The latter condition could slow migration of fish through the facility. (3) Screen and seal materials generally were in good condition. (4) Automated cleaning brushes generally functioned properly; chains and other moving parts were typically well-greased and operative. (5) Washington Department of Fish and Wildlife (WDFW) and U.S. Bureau of Reclamation (USBR) generally operate and maintain fish screen facilities in a way that provides safe passage for juvenile fish. (6) In some instances, irrigators responsible for specific maintenance at their sites (e.g., debris removal) are not performing their tasks in a way that provides optimum operation of the fish screen facility. New ways need to be found to encourage them to maintain their facilities properly. (7) We recommend placing datasheets providing up-to-date operating criteria and design flows in each sites logbox. The datasheet should include bypass design flows and a table showing depths of water over the weir and corresponding bypass flow. This information is available at some of the sites but may be outdated. These data are used to determine if the site is running within design criteria. (8) Modifying use of debris control plates at Gleed helped minimize the extreme fluctuations in flow, but approach velocities are still too high. Other ways to reduce the approach velocities need to be tried, possibly including redesign of the site. (9) Alternatives to a screen site at Taylor should be considered. A lot of effort was spent trying to increase water to the site, but it still was unable to operate within NMFS criteria for most of the year and may be a hazard to juvenile salmonids. We conclude that the conditions at most of the Phase II fish screen facilities we evaluated in 2005 would be expected to provide safe passage for juvenile fish. For those sites where conditions are not always optimum for safe fish passage, PNNL researchers will try to coordinate with the WDFW and USBR in 2006 to find solutions to the problems. Some of those problems are consistently high approach velocities at specific sites, including Congdon, Naches-Selah, Union Gap, and Yakima-Tieton. We would like to be able to monitor changes in velocities as soon as operations and maintenance personnel adjust the louvers or porosity boards at these sites. This will give them immediate feedback on the results of their modifications and allow additional adjustments as necessary until the conditions meet NMFS criteria. Pacific Northwest National Laboratory has performed evaluations at many of these sites over the past 8 years, providing information WDFW and USBR personnel can use to perform their operations and maintenance more effectively. Consequently, overall effectiveness of the screens facilities has improved over time.« less

Efficient one-cycle affinity selection of binding proteins or peptides specific for a small-molecule using a T7 phage display pool.

PubMed

Takakusagi, Yoichi; Kuramochi, Kouji; Takagi, Manami; Kusayanagi, Tomoe; Manita, Daisuke; Ozawa, Hiroko; Iwakiri, Kanako; Takakusagi, Kaori; Miyano, Yuka; Nakazaki, Atsuo; Kobayashi, Susumu; Sugawara, Fumio; Sakaguchi, Kengo

2008-11-15

Here, we report an efficient one-cycle affinity selection using a natural-protein or random-peptide T7 phage pool for identification of binding proteins or peptides specific for small-molecules. The screening procedure involved a cuvette type 27-MHz quartz-crystal microbalance (QCM) apparatus with introduction of self-assembled monolayer (SAM) for a specific small-molecule immobilization on the gold electrode surface of a sensor chip. Using this apparatus, we attempted an affinity selection of proteins or peptides against synthetic ligand for FK506-binding protein (SLF) or irinotecan (Iri, CPT-11). An affinity selection using SLF-SAM and a natural-protein T7 phage pool successfully detected FK506-binding protein 12 (FKBP12)-displaying T7 phage after an interaction time of only 10 min. Extensive exploration of time-consuming wash and/or elution conditions together with several rounds of selection was not required. Furthermore, in the selection using a 15-mer random-peptide T7 phage pool and subsequent analysis utilizing receptor ligand contact (RELIC) software, a subset of SLF-selected peptides clearly pinpointed several amino-acid residues within the binding site of FKBP12. Likewise, a subset of Iri-selected peptides pinpointed part of the positive amino-acid region of residues from the Iri-binding site of the well-known direct targets, acetylcholinesterase (AChE) and carboxylesterase (CE). Our findings demonstrate the effectiveness of this method and general applicability for a wide range of small-molecules.

Clinical Costs of Colorectal Cancer Screening in 5 Federally Funded Demonstration Programs

PubMed Central

Tangka, Florence K. L.; Subramanian, Sujha; Beebe, Maggie C.; Hoover, Sonja; Royalty, Janet; Seeff, Laura C.

2016-01-01

BACKGROUND The Centers for Disease Control and Prevention initiated the Colorectal Cancer Screening Demonstration Program (CRCSDP) to explore the feasibility of establishing a large-scale colorectal cancer (CRC) screening program for underserved populations in the United States. The authors of this report assessed the clinical costs incurred at each of the 5 participating sites during the demonstration period. METHODS By using data on payments to providers by each of the 5 CRCSDP sites, the authors estimated costs for specific clinical services and overall clinical costs for each of the 2 CRC screening methods used by the sites: colonoscopy and fecal occult blood test (FOBT). RESULTS Among CRCSDP clients who were at average risk for CRC and for whom complete cost data were available, 2131 were screened by FOBT, and 1888 were screened by colonoscopy. The total average clinical cost per individual screened by FOBT (including costs for screening, diagnosis, initial surveillance, office visits, and associated clinical services averaged across all individuals who received screening FOBT) ranged from $48 in Nebraska to $149 in Greater Seattle. This compared with an average clinical cost per individual for all services related to the colonoscopy screening ranging from $654 in St. Louis to $1600 in Baltimore City. CONCLUSIONS Variations in how sites contracted with providers and in the services provided through CRCSDP affected the cost of clinical services and the complexity of collecting cost data. Health officials may find these data useful in program planning and budgeting. PMID:23868481

Rapid assessment of environmental health risks posed by mining operations in low- and middle-income countries: selected case studies.

PubMed

Caravanos, Jack; Ericson, Bret; Ponce-Canchihuamán, Johny; Hanrahan, David; Block, Meredith; Susilorini, Budi; Fuller, Richard

2013-11-01

Previous studies have evaluated associated health risks and human exposure pathways at mining sites. Others have provided estimates of the scale of the issue based in part on surveys. However, a global census of mining-related hazardous waste sites has been lacking. The Toxic Sites Identification Program (TSIP) implemented by Blacksmith Institute (New York, NY, USA) since 2009 is an ongoing effort to catalogue a wide range of chemically contaminated sites with a potential human health risk (Ericson et al., Environ Monit Assess doi:10.1007/s 10661-012-2665-2, 2012). The TSIP utilizes a rapid assessment instrument, the Initial Site Screening (ISS), to quickly and affordably identify key site criteria including human exposure pathways, estimated populations at risk, and sampling information. The resulting ISS allows for comparison between sites exhibiting different contaminants and pollution sources. This paper explores the results of a subset of ISSs completed at 131 artisanal and small-scale gold mining areas and 275 industrial mining and ore processing sites in 45 countries. The authors show that the ISS captures key data points, allowing for prioritization of sites for further investigation or remedial activity.

Computational Optimization and Characterization of Molecularly Imprinted Polymers

NASA Astrophysics Data System (ADS)

Terracina, Jacob J.

Molecularly imprinted polymers (MIPs) are a class of materials containing sites capable of selectively binding to the imprinted target molecule. Computational chemistry techniques were used to study the effect of different fabrication parameters (the monomer-to-target ratios, pre-polymerization solvent, temperature, and pH) on the formation of the MIP binding sites. Imprinted binding sites were built in silico for the purposes of better characterizing the receptor - ligand interactions. Chiefly, the sites were characterized with respect to their selectivities and the heterogeneity between sites. First, a series of two-step molecular mechanics (MM) and quantum mechanics (QM) computational optimizations of monomer -- target systems was used to determine optimal monomer-to-target ratios for the MIPs. Imidazole- and xanthine-derived target molecules were studied. The investigation included both small-scale models (one-target) and larger scale models (five-targets). The optimal ratios differed between the small and larger scales. For the larger models containing multiple targets, binding-site surface area analysis was used to evaluate the heterogeneity of the sites. The more fully surrounded sites had greater binding energies. Molecular docking was then used to measure the selectivities of the QM-optimized binding sites by comparing the binding energies of the imprinted target to that of a structural analogue. Selectivity was also shown to improve as binding sites become more fully encased by the monomers. For internal sites, docking consistently showed selectivity favoring the molecules that had been imprinted via QM geometry optimizations. The computationally imprinted sites were shown to exhibit size-, shape-, and polarity-based selectivity. This represented a novel approach to investigate the selectivity and heterogeneity of imprinted polymer binding sites, by applying the rapid orientation screening of MM docking to the highly accurate QM-optimized geometries. Next, we sought to computationally construct and investigate binding sites for their enantioselectivity. Again, a two-step MM [special characters removed] QM optimization scheme was used to "computationally imprint" chiral molecules. Using docking techniques, the imprinted binding sites were shown to exhibit an enantioselective preference for the imprinted molecule over its enantiomer. Docking of structurally similar chiral molecules showed that the sites computationally imprinted with R- or S-tBOC-tyrosine were able to differentiate between R- and S-forms of other tyrosine derivatives. The cross-enantioselectivity did not hold for chiral molecules that did not share the tyrosine H-bonding functional group orientations. Further analysis of the individual monomer - target interactions within the binding site led us to conclude that H-bonding functional groups that are located immediately next to the target's chiral center, and therefore spatially fixed relative to the chiral center, will have a stronger contribution to the enantioselectivity of the site than those groups separated from the chiral center by two or more rotatable bonds. These models were the first computationally imprinted binding sites to exhibit this enantioselective preference for the imprinted target molecules. Finally, molecular dynamics (MD) was used to quantify H-bonding interactions between target molecules, monomers, and solvents representative of the pre-polymerization matrix. It was found that both target dimerization and solvent interference decrease the number of monomer - target H-bonds present. Systems were optimized via simulated annealing to create binding sites that were then subjected to molecular docking analysis. Docking showed that the presence of solvent had a detrimental effect on the sensitivity and selectivity of the sites, and that solvents with more H-bonding capabilities were more disruptive to the binding properties of the site. Dynamic simulations also showed that increasing the temperature of the solution can significantly decrease the number of H-bonds formed between the targets and monomers. It is believed that the monomer - target complexes formed within the pre-polymerization matrix are translated into the selective binding cavities formed during polymerization. Elucidating the nature of these interactions in silico improves our understanding of MIPs, ultimately allowing for more optimized sensing materials.

Role of genetic improvement in the Short Rotation Woody Crops Program

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

Layton, P.A.; Wright, L.L.

1986-01-01

A major effort in the Short Rotation Woody Crops Program (SRWCP) is species screening and genetic improvement of selected species. Of the 125 species initially evaluated for SRIC, 20 are being seriously considered with most of emphasis on 16 hardwood species. Range-wide seed collections of 12 species were provenance tested; these include Platanus occidentalis (sycamore), Alnus glutinosa (European black alder), and Robinia pseudoacacia (black locust). Based on the results of these tests, highly productive, site-specific seed sources are being chosen for several geographic regions. Three of these species re currently being bred for increased productivity in SRIC systems. Genetic improvementmore » is viewed as a tool for increasing productivity, having anticipated gains of 40 to 50%. The techniques of somaclonal screening and genetic engineering are being evaluated for their usefulness in the SRIC improvement program. Currently, salt-tolerant Atriplex canescens (four-wing saltbush) and herbicide-resistant Populus spp. are being sought via somaclonal screening. 35 refs., 4 figs., 3 tabs.« less

Using intervention mapping as a participatory strategy: development of a cervical cancer screening intervention for Hispanic women.

PubMed

Byrd, Theresa L; Wilson, Katherine M; Smith, Judith Lee; Heckert, Andrea; Orians, Carlyn E; Vernon, Sally W; Fernandez-Esquer, Maria E; Fernandez, Maria E

2012-10-01

Cervical cancer is preventable with treatment of precancerous lesions and treatable at early stages. Hispanics have higher rates of cervical cancer and lower rates of screening. Ayudando a las Mujeres con Informacción, Guía, y Amor para su Salud (AMIGAS) is an intervention to increase cervical cancer screening in U.S. women of Mexican origin. AMIGAS was developed with the participation of the community using intervention mapping (IM). Following the IM process, the authors completed a needs assessment, development of program objectives, selection of intervention methods and strategies, and program design. A benefit of IM is its linkage with community-based participatory research as it includes engagement of community members to identify and refine priority areas. The success of this strategy suggests it a useful tool for other populations. The resulting intervention program is currently being tested for efficacy and cost-effectiveness in three sites: El Paso, Texas; Houston, Texas; and Yakima, Washington.

Assessment of training and technical assistance needs of Colorectal Cancer Control Program Grantees in the U.S.

PubMed

Escoffery, Cam; Hannon, Peggy; Maxwell, Annette E; Vu, Thuy; Leeman, Jennifer; Dwyer, Andrea; Mason, Caitlin; Sowles, Shaina; Rice, Ketra; Gressard, Lindsay

2015-01-31

Practitioners often require training and technical assistance to build their capacity to select, adapt, and implement evidence-based interventions (EBIs). The CDC Colorectal Cancer Control Program (CRCCP) aims to promote CRC screening to increase population-level screening. This study identified the training and technical assistance (TA) needs and preferences for training related to the implementation of EBIs among CRCCP grantees. Twenty-nine CRCCP grantees completed an online survey about their screening activities, training and technical assistance in 2012. They rated desire for training on various evidence-based strategies to increase cancer screening, evidence-based competencies, and program management topics. They also reported preferences for training formats and facilitators and barriers to trainings. Many CRCCP grantees expressed the need for training with regards to specific EBIs, especially system-level and provider-directed EBIs to promote CRC screening. Grantees rated these EBIs as more difficult to implement than client-oriented EBIs. Grantees also reported a moderate need for training regarding finding EBIs, assessing organizational capacity, implementing selected EBIs, and conducting process and outcome evaluations. Other desired training topics reported with higher frequency were partnership development and data collection/evaluation. Grantees preferred training formats that were interactive such as on-site trainings, webinars or expert consultants. Public health organizations need greater supports for adopting evidence-based interventions, working with organizational-level change, partnership development and data management. Future capacity building efforts for the adoption of EBIs should focus on systems or provider level interventions and key processes for health promotion and should be delivered in a variety of ways to assist local organizations in cancer prevention and control.

Virtual screening filters for the design of type II p38 MAP kinase inhibitors: a fragment based library generation approach.

PubMed

Badrinarayan, Preethi; Sastry, G Narahari

2012-04-01

In this work, we introduce the development and application of a three-step scoring and filtering procedure for the design of type II p38 MAP kinase leads using allosteric fragments extracted from virtual screening hits. The design of the virtual screening filters is based on a thorough evaluation of docking methods, DFG-loop conformation, binding interactions and chemotype specificity of the 138 p38 MAP kinase inhibitors from Protein Data Bank bound to DFG-in and DFG-out conformations using Glide, GOLD and CDOCKER. A 40 ns molecular dynamics simulation with the apo, type I with DFG-in and type II with DFG-out forms was carried out to delineate the effects of structural variations on inhibitor binding. The designed docking-score and sub-structure filters were first tested on a dataset of 249 potent p38 MAP kinase inhibitors from seven diverse series and 18,842 kinase inhibitors from PDB, to gauge their capacity to discriminate between kinase and non-kinase inhibitors and likewise to selectively filter-in target-specific inhibitors. The designed filters were then applied in the virtual screening of a database of ten million (10⁷) compounds resulting in the identification of 100 hits. Based on their binding modes, 98 allosteric fragments were extracted from the hits and a fragment library was generated. New type II p38 MAP kinase leads were designed by tailoring the existing type I ATP site binders with allosteric fragments using a common urea linker. Target specific virtual screening filters can thus be easily developed for other kinases based on this strategy to retrieve target selective compounds. Copyright © 2012 Elsevier Inc. All rights reserved.

The Use of Routine Postoperative Microscopy and Culture Screening Following Elective Hip and Knee Arthroplasty: An Unnecessary Cost With No Effect on Clinical Management?

PubMed

Kemp, Mark A; Martina, Ka; Collins, Claire L; Salmon, Lucy J; Gooden, Benjamin R; Lyons, Matthew C

2017-04-01

The use of microscopy and culture screening to detect pathogenic microorganisms followed by a decolonization protocol is a widely performed practice prior to elective hip and knee arthroplasty. In our center, the routine care of hip and knee arthroplasty also involves postoperative screening including direct culture of the surgical site. The aim of this study was to assess the frequency of pathogen detection following these tests and to determine whether routine postoperative screening, with particular reference to postoperative surgical site culture, led to any change in clinical management of these patients. A series of 1000 patients undergoing hip or knee arthroplasty at The Mater Hospital between January 2014 and December 2015 were identified from our arthroplasty database. Results of preoperative and postoperative microscopy and culture screening were reviewed by 2 independent researchers. Of the 1000 subjects, positive microscopy and culture results were identified in 88 patients (8.8%) preoperatively and 5 patients (0.5%) postoperatively. None of the 1000 postoperative surgical site swabs had a positive microscopy and culture screen. All the 5 positive postoperative microscopy and culture screen results were in patients who had positive cultures preoperatively. There were no positive postoperative microscopy and culture screen results in patients who had had negative preoperative results. Postoperative screening was performed at a cost of AUS$213 per patient. Routine postoperative surgical site culture following hip and knee arthroplasty does not alter clinical management, has a significant associated financial cost, and has the potential to expose the patient to a risk of surgical site infection and is therefore not supported. Copyright © 2016 Elsevier Inc. All rights reserved.

Variable screening via quantile partial correlation

PubMed Central

Ma, Shujie; Tsai, Chih-Ling

2016-01-01

In quantile linear regression with ultra-high dimensional data, we propose an algorithm for screening all candidate variables and subsequently selecting relevant predictors. Specifically, we first employ quantile partial correlation for screening, and then we apply the extended Bayesian information criterion (EBIC) for best subset selection. Our proposed method can successfully select predictors when the variables are highly correlated, and it can also identify variables that make a contribution to the conditional quantiles but are marginally uncorrelated or weakly correlated with the response. Theoretical results show that the proposed algorithm can yield the sure screening set. By controlling the false selection rate, model selection consistency can be achieved theoretically. In practice, we proposed using EBIC for best subset selection so that the resulting model is screening consistent. Simulation studies demonstrate that the proposed algorithm performs well, and an empirical example is presented. PMID:28943683

Evaluation of sexual history-based screening of anatomic sites for chlamydia trachomatis and neisseria gonorrhoeae infection in men having sex with men in routine practice.

PubMed

Peters, Remco P H; Verweij, Stephan P; Nijsten, Noëmi; Ouburg, Sander; Mutsaers, Johan; Jansen, Casper L; van Leeuwen, A Petra; Morré, Servaas A

2011-07-26

Sexually transmitted infection (STI) screening programmes are implemented in many countries to decrease burden of STI and to improve sexual health. Screening for Chlamydia trachomatis and Neisseria gonorrhoeae has a prominent role in these protocols. Most of the screening programmes concerning men having sex with men (MSM) are based on opportunistic urethral testing. In The Netherlands, a history-based approach is used. The aim of this study is to evaluate the protocol of screening anatomic sites for C. trachomatis and N. gonorrhoeae infection based on sexual history in MSM in routine practice in The Netherlands. All MSM visiting the clinic for STI in The Hague are routinely asked about their sexual practice during consulting. As per protocol, tests for urogenital, oropharyngeal and anorectal infection are obtained based on reported site(s) of sexual contact. All consultations are entered into a database as part of the national STI monitoring system. Data of an 18 months period were retrieved from this database and analysed. A total of 1455 consultations in MSM were registered during the study period. The prevalence of C. trachomatis and N. gonorrhoeae per anatomic site was: urethral infection 4.0% respectively and 2.8%, oropharynx 1.5% and 4.2%, and anorectum 8.2% and 6.0%. The majority of chlamydia cases (72%) involved a single anatomic site, which was especially manifest for anorectal infections (79%), while 42% of gonorrhoea cases were single site. Twenty-six percent of MSM with anorectal chlamydia and 17% with anorectal gonorrhoea reported symptoms of proctitis; none of the oropharyngeal infections were symptomatic. Most cases of anorectal infection (83%) and oropharyngeal infection (100%) would have remained undiagnosed with a symptom-based protocol. The current strategy of sexual-history based screening of multiple anatomic sites for chlamydia and gonorrhoea in MSM is a useful and valid guideline which is to be preferred over a symptom-based screening protocol.

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.

Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae

PubMed Central

Mesarich, Carl H.; Rees-George, Jonathan; Gardner, Paul P.; Ghomi, Fatemeh Ashari; Gerth, Monica L.; Andersen, Mark T.; Rikkerink, Erik H. A.; Fineran, Peter C.

2017-01-01

Pseudomonas syringae pv. actinidiae (Psa), the causal agent of kiwifruit canker, is one of the most devastating plant diseases of recent times. We have generated two mini-Tn5-based random insertion libraries of Psa ICMP 18884. The first, a ‘phenotype of interest’ (POI) library, consists of 10,368 independent mutants gridded into 96-well plates. By replica plating onto selective media, the POI library was successfully screened for auxotrophic and motility mutants. Lipopolysaccharide (LPS) biosynthesis mutants with ‘Fuzzy-Spreader’-like morphologies were also identified through a visual screen. The second, a ‘mutant of interest’ (MOI) library, comprises around 96,000 independent mutants, also stored in 96-well plates, with approximately 200 individuals per well. The MOI library was sequenced on the Illumina MiSeq platform using Transposon-Directed Insertion site Sequencing (TraDIS) to map insertion sites onto the Psa genome. A grid-based PCR method was developed to recover individual mutants, and using this strategy, the MOI library was successfully screened for a putative LPS mutant not identified in the visual screen. The Psa chromosome and plasmid had 24,031 and 1,236 independent insertion events respectively, giving insertion frequencies of 3.65 and 16.6 per kb respectively. These data suggest that the MOI library is near saturation, with the theoretical probability of finding an insert in any one chromosomal gene estimated to be 97.5%. However, only 47% of chromosomal genes had insertions. This surprisingly low rate cannot be solely explained by the lack of insertions in essential genes, which would be expected to be around 5%. Strikingly, many accessory genes, including most of those encoding type III effectors, lacked insertions. In contrast, 94% of genes on the Psa plasmid had insertions, including for example, the type III effector HopAU1. These results suggest that some chromosomal sites are rendered inaccessible to transposon insertion, either by DNA-binding proteins or by the architecture of the nucleoid. PMID:28249011

Sensitivity of ecological soil-screening levels for metals to exposure model parameterization and toxicity reference values.

PubMed

Sample, Bradley E; Fairbrother, Anne; Kaiser, Ashley; Law, Sheryl; Adams, Bill

2014-10-01

Ecological soil-screening levels (Eco-SSLs) were developed by the United States Environmental Protection Agency (USEPA) for the purposes of setting conservative soil screening values that can be used to eliminate the need for further ecological assessment for specific analytes at a given site. Ecological soil-screening levels for wildlife represent a simplified dietary exposure model solved in terms of soil concentrations to produce exposure equal to a no-observed-adverse-effect toxicity reference value (TRV). Sensitivity analyses were performed for 6 avian and mammalian model species, and 16 metals/metalloids for which Eco-SSLs have been developed. The relative influence of model parameters was expressed as the absolute value of the range of variation observed in the resulting soil concentration when exposure is equal to the TRV. Rank analysis of variance was used to identify parameters with greatest influence on model output. For both birds and mammals, soil ingestion displayed the broadest overall range (variability), although TRVs consistently had the greatest influence on calculated soil concentrations; bioavailability in food was consistently the least influential parameter, although an important site-specific variable. Relative importance of parameters differed by trophic group. Soil ingestion ranked 2nd for carnivores and herbivores, but was 4th for invertivores. Different patterns were exhibited, depending on which parameter, trophic group, and analyte combination was considered. The approach for TRV selection was also examined in detail, with Cu as the representative analyte. The underlying assumption that generic body-weight-normalized TRVs can be used to derive protective levels for any species is not supported by the data. Whereas the use of site-, species-, and analyte-specific exposure parameters is recommended to reduce variation in exposure estimates (soil protection level), improvement of TRVs is more problematic. © 2014 The Authors. Environmental Toxicology and Chemistry Published by Wiley Periodicals, Inc.

Sensitivity of ecological soil-screening levels for metals to exposure model parameterization and toxicity reference values

PubMed Central

Sample, Bradley E; Fairbrother, Anne; Kaiser, Ashley; Law, Sheryl; Adams, Bill

2014-01-01

Ecological soil-screening levels (Eco-SSLs) were developed by the United States Environmental Protection Agency (USEPA) for the purposes of setting conservative soil screening values that can be used to eliminate the need for further ecological assessment for specific analytes at a given site. Ecological soil-screening levels for wildlife represent a simplified dietary exposure model solved in terms of soil concentrations to produce exposure equal to a no-observed-adverse-effect toxicity reference value (TRV). Sensitivity analyses were performed for 6 avian and mammalian model species, and 16 metals/metalloids for which Eco-SSLs have been developed. The relative influence of model parameters was expressed as the absolute value of the range of variation observed in the resulting soil concentration when exposure is equal to the TRV. Rank analysis of variance was used to identify parameters with greatest influence on model output. For both birds and mammals, soil ingestion displayed the broadest overall range (variability), although TRVs consistently had the greatest influence on calculated soil concentrations; bioavailability in food was consistently the least influential parameter, although an important site-specific variable. Relative importance of parameters differed by trophic group. Soil ingestion ranked 2nd for carnivores and herbivores, but was 4th for invertivores. Different patterns were exhibited, depending on which parameter, trophic group, and analyte combination was considered. The approach for TRV selection was also examined in detail, with Cu as the representative analyte. The underlying assumption that generic body-weight–normalized TRVs can be used to derive protective levels for any species is not supported by the data. Whereas the use of site-, species-, and analyte-specific exposure parameters is recommended to reduce variation in exposure estimates (soil protection level), improvement of TRVs is more problematic. Environ Toxicol Chem 2014;33:2386–2398. PMID:24944000

Geohydrologic and water-quality data in the vicinity of the Rialto-Colton Fault, San Bernardino, California

USGS Publications Warehouse

Teague, Nicholas F.; Brown, Anthony A.; Woolfenden, Linda R.

2014-01-01

The Rialto-Colton Basin is in western San Bernardino County, about 60 miles east of Los Angeles, California. The basin is bounded by faults on the northeast and southwest sides and contains multiple barriers to groundwater flow. The structural geology of the basin leads to complex hydrology. Between 2001 and 2008, in an effort to better understand the complex hydrologic system of the Rialto-Colton Basin, seven multiple-well monitoring sites were constructed. Two to six observation wells were installed in the borehole at each site; a total of 32 observation wells were installed. This report presents geologic, hydrologic, and water-quality data collected from these seven multiple-well monitoring sites. Descriptions of the collected drill cuttings were compiled into lithologic logs for each monitoring site. The lithologic logs are summarized along with the geophysical logs, including gamma-ray, spontaneous potential, resistivity, and electromagnetic induction tool logs. At selected sites, sonic tool logs also were recorded. Periodic water-level measurements are reported, and water-level data are displayed on hydrographs. Water levels at multiple-well monitoring sites in the northern part of the study area differed between the shallow and deep observation wells; in the remaining multiple-well monitoring sites, water levels differed little with depth. Along the southern trace of the Rialto-Colton Fault, water levels are slightly higher east of the fault than west of the fault. Selected water-quality data for 21 of the observation wells show water from wells in the northern and central parts of the study area is calcium-carbonate water. In the southern part of the study area, water from wells screened above 400 feet below land surface is of mixed type or is calcium-carbonate water. Water from wells screened greater than 400 feet below land surface in the southern part of the study area is sodium-carbonate or sodium-mixed anion water. Water from most wells in the study area plots above the Global Meteoric Water Line along an apparent local meteoric water line, indicating the water has not experienced substantial evaporation before infiltration. A few samples from shallow wells in the study area plot slightly to the right of the Global Meteoric Water Line, possibly indicating the water experienced some evaporation before recharge.

Using MCDA and GIS for hazardous waste landfill siting considering land scarcity for waste disposal

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

Feo, Giovanni De, E-mail: g.defeo@unisa.it; Gisi, Sabino De

Highlights: • Wasting land for the siting of hazardous waste landfills must be avoided. • The siting procedure is based on a land use map of potentially suitable areas. • All the waste facilities of the management system are simultaneously considered. • A case study is developed considering two multi-criteria techniques. • An innovative criteria weighting tool (PSW) is used in combination with the AHP. - Abstract: The main aim of this study was to develop a procedure that minimizes the wasting of space for the siting of hazardous waste landfills as part of a solid waste management system. Wemore » wanted to tackle the shortage of land for waste disposal that is a serious and growing problem in most large urban regions. The procedure combines a multi-criteria decision analysis (MCDA) approach with a geographical information system (GIS). The GIS was utilised to obtain an initial screening in order to eliminate unsuitable areas, whereas the MCDA was developed to select the most suitable sites. The novelty of the proposed siting procedure is the introduction of a new screening phase before the macro-siting step aimed at producing a “land use map of potentially suitable areas” for the siting of solid waste facilities which simultaneously takes into consideration all plant types. The issue of obtaining sites evaluations of a specific facility was coupled with the issue of not wasting land appropriate to facilitate other types of waste management options. In the developed case study, the use of an innovative criteria weighting tool (the “Priority Scale”) in combination with the Analytic Hierarchy Process was useful to easier define the priorities of the evaluation criteria in comparison with other classic methods such as the Paired Comparison Technique in combination with the Simple Additive Weighting method.« less

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

Yoo, Yong Kyoung; Center for Biomicrosystems, Korea Institute of Science and Technology, Seoul 136-791; Lee, Sang-Myung

Combining a highly sensitive sensor platform with highly selective recognition elements is essential for micro/nanotechnology-based electronic nose applications. Particularly, the regeneration sensor surface and its conditions are key issues for practical e-nose applications. We propose a highly sensitive piezoelectric-driven microcantilever array chip with highly selective peptide receptors. By utilizing the peptide receptor, which was discovered by a phase display screening process, we immobilized a dinitrotoluene (DNT) specific peptide as well as a DNT nonspecific peptide on the surface of the cantilever array. The delivery of DNT gas via pressure-driven flow led to a greater instant response of ∼30 Hz, compared tomore » diffusion only (∼15 Hz for 15 h). Using a simple pressure-driven air flow of ∼50 sccm, we confirmed that a ratio of ∼70% of the specific-bounded sites from DNT gas molecules could be regenerated, showing re-usability of the peptide receptor in on-site monitoring for electronic nose applications.« less

Seismic aftershock monitoring for on-site inspection purposes. Experience from Integrated Field Exercise 2008.

NASA Astrophysics Data System (ADS)

Labak, P.; Arndt, R.; Villagran, M.

2009-04-01

One of the sub-goals of the Integrated Field Experiment in 2008 (IFE08) in Kazakhstan was testing the prototype elements of the Seismic aftershock monitoring system (SAMS) for on-site inspection purposes. The task of the SAMS is to collect the facts, which should help to clarify nature of the triggering event. Therefore the SAMS has to be capable to detect and identify events as small as magnitude -2 in the inspection area size up to 1000 km2. Equipment for 30 mini-arrays and 10 3-component stations represented the field equipment of the SAMS. Each mini-array consisted of a central 3-component seismometer and 3 vertical seismometers at the distance about 100 m from the central seismometer. The mini-arrays covered approximately 80% of surrogate inspection area (IA) on the territory of former Semipalatinsk test site. Most of the stations were installed during the first four days of field operations by the seismic sub-team, which consisted of 10 seismologists. SAMS data center comprised 2 IBM Blade centers and 8 working places for data archiving, detection list production and event analysis. A prototype of SAMS software was tested. Average daily amount of collected raw data was 15-30 GB and increased according to the amount of stations entering operation. Routine manual data screening and data analyses were performed by 2-6 subteam members. Automatic screening was used for selected time intervals. Screening was performed using the Sonoview program in frequency domain and using the Geotool and Hypolines programs for screening in time domain. The screening results were merged into the master event list. The master event list served as a basis of detailed analysis of unclear events and events identified to be potentially in the IA. Detailed analysis of events to be potentially in the IA was performed by the Hypoline and Geotool programs. In addition, the Hyposimplex and Hypocenter programs were also used for localization of events. The results of analysis were integrated in the visual form using the Seistrain/geosearch program. Data were fully screened for the period 5.-13.9.2008. 360 teleseismic, regional and local events were identified. Results of the detection and analysis will be presented and consequences for further SAMS development will be discussed.

Screening and management of mental health and substance use disorders in HIV treatment settings in low- and middle-income countries within the global IeDEA consortium.

PubMed

Parcesepe, Angela M; Mugglin, Catrina; Nalugoda, Fred; Bernard, Charlotte; Yunihastuti, Evy; Althoff, Keri; Jaquet, Antoine; Haas, Andreas D; Duda, Stephany N; Wester, C William; Nash, Denis

2018-03-01

Integration of services to screen and manage mental health and substance use disorders (MSDs) into HIV care settings has been identified as a promising strategy to improve mental health and HIV treatment outcomes among people living with HIV/AIDS (PLWHA) in low- and middle-income countries (LMICs). Data on the extent to which HIV treatment sites in LMICs screen and manage MSDs are limited. The objective of this study was to assess practices for screening and treatment of MSDs at HIV clinics in LMICs participating in the International epidemiology Databases to Evaluate AIDS (IeDEA) consortium. We surveyed a stratified random sample of 95 HIV clinics in 29 LMICs in the Caribbean, Central and South America, Asia-Pacific and sub-Saharan Africa. The survey captured information onsite characteristics and screening and treatment practices for depression, post-traumatic stress disorder (PTSD), substance use disorders (SUDs) and other mental health disorders. Most sites (n = 76, 80%) were in urban areas. Mental health screening varied by disorder: 57% of sites surveyed screened for depression, 19% for PTSD, 55% for SUDs and 29% for other mental health disorders. Depression, PTSD, SUDs and other mental health disorders were reported as managed on site (having services provided at the HIV clinic or same health facility) at 70%, 51%, 41% and 47% of sites respectively. Combined availability of screening and on-site management of depression, PTSD, and SUDs, and other mental health disorders was reported by 42%, 14%, 26% and 19% of sites, respectively. On-site management of depression and PTSD was reported significantly less often in rural as compared to urban settings (depression: 33% and 78% respectively; PTSD: 24% and 58% respectively). Screening for depression and SUDs was least commonly reported by HIV programmes that treated only children as compared to HIV programmes that treated only adults or treated both adults and children. Significant gaps exist in the management of MSDs in HIV care settings in LMICs, particularly in rural settings. Identification and evaluation of optimal implementation strategies to scale and sustain integrated MSDs and HIV care is needed. © 2018 The Authors. Journal of the International AIDS Society published by John Wiley & sons Ltd on behalf of the International AIDS Society.

Quantifying and visualizing site performance in clinical trials.

PubMed

Yang, Eric; O'Donovan, Christopher; Phillips, JodiLyn; Atkinson, Leone; Ghosh, Krishnendu; Agrafiotis, Dimitris K

2018-03-01

One of the keys to running a successful clinical trial is the selection of high quality clinical sites, i.e., sites that are able to enroll patients quickly, engage them on an ongoing basis to prevent drop-out, and execute the trial in strict accordance to the clinical protocol. Intuitively, the historical track record of a site is one of the strongest predictors of its future performance; however, issues such as data availability and wide differences in protocol complexity can complicate interpretation. Here, we demonstrate how operational data derived from central laboratory services can provide key insights into the performance of clinical sites and help guide operational planning and site selection for new clinical trials. Our methodology uses the metadata associated with laboratory kit shipments to clinical sites (such as trial and anonymized patient identifiers, investigator names and addresses, sample collection and shipment dates, etc.) to reconstruct the complete schedule of patient visits and derive insights about the operational performance of those sites, including screening, enrollment, and drop-out rates and other quality indicators. This information can be displayed in its raw form or normalized to enable direct comparison of site performance across studies of varied design and complexity. Leveraging Covance's market leadership in central laboratory services, we have assembled a database of operational metrics that spans more than 14,000 protocols, 1400 indications, 230,000 unique investigators, and 23 million patient visits and represents a significant fraction of all clinical trials run globally in the last few years. By analyzing this historical data, we are able to assess and compare the performance of clinical investigators across a wide range of therapeutic areas and study designs. This information can be aggregated across trials and geographies to gain further insights into country and regional trends, sometimes with surprising results. The use of operational data from Covance Central Laboratories provides a unique perspective into the performance of clinical sites with respect to many important metrics such as patient enrollment and retention. These metrics can, in turn, be used to guide operational planning and site selection for new clinical trials, thereby accelerating recruitment, improving quality, and reducing cost.

[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.

Safety performance functions for intersections : final report, December 2009.

DOT National Transportation Integrated Search

2009-12-01

Road safety management activities include screening the network for sites with a potential for safety improvement (Network : Screening), diagnosing safety problems at specific sites, and evaluating the safety effectiveness of implemented : countermea...

Equal Employment Opportunity and ADA Implications of Screening and Selection.

ERIC Educational Resources Information Center

Norton, Steven D.; Hundley, John R.

1995-01-01

The process of screening and selecting new employees is viewed as one having discrete steps, each with implications concerning Equal Employment Opportunity and the Americans with Disabilities Act. Several screening and selection methods are examined, with questionnaire forms used by Indiana University, South Bend provided for illustration. Typical…

Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor.

PubMed

Lenselink, Eelke B; Beuming, Thijs; Sherman, Woody; van Vlijmen, Herman W T; IJzerman, Adriaan P

2014-06-23

A major challenge in structure-based virtual screening (VS) involves the treatment of explicit water molecules during docking in order to improve the enrichment of active compounds over decoys. Here we have investigated this in the context of the adenosine A2A receptor, where water molecules have previously been shown to be important for achieving high enrichment rates with docking, and where the positions of some binding site waters are known from a high-resolution crystal structure. The effect of these waters (both their presence and orientations) on VS enrichment was assessed using a carefully curated set of 299 high affinity A2A antagonists and 17,337 decoys. We show that including certain crystal waters greatly improves VS enrichment and that optimization of water hydrogen positions is needed in order to achieve the best results. We also show that waters derived from a molecular dynamics simulation - without any knowledge of crystallographic waters - can improve enrichments to a similar degree as the crystallographic waters, which makes this strategy applicable to structures without experimental knowledge of water positions. Finally, we used decision trees to select an ensemble of structures with different water molecule positions and orientations that outperforms any single structure with water molecules. The approach presented here is validated against independent test sets of A2A receptor antagonists and decoys from the literature. In general, this water optimization strategy could be applied to any target with waters-mediated protein-ligand interactions.

Development of a High-Throughput Ion-Exchange Resin Characterization Workflow.

PubMed

Liu, Chun; Dermody, Daniel; Harris, Keith; Boomgaard, Thomas; Sweeney, Jeff; Gisch, Daryl; Goltz, Bob

2017-06-12

A novel high-throughout (HTR) ion-exchange (IEX) resin workflow has been developed for characterizing ion exchange equilibrium of commercial and experimental IEX resins against a range of different applications where water environment differs from site to site. Because of its much higher throughput, design of experiment (DOE) methodology can be easily applied for studying the effects of multiple factors on resin performance. Two case studies will be presented to illustrate the efficacy of the combined HTR workflow and DOE method. In case study one, a series of anion exchange resins have been screened for selective removal of NO 3 - and NO 2 - in water environments consisting of multiple other anions, varied pH, and ionic strength. The response surface model (RSM) is developed to statistically correlate the resin performance with the water composition and predict the best resin candidate. In case study two, the same HTR workflow and DOE method have been applied for screening different cation exchange resins in terms of the selective removal of Mg 2+ , Ca 2+ , and Ba 2+ from high total dissolved salt (TDS) water. A master DOE model including all of the cation exchange resins is created to predict divalent cation removal by different IEX resins under specific conditions, from which the best resin candidates can be identified. The successful adoption of HTR workflow and DOE method for studying the ion exchange of IEX resins can significantly reduce the resources and time to address industry and application needs.

Chemical biology of natural indolocarbazole products: 30 years since the discovery of staurosporine.

PubMed

Nakano, Hirofumi; Omura, Satoshi

2009-01-01

Staurosporine was discovered at the Kitasato Institute in 1977 while screening for microbial alkaloids using chemical detection methods. It was during the same era that protein kinase C was discovered and oncogene v-src was shown to have protein kinase activity. Staurosporine was first isolated from a culture of Actinomyces that originated in a soil sample collected in Mizusawa City, Japan. Thereafter, indolocarbazole compounds have been isolated from a variety of organisms. The biosynthesis of staurosporine and related indolocarbazoles was finally elucidated during the past decade through genetic and biochemical studies. Subsequently, several novel indolocarbazoles have been produced using combinatorial biosynthesis. In 1986, 9 years since its discovery, staurosporine and related indolocarbazoles were shown to be nanomolar inhibitors of protein kinases. They can thus be viewed as forerunners of today's crop of novel anticancer drugs. The finding led many pharmaceutical companies to search for selective protein kinase inhibitors by screening natural products and through chemical synthesis. In the 1990s, imatinib, a Bcr-Abl tyrosine kinase inhibitor, was synthesized and, following human clinical trials for chronic myelogenous leukemia, it was approved for use in the USA in 2001. In 1992, mammalian topoisomerases were shown to be targets for indolocarbazoles. This opened up new possibilities in that indolocarbazole compounds could selectively interact with ATP-binding sites of not only protein kinases but also other proteins that had slight differences in ATP-binding sites. ABCG2, an ATP-binding cassette transporter, was recently identified as an important new target for indolocarbazoles.

Oncological screening for Bilateral Breast Reduction: a survey of practice variations in UK Breast and Plastics surgeons 2009.

PubMed

Hennedige, Anusha A; Kong, Tze Yean; Gandhi, Ashu

2011-07-01

Bilateral Breast Reduction (BBR) is a common procedure performed by Breast and Plastic surgeons in the UK. No consensus exists regarding preoperative screening for malignancy or for selective criteria for such screening. Preoperative BBR screening practices among UK Breast and Plastic surgeons are unknown. Ascertain the preoperative and postoperative BBR screening practices of UK Breast and Plastic surgeons. A questionnaire was posted to all 434 Breast and 335 Plastic surgeons in the UK. All results were analysed with relevant statistical methods. 64% of Breast surgeons and 72% of Plastic surgeons responded. 40% of Breast surgeons and 91% of Plastic surgeons perform BBR. Routine radiological screening: 92% Breast 41% Plastic (p < 0.05). Routine breast examination prior to BBR: 98% Breast 91% Plastic. Routine histology for BBR specimens: 96% Breast 90% Plastic. Selective screening of patients aged 30-40 years old: Breast 38% Plastic 10%. Selective screening of patients aged 40-50: Breast 78%, Plastic 53%. Selective screening of patients with strong family history of breast cancer: Breast 72%, Plastic 91%. Selective screening of patients with previous breast cancer: Breast 77%, Plastic 93%. There are significant differences in practice between UK Breast surgeons and Plastic surgeons in preoperative oncological screening for BBR. The large discrepancy in preoperative radiological screening, reflects a ubiquitous pro-screening ideology among Breast surgeons not prevalent among Plastic surgeons. These results will provoke debate towards the direction of consensus to ultimately reflect best practice. Copyright © 2010. Published by Elsevier Ltd.

Implementation of a DOD ELAP Conforming Quality System at a FUSRAP Site Field Temporary Radiological Screening Laboratory - 13500

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

Winters, M.S.; McElheny, G.; Houston, L.M.

2013-07-01

A case study is presented on specific program elements that supported the transition of a temporary field radiological screening lab to an accredited operation capable of meeting client quality objectives for definitive results data. The temporary field lab is located at the Formerly Utilized Sites Remedial Action Program Linde Site in Tonawanda, NY. The site is undergoing remediation under the direction of the United States Army Corps of Engineers - Buffalo District, with Cabrera Services Inc. as the remediation contractor and operator of the on-site lab. Analysis methods employed in the on-site lab include gross counting of alpha and betamore » particle activity on swipes and air filters and gamma spectroscopy of soils and other solid samples. A discussion of key program elements and lessons learned may help other organizations considering pursuit of accreditation for on-site screening laboratories. (authors)« less

On the applicability of surrogate-based Markov chain Monte Carlo-Bayesian inversion to the Community Land Model: Case studies at flux tower sites: SURROGATE-BASED MCMC FOR CLM

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

Huang, Maoyi; Ray, Jaideep; Hou, Zhangshuan

2016-07-04

The Community Land Model (CLM) has been widely used in climate and Earth system modeling. Accurate estimation of model parameters is needed for reliable model simulations and predictions under current and future conditions, respectively. In our previous work, a subset of hydrological parameters has been identified to have significant impact on surface energy fluxes at selected flux tower sites based on parameter screening and sensitivity analysis, which indicate that the parameters could potentially be estimated from surface flux observations at the towers. To date, such estimates do not exist. In this paper, we assess the feasibility of applying a Bayesianmore » model calibration technique to estimate CLM parameters at selected flux tower sites under various site conditions. The parameters are estimated as a joint probability density function (PDF) that provides estimates of uncertainty of the parameters being inverted, conditional on climatologically-average latent heat fluxes derived from observations. We find that the simulated mean latent heat fluxes from CLM using the calibrated parameters are generally improved at all sites when compared to those obtained with CLM simulations using default parameter sets. Further, our calibration method also results in credibility bounds around the simulated mean fluxes which bracket the measured data. The modes (or maximum a posteriori values) and 95% credibility intervals of the site-specific posterior PDFs are tabulated as suggested parameter values for each site. Analysis of relationships between the posterior PDFs and site conditions suggests that the parameter values are likely correlated with the plant functional type, which needs to be confirmed in future studies by extending the approach to more sites.« less

On the applicability of surrogate-based MCMC-Bayesian inversion to the Community Land Model: Case studies at Flux tower sites

DOE PAGES

Huang, Maoyi; Ray, Jaideep; Hou, Zhangshuan; ...

2016-06-01

The Community Land Model (CLM) has been widely used in climate and Earth system modeling. Accurate estimation of model parameters is needed for reliable model simulations and predictions under current and future conditions, respectively. In our previous work, a subset of hydrological parameters has been identified to have significant impact on surface energy fluxes at selected flux tower sites based on parameter screening and sensitivity analysis, which indicate that the parameters could potentially be estimated from surface flux observations at the towers. To date, such estimates do not exist. In this paper, we assess the feasibility of applying a Bayesianmore » model calibration technique to estimate CLM parameters at selected flux tower sites under various site conditions. The parameters are estimated as a joint probability density function (PDF) that provides estimates of uncertainty of the parameters being inverted, conditional on climatologically average latent heat fluxes derived from observations. We find that the simulated mean latent heat fluxes from CLM using the calibrated parameters are generally improved at all sites when compared to those obtained with CLM simulations using default parameter sets. Further, our calibration method also results in credibility bounds around the simulated mean fluxes which bracket the measured data. The modes (or maximum a posteriori values) and 95% credibility intervals of the site-specific posterior PDFs are tabulated as suggested parameter values for each site. As a result, analysis of relationships between the posterior PDFs and site conditions suggests that the parameter values are likely correlated with the plant functional type, which needs to be confirmed in future studies by extending the approach to more sites.« less

On the applicability of surrogate-based MCMC-Bayesian inversion to the Community Land Model: Case studies at Flux tower sites

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

Huang, Maoyi; Ray, Jaideep; Hou, Zhangshuan

The Community Land Model (CLM) has been widely used in climate and Earth system modeling. Accurate estimation of model parameters is needed for reliable model simulations and predictions under current and future conditions, respectively. In our previous work, a subset of hydrological parameters has been identified to have significant impact on surface energy fluxes at selected flux tower sites based on parameter screening and sensitivity analysis, which indicate that the parameters could potentially be estimated from surface flux observations at the towers. To date, such estimates do not exist. In this paper, we assess the feasibility of applying a Bayesianmore » model calibration technique to estimate CLM parameters at selected flux tower sites under various site conditions. The parameters are estimated as a joint probability density function (PDF) that provides estimates of uncertainty of the parameters being inverted, conditional on climatologically average latent heat fluxes derived from observations. We find that the simulated mean latent heat fluxes from CLM using the calibrated parameters are generally improved at all sites when compared to those obtained with CLM simulations using default parameter sets. Further, our calibration method also results in credibility bounds around the simulated mean fluxes which bracket the measured data. The modes (or maximum a posteriori values) and 95% credibility intervals of the site-specific posterior PDFs are tabulated as suggested parameter values for each site. As a result, analysis of relationships between the posterior PDFs and site conditions suggests that the parameter values are likely correlated with the plant functional type, which needs to be confirmed in future studies by extending the approach to more sites.« less

On the applicability of surrogate-based Markov chain Monte Carlo-Bayesian inversion to the Community Land Model: Case studies at flux tower sites

NASA Astrophysics Data System (ADS)

Huang, Maoyi; Ray, Jaideep; Hou, Zhangshuan; Ren, Huiying; Liu, Ying; Swiler, Laura

2016-07-01

The Community Land Model (CLM) has been widely used in climate and Earth system modeling. Accurate estimation of model parameters is needed for reliable model simulations and predictions under current and future conditions, respectively. In our previous work, a subset of hydrological parameters has been identified to have significant impact on surface energy fluxes at selected flux tower sites based on parameter screening and sensitivity analysis, which indicate that the parameters could potentially be estimated from surface flux observations at the towers. To date, such estimates do not exist. In this paper, we assess the feasibility of applying a Bayesian model calibration technique to estimate CLM parameters at selected flux tower sites under various site conditions. The parameters are estimated as a joint probability density function (PDF) that provides estimates of uncertainty of the parameters being inverted, conditional on climatologically average latent heat fluxes derived from observations. We find that the simulated mean latent heat fluxes from CLM using the calibrated parameters are generally improved at all sites when compared to those obtained with CLM simulations using default parameter sets. Further, our calibration method also results in credibility bounds around the simulated mean fluxes which bracket the measured data. The modes (or maximum a posteriori values) and 95% credibility intervals of the site-specific posterior PDFs are tabulated as suggested parameter values for each site. Analysis of relationships between the posterior PDFs and site conditions suggests that the parameter values are likely correlated with the plant functional type, which needs to be confirmed in future studies by extending the approach to more sites.

[Application of multiplex PCR for the screening of genotyping system for the rare blood groups Fy(a-), s-,k-,Di(b-) and Js(b-)].

PubMed

Jiao, Wei; Xie, Li; Li, Hailan; Lan, Jiao; Mo, Zhuning; Yang, Ziji; Liu, Fei; Xiao, Ruiping; He, Yunlei; Ye, Luyi; Zhu, Ziyan

2014-04-01

To screen rare blood groups Fy(a-), s-, k-, Di(b-) and Js(b-) in an ethnic Zhuang population. Sequence-specific primers were designed based on single nucleotide polymorphism (SNP) sites of blood group antigens Fy(b) and s. A specific multiplex PCR system I was established. Multiplex PCR system II was applied to detect alleles antigens Di(b), k, Js(b)1910 and Js(b) 2019 at the same time. The two systems was were used to screen for rare blood group antigens in 4490 randomly selected healthy donors of Guangxi Zhuang ethnic origin. We successfully made the multiplex PCR system I. We detected the rare blood group antigens using the two PCR system. There are five Fy(a-), three s(-), two Di(b-) in 4490 Guangxi zhuang random samples. The multiplex PCR system I has achieved good accuracy and stability. With multiplex PCR systems I and II, 4490 samples were screened. Five Fy(a-), three s(-) and two Di(b-) samples were discovered. Multiplex PCR is an effective methods, which can be used for high throughput screening of rare blood groups. The rare blood types of Guangxi Zhuang ethnic origin obtained through the screening can provide valuable information for compatible blood transfusion. Through screening we obtained precious rare blood type materials which can be used to improve the capability of compatible infusion and reduce the transfusion reactions.

Experimental Seismic Event-screening Criteria at the Prototype International Data Center

NASA Astrophysics Data System (ADS)

Fisk, M. D.; Jepsen, D.; Murphy, J. R.

- Experimental seismic event-screening capabilities are described, based on the difference of body-and surface-wave magnitudes (denoted as Ms:mb) and event depth. These capabilities have been implemented and tested at the prototype International Data Center (PIDC), based on recommendations by the IDC Technical Experts on Event Screening in June 1998. Screening scores are presented that indicate numerically the degree to which an event meets, or does not meet, the Ms:mb and depth screening criteria. Seismic events are also categorized as onshore, offshore, or mixed, based on their 90% location error ellipses and an onshore/offshore grid with five-minute resolution, although this analysis is not used at this time to screen out events.Results are presented of applications to almost 42,000 events with mb>=3.5 in the PIDC Standard Event Bulletin (SEB) and to 121 underground nuclear explosions (UNE's) at the U.S. Nevada Test Site (NTS), the Semipalatinsk and Novaya Zemlya test sites in the Former Soviet Union, the Lop Nor test site in China, and the Indian, Pakistan, and French Polynesian test sites. The screening criteria appear to be quite conservative. None of the known UNE's are screened out, while about 41 percent of the presumed earthquakes in the SEB with mb>=3.5 are screened out. UNE's at the Lop Nor, Indian, and Pakistan test sites on 8 June 1996, 11 May 1998, and 28 May 1998, respectively, have among the lowest Ms:mb scores of all events in the SEB.To assess the validity of the depth screening results, comparisons are presented of SEB depth solutions to those in other bulletins that are presumed to be reliable and independent. Using over 1600 events, the comparisons indicate that the SEB depth confidence intervals are consistent with or shallower than over 99.8 percent of the corresponding depth estimates in the other bulletins. Concluding remarks are provided regarding the performance of the experimental event-screening criteria, and plans for future improvements, based on recent recommendations by the IDC Technical Experts on Event Screening in May 1999.

Solar and Wind Site Screening Decision Trees

EPA Pesticide Factsheets

EPA and NREL created a decision tree to guide state and local governments and other stakeholders through a process for screening sites for their suitability for future redevelopment with solar photovoltaic (PV) energy and wind energy.

Identification of novel target sites and an inhibitor of the dengue virus E protein.

PubMed

Yennamalli, Ragothaman; Subbarao, Naidu; Kampmann, Thorsten; McGeary, Ross P; Young, Paul R; Kobe, Bostjan

2009-06-01

Dengue and related flaviviruses represent a significant global health threat. The envelope glycoprotein E mediates virus attachment to a host cell and the subsequent fusion of viral and host cell membranes. The fusion process is driven by conformational changes in the E protein and is an essential step in the virus life cycle. In this study, we analyzed the pre-fusion and post-fusion structures of the dengue virus E protein to identify potential novel sites that could bind small molecules, which could interfere with the conformational transitions that mediate the fusion process. We used an in silico virtual screening approach combining three different docking algorithms (DOCK, GOLD and FlexX) to identify compounds that are likely to bind to these sites. Seven structurally diverse molecules were selected to test experimentally for inhibition of dengue virus propagation. The best compound showed an IC(50) in the micromolar range against dengue virus type 2.

Identification of novel target sites and an inhibitor of the dengue virus E protein

NASA Astrophysics Data System (ADS)

Yennamalli, Ragothaman; Subbarao, Naidu; Kampmann, Thorsten; McGeary, Ross P.; Young, Paul R.; Kobe, Bostjan

2009-06-01

Dengue and related flaviviruses represent a significant global health threat. The envelope glycoprotein E mediates virus attachment to a host cell and the subsequent fusion of viral and host cell membranes. The fusion process is driven by conformational changes in the E protein and is an essential step in the virus life cycle. In this study, we analyzed the pre-fusion and post-fusion structures of the dengue virus E protein to identify potential novel sites that could bind small molecules, which could interfere with the conformational transitions that mediate the fusion process. We used an in silico virtual screening approach combining three different docking algorithms (DOCK, GOLD and FlexX) to identify compounds that are likely to bind to these sites. Seven structurally diverse molecules were selected to test experimentally for inhibition of dengue virus propagation. The best compound showed an IC50 in the micromolar range against dengue virus type 2.

Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets.

PubMed

Feinstein, Wei P; Brylinski, Michal

2015-01-01

Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the critical parameters for ligand docking is the size of a search space used to identify low-energy binding poses of drug candidates. Currently available docking packages often come with a default protocol for calculating the box size, however, many of these procedures have not been systematically evaluated. In this study, we investigate how the docking accuracy of AutoDock Vina is affected by the selection of a search space. We propose a new procedure for calculating the optimal docking box size that maximizes the accuracy of binding pose prediction against a non-redundant and representative dataset of 3,659 protein-ligand complexes selected from the Protein Data Bank. Subsequently, we use the Directory of Useful Decoys, Enhanced to demonstrate that the optimized docking box size also yields an improved ranking in virtual screening. Binding pockets in both datasets are derived from the experimental complex structures and, additionally, predicted by eFindSite. A systematic analysis of ligand binding poses generated by AutoDock Vina shows that the highest accuracy is achieved when the dimensions of the search space are 2.9 times larger than the radius of gyration of a docking compound. Subsequent virtual screening benchmarks demonstrate that this optimized docking box size also improves compound ranking. For instance, using predicted ligand binding sites, the average enrichment factor calculated for the top 1 % (10 %) of the screening library is 8.20 (3.28) for the optimized protocol, compared to 7.67 (3.19) for the default procedure. Depending on the evaluation metric, the optimal docking box size gives better ranking in virtual screening for about two-thirds of target proteins. This fully automated procedure can be used to optimize docking protocols in order to improve the ranking accuracy in production virtual screening simulations. Importantly, the optimized search space systematically yields better results than the default method not only for experimental pockets, but also for those predicted from protein structures. A script for calculating the optimal docking box size is freely available at www.brylinski.org/content/docking-box-size. Graphical AbstractWe developed a procedure to optimize the box size in molecular docking calculations. Left panel shows the predicted binding pose of NADP (green sticks) compared to the experimental complex structure of human aldose reductase (blue sticks) using a default protocol. Right panel shows the docking accuracy using an optimized box size.

Selection of Rear Projection Screens for Learning Carrels.

ERIC Educational Resources Information Center

Smith, Edgar A.

The selection of a rear projection screen for a learning carrel should take into account the viewing angle involved. In some carrels, the viewer can be seated in front of the screen (i.e., on the normal axis) since the screen is used primarily to present information. In these cases, where the screen will be viewed only from a restricted range, a…

Vitual screening and binding mode elucidation of curcumin analogues on Cyclooxygenase-2 using AYO_COX2_V1.1 protocol

NASA Astrophysics Data System (ADS)

Mulatsari, E.; Mumpuni, E.; Herfian, A.

2017-05-01

Curcumin is yellow colored phenolic compounds contained in Curcuma longa. Curcumin is known to have biological activities as anti-inflammatory, antiviral, antioxidant, and anti-infective agent [1]. Synthesis of curcumin analogue compounds has been done and some of them had biological activity like curcumin. In this research, the virtual screening of curcumin analogue compounds has been conducted. The purpose of this research was to determine the activity of these compounds as selective Cyclooxygenase-2inhibitors in in-silico. Binding mode elucidation was made by active and inactive representative compounds to see the interaction of the amino acids in the binding site of the compounds. This research used AYO_COX2_V.1.1, a structure-based virtual screening protocol (SBVS) that has been validated by Mumpuni E et al, 2014 [2]. AYO_COX2_V.1.1 protocol using a variety of integrated applications such as SPORES, PLANTS, BKchem, OpenBabel and PyMOL. The results of virtual screening conducted on 49 curcumin analogue compounds obtained 8 compounds with 4 active amino acid residues (GLY340, ILE503, PHE343, and PHE367) that were considered active as COX-2 inhibitor.

Effectiveness of peer education for breast cancer screening and health beliefs in eastern Turkey.

PubMed

Gözüm, Sebahat; Karayurt, Ozgul; Kav, Sultan; Platin, Nurgun

2010-01-01

The primary site of cancer in Turkish women is breast cancer. The incidence of breast cancer is increasing in Turkey. The aim of the research was to educate women 40 years and older to increase their awareness on early detection and diagnosis, to facilitate the use of the early diagnosis methods, to improve the women's beliefs in relation breast cancer, and to increase the use of Cancer Early Diagnosis and Screening Centers available in the city. The target population of the research was 5000 women. Forty selected women were educated as peer educators. Twenty-five of them were selected as principal peer educator. Each peer educator was expected to educate 200 women. Peer trainers educated their peer and also arranged for the mammography appointment of the women who decided to have theirs taken. Data were obtained before and after the training by Champion's Health Belief Model Scale, questionnaire forms, and Cancer Early Diagnosis and Screening Centers data for mammography practice. Breast cancer was detected in 8 women. Statistical analyses showed positive changes in women's health beliefs and breast self-examination knowledge. There were 20.4% of women (n = 1040) who did get mammograms, and 8% (n = 8) of women were found to have cancer in all of those screened. Peer education was found to be effective for increasing the knowledge, beliefs, and practice of women related to breast cancer. Peers can reinforce learning through ongoing contact. Peer education can be used to improve early diagnosis of breast cancer and breast cancer awareness in asymptomatic women.

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning

PubMed Central

Bacik, John-Paul; Wrenbeck, Emily E.; Michalczyk, Ryszard; Whitehead, Timothy A.

2017-01-01

Proteins are marginally stable, and an understanding of the sequence determinants for improved protein solubility is highly desired. For enzymes, it is well known that many mutations that increase protein solubility decrease catalytic activity. These competing effects frustrate efforts to design and engineer stable, active enzymes without laborious high-throughput activity screens. To address the trade-off between enzyme solubility and activity, we performed deep mutational scanning using two different screens/selections that purport to gauge protein solubility for two full-length enzymes. We assayed a TEM-1 beta-lactamase variant and levoglucosan kinase (LGK) using yeast surface display (YSD) screening and a twin-arginine translocation pathway selection. We then compared these scans with published experimental fitness landscapes. Results from the YSD screen could explain 37% of the variance in the fitness landscapes for one enzyme. Five percent to 10% of all single missense mutations improve solubility, matching theoretical predictions of global protein stability. For a given solubility-enhancing mutation, the probability that it would retain wild-type fitness was correlated with evolutionary conservation and distance to active site, and anticorrelated with contact number. Hybrid classification models were developed that could predict solubility-enhancing mutations that maintain wild-type fitness with an accuracy of 90%. The downside of using such classification models is the removal of rare mutations that improve both fitness and solubility. To reveal the biophysical basis of enhanced protein solubility and function, we determined the crystallographic structure of one such LGK mutant. Beyond fundamental insights into trade-offs between stability and activity, these results have potential biotechnological applications. PMID:28196882

Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation.

PubMed

Zhyvoloup, Alexander; Melamed, Anat; Anderson, Ian; Planas, Delphine; Lee, Chen-Hsuin; Kriston-Vizi, Janos; Ketteler, Robin; Merritt, Andy; Routy, Jean-Pierre; Ancuta, Petronela; Bangham, Charles R M; Fassati, Ariberto

2017-07-01

HIV-1 integrates more frequently into transcribed genes, however the biological significance of HIV-1 integration targeting has remained elusive. Using a selective high-throughput chemical screen, we discovered that the cardiac glycoside digoxin inhibits wild-type HIV-1 infection more potently than HIV-1 bearing a single point mutation (N74D) in the capsid protein. We confirmed that digoxin repressed viral gene expression by targeting the cellular Na+/K+ ATPase, but this did not explain its selectivity. Parallel RNAseq and integration mapping in infected cells demonstrated that digoxin inhibited expression of genes involved in T-cell activation and cell metabolism. Analysis of >400,000 unique integration sites showed that WT virus integrated more frequently than N74D mutant within or near genes susceptible to repression by digoxin and involved in T-cell activation and cell metabolism. Two main gene networks down-regulated by the drug were CD40L and CD38. Blocking CD40L by neutralizing antibodies selectively inhibited WT virus infection, phenocopying digoxin. Thus the selectivity of digoxin depends on a combination of integration targeting and repression of specific gene networks. The drug unmasked a functional connection between HIV-1 integration and T-cell activation. Our results suggest that HIV-1 evolved integration site selection to couple its early gene expression with the status of target CD4+ T-cells, which may affect latency and viral reactivation.

Model for screened, charge-regulated electrostatics of an eye lens protein: Bovine gammaB-crystallin

PubMed Central

Wahle, Christopher W.; Martini, K. Michael; Hollenbeck, Dawn M.; Langner, Andreas; Ross, David S.; Hamilton, John F.; Thurston, George M.

2018-01-01

We model screened, site-specific charge regulation of the eye lens protein bovine gammaB-crystallin (γ B) and study the probability distributions of its proton occupancy patterns. Using a simplified dielectric model, we solve the linearized Poisson-Boltzmann equation to calculate a 54 × 54 work-of-charging matrix, each entry being the modeled voltage at a given titratable site, due to an elementary charge at another site. The matrix quantifies interactions within patches of sites, including γB charge pairs. We model intrinsic pK values that would occur hypothetically in the absence of other charges, with use of experimental data on the dependence of pK values on aqueous solution conditions, the dielectric model, and literature values. We use Monte Carlo simulations to calculate a model grand-canonical partition function that incorporates both the work-of-charging and the intrinsic pK values for isolated γB molecules and we calculate the probabilities of leading proton occupancy configurations, for 4 < pH < 8 and Debye screening lengths from 6 to 20 Å. We select the interior dielectric value to model γB titration data. At pH 7.1 and Debye length 6.0 Å, on a given γB molecule the predicted top occupancy pattern is present nearly 20% of the time, and 90% of the time one or another of the first 100 patterns will be present. Many of these occupancy patterns differ in net charge sign as well as in surface voltage profile. We illustrate how charge pattern probabilities deviate from the multinomial distribution that would result from use of effective pK values alone and estimate the extents to which γB charge pattern distributions broaden at lower pH and narrow as ionic strength is lowered. These results suggest that for accurate modeling of orientation-dependent γB-γB interactions, consideration of numerous pairs of proton occupancy patterns will be needed. PMID:29346981

Model for screened, charge-regulated electrostatics of an eye lens protein: Bovine gammaB-crystallin.

PubMed

Wahle, Christopher W; Martini, K Michael; Hollenbeck, Dawn M; Langner, Andreas; Ross, David S; Hamilton, John F; Thurston, George M

2017-09-01

We model screened, site-specific charge regulation of the eye lens protein bovine gammaB-crystallin (γB) and study the probability distributions of its proton occupancy patterns. Using a simplified dielectric model, we solve the linearized Poisson-Boltzmann equation to calculate a 54×54 work-of-charging matrix, each entry being the modeled voltage at a given titratable site, due to an elementary charge at another site. The matrix quantifies interactions within patches of sites, including γB charge pairs. We model intrinsic pK values that would occur hypothetically in the absence of other charges, with use of experimental data on the dependence of pK values on aqueous solution conditions, the dielectric model, and literature values. We use Monte Carlo simulations to calculate a model grand-canonical partition function that incorporates both the work-of-charging and the intrinsic pK values for isolated γB molecules and we calculate the probabilities of leading proton occupancy configurations, for 4

Model for screened, charge-regulated electrostatics of an eye lens protein: Bovine gammaB-crystallin

NASA Astrophysics Data System (ADS)

Wahle, Christopher W.; Martini, K. Michael; Hollenbeck, Dawn M.; Langner, Andreas; Ross, David S.; Hamilton, John F.; Thurston, George M.

2017-09-01

We model screened, site-specific charge regulation of the eye lens protein bovine gammaB-crystallin (γ B ) and study the probability distributions of its proton occupancy patterns. Using a simplified dielectric model, we solve the linearized Poisson-Boltzmann equation to calculate a 54 ×54 work-of-charging matrix, each entry being the modeled voltage at a given titratable site, due to an elementary charge at another site. The matrix quantifies interactions within patches of sites, including γ B charge pairs. We model intrinsic p K values that would occur hypothetically in the absence of other charges, with use of experimental data on the dependence of p K values on aqueous solution conditions, the dielectric model, and literature values. We use Monte Carlo simulations to calculate a model grand-canonical partition function that incorporates both the work-of-charging and the intrinsic p K values for isolated γ B molecules and we calculate the probabilities of leading proton occupancy configurations, for 4

Eastern Chimpanzees, but Not Bonobos, Represent a Simian Immunodeficiency Virus Reservoir

PubMed Central

Li, Yingying; Ndjango, Jean-Bosco; Learn, Gerald H.; Ramirez, Miguel A.; Keele, Brandon F.; Bibollet-Ruche, Frederic; Liu, Weimin; Easlick, Juliet L.; Decker, Julie M.; Rudicell, Rebecca S.; Inogwabini, Bila-Isia; Ahuka-Mundeke, Steve; Leendertz, Fabian H.; Reynolds, Vernon; Muller, Martin N.; Chancellor, Rebecca L.; Rundus, Aaron S.; Simmons, Nicole; Worobey, Michael; Shaw, George M.; Peeters, Martine; Sharp, Paul M.

2012-01-01

Chimpanzees in west central Africa (Pan troglodytes troglodytes) are endemically infected with simian immunodeficiency viruses (SIVcpzPtt) that have crossed the species barrier to humans and gorillas on at least five occasions, generating pandemic and nonpandemic forms of human immunodeficiency virus type 1 (HIV-1) as well as gorilla SIV (SIVgor). Chimpanzees in east Africa (Pan troglodytes schweinfurthii) are also infected with SIVcpz; however, their viruses (SIVcpzPts) have never been found in humans. To examine whether this is due to a paucity of natural infections, we used noninvasive methods to screen wild-living eastern chimpanzees in the Democratic Republic of the Congo (DRC), Uganda, and Rwanda. We also screened bonobos (Pan paniscus) in the DRC, a species not previously tested for SIV in the wild. Fecal samples (n = 3,108) were collected at 50 field sites, tested for species and subspecies origin, and screened for SIVcpz antibodies and nucleic acids. Of 2,565 samples from eastern chimpanzees, 323 were antibody positive and 92 contained viral RNA. The antibody-positive samples represented 76 individuals from 19 field sites, all sampled north of the Congo River in an area spanning 250,000 km2. In this region, SIVcpzPts was common and widespread, with seven field sites exhibiting infection rates of 30% or greater. The overall prevalence of SIVcpzPts infection was 13.4% (95% confidence interval, 10.7% to 16.5%). In contrast, none of the 543 bonobo samples from six sites was antibody positive. All newly identified SIVcpzPts strains clustered in strict accordance to their subspecies origin; however, they exhibited considerable genetic diversity, especially in protein domains known to be under strong host selection pressure. Thus, the absence of SIVcpzPts zoonoses cannot be explained by an insufficient primate reservoir. Instead, greater adaptive hurdles may have prevented the successful colonization of humans by P. t. schweinfurthii viruses. PMID:22837215

Risk assessment of water quality in three North Carolina, USA, streams supporting federally endangered freshwater mussels (Unionidae)

USGS Publications Warehouse

Ward, S.; Augspurger, T.; Dwyer, F.J.; Kane, C.; Ingersoll, C.G.

2007-01-01

Water quality data were collected from three drainages supporting the endangered Carolina heelsplitter (Lasmigona decorata) and dwarf wedgemussel (Alasmidonta heterodon) to determine the potential for impaired water quality to limit the recovery of these freshwater mussels in North Carolina, USA. Total recoverable copper, total residual chlorine, and total ammonia nitrogen were measured every two months for approximately a year at sites bracketing wastewater sources and mussel habitat. These data and state monitoring datasets were compared with ecological screening values, including estimates of chemical concentrations likely to be protective of mussels, and federal ambient water quality criteria to assess site risks following a hazard quotient approach. In one drainage, the site-specific ammonia ecological screening value for acute exposures was exceeded in 6% of the samples, and 15% of samples exceeded the chronic ecological screening value; however, ammonia concentrations were generally below levels of concern in other drainages. In all drainages, copper concentrations were higher than ecological screening values most frequently (exceeding the ecological screening values for acute exposures in 65-94% of the samples). Chlorine concentrations exceeding the acute water quality criterion were observed in 14 and 35% of samples in two of three drainages. The ecological screening values were exceeded most frequently in Goose Creek and the Upper Tar River drainages; concentrations rarely exceeded ecological screening values in the Swift Creek drainage except for copper. The site-specific risk assessment approach provides valuable information (including site-specific risk estimates and ecological screening values for protection) that can be applied through regulatory and nonregulatory means to improve water quality for mussels where risks are indicated and pollutant threats persist. ?? 2007 SETAC.

Semirational Approach for Ultrahigh Poly(3-hydroxybutyrate) Accumulation in Escherichia coli by Combining One-Step Library Construction and High-Throughput Screening.

PubMed

Li, Teng; Ye, Jianwen; Shen, Rui; Zong, Yeqing; Zhao, Xuejin; Lou, Chunbo; Chen, Guo-Qiang

2016-11-18

As a product of a multistep enzymatic reaction, accumulation of poly(3-hydroxybutyrate) (PHB) in Escherichia coli (E. coli) can be achieved by overexpression of the PHB synthesis pathway from a native producer involving three genes phbC, phbA, and phbB. Pathway optimization by adjusting expression levels of the three genes can influence properties of the final product. Here, we reported a semirational approach for highly efficient PHB pathway optimization in E. coli based on a phbCAB operon cloned from the native producer Ralstonia entropha (R. entropha). Rationally designed ribosomal binding site (RBS) libraries with defined strengths for each of the three genes were constructed based on high or low copy number plasmids in a one-pot reaction by an oligo-linker mediated assembly (OLMA) method. Strains with desired properties were evaluated and selected by three different methodologies, including visual selection, high-throughput screening, and detailed in-depth analysis. Applying this approach, strains accumulating 0%-92% PHB contents in cell dry weight (CDW) were achieved. PHB with various weight-average molecular weights (M w ) of 2.7-6.8 × 10 6 were also efficiently produced in relatively high contents. These results suggest that the semirational approach combining library design, construction, and proper screening is an efficient way to optimize PHB and other multienzyme pathways.

Evaluation of feedback interventions for improving the quality assurance of cancer screening in Japan: study design and report of the baseline survey.

PubMed

Machii, Ryoko; Saika, Kumiko; Higashi, Takahiro; Aoki, Ayako; Hamashima, Chisato; Saito, Hiroshi

2012-02-01

The importance of quality assurance in cancer screening has recently gained increasing attention in Japan. To evaluate and improve quality, checklists and process indicators have been developed. To explore effective methods of enhancing quality in cancer screening, we started a randomized control study of the methods of evaluation and feedback for cancer control from 2009 to 2014. We randomly assigned 1270 municipal governments, equivalent to 71% of all Japanese municipal governments that performed screening programs, into three groups. The high-intensity intervention groups (n = 425) were individually evaluated using both checklist performance and process indicator values, while the low-intensity intervention groups (n= 421) were individually evaluated on the basis of only checklist performance. The control group (n = 424) received only a basic report that included the national average of checklist performance scores. We repeated the survey for each municipality's quality assurance activity performance using checklists and process indicators. In this paper, we report our study design and the result of the baseline survey. The checklist adherence rates were especially low in the checklist elements related to invitation of individuals, detailed monitoring of process indicators such as cancer detection rates according to screening histories and appropriate selection of screening facilities. Screening rate and percentage of examinees who underwent detailed examination tended to be lower for large cities when compared with smaller cities for all cancer sites. The performance of the Japanese cancer screening program in 2009 was identified for the first time.

Ab initio study of the Coulomb interaction in NbxCo clusters: Strong on-site versus weak nonlocal screening

NASA Astrophysics Data System (ADS)

Peters, L.; Şaşıoǧlu, E.; Mertig, I.; Katsnelson, M. I.

2018-01-01

By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the full-potential linearized augmented plane wave method, we study the screening of the Coulomb interaction in NbxCo (1 ≤x ≤9 ) clusters. In addition, these results are compared with pure bcc Nb bulk. We find that for all clusters the on-site Coulomb interaction in RPA is strongly screened, whereas the intersite nonlocal Coulomb interaction is weakly screened and for some clusters it is unscreened or even antiscreened. This is in strong contrast with pure Nb bulk, where the intersite Coulomb interaction is almost completely screened. Furthermore, constrained RPA calculations reveal that the contribution of the Co 3 d → 3 d channel to the total screening of the Co 3 d electrons is small. Moreover, we find that both the on-site and intersite Coulomb interaction parameters decrease in a reasonable approximation linearly with the cluster size and for clusters having more than 20 Nb atoms a transition from 0D to 3D screening is expected to take place.

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

PubMed Central

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

2013-01-01

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

Design, synthesis and antimalarial screening of some hybrid 4-aminoquinoline-triazine derivatives against pf-DHFR-TS.

PubMed

Sahu, Supriya; Ghosh, Surajit Kumar; Kalita, Junmoni; Dutta, Mayurakhi; Bhat, Hans Raj

2016-04-01

Existing antifolate antimalarial drugs have shown resistance due to the mutations at some amino acid positions of Plasmodium falciparum DHFR-TS. In the present study, to overcome this resistance, a new series of hybrid 4-aminoquinoline-triazine derivatives were designed and docked into the active site of Pf-DHFR-TS (PDB i.d. 1J3K) using validated CDOCKER protocol. Binding energy was calculated by applying CHARMm forcefield. Binding energy and the pattern of interaction of the docked compounds were analysed. Fifteen compounds were selected for synthesis based on their binding energy values and docking poses. Synthesized compounds were characterised by FTIR, (1)H NMR, (13)C NMR, mass spectroscopy and were screened for antimalarial activity against 3D7 strain of Plasmodium falciparum. Copyright © 2016 Elsevier Inc. All rights reserved.

Construction of CRISPR Libraries for Functional Screening.

PubMed

Carstens, Carsten P; Felts, Katherine A; Johns, Sarah E

2018-01-01

Identification of gene function has been aided by the ability to generate targeted gene knockouts or transcriptional repression using the CRISPR/CAS9 system. Using pooled libraries of guide RNA expression vectors that direct CAS9 to a specific genomic site allows identification of genes that are either enriched or depleted in response to a selection scheme, thus linking the affected gene to the chosen phenotype. The quality of the data generated by the screening is dependent on the quality of the guide RNA delivery library with regards to error rates and especially evenness of distribution of the guides. Here, we describe a method for constructing complex plasmid libraries based on pooled designed oligomers with high representation and tight distributions. The procedure allows construction of plasmid libraries of >60,000 members with a 95th/5th percentile ratio of less than 3.5.

CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction.

PubMed

Xu, Youjun; Wang, Shiwei; Hu, Qiwan; Gao, Shuaishi; Ma, Xiaomin; Zhang, Weilin; Shen, Yihang; Chen, Fangjin; Lai, Luhua; Pei, Jianfeng

2018-05-10

CavityPlus is a web server that offers protein cavity detection and various functional analyses. Using protein three-dimensional structural information as the input, CavityPlus applies CAVITY to detect potential binding sites on the surface of a given protein structure and rank them based on ligandability and druggability scores. These potential binding sites can be further analysed using three submodules, CavPharmer, CorrSite, and CovCys. CavPharmer uses a receptor-based pharmacophore modelling program, Pocket, to automatically extract pharmacophore features within cavities. CorrSite identifies potential allosteric ligand-binding sites based on motion correlation analyses between cavities. CovCys automatically detects druggable cysteine residues, which is especially useful to identify novel binding sites for designing covalent allosteric ligands. Overall, CavityPlus provides an integrated platform for analysing comprehensive properties of protein binding cavities. Such analyses are useful for many aspects of drug design and discovery, including target selection and identification, virtual screening, de novo drug design, and allosteric and covalent-binding drug design. The CavityPlus web server is freely available at http://repharma.pku.edu.cn/cavityplus or http://www.pkumdl.cn/cavityplus.

EPA RE-Powering Mapper: Alternative Energy Potential at Cleanup Sites

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management??s (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

The value of testing multiple anatomic sites for gonorrhoea and chlamydia in sexually transmitted infection centres in the Netherlands, 2006-2010.

PubMed

Koedijk, F D H; van Bergen, J E A M; Dukers-Muijrers, N H T M; van Leeuwen, A P; Hoebe, C J P A; van der Sande, M A B

2012-09-01

National surveillance data from 2006 to 2010 of the Dutch sexually transmitted infection (STI) centres were used to analyse current practices on testing extragenital sites for chlamydia and gonorrhoea in men who have sex with men (MSM) and women. In MSM, 76.0% and 88.9% were tested at least at one extragenital site (pharyngeal and/or anorectal) for chlamydia and gonorrhoea, respectively; for women this was 20.5% and 30.2%. Testing more than one anatomic site differed by STI centre, ranging from 2% to 100%. In MSM tested at multiple sites, 63.0% and 66.5% of chlamydia and gonorrhoea diagnoses, respectively, would have been missed if screened at the urogenital site only, mainly anorectal infections. For women tested at multiple sites, the proportions of missed chlamydia and gonorrhoea diagnoses would have been 12.9% and 30.0%, respectively. Testing extragenital sites appears warranted, due to the numerous infections that would have been missed. Adding anorectal screening to urogenital screening for all MSM visiting an STI centre should be recommended. Since actual testing practices differ by centre, there is a need for clearer guidelines. Routine gonorrhoea and chlamydia screening at multiple sites in STI centres should be investigated further as this might be a more effective approach to reduce transmission than current practice.

Identification of STAT1 and STAT3 Specific Inhibitors Using Comparative Virtual Screening and Docking Validation

PubMed Central

Szelag, Malgorzata; Czerwoniec, Anna; Wesoly, Joanna; Bluyssen, Hans A. R.

2015-01-01

Signal transducers and activators of transcription (STATs) facilitate action of cytokines, growth factors and pathogens. STAT activation is mediated by a highly conserved SH2 domain, which interacts with phosphotyrosine motifs for specific STAT-receptor contacts and STAT dimerization. The active dimers induce gene transcription in the nucleus by binding to a specific DNA-response element in the promoter of target genes. Abnormal activation of STAT signaling pathways is implicated in many human diseases, like cancer, inflammation and auto-immunity. Searches for STAT-targeting compounds, exploring the phosphotyrosine (pTyr)-SH2 interaction site, yielded many small molecules for STAT3 but sparsely for other STATs. However, many of these inhibitors seem not STAT3-specific, thereby questioning the present modeling and selection strategies of SH2 domain-based STAT inhibitors. We generated new 3D structure models for all human (h)STATs and developed a comparative in silico docking strategy to obtain further insight into STAT-SH2 cross-binding specificity of a selection of previously identified STAT3 inhibitors. Indeed, by primarily targeting the highly conserved pTyr-SH2 binding pocket the majority of these compounds exhibited similar binding affinity and tendency scores for all STATs. By comparative screening of a natural product library we provided initial proof for the possibility to identify STAT1 as well as STAT3-specific inhibitors, introducing the ‘STAT-comparative binding affinity value’ and ‘ligand binding pose variation’ as selection criteria. In silico screening of a multi-million clean leads (CL) compound library for binding of all STATs, likewise identified potential specific inhibitors for STAT1 and STAT3 after docking validation. Based on comparative virtual screening and docking validation, we developed a novel STAT inhibitor screening tool that allows identification of specific STAT1 and STAT3 inhibitory compounds. This could increase our understanding of the functional role of these STATs in different diseases and benefit the clinical need for more drugable STAT inhibitors with high specificity, potency and excellent bioavailability. PMID:25710482

Establishing physico-chemical reference conditions in Mediterranean streams according to the European Water Framework Directive.

PubMed

Sánchez-Montoya, María del Mar; Arce, Maria Isabel; Vidal-Abarca, María Rosario; Suárez, María Luisa; Prat, Narcís; Gómez, Rosa

2012-05-01

Type-specific physico-chemical reference conditions are required for the assessment of ecological status in the Water Framework Directive context, similarly to the biological and hydro-morphological elements. This directive emphasises that natural variability of quality elements in high status (reference condition) needs to be quantified. Mediterranean streams often present a marked seasonal pattern in hydrological, biological and geochemical processes which could affect physico-chemical reference conditions. This study establishes general physico-chemical reference conditions (oxygenation, nutrient, salinity and acidification conditions) for different Mediterranean stream types. 116 potential reference sites located in 23 Mediterranean catchments in Spain were sampled in spring, summer and autumn in 2003. All sites were subjected to a screening method for the selection of reference sites in Mediterranean streams (Mediterranean Reference Criteria) and classified using a pre-established stream typology that establishes five different stream types (temporary streams, evaporite-calcareous at medium altitude, siliceous headwaters, calcareous headwaters and large watercourses). Reference conditions (reference value and reference threshold equivalents to high-good class boundary) were calculated using two different methods according to the availability of reference sites: the reference site 75th percentile approach of all reference sites and the 25th percentile of the population approach. The majority of the studied potential reference sites (76 out of 116) were selected as reference sites. Regarding type-specific reference conditions, only siliceous headwaters could be considered different from the rest of stream types because lower conductivity and pH. All reference stream types presented seasonal differences as regards some parameters, except for temporary streams due to the high natural variation of this stream type. For those parameters which presented seasonal differences in a specific stream type, the least restrictive values were proposed as reference conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Screening, Brief Intervention, and Referral to Treatment for Older Adults With Substance Misuse

PubMed Central

Hazlett, Robert W.; Hedgecock, Deborah K.; Duchene, Darran M.; Burns, L. Vance; Gum, Amber M.

2015-01-01

Objectives. We compared substance use and SBIRT (Screening, Brief Intervention, and Referral to Treatment) services received for older adults screened by the Florida BRITE (BRief Intervention and Treatment of Elders) Project, across 4 categories of service providers. Methods. Staff from 29 agencies screened for substance use risk in 75 sites across 18 Florida counties. Clients at no or low risk received feedback about screening; moderate risk led to brief intervention, moderate or high risk led to brief treatment, and highest severity led to referral to treatment. Six-month follow-ups were conducted with a random sample of clients. Results. Over 5 years (September 15, 2006–September 14, 2011), 85 001 client screenings were recorded. Of these, 8165 clients were at moderate or high risk. Most received brief intervention for alcohol or medication misuse. Differences were observed across 4 categories of agencies. Health educators screening solely within medical sites recorded fewer positive screens than those from mental health, substance abuse, or aging services that screened in a variety of community-based and health care sites. Six-month follow-ups revealed a significant decrease in substance use. Conclusions. The Florida BRITE Project demonstrated that SBIRT can be extended to nonmedical services that serve older adults. PMID:24832147

Disappointing performance of literature-derived selective screening criteria for asymptomatic Chlamydia trachomatis infection in an inner-city population.

PubMed

van Valkengoed, I G; Boeke, A J; Morré, S A; van den Brule, A J; Meijer, C J; Devillé, W; Bouter, L M

2000-10-01

In an inner-city population with a low prevalence of Chlamydia trachomatis infection, selective screening may be indicated to increase the efficiency of screening. To evaluate the performance of sets of selective screening criteria for asymptomatic Chlamydia trachomatis infection in an inner-city population. The criteria were derived from reports of studies carried out in various settings. A total of 5714 women age 15 to 40 years living in Amsterdam were invited for a screening based on home-obtained urine specimens. Criteria identified from the literature were applied to the screening population. A calculated area under the receiver-operator characteristic curve (AUC) of greater than 0.75 was considered a good measure of diagnostic accuracy. Of the four sets of criteria, selection based on the following determinants showed the highest diagnostic accuracy: younger than 25 years, being unmarried, number of partners during the previous 6 months, Surinam or Antillean origin (black), and vaginal douching (AUC, 0.67; 95% CI, 0.65-0.69). Selection based on age alone showed an AUC of 0.57 (95% CI, 0.55-0.69). The performance of selective screening criteria for asymptomatic C trachomatis infection in an inner-city population in Amsterdam was insufficient to recommend its implementation in practice.

Non-visual Web Browsing: Beyond Web Accessibility

PubMed Central

Ramakrishnan, I.V.; Ashok, Vikas

2017-01-01

People with vision impairments typically use screen readers to browse the Web. To facilitate non-visual browsing, web sites must be made accessible to screen readers, i.e., all the visible elements in the web site must be readable by the screen reader. But even if web sites are accessible, screen-reader users may not find them easy to use and/or easy to navigate. For example, they may not be able to locate the desired information without having to listen to a lot of irrelevant contents. These issues go beyond web accessibility and directly impact web usability. Several techniques have been reported in the accessibility literature for making the Web usable for screen reading. This paper is a review of these techniques. Interestingly, the review reveals that understanding the semantics of the web content is the overarching theme that drives these techniques for improving web usability. PMID:29202137

Non-visual Web Browsing: Beyond Web Accessibility.

PubMed

Ramakrishnan, I V; Ashok, Vikas; Billah, Syed Masum

2017-07-01

People with vision impairments typically use screen readers to browse the Web. To facilitate non-visual browsing, web sites must be made accessible to screen readers, i.e., all the visible elements in the web site must be readable by the screen reader. But even if web sites are accessible, screen-reader users may not find them easy to use and/or easy to navigate. For example, they may not be able to locate the desired information without having to listen to a lot of irrelevant contents. These issues go beyond web accessibility and directly impact web usability. Several techniques have been reported in the accessibility literature for making the Web usable for screen reading. This paper is a review of these techniques. Interestingly, the review reveals that understanding the semantics of the web content is the overarching theme that drives these techniques for improving web usability.

Computer-assisted identification of novel small molecule inhibitors targeting GLUT1

NASA Astrophysics Data System (ADS)

Wan, Zhining; Li, Xin; Sun, Rong; Li, Yuanyuan; Wang, Xiaoyun; Li, Xinru; Rong, Li; Shi, Zheng; Bao, Jinku

2015-12-01

Glucose transporters (GLUTs) are the main carriers of glucose that facilitate the diffusion of glucose in mammalian cells, especially GLUT1. Notably, GLUT1 is a rate-limiting transporter for glucose uptake, and its overexpression is a common characteristic in most cancers. Thus, the inhibition of GLUT1 by novel small compounds to lower glucose levels for cancer cells has become an emerging strategy. Herein, we employed high-throughput screening approaches to identify potential inhibitors against the sugar-binding site of GLUT1. Firstly, molecular docking screening was launched against the specs products, and three molecules (ZINC19909927, ZINC19908826, and ZINC19815451) were selected as candidate GLUT1 inhibitors for further analysis. Then, taking the initial ligand β-NG as a reference, molecular dynamic (MD) simulations and molecular mechanics/generalized born surface area (MM/GBSA) method were applied to evaluate the binding stability and affinity of the three candidates towards GLUT1. Finally, we found that ZINC19909927 might have the highest affinity to occupy the binding site of GLUT1. Meanwhile, energy decomposition analysis identified several residues located in substrate-binding site that might provide clues for future inhibitor discovery towards GLUT1. Taken together, these results in our study may provide valuable information for identifying new inhibitors targeting GLUT1-mediated glucose transport and metabolism for cancer therapeutics.

A tiered approach to distinguish sources of gasoline and diesel spills.

PubMed

Xiong, Wenhui; Bernesky, Ryan; Bechard, Robert; Michaud, Guy; Lang, Jeremy

2014-07-15

Approximately 11% and 25% of annual Canadian oil spill accidents are gasoline and diesel spills, respectively. Gasoline and diesel spills are a challenge to conventional environmental forensic techniques because refinery processes remove most of the higher molecular weight biomarkers. This study presents a tiered environmental forensics strategy that includes such information as site operational history, geology/hydrogeology, GC/FID pre-screening, volatile GC/MS, semi-volatile GC/MS, and GC/MS selected ion monitoring (SIM) chromatograms for fingerprinting of gasoline and diesel spills. GC/FID pre-screening analysis identified the presence of two individual gasoline and diesel plumes at a fuel service station (study site). The gasoline plume is present between the upgradient fuel underground storage tanks (USTs) and the downgradient diesel plume, suggesting that the diesel impacts to groundwater may not be originated from the current UST leakage. Similar distribution of C3-alkylbenzenes (the most stable chemicals in gasoline) and the consistent diagnostic ratios of the analyte pairs with similar solubility indicate that the source for the dissolved gasoline constituents in the gasoline impacted zone likely originated from a gasoline leakage from the current USTs on the study site. In the diesel impacted zone, the distinct distribution and diagnostic ratios of sesquiterpanes (biomarkers for diesel) and alkylated PAHs confirm that the diesel plume originate from different crude oil sources than the current USTs. Copyright © 2014 Elsevier B.V. All rights reserved.

Scheme for the selection of measurement uncertainty models in blood establishments' screening immunoassays.

PubMed

Pereira, Paulo; Westgard, James O; Encarnação, Pedro; Seghatchian, Jerard; de Sousa, Gracinda

2015-02-01

Blood establishments routinely perform screening immunoassays to assess safety of the blood components. As with any other screening test, results have an inherent uncertainty. In blood establishments the major concern is the chance of false negatives, due to its possible impact on patients' health. This article briefly reviews GUM and diagnostic accuracy models for screening immunoassays, recommending a scheme to support the screening laboratories' staffs on the selection of a model considering the intended use of the screening results (i.e., post-transfusion safety). The discussion is grounded on a "risk-based thinking", risk being considered from the blood donor selection to the screening immunoassays. A combination of GUM and diagnostic accuracy models to evaluate measurement uncertainty in blood establishments is recommended. Copyright © 2014 Elsevier Ltd. All rights reserved.

Retrovolution: HIV-driven evolution of cellular genes and improvement of anticancer drug activation.

PubMed

Rossolillo, Paola; Winter, Flore; Simon-Loriere, Etienne; Gallois-Montbrun, Sarah; Negroni, Matteo

2012-08-01

In evolution strategies aimed at isolating molecules with new functions, screening for the desired phenotype is generally performed in vitro or in bacteria. When the final goal of the strategy is the modification of the human cell, the mutants selected with these preliminary screenings may fail to confer the desired phenotype, due to the complex networks that regulate gene expression in higher eukaryotes. We developed a system where, by mimicking successive infection cycles with HIV-1 derived vectors containing the gene target of the evolution in their genome, libraries of gene mutants are generated in the human cell, where they can be directly screened. As a proof of concept we created a library of mutants of the human deoxycytidine kinase (dCK) gene, involved in the activation of nucleoside analogues used in cancer treatment, with the aim of isolating a variant sensitizing cancer cells to the chemotherapy compound Gemcitabine, to be used in gene therapy for anti-cancer approaches or as a poorly immunogenic negative selection marker for cell transplantation approaches. We describe the isolation of a dCK mutant, G12, inducing a 300-fold sensitization to Gemcitabine in cells originally resistant to the prodrug (Messa 10K), an effect 60 times stronger than the one induced by the wt enzyme. The phenotype is observed in different tumour cell lines irrespective of the insertion site of the transgene and is due to a change in specificity of the mutated kinase in favour of the nucleoside analogue. The mutations characterizing G12 are distant from the active site of the enzyme and are unpredictable on a rational basis, fully validating the pragmatic approach followed. Besides the potential interest of the G12 dCK variant for therapeutic purposes, the methodology developed is of interest for a large panel of applications in biotechnology and basic research.

Walla Walla River Basin Fish Screen Evaluations, 2003: Nursery Bridge Fishway and Garden City-Lowden II

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

Vucelick, Jessica A.; McMichael, Geoffrey A.

2003-11-01

The Pacific Northwest National Laboratory (PNNL) evaluated the fish screens at the Nursery Bridge Fishway and at the newly constructed Garden City-Lowden II site west of Walla Walla, Washington in the Walla Walla River Basin during the spring and summer of 2003. Both fish screen facilities were examined to determine if they were being effectively operated and maintained to provide for safe fish passage. At the Nursery Bridge Fishway, the screens were evaluated specifically to determine whether the louvers that aid in controlling water flow from behind the screens could be adjusted so that the screens would meet fish protectionmore » criteria. Data were collected to determine whether velocities in front of the screens and in the bypasses met current National Oceanic and Atmospheric Administration Fisheries ((NOAA Fisheries), formerly National Marine Fisheries Service (NMFS)) criteria to promote safe and timely fish passage before and after changing the louver settings. Rock weirs downstream of the dam were also evaluated to determine whether they might impede upstream migration of juvenile salmonids during low flow conditions. At the Garden City-Lowden II site, data were collected to establish a baseline for operating conditions and to determine whether any changes in the baffle settings were needed. Based on the results of our studies in 2003, we concluded: Nursery Bridge Site: (1) 68% of the initial velocity measurements on the west screen exceeded the NOAA Fisheries criteria of 0.4 ft/s for approach velocity; (2) A simple adjustment of the existing louvers was not sufficient to fix the problem; (3) The sediment and debris load in the river upstream of the screens exceeded the design criteria for the site, which had frequent breakdowns in the screen cleaning systems; and (4) The rock weirs downstream of the dam would not be expected to impede upstream movement of juvenile fish during low flow conditions. Garden City-Lowden II: (1) The flat inclined-plate screen design appeared to be efficiently protecting juvenile fish from entrainment, impingement and migration delay; (2) Approach velocities met the NMFS criteria of less than 0.4 ft/s in June, and no change in baffle settings was needed; (3) Sweep velocities were generally lower than approach velocities and did not increase toward the downstream end of the site; and (4) The automated cleaning system at the Garden City-Lowden II site works adequately when sediment loads are low, though its effectiveness at cleaning the screens decreases as sediment and debris loads and algal growth increase.« less

Combinatorial Methodology for Screening Selectivity in Polymeric Pervaporation Membranes.

PubMed

Godbole, Rutvik V; Ma, Lan; Doerfert, Michael D; Williams, Porsche; Hedden, Ronald C

2015-11-09

Combinatorial methodology is described for rapid screening of selectivity in polymeric pervaporation membrane materials for alcohol-water separations. The screening technique is demonstrated for ethanol-water separation using a model polyacrylate system. The materials studied are cross-linked random copolymers of a hydrophobic comonomer (n-butyl acrylate, B) and a hydrophilic comonomer (2-hydroxyethyl acrylate, H). A matrix of materials is prepared that has orthogonal variations in two key variables, H:B ratio and cross-linker concentration. For mixtures of ethanol and water, equilibrium selectivities and distribution coefficients are obtained by combining swelling measurements with high-throughput HPLC analysis. Based on the screening results, two copolymers are selected for further study as pervaporation membranes to quantify permeability selectivity and the flux of ethanol. The screening methodology described has good potential to accelerate the search for new membrane materials, as it is adaptable to a broad range of polymer chemistries.

EPA RE-Powering Mapper Region 10

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 4

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Large Scale

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 2

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 6

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 8

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 7

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 5

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 3

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Solar on Landfills

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 9

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Utility Scale

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 1

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

Zebrafish embryos as a screen for DNA methylation modifications after compound exposure.

PubMed

Bouwmeester, Manon C; Ruiter, Sander; Lommelaars, Tobias; Sippel, Josefine; Hodemaekers, Hennie M; van den Brandhof, Evert-Jan; Pennings, Jeroen L A; Kamstra, Jorke H; Jelinek, Jaroslav; Issa, Jean-Pierre J; Legler, Juliette; van der Ven, Leo T M

2016-01-15

Modified epigenetic programming early in life is proposed to underlie the development of an adverse adult phenotype, known as the Developmental Origins of Health and Disease (DOHaD) concept. Several environmental contaminants have been implicated as modifying factors of the developing epigenome. This underlines the need to investigate this newly recognized toxicological risk and systematically screen for the epigenome modifying potential of compounds. In this study, we examined the applicability of the zebrafish embryo as a screening model for DNA methylation modifications. Embryos were exposed from 0 to 72 h post fertilization (hpf) to bisphenol-A (BPA), diethylstilbestrol, 17α-ethynylestradiol, nickel, cadmium, tributyltin, arsenite, perfluoroctanoic acid, valproic acid, flusilazole, 5-azacytidine (5AC) in subtoxic concentrations. Both global and site-specific methylation was examined. Global methylation was only affected by 5AC. Genome wide locus-specific analysis was performed for BPA exposed embryos using Digital Restriction Enzyme Analysis of Methylation (DREAM), which showed minimal wide scale effects on the genome, whereas potential informative markers were not confirmed by pyrosequencing. Site-specific methylation was examined in the promoter regions of three selected genes vasa, vtg1 and cyp19a2, of which vasa (ddx4) was the most responsive. This analysis distinguished estrogenic compounds from metals by direction and sensitivity of the effect compared to embryotoxicity. In conclusion, the zebrafish embryo is a potential screening tool to examine DNA methylation modifications after xenobiotic exposure. The next step is to examine the adult phenotype of exposed embryos and to analyze molecular mechanisms that potentially link epigenetic effects and altered phenotypes, to support the DOHaD hypothesis. Copyright © 2015 Elsevier Inc. All rights reserved.

Analytical Validation of a Portable Mass Spectrometer Featuring Interchangeable, Ambient Ionization Sources for High Throughput Forensic Evidence Screening

NASA Astrophysics Data System (ADS)

Lawton, Zachary E.; Traub, Angelica; Fatigante, William L.; Mancias, Jose; O'Leary, Adam E.; Hall, Seth E.; Wieland, Jamie R.; Oberacher, Herbert; Gizzi, Michael C.; Mulligan, Christopher C.

2017-06-01

Forensic evidentiary backlogs are indicative of the growing need for cost-effective, high-throughput instrumental methods. One such emerging technology that shows high promise in meeting this demand while also allowing on-site forensic investigation is portable mass spectrometric (MS) instrumentation, particularly that which enables the coupling to ambient ionization techniques. While the benefits of rapid, on-site screening of contraband can be anticipated, the inherent legal implications of field-collected data necessitates that the analytical performance of technology employed be commensurate with accepted techniques. To this end, comprehensive analytical validation studies are required before broad incorporation by forensic practitioners can be considered, and are the focus of this work. Pertinent performance characteristics such as throughput, selectivity, accuracy/precision, method robustness, and ruggedness have been investigated. Reliability in the form of false positive/negative response rates is also assessed, examining the effect of variables such as user training and experience level. To provide flexibility toward broad chemical evidence analysis, a suite of rapidly-interchangeable ion sources has been developed and characterized through the analysis of common illicit chemicals and emerging threats like substituted phenethylamines. [Figure not available: see fulltext.

Comparison of a rational vs. high throughput approach for rapid salt screening and selection.

PubMed

Collman, Benjamin M; Miller, Jonathan M; Seadeek, Christopher; Stambek, Julie A; Blackburn, Anthony C

2013-01-01

In recent years, high throughput (HT) screening has become the most widely used approach for early phase salt screening and selection in a drug discovery/development setting. The purpose of this study was to compare a rational approach for salt screening and selection to those results previously generated using a HT approach. The rational approach involved a much smaller number of initial trials (one salt synthesis attempt per counterion) that were selected based on a few strategic solubility determinations of the free form combined with a theoretical analysis of the ideal solvent solubility conditions for salt formation. Salt screening results for sertraline, tamoxifen, and trazodone using the rational approach were compared to those previously generated by HT screening. The rational approach produced similar results to HT screening, including identification of the commercially chosen salt forms, but with a fraction of the crystallization attempts. Moreover, the rational approach provided enough solid from the very initial crystallization of a salt for more thorough and reliable solid-state characterization and thus rapid decision-making. The crystallization techniques used in the rational approach mimic larger-scale process crystallization, allowing smoother technical transfer of the selected salt to the process chemist.

Entertainment education for prostate cancer screening: a randomized trial among primary care patients with low health literacy.

PubMed

Volk, Robert J; Jibaja-Weiss, Maria L; Hawley, Sarah T; Kneuper, Suzanne; Spann, Stephen J; Miles, Brian J; Hyman, David J

2008-12-01

To evaluate an entertainment-based patient decision aid for prostate cancer screening among patients with low or high health literacy. Male primary care patients from two clinical sites, one characterized as serving patients with low health literacy (n=149) and the second as serving patients with high health literacy (n=301), were randomized to receive an entertainment-based decision aid for prostate cancer screening or an audiobooklet-control aid with the same learner content but without the entertainment features. Postintervention and 2-week follow-up assessments were conducted. Patients at the low-literacy site were more engaged with the entertainment-based aid than patients at the high-literacy site. Overall, knowledge improved for all patients. Among patients at the low-literacy site, the entertainment-based aid was associated with lower decisional conflict and greater self-advocacy (i.e., mastering and obtaining information about screening) when compared to patients given the audiobooklet. No differences between the aids were observed for patients at the high-literacy site. Entertainment education may be an effective strategy for promoting informed decision making about prostate cancer screening among patients with lower health literacy. As barriers to implementing computer-based patient decision support programs decrease, alternative models for delivering these programs should be explored.

Challenges in fecal donor selection and screening for fecal microbiota transplantation: A review.

PubMed

Woodworth, Michael H; Carpentieri, Cynthia; Sitchenko, Kaitlin L; Kraft, Colleen S

2017-05-04

Fecal microbiota transplantation is best understood as an effective and inexpensive therapy for recurrent Clostridium difficile infection but fecal donor selection and screening should be periodically revised. Here, we review current recommendations for selection and screening of fecal donors for fecal microbiota transplantation. We recommend considering diabetes mellitus, prior cardiovascular events, and clinical healthcare exposure as fecal donor exclusion criteria until more is known about the association of these conditions with the human gut microbiome. We review the non-bacterial members of the human gut microbiome, associations of the gut microbiome with colorectal malignancies, the human gut resistome and how these may impact future donor screening recommendations. Collaboration between clinicians, clinical laboratory scientists, industry and regulatory agencies will be critically important for continued improvement in donor selection and screening.

The siting program of geological repository for spent fuel/high-level waste in Czech Republic

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

Novotny, P.

1993-12-31

The management of high-level waste in Czech Republic have a very short history, because before the year 1989 spent nuclear fuel was re-exported back to USSR. The project ``Geological research of HLW repository in Czech Republic`` was initiated during 1990 by the Ministry of the Environment of the Czech Republic and by this project delegated the Czech Geological Survey (CGU) Prague. The first CGU project late in 1990 for multibarrier concept has proposed a geological repository to be located at a depth of about 500 m. Screening and studies of potential sites for repository started in 1991. First stage representedmore » regional siting of the Czech Republic for perspective rock types and massifs. In cooperation with GEOPHYSICS Co., Geophysical Institute of the Czech Academy of Sciences and Charles University Prague 27 perspective regions were selected, using criteria IAEA. This work in the Czech Republic was possible thanks to the detailed geological studies done in the past and thanks to the numerous archive data, concentrated in the central geological archive GEOFOND. Selection of perspective sites also respected natural conservation regions, regions conserving water and mineral waters resources. CGU opened up contact with countries with similar geological situation and started cooperation with SKB (Swedish Nuclear Fuel and Waste Management Co.). The Project of geological research for the next 10 years is a result of these activities.« less

Discovery and structure-activity relationship of oxalylarylaminobenzoic acids as inhibitors of protein tyrosine phosphatase 1B.

PubMed

Liu, Gang; Szczepankiewicz, Bruce G; Pei, Zhonghua; Janowick, David A; Xin, Zhili; Hajduk, Philip J; Abad-Zapatero, Cele; Liang, Heng; Hutchins, Charles W; Fesik, Stephen W; Ballaron, Steve J; Stashko, Mike A; Lubben, Tom; Mika, Amanda K; Zinker, Bradley A; Trevillyan, James M; Jirousek, Michael R

2003-05-22

Protein Tyrosine phosphatase 1B (PTP1B) has been implicated as a key negative regulator of both insulin and leptin signaling pathways. Using an NMR-based screening approach with 15N- and 13C-labeled PTP1B, we have identified 2,3-dimethylphenyloxalylaminobenzoic acid (1) as a general, reversible, and competitive PTPase inhibitor. Structure-based approach guided by X-ray crystallography facilitated the development of 1 into a novel series of potent and selective PTP1B inhibitors occupying both the catalytic site and a portion of the noncatalytic, second phosphotyrosine binding site. Interestingly, oral biovailability has been observed in rats for some compounds. Furthermore, we demonstrated in vivo plasma glucose lowering effects with compound 12d in ob/ob mice.

Screening for Psychopathology Versus Selecting for Suitability: Ethical and Legal Considerations

NASA Technical Reports Server (NTRS)

Holland, Albert W.; Galarza, Laura; Arvey, Richard; Hysong, Sylvia; Sackett, Paul; Cascio, Wayne

2000-01-01

The current system for psychological selection of U.S. astronauts is divided into two phases: The select-out phase and the select-in phase. The select-out phase screens candidates for psychopathology; candidates who do not meet the baseline psychiatric requirements are immediately disqualified. The select-in phase assesses candidates for suitability to fly short- and long-duration missions. Suitability ratings are given for ten factors found to be critical for short and long-duration space missions. There are qualitative differences in the purpose of the two phases (select-in vs. select-out) and in the nature of the information collected in each phase. Furthermore, there are different logistic, ethical, and legal issues related to a medical or psychiatric (select-out) screening versus a suitability (select-in) psychological screening process . The purpose of this presentation is to contrast the ethical and legal environment surrounding the select-out and select-in phases of the psychological selection system. Issues such as data collection, data storage and management, the federal statutory environment, and personnel training will be discussed. Further, a summary of the new standards for psychological testing is presented, along with their implications for astronaut selection.

Sulfated Pentagalloylglucoside is a Potent, Allosteric, and Selective Inhibitor of Factor XIa

PubMed Central

Al-Horani, Rami A.; Ponnusamy, Pooja; Mehta, Akul Y.; Gailani, David; Desai, Umesh R.

2013-01-01

Inhibition of factor XIa (FXIa) is a novel paradigm for developing anticoagulants without major bleeding consequences. We present the discovery of sulfated pentagalloylglucoside (6) as a highly selective inhibitor of human FXIa. Biochemical screening of a focused library led to the identification of 6, a sulfated aromatic mimetic of heparin. Inhibitor 6 displayed a potency of 551 nM against FXIa, which was at least 200-fold more selective than other relevant enzymes. It also prevented activation of factor IX and prolonged human plasma and whole blood clotting. Inhibitor 6 reduced VMAX of FXIa hydrolysis of chromogenic substrate without affecting the KM suggesting an allosteric mechanism. Competitive studies showed that 6 bound in the heparin-binding site of FXIa. No allosteric small molecule has been discovered to date that exhibits equivalent potency against FXIa. Inhibitor 6 is expected to open up a major route to allosteric FXIa anticoagulants with clinical relevance. PMID:23316863

Field test of on-site drug detection devices

DOT National Transportation Integrated Search

2000-10-01

This NHTSA-sponsored study reports the findings of a field evaluation of five on-site drug screening devices used by law enforcement to screen for illicit drugs among drivers suspected of driving under the influence (DUI) of alcohol or other drugs. I...

Walla Walla River Basin Fish Screen Evaluations; Nursery Bridge Fishway and Garden City/Lowden II Sites, 2005-2006 Progress Report.

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

Chamness, Mickie

2006-06-01

Pacific Northwest National Laboratory (PNNL) evaluated two fish screen facilities in the Walla Walla River basin in 2005 and early 2006. The Garden City/Lowden screen site was evaluated in April and June 2005 to determine whether the fish screens met National Marine Fisheries Service criteria to provide safe passage for juvenile salmonids. Louvers behind the screens at the Nursery Bridge Fishway were modified in fall 2005 in an attempt to minimize high approach velocities. PNNL evaluated the effects of those modifications in March 2006. Results of the Garden City/Lowden evaluations indicate the site performs well at varying river levels andmore » canal flows. Approach velocities did not exceed 0.4 feet per second (fps) at any time. Sweep velocities increased toward the fish ladder in March but not in June. The air-burst mechanism appears to keep large debris off the screens, although it does not prevent algae and periphyton from growing on the screen face, especially near the bottom of the screens. At Nursery Bridge, results indicate all the approach velocities were below 0.4 fps under the moderate river levels and operational conditions encountered on March 7, 2006. Sweep did not consistently increase toward the fish ladder, but the site generally met the criteria for safe passage of juvenile salmonids. Modifications to the louvers seem to allow more control over the amount of water moving through the screens. We will measure approach velocities when river levels are higher to determine whether the louver modifications can help correct excessive approach velocities under a range of river levels and auxiliary water supply flows.« less

[Chemical databases and virtual screening].

PubMed

Rognan, Didier; Bonnet, Pascal

2014-12-01

A prerequisite to any virtual screening is the definition of compound libraries to be screened. As we describe here, various sources are available. The selection of the proper library is usually project-dependent but at least as important as the screening method itself. This review details the main compound libraries that are available for virtual screening and guide the reader to the best possible selection according to its needs. © 2014 médecine/sciences – Inserm.

Discrete Fourier Transform-Based Multivariate Image Analysis: Application to Modeling of Aromatase Inhibitory Activity.

PubMed

Barigye, Stephen J; Freitas, Matheus P; Ausina, Priscila; Zancan, Patricia; Sola-Penna, Mauro; Castillo-Garit, Juan A

2018-02-12

We recently generalized the formerly alignment-dependent multivariate image analysis applied to quantitative structure-activity relationships (MIA-QSAR) method through the application of the discrete Fourier transform (DFT), allowing for its application to noncongruent and structurally diverse chemical compound data sets. Here we report the first practical application of this method in the screening of molecular entities of therapeutic interest, with human aromatase inhibitory activity as the case study. We developed an ensemble classification model based on the two-dimensional (2D) DFT MIA-QSAR descriptors, with which we screened the NCI Diversity Set V (1593 compounds) and obtained 34 chemical compounds with possible aromatase inhibitory activity. These compounds were docked into the aromatase active site, and the 10 most promising compounds were selected for in vitro experimental validation. Of these compounds, 7419 (nonsteroidal) and 89 201 (steroidal) demonstrated satisfactory antiproliferative and aromatase inhibitory activities. The obtained results suggest that the 2D-DFT MIA-QSAR method may be useful in ligand-based virtual screening of new molecular entities of therapeutic utility.

Summary of Organic Wastewater Compounds and Other Water-Quality Data in Charles County, Maryland, October 2007 through August 2008

USGS Publications Warehouse

Lorah, Michelle M.; Soeder, Daniel J.; Teunis, Jessica A.

2010-01-01

The U.S. Geological Survey, in cooperation with the government of Charles County, Maryland, and the Port Tobacco River Conservancy, Inc., conducted a water-quality reconnaissance and sampling investigation of the Port Tobacco River and Nanjemoy Creek watersheds in Charles County during October 2007 and June-August 2008. Samples were collected and analyzed for major ions, nutrients, organic wastewater compounds, and other selected constituents from 17 surface-water sites and 11 well sites (5 of which were screened in streambed sediments to obtain porewater samples). Most of the surface-water sites were relatively widely spaced throughout the Port Tobacco River and Nanjemoy Creek watersheds, although the well sites and some associated surface-water sites were concentrated in one residential community along the Port Tobacco River that has domestic septic systems. Sampling for enterococci bacteria was conducted by the Port Tobacco River Conservancy, Inc., at each site to coordinate with the sampling for chemical constituents. The purpose of the coordinated sampling was to determine correlations between historically high, in-stream bacteria counts and human wastewater inputs. Chemical data for the groundwater, porewater, and surface-water samples are presented in this report.

Directed divergent evolution of a thermostable D-tagatose epimerase towards improved activity for two hexose substrates.

PubMed

Bosshart, Andreas; Hee, Chee Seng; Bechtold, Matthias; Schirmer, Tilman; Panke, Sven

2015-03-02

Functional promiscuity of enzymes can often be harnessed as the starting point for the directed evolution of novel biocatalysts. Here we describe the divergent morphing of an engineered thermostable variant (Var8) of a promiscuous D-tagatose epimerase (DTE) into two efficient catalysts for the C3 epimerization of D-fructose to D-psicose and of L-sorbose to L-tagatose. Iterative single-site randomization and screening of 48 residues in the first and second shells around the substrate-binding site of Var8 yielded the eight-site mutant IDF8 (ninefold improved kcat for the epimerization of D-fructose) and the six-site mutant ILS6 (14-fold improved epimerization of L-sorbose), compared to Var8. Structure analysis of IDF8 revealed a charged patch at the entrance of its active site; this presumably facilitates entry of the polar substrate. The improvement in catalytic activity of variant ILS6 is thought to relate to subtle changes in the hydration of the bound substrate. The structures can now be used to select additional sites for further directed evolution of the ketohexose epimerase. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Attitudes to Chlamydia screening elicited using the social networking site Facebook for subject recruitment.

PubMed

Ahmed, Navera; Jayasinghe, Yasmin; Wark, John D; Fenner, Yeshe; Moore, Elya E; Tabrizi, Sepehr N; Fletcher, Ashley; Garland, Suzanne M

2013-07-01

Chlamydia (Chlamydia trachomatis) is the commonest bacterial sexually transmissible infection worldwide and contributes to significant morbidity in females. We examined potential barriers and facilitating factors for screening in young Victorian women, using the social networking site, Facebook to recruit participants. This was part of a larger study on young women's health that assessed the feasibility of using social networking sites for recruitment. An advertisement was placed on Facebook between May and September 2010, and was visible to eligible women. Women who clicked on the advertisement and expressed their interest in participating were invited to complete a questionnaire either at a study site or online. In total, 278 participants completed the survey, with 76% reporting willingness to participate in chlamydia screening by recruitment via an online system. Overall, 73% of participants indicated they were comfortable providing a urine sample collected at home for chlamydia screening, with older participants less comfortable with this method (P=0.02, odds ratio (OR)=0.09, 95% confidence interval (CI)=0.01-0.7). Participants expressed comfort with their Pap smear and chlamydia screening being performed together (92.7%), especially those who were aware of human papillomavirus (P<0.01, OR=2.5, 95% CI=1.3-4.7). This study demonstrated willingness by young Victorian women using Facebook to participate in screening for chlamydia. There was strong acceptance of self-collected sampling, and of combined chlamydia and cervical cytology screening. Facebook may therefore be a feasible way for improving screening coverage at a population level.

Neuron-specific feeding RNAi in C. elegans and its use in a screen for essential genes required for GABA neuron function.

PubMed

Firnhaber, Christopher; Hammarlund, Marc

2013-11-01

Forward genetic screens are important tools for exploring the genetic requirements for neuronal function. However, conventional forward screens often have difficulty identifying genes whose relevant functions are masked by pleiotropy. In particular, if loss of gene function results in sterility, lethality, or other severe pleiotropy, neuronal-specific functions cannot be readily analyzed. Here we describe a method in C. elegans for generating cell-specific knockdown in neurons using feeding RNAi and its application in a screen for the role of essential genes in GABAergic neurons. We combine manipulations that increase the sensitivity of select neurons to RNAi with manipulations that block RNAi in other cells. We produce animal strains in which feeding RNAi results in restricted gene knockdown in either GABA-, acetylcholine-, dopamine-, or glutamate-releasing neurons. In these strains, we observe neuron cell-type specific behavioral changes when we knock down genes required for these neurons to function, including genes encoding the basal neurotransmission machinery. These reagents enable high-throughput, cell-specific knockdown in the nervous system, facilitating rapid dissection of the site of gene action and screening for neuronal functions of essential genes. Using the GABA-specific RNAi strain, we screened 1,320 RNAi clones targeting essential genes on chromosomes I, II, and III for their effect on GABA neuron function. We identified 48 genes whose GABA cell-specific knockdown resulted in reduced GABA motor output. This screen extends our understanding of the genetic requirements for continued neuronal function in a mature organism.

A screen for kinase inhibitors identifies antimicrobial imidazopyridine aminofurazans as specific inhibitors of the Listeria monocytogenes PASTA kinase PrkA

PubMed Central

Schaenzer, Adam J.; Wlodarchak, Nathan; Drewry, David H.; Zuercher, William J.; Rose, Warren E.; Striker, Rob; Sauer, John-Demian

2017-01-01

Bacterial signaling systems such as protein kinases and quorum sensing have become increasingly attractive targets for the development of novel antimicrobial agents in a time of rising antibiotic resistance. The family of bacterial Penicillin-binding-protein And Serine/Threonine kinase-Associated (PASTA) kinases is of particular interest due to the role of these kinases in regulating resistance to β-lactam antibiotics. As such, small-molecule kinase inhibitors that target PASTA kinases may prove beneficial as treatments adjunctive to β-lactam therapy. Despite this interest, only limited progress has been made in identifying functional inhibitors of the PASTA kinases that have both activity against the intact microbe and high kinase specificity. Here, we report the results of a small-molecule screen that identified GSK690693, an imidazopyridine aminofurazan-type kinase inhibitor that increases the sensitivity of the intracellular pathogen Listeria monocytogenes to various β-lactams by inhibiting the PASTA kinase PrkA. GSK690693 potently inhibited PrkA kinase activity biochemically and exhibited significant selectivity for PrkA relative to the Staphylococcus aureus PASTA kinase Stk1. Furthermore, other imidazopyridine aminofurazans could effectively inhibit PrkA and potentiate β-lactam antibiotic activity to varying degrees. The presence of the 2-methyl-3-butyn-2-ol (alkynol) moiety was important for both biochemical and antimicrobial activity. Finally, mutagenesis studies demonstrated residues in the back pocket of the active site are important for GSK690693 selectivity. These data suggest that targeted screens can successfully identify PASTA kinase inhibitors with both biochemical and antimicrobial specificity. Moreover, the imidazopyridine aminofurazans represent a family of PASTA kinase inhibitors that have the potential to be optimized for selective PASTA kinase inhibition. PMID:28821610

A screen for kinase inhibitors identifies antimicrobial imidazopyridine aminofurazans as specific inhibitors of the Listeria monocytogenes PASTA kinase PrkA.

PubMed

Schaenzer, Adam J; Wlodarchak, Nathan; Drewry, David H; Zuercher, William J; Rose, Warren E; Striker, Rob; Sauer, John-Demian

2017-10-13

Bacterial signaling systems such as protein kinases and quorum sensing have become increasingly attractive targets for the development of novel antimicrobial agents in a time of rising antibiotic resistance. The family of bacterial P enicillin-binding-protein A nd S erine/ T hreonine kinase- A ssociated (PASTA) kinases is of particular interest due to the role of these kinases in regulating resistance to β-lactam antibiotics. As such, small-molecule kinase inhibitors that target PASTA kinases may prove beneficial as treatments adjunctive to β-lactam therapy. Despite this interest, only limited progress has been made in identifying functional inhibitors of the PASTA kinases that have both activity against the intact microbe and high kinase specificity. Here, we report the results of a small-molecule screen that identified GSK690693, an imidazopyridine aminofurazan-type kinase inhibitor that increases the sensitivity of the intracellular pathogen Listeria monocytogenes to various β-lactams by inhibiting the PASTA kinase PrkA. GSK690693 potently inhibited PrkA kinase activity biochemically and exhibited significant selectivity for PrkA relative to the Staphylococcus aureus PASTA kinase Stk1. Furthermore, other imidazopyridine aminofurazans could effectively inhibit PrkA and potentiate β-lactam antibiotic activity to varying degrees. The presence of the 2-methyl-3-butyn-2-ol (alkynol) moiety was important for both biochemical and antimicrobial activity. Finally, mutagenesis studies demonstrated residues in the back pocket of the active site are important for GSK690693 selectivity. These data suggest that targeted screens can successfully identify PASTA kinase inhibitors with both biochemical and antimicrobial specificity. Moreover, the imidazopyridine aminofurazans represent a family of PASTA kinase inhibitors that have the potential to be optimized for selective PASTA kinase inhibition.

Screening of HIV-1 Protease Using a Combination of an Ultra-High-Throughput Fluorescent-Based Assay and RapidFire Mass Spectrometry.

PubMed

Meng, Juncai; Lai, Ming-Tain; Munshi, Vandna; Grobler, Jay; McCauley, John; Zuck, Paul; Johnson, Eric N; Uebele, Victor N; Hermes, Jeffrey D; Adam, Gregory C

2015-06-01

HIV-1 protease (PR) represents one of the primary targets for developing antiviral agents for the treatment of HIV-infected patients. To identify novel PR inhibitors, a label-free, high-throughput mass spectrometry (HTMS) assay was developed using the RapidFire platform and applied as an orthogonal assay to confirm hits identified in a fluorescence resonance energy transfer (FRET)-based primary screen of > 1 million compounds. For substrate selection, a panel of peptide substrates derived from natural processing sites for PR was evaluated on the RapidFire platform. As a result, KVSLNFPIL, a new substrate measured to have a ~ 20- and 60-fold improvement in k cat/K m over the frequently used sequences SQNYPIVQ and SQNYPIV, respectively, was identified for the HTMS screen. About 17% of hits from the FRET-based primary screen were confirmed in the HTMS confirmatory assay including all 304 known PR inhibitors in the set, demonstrating that the HTMS assay is effective at triaging false-positives while capturing true hits. Hence, with a sampling rate of ~7 s per well, the RapidFire HTMS assay enables the high-throughput evaluation of peptide substrates and functions as an efficient tool for hits triage in the discovery of novel PR inhibitors. © 2015 Society for Laboratory Automation and Screening.

Nationwide genetic analysis for molecularly unresolved cystic fibrosis patients in a multiethnic society: implications for preconception carrier screening.

PubMed

Behar, Doron M; Inbar, Ori; Shteinberg, Michal; Gur, Michal; Mussaffi, Huda; Shoseyov, David; Ashkenazi, Moshe; Alkrinawi, Soliman; Bormans, Concetta; Hakim, Fahed; Mei-Zahav, Meir; Cohen-Cymberknoh, Malena; Dagan, Adi; Prais, Dario; Sarouk, Ifat; Stafler, Patrick; Bar Aluma, Bat El; Akler, Gidon; Picard, Elie; Aviram, Micha; Efrati, Ori; Livnat, Galit; Rivlin, Joseph; Bentur, Lea; Blau, Hannah; Kerem, Eitan; Singer, Amihood

2017-05-01

Preconception carrier screening for cystic fibrosis (CF) is usually performed using ethnically targeted panels of selected mutations. This has been recently challenged by the use of expanded, ethnically indifferent, pan-population panels. Israel is characterized by genetically heterogeneous populations carrying a wide range of CFTR mutations. To assess the potential of expanding the current Israeli preconception screening program, we sought the subset of molecularly unresolved CF patients listed in the Israeli CF data registry comprising ~650 patients. An Israeli nationwide genotyping of 152 CF cases, representing 176 patients lacking molecular diagnosis, was conducted. Molecular analysis included Sanger sequencing for all exons and splice sites, multiplex ligation probe amplification (MLPA), and next-generation sequencing of the poly-T/TG tracts. We identified 54 different mutations, of which only 16 overlapped the 22 mutations included in the Israeli preconception screening program. A total of 29/54 (53.7%) mutations were already listed as CF causing by the CFTR2 database, and only 4/54 (7.4%) were novel. Molecular diagnosis was reached in 78/152 (51.3%) cases. Prenatal diagnosis of 24/78 (30.8%) cases could have been achieved by including all CFTR2-causing mutations in the Israeli panel. Our data reveal an overwhelming hidden abundance of CFTR gene mutations suggesting that expanded preconception carrier screening might achieve higher preconception detection rates.

Evaluation of a new website design for iwantthekit for chlamydia, gonorrhea, and trichomonas screening.

PubMed

Kuder, Margaret; Goheen, Mary Jett; Dize, Laura; Barnes, Mathilda; Gaydos, Charlotte A

2015-05-01

The www.iwantthekit.org provides Internet-based, at-home sexually transmitted infection screening. The Web site implemented an automated test result access system. To evaluate potential deleterious effects of the new system, we analyzed demographics, Web site usage, and treatment. The post-Web site design captured more participant information and no decrease in requests, kit return, or treatment adherence.

A genome-wide map of hyper-edited RNA reveals numerous new sites.

PubMed

Porath, Hagit T; Carmi, Shai; Levanon, Erez Y

2014-08-27

Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive ('hyper') editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites.

A rapid, controlled-environment seedling root screen for wheat correlates well with rooting depths at vegetative, but not reproductive, stages at two field sites

PubMed Central

Watt, M.; Moosavi, S.; Cunningham, S. C.; Kirkegaard, J. A.; Rebetzke, G. J.; Richards, R. A.

2013-01-01

Background and Aims Root length and depth determine capture of water and nutrients by plants, and are targets for crop improvement. Here we assess a controlled-environment wheat seedling screen to determine speed, repeatability and relatedness to performance of young and adult plants in the field. Methods Recombinant inbred lines (RILs) and diverse genotypes were grown in rolled, moist germination paper in growth cabinets, and primary root number and length were measured when leaf 1 or 2 were fully expanded. For comparison, plants were grown in the field and root systems were harvested at the two-leaf stage with either a shovel or a soil core. From about the four-leaf stage, roots were extracted with a steel coring tube only, placed directly over the plant and pushed to the required depth with a hydraulic ram attached to a tractor. Key Results In growth cabinets, repeatability was greatest (r = 0·8, P < 0·01) when the paper was maintained moist and seed weight, pathogens and germination times were controlled. Scanned total root length (slow) was strongly correlated (r = 0·7, P < 0·01) with length of the two longest seminal axile roots measured with a ruler (fast), such that 100–200 genotypes were measured per day. Correlation to field-grown roots at two sites at two leaves was positive and significant within the RILs and cultivars (r = 0·6, P = 0·01), and at one of the two sites at the five-leaf stage within the RILs (r = 0·8, P = 0·05). Measurements made in the field with a shovel or extracted soil cores were fast (5 min per core) and had significant positive correlations to scanner measurements after root washing and cleaning (>2 h per core). Field measurements at two- and five-leaf stages did not correlate with root depth at flowering. Conclusions The seedling screen was fast, repeatable and reliable for selecting lines with greater total root length in the young vegetative phase in the field. Lack of significant correlation with reproductive stage root system depth at the field sites used in this study reflected factors not captured in the screen such as time, soil properties, climate variation and plant phenology. PMID:23821620

Uptake and Predictors of Anal Cancer Screening in Men Who Have Sex With Men

PubMed Central

D'Souza, Gypsyamber; Rajan, Shirani D.; Bhatia, Rohini; Cranston, Ross D.; Plankey, Michael W.; Silvestre, Anthony; Ostrow, David G.; Wiley, Dorothy; Shah, Nisha; Brewer, Noel T.

2013-01-01

Objectives. We investigated attitudes about and acceptance of anal Papanicolaou (Pap) screening among men who have sex with men (MSM). Methods. Free anal Pap screening (cytology) was offered to 1742 MSM in the Multicenter AIDS Cohort Study, who reported history of, attitudes about, and experience with screening. We explored predictors of declining screening with multivariate logistic regression. Results. A history of anal Pap screening was uncommon among non–HIV-infected MSM, but more common among HIV-infected MSM (10% vs 39%; P < .001). Most participants expressed moderate or strong interest in screening (86%), no anxiety about screening (66%), and a strong belief in the utility of screening (65%). Acceptance of screening during this study was high (85%) across all 4 US sites. Among those screened, most reported it was “not a big deal” or “not as bad as expected,” and 3% reported that it was “scary.” Declining to have screening was associated with Black race, anxiety about screening, and low interest, but not age or HIV status. Conclusions. This study demonstrated high acceptance of anal Pap screening among both HIV-infected and non–HIV-infected MSM across 4 US sites. PMID:23865658

A reliable computational workflow for the selection of optimal screening libraries.

PubMed

Gilad, Yocheved; Nadassy, Katalin; Senderowitz, Hanoch

2015-01-01

The experimental screening of compound collections is a common starting point in many drug discovery projects. Successes of such screening campaigns critically depend on the quality of the screened library. Many libraries are currently available from different vendors yet the selection of the optimal screening library for a specific project is challenging. We have devised a novel workflow for the rational selection of project-specific screening libraries. The workflow accepts as input a set of virtual candidate libraries and applies the following steps to each library: (1) data curation; (2) assessment of ADME/T profile; (3) assessment of the number of promiscuous binders/frequent HTS hitters; (4) assessment of internal diversity; (5) assessment of similarity to known active compound(s) (optional); (6) assessment of similarity to in-house or otherwise accessible compound collections (optional). For ADME/T profiling, Lipinski's and Veber's rule-based filters were implemented and a new blood brain barrier permeation model was developed and validated (85 and 74 % success rate for training set and test set, respectively). Diversity and similarity descriptors which demonstrated best performances in terms of their ability to select either diverse or focused sets of compounds from three databases (Drug Bank, CMC and CHEMBL) were identified and used for diversity and similarity assessments. The workflow was used to analyze nine common screening libraries available from six vendors. The results of this analysis are reported for each library providing an assessment of its quality. Furthermore, a consensus approach was developed to combine the results of these analyses into a single score for selecting the optimal library under different scenarios. We have devised and tested a new workflow for the rational selection of screening libraries under different scenarios. The current workflow was implemented using the Pipeline Pilot software yet due to the usage of generic components, it can be easily adapted and reproduced by computational groups interested in rational selection of screening libraries. Furthermore, the workflow could be readily modified to include additional components. This workflow has been routinely used in our laboratory for the selection of libraries in multiple projects and consistently selects libraries which are well balanced across multiple parameters.Graphical abstract.

Correction factors for self-selection when evaluating screening programmes.

PubMed

Spix, Claudia; Berthold, Frank; Hero, Barbara; Michaelis, Jörg; Schilling, Freimut H

2016-03-01

In screening programmes there is recognized bias introduced through participant self-selection (the healthy screenee bias). Methods used to evaluate screening programmes include Intention-to-screen, per-protocol, and the "post hoc" approach in which, after introducing screening for everyone, the only evaluation option is participants versus non-participants. All methods are prone to bias through self-selection. We present an overview of approaches to correct for this bias. We considered four methods to quantify and correct for self-selection bias. Simple calculations revealed that these corrections are actually all identical, and can be converted into each other. Based on this, correction factors for further situations and measures were derived. The application of these correction factors requires a number of assumptions. Using as an example the German Neuroblastoma Screening Study, no relevant reduction in mortality or stage 4 incidence due to screening was observed. The largest bias (in favour of screening) was observed when comparing participants with non-participants. Correcting for bias is particularly necessary when using the post hoc evaluation approach, however, in this situation not all required data are available. External data or further assumptions may be required for estimation. © The Author(s) 2015.

Direct and selective small-molecule inhibition of photosynthetic PEP carboxylase: New approach to combat C4 weeds in arable crops.

PubMed

Paulus, Judith Katharina; Förster, Kerstin; Groth, Georg

2014-06-05

Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme of C4 photosynthesis. Besides, non-photosynthetic isoforms of PEPC are found in bacteria and all types of plants, although not in animals or fungi. A single residue in the allosteric feedback inhibitor site of PEPC was shown to adjust the affinity of the photosynthetic and non-photosynthetic isoforms for feedback inhibition by metabolites of the C4 pathway. Here, we applied computational screening and biochemical analyses to identify molecules that selectively inhibit C4 PEPC, but have no effect on the activity of non-photosynthetic PEPCs. We found two types of selective inhibitors, catechins and quinoxalines. Binding constants in the lower μM range and a strong preference for C4 PEPC qualify the quinoxaline compounds as potential selective herbicides to combat C4 weeds. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Canopy water balance of windward and leeward Hawaiian cloud forests on Haleakalā, Maui, Hawai'i

USGS Publications Warehouse

Giambelluca, Thomas W.; DeLay, John K.; Nullet, Michael A.; Scholl, Martha A.; Gingerich, Stephen B.

2011-01-01

The contribution of intercepted cloud water to precipitation at windward and leeward cloud forest sites on the slopes of Haleakalā, Maui was assessed using two approaches. Canopy water balance estimates based on meteorological monitoring were compared with interpretations of fog screen measurements collected over a 2-year period at each location. The annual incident rainfall was 973 mm at the leeward site (Auwahi) and 2550 mm at the windward site (Waikamoi). At the leeward, dry forest site, throughfall was less than rainfall (87%), and, at the windward, wet forest site, throughfall exceeded rainfall (122%). Cloud water interception estimated from canopy water balance was 166 mm year−1 at Auwahi and 1212 mm year−1 at Waikamoi. Annual fog screen measurements of cloud water flux, corrected for wind-blown rainfall, were 132 and 3017 mm for the dry and wet sites respectively. Event totals of cloud water flux based on fog screen measurements were poorly correlated with event cloud water interception totals derived from the canopy water balance. Hence, the use of fixed planar fog screens to estimate cloud water interception is not recommended. At the wet windward site, cloud water interception made up 32% of the total precipitation, adding to the already substantial amount of rainfall. At the leeward dry site, cloud water interception was 15% of the total precipitation. Vegetation at the dry site, where trees are more exposed and isolated, was more efficient at intercepting the available cloud water than at the rainy site, but events were less frequent, shorter in duration and lower in intensity. A large proportion of intercepted cloud water, 74% and 83%, respectively for the two sites, was estimated to become throughfall, thus adding significantly to soil water at both sites

Allosteric activation of the follicle-stimulating hormone (FSH) receptor by selective, nonpeptide agonists.

PubMed

Yanofsky, Stephen D; Shen, Emily S; Holden, Frank; Whitehorn, Erik; Aguilar, Barbara; Tate, Emily; Holmes, Christopher P; Scheuerman, Randall; MacLean, Derek; Wu, May M; Frail, Donald E; López, Francisco J; Winneker, Richard; Arey, Brian J; Barrett, Ronald W

2006-05-12

The pituitary glycoprotein hormones, luteinizing hormone and follicle-stimulating hormone (FSH), act through their cognate receptors to initiate a series of coordinated physiological events that results in germ cell maturation. Given the importance of FSH in regulating folliculogenesis and fertility, the development of FSH mimetics has been sought to treat infertility. Currently, purified and recombinant human FSH are the only FSH receptor (FSH-R) agonists available for infertility treatment. By screening unbiased combinatorial chemistry libraries, using a cAMP-responsive luciferase reporter assay, we discovered thiazolidinone agonists (EC50's = 20 microm) of the human FSH-R. Subsequent analog library screening and parallel synthesis optimization resulted in the identification of a potent agonist (EC50 = 2 nm) with full efficacy compared with FSH that was FSH-R-selective and -dependent. The compound mediated progesterone production in Y1 cells transfected with the human FSH-R (EC50 = 980 nm) and estradiol production from primary rat ovarian granulosa cells (EC50 = 10.5 nm). This and related compounds did not compete with FSH for binding to the FSH-R. Use of human FSH/thyroid-stimulating hormone (TSH) receptor chimeras suggested a novel mechanism for receptor activation through a binding site independent of the natural hormone binding site. This study is the first report of a high affinity small molecule agonist that activates a glycoprotein hormone receptor through an allosteric mechanism. The small molecule FSH receptor agonists described here could lead to an oral alternative to the current parenteral FSH treatments used clinically to induce ovarian stimulation for both in vivo and in vitro fertilization therapy.

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.

A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity

PubMed Central

2016-01-01

Recent outbreaks of highly pathogenic and occasional drug-resistant influenza strains have highlighted the need to develop novel anti-influenza therapeutics. Here, we report computational and experimental efforts to identify influenza neuraminidase inhibitors from among the 3000 natural compounds in the Malaysian-Plants Natural-Product (NADI) database. These 3000 compounds were first docked into the neuraminidase active site. The five plants with the largest number of top predicted ligands were selected for experimental evaluation. Twelve specific compounds isolated from these five plants were shown to inhibit neuraminidase, including two compounds with IC50 values less than 92 μM. Furthermore, four of the 12 isolated compounds had also been identified in the top 100 compounds from the virtual screen. Together, these results suggest an effective new approach for identifying bioactive plant species that will further the identification of new pharmacologically active compounds from diverse natural-product resources. PMID:25555059

Footprinting of Inhibitor Interactions of In Silico Identified Inhibitors of Trypanothione Reductase of Leishmania Parasite

PubMed Central

Venkatesan, Santhosh K.; Dubey, Vikash Kumar

2012-01-01

Structure-based virtual screening of NCI Diversity set II compounds was performed to indentify novel inhibitor scaffolds of trypanothione reductase (TR) from Leishmania infantum. The top 50 ranked hits were clustered using the AuPoSOM tool. Majority of the top-ranked compounds were Tricyclic. Clustering of hits yielded four major clusters each comprising varying number of subclusters differing in their mode of binding and orientation in the active site. Moreover, for the first time, we report selected alkaloids and dibenzothiazepines as inhibitors of Leishmania infantum TR. The mode of binding observed among the clusters also potentiates the probable in vitro inhibition kinetics and aids in defining key interaction which might contribute to the inhibition of enzymatic reduction of T[S] 2. The method provides scope for automation and integration into the virtual screening process employing docking softwares, for clustering the small molecule inhibitors based upon protein-ligand interactions. PMID:22550471

Methodology Development in Directed Evolution: Exploring Options when Applying Triple-Code Saturation Mutagenesis.

PubMed

Qu, Ge; Lonsdale, Richard; Yao, Peiyuan; Li, Guangyue; Liu, Beibei; Reetz, Manfred T; Sun, Zhoutong

2018-02-02

Directed evolution of stereo- or regioselective enzymes as catalysts in asymmetric transformations is of particular interest in organic synthesis. Upon evolving these biocatalysts, screening is the bottleneck. To beat the numbers problem most effectively, methods and strategies for building "small but smart" mutant libraries have been developed. Herein, we compared two different strategies regarding the application of triple-code saturation mutagenesis (TCSM) at multiresidue sites of the Thermoanaerobacter brockii alcohol dehydrogenase by using distinct reduced amino-acid alphabets. By using the synthetically difficult-to-reduce prochiral ketone tetrahydrofuran-3-one as a substrate, highly R- and S-selective variants were obtained (92-99 % ee) with minimal screening. The origin of stereoselectivity was provided by molecular dynamics analyses, which is discussed in terms of the Bürgi-Dunitz trajectory. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Methyl parathion detection in vegetables and fruits using silver@graphene nanoribbons nanocomposite modified screen printed electrode

NASA Astrophysics Data System (ADS)

Govindasamy, Mani; Mani, Veerappan; Chen, Shen-Ming; Chen, Tse-Wei; Sundramoorthy, Ashok Kumar

2017-04-01

We have developed a sensitive electrochemical sensor for Organophosphorus pesticide methyl parathion (MP) using silver particles supported graphene nanoribbons (Ag@GNRs). The Ag@GNRs nanocomposite was prepared through facile wet chemical strategy and characterized by TEM, EDX, XRD, Raman, UV-visible, electrochemical and impedance spectroscopies. The Ag@GNRs film modified screen printed carbon electrode (SPCE) delivers excellent electrocatalytic ability to the reduction of MP. The Ag@GNRs/SPCE detects sub-nanomolar concentrations of MP with excellent selectivity. The synergic effects between special electrocatalytic ability of Ag and excellent physicochemical properties of GNRs (large surface area, high conductivity, high area-normalized edge-plane structures and abundant catalytic sites) make the composite highly suitable for MP sensing. Most importantly, the method is successfully demonstrated in vegetables and fruits which revealed its potential real-time applicability in food analysis.

Therapeutic Targeting of Spliceosomal-Mutant Acquired Bone Marrow Failure Disorders

DTIC Science & Technology

2017-05-01

we have completed both a negative selection shRNA screen and a genome-wide CRISPR dropout screen to identify genes selectively required in...level of protein. Aim 2: We have recently completed a genome-wide CRISPR dropout screen in the same cells in which the shRNA screen was performed...Project: Janine performed the CRISPR screen in Aim 2. Funding Support: US National Institutes of Health (NIH)-NHLBI grant R01 HL128239 10

Reasons for non-participation in an international multicenter trial of a new drug for tuberculosis treatment.

PubMed

Lamunu, D; Chapman, K N; Nsubuga, P; Muzanyi, G; Mulumba, Y; Mugerwa, M A; Goldberg, S; Bozeman, L; Engle, M; Saukkonen, J; Mastranunzio, S; Mayanja-Kizza, H; Johnson, J L

2012-04-01

Clinical trials can provide a high standard of patient care and contribute to scientific knowledge; however, only a fraction of the patients screened participate and receive treatment as part of a trial. To explore reasons why patients were not enrolled in an international tuberculosis (TB) treatment trial and to compare experiences among study sites. An analysis of reasons why patients were not enrolled was conducted among patients screened for a TB clinical trial at 26 sites in North and South America, Africa, and Europe. Staff at study sites screened 1119 potential candidates for the trial: 61% (n = 686) were not enrolled due to 1) failure to meet eligibility criteria (n = 405, 59%), 2) site's decision (n = 168, 24%), or 3) candidate's choice (n = 113, 16%). Study staff recorded a total of 144 reasons for why they believed patients chose not to participate, including concerns over research (28%), conflicts with work or school (21%), and lifestyle and family issues (20%). Socio-demographic and geographic factors also influenced participation. Increased evaluation of screening outcomes and of specific interventions, such as improved education and communication about trial procedures, may increase the efficiency of screening and enrollment in clinical trials.

Structure Based Library Design (SBLD) for new 1,4-dihydropyrimidine scaffold as simultaneous COX-1/COX-2 and 5-LOX inhibitors.

PubMed

Lokwani, Deepak; Azad, Rajaram; Sarkate, Aniket; Reddanna, Pallu; Shinde, Devanand

2015-08-01

The various scaffolds containing 1,4-dihydropyrimidine ring were designed by considering the environment of the active site of COX-1/COX-2 and 5-LOX enzymes. The structure-based library design approach, including the focused library design (Virtual Combinatorial Library Design) and virtual screening was used to select the 1,4-dihydropyrimidine scaffold for simultaneous inhibition of both enzyme pathways (COX-1/COX-2 and 5-LOX). The virtual library on each 1,4-dihydropyrimidine scaffold was enumerated in two alternative ways. In first way, the chemical reagents at R groups were filtered by docking of scaffold with single position substitution, that is, only at R1, or R2, or R3, … Rn on COX-2 enzyme using Glide XP docking mode. The structures that do not dock well were removed and the library was enumerated with filtered chemical reagents. In second alternative way, the single position docking stage was bypassed, and the entire library was enumerated using all chemical reagents by docking on the COX-2 enzyme. The entire library of approximately 15,629 compounds obtained from both ways after screening for drug like properties, were further screened for their binding affinity against COX-1 and 5-LOX enzymes using Virtual Screening Workflow. Finally, 142 hits were obtained and divided into two groups based on their binding affinity for COX-1/COX-2 and for both enzyme pathways (COX-1/COX-2 and 5-LOX). The ten molecules were selected, synthesized and evaluated for their COX-1, COX-2 and 5-LOX inhibiting activity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Screening of seaweeds in the East China Sea as potential bio-monitors of heavy metals.

PubMed

Pan, Yaoru; Wernberg, Thomas; de Bettignies, Thibaut; Holmer, Marianne; Li, Ke; Wu, Jiaping; Lin, Fang; Yu, Yan; Xu, Jiang; Zhou, Chaosheng; Huang, Zhixing; Xiao, Xi

2018-06-01

Seaweeds are good bio-monitors of heavy metal pollution and have been included in European coastal monitoring programs. However, data for seaweed species in China are scarce or missing. In this study, we explored the potential of seaweeds as bio-monitor by screening the natural occurring seaweeds in the "Kingdom of seaweed and shellfish" at Dongtou Islands, the East China Sea. Totally, 12 seaweed species were collected from six sites, with richness following the sequence of Rhodophyta > Phaeophyta > Chlorophyta. The concentration of heavy metals (Cu, Cr, Ni, Zn, Pb, Cd, As) in the seaweeds was determined, and the bioaccumulation coefficient was calculated. A combination of four seaweeds, Pachydictyon coriaceum, Gelidium divaricatum, Sargassum thunbergii, and Pterocladiella capillacea, were proposed as bio-monitors due to their high bioaccumulation capabilities of specific heavy metals in the East China Sea and hence hinted the importance of using seaweed community for monitoring of pollution rather than single species. Our results provide first-hand data for the selection of bio-monitor species for heavy metals in the East China Sea and contribute to selection of cosmopolitan bio-monitor communities over geographical large area, which will benefit the establishment of monitoring programs for coastal heavy metal contamination.

An enzyme-mediated protein-fragment complementation assay for substrate screening of sortase A.

PubMed

Li, Ning; Yu, Zheng; Ji, Qun; Sun, Jingying; Liu, Xiao; Du, Mingjuan; Zhang, Wei

2017-04-29

Enzyme-mediated protein conjugation has gained great attention recently due to the remarkable site-selectivity and mild reaction condition affected by the nature of enzyme. Among all sorts of enzymes reported, sortase A from Staphylococcus aureus (SaSrtA) is the most popular enzyme due to its selectivity and well-demonstrated applications. Position scanning has been widely applied to understand enzyme substrate specificity, but the low throughput of chemical synthesis of peptide substrates and analytical methods (HPLC, LC-ESI-MS) have been the major hurdle to fully decode enzyme substrate profile. We have developed a simple high-throughput substrate profiling method to reveal novel substrates of SaSrtA 7M, a widely used hyperactive peptide ligase, by modified protein-fragment complementation assay (PCA). A small library targeting the LPATG motif recognized by SaSrtA 7M was generated and screened against proteins carrying N-terminal glycine. Using this method, we have confirmed all currently known substrates of the enzyme, and moreover identified some previously unknown substrates with varying activities. The method provides an easy, fast and highly-sensitive way to determine substrate profile of a peptide ligase in a high-throughput manner. Copyright © 2017 Elsevier Inc. All rights reserved.

Bioprospecting for hyper-lipid producing microalgal strains for sustainable biofuel production.

PubMed

Mutanda, T; Ramesh, D; Karthikeyan, S; Kumari, S; Anandraj, A; Bux, F

2011-01-01

Global petroleum reserves are shrinking at a fast pace, increasing the demand for alternate fuels. Microalgae have the ability to grow rapidly, and synthesize and accumulate large amounts (approximately 20-50% of dry weight) of neutral lipid stored in cytosolic lipid bodies. A successful and economically viable algae based biofuel industry mainly depends on the selection of appropriate algal strains. The main focus of bioprospecting for microalgae is to identify unique high lipid producing microalgae from different habitats. Indigenous species of microalgae with high lipid yields are especially valuable in the biofuel industry. Isolation, purification and identification of natural microalgal assemblages using conventional techniques is generally time consuming. However, the recent use of micromanipulation as a rapid isolating tool allows for a higher screening throughput. The appropriate media and growth conditions are also important for successful microalgal proliferation. Environmental parameters recorded at the sampling site are necessary to optimize in vitro growth. Identification of species generally requires a combination of morphological and genetic characterization. The selected microalgal strains are grown in upscale systems such as raceway ponds or photobireactors for biomass and lipid production. This paper reviews the recent methodologies adopted for site selection, sampling, strain selection and identification, optimization of cultural conditions for superior lipid yield for biofuel production. Energy generation routes of microalgal lipids and biomass are discussed in detail. Copyright © 2010 Elsevier Ltd. All rights reserved.

Site-saturation mutagenesis of Glomerella cingulata cutinase gene for enhanced enzyme thermostability

NASA Astrophysics Data System (ADS)

Hanapi, Wan Nurhidayah Wan; Iuan-Sheau, Chin; Mahadi, Nor Muhammad; Murad, Abdul Munir Abdul; Bakar, Farah Diba Abu

2015-09-01

Cutinase is an important biocatalyst for various industrial applications. This enzyme which has dual functionality comparable to esterases and lipases, is efficient in the hydrolysis of soluble esters and emulsified triacylglycerols. Naturally-occurring enzymes usually have disadvantages when applied in non-natural catalysis due to Glomerella cingulata cutinase enzyme thermostability. It is postulated that by increasing the rigidity at certain amino acid positions showing high mobility based on the three-dimensional structure of G. cingulata cutinase, the improvement in thermostability will be achieved. The amino acid N82 of G. cingulata cutinase was selected based on its high B-factor value determined via the B-FITTER program. Megaprimer PCR was employed to introduce mutations at the chosen site by randomization using NNK degenerate primers. About 300 transformants were selected for screening of positive cutinase variants. The N82_V14 cutinase variant was observed to be more thermostable at an almost 2-fold increase when exposed at 50°C for 1 hr as compared to the wild-type enzyme. This study may provide valuable information regarding thermal stability of cutinases denaturation at high temperatures.

Aedes albopictus (Diptera: Culicidae) Oviposition Preference as Influenced by Container Size and Buddleja davidii Plants.

PubMed

Davis, Timothy J; Kline, Daniel L; Kaufman, Phillip E

2016-03-01

Aedes albopictus (Skuse) is a container-breeding mosquito commonly found in residential areas of its range in the United States. Mosquitoes are known to utilize flowering plants for sugar acquisition. Limited information is known about the influences on oviposition site selection, outside of container size. Residential areas are often landscaped with a variety of flowering plants and are known to provide numerous sizes of potential larval developmental sites for container-breeding mosqutioes. Through screened enclosure and field studies, the oviposition preference of Ae. albopictus for containers of three selected sizes (473, 946 and 1,892 ml) and the influence of flowering butterfly bush (Buddleja davidii Franchett cultivar 'Guinevere') plants were examined. Our results document that significantly more eggs were oviposited in the largest containers. Additionally, significantly more eggs were oviposited in containers adjacent to flowering butterfly bushes than in those without a flowering butterfly bush. Finally, our results document that flowering butterfly bushes exerted greater influence over Ae. albopictus oviposition decisions than did container size. Our findings can be applied to several aspects of Ae. albopictus surveillance and control.

Focused Screening of ECM-Selective Adhesion Peptides on Cellulose-Bound Peptide Microarrays.

PubMed

Kanie, Kei; Kondo, Yuto; Owaki, Junki; Ikeda, Yurika; Narita, Yuji; Kato, Ryuji; Honda, Hiroyuki

2016-11-19

The coating of surfaces with bio-functional proteins is a promising strategy for the creation of highly biocompatible medical implants. Bio-functional proteins from the extracellular matrix (ECM) provide effective surface functions for controlling cellular behavior. We have previously screened bio-functional tripeptides for feasibility of mass production with the aim of identifying those that are medically useful, such as cell-selective peptides. In this work, we focused on the screening of tripeptides that selectively accumulate collagen type IV (Col IV), an ECM protein that accelerates the re-endothelialization of medical implants. A SPOT peptide microarray was selected for screening owing to its unique cellulose membrane platform, which can mimic fibrous scaffolds used in regenerative medicine. However, since the library size on the SPOT microarray was limited, physicochemical clustering was used to provide broader variation than that of random peptide selection. Using the custom focused microarray of 500 selected peptides, we assayed the relative binding rates of tripeptides to Col IV, collagen type I (Col I), and albumin. We discovered a cluster of Col IV-selective adhesion peptides that exhibit bio-safety with endothelial cells. The results from this study can be used to improve the screening of regeneration-enhancing peptides.

Focused Screening of ECM-Selective Adhesion Peptides on Cellulose-Bound Peptide Microarrays

PubMed Central

Kanie, Kei; Kondo, Yuto; Owaki, Junki; Ikeda, Yurika; Narita, Yuji; Kato, Ryuji; Honda, Hiroyuki

2016-01-01

The coating of surfaces with bio-functional proteins is a promising strategy for the creation of highly biocompatible medical implants. Bio-functional proteins from the extracellular matrix (ECM) provide effective surface functions for controlling cellular behavior. We have previously screened bio-functional tripeptides for feasibility of mass production with the aim of identifying those that are medically useful, such as cell-selective peptides. In this work, we focused on the screening of tripeptides that selectively accumulate collagen type IV (Col IV), an ECM protein that accelerates the re-endothelialization of medical implants. A SPOT peptide microarray was selected for screening owing to its unique cellulose membrane platform, which can mimic fibrous scaffolds used in regenerative medicine. However, since the library size on the SPOT microarray was limited, physicochemical clustering was used to provide broader variation than that of random peptide selection. Using the custom focused microarray of 500 selected peptides, we assayed the relative binding rates of tripeptides to Col IV, collagen type I (Col I), and albumin. We discovered a cluster of Col IV-selective adhesion peptides that exhibit bio-safety with endothelial cells. The results from this study can be used to improve the screening of regeneration-enhancing peptides. PMID:28952593

Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation

PubMed Central

Planas, Delphine; Merritt, Andy; Routy, Jean-Pierre; Ancuta, Petronela; Bangham, Charles R. M.

2017-01-01

HIV-1 integrates more frequently into transcribed genes, however the biological significance of HIV-1 integration targeting has remained elusive. Using a selective high-throughput chemical screen, we discovered that the cardiac glycoside digoxin inhibits wild-type HIV-1 infection more potently than HIV-1 bearing a single point mutation (N74D) in the capsid protein. We confirmed that digoxin repressed viral gene expression by targeting the cellular Na+/K+ ATPase, but this did not explain its selectivity. Parallel RNAseq and integration mapping in infected cells demonstrated that digoxin inhibited expression of genes involved in T-cell activation and cell metabolism. Analysis of >400,000 unique integration sites showed that WT virus integrated more frequently than N74D mutant within or near genes susceptible to repression by digoxin and involved in T-cell activation and cell metabolism. Two main gene networks down-regulated by the drug were CD40L and CD38. Blocking CD40L by neutralizing antibodies selectively inhibited WT virus infection, phenocopying digoxin. Thus the selectivity of digoxin depends on a combination of integration targeting and repression of specific gene networks. The drug unmasked a functional connection between HIV-1 integration and T-cell activation. Our results suggest that HIV-1 evolved integration site selection to couple its early gene expression with the status of target CD4+ T-cells, which may affect latency and viral reactivation. PMID:28727807

Spatial distribution of jet fuel in the vadoze zone of a heterogeneous and fractured soil.

PubMed

Tzovolou, D N; Benoit, Y; Haeseler, F; Klint, K E; Tsakiroglou, C D

2009-04-01

The goal of the present work is to screen and evaluate all available data before selecting and testing remediation technologies on heterogeneous soils polluted by jet fuel. The migration pathways of non-aqueous phase liquids (NAPLs) in the subsurface relate closely with soil properties. A case study is performed on the vadoze zone of a military airport of north-west Poland contaminated by jet fuel. Soil samples are collected from various depths of two cells, and on-site and off-site chemical analyses of hydrocarbons are conducted by using Pollut Eval apparatus and GC-MS, respectively. The geological conceptual model of the site along with microscopic and hydraulic properties of the porous matrix and fractures enable us to interpret the non-uniform spatial distribution of jet fuel constituents. The total concentration of the jet fuel and its main hydrocarbon families (n-paraffins, major aromatics) over the two cells is governed by the slow preferential flow of NAPL through the porous matrix, the rapid NAPL convective flow through vertical desiccation and sub-horizontal glaciotectonic fractures, and n-paraffin biodegradation in upper layers where the rates of oxygen transfer is not limited by complexities of the pore structure. The information collected is valuable for the selection, implementation and evaluation of two in situ remediation methods.

Identification and Characterization of Influenza Virus Entry Inhibitors through Dual Myxovirus High-Throughput Screening.

PubMed

Weisshaar, Marco; Cox, Robert; Morehouse, Zachary; Kumar Kyasa, Shiva; Yan, Dan; Oberacker, Phil; Mao, Shuli; Golden, Jennifer E; Lowen, Anice C; Natchus, Michael G; Plemper, Richard K

2016-08-15

Influenza A virus (IAV) infections cause major morbidity and mortality, generating an urgent need for novel antiviral therapeutics. We recently established a dual myxovirus high-throughput screening protocol that combines a fully replication-competent IAV-WSN strain and a respiratory syncytial virus reporter strain for the simultaneous identification of IAV-specific, paramyxovirus-specific, and broad-spectrum inhibitors. In the present study, this protocol was applied to a screening campaign to assess a diverse chemical library with over 142,000 entries. Focusing on IAV-specific hits, we obtained a hit rate of 0.03% after cytotoxicity testing and counterscreening. Three chemically distinct hit classes with nanomolar potency and favorable cytotoxicity profiles were selected. Time-of-addition, minigenome, and viral entry studies demonstrated that these classes block hemagglutinin (HA)-mediated membrane fusion. Antiviral activity extends to an isolate from the 2009 pandemic and, in one case, another group 1 subtype. Target identification through biolayer interferometry confirmed binding of all hit compounds to HA. Resistance profiling revealed two distinct escape mechanisms: primary resistance, associated with reduced compound binding, and secondary resistance, associated with unaltered binding. Secondary resistance was mediated, unusually, through two different pairs of cooperative mutations, each combining a mutation eliminating the membrane-proximal stalk N-glycan with a membrane-distal change in HA1 or HA2. Chemical synthesis of an analog library combined with in silico docking extracted a docking pose for the hit classes. Chemical interrogation spotlights IAV HA as a major druggable target for small-molecule inhibition. Our study identifies novel chemical scaffolds with high developmental potential, outlines diverse routes of IAV escape from entry inhibition, and establishes a path toward structure-aided lead development. This study is one of the first to apply a fully replication-competent third-generation IAV reporter strain to a large-scale high-throughput screen (HTS) drug discovery campaign, allowing multicycle infection and screening in physiologically relevant human respiratory cells. A large number of potential druggable targets was thus chemically interrogated, but mechanistic characterization, positive target identification, and resistance profiling demonstrated that three chemically promising and structurally distinct hit classes selected for further analysis all block HA-mediated membrane fusion. Viral escape from inhibition could be achieved through primary and secondary resistance mechanisms. In silico docking predicted compound binding to a microdomain located at the membrane-distal site of the prefusion HA stalk that was also previously suggested as a target site for chemically unrelated HA inhibitors. This study identifies an unexpected chemodominance of the HA stalk microdomain for small-molecule inhibitors in IAV inhibitor screening campaigns and highlights a novel mechanism of cooperative resistance to IAV entry blockers. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Identification and Characterization of Influenza Virus Entry Inhibitors through Dual Myxovirus High-Throughput Screening

PubMed Central

Weisshaar, Marco; Cox, Robert; Morehouse, Zachary; Kumar Kyasa, Shiva; Yan, Dan; Oberacker, Phil; Mao, Shuli; Lowen, Anice C.; Natchus, Michael G.

2016-01-01

ABSTRACT Influenza A virus (IAV) infections cause major morbidity and mortality, generating an urgent need for novel antiviral therapeutics. We recently established a dual myxovirus high-throughput screening protocol that combines a fully replication-competent IAV-WSN strain and a respiratory syncytial virus reporter strain for the simultaneous identification of IAV-specific, paramyxovirus-specific, and broad-spectrum inhibitors. In the present study, this protocol was applied to a screening campaign to assess a diverse chemical library with over 142,000 entries. Focusing on IAV-specific hits, we obtained a hit rate of 0.03% after cytotoxicity testing and counterscreening. Three chemically distinct hit classes with nanomolar potency and favorable cytotoxicity profiles were selected. Time-of-addition, minigenome, and viral entry studies demonstrated that these classes block hemagglutinin (HA)-mediated membrane fusion. Antiviral activity extends to an isolate from the 2009 pandemic and, in one case, another group 1 subtype. Target identification through biolayer interferometry confirmed binding of all hit compounds to HA. Resistance profiling revealed two distinct escape mechanisms: primary resistance, associated with reduced compound binding, and secondary resistance, associated with unaltered binding. Secondary resistance was mediated, unusually, through two different pairs of cooperative mutations, each combining a mutation eliminating the membrane-proximal stalk N-glycan with a membrane-distal change in HA1 or HA2. Chemical synthesis of an analog library combined with in silico docking extracted a docking pose for the hit classes. Chemical interrogation spotlights IAV HA as a major druggable target for small-molecule inhibition. Our study identifies novel chemical scaffolds with high developmental potential, outlines diverse routes of IAV escape from entry inhibition, and establishes a path toward structure-aided lead development. IMPORTANCE This study is one of the first to apply a fully replication-competent third-generation IAV reporter strain to a large-scale high-throughput screen (HTS) drug discovery campaign, allowing multicycle infection and screening in physiologically relevant human respiratory cells. A large number of potential druggable targets was thus chemically interrogated, but mechanistic characterization, positive target identification, and resistance profiling demonstrated that three chemically promising and structurally distinct hit classes selected for further analysis all block HA-mediated membrane fusion. Viral escape from inhibition could be achieved through primary and secondary resistance mechanisms. In silico docking predicted compound binding to a microdomain located at the membrane-distal site of the prefusion HA stalk that was also previously suggested as a target site for chemically unrelated HA inhibitors. This study identifies an unexpected chemodominance of the HA stalk microdomain for small-molecule inhibitors in IAV inhibitor screening campaigns and highlights a novel mechanism of cooperative resistance to IAV entry blockers. PMID:27252534

Simultaneous fluorescence light-up and selective multicolor nucleobase recognition based on sequence-dependent strong binding of berberine to DNA abasic site.

PubMed

Wu, Fei; Shao, Yong; Ma, Kun; Cui, Qinghua; Liu, Guiying; Xu, Shujuan

2012-04-28

Label-free DNA nucleobase recognition by fluorescent small molecules has received much attention due to its simplicity in mutation identification and drug screening. However, sequence-dependent fluorescence light-up nucleobase recognition and multicolor emission with individual emission energy for individual nucleobases have been seldom realized. Herein, an abasic site (AP site) in a DNA duplex was employed as a binding field for berberine, one of isoquinoline alkaloids. Unlike weak binding of berberine to the fully matched DNAs without the AP site, strong binding of berberine to the AP site occurs and the berberine's fluorescence light-up behaviors are highly dependent on the target nucleobases opposite the AP site in which the targets thymine and cytosine produce dual emission bands, while the targets guanine and adenine only give a single emission band. Furthermore, more intense emissions are observed for the target pyrimidines than purines. The flanking bases of the AP site also produce some modifications of the berberine's emission behavior. The binding selectivity of berberine at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, excited-state lifetime, DNA melting and fluorescence quenching by ferrocyanide and sodium chloride. It is expected that the target pyrimidines cause berberine to be stacked well within DNA base pairs near the AP site, which results in a strong resonance coupling of the electronic transitions to the particular vibration mode to produce the dual emissions. The fluorescent signal-on and emission energy-modulated sensing for nucleobases based on this fluorophore is substantially advantageous over the previously used fluorophores. We expect that this approach will be developed as a practical device for differentiating pyrimidines from purines by positioning an AP site toward a target that is available for readout by this alkaloid probe. This journal is © The Royal Society of Chemistry 2012

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

Entertainment Education for Prostate Cancer Screening: A Randomized Trial among Primary Care Patients with Low Health Literacy

PubMed Central

Volk, Robert J.; Jibaja-Weiss, Maria L.; Hawley, Sarah T.; Kneuper, Suzanne; Spann, Stephen J.; Miles, Brian J.; Hyman, David J.

2008-01-01

Objective To evaluate an entertainment-based patient decision aid for prostate cancer screening among patients with low or high health literacy. Methods Male primary care patients from two clinical sites, one characterized as serving patients with low health literacy (n=149) and the second as serving patients with high health literacy (n=301), were randomized to receive an entertainment-based decision aid for prostate cancer screening or an audiobooklet-control aid with the same learner content but without the entertainment features. Postintervention and 2-week follow-up assessments were conducted. Results Patients at the low-literacy site were more engaged with the entertainment-based aid than patients at the high-literacy site. Overall, knowledge improved for all patients. Among patients at the low-literacy site, the entertainment-based aid was associated with lower decisional conflict and greater self-advocacy (i.e., mastering and obtaining information about screening) when compared to patients given the audiobooklet. No differences between the aids were observed for patients at the high-literacy site. Conclusions Entertainment education may be an effective strategy for promoting informed decision making about prostate cancer screening among patients with lower health literacy. Practice Implications As barriers to implementing computer-based patient decision support programs decrease, alternative models for delivering these programs should be explored. PMID:18760888

Confirmation of high-throughput screening data and novel mechanistic insights into VDR-xenobiotic interactions by orthogonal assays.

PubMed

Mahapatra, Debabrata; Franzosa, Jill A; Roell, Kyle; Kuenemann, Melaine Agnes; Houck, Keith A; Reif, David M; Fourches, Denis; Kullman, Seth W

2018-06-11

High throughput screening (HTS) programs have demonstrated that the Vitamin D receptor (VDR) is activated and/or antagonized by a wide range of structurally diverse chemicals. In this study, we examined the Tox21 qHTS data set generated against VDR for reproducibility and concordance and elucidated functional insights into VDR-xenobiotic interactions. Twenty-one potential VDR agonists and 19 VDR antagonists were identified from a subset of >400 compounds with putative VDR activity and examined for VDR functionality utilizing select orthogonal assays. Transient transactivation assay (TT) using a human VDR plasmid and Cyp24 luciferase reporter construct revealed 20/21 active VDR agonists and 18/19 active VDR antagonists. Mammalian-2-hybrid assay (M2H) was then used to evaluate VDR interactions with co-activators and co-regulators. With the exception of a select few compounds, VDR agonists exhibited significant recruitment of co-regulators and co-activators whereas antagonists exhibited considerable attenuation of recruitment by VDR. A unique set of compounds exhibiting synergistic activity in antagonist mode and no activity in agonist mode was identified. Cheminformatics modeling of VDR-ligand interactions were conducted and revealed selective ligand VDR interaction. Overall, data emphasizes the molecular complexity of ligand-mediated interactions with VDR and suggest that VDR transactivation may be a target site of action for diverse xenobiotics.

Installation Restoration Program. Feasibility Study for Sites 1, 3, 5, 6, 7, 8, and 9. Michigan Air National Guard. Alpena Combat Readiness Training Center, Alpena, Michigan.

DTIC Science & Technology

1996-04-01

This study is to screen and evaluate remediation alternatives for IRP sites at Alpena CR TC, Alpena , MI. The purpose of this FS is to develop, screen... Alpena CRTC. The first step in the PS process is to identify the RAOs and general response actions (GRAs). RAOs consist of medium-specific or site

Use of the heteroduplex mobility assay and cell sorting to select genome sequences of the CCR5 gene in HEK 293T cells edited by transcription activator-like effector nucleases.

PubMed

Nerys-Junior, Arildo; Costa, Lendel C; Braga-Dias, Luciene P; Oliveira, Márcia; Rossi, Atila D; da Cunha, Rodrigo Delvecchio; Gonçalves, Gabriel S; Tanuri, Amilcar

2014-03-01

Engineered nucleases such as zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) are one of the most promising tools for modifying genomes. These site-specific enzymes cause double-strand breaks that allow gene disruption or gene insertion, thereby facilitating genetic manipulation. The major problem associated with this approach is the labor-intensive procedures required to screen and confirm the cellular modification by nucleases. In this work, we produced a TALEN that targets the human CCR5 gene and developed a heteroduplex mobility assay for HEK 293T cells to select positive colonies for sequencing. This approach provides a useful tool for the quick detection and easy assessment of nuclease activity.

Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives

NASA Astrophysics Data System (ADS)

Fogel, Gary B.; Cheung, Mars; Pittman, Eric; Hecht, David

2008-01-01

Modeling studies were performed on known inhibitors of the quadruple mutant Plasmodium falciparum dihydrofolate reductase (DHFR). GOLD was used to dock 32 pyrimethamine derivatives into the active site of DHFR obtained from the x-ray crystal structure 1J3K.pdb. Several scoring functions were evaluated and the Molegro Protein-Ligand Interaction Score was determined to have one of the best correlation to experimental p K i . In conjunction with Protein-Ligand Interaction scores, predicted binding modes and key protein-ligand interactions were evaluated and analyzed in order to develop criteria for selecting compounds having a greater chance of activity versus resistant strains of Plasmodium falciparum. This methodology will be used in future studies for selection of compounds for focused screening libraries.

Screening lactic acid bacteria strains with ability to bind di-n-butyl phthalate via Turbiscan technique.

PubMed

Lili, Zhao; Hongfei, Zhao; Shoukat, Sana; Xiaochen, Zhang; Bolin, Zhang

2017-06-01

Di-n-butyl phthalate (DBP) is a ubiquitous environmental contaminant that poses a risk to humans. Previous work indicates that the ability of lactic acid bacteria (LAB) to bind phthalic acid esters is strain-specific. As cell suspensions of LAB strains in aqueous solution are likely to be colloidal dispersions, this study provided a technique to efficiently screen LAB strains that bind DBP via Turbiscan, which has been widely used to measure the stability of emulsions or colloidal dispersions. Eleven LAB strains belonging to Lactobacillus plantarum, Lb. pentosus, Lb. paralimentarius, Lb. helveticus, Leuconostoc mesenteroides, Lb. acidophilus, Bifidobacterium lactis, and Bifidobacterium bifidum species were used in this study, and seven of them were selected to test in an earlier stage of exploring the process for finding a screening method; others were used for a validation test. It was observed that the various values of the 10 h Turbiscan Stability Index (TSI) of the cell suspension from each strain, at the equilibrium time of dispersed particles according to the peak thickness of cell-suspensions as measured by Turbiscan, had significant negative correlations with the DBP-binding percentage of LAB strains. Higher TSI values are correlated with lower binding of bacteria strains to DBP with a correlation coefficient of 0.8292. Cell surface hydrocarbons of LAB strains and their adherence were observed to correlate with DBP-binding percentages and may lead to the different states of aggregation or equilibrium of bacterial cell-suspensions, and the aggregation of bacterial cells resulted in fewer binding sites in the cell wall for DBP. Finally, four LAB strains were randomly selected to verify the feasibility of the method. In all, the findings demonstrate that TSI might be used as a tool to quickly screen strains that bind DBP. The present work could be extended to the removal of other toxic compounds, when screening of high-efficiency strains is required.

Ranking targets in structure-based virtual screening of three-dimensional protein libraries: methods and problems.

PubMed

Kellenberger, Esther; Foata, Nicolas; Rognan, Didier

2008-05-01

Structure-based virtual screening is a promising tool to identify putative targets for a specific ligand. Instead of docking multiple ligands into a single protein cavity, a single ligand is docked in a collection of binding sites. In inverse screening, hits are in fact targets which have been prioritized within the pool of best ranked proteins. The target rate depends on specificity and promiscuity in protein-ligand interactions and, to a considerable extent, on the effectiveness of the scoring function, which still is the Achilles' heel of molecular docking. In the present retrospective study, virtual screening of the sc-PDB target library by GOLD docking was carried out for four compounds (biotin, 4-hydroxy-tamoxifen, 6-hydroxy-1,6-dihydropurine ribonucleoside, and methotrexate) of known sc-PDB targets and, several ranking protocols based on GOLD fitness score and topological molecular interaction fingerprint (IFP) comparison were evaluated. For the four investigated ligands, the fusion of GOLD fitness and two IFP scores allowed the recovery of most targets, including the rare proteins which are not readily suitable for statistical analysis, while significantly filtering out most false positive entries. The current survey suggests that selecting a small number of targets (<20) for experimental evaluation is achievable with a pure structure-based approach.

Trypanosoma Cruzi Cyp51 Inhibitor Derived from a Mycobacterium Tuberculosis Screen Hit

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

Chen, Chiung-Kuang; Doyle, Patricia S.; Yermalitskaya, Liudmila V.

2009-02-18

The two front-line drugs for chronic Trypanosoma cruzi infections are limited by adverse side-effects and declining efficacy. One potential new target for Chagas disease chemotherapy is sterol 14{alpha}-demethylase (CYP51), a cytochrome P450 enzyme involved in biosynthesis of membrane sterols. In a screening effort targeting Mycobacterium tuberculosis CYP51 (CYP51{sub Mt}), we previously identified the N-[4-pyridyl]-formamide moiety as a building block capable of delivering a variety of chemotypes into the CYP51 active site. In that work, the binding modes of several second generation compounds carrying this scaffold were determined by high-resolution co-crystal structures with CYP51{sub Mt}. Subsequent assays against the CYP51 orthologuemore » in T. cruzi, CYP51{sub Tc}, demonstrated that two of the compounds tested in the earlier effort bound tightly to this enzyme. Both were tested in vitro for inhibitory effects against T. cruzi and the related protozoan parasite Trypanosoma brucei, the causative agent of African sleeping sickness. One of the compounds had potent, selective anti-T. cruzi activity in infected mouse macrophages. Cure of treated host cells was confirmed by prolonged incubation in the absence of the inhibiting compound. Discrimination between T. cruzi and T. brucei CYP51 by the inhibitor was largely based on the variability (phenylalanine versus isoleucine) of a single residue at a critical position in the active site. CYP51{sub Mt}-based crystal structure analysis revealed that the functional groups of the two tightly bound compounds are likely to occupy different spaces in the CYP51 active site, suggesting the possibility of combining the beneficial features of both inhibitors in a third generation of compounds to achieve more potent and selective inhibition of CYP51{sub Tc}. Enzyme sterol 14{alpha}-demethylase (CYP51) is a well-established target for anti-fungal therapy and is a prospective target for Chagas disease therapy. We previously identified a chemical scaffold capable of delivering a variety of chemical structures into the CYP51 active site. In this work the binding modes of several second generation compounds carrying this scaffold were determined in high-resolution co-crystal structures with CYP51 of Mycobacterium tuberculosis. Subsequent assays against CYP51 in Trypanosoma cruzi, the agent of Chagas disease, demonstrated that two of the compounds bound tightly to the enzyme. Both were tested for inhibitory effects against T. cruzi and the related protozoan parasite Trypanosoma brucei. One of the compounds had potent, selective anti-T. cruzi activity in infected mouse macrophages. This compound is currently being evaluated in animal models of Chagas disease. Discrimination between T. cruzi and T. brucei CYP51 by the inhibitor was largely based on the variability of a single amino acid residue at a critical position in the active site. Our work is aimed at rational design of potent and highly selective CYP51 inhibitors with potential to become therapeutic drugs. Drug selectivity to prevent host-pathogen cross-reactivity is pharmacologically important, because CYP51 is present in human host.« less

USING DIRECT-PUSH TOOLS TO MAP HYDROSTRATIGRAPHY AND PREDICT MTBE PLUME DIVING

EPA Science Inventory

Conventional wells for monitoring MTBE contamination at underground storage tank sites are screened a few feet above and a few feet below the water table. At some sites, a plume of contamination in ground water may dive below the screen of conventional monitoring wells and escap...

Selection, application, and validation of a set of molecular descriptors for nuclear receptor ligands.

PubMed

Stewart, Eugene L; Brown, Peter J; Bentley, James A; Willson, Timothy M

2004-08-01

A methodology for the selection and validation of nuclear receptor ligand chemical descriptors is described. After descriptors for a targeted chemical space were selected, a virtual screening methodology utilizing this space was formulated for the identification of potential NR ligands from our corporate collection. Using simple descriptors and our virtual screening method, we are able to quickly identify potential NR ligands from a large collection of compounds. As validation of the virtual screening procedure, an 8, 000-membered NR targeted set and a 24, 000-membered diverse control set of compounds were selected from our in-house general screening collection and screened in parallel across a number of orphan NR FRET assays. For the two assays that provided at least one hit per set by the established minimum pEC(50) for activity, the results showed a 2-fold increase in the hit-rate of the targeted compound set over the diverse set.

Pain, pain intensity and pain disability in high school students are differently associated with physical activity, screening hours and sleep.

PubMed

Silva, Anabela G; Sa-Couto, Pedro; Queirós, Alexandra; Neto, Maritza; Rocha, Nelson P

2017-05-16

Studies exploring the association between physical activity, screen time and sleep and pain usually focus on a limited number of painful body sites. Nevertheless, pain at different body sites is likely to be of different nature. Therefore, this study aims to explore and compare the association between time spent in self-reported physical activity, in screen based activities and sleeping and i) pain presence in the last 7-days for 9 different body sites; ii) pain intensity at 9 different body sites and iii) global disability. Nine hundred sixty nine students completed a questionnaire on pain, time spent in moderate and vigorous physical activity, screen based time watching TV/DVD, playing, using mobile phones and computers and sleeping hours. Univariate and multivariate associations between pain presence, pain intensity and disability and physical activity, screen based time and sleeping hours were investigated. Pain presence: sleeping remained in the multivariable model for the neck, mid back, wrists, knees and ankles/feet (OR 1.17 to 2.11); moderate physical activity remained in the multivariate model for the neck, shoulders, wrists, hips and ankles/feet (OR 1.06 to 1.08); vigorous physical activity remained in the multivariate model for mid back, knees and ankles/feet (OR 1.05 to 1.09) and screen time remained in the multivariate model for the low back (OR = 2.34. Pain intensity: screen time and moderate physical activity remained in the multivariable model for pain intensity at the neck, mid back, low back, shoulder, knees and ankles/feet (Rp 2 0.02 to 0.04) and at the wrists (Rp 2  = 0.04), respectively. Disability showed no association with sleeping, screen time or physical activity. This study suggests both similarities and differences in the patterns of association between time spent in physical activity, sleeping and in screen based activities and pain presence at 8 different body sites. In addition, they also suggest that the factors associated with the presence of pain, pain intensity and pain associated disability are different.

Hospital evaluation of health literacy and associated outcomes in patients after acute myocardial infarction.

PubMed

Rymer, Jennifer A; Kaltenbach, Lisa A; Anstrom, Kevin J; Fonarow, Gregg C; Erskine, Nathaniel; Peterson, Eric D; Wang, Tracy Y

2018-04-01

Low health literacy is common in the United States and may affect outcomes after myocardial infarction (MI). How often hospitals screen for low health literacy is unknown. We surveyed 122 hospitals in the TRANSLATE-ACS study and divided them into those that reported routinely (>75% of patients), selectively (1%-75%), or never (0%) screening MI patients for low health literacy prior to discharge. We performed logistic regression with random intercepts to compare 6-week and 6-month patient-reported medication adherence and multivariable Cox regression to compare 1-year major adverse cardiovascular events and all-cause readmission risks between hospital groups. Overall, 25 (20.5%), 47 (38.5%), and 50 (41.0%) hospitals reported routinely, selectively, or never screening patients for low health literacy, respectively. Patients discharged from hospitals that routinely screened were more likely to report 6-week medication adherence [routinely: adjusted odds ratio (OR) 1.26, 95% CI 1.01-1.57; selectively: adjusted OR 1.19, 95% CI 1.00-1.43, both referenced to those discharged from hospitals that never screened]. Compared with hospitals that never screened health literacy, 1-year major adverse cardiovascular events were similar for hospitals that reported routinely screening (adjusted HR 0.92, 95% CI 0.75-1.14) or selectively screening (adjusted HR 1.01, 95% CI 0.84-1.21). Hospitals that reported selectively screening health literacy were associated with a lower adjusted risk of 1-year all-cause readmission (adjusted HR 0.89, 95% CI 0.79-1.00, P=.041). Only a minority of US hospitals routinely screen MI patients for low health literacy. Hospital screening was associated with higher medication adherence and lower readmission risk. Further investigation is needed to understand how inpatient screening can be implemented to improve longitudinal post-MI care. Copyright © 2017 Elsevier Inc. All rights reserved.

78 FR 18595 - Agency Forms Undergoing Paperwork Reduction Act Review

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-27

... indicates that regular screening is effective in reducing CRC incidence and mortality, regular CRC screening... disparities in CRC screening, incidence and mortality. Funded sites implement evidence-based interventions to...

Protein-protein interaction site predictions with minimum covariance determinant and Mahalanobis distance.

PubMed

Qiu, Zhijun; Zhou, Bo; Yuan, Jiangfeng

2017-11-21

Protein-protein interaction site (PPIS) prediction must deal with the diversity of interaction sites that limits their prediction accuracy. Use of proteins with unknown or unidentified interactions can also lead to missing interfaces. Such data errors are often brought into the training dataset. In response to these two problems, we used the minimum covariance determinant (MCD) method to refine the training data to build a predictor with better performance, utilizing its ability of removing outliers. In order to predict test data in practice, a method based on Mahalanobis distance was devised to select proper test data as input for the predictor. With leave-one-validation and independent test, after the Mahalanobis distance screening, our method achieved higher performance according to Matthews correlation coefficient (MCC), although only a part of test data could be predicted. These results indicate that data refinement is an efficient approach to improve protein-protein interaction site prediction. By further optimizing our method, it is hopeful to develop predictors of better performance and wide range of application. Copyright © 2017 Elsevier Ltd. All rights reserved.

Miscellaneous chemical basin expedited site characterization report

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

Riha, B.D.; Pemberton, B.E.; Rossabi, J.

1996-12-01

A total of twenty nine cone penetrometer test (CPT) pushes in three weeks were conducted for vadose zone characterization of the Miscellaneous Chemical Basin (MCB) waste unit at the Savannah River Site. The shallow, unlined basin received liquid chemical wastes over an 18 year period beginning in 1956. This characterization was initiated to determine the vertical and lateral extent of contamination in the vadose zone and to install vadose zone wells for remediation by barometric pumping or active vapor extraction to help prevent further contamination of groundwater. The CPT locations within the waste site were selected based on results frommore » previous shallow soil gas surveys, groundwater contamination data, and the suspected basin center. Geophysical data and soil gas samples were collected at twenty five locations and twenty five vadose zone wells were installed. The wells were screened to target the clay zones and areas of higher soil gas concentrations. The well construction diagrams are provided in Appendix B. Baro-Ball{trademark} valves for enhanced barometric pumping were installed on each well upon completion to immediately begin the remediation treatability study at the site.« less

Screening uptake rates and the clinical and cost effectiveness of screening for gestational diabetes mellitus in primary versus secondary care: study protocol for a randomised controlled trial

PubMed Central

2014-01-01

Background The risks associated with gestational diabetes mellitus (GDM) are well recognized, and there is increasing evidence to support treatment of the condition. However, clear guidance on the ideal approach to screening for GDM is lacking. Professional groups continue to debate whether selective screening (based on risk factors) or universal screening is the most appropriate approach. Additionally, there is ongoing debate about what levels of glucose abnormalities during pregnancy respond best to treatment and which maternal and neonatal outcomes benefit most from treatment. Furthermore, the implications of possible screening options on health care costs are not well established. In response to this uncertainty there have been repeated calls for well-designed, randomised trials to determine the efficacy of screening, diagnosis, and management plans for GDM. We describe a randomised controlled trial to investigate screening uptake rates and the clinical and cost effectiveness of screening in primary versus secondary care settings. Methods/Design This will be an unblinded, two-group, parallel randomised controlled trial (RCT). The target population includes 784 women presenting for their first antenatal visit at 12 to 18 weeks gestation at two hospitals in the west of Ireland: Galway University Hospital and Mayo General Hospital. Participants will be offered universal screening for GDM at 24 to 28 weeks gestation in either primary care (n = 392) or secondary care (n = 392) locations. The primary outcome variable is the uptake rate of screening. Secondary outcomes include indicators of clinical effectiveness of screening at each screening site (primary and secondary) including gestational week at time of screening, time to access antenatal diabetes services for women diagnosed with GDM, and pregnancy and neonatal outcomes for women with GDM. In addition, parallel economic and qualitative evaluations will be conducted. The trial will cover the period from the woman’s first hospital antenatal visit at 12 to 18 weeks gestation, until the completion of the pregnancy. Trial registration Current Controlled Trials: ISRCTN02232125 PMID:24438478

Statistical analysis of long-term hydrologic records for selection of drought-monitoring sites on Long Island, New York

USGS Publications Warehouse

Busciolano, Ronald J.

2005-01-01

Ground water is the sole source of water supply for more than 3 million people on Long Island, New York. Large-scale ground-water pumpage, sewering systems, and prolonged periods of below-normal precipitation have lowered ground-water levels and decreased stream-discharge in western and central Long Island. No method is currently (2004) available on Long Island that can assess data from the ground-water-monitoring network to enable water managers and suppliers with the ability to give timely warning of severe water-level declines.This report (1) quantifies past drought- and human-induced changes in the ground-water system underlying Long Island by applying statistical and graphical methods to precipitation, stream-discharge, and ground-water-level data from selected monitoring sites; (2) evaluates the relation between water levels in the upper glacial aquifer and those in the underlying Magothy aquifer; (3) defines trends in stream discharge and ground-water levels that might indicate the onset of drought conditions or the effects of excessive pumping; and (4) discusses the long-term records that were used to select sites for a Long Island drought-monitoring network.Long Island’s long-term hydrologic records indicated that the available data provide a basis for development of a drought-monitoring network. The data from 36 stations that were selected as possible drought-monitoring sites—8 precipitation-monitoring stations, 8 streamflow-gaging (discharge) stations, 15 monitoring wells screened in the upper glacial aquifer under water-table (unconfined) conditions, and 5 monitoring wells screened in the underlying Magothy aquifer under semi-confined conditions—indicate that water levels in western parts of Long Island have fallen and risen markedly (more than 15 ft) in response to fluctuations in pumpage, and have declined from the increased use of sanitary- and storm-sewer systems. Water levels in the central and eastern parts, in contrast, remain relatively unaffected compared to the western parts, although the effects of human activity are discernible in the records.The value of each site as a drought-monitoring indicator was assessed through an analysis of trends in the records. Fifty-year annual and monthly data sets were created and combined into three composite-average hydrographs—precipitation, stream discharge, and ground-water levels. Three zones representing the range of human effect on ground-water levels were delineated to help evaluate islandwide hydrologic conditions and to quantify the indices. Data from the three indices can be used to assess current conditions in the ground-water system underlying Long Island and evaluate water-level declines during periods of drought.

Using FEP's List and a PA Methodology for Evaluating Suitable Areas for the LLW Repository in Italy

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

Risoluti, P.; Ciabatti, P.; Mingrone, G.

2002-02-26

In Italy following a referendum held in 1987, nuclear energy has been phased out. Since 1998, a general site selection process covering the whole Italian territory has been under way. A GIS (Geographic Information System) methodology was implemented in three steps using the ESRI Arc/Info and Arc/View platforms. The screening identified approximately 0.8% of the Italian territory as suitable for locating the LLW Repository. 200 areas have been identified as suitable for the location of the LLW Repository, using a multiple exclusion criteria procedure (1:500,000), regional scale (1:100.000) and local scale (1:25,000-1:10,000). A methodology for evaluating these areas has beenmore » developed allowing, along with the evaluation of the long term efficiency of the engineered barrier system (EBS), the characterization of the selected areas in terms of physical and safety factors and planning factors. The first step was to identify, on a referenced FEPs list, a group of geomorphological, geological, hydrogeological, climatic and human behavior caused process and/or events, which were considered of importance for the site evaluation, taking into account the Italian situation. A site evaluation system was established ascribing weighted scores to each of these processes and events, which were identified as parameters of the new evaluation system. The score of each parameter is ranging from 1 (low suitability) to 3 (high suitability). The corresponding weight is calculated considering the effect of the parameter in terms of total dose to the critical group, using an upgraded AMBER model for PA calculation. At the end of the process an index obtained by a score weighted sum gives the degree of suitability of the selected areas for the LLW Repository location. The application of the methodology to two selected sites is given in the paper.« less

Rapid assessment of the geographical distribution of lymphatic filariasis in Uganda, by screening of schoolchildren for circulating filarial antigens.

PubMed

Onapa, A W; Simonsen, P E; Baehr, I; Pedersen, E M

2005-03-01

To permit improvements in the targeting of control activities, the geographical distribution of lymphatic filariasis in Uganda was assessed by using a rapid immunochromatographic card test to check school-aged children for Wuchereria bancrofti-specific circulating filarial antigens (CFA). Survey sites were selected to represent the various ecological and topographical diversities in the country. Overall, 17,533 children from 76 sites were examined. CFA-positive cases were detected at 31 of the sites, with prevalences ranging from 0.4% to 30.7%. There appeared to be strikingly more lymphatic filariasis in the north of the country than in the south. The main focus was north of the Victoria Nile, where 27 (66%) of 41 sites had CFA-positive cases, often at high prevalences. Only four (11.4%) of the 35 sites south of the Victoria Nile had CFA-positive cases, and all four were along the western rift valley and had relatively low CFA prevalences. Geostatistical interpolation was used to create a map showing the geographical distribution of CFA prevalences in Uganda (by ordinary kriging), and to assess the population exposed to W. bancrofti transmission. Estimates based on population data from 2002 indicated that approximately 8.7 million people (35.3% of the national population) lived in areas where > 1% of the school-aged children were CFA-positive. CFA prevalences generally decreased with increasing altitude, and no CFA-positive cases were found at sites that were > 1300 m above sea level. Although it gives an under-estimate of the overall community prevalence (a fact that should be taken into account when interpreting the present results and comparing them with the results of other surveys), the screening of schoolchildren for CFA was found to be a simple and useful approach for mapping the geographical distribution of lymphatic filariasis.

Diverse Actions and Target-Site Selectivity of Neonicotinoids: Structural Insights

PubMed Central

Matsuda, Kazuhiko; Kanaoka, Satoshi; Akamatsu, Miki; Sattelle, David B.

2009-01-01

The nicotinic acetylcholine receptors (nAChRs) are targets for human and veterinary medicines as well as insecticides. Subtype-selectivity among the diverse nAChR family members is important for medicines targeting particular disorders, and pest-insect selectivity is essential for the development of safer, environmentally acceptable insecticides. Neonicotinoid insecticides selectively targeting insect nAChRs have important applications in crop protection and animal health. Members of this class exhibit strikingly diverse actions on their nAChR targets. Here we review the chemistry and diverse actions of neonicotinoids on insect and mammalian nAChRs. Electrophysiological studies on native nAChRs and on wild-type and mutagenized recombinant nAChRs have shown that basic residues particular to loop D of insect nAChRs are likely to interact electrostatically with the nitro group of neonicotinoids. In 2008, the crystal structures were published showing neonicotinoids docking into the acetylcholine binding site of molluscan acetylcholine binding proteins with homology to the ligand binding domain (LBD) of nAChRs. The crystal structures showed that 1) glutamine in loop D, corresponding to the basic residues of insect nAChRs, hydrogen bonds with the NO2 group of imidacloprid and 2) neonicotinoid-unique stacking and CH-π bonds at the LBD. A neonicotinoid-resistant strain obtained by laboratory-screening has been found to result from target site mutations, and possible reasons for this are also suggested by the crystal structures. The prospects of designing neonicotinoids that are safe not only for mammals but also for beneficial insects such as honey bees (Apis mellifera) are discussed in terms of interactions with non-α nAChR subunits. PMID:19321668

Interaction of antithrombin with sulfated, low molecular weight lignins: opportunities for potent, selective modulation of antithrombin function.

PubMed

Henry, Brian L; Connell, Justin; Liang, Aiye; Krishnasamy, Chandravel; Desai, Umesh R

2009-07-31

Antithrombin, a major regulator of coagulation and angiogenesis, is known to interact with several natural sulfated polysaccharides. Previously, we prepared sulfated low molecular weight variants of natural lignins, called sulfated dehydrogenation polymers (DHPs) (Henry, B. L., Monien, B. H., Bock, P. E., and Desai, U. R. (2007) J. Biol. Chem. 282, 31891-31899), which have now been found to exhibit interesting antithrombin binding properties. Sulfated DHPs represent a library of diverse noncarbohydrate aromatic scaffolds that possess structures completely different from heparin and heparan sulfate. Fluorescence binding studies indicate that sulfated DHPs bind to antithrombin with micromolar affinity under physiological conditions. Salt dependence of binding affinity indicates that the antithrombin-sulfated DHP interaction involves a massive 80-87% non-ionic component to the free energy of binding. Competitive binding studies with heparin pentasaccharide, epicatechin sulfate, and full-length heparin indicate that sulfated DHPs bind to both the pentasaccharide-binding site and extended heparin-binding site of antithrombin. Affinity capillary electrophoresis resolves a limited number of peaks of antithrombin co-complexes suggesting preferential binding of selected DHP structures to the serpin. Computational genetic algorithm-based virtual screening study shows that only one sulfated DHP structure, out of the 11 present in a library of plausible sequences, bound in the heparin-binding site with a high calculated score supporting selectivity of recognition. Enzyme inhibition studies indicate that only one of the three sulfated DHPs studied is a potent inhibitor of free factor VIIa in the presence of antithrombin. Overall, the chemo-enzymatic origin and antithrombin binding properties of sulfated DHPs present novel opportunities for potent and selective modulation of the serpin function, especially for inhibiting the initiation phase of hemostasis.

Use of a Recombinant Fluorescent Substrate with Cleavage Sites for All Botulinum Neurotoxins in High-Throughput Screening of Natural Product Extracts for Inhibitors of Serotypes A, B, and E7

DTIC Science & Technology

2007-12-14

contained dried residues from a collection of terrestrial plants , marine inver- tebrates, and various fungi. NCI plate numbers, sources of extracts, and... plants ), while Fig. 3B displays results from row G of the same plate. In these examples, wells B3, B5, B9, G9, and G12 were selected for further...sources of extracts Plate no. Source Extraction solvent 96110120 Terrestrial plants Water 96110125 Terrestrial plants CH3OH-CH2Cl2 12000707 Marine

Walla Walla River Basin Fish Screen Evaluations; Nursery Bridge Fishway and Garden City/Lowden II Sites, 2003 Technical Report.

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

Vucelick, J.; McMichael, G.

2003-11-01

Pacific Northwest National Laboratory evaluated the fish screens at the Nursery Bridge Fishway and the newly constructed Garden City/Lowden II site west of Walla Walla, Washington, in the Walla Walla River Basin during spring and summer 2003. Both fish screen facilities were examined to determine if they were being effectively operated and maintained to provide for safe fish passage. At the Nursery Bridge Fishway, the screens were evaluated specifically to determine whether the louvers that aid in controlling water flow from behind the screens could be adjusted so that the screens would meet fish protection criteria. Data were collected tomore » determine whether velocities in front of the screens and in the bypasses met current National Oceanic and Atmospheric Administration Fisheries (NOAA Fisheries) (formerly National Marine Fisheries Service (NMFS)) criteria to promote safe and timely fish passage before and after changing the louver settings. Rock weirs downstream of the dam were also evaluated to determine whether they might impede upstream migration of juvenile salmonids during low flow conditions. At the Garden City/Lowden II site, data were collected to establish a baseline for operating conditions and to determine whether any changes in the baffle settings were needed.« less

Development of a liquefaction hazard screening tool for caltrans bridge sites

USGS Publications Warehouse

Knudsen, K.-L.; Bott, J.D.J.; Woods, M.O.; McGuire, T.L.

2009-01-01

We have developed a liquefaction hazard screening tool for the California Department of Transportation (Caltrans) that is being used to evaluate the liquefaction hazard to approximately 13,000 bridge sites in California. Because of the large number of bridge sites to be evaluated, we developed a tool that makes use of parameters not typically considered in site-specific liquefaction investigations. We assessed geologic, topographic, seismic hazard, and subsurface conditions at about 100 sites of past liquefaction in California. Among the parameters we found common to many of these sites are: (a) low elevations, (b) proximity to a water body, and (c) presence of geologically youthful deposits or artificial fill materials. The nature of the study necessitated the use of readily available data, preferably datasets that are consistent across the state. The screening tool we provided to Caltrans makes use of the following parameters: (1) proximity to a water body, (2) whether the bridge crosses a water body, (3) the age of site geologic materials and the environment in which the materials were deposited, as discerned from available digital geologic maps, (4) probabilistic shaking estimates, (5) the site elevation, (6) information from available liquefaction hazard maps [covering the 9-county San Francisco Bay Area and Ventura County] and California Geological Survey (CGS) Zones of Required Investigation. For bridge sites at which subsurface boring data were available (from CGS' existing database), we calculated Displacement Potential Index values using a methodology developed by Allison Faris and Jiaer Wu. Caltrans' staff will use this hazard-screening tool, along with other tools focused on bridges and foundations, to prioritize site-specific investigations. ?? 2009 ASCE.

Time- and Cost-Efficient Identification of T-DNA Insertion Sites through Targeted Genomic Sequencing

PubMed Central

Lepage, Étienne; Zampini, Éric; Boyle, Brian; Brisson, Normand

2013-01-01

Forward genetic screens enable the unbiased identification of genes involved in biological processes. In Arabidopsis, several mutant collections are publicly available, which greatly facilitates such practice. Most of these collections were generated by agrotransformation of a T-DNA at random sites in the plant genome. However, precise mapping of T-DNA insertion sites in mutants isolated from such screens is a laborious and time-consuming task. Here we report a simple, low-cost and time efficient approach to precisely map T-DNA insertions simultaneously in many different mutants. By combining sequence capture, next-generation sequencing and 2D-PCR pooling, we developed a new method that allowed the rapid localization of T-DNA insertion sites in 55 out of 64 mutant plants isolated in a screen for gyrase inhibition hypersensitivity. PMID:23951038

Occurrence and Distribution of Pesticides in the St. Lucie River Watershed, South-Central Florida, 2000-01, Based on Enzyme-Linked Immunosorbent Assay (ELISA) Screening

USGS Publications Warehouse

Lietz, A.C.

2003-01-01

The St. Lucie River watershed is a valuable estuarine ecosystem and resource in south-central Florida. The watershed has undergone extensive changes over the last century because of anthropogenic activities. These activities have resulted in a complex urban and agricultural drainage network that facilitates the transport of contaminants, including pesticides, to the primary canals and then to the estuary. Historical data indicate that aquatic life criteria for selected pesticides have been exceeded. To address this concern, a reconnaissance was conducted to assess the occurrence and distribution of selected pesticides within the St. Lucie River watershed. Numerous water samples were collected from 37 sites among various land-use categories (urban/built-up, citrus, cropland/pastureland, and inte-grated). Samples were collected at inflow points to primary canals (C-23, C-24, and C-44) and at control structures along these canals from October 2000 to September 2001. Samples were screened for four pesticide classes (triazines, chloroacetanilides, chlorophenoxy compounds, and organophosphates) by using Enzyme-Linked Immunosorbent Assay (ELISA) screening. A temporal distribution of pesticides within the watershed was made based on samples collected at the integrated sites during different rainfall events between October 2000 and September 2001. Triazines were detected in 32 percent of the samples collected at the integrated sites. Chloroacetanilides were detected in 60 percent of the samples collected at the integrated sites, with most detections occurring at one site. Chlorophenoxy compounds were detected in 17 percent of the samples collected at the integrated sites. Organophosphates were detected in only one sample. A spatial distribution and range of concentration of pesticides at the 37 sampling sites in the watershed were determined among land-use categories. Triazine concentrations ranged from highest to lowest in the citrus, urban/built-up, and integrated areas, respectively. The highest median triazine concentration was found in the cropland/pastureland area. Chloroacetanilide concentra-tions ranged from highest to lowest in the citrus, integrated, urban/built-up, and cropland/pastureland areas, respectively. Chlorophenoxy compound concentrations ranged from highest to lowest in the urban/built-up, integrated, citrus, and cropland/pastureland areas, respectively. The maximum concentrations of triazines, chloroacetanilides, and chlorophenoxy compounds were 0.63, 1.0, and 14 micrograms per liter, respectively. Organophosphate was detected once at an integrated site at a concentration of 0.20 microgram per liter. Currently, the U.S. Environmental Protection Agency has no aquatic life guidelines for atrazine and metolachlor. However, assuming that all triazine and metolachlor concentrations from ELISA and gas chromatography/mass spectrometry (GC/MS) analyses were the result of atrazine and metolachlor detections, no concentrations exceeded the Canadian aquatic life guidelines for atrazine and metolachlor. One organophosphate detection (0.2 microgram per liter) did exceed the U.S. Environmental Protection Agency aquatic life guideline for chlorpyrifos. The deethylatrazine/atrazine ratio (DAR) is an important indicator of atrazine transport in the environment. The DAR ranged from 0.25 to 0.33, indicating that postapplication runoff was the most likely source of atrazine to the environment at the time of sampling. Deisopropylatrazine is a metabolite of atrazine and structurally similar compounds, such as simazine and cyanazine. The deisopropylatrazine/deethylatrazine ratio (D2R) is an indicator of nonpoint sources of deisopropylatrazine to the environment. The ratio ranged from 1 to 3 in this study, indicating simazine was an important source of deisopropylatrazine to the environment at the time of sampling, as opposed to atrazine alone. Confirmation analyses by GC/MS for triazines detected by ELISA indicated t

High-throughput screening (HTPS) of ToxCast Phase II chemical library for sodium iodide symporter (NIS) Inhibitors

EPA Science Inventory

In support of the Endocrine Disruptor Screening Program (EDSP), the U.S. EPA’s Office of Research and Development (ORD) is currently developing HTPS approaches to identify chemicals that may alter target sites in the thyroid hormone pathway. One target site is the sodium io...

A fast stimulability screening protocol for neuronal cultures on microelectrode arrays.

PubMed

Kapucu, Fikret E; Tanskanen, Jarno M A; Yuan, Yuting; Hyttinen, Jari A K

2015-01-01

Microelectrode arrays (MEAs) are used to study the electrical activity in brain slices and neuronal cultures. MEA experiments for the analysis of electrical stimulation responses require the tissue or culture to be prone to stimulation. For brain slices, potential stimulation sites may be directly visible in microscope, in which case the determination of stimulability at those locations is sufficient. In unstructured neuronal cultures, potential stimulation sites may not be known a priori, and spatial stimulability screening should be performed. Considering, e.g., 59 microelectrode sites, each to be stimulated several times, may result in long screening times, unacceptable with a MEA system without an integrated CO2 incubator, or in high stimulation effects on the networks. Here, we describe an implementation of a fast stimulation protocol employing pseudorandom stimulation site switching aiming at alleviating the network effects of the stimulability screening. In this paper, we show the usability of the proposed protocol by first detecting stimulable locations and subsequently apply repeated stimulation on the identified potentially stimulable locations to observe an exemplary neuronal pathway.

Computational Screening of Nanoporous Materials for Hexane and Heptane Isomer Separation

DOE PAGES

Chung, Yongchul G.; Bai, Peng; Haranczyk, Maciej; ...

2017-07-05

Computational high-throughput screening was carried out to assess a large number of experimentally reported metal–organic frameworks (MOFs) and zeolites for their utility in hexane isomer separation. Through the paper, we identified many MOFs and zeolites with high selectivity (S L+M > 10) for the group of n-hexane, 2-methylpentane, and 3-methylpentane (linear and monobranched isomers) versus 2,2-dimethylbutane and 2,3-dimethylbutane (dibranched isomers). This group of selective sorbents includes VICDOC (Fe 2(BDP) 3), a MOF with triangular pores that is known to exhibit high isomer selectivity and capacity. For three of these structures, the adsorption isotherms for a 10-component mixture of hexane andmore » heptane isomers were calculated. Subsequent simulations of column breakthrough curves showed that the DEYVUA MOF exhibits a longer process cycle time than VICDOC MOF or MRE zeolite, which are previously reported, high-performing materials, illustrating the importance of capacity in designing MOFs for practical applications. Among the identified candidates, we synthesized and characterized a MOF in a new copper form with high predicted adsorbent capacity (q L+M > 1.2 mol/L) and moderately high selectivity (S L+M ≈ 10). In conclusion, we examined the role of pore shape in hexane isomer separations, especially of triangular-shaped pores. We show through the potential energy surface and three-dimensional siting analyses that linear alkanes do not populate the corners of narrow triangular channels and that structures with nontriangular pores can efficiently separate hexane isomers. Detailed thermodynamic analysis illustrates how differences in the free energy of adsorption contribute to shape-selective separation in nanoporous materials.« less

Computational Screening of Nanoporous Materials for Hexane and Heptane Isomer Separation

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

Chung, Yongchul G.; Bai, Peng; Haranczyk, Maciej

Computational high-throughput screening was carried out to assess a large number of experimentally reported metal–organic frameworks (MOFs) and zeolites for their utility in hexane isomer separation. Through the paper, we identified many MOFs and zeolites with high selectivity (S L+M > 10) for the group of n-hexane, 2-methylpentane, and 3-methylpentane (linear and monobranched isomers) versus 2,2-dimethylbutane and 2,3-dimethylbutane (dibranched isomers). This group of selective sorbents includes VICDOC (Fe 2(BDP) 3), a MOF with triangular pores that is known to exhibit high isomer selectivity and capacity. For three of these structures, the adsorption isotherms for a 10-component mixture of hexane andmore » heptane isomers were calculated. Subsequent simulations of column breakthrough curves showed that the DEYVUA MOF exhibits a longer process cycle time than VICDOC MOF or MRE zeolite, which are previously reported, high-performing materials, illustrating the importance of capacity in designing MOFs for practical applications. Among the identified candidates, we synthesized and characterized a MOF in a new copper form with high predicted adsorbent capacity (q L+M > 1.2 mol/L) and moderately high selectivity (S L+M ≈ 10). In conclusion, we examined the role of pore shape in hexane isomer separations, especially of triangular-shaped pores. We show through the potential energy surface and three-dimensional siting analyses that linear alkanes do not populate the corners of narrow triangular channels and that structures with nontriangular pores can efficiently separate hexane isomers. Detailed thermodynamic analysis illustrates how differences in the free energy of adsorption contribute to shape-selective separation in nanoporous materials.« less

CORRECTIVE ACTION DECISION DOCUMENT FOR CORRECTIVE ACTION UNIT 383: AREA 12 E-TUNNEL SITES, NEVADA TEST SITE, REV. NO. 0

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

Mark McLane

2005-03-01

This Corrective Action Decision Document (CADD) was prepared by the Defense Threat Reduction Agency (DTRA) and the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO). The recommendations and corrective actions described within this document apply to the future closure of Corrective Action Unit (CAU) 383, Area 12 E-Tunnel Sites, which is a joint DTRA and NNSA/NSO site. The CAU consists of three (3) Corrective Action Sites (CASs): CAS 12-06-06 (Muckpile); CAS 12-25-02 (Oil Spill); and CAS 12-28-02 (Radioactive Material). In addition to these CASs, E-Tunnel Ponds One, Two, and Three, and the Drainage Area above themore » ponds were included since closure of the Muckpile will impact these areas. This CADD is consistent with the requirements of the ''Federal Facility Agreement and Consent Order'' agreed to by the State of Nevada, the U.S. Department of Energy, and the U.S. Department of Defense. The DTRA point of contact is the Nevada Operations Office, Environmental Project Manager; currently Ms. Tiffany A. Lantow. The NNSA/NSO point of contact is the Environmental Restoration, Industrial Sites Project Manager; currently Ms. Janet Appenzeller-Wing. The purpose of this CADD is to identify and provide the rationale for the selection of a recommended corrective action alternative for CAU 383. This document presents the recommended corrective action for CAU 383 (E-Tunnel Sites); however, implementation may be affected by the corrective action (to be determined) for CAU 551 (Area 12 Muckpiles) due to the close proximity of B, C, D, and F-Tunnels. The scope of this CADD consists of the following tasks: (1) Develop corrective action objectives; (2) Identify corrective action alternative screening criteria; (3) Develop corrective action alternatives; (4) Perform detailed and comparative evaluations of the corrective action alternatives in relation to the corrective action objectives and screening criteria; and (5) Recommend and justify a preferred corrective action alternative for CAU 383.« less

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

PubMed Central

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

2009-01-01

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

Ligand-based virtual screening under partial shape constraints.

PubMed

von Behren, Mathias M; Rarey, Matthias

2017-04-01

Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).

Ligand-based virtual screening under partial shape constraints

NASA Astrophysics Data System (ADS)

von Behren, Mathias M.; Rarey, Matthias

2017-04-01

Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise).

Recruitment of participants to a multiple sclerosis trial: The CombiRx experience

PubMed Central

Bhanushali, Minal J; Gustafson, Tarah; Powell, Steve; Conwit, Robin A; Wolinsky, Jerry S; Cutter, Gary R; Lublin, Fred; Cofield, Stacey S

2014-01-01

Background and Purpose: Participant recruitment is central to all clinical trials. Any delay in recruitment affects the completion and ultimate success of the trial. We report our experience with patient screening and randomization in CombiRx, which may inform the design of other trials. CombiRx was a multi-center, phase III, double-blind, randomized clinical trial comparing the combined use of interferon beta-1a and glatiramer acetate to either agent alone in patients with relapsing-remitting multiple sclerosis (RRMS). This trial was launched in January 2005 in 69 centers in the U.S. and Canada under a co-operative agreement with the National Institute of Neurological Disorders and Stroke (NINDS). The goal was to recruit 1000 patients over 1.5 years after a 6 month startup period. Instead, the investigators required 4.25 years to enroll 1008 patients. Methods: During this trial, we assessed the effectiveness of various recruitment strategies, utility of rescreening prior screen failures, and potential factors and strategies used in study conduct, research and infrastructure, all of which affected recruitment of participants and ultimately time to completion of CombiRx. We particularly were interested in the variability in time to site initiation between academic centers and private practice sites. Results: Physicians who were directly involved in the medical care of patients with RRMS were the primary source of patients recruited to CombiRx. A flexible study design that allowed for re-screening of the initial screen failures after a period of time was useful due to the relapsing/remitting course of the disease. Academic centers took longer to implement the trial than the private practice centers, but once sites were approved for enrollment, there was no important difference in the number of participants enrolled. Limitations: The CombiRx trial was conducted during a period when multiple new medications were being tested, thus affecting the pace of recruitment and limiting ability to generalize our experiences. However, the lessons we learned about process are relevant. Conclusion: Participants can be enrolled successfully in a clinical trial for RRMS, but factors affecting the time to achieve the requirements needed to start screening can be unpredictable and problematic. Prospective planning by the sponsors and investigators, use of central IRBs, master trial agreements and secure remote desktop access to the trial database may expedite trial implementation and participant recruitment. A good scientific research question with flexible study design and active involvement of the clinicians are important factors driving recruitment. Clinical trials can be implemented successfully both in private practices and at academic centers, a consideration when selecting sites. PMID:24686106

Reconnaissance soil geochemistry at the Riverton Uranium Mill Tailings Remedial Action Site, Fremont County, Wyoming

USGS Publications Warehouse

Smith, David B.; Sweat, Michael J.

2012-01-01

Soil samples were collected and chemically analyzed from the Riverton Uranium Mill Tailings Remedial Action Site, which lies within the Wind River Indian Reservation in Fremont County, Wyoming. Nineteen soil samples from a depth of 0 to 5 centimeters were collected in August 2011 from the site. The samples were sieved to less than 2 millimeters and analyzed for 44 major and trace elements following a near-total multi-acid extraction. Soil pH was also determined. The geochemical data were compared to a background dataset consisting of 160 soil samples previously collected from the same depth throughout the State of Wyoming as part of another ongoing study by the U.S. Geological Survey. Risk from potentially toxic elements in soil from the site to biologic receptors and humans was estimated by comparing the concentration of these elements with soil screening values established by the U.S. Environmental Protection Agency. All 19 samples exceeded the carcinogenic human health screening level for arsenic in residential soils of 0.39 milligrams per kilogram (mg/kg), which represents a one-in-one-million cancer risk (median arsenic concentration in the study area is 2.7 mg/kg). All 19 samples also exceeded the lead and vanadium screening levels for birds. Eighteen of the 19 samples exceeded the manganese screening level for plants, 13 of the 19 samples exceeded the antimony screening level for mammals, and 10 of 19 samples exceeded the zinc screening level for birds. However, these exceedances are also found in soils at most locations in the Wyoming Statewide soil database, and elevated concentrations alone are not necessarily cause for alarm. Uranium and thorium, two other elements of environmental concern, are elevated in soils at the site as compared to the Wyoming dataset, but no human or ecological soil screening levels have been established for these elements.

Identifiability in N-mixture models: a large-scale screening test with bird data.

PubMed

Kéry, Marc

2018-02-01

Binomial N-mixture models have proven very useful in ecology, conservation, and monitoring: they allow estimation and modeling of abundance separately from detection probability using simple counts. Recently, doubts about parameter identifiability have been voiced. I conducted a large-scale screening test with 137 bird data sets from 2,037 sites. I found virtually no identifiability problems for Poisson and zero-inflated Poisson (ZIP) binomial N-mixture models, but negative-binomial (NB) models had problems in 25% of all data sets. The corresponding multinomial N-mixture models had no problems. Parameter estimates under Poisson and ZIP binomial and multinomial N-mixture models were extremely similar. Identifiability problems became a little more frequent with smaller sample sizes (267 and 50 sites), but were unaffected by whether the models did or did not include covariates. Hence, binomial N-mixture model parameters with Poisson and ZIP mixtures typically appeared identifiable. In contrast, NB mixtures were often unidentifiable, which is worrying since these were often selected by Akaike's information criterion. Identifiability of binomial N-mixture models should always be checked. If problems are found, simpler models, integrated models that combine different observation models or the use of external information via informative priors or penalized likelihoods, may help. © 2017 by the Ecological Society of America.

A rapid generation of adenovirus vector with a genetic modification in hexon protein.

PubMed

Di, Bingyan; Mao, Qinwen; Zhao, Junli; Li, Xing; Wang, Dongyang; Xia, Haibin

2012-02-10

The generation of hexon-modified adenovirus vector has proven difficult. In this paper, we developed a novel method for rapid generation of hexon-modified adenoviral vector via one step ligation in vitro followed by quick white/blue color screening. The new system has the following features. First, eGFP expression driven by the CMV promoter in E1 region functions as a reporter to evaluate the tropism of hexon-modified adenovirus in vitro. Second, it has two unique restriction enzyme sites with sticky ends located in the hexon HVR5 region. Third, a lacZ expression cassette under the control of plac promoter is placed between the two restriction enzyme sites, which allows recombinants to be selected using blue/white screening. To prove the principle of the method, genetically modified adenoviruses were successfully produced by insertion of NGR, RGD or Tat PTD peptide into hexon HVR5. Furthermore, the transduction efficiency of the Tat PTD modified virus was shown to be a significant enhancement in A172 and CHO-K1 cells. In conclusion, the novel system makes the production of truly retargeted vectors more promising, which would be of substantial benefit for cancer gene therapy. Copyright © 2012 Elsevier B.V. All rights reserved.

In Silico Discovery of a Substituted 6-Methoxy-quinalidine with Leishmanicidal Activity in Leishmania infantum.

PubMed

Stevanović, Strahinja; Perdih, Andrej; Senćanski, Milan; Glišić, Sanja; Duarte, Margarida; Tomás, Ana M; Sena, Filipa V; Sousa, Filipe M; Pereira, Manuela M; Solmajer, Tom

2018-03-27

There is an urgent need for the discovery of new antileishmanial drugs with a new mechanism of action. Type 2 NADH dehydrogenase from Leishmania infantum ( Li NDH2) is an enzyme of the parasite's respiratory system, which catalyzes the electron transfer from NADH to ubiquinone without coupled proton pumping. In previous studies of the related NADH: ubiquinone oxidoreductase crystal structure from Saccharomyces cerevisiae , two ubiquinone-binding sites (UQ I and UQ II ) were identified and shown to play an important role in the NDH-2-catalyzed oxidoreduction reaction. Based on the available structural data, we developed a three-dimensional structural model of Li NDH2 using homology detection methods and performed an in silico virtual screening campaign to search for potential inhibitors targeting the Li NDH2 ubiquinone-binding site 1-UQ I . Selected compounds displaying favorable properties in the computational screening experiments were assayed for inhibitory activity in the structurally similar recombinant NDH-2 from S. aureus and leishmanicidal activity was determined in the wild-type axenic amastigotes and promastigotes of L. infantum . The identified compound, a substituted 6-methoxy-quinalidine, showed promising nanomolar leishmanicidal activity on wild-type axenic promastigotes and amastigotes of L. infantum and the potential for further development.

Screening of a library of T7 phage-displayed peptides identifies alphaC helix in 14-3-3 protein as a CBP501-binding site.

PubMed

Matsumoto, Yuki; Shindo, Yosuke; Takakusagi, Yoichi; Takakusagi, Kaori; Tsukuda, Senko; Kusayanagi, Tomoe; Sato, Hitoshi; Kawabe, Takumi; Sugawara, Fumio; Sakaguchi, Kengo

2011-12-01

CBP501 is a chemically modified peptide composed of twelve unnatural d-amino acids, which inhibits Chk kinase and abrogates G2 arrest induced by DNA-damaging agents. Here we identified an alphaC helix in 14-3-3 protein as a CBP501-binding site using T7 phage display technology. An affinity selection of T7 phage-displayed peptide using biotinylated CBP501 identified a 14-mer peptide NSDCIISRKIEQKE. This peptide sequence showed similarity to a portion of the alphaC helix of human 14-3-3ε, suggesting that CBP501 may bind to this region. Surface plasmon resonance (SPR) and ELISA demonstrated that CBP501 interacts with 14-3-3ε specifically at the screen-guided region. An avidin-agarose bead pull-down assay showed that CBP501 also binds to other 14-3-3 isoforms in Jurkat cells. Among the other known Chk kinase inhibitors tested, CBP501 showed the strongest affinity for 14-3-3ε. Thus, we conclude that in addition to the direct inhibition of Chk kinase activity, CBP501 directly binds to cellular 14-3-3 proteins through alphaC helix. Copyright © 2011 Elsevier Ltd. All rights reserved.

Conformational flexibility of DENV NS2B/NS3pro: from the inhibitor effect to the serotype influence

NASA Astrophysics Data System (ADS)

Piccirillo, Erika; Merget, Benjamin; Sotriffer, Christoph A.; do Amaral, Antonia T.

2016-03-01

The dengue virus (DENV) has four well-known serotypes, namely DENV1 to DENV4, which together cause 50-100 million infections worldwide each year. DENV NS2B/NS3pro is a protease recognized as a valid target for DENV antiviral drug discovery. However, NS2B/NS3pro conformational flexibility, involving in particular the NS2B region, is not yet completely understood and, hence, a big challenge for any virtual screening (VS) campaign. Molecular dynamics (MD) simulations were performed in this study to explore the DENV3 NS2B/NS3pro binding-site flexibility and obtain guidelines for further VS studies. MD simulations were done with and without the Bz-nKRR-H inhibitor, showing that the NS2B region stays close to the NS3pro core even in the ligand-free structure. Binding-site conformational states obtained from the simulations were clustered and further analysed using GRID/PCA, identifying four conformations of potential importance for VS studies. A virtual screening applied to a set of 31 peptide-based DENV NS2B/NS3pro inhibitors, taken from literature, illustrated that selective alternative pharmacophore models can be constructed based on conformations derived from MD simulations. For the first time, the NS2B/NS3pro binding-site flexibility was evaluated for all DENV serotypes using homology models followed by MD simulations. Interestingly, the number of NS2B/NS3pro conformational states differed depending on the serotype. Binding-site differences could be identified that may be crucial to subsequent VS studies.

Development of a Comprehensive Database System for Safety Analyst

PubMed Central

Paz, Alexander; Veeramisti, Naveen; Khanal, Indira; Baker, Justin

2015-01-01

This study addressed barriers associated with the use of Safety Analyst, a state-of-the-art tool that has been developed to assist during the entire Traffic Safety Management process but that is not widely used due to a number of challenges as described in this paper. As part of this study, a comprehensive database system and tools to provide data to multiple traffic safety applications, with a focus on Safety Analyst, were developed. A number of data management tools were developed to extract, collect, transform, integrate, and load the data. The system includes consistency-checking capabilities to ensure the adequate insertion and update of data into the database. This system focused on data from roadways, ramps, intersections, and traffic characteristics for Safety Analyst. To test the proposed system and tools, data from Clark County, which is the largest county in Nevada and includes the cities of Las Vegas, Henderson, Boulder City, and North Las Vegas, was used. The database and Safety Analyst together help identify the sites with the potential for safety improvements. Specifically, this study examined the results from two case studies. The first case study, which identified sites having a potential for safety improvements with respect to fatal and all injury crashes, included all roadway elements and used default and calibrated Safety Performance Functions (SPFs). The second case study identified sites having a potential for safety improvements with respect to fatal and all injury crashes, specifically regarding intersections; it used default and calibrated SPFs as well. Conclusions were developed for the calibration of safety performance functions and the classification of site subtypes. Guidelines were provided about the selection of a particular network screening type or performance measure for network screening. PMID:26167531

The myth of the normal, average human brain--the ICBM experience: (1) subject screening and eligibility.

PubMed

Mazziotta, John C; Woods, Roger; Iacoboni, Marco; Sicotte, Nancy; Yaden, Kami; Tran, Mary; Bean, Courtney; Kaplan, Jonas; Toga, Arthur W

2009-02-01

In the course of developing an atlas and reference system for the normal human brain throughout the human age span from structural and functional brain imaging data, the International Consortium for Brain Mapping (ICBM) developed a set of "normal" criteria for subject inclusion and the associated exclusion criteria. The approach was to minimize inclusion of subjects with any medical disorders that could affect brain structure or function. In the past two years, a group of 1685 potential subjects responded to solicitation advertisements at one of the consortium sites (UCLA). Subjects were screened by a detailed telephone interview and then had an in-person history and physical examination. Of those who responded to the advertisement and considered themselves to be normal, only 31.6% (532 subjects) passed the telephone screening process. Of the 348 individuals who submitted to in-person history and physical examinations, only 51.7% passed these screening procedures. Thus, only 10.7% of those individuals who responded to the original advertisement qualified for imaging. The most frequent cause for exclusion in the second phase of subject screening was high blood pressure followed by abnormal signs on neurological examination. It is concluded that the majority of individuals who consider themselves normal by self-report are found not to be so by detailed historical interviews about underlying medical conditions and by thorough medical and neurological examinations. Recommendations are made with regard to the inclusion of subjects in brain imaging studies and the criteria used to select them.

Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target.

PubMed

Ulrich, Julia; Dao, Van Anh; Majumdar, Upalparna; Schmitt-Engel, Christian; Schwirz, Jonas; Schultheis, Dorothea; Ströhlein, Nadi; Troelenberg, Nicole; Grossmann, Daniela; Richter, Tobias; Dönitz, Jürgen; Gerischer, Lizzy; Leboulle, Gérard; Vilcinskas, Andreas; Stanke, Mario; Bucher, Gregor

2015-09-03

Insect pest control is challenged by insecticide resistance and negative impact on ecology and health. One promising pest specific alternative is the generation of transgenic plants, which express double stranded RNAs targeting essential genes of a pest species. Upon feeding, the dsRNA induces gene silencing in the pest resulting in its death. However, the identification of efficient RNAi target genes remains a major challenge as genomic tools and breeding capacity is limited in most pest insects impeding whole-animal-high-throughput-screening. We use the red flour beetle Tribolium castaneum as a screening platform in order to identify the most efficient RNAi target genes. From about 5,000 randomly screened genes of the iBeetle RNAi screen we identify 11 novel and highly efficient RNAi targets. Our data allowed us to determine GO term combinations that are predictive for efficient RNAi target genes with proteasomal genes being most predictive. Finally, we show that RNAi target genes do not appear to act synergistically and that protein sequence conservation does not correlate with the number of potential off target sites. Our results will aid the identification of RNAi target genes in many pest species by providing a manageable number of excellent candidate genes to be tested and the proteasome as prime target. Further, the identified GO term combinations will help to identify efficient target genes from organ specific transcriptomes. Our off target analysis is relevant for the sequence selection used in transgenic plants.

Amino acid screening based on structural modeling identifies critical residues for the function, ion selectivity and structure of Arabidopsis MTP1.

PubMed

Kawachi, Miki; Kobae, Yoshihiro; Kogawa, Sayaka; Mimura, Tetsuro; Krämer, Ute; Maeshima, Masayoshi

2012-07-01

Arabidopsis thaliana MTP1 is a vacuolar membrane Zn(2+)/H(+) antiporter of the cation diffusion facilitator family. Here we present a structure-function analysis of AtMTP1-mediated transport and its remarkable Zn(2+) selectivity by functional complementation tests of more than 50 mutant variants in metal-sensitive yeast strains. This was combined with homology modeling of AtMTP1 based on the crystal structure of the Escherichia coli broad-specificity divalent cation transporter YiiP. The Zn(2+)-binding sites of EcYiiP in the cytoplasmic C-terminus, and the pore formed by transmembrane helices TM2 and TM5, are conserved in AtMTP1. Although absent in EcYiiP, Cys31 and Cys36 in the extended N-terminal cytosolic domain of AtMTP1 are necessary for complementation of a Zn-sensitive yeast strain. On the cytosolic side of the active Zn(2+)-binding site inside the transmembrane pore, Ala substitution of either Asn258 in TM5 or Ser101 in TM2 non-selectively enhanced the metal tolerance conferred by AtMTP1. Modeling predicts that these residues obstruct the movement of cytosolic Zn(2+) into the intra-membrane Zn(2+)-binding site of AtMTP1. A conformational change in the immediately preceding His-rich cytosolic loop may displace Asn258 and permit Zn(2+) entry into the pore. This would allow dynamic coupling of Zn(2+) transport to the His-rich loop, thus acting as selectivity filter or sensor of cytoplasmic Zn(2+) levels. Individual mutations at diverse sites within AtMTP1 conferred Co and Cd tolerance in yeast, and included deletions in N-terminal and His-rich intra-molecular cytosolic domains, and mutations of single residues flanking the transmembrane pore or participating in intra- or inter-molecular domain interactions, all of which are not conserved in the non-selective EcYiiP. © 2012 The Authors Journal compilation © 2012 FEBS.

Engineering more stable, selectable marker-free autoluminescent mycobacteria by one step.

PubMed

Yang, Feng; Njire, Moses M; Liu, Jia; Wu, Tian; Wang, Bangxing; Liu, Tianzhou; Cao, Yuanyuan; Liu, Zhiyong; Wan, Junting; Tu, Zhengchao; Tan, Yaoju; Tan, Shouyong; Zhang, Tianyu

2015-01-01

In our previous study, we demonstrated that the use of the autoluminescent Mycobacterium tuberculosis as a reporter strain had the potential to drastically reduce the time, effort, animals and costs consumed in evaluation of the activities of drugs and vaccines in live mice. However, the strains were relatively unstable and lost reporter with time without selection. The kanamycin selection marker used wasn't the best choice as it provides resistance to amino glycosides which are an important class of second line drugs used in tuberculosis treatment. In addition, the marker could limit utility of the strains for screening of new potential drugs or evaluating drug combinations for tuberculosis treatment. Limited selection marker genes for mycobacterial genetic manipulation is a major drawback for such a marker-containing strain in many research fields. Therefore, selectable marker-free, more stable autoluminescent mycobacteria are highly needed. After trying several strategies, we created such mycobacterial strains successfully by using an integrative vector and removing both the resistance maker and integrase genes by Xer site-specific recombination in one step. The corresponding plasmid vectors developed in this study could be very convenient in constructing other selectable marker-free, more stable reporter mycobacteria with diverse applications.

Improving compliance to colorectal cancer screening using blood and stool based tests in patients refusing screening colonoscopy in Germany.

PubMed

Adler, Andreas; Geiger, Sebastian; Keil, Anne; Bias, Harald; Schatz, Philipp; deVos, Theo; Dhein, Jens; Zimmermann, Mathias; Tauber, Rudolf; Wiedenmann, Bertram

2014-10-17

Despite strong recommendations for colorectal cancer (CRC) screening, participation rates are low. Understanding factors that affect screening choices is essential to developing future screening strategies. Therefore, this study assessed patient willingness to use non-invasive stool or blood based screening tests after refusing colonoscopy. Participants were recruited during regular consultations. Demographic, health, psychological and socioeconomic factors were recorded. All subjects were advised to undergo screening by colonoscopy. Subjects who refused colonoscopy were offered a choice of non-invasive tests. Subjects who selected stool testing received a collection kit and instructions; subjects who selected plasma testing had a blood draw during the office visit. Stool samples were tested with the Hb/Hp Complex Elisa test, and blood samples were tested with the Epi proColon® 2.0 test. Patients who were positive for either were advised to have a diagnostic colonoscopy. 63 of 172 subjects were compliant to screening colonoscopy (37%). 106 of the 109 subjects who refused colonoscopy accepted an alternative non-invasive method (97%). 90 selected the Septin9 blood test (83%), 16 selected a stool test (15%) and 3 refused any test (3%). Reasons for blood test preference included convenience of an office draw, overall convenience and less time consuming procedure. 97% of subjects refusing colonoscopy accepted a non-invasive screening test of which 83% chose the Septin9 blood test. The observation that participation can be increased by offering non-invasive tests, and that a blood test is the preferred option should be validated in a prospective trial in the screening setting.

Analysis of Parametric Adaptive Signal Detection with Applications to Radars and Hyperspectral Imaging

DTIC Science & Technology

2010-02-01

98 8.4.5 Training Screening ............................. .................................................................99 8.5 Experimental...associated with the proposed parametric model. Several im- portant issues are discussed, including model order selection, training screening , and time...parameters associated with the NS-AR model. In addition, we develop model order selection, training screening , and time-series based whitening and

Reasons for non-recruitment of eligible patients to a randomised controlled trial of secondary prevention after intracerebral haemorrhage: observational study.

PubMed

Maxwell, Amy E; MacLeod, Mary Joan; Joyson, Anu; Johnson, Sharon; Ramadan, Hawraman; Bellfield, Ruth; Byrne, Anthony; McGhee, Caroline; Rudd, Anthony; Price, Fiona; Vasileiadis, Evangelos; Holden, Melinda; Hewitt, Jonathan; Carpenter, Michael; Needle, Ann; Valentine, Stacey; Patel, Farzana; Harrington, Frances; Mudd, Paul; Emsley, Hedley; Gregary, Bindu; Kane, Ingrid; Muir, Keith; Tiwari, Divya; Owusu-Agyei, Peter; Temple, Natalie; Sekaran, Lakshmanan; Ragab, Suzanne; England, Timothy; Hedstrom, Amanda; Jones, Phil; Jones, Sarah; Doherty, Mandy; McCarron, Mark O; Cohen, David L; Tysoe, Sharon; Al-Shahi Salman, Rustam

2017-04-05

Recruitment to randomised prevention trials is challenging, not least for intracerebral haemorrhage (ICH) associated with antithrombotic drug use. We investigated reasons for not recruiting apparently eligible patients at hospital sites that keep screening logs in the ongoing REstart or STop Antithrombotics Randomised Trial (RESTART), which seeks to determine whether to start antiplatelet drugs after ICH. By the end of May 2015, 158 participants had been recruited at 108 active sites in RESTART. The trial coordinating centre invited all sites that kept screening logs to submit screening log data, followed by one reminder. We checked the integrity of data, focused on the completeness of data about potentially eligible patients and categorised the reasons they were not randomised. Of 108 active sites, 39 (36%) provided usable screening log data over a median of ten (interquartile range = 5-13) months of recruitment per site. During this time, sites screened 633 potentially eligible patients and randomised 53 (8%) of them. The main reasons why 580 patients were not randomised were: 43 (7%) patients started anticoagulation, 51 (9%) patients declined, 148 (26%) patients' stroke physicians were not uncertain about using antiplatelet drugs, 162 (28%) patients were too unwell and 176 (30%) patients were not randomised due to other reasons. RESTART recruited ~8% of eligible patients. If more physicians were uncertain about the therapeutic dilemma that RESTART is addressing, RESTART could have recruited up to four times as many participants. The trial coordinating centre continues to engage with physicians about their uncertainty. EU Clinical Trials, EudraCT 2012-003190-26 . Registered on 3 July 2012.

Body mass index is not a good predictor of bone density: results from WHI, CHS, and EPIDOS.

PubMed

Robbins, John; Schott, Anne-Marie; Azari, Rahman; Kronmal, Richard

2006-01-01

Body mass index (BMI) is often used to predict bone mineral density (BMD). This may be flawed. Large epidemiologic studies with BMI and BMD data were analyzed. Weight alone is a better predictor of BMD than BMI. Thus, when selecting individuals for dual-energy X-ray absorptiometry, weight should be used instead of BMI. Low body mass index (BMI) is frequently suggested as one of the factors that indicates the need for bone mineral density (BMD) screening for osteoporosis. The inclusion of the height-squared term in the denominator of this predictive factor is taken on faith or from other data, but it may not be reasonable in this case. We used data from three large epidemiologic studies to test the BMI, height, and weight as predictors of BMD: (1) the Women's Health Initiative (WHI) with 11,390 women; (2) the Cardiovascular Health Study (CHS) with 1,578 men and women; (3) and EPIDOS with 7,598 women. Dual-energy X-ray absorptiometry data on one or more BMD sites, the total hip, the femoral neck, and the lumbar spine from the three studies, as well as height and weight were examined. Correlation coefficients for BMI and weight with BMD were compared. Log transformed models were evaluated to compare the strengths of the models. The result of weight alone was a much better predictor of BMD for all sites in the three studies than BMI. Taller participants had larger BMDs than would have been predicted by BMI. In conclusion, BMIs should not be used to select individuals for BMD screening. A regression model using weight alone or weight and height is a better predictor of BMD in all three populations.

Hydrogeologic framework and ground-water resources at Seymour Johnson Air Force Base, North Carolina

USGS Publications Warehouse

Cardinell, A.P.; Howe, S.S.

1997-01-01

A preliminary hydrogeologic framework of the Seymour Johnson Air Force Base was constructed from published data, available well data, and reports from Air Base files, City of Goldsboro and Wayne County records, and North Carolina Geological Survey files. Borehole geophysical logs were run in selected wells; and the surficial, Black Creek, and upper Cape Fear aquifers were mapped. Results indicate that the surficial aquifer appears to have the greatest lateral variability of clay units and aquifer material of the three aquifers. A surficial aquifer water-level surface map, constructed from selected monitoring wells screened exclusively in the surficial aquifer, indicates the general direction of ground-water movement in this mostly unconfined aquifer is toward the Neuse River and Stoney Creek. However, water-level gradient data from a few sites in the surficial aquifer did not reflect this trend, and there are insufficient hydrologic and hydrogeologic data to determine the cause of these few anamalous measurements. The Black Creek aquifer underlies the surficial aquifer and is believed to underlie most of Wayne County, including the Air Base where the aquifer and overlying confining unit are estimated from well log data to be as much as 100 feet thick. The Black Creek confining unit ranges in thickness from less than 8 feet to more than 20 feet. There are currently no accessible wells screened exclusively in the Black Creek aquifer from which to measure water levels. The upper Cape Fear aquifer and confining unit are generally found at depths greater than 80 feet below land surface at the Air Base, and are estimated to be as much as 70 feet thick. Hydrologic and hydrogeologic data are insufficient to determine localized surficial aquifer hydrogeology, ground-water movement at several sites, or hydraulic head differences between the three aquifers.

Mapping Near-Surface Salinization Using Long-wavelength AIRSAR

NASA Technical Reports Server (NTRS)

Paine, Jeffery G.

2003-01-01

In May 1999, NASA's Jet Propulsion Laboratory acquired airborne synthetic aperture radar (AIRSAR) data over the Hatchel and Montague Test Sites in Texas. We analyzed P- and L-band polarimetric radar data from these AIRSAR missions to assess whether AIRSAR could be used as a rapid and remote platform for screening large areas at risk for near-surface soil and water salinization. Ongoing geological, geophysical, and hydrological studies at the Hatchel Test Site in Runnels County and the Montague Test Site in Montague County have demonstrated the utility of high-resolution airborne electromagnetic (EM) induction in mapping electrical conductivity changes that accompany shallow natural and oil-field related salinization at these sites in the Colorado and Red River basins. We compared AIRSAR and airborne EM data quantitatively by (1) selecting representative flight lines from airborne EM surveys of the Hatchel and Montague sites, (2) extracting measurement locations and apparent conductivities at the highest available EM frequency, (3) identifying and extracting all P- and L-band backscatter intensities for all locations within 5 m of an airborne EM measurement, and (4) examining the spatial and magnitude relationships between apparent conductivity and all radar polarization and polarization-ratio combinations. For both test sites, backscatter intensity in all individual P- and L-band polarizations was slightly negatively correlated with apparent conductivity. In most modes this was manifested as a decrease in the range and magnitude of backscatter intensity as apparent conductivity increased. Select single-band and cross-band polarization ratios exhibited somewhat higher correlation with apparent conductivity by partly diminishing the dominance of the vegetation contribution to V backscatter intensity. The highest correlation with conductivity was obtained using the L-band vertical- to cross-polarization ratio, the P-band vertical- to L-band cross-polarization ratio, and the P-band vertical-to cross-polarization ratio. These correlations were higher for the more arid (and less electrically conductive) Hatchel Test Site than they were for the Montague Test Site.

75 FR 37519 - 30-Day Notice of Proposed Information Collection: Forms DS-4138, Request for Escort Screening...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-29

... to obtain or retain a benefit. Title of Information Collection: Application for OFM Web site Account...] 30-Day Notice of Proposed Information Collection: Forms DS-4138, Request for Escort Screening Courtesies; DS-4139, Photograph and Signature Card; & DS-4140, Application for OFM Web Site Account; DS- 1504...

RNA interference as a method for target-site screening in the Western Corn Rootworm, Diabrotica virgifera virgifera

USDA-ARS?s Scientific Manuscript database

RNA interference (RNAi) is one of the most powerful and extraordinarily-specific means by which to silence genes. The ability of RNAi to silence genes makes it possible to ascertain function from genomic data, thereby making it an excellent choice for target-site screening. To test the efficacy of...

Use of the heteroduplex mobility assay and cell sorting to select genome sequences of the CCR5 gene in HEK 293T cells edited by transcription activator-like effector nucleases

PubMed Central

Nerys-Junior, Arildo; Costa, Lendel C.; Braga-Dias, Luciene P.; Oliveira, Márcia; Rossi, Átila D.; da Cunha, Rodrigo Delvecchio; Gonçalves, Gabriel S.; Tanuri, Amilcar

2014-01-01

Engineered nucleases such as zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) are one of the most promising tools for modifying genomes. These site-specific enzymes cause double-strand breaks that allow gene disruption or gene insertion, thereby facilitating genetic manipulation. The major problem associated with this approach is the labor-intensive procedures required to screen and confirm the cellular modification by nucleases. In this work, we produced a TALEN that targets the human CCR5 gene and developed a heteroduplex mobility assay for HEK 293T cells to select positive colonies for sequencing. This approach provides a useful tool for the quick detection and easy assessment of nuclease activity. PMID:24688299

Discovery of Clinical Candidate 1-{[(2 S ,3 S ,4 S )-3-Ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide (PF-06650833), a Potent, Selective Inhibitor of Interleukin-1 Receptor Associated Kinase 4 (IRAK4), by Fragment-Based Drug Design

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

Lee, Katherine L.; Ambler, Catherine M.; Anderson, David R.

Through fragment-based drug design focused on engaging the active site of IRAK4 and leveraging three-dimensional topology in a ligand-efficient manner, a micromolar hit identified from a screen of a Pfizer fragment library was optimized to afford IRAK4 inhibitors with nanomolar potency in cellular assays. The medicinal chemistry effort featured the judicious placement of lipophilicity, informed by co-crystal structures with IRAK4 and optimization of ADME properties to deliver clinical candidate PF-06650833 (compound 40). This compound displays a 5-unit increase in lipophilic efficiency from the fragment hit, excellent kinase selectivity, and pharmacokinetic properties suitable for oral administration.

Implementation of Tuberculosis Intensive Case Finding, Isoniazid Preventive Therapy, and Infection Control ("Three I's") and HIV-Tuberculosis Service Integration in Lower Income Countries.

PubMed

Charles, M Katherine; Lindegren, Mary Lou; Wester, C William; Blevins, Meridith; Sterling, Timothy R; Dung, Nguyen Thi; Dusingize, Jean Claude; Avit-Edi, Divine; Durier, Nicolas; Castelnuovo, Barbara; Nakigozi, Gertrude; Cortes, Claudia P; Ballif, Marie; Fenner, Lukas

2016-01-01

World Health Organization advocates for integration of HIV-tuberculosis (TB) services and recommends intensive case finding (ICF), isoniazid preventive therapy (IPT), and infection control ("Three I's") for TB prevention and control among persons living with HIV. To assess the implementation of the "Three I's" of TB-control at HIV treatment sites in lower income countries. Survey conducted between March-July, 2012 at 47 sites in 26 countries: 6 (13%) Asia Pacific, 7 (15%), Caribbean, Central and South America, 5 (10%) Central Africa, 8 (17%) East Africa, 14 (30%) Southern Africa, and 7 (15%) West Africa. ICF using symptom-based screening was performed at 38% of sites; 45% of sites used symptom-screening plus additional diagnostics. IPT at enrollment or ART initiation was implemented in only 17% of sites, with 9% of sites providing IPT to tuberculin-skin-test positive patients. Infection control measures varied: 62% of sites separated smear-positive patients, and healthcare workers used masks at 57% of sites. Only 12 (26%) sites integrated HIV-TB services. Integration was not associated with implementation of TB prevention measures except for IPT provision at enrollment (42% integrated vs. 9% non-integrated; p = 0.03). Implementation of TB screening, IPT provision, and infection control measures was low and variable across regional HIV treatment sites, regardless of integration status.

Biosensor-based small molecule fragment screening with biolayer interferometry

NASA Astrophysics Data System (ADS)

Wartchow, Charles A.; Podlaski, Frank; Li, Shirley; Rowan, Karen; Zhang, Xiaolei; Mark, David; Huang, Kuo-Sen

2011-07-01

Biosensor-based fragment screening is a valuable tool in the drug discovery process. This method is advantageous over many biochemical methods because primary hits can be distinguished from non-specific or non-ideal interactions by examining binding profiles and responses, resulting in reduced false-positive rates. Biolayer interferometry (BLI), a technique that measures changes in an interference pattern generated from visible light reflected from an optical layer and a biolayer containing proteins of interest, is a relatively new method for monitoring small molecule interactions. The BLI format is based on a disposable sensor that is immersed in 96-well or 384-well plates. BLI has been validated for small molecule detection and fragment screening with model systems and well-characterized targets where affinity constants and binding profiles are generally similar to those obtained with surface plasmon resonsance (SPR). Screens with challenging targets involved in protein-protein interactions including BCL-2, JNK1, and eIF4E were performed with a fragment library of 6,500 compounds, and hit rates were compared for these targets. For eIF4E, a protein containing a PPI site and a nucleotide binding site, results from a BLI fragment screen were compared to results obtained in biochemical HTS screens. Overlapping hits were observed for the PPI site, and hits unique to the BLI screen were identified. Hit assessments with SPR and BLI are described.

Rapid microfluidic analysis of a Y-STR multiplex for screening of forensic samples.

PubMed

Gibson-Daw, Georgiana; Albani, Patricia; Gassmann, Marcus; McCord, Bruce

2017-02-01

In this paper, we demonstrate a rapid analysis procedure for use with a small set of rapidly mutating Y chromosomal short tandem repeat (Y-STR) loci that combines both rapid polymerase chain reaction (PCR) and microfluidic separation elements. The procedure involves a high-speed polymerase and a rapid cycling protocol to permit PCR amplification in 16 min. The resultant amplified sample is next analysed using a short 1.8-cm microfluidic electrophoresis system that permits a four-locus Y-STR genotype to be produced in 80 s. The entire procedure takes less than 25 min from sample collection to result. This paper describes the rapid amplification protocol as well as studies of the reproducibility and sensitivity of the procedure and its optimisation. The amplification process utilises a small high-speed thermocycler, microfluidic device and compact laptop, making it portable and potentially useful for rapid, inexpensive on-site genotyping. The four loci used for the multiplex were selected due to their rapid mutation rates and should proved useful in preliminary screening of samples and suspects. Overall, this technique provides a method for rapid sample screening of suspect and crime scene samples in forensic casework. Graphical abstract ᅟ.

Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries.

PubMed

Lamichhane, Tek N; Abeydeera, N Dinuka; Duc, Anne-Cécile E; Cunningham, Philip R; Chow, Christine S

2011-01-28

Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this region in translation. In this work, a heptapeptide M13 phage-display library was screened for ligands that target the wild-type, naturally modified bacterial helix 31. Several peptides, including TYLPWPA, CVRPFAL, TLWDLIP, FVRPFPL, ATPLWLK, and DIRTQRE, were found to be prevalent after several rounds of screening. Several of the peptides exhibited moderate affinity (in the high nM to low µM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays.

Acceptability of Cervical Cancer Screening in Rural Mozambique

ERIC Educational Resources Information Center

Audet, Carolyn M.; Matos, Carla Silva; Blevins, Meridith; Cardoso, Aventina; Moon, Troy D.; Sidat, Mohsin

2012-01-01

In Zambezia province, Mozambique, cervical cancer (CC) screening was introduced to rural communities in 2010. Our study sought to determine whether women would accept screening via pelvic examination and visual inspection with acetic acid (VIA) at two clinical sites near the onset of a new CC screening program. A cross-sectional descriptive study…

City and County Solar PV Training Program, Module 2: Screening and Identifying PV Projects

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

Elgqvist, Emma M

When screening and identifying PV projects, cities and counties should understand the different factors that impact the technical and economic potential of a PV project, the steps of the PV screening process, and how to use REopt Lite to screen a site for PV and storage project potential.

Assembly of ordered contigs of cosmids selected with YACs of human chromosome 13

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

Fischer, S.G.; Cayanis, E.; Boukhgalter, B.

1994-06-01

The authors have developed an efficient method for assembling ordered cosmid contigs aligned to mega-YACs and midi-YACs (average insert sizes of 1.0 and 0.35 Mb, respectively) and used this general method to initiate high-resolution physical mapping of human chromosome 13 (Chr 13). Chr 13-enriched midi-YAC (mYAC) and mega-YAC (MYAC) sublibraries were obtained from corresponding CEPH total human YAC libraries by selecting colonies with inter-Alu PCR probes derived from Chr 13 monochromosomal cell hybrid DNA. These sublibraries were arrayed on filters at high density. In this approach, the MYAC 13 sublibrary is screened by hybridization with cytogenetically assigned Chr 13 DNAmore » probes to select one or a small subset of MYACs. Inter-Alu PCR products from each mYAC are then hybridized to the MYAC and mYAC sublibraries to identify overlapping YACs and to an arrayed Chr 13-specific cosmid library to select corresponding cosmids. The set of selected cosmids, gridded on filters at high density, is hybridized with inter-Alu PCR products from each of the overlapping YACs to identify subsets of cosmids and also with riboprobes from each cosmid of the arrayed set ({open_quotes}cosmid matrix cross-hybridization{close_quotes}). From these data, cosmid contigs are assembled by a specifically designed computer program. Application of this method generates cosmid contigs spanning the length of a MYAC with few gaps. To provide a high-resolution map, ends of cosmids are sequenced at preselected sites to position densely spaced sequence-tagged sites. 33 refs., 7 figs., 1 tab.« less

An Automated Algorithm to Screen Massive Training Samples for a Global Impervious Surface Classification

NASA Technical Reports Server (NTRS)

Tan, Bin; Brown de Colstoun, Eric; Wolfe, Robert E.; Tilton, James C.; Huang, Chengquan; Smith, Sarah E.

2012-01-01

An algorithm is developed to automatically screen the outliers from massive training samples for Global Land Survey - Imperviousness Mapping Project (GLS-IMP). GLS-IMP is to produce a global 30 m spatial resolution impervious cover data set for years 2000 and 2010 based on the Landsat Global Land Survey (GLS) data set. This unprecedented high resolution impervious cover data set is not only significant to the urbanization studies but also desired by the global carbon, hydrology, and energy balance researches. A supervised classification method, regression tree, is applied in this project. A set of accurate training samples is the key to the supervised classifications. Here we developed the global scale training samples from 1 m or so resolution fine resolution satellite data (Quickbird and Worldview2), and then aggregate the fine resolution impervious cover map to 30 m resolution. In order to improve the classification accuracy, the training samples should be screened before used to train the regression tree. It is impossible to manually screen 30 m resolution training samples collected globally. For example, in Europe only, there are 174 training sites. The size of the sites ranges from 4.5 km by 4.5 km to 8.1 km by 3.6 km. The amount training samples are over six millions. Therefore, we develop this automated statistic based algorithm to screen the training samples in two levels: site and scene level. At the site level, all the training samples are divided to 10 groups according to the percentage of the impervious surface within a sample pixel. The samples following in each 10% forms one group. For each group, both univariate and multivariate outliers are detected and removed. Then the screen process escalates to the scene level. A similar screen process but with a looser threshold is applied on the scene level considering the possible variance due to the site difference. We do not perform the screen process across the scenes because the scenes might vary due to the phenology, solar-view geometry, and atmospheric condition etc. factors but not actual landcover difference. Finally, we will compare the classification results from screened and unscreened training samples to assess the improvement achieved by cleaning up the training samples. Keywords:

Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins.

PubMed

Sun, Yan-Bo; Zhou, Wei-Ping; Liu, He-Qun; Irwin, David M; Shen, Yong-Yi; Zhang, Ya-Ping

2013-01-01

Since their divergence from the terrestrial artiodactyls, cetaceans have fully adapted to an aquatic lifestyle, which represents one of the most dramatic transformations in mammalian evolutionary history. Numerous morphological and physiological characters of cetaceans have been acquired in response to this drastic habitat transition, such as thickened blubber, echolocation, and ability to hold their breath for a long period of time. However, knowledge about the molecular basis underlying these adaptations is still limited. The sequence of the genome of Tursiops truncates provides an opportunity for a comparative genomic analyses to examine the molecular adaptation of this species. Here, we constructed 11,838 high-quality orthologous gene alignments culled from the dolphin and four other terrestrial mammalian genomes and screened for positive selection occurring in the dolphin lineage. In total, 368 (3.1%) of the genes were identified as having undergone positive selection by the branch-site model. Functional characterization of these genes showed that they are significantly enriched in the categories of lipid transport and localization, ATPase activity, sense perception of sound, and muscle contraction, areas that are potentially related to cetacean adaptations. In contrast, we did not find a similar pattern in the cow, a closely related species. We resequenced some of the positively selected sites (PSSs), within the positively selected genes, and showed that most of our identified PSSs (50/52) could be replicated. The results from this study should have important implications for our understanding of cetacean evolution and their adaptations to the aquatic environment.

Implications of Nine Risk Prediction Models for Selecting Ever-Smokers for Computed Tomography Lung Cancer Screening.

PubMed

Katki, Hormuzd A; Kovalchik, Stephanie A; Petito, Lucia C; Cheung, Li C; Jacobs, Eric; Jemal, Ahmedin; Berg, Christine D; Chaturvedi, Anil K

2018-05-15

Lung cancer screening guidelines recommend using individualized risk models to refer ever-smokers for screening. However, different models select different screening populations. The performance of each model in selecting ever-smokers for screening is unknown. To compare the U.S. screening populations selected by 9 lung cancer risk models (the Bach model; the Spitz model; the Liverpool Lung Project [LLP] model; the LLP Incidence Risk Model [LLPi]; the Hoggart model; the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial Model 2012 [PLCOM2012]; the Pittsburgh Predictor; the Lung Cancer Risk Assessment Tool [LCRAT]; and the Lung Cancer Death Risk Assessment Tool [LCDRAT]) and to examine their predictive performance in 2 cohorts. Population-based prospective studies. United States. Models selected U.S. screening populations by using data from the National Health Interview Survey from 2010 to 2012. Model performance was evaluated using data from 337 388 ever-smokers in the National Institutes of Health-AARP Diet and Health Study and 72 338 ever-smokers in the CPS-II (Cancer Prevention Study II) Nutrition Survey cohort. Model calibration (ratio of model-predicted to observed cases [expected-observed ratio]) and discrimination (area under the curve [AUC]). At a 5-year risk threshold of 2.0%, the models chose U.S. screening populations ranging from 7.6 million to 26 million ever-smokers. These disagreements occurred because, in both validation cohorts, 4 models (the Bach model, PLCOM2012, LCRAT, and LCDRAT) were well-calibrated (expected-observed ratio range, 0.92 to 1.12) and had higher AUCs (range, 0.75 to 0.79) than 5 models that generally overestimated risk (expected-observed ratio range, 0.83 to 3.69) and had lower AUCs (range, 0.62 to 0.75). The 4 best-performing models also had the highest sensitivity at a fixed specificity (and vice versa) and similar discrimination at a fixed risk threshold. These models showed better agreement on size of the screening population (7.6 million to 10.9 million) and achieved consensus on 73% of persons chosen. No consensus on risk thresholds for screening. The 9 lung cancer risk models chose widely differing U.S. screening populations. However, 4 models (the Bach model, PLCOM2012, LCRAT, and LCDRAT) most accurately predicted risk and performed best in selecting ever-smokers for screening. Intramural Research Program of the National Institutes of Health/National Cancer Institute.

Regulatory requirements and tools for environmental assessment of hazardous wastes: Understanding tribal and stakeholder concerns using Department of Energy sites

PubMed Central

Burger, Joanna; Powers, Charles; Gochfeld, Michael

2014-01-01

Many US governmental and Tribal Nation agencies, as well as state and local entities, deal with hazardous wastes within regulatory frameworks that require specific environmental assessments. In this paper we use Department of Energy (DOE) sites as examples to examine the relationship between regulatory requirements and environmental assessments for hazardous waste sites and give special attention to how assessment tools differ. We consider federal laws associated with environmental protection include the National Environmental Policy Act (NEPA), the Resource Conservation and Recovery Act (RCRA), the Comprehensive Environmental Response Compensation and Liability Act (CERCLA), as well as regulations promulgated by the Nuclear Regulatory Commission, Tribal Nations and state agencies. These regulatory regimes require different types of environmental assessments and remedial investigations, dose assessments and contaminant pathways. The DOE case studies illustrate the following points: 1) there is often understandable confusion about what regulatory requirements apply to the site resources, and what environmental assessments are required by each, 2) the messages sent on site safety issued by different regulatory agencies are sometimes contradictory or confusing (e.g. Oak Ridge Reservation), 3) the regulatory frameworks being used to examine the same question can be different, leading to different conclusions (e.g. Brookhaven National Laboratory), 4) computer models used in support of groundwater models or risk assessments are not necessarily successful in convincing Native Americans and others that there is no possibility of risk from contaminants (e.g. Amchitka Island), 5) when given the opportunity to choose between relying on a screening risk assessments or waiting for a full site-specific analysis of contaminants in biota, the screening risk assessment option is rarely selected (e.g. Amchitka, Hanford Site), and finally, 6) there needs to be agreement on whether there has been adequate characterization to support the risk assessment (e.g. Hanford). The assessments need to be transparent and to accommodate different opinions about the relationship between characterizations and risk assessments. This paper illustrates how many of the problems at DOE sites, and potentially at other sites in the U.S. and elsewhere, derive from a lack of either understanding of, or consensus about, the regulatory process, including the timing and types of required characterizations and data in support of site characterizations and risk assessments. PMID:20719428

How to select the correct education strategy: when not to go online.

PubMed

Klingbeil, Carol G; Johnson, Norah L; Totka, Joan P; Doyle, Lynn

2009-01-01

Screening for intimate partner violence is an important injury prevention strategy. Nurses who develop staff education, to promote screening, need to select a method that is sensitive to learners. Online learning, although convenient, is not well suited to sensitive topics such as screening for intimate partner violence. The purpose of this article is to describe a curriculum for intimate partner violence screening based on self-efficacy theory, which includes a hospital-produced video, a role play, and a discussion.

Comparison of Cardiovascular Risk Screening Methods and Mortality Data among Hungarian Primary Care Population: Preliminary Results of the First Government-Financed Managed Care Program.

PubMed

Móczár, Csaba; Rurik, Imre

2015-09-01

Besides participation in the primary prevention, screening as secondary prevention is an important requirement for primary care services. The effect of this work is influenced by the characteristics of individual primary care practices and doctors' screening habits, as well as by the regulation of screening processes and available financial resources. Between 1999 and 2009, a managed care program was introduced and carried out in Hungary, financed by the government. This financial support and motivation gave the opportunity to increase the number of screenings. 4,462 patients of 40 primary care practices were screened on the basis of SCORE risk assessment. The results of the screening were compared on the basis of two groups of patients, namely: those who had been pre-screened (pre-screening method) for known risk factors in their medical history (smoking, BMI, age, family cardiovascular history), and those randomly screened. The authors also compared the mortality data of participating primary care practices with the regional and national data. The average score was significantly higher in the pre-screened group of patients, regardless of whether the risk factors were considered one by one or in combination. Mortality was significantly lower in the participating primary practices than had been expected on the basis of the national mortality data. This government-financed program was a big step forward to establish a proper screening method within Hungarian primary care. Performing cardiovascular screening of a selected target group is presumably more appropriate than screening within a randomly selected population. Both methods resulted in a visible improvement in regional mortality data, though it is very likely that with pre-screening a more cost-effective selection for screening may be obtained.

["Local" or "mobile" screening for diabetic retinopathy in general practice by non-mydriatic digital cameras? about the Diabetes Midi-Pyrénées network activity between 2005 and 2010].

PubMed

Bismuth, Pierre; Bismuth, Michel; Dupouy, Julie; Rougé-Bugat, Marie-Eve; Poutrain, Jean-Christophe; Escourrou, Brigitte; Hanaire, Hélène; Oustric, Stéphane

2012-12-01

Fundus photographs using non-mydriatic digital cameras for diabetic retinopathy screening have been studied in France during the past 10 years. Nevertheless, the different screening modalities have not been compared. The main goal of this study was to compare patient recruitment with two different screening modalities, and secondarily to compare diagnostic effectiveness and cost. A retrospective study analyzed data from the Diabetes Midi Pyrenees Network in 2005 and between 2006 and 2010. In 2005, a vehicle with digital camera traveled through a rural department in order to screen diabetic patients whose last fundus examination was performed greater than 1 year previously. Between 2006 and 2010, general practitioners sent their diabetic patients whose last fundus examination was performed greater than 1 year previously to a "local" screening site. In the two cases, fundus photographs were made by trained operator at screening site and analyzed by an ophthalmologist. The "mobile" screening recruited 698 patients, and the "local" screening 345 patients. Patients recruited by "mobile" screening were older than those recruited by "local" screening. They were preferentially men and suffered from diabetes from far longer The diagnostic performance of "local" screening was 26.8%, and it was 28.6% for "mobile" screening (p = 0.47). The cost of screening was higher for "mobile" screening: 116 Euro against 61 Euro for "local" screening. "Mobile" screening could allow more patient recruitment than "local" screening when geographic and demographic constraints are more important.

Toward the understanding of the molecular basis for the inhibition of COX-1 and COX-2 by phenolic compounds present in Uruguayan propolis and grape pomace.

PubMed

Paulino, Margot; Alvareda, Elena; Iribarne, Federico; Miranda, Pablo; Espinosa, Victoria; Aguilera, Sara; Pardo, Helena

2016-12-01

Propolis and grape pomace have significant amounts of phenols which can take part in anti-inflammatory mechanisms. As the cyclooxygenases 1 and 2 (COX-1 and COX-2) are involved in said mechanisms, the possibility for a selective inhibition of COX-2 was analyzed in vitro and in silico. Propolis and grape pomace from Uruguayan species were collected, extracted in hydroalcoholic mixture and analyzed. Based on phenols previously identified, and taking as reference the crystallographic structures of COX-1 and COX-2 in complex with the commercial drug Celecoxib, a molecular docking procedure was devised to adjust 123 phenolic molecular models at the enzyme-binding sites. The most important results of this work are that the extracts have an overall inhibition activity very similar in COX-1 and COX-2, i.e. they do not possess selective inhibition activity for COX-2. Nevertheless, 10 compounds of the phenolic database turned out to be more selective and 94 phenols resulted with similar selectivity than Celecoxib, an outcome that accounts for the overall experimental inhibition measures. Binding site environment observations showed increased polarity in COX-2 as compared with COX-1, suggesting that polarity is the key for selectivity. Accordingly, the screening of molecular contacts pointed to the residues: Arg106, Gln178, Leu338, Ser339, Tyr341, Tyr371, Arg499, Ala502, Val509, and Ser516, which would explain, at the atomic level, the anti-inflammatory effect of the phenolic compounds. Among them, Gln178 and Arg499 appear to be essential for the selective inhibition of COX-2.

A concept for making EMO mobile

NASA Astrophysics Data System (ADS)

Kumar, Mukesh

2012-01-01

The current selected features and profiles in a mobile device is usually set manually and do not use the external environment automatically to change it. The features and profile can be switching to silent mode in office, selecting a formal ringtone in office, describing the mood in the social network sites and a whole lot of similar things. These features and profiles of the mobile is usually related to facial expression of the person (happiness, sadness, disgust, anger, fear, and surprise), external appearance (different clothes in office and home) and surroundings of the person (office, home, park etc). The idea of the paper is to the use the above mentioned external events and changes the theme of the mobile phone. The change may be changing the color of mobile screen, select particular category of word suggestion during writing SMS, notes or document, select music playlist, call buddy with whom user would like to share stuff. Basically user will have a mobile that can understand user's emotion and do accordingly. The paper presents details about emotion reading and implementation using patter recognition technique to capture.

A concept for making EMO mobile

NASA Astrophysics Data System (ADS)

Kumar, Mukesh

2011-12-01

The current selected features and profiles in a mobile device is usually set manually and do not use the external environment automatically to change it. The features and profile can be switching to silent mode in office, selecting a formal ringtone in office, describing the mood in the social network sites and a whole lot of similar things. These features and profiles of the mobile is usually related to facial expression of the person (happiness, sadness, disgust, anger, fear, and surprise), external appearance (different clothes in office and home) and surroundings of the person (office, home, park etc). The idea of the paper is to the use the above mentioned external events and changes the theme of the mobile phone. The change may be changing the color of mobile screen, select particular category of word suggestion during writing SMS, notes or document, select music playlist, call buddy with whom user would like to share stuff. Basically user will have a mobile that can understand user's emotion and do accordingly. The paper presents details about emotion reading and implementation using patter recognition technique to capture.

A novel sgRNA selection system for CRISPR-Cas9 in mammalian cells.

PubMed

Zhang, Haiwei; Zhang, Xixi; Fan, Cunxian; Xie, Qun; Xu, Chengxian; Zhao, Qun; Liu, Yongbo; Wu, Xiaoxia; Zhang, Haibing

2016-03-18

CRISPR-Cas9 mediated genome editing system has been developed as a powerful tool for elucidating the function of genes through genetic engineering in multiple cells and organisms. This system takes advantage of a single guide RNA (sgRNA) to direct the Cas9 endonuclease to a specific DNA site to generate mutant alleles. Since the targeting efficiency of sgRNAs to distinct DNA loci can vary widely, there remains a need for a rapid, simple and efficient sgRNA selection method to overcome this limitation of the CRISPR-Cas9 system. Here we report a novel system to select sgRNA with high efficacy for DNA sequence modification by a luciferase assay. Using this sgRNAs selection system, we further demonstrated successful examples of one sgRNA for generating one gene knockout cell lines where the targeted genes are shown to be functionally defective. This system provides a potential application to optimize the sgRNAs in different species and to generate a powerful CRISPR-Cas9 genome-wide screening system with minimum amounts of sgRNAs. Copyright © 2016 Elsevier Inc. All rights reserved.

A Discovery Strategy for Selective Inhibitors of c-Src in Complex with the Focal Adhesion Kinase SH3/SH2-binding Region.

PubMed

Moroco, Jamie A; Baumgartner, Matthew P; Rust, Heather L; Choi, Hwan Geun; Hur, Wooyoung; Gray, Nathanael S; Camacho, Carlos J; Smithgall, Thomas E

2015-08-01

The c-Src tyrosine kinase co-operates with the focal adhesion kinase to regulate cell adhesion and motility. Focal adhesion kinase engages the regulatory SH3 and SH2 domains of c-Src, resulting in localized kinase activation that contributes to tumor cell metastasis. Using assay conditions where c-Src kinase activity required binding to a tyrosine phosphopeptide based on the focal adhesion kinase SH3-SH2 docking sequence, we screened a kinase-biased library for selective inhibitors of the Src/focal adhesion kinase peptide complex versus c-Src alone. This approach identified an aminopyrimidinyl carbamate compound, WH-4-124-2, with nanomolar inhibitory potency and fivefold selectivity for c-Src when bound to the phospho-focal adhesion kinase peptide. Molecular docking studies indicate that WH-4-124-2 may preferentially inhibit the 'DFG-out' conformation of the kinase active site. These findings suggest that interaction of c-Src with focal adhesion kinase induces a unique kinase domain conformation amenable to selective inhibition. © 2014 John Wiley & Sons A/S.

Risk-Based Prioritization Method for the Classification of Groundwater Pollution from Hazardous Waste Landfills.

PubMed

Yang, Yu; Jiang, Yong-Hai; Lian, Xin-Ying; Xi, Bei-Dou; Ma, Zhi-Fei; Xu, Xiang-Jian; An, Da

2016-12-01

Hazardous waste landfill sites are a significant source of groundwater pollution. To ensure that these landfills with a significantly high risk of groundwater contamination are properly managed, a risk-based ranking method related to groundwater contamination is needed. In this research, a risk-based prioritization method for the classification of groundwater pollution from hazardous waste landfills was established. The method encompasses five phases, including risk pre-screening, indicator selection, characterization, classification and, lastly, validation. In the risk ranking index system employed here, 14 indicators involving hazardous waste landfills and migration in the vadose zone as well as aquifer were selected. The boundary of each indicator was determined by K-means cluster analysis and the weight of each indicator was calculated by principal component analysis. These methods were applied to 37 hazardous waste landfills in China. The result showed that the risk for groundwater contamination from hazardous waste landfills could be ranked into three classes from low to high risk. In all, 62.2 % of the hazardous waste landfill sites were classified in the low and medium risk classes. The process simulation method and standardized anomalies were used to validate the result of risk ranking; the results were consistent with the simulated results related to the characteristics of contamination. The risk ranking method was feasible, valid and can provide reference data related to risk management for groundwater contamination at hazardous waste landfill sites.

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

Assessing technical performance at diverse ambulatory care sites.

PubMed

Osterweis, M; Bryant, E

1978-01-01

The purpose of the large study reported here was to develop and test methods for assessing the quality of health care that would be broadly applicable to diverse ambulatory care organizations for periodic comparative review. Methodological features included the use of an age-sex stratified random sampling scheme, dependence on medical records as the source of data, a fixed study period year, use of Kessner's tracer methodology (including not only acute and chronic diseases but also screening and immunization rates as indicators), and a fixed tracer matrix at all test sites. This combination of methods proved more efficacious in estimating certain parameters for the total patient populations at each site (including utilization patterns, screening, and immunization rates) and the process of care for acute conditions than it did in examining the process of care for the selected chronic condition. It was found that the actual process of care at all three sites for the three acute conditions (streptococcal pharyngitis, urinary tract infection, and iron deficiency anemia) often differed from the expected process in terms of both diagnostic procedures and treatment. For hypertension, the chronic disease tracer, medical records were frequently a deficient data source from which to draw conclusions about the adequacy of treatment. Several aspects of the study methodology were found to be detrimental to between-site comparisons of the process of care for chronic disease management. The use of an age-sex stratified random sampling scheme resulted in the identification of too few cases of hypertension at some sites for analytic purposes, thereby necessitating supplementary sampling by diagnosis. The use of a fixed study period year resulted in an arbitrary starting point in the course of the disease. Furthermore, in light of the diverse sociodemographic characteristics of the patient populations, the use of a fixed matrix of tracer conditions for all test sites is questionable. The discussion centers on these and other problems encountered in attempting to compare technical performance within diverse ambulatory care organizations and provides some guidelines as to the utility of alternative methods for assessing the quality of health care.

Elaboration of a fragment library hit produces potent and selective aspartate semialdehyde dehydrogenase inhibitors.

PubMed

Thangavelu, Bharani; Bhansali, Pravin; Viola, Ronald E

2015-10-15

Aspartate-β-semialdehyde dehydrogenase (ASADH) lies at the first branch point in the aspartate metabolic pathway which leads to the biosynthesis of several essential amino acids and some important metabolites. This pathway is crucial for many metabolic processes in plants and microbes like bacteria and fungi, but is absent in mammals. Therefore, the key microbial enzymes involved in this pathway are attractive potential targets for development of new antibiotics with novel modes of action. The ASADH enzyme family shares the same substrate binding and active site catalytic groups; however, the enzymes from representative bacterial and fungal species show different inhibition patterns when previously screened against low molecular weight inhibitors identified from fragment library screening. In the present study several approaches, including fragment based drug discovery (FBDD), inhibitor docking, kinetic, and structure-activity relationship (SAR) studies have been used to guide ASADH inhibitor development. Elaboration of a core structure identified by FBDD has led to the synthesis of low micromolar inhibitors of the target enzyme, with high selectivity introduced between the Gram-negative and Gram-positive orthologs of ASADH. This new set of structures open a novel direction for the development of inhibitors against this validated drug-target enzyme. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computational approaches in the design of synthetic receptors - A review.

PubMed

Cowen, Todd; Karim, Kal; Piletsky, Sergey

2016-09-14

The rational design of molecularly imprinted polymers (MIPs) has been a major contributor to their reputation as "plastic antibodies" - high affinity robust synthetic receptors which can be optimally designed, and produced for a much reduced cost than their biological equivalents. Computational design has become a routine procedure in the production of MIPs, and has led to major advances in functional monomer screening, selection of cross-linker and solvent, optimisation of monomer(s)-template ratio and selectivity analysis. In this review the various computational methods will be discussed with reference to all the published relevant literature since the end of 2013, with each article described by the target molecule, the computational approach applied (whether molecular mechanics/molecular dynamics, semi-empirical quantum mechanics, ab initio quantum mechanics (Hartree-Fock, Møller-Plesset, etc.) or DFT) and the purpose for which they were used. Detailed analysis is given to novel techniques including analysis of polymer binding sites, the use of novel screening programs and simulations of MIP polymerisation reaction. The further advances in molecular modelling and computational design of synthetic receptors in particular will have serious impact on the future of nanotechnology and biotechnology, permitting the further translation of MIPs into the realms of analytics and medical technology. Copyright © 2016 Elsevier B.V. All rights reserved.

A Synthetic Interaction Screen Identifies Factors Selectively Required for Proliferation and TERT Transcription in p53-Deficient Human Cancer Cells

PubMed Central

Park, Sung Mi; Zhu, Lihua J.; Debily, Marie-anne; Kittler, Ellen L. W.; Zapp, Maria L.; Lapointe, David; Gobeil, Stephane; Virbasius, Ching-Man; Green, Michael R.

2012-01-01

Numerous genetic and epigenetic alterations render cancer cells selectively dependent on specific genes and regulatory pathways, and represent potential vulnerabilities that can be therapeutically exploited. Here we describe an RNA interference (RNAi)–based synthetic interaction screen to identify genes preferentially required for proliferation of p53-deficient (p53−) human cancer cells. We find that compared to p53-competent (p53+) human cancer cell lines, diverse p53− human cancer cell lines are preferentially sensitive to loss of the transcription factor ETV1 and the DNA damage kinase ATR. In p53− cells, RNAi–mediated knockdown of ETV1 or ATR results in decreased expression of the telomerase catalytic subunit TERT leading to growth arrest, which can be reversed by ectopic TERT expression. Chromatin immunoprecipitation analysis reveals that ETV1 binds to a region downstream of the TERT transcriptional start-site in p53− but not p53+ cells. We find that the role of ATR is to phosphorylate and thereby stabilize ETV1. Our collective results identify a regulatory pathway involving ETV1, ATR, and TERT that is preferentially important for proliferation of diverse p53− cancer cells. PMID:23284306

Potential human cholesterol esterase inhibitor design: benefits from the molecular dynamics simulations and pharmacophore modeling studies.

PubMed

John, Shalini; Thangapandian, Sundarapandian; Lee, Keun Woo

2012-01-01

Human pancreatic cholesterol esterase (hCEase) is one of the lipases found to involve in the digestion of large and broad spectrum of substrates including triglycerides, phospholipids, cholesteryl esters, etc. The presence of bile salts is found to be very important for the activation of hCEase. Molecular dynamic simulations were performed for the apoform and bile salt complexed form of hCEase using the co-ordinates of two bile salts from bovine CEase. The stability of the systems throughout the simulation time was checked and two representative structures from the highly populated regions were selected using cluster analysis. These two representative structures were used in pharmacophore model generation. The generated pharmacophore models were validated and used in database screening. The screened hits were refined for their drug-like properties based on Lipinski's rule of five and ADMET properties. The drug-like compounds were further refined by molecular docking simulation using GOLD program based on the GOLD fitness score, mode of binding, and molecular interactions with the active site amino acids. Finally, three hits of novel scaffolds were selected as potential leads to be used in novel and potent hCEase inhibitor design. The stability of binding modes and molecular interactions of these final hits were re-assured by molecular dynamics simulations.

Failure and Redemption of Multifilter Rotating Shadowband Radiometer (MFRSR)/Normal Incidence Multifilter Radiometer (NIMFR) Cloud Screening: Contrasting Algorithm Performance at Atmospheric Radiation Measurement (ARM) North Slope of Alaska (NSA) and Southern Great Plains (SGP) Sites

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

Kassianov, Evgueni I.; Flynn, Connor J.; Koontz, Annette S.

2013-09-11

Well-known cloud-screening algorithms, which are designed to remove cloud-contaminated aerosol optical depths (AOD) from AOD measurements, have shown great performance at many middle-to-low latitude sites around the world. However, they may occasionally fail under challenging observational conditions, such as when the sun is low (near the horizon) or when optically thin clouds with small spatial inhomogeneity occur. Such conditions have been observed quite frequently at the high-latitude Atmospheric Radiation Measurement (ARM) North Slope of Alaska (NSA) sites. A slightly modified cloud-screening version of the standard algorithm is proposed here with a focus on the ARM-supported Multifilter Rotating Shadowband Radiometer (MFRSR)more » and Normal Incidence Multifilter Radiometer (NIMFR) data. The modified version uses approximately the same techniques as the standard algorithm, but it additionally examines the magnitude of the slant-path line of sight transmittance and eliminates points when the observed magnitude is below a specified threshold. Substantial improvement of the multi-year (1999-2012) aerosol product (AOD and its Angstrom exponent) is shown for the NSA sites when the modified version is applied. Moreover, this version reproduces the AOD product at the ARM Southern Great Plains (SGP) site, which was originally generated by the standard cloud-screening algorithms. The proposed minor modification is easy to implement and its application to existing and future cloud-screening algorithms can be particularly beneficial for challenging observational conditions.« less

Online information about risks and benefits of screening mammography in 10 European countries: An observational Web sites analysis.

PubMed

Spagnoli, Laura; Navaro, Monica; Ferrara, Pietro; Del Prete, Viola; Attena, Francesco

2018-06-01

Most publications about breast cancer do not provide accurate and comprehensive information, giving few or no data about risk/benefit ratios. We conducted a comparative study among 10 European countries about health information on breast cancer screening, assessing the first 10 Web sites addressing the general public that appeared following an Internet search.With the help of medical residents involved in the EuroNet MRPH Association, we analyzed the first 30 results of an Internet search in 10 European countries to determine the first 10 sites that offered screening mammography. We searched for the following information: source of information, general information on mammography and breast cancer screening, potential harms and risks (false positives, false positives after biopsy, false negatives, interval cancer, overdiagnosis, lead-time bias, and radiation exposure), and potential benefits (reduced mortality and increased survival).The United Kingdom provided the most information: 39 of all 70 possible identified risks (56%) were reported on its sites. Five nations presented over 35% of the possible information (United Kingdom, Spain, France, Ireland, and Italy); the others were under 30% (Portugal, Poland, Slovenia, Netherlands, and Croatia). Regarding the benefits, sites offering the most complete information were those in France (95%) and Poland (90%).Our results suggest that, despite consensus in the scientific community about providing better information to citizens, further efforts are needed to improve information about breast cancer screening. That conclusion also applies to countries showing better results. We believe that there should be greater coordination in this regard throughout Europe.

The MORPHEUS II protein crystallization screen

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

Gorrec, Fabrice, E-mail: fgorrec@mrc-lmb.cam.ac.uk

2015-06-27

MORPHEUS II is a 96-condition initial crystallization screen formulated de novo. The screen incorporates reagents selected from the Protein Data Bank to yield crystals that are not observed in traditional conditions. In addition, the formulation facilitates the optimization and cryoprotection of crystals. High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected frommore » the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.« less

Assessment of Uncertainty-Based Screening Volumes for NASA Robotic LEO and GEO Conjunction Risk Assessment

NASA Technical Reports Server (NTRS)

Narvet, Steven W.; Frigm, Ryan C.; Hejduk, Matthew D.

2011-01-01

Conjunction Assessment operations require screening assets against the space object catalog by placing a pre-determined spatial volume around each asset and predicting when another object will violate that volume. The selection of the screening volume used for each spacecraft is a trade-off between observing all conjunction events that may pose a potential risk to the primary spacecraft and the ability to analyze those predicted events. If the screening volumes are larger, then more conjunctions can be observed and therefore the probability of a missed detection of a high risk conjunction event is small; however, the amount of data which needs to be analyzed increases. This paper characterizes the sensitivity of screening volume size to capturing typical orbit uncertainties and the expected number of conjunction events observed. These sensitivities are quantified in the form of a trade space that allows for selection of appropriate screen-ing volumes to fit the desired concept of operations, system limitations, and tolerable analyst workloads. This analysis will specifically highlight the screening volume determination and selection process for use in the NASA Conjunction Assessment Risk Analysis process but will also provide a general framework for other Owner / Operators faced with similar decisions.

Which risk models perform best in selecting ever-smokers for lung cancer screening?

Cancer.gov

A new analysis by scientists at NCI evaluates nine different individualized lung cancer risk prediction models based on their selections of ever-smokers for computed tomography (CT) lung cancer screening.

Type 2 diabetes and cardiac autonomic neuropathy screening using dynamic pupillometry

PubMed Central

Lerner, Alana G.; Bernabé-Ortiz, Antonio; Ticse, Ray; Hernandez, Arturo; Huaylinos, Yvonne; Pinto, Miguel E.; Málaga, Germán; Checkley, William; Gilman, Robert H.; Miranda, J. Jaime

2015-01-01

Aim To determine if changes in pupillary response are useful as a screening tool for diabetes and to assess whether pupillometry is associated with cardiac autonomic neuropathy. Methods We conducted a cross-sectional study with participants drawn from two settings: a hospital and a community site. At the community site, individuals with newly diagnosed diabetes as well as a random sample of control individuals without diabetes, confirmed by oral glucose tolerance test, were selected. Participants underwent an LED light stimulus test and eight pupillometry variables were measured. Outcomes were diabetes, defined by oral glucose tolerance test, and cardiac autonomic dysfunction, determined by a positive readout on two of four diagnostic tests: heart rate response to the Valsalva manoeuvre; orthostatic hypotension; 30:15 ratio; and expiration-to-inspiration ratio. The area under the curve, best threshold, sensitivity and specificity of each pupillometry variable was calculated. Results Data from 384 people, 213 with diabetes, were analysed. The mean (±SD) age of the people with diabetes was 58.6 (±8.2) years and in the control subjects it was 56.1 (±8.6) years. When comparing individuals with and without diabetes, the amplitude of the pupil reaction had the highest area under the curve [0.69 (sensitivity: 78%; specificity: 55%)]. Cardiac autonomic neuropathy was present in 51 of the 138 people evaluated (37.0%; 95% CI 28.8–45.1). To diagnose cardiac autonomic neuropathy, two pupillometry variables had the highest area under the curve: baseline pupil radius [area under the curve: 0.71 (sensitivity: 51%; specificity: 84%)], and amplitude of the pupil reaction [area under the curve: 070 (sensitivity: 82%; specificity: 55%)]. Conclusions Pupillometry is an inexpensive technique to screen for diabetes and cardiac autonomic neuropathy, but it does not have sufficient accuracy for clinical use as a screening tool. PMID:25761508

Type 2 diabetes and cardiac autonomic neuropathy screening using dynamic pupillometry.

PubMed

Lerner, A G; Bernabé-Ortiz, A; Ticse, R; Hernandez, A; Huaylinos, Y; Pinto, M E; Málaga, G; Checkley, W; Gilman, R H; Miranda, J J

2015-11-01

To determine if changes in pupillary response are useful as a screening tool for diabetes and to assess whether pupillometry is associated with cardiac autonomic neuropathy. We conducted a cross-sectional study with participants drawn from two settings: a hospital and a community site. At the community site, individuals with newly diagnosed diabetes as well as a random sample of control individuals without diabetes, confirmed by oral glucose tolerance test, were selected. Participants underwent an LED light stimulus test and eight pupillometry variables were measured. Outcomes were diabetes, defined by oral glucose tolerance test, and cardiac autonomic dysfunction, determined by a positive readout on two of four diagnostic tests: heart rate response to the Valsalva manoeuvre; orthostatic hypotension; 30:15 ratio; and expiration-to-inspiration ratio. The area under the curve, best threshold, sensitivity and specificity of each pupillometry variable was calculated. Data from 384 people, 213 with diabetes, were analysed. The mean (±sd) age of the people with diabetes was 58.6 (±8.2) years and in the control subjects it was 56.1 (±8.6) years. When comparing individuals with and without diabetes, the amplitude of the pupil reaction had the highest area under the curve [0.69 (sensitivity: 78%; specificity: 55%)]. Cardiac autonomic neuropathy was present in 51 of the 138 people evaluated (37.0%; 95% CI 28.8-45.1). To diagnose cardiac autonomic neuropathy, two pupillometry variables had the highest area under the curve: baseline pupil radius [area under the curve: 0.71 (sensitivity: 51%; specificity: 84%)], and amplitude of the pupil reaction [area under the curve: 0.70 (sensitivity: 82%; specificity: 55%)]. Pupillometry is an inexpensive technique to screen for diabetes and cardiac autonomic neuropathy, but it does not have sufficient accuracy for clinical use as a screening tool. © 2015 The Authors. Diabetic Medicine © 2015 Diabetes UK.

Northeast Oregon Hatchery Project, Final Siting Report.

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

Watson, Montgomery

1995-03-01

This report presents the results of site analysis for the Bonneville Power Administration Northeast Oregon Hatchery Project. The purpose of this project is to provide engineering services for the siting and conceptual design of hatchery facilities for the Bonneville Power Administration. The hatchery project consists of artificial production facilities for salmon and steelhead to enhance production in three adjacent tributaries to the Columbia River in northeast Oregon: the Grande Ronde, Walla Walla, and Imnaha River drainage basins. Facilities identified in the master plan include adult capture and holding facilities; spawning incubation, and early rearing facilities; full-term rearing facilities; and directmore » release or acclimation facilities. The evaluation includes consideration of a main production facility for one or more of the basins or several smaller satellite production facilities to be located within major subbasins. The historic and current distribution of spring and fall chinook salmon and steelhead was summarized for the Columbia River tributaries. Current and future production and release objectives were reviewed. Among the three tributaries, forty seven sites were evaluated and compared to facility requirements for water and space. Site screening was conducted to identify the sites with the most potential for facility development. Alternative sites were selected for conceptual design of each facility type. A proposed program for adult holding facilities, final rearing/acclimation, and direct release facilities was developed.« less

Screen Twice, Cut Once: Assessing the Predictive Validity of Applicant Selection Tools

ERIC Educational Resources Information Center

Goldhaber, Dan; Grout, Cyrus; Huntington-Klein, Nick

2017-01-01

Despite their widespread use, there is little academic evidence on whether applicant selection instruments can improve teacher hiring. We examine the relationship between two screening instruments used by Spokane Public Schools to select classroom teachers and three teacher outcomes: value added, absences, and attrition. We observe all applicants…

Standardised method of determining vibratory perception thresholds for diagnosis and screening in neurological investigation.

PubMed Central

Goldberg, J M; Lindblom, U

1979-01-01

Vibration threshold determinations were made by means of an electromagnetic vibrator at three sites (carpal, tibial, and tarsal), which were primarily selected for examining patients with polyneuropathy. Because of the vast variation demonstrated for both vibrator output and tissue damping, the thresholds were expressed in terms of amplitude of stimulator movement measured by means of an accelerometer, instead of applied voltage which is commonly used. Statistical analysis revealed a higher power of discimination for amplitude measurements at all three stimulus sites. Digital read-out gave the best statistical result and was also most practical. Reference values obtained from 110 healthy males, 10 to 74 years of age, were highly correlated with age for both upper and lower extremities. The variance of the vibration perception threshold was less than that of the disappearance threshold, and determination of the perception threshold alone may be sufficient in most cases. PMID:501379

Estimates of long-term mean-annual nutrient loads considered for use in SPARROW models of the Midcontinental region of Canada and the United States, 2002 base year

USGS Publications Warehouse

Saad, David A.; Benoy, Glenn A.; Robertson, Dale M.

2018-05-11

Streamflow and nutrient concentration data needed to compute nitrogen and phosphorus loads were compiled from Federal, State, Provincial, and local agency databases and also from selected university databases. The nitrogen and phosphorus loads are necessary inputs to Spatially Referenced Regressions on Watershed Attributes (SPARROW) models. SPARROW models are a way to estimate the distribution, sources, and transport of nutrients in streams throughout the Midcontinental region of Canada and the United States. After screening the data, approximately 1,500 sites sampled by 34 agencies were identified as having suitable data for calculating the long-term mean-annual nutrient loads required for SPARROW model calibration. These final sites represent a wide range in watershed sizes, types of nutrient sources, and land-use and watershed characteristics in the Midcontinental region of Canada and the United States.

Gene trap and gene inversion methods for conditional gene inactivation in the mouse

PubMed Central

Xin, Hong-Bo; Deng, Ke-Yu; Shui, Bo; Qu, Shimian; Sun, Qi; Lee, Jane; Greene, Kai Su; Wilson, Jason; Yu, Ying; Feldman, Morris; Kotlikoff, Michael I.

2005-01-01

Conditional inactivation of individual genes in mice using site-specific recombinases is an extremely powerful method for determining the complex roles of mammalian genes in developmental and tissue-specific contexts, a major goal of post-genomic research. However, the process of generating mice with recombinase recognition sequences placed at specific locations within a gene, while maintaining a functional allele, is time consuming, expensive and technically challenging. We describe a system that combines gene trap and site-specific DNA inversion to generate mouse embryonic stem (ES) cell clones for the rapid production of conditional knockout mice, and the use of this system in an initial gene trap screen. Gene trapping should allow the selection of thousands of ES cell clones with defined insertions that can be used to generate conditional knockout mice, thereby providing extensive parallelism that eliminates the time-consuming steps of targeting vector construction and homologous recombination for each gene. PMID:15659575

Performance evaluation of structure based and ligand based virtual screening methods on ten selected anti-cancer targets.

PubMed

Ramasamy, Thilagavathi; Selvam, Chelliah

2015-10-15

Virtual screening has become an important tool in drug discovery process. Structure based and ligand based approaches are generally used in virtual screening process. To date, several benchmark sets for evaluating the performance of the virtual screening tool are available. In this study, our aim is to compare the performance of both structure based and ligand based virtual screening methods. Ten anti-cancer targets and their corresponding benchmark sets from 'Demanding Evaluation Kits for Objective In silico Screening' (DEKOIS) library were selected. X-ray crystal structures of protein-ligand complexes were selected based on their resolution. Openeye tools such as FRED, vROCS were used and the results were carefully analyzed. At EF1%, vROCS produced better results but at EF5% and EF10%, both FRED and ROCS produced almost similar results. It was noticed that the enrichment factor values were decreased while going from EF1% to EF5% and EF10% in many cases. Published by Elsevier Ltd.

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.

Apparel Research Network (ARN); Apparel Order Processing Module (AOPM): Field User Manual, Version 1

DTIC Science & Technology

1997-09-30

changes. Cancel Button Closes the Site Information Screen, abandoning changes. APPAREL ORDER PROCESSING MODULE FIELD USER MANUAL Ordering Official...on the Ordering Official Information Screen. APPAREL ORDER PROCESSING MODULE FIELD USER MANUAL Ordering Official Information Screen (Jjj

10 CFR 960.3-2 - Siting process.

Code of Federal Regulations, 2010 CFR

2010-01-01

... REPOSITORY Implementation Guidelines § 960.3-2 Siting process. The siting process begins with site screening... first repository before the enactment of the Act, and the identification of such sites was made after... identification of potentially acceptable sites for the second and subsequent repositories shall be conducted in...

Macroinvertebrate-based assessment of biological condition at selected sites in the Eagle River watershed, Colorado, 2000-07

USGS Publications Warehouse

Zuellig, Robert E.; Bruce, James F.; Healy, Brian D.; Williams, Cory A.

2010-01-01

The U.S. Geological Survey (USGS), in cooperation with the Colorado River Water Conservation District, Eagle County, Eagle River Water and Sanitation District, Upper Eagle Regional Water Authority, Colorado Department of Transportation, City of Aurora, Town of Eagle, Town of Gypsum, Town of Minturn, Town of Vail, Vail Resorts, Colorado Springs Utilities, Denver Water, and the U.S. Department of Agriculture Forest Service (FS), compiled macroinvertebrate (73 sites, 124 samples) data previously collected in the Eagle River watershed from selected USGS and FS studies, 2000-07. These data were analyzed to assess the biological condition (that is, biologically ?degraded? or ?good?) at selected sites in the Eagle River watershed and determine if site class (for example, urban or undeveloped) described biological condition. An independently developed predictive model was applied to calculate a site-specific measure of taxonomic completeness for macroinvertebrate communities, where taxonomic completeness was expressed as the ratio of observed (O) taxa to those expected (E) to occur at each site. Macroinvertebrate communities were considered degraded at sites were O/E values were less than 0.80, indicating that at least 20 percent of expected taxa were not observed. Sites were classified into one of four classes (undeveloped, adjacent road or highway or both, mixed, urban) using a combination of riparian land-cover characteristics, examination of topographic maps and aerial imagery, screening for exceedances in water-quality standards, and best professional judgment. Analysis of variance was used to determine if site class accounted for variability in mean macroinvertebrate O/E values. Finally, macroinvertebrate taxa observed more or less frequently than expected at urban sites were indentified. This study represents the first standardized assessment of biological condition of selected sites distributed across the Eagle River watershed. Of the 73 sites evaluated, just over half (55 percent) were considered in good biological condition (O/E greater than 0.80). The remaining sites were either consistently biologically degraded (30 percent; O/E less than 0.80) or varied annually between good and degraded condition (15 percent; O/E is less than or greater than 0.80). Sites primarily affected by urbanization were among the most severely degraded (lowest O/E values) when compared to other site classes. Although most urban sites were among the most severely degraded (lowest O/E values), a few sites had nearly intact macroinvertebrate communities (O/E near 1.0). Similar observations were noted among sites classified as mixed. Thirteen macroinvertebrate taxa were indentified that occurred more or less frequently than expected at urban sites. Additionally, six other taxa were impartial (tolerant) to the same conditions. Combined, these 19 taxa provide an opportunity to enhance the interpretation of future studies in the Eagle River watershed, but will require better insight into the responses of these taxa to specific stressors. Understanding the sources of variability affecting biological condition along with why some sites expected to be degraded, but showed otherwise, will have clear implications for mitigation efforts. Integrating results of this study with field and laboratory investigations will greatly enhance the ability to identify causal factors affecting biological condition at degraded sites, the logical next step. Information generated from such integrative studies will be imperative for well targeted mitigation efforts in the Eagle River watershed.

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

Involvement of Sp1 and Microsatellite Repressor Sequences in the Transcriptional Control of the Human CD30 Gene

PubMed Central

Croager, Emma J.; Gout, Alexander M.; Abraham, Lawrence J.

2000-01-01

CD30, as a member of the tumor necrosis factor (TNF) receptor family, is expressed on the surface of activated lymphoid cells. CD30 overexpression is a characteristic of lymphoproliferative diseases such as Hodgkin’s/non-Hodgkin’s lymphomas, embryonal carcinoma, and a number of Th2-associated diseases. The CD30 gene has been mapped to a region of the murine genome that is involved in susceptibility to systemic lupus erythematosus. Functionally, CD30 may play a role in the deletion of autoreactive T cells. We were interested in determining the molecular nature of CD30 overexpression. Sequence comparison has revealed significant identity between the TATA-less human and murine CD30 promoters; they share a number of common consensus binding motifs. Transfection assays identified three regions of transcriptional importance; the region between position −1.2 kb and −336 bp, containing a CCAT microsatellite sequence, a conserved Sp1 site at positions −43 to −38, and a downstream promoter element (DPE) at positions +24 to +29. EMSA and DNase I footprinting showed specific DNA-protein interactions of the CD30 promoter with the Sp1 site and the CCAT repeat region. The DPE element was shown to be essential for start site selection. We conclude that the conserved Sp1 site at −43 to −38 is associated with maximum reporter gene activity, the DPE element is required for start site selection, and the CCAT tetranucleotide repeats act to repress transcription. We also have shown that the microsatellite is multiallelic, when we screened a random healthy population. Further studies are required to determine whether microsatellite instability in the repressor predisposes susceptible individuals to CD30 overexpression. PMID:10793083

Large datasets, logistics, sharing and workflow in screening.

PubMed

Cook, Tessa S

2018-03-29

Cancer screening initiatives exist around the world for different malignancies, most frequently breast, colorectal, and cervical cancer. A number of cancer registries exist to collect relevant data, but while these data may include imaging findings, they rarely, if ever, include actual images. Additionally, the data submitted to the registry are usually correlated with eventual cancer diagnoses and patient outcomes, rather than used with the individual's future screenings. Developing screening programs that allow for images to be submitted to a central location in addition to patient meta data and used for comparison to future screening exams would be very valuable in increasing access to care and ensuring that individuals are effectively screened at appropriate intervals. It would also change the way imaging results and additional patient data are correlated to eventual outcomes. However, it introduces logistical challenges surrounding secure storage and transmission of data to subsequent screening sites. In addition, in the absence of standardized protocols for screening, comparing current and prior imaging, especially from different equipment, can be challenging. Implementing a large-scale screening program with an image-enriched screening registry-effectively, an image-enriched electronic screening record-also requires that incentives exist for screening sites, physicians, and patients to participate; to maximize coverage, participation may have to be supported by government agencies. Workflows will also have to be adjusted to support registry participation for all screening patients in an effort to create a large, robust data set that can be used for future screening efforts as well as research initiatives.center.

General M13 phage display: M13 phage display in identification and characterization of protein-protein interactions.

PubMed

Hertveldt, Kirsten; Beliën, Tim; Volckaert, Guido

2009-01-01

In M13 phage display, proteins and peptides are exposed on one of the surface proteins of filamentous phage particles and become accessible to affinity enrichment against a bait of interest. We describe the construction of fragmented whole genome and gene fragment phage display libraries and interaction selection by panning. This strategy allows the identification and characterization of interacting proteins on a genomic scale by screening the fragmented "proteome" against protein baits. Gene fragment libraries allow a more in depth characterization of the protein-protein interaction site by identification of the protein region involved in the interaction.

1,2-ethane bis-1-amino-4-benzamidine is active against several brain insult and seizure challenges through anti-NMDA mechanisms targeting the 3H-TCP binding site and antioxidant action.

PubMed

Vamecq, Joseph; Maurois, Pierre; Pages, Nicole; Bac, Pierre; Stables, James P; Gressens, Pierre; Stanicki, Dimitri; Vanden Eynde, Jean Jacques

2010-07-01

Five bis-benzamidines were screened towards murine magnesium deficiency-dependent audiogenic seizures, unravelling two compounds with efficacious doses 50 (ED(50)) less than 10mg/kg. They were also screened against maximal electroshock and subcutaneous pentylenetetrazole-induced seizures, and explored for superoxide -scavenging activity. 1,2-Ethane bis-1-amino-4-benzamidine (EBAB) was selected and evaluated in 6 Hz seizure test (ED(50)=49 mg/kg) and at 4 microg/kg in focal cerebral ibotenate poisoning in pups (sizes of both white and grey matter wounds were halved). EBAB was further tested on NMDA-induced seizures in mice (ED(50)=6 mg/kg) and on (3)H-TC -binding to a rodent cerebral preparation (IC(50)=1.4 microM). Taken as a whole, present data emphasise the suitability of bis-benzamidines as templates for designing brain protective compounds. Copyright (c) 2010 Elsevier Masson SAS. All rights reserved.

Ensemble-based ADME-Tox profiling and virtual screening for the discovery of new inhibitors of the Leishmania mexicana cysteine protease CPB2.8ΔCTE.

PubMed

Scala, Angela; Rescifina, Antonio; Micale, Nicola; Piperno, Anna; Schirmeister, Tanja; Maes, Louis; Grassi, Giovanni

2018-02-01

In an effort to identify novel molecular warheads able to inhibit Leishmania mexicana cysteine protease CPB2.8ΔCTE, fused benzo[b]thiophenes and β,β'-triketones emerged as covalent inhibitors binding the active site cysteine residue. Enzymatic screening showed a moderate-to-excellent activity (12%-90% inhibition of the target enzyme at 20 μm). The most promising compounds were selected for further profiling including in vitro cell-based assays and docking studies. Computational data suggest that benzo[b]thiophenes act immediately as non-covalent inhibitors and then as irreversible covalent inhibitors, whereas a reversible covalent mechanism emerged for the 1,3,3'-triketones with a Y-topology. Based on the predicted physicochemical and ADME-Tox properties, compound 2b has been identified as a new drug-like, non-mutagen, non-carcinogen, and non-neurotoxic lead candidate. © 2017 John Wiley & Sons A/S.

A method for multi-codon scanning mutagenesis of proteins based on asymmetric transposons.

PubMed

Liu, Jia; Cropp, T Ashton

2012-02-01

Random mutagenesis followed by selection or screening is a commonly used strategy to improve protein function. Despite many available methods for random mutagenesis, nearly all generate mutations at the nucleotide level. An ideal mutagenesis method would allow for the generation of 'codon mutations' to change protein sequence with defined or mixed amino acids of choice. Herein we report a method that allows for mutations of one, two or three consecutive codons. Key to this method is the development of a Mu transposon variant with asymmetric terminal sequences. As a demonstration of the method, we performed multi-codon scanning on the gene encoding superfolder GFP (sfGFP). Characterization of 50 randomly chosen clones from each library showed that more than 40% of the mutants in these three libraries contained seamless, in-frame mutations with low site preference. By screening only 500 colonies from each library, we successfully identified several spectra-shift mutations, including a S205D variant that was found to bear a single excitation peak in the UV region.

Corrective Action Decision Document for Corrective Action Unit 204: Storage Bunkers, Nevada Test Site, Nevada, Rev. No. 0

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

Robert Boehlecke

2004-04-01

The six bunkers included in CAU 204 were primarily used to monitor atmospheric testing or store munitions. The ''Corrective Action Investigation Plan (CAIP) for Corrective Action Unit 204: Storage Bunkers, Nevada Test Site, Nevada'' (NNSA/NV, 2002a) provides information relating to the history, planning, and scope of the investigation; therefore, it will not be repeated in this CADD. This CADD identifies potential corrective action alternatives and provides a rationale for the selection of a recommended corrective action alternative for each CAS within CAU 204. The evaluation of corrective action alternatives is based on process knowledge and the results of investigative activitiesmore » conducted in accordance with the CAIP (NNSA/NV, 2002a) that was approved prior to the start of the Corrective Action Investigation (CAI). Record of Technical Change (ROTC) No. 1 to the CAIP (approval pending) documents changes to the preliminary action levels (PALs) agreed to by the Nevada Division of Environmental Protection (NDEP) and DOE, National Nuclear Security Administration Nevada Site Office (NNSA/NSO). This ROTC specifically discusses the radiological PALs and their application to the findings of the CAU 204 corrective action investigation. The scope of this CADD consists of the following: (1) Develop corrective action objectives; (2) Identify corrective action alternative screening criteria; (3) Develop corrective action alternatives; (4) Perform detailed and comparative evaluations of corrective action alternatives in relation to corrective action objectives and screening criteria; and (5) Recommend and justify a preferred corrective action alternative for each CAS within CAU 204.« less

Diabetes Screening Reminder for Women With Prior Gestational Diabetes: A Randomized Controlled Trial.

PubMed

Zera, Chloe A; Bates, David W; Stuebe, Alison M; Ecker, Jeffrey L; Seely, Ellen W

2015-07-01

To evaluate whether an electronic health record (EHR) reminder improves rates of screening for type 2 diabetes in women with prior gestational diabetes. We randomly allocated primary care providers (by clinic site) to a reminder for type 2 diabetes screening within the EHR or to usual care. Women with previous gestational diabetes mellitus were identified through an automated search of laboratory results and the problem list. We compared rates of screening during the study period (2010-2012) in women at intervention sites with those at control sites. With a sample size of 850 participants, we had 80% power to detect a 15% difference in screening rates. We included 847 individuals seen at a participating clinic during the study period, of whom 471 were at a reminder clinic and 376 were at a control clinic. A similar proportion of women were screened for type 2 diabetes in both groups (n=265, 56.3% of the reminder group compared with n=206, 54.8% of the control group, P=.67; adjusted odds ratio [OR] 1.04, 95% confidence interval [CI] 0.79-1.38). Patient characteristics associated with risk for diabetes including body mass index (adjusted OR per kg/m 1.05, 95% CI 1.01-1.08) and race (adjusted OR for nonwhite race 2.14, 95% CI 1.57-2.92) were significantly associated with screening. A simple EHR reminder did not increase the rate of diabetes screening in women with prior gestational diabetes mellitus. ClinicalTrials.gov, www.clinicaltrials.gov, NCT01288144. I.

A Multi-Center Diabetes Eye Screening Study in Community Settings: Study Design and Methodology.

PubMed

Murchison, Ann P; Friedman, David S; Gower, Emily W; Haller, Julia A; Lam, Byron L; Lee, David J; McGwin, Gerald; Owsley, Cynthia; Saaddine, Jinan; Insight Study Group

2016-01-01

Diabetes is the leading cause of new cases of blindness among adults aged 20-74 years within the United States. The Innovative Network for Sight Research group (INSIGHT) designed the Diabetic Eye Screening Study (DESS) to examine the feasibility and short-term effectiveness of non-mydriatic diabetic retinopathy (DR) screening for adults with diabetes in community-based settings. Study enrollment began in December 2011 at four sites: an internal medicine clinic at a county hospital in Birmingham, Alabama; a Federally-qualified community healthcare center in Miami-Dade County, Florida; a university-affiliated outpatient pharmacy in Philadelphia, Pennsylvania; and a medical home in Winston-Salem, North Carolina. People 18 years or older with previously diagnosed diabetes were offered free DR screening using non-mydriatic retinal photography that was preceded by a brief questionnaire addressing demographic information and previous eye care use. Visual acuity was also measured for each eye. Images were evaluated at a telemedicine reading center by trained evaluators using the National Health System DR grading classification. Participants and their physicians were sent screening report results and telephoned for a follow-up survey 3 months post-screening to determine whether participants had sought follow-up comprehensive eye care and their experiences with the screening process. Target enrollment at each site was a minimum of 500 persons. Three of the four sites met this enrollment goal. The INSIGHT/DESS is intended to establish the feasibility and short-term effectiveness of DR screening using non-mydriatic retinal photography in persons with diabetes who seek services in community-based clinic and pharmacy settings.

Discovery and Mechanistic Characterization of Selective Inhibitors of H2S-producing Enzyme: 3-Mercaptopyruvate Sulfurtransferase (3MST) Targeting Active-site Cysteine Persulfide

PubMed Central

Hanaoka, Kenjiro; Sasakura, Kiyoshi; Suwanai, Yusuke; Toma-Fukai, Sachiko; Shimamoto, Kazuhito; Takano, Yoko; Shibuya, Norihiro; Terai, Takuya; Komatsu, Toru; Ueno, Tasuku; Ogasawara, Yuki; Tsuchiya, Yukihiro; Watanabe, Yasuo; Kimura, Hideo; Wang, Chao; Uchiyama, Masanobu; Kojima, Hirotatsu; Okabe, Takayoshi; Urano, Yasuteru; Shimizu, Toshiyuki; Nagano, Tetsuo

2017-01-01

Very recent studies indicate that sulfur atoms with oxidation state 0 or −1, called sulfane sulfurs, are the actual mediators of some physiological processes previously considered to be regulated by hydrogen sulfide (H2S). 3-Mercaptopyruvate sulfurtransferase (3MST), one of three H2S-producing enzymes, was also recently shown to produce sulfane sulfur (H2Sn). Here, we report the discovery of several potent 3MST inhibitors by means of high-throughput screening (HTS) of a large chemical library (174,118 compounds) with our H2S-selective fluorescent probe, HSip-1. Most of the identified inhibitors had similar aromatic ring-carbonyl-S-pyrimidone structures. Among them, compound 3 showed very high selectivity for 3MST over other H2S/sulfane sulfur-producing enzymes and rhodanese. The X-ray crystal structures of 3MST complexes with two of the inhibitors revealed that their target is a persulfurated cysteine residue located in the active site of 3MST. Precise theoretical calculations indicated the presence of a strong long-range electrostatic interaction between the persulfur anion of the persulfurated cysteine residue and the positively charged carbonyl carbon of the pyrimidone moiety of the inhibitor. Our results also provide the experimental support for the idea that the 3MST-catalyzed reaction with 3-mercaptopyruvate proceeds via a ping-pong mechanism. PMID:28079151

Motivation, recruitment, and screening of volunteers for a phase I/II HIV preventive vaccine trial in Thailand.

PubMed

Jenkins, R A; Chinaworapong, S; Morgan, P A; Ruangyuttikarn, C; Sontirat, A; Chiu, J; Michael, R A; Nitayaphan, S; Khamboonruang, C

1998-06-01

Data from recruitment and screening for a phase I/II preventive HIV-1 vaccine trial in Thailand were evaluated with respect to correlates of participation at each phase. Correlates included demographic variables, motivation for interest in the trial, and factors related to communication and contact. Participants were recruited at two sites through varied methods. The majority of prescreenees reported altruistic motives for interest in the trial and blood donors emerged as a group that may have been particularly altruistic. Findings indicated site differences in attrition during recruitment and screening, but not in enrollment into the vaccine trial. Blood donation and willingness to be contacted by phone at home were significantly related to making and keeping screening appointments.

CHRONIC ZINC SCREENING WATER EFFECT RATIO FOR THE H-12 OUTFALL, SAVANNAH RIVER SITE

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

Coughlin, D.; Looney, B.; Millings, M.

2009-01-13

In response to proposed Zn limits for the NPDES outfall H-12, a Zn screening Water Effects Ratio (WER) study was conducted to determine if a full site-specific WER is warranted. Using standard assumptions for relating the lab results to the stream, the screening WER data were consistent with the proposed Zn limit and suggest that a full WER would result in a similar limit. Addition of a humate amendment to the outfall water reduced Zn toxicity, but the toxicity reduction was relatively small and unlikely to impact proposed Zn limits. The screening WER data indicated that the time and expensemore » required to perform a full WER for Zn is not warranted.« less

Immobilized magnetic beads-based multi-target affinity selection coupled with HPLC-MS for screening active compounds from traditional Chinese medicine and natural products.

PubMed

Chen, Yaqi; Chen, Zhui; Wang, Yi

2015-01-01

Screening and identifying active compounds from traditional Chinese medicine (TCM) and other natural products plays an important role in drug discovery. Here, we describe a magnetic beads-based multi-target affinity selection-mass spectrometry approach for screening bioactive compounds from natural products. Key steps and parameters including activation of magnetic beads, enzyme/protein immobilization, characterization of functional magnetic beads, screening and identifying active compounds from a complex mixture by LC/MS, are illustrated. The proposed approach is rapid and efficient in screening and identification of bioactive compounds from complex natural products.

Civil Legal Services and Medical-Legal Partnerships Needed by the Homeless Population: A National Survey.

PubMed

Tsai, Jack; Jenkins, Darlene; Lawton, Ellen

2017-03-01

To examine civil legal needs among people experiencing homelessness and the extent to which medical-legal partnerships exist in homeless service sites, which promote the integration of civil legal aid professionals into health care settings. We surveyed a national sample of 48 homeless service sites across 26 states in November 2015. The survey asked about needs, attitudes, and practices related to civil legal issues, including medical-legal partnerships. More than 90% of the homeless service sites reported that their patients experienced at least 1 civil legal issue, particularly around housing, employment, health insurance, and disability benefits. However, only half of all sites reported screening patients for civil legal issues, and only 10% had a medical-legal partnership. The large majority of sites reported interest in receiving training on screening for civil legal issues and developing medical-legal partnerships. There is great need and potential to deploy civil legal services in health settings to serve unstably housed populations. Training homeless service providers how to screen for civil legal issues and how to develop medical-legal partnerships would better equip them to provide comprehensive care.

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

Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.).

PubMed

Keyte, Anna L; Percifield, Ryan; Liu, Bao; Wendel, Jonathan F

2006-01-01

Cytosine methylation is important in the epigenetic regulation of gene expression and development in plants and has been implicated in silencing duplicate genes after polyploid formation in several plant groups. Relatively little information exists, however, on levels and patterns of methylation polymorphism (MP) at homologous loci within species. Here we explored the levels and patterns of methylation-polymorphism diversity at CCGG sites within allotetraploid cotton, Gossypium hirsutum, using a methylation-sensitive amplified fragment length polymorphism screen and a selected set of 20 G. hirsutum accessions for which we have information on genetic polymorphism levels and relationships. Methylation and MP exist at high levels within G. hirsutum: of 150 HpaII/MspI sites surveyed, 48 were methylated at the inner cytosine (32%) and 32 of these were polymorphic (67%). Both these values are higher than comparable measures of genetic diversity using restriction fragment length polymorphisms. The high percentage of methylation-polymorphic sites and potential relationship to gene expression underscore the potential significance of MP within and among populations. We speculate that biased correlation of methylation-polymorphic sites and genes in cotton may be a consequence of polyploidy and the attendant doubling of all genes.

Recognition of DNA abasic site nanocavity by fluorophore-switched probe: Suitable for all sequence environments

NASA Astrophysics Data System (ADS)

Wang, Ying; Hu, Yuehua; Wu, Tao; Zhang, Lihua; Liu, Hua; Zhou, Xiaoshun; Shao, Yong

2016-01-01

Removal of a damaged base in DNA produces an abasic site (AP site) nanocavity. If left un-repaired in vivo by the specific enzyme, this nanocavity will result in nucleotide mutation in the following DNA replication. Therefore, selective recognition of AP site nanocavity by small molecules is important for identification of such DNA damage and development of genetic drugs. In this work, we investigate the fluorescence behavior of isoquinoline alkaloids including palmatine (PAL), berberine (BER), epiberberine (EPI), jatrorrhizine (JAT), coptisine (COP), coralyne (COR), worenine (WOR), berberrubine (BEU), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT) upon binding with the AP nanocavity. PAL is screened out as the most efficient fluorophore-switched probe to recognize the AP nanocavity over the fully matched DNA. Its fluorescence enhancement occurs for all of the AP nanocavity sequence environments, which has not been achieved by the previously used probes. The bridged π conjugation effect should partially contribute to the AP nanocavity-specific fluorescence, as opposed to the solvent effect. Due to the strong binding with the AP nanocavity, PAL will find wide applications in the DNA damage recognition and sensor development.

Mesoscale carbon sequestration site screening and CCS infrastructure analysis.

PubMed

Keating, Gordon N; Middleton, Richard S; Stauffer, Philip H; Viswanathan, Hari S; Letellier, Bruce C; Pasqualini, Donatella; Pawar, Rajesh J; Wolfsberg, Andrew V

2011-01-01

We explore carbon capture and sequestration (CCS) at the meso-scale, a level of study between regional carbon accounting and highly detailed reservoir models for individual sites. We develop an approach to CO(2) sequestration site screening for industries or energy development policies that involves identification of appropriate sequestration basin, analysis of geologic formations, definition of surface sites, design of infrastructure, and analysis of CO(2) transport and storage costs. Our case study involves carbon management for potential oil shale development in the Piceance-Uinta Basin, CO and UT. This study uses new capabilities of the CO(2)-PENS model for site screening, including reservoir capacity, injectivity, and cost calculations for simple reservoirs at multiple sites. We couple this with a model of optimized source-sink-network infrastructure (SimCCS) to design pipeline networks and minimize CCS cost for a given industry or region. The CLEAR(uff) dynamical assessment model calculates the CO(2) source term for various oil production levels. Nine sites in a 13,300 km(2) area have the capacity to store 6.5 GtCO(2), corresponding to shale-oil production of 1.3 Mbbl/day for 50 years (about 1/4 of U.S. crude oil production). Our results highlight the complex, nonlinear relationship between the spatial deployment of CCS infrastructure and the oil-shale production rate.

When public health intervention is not successful: Cost sharing, crowd-out, and selection in Korea's National Cancer Screening Program.

PubMed

Kim, Hyuncheol Bryant; Lee, Sun-Mi

2017-05-01

This study investigates the impact of and behavioral responses to cost sharing in Korea's National Cancer Screening Program, which provides free stomach and breast cancer screenings to those with an income below a certain cutoff. Free cancer screening substantially increases the screening take up rate, yielding more cancer detections. However, the increase in cancer detection is quickly crowded out by cancer detection through other channels such as diagnostic testing and private cancer screening. Further, compliers are much less likely to have cancer than never takers. Crowd-out and selection help explain why the program has been unable to reduce cancer mortality. Copyright © 2017 Elsevier B.V. All rights reserved.

REopt Screenings Catalyze Development of Hundreds of Megawatts of Renewable Energy for Federal Agencies

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

None

The Federal Energy Management Program (FEMP) offers renewable energy project assistance to federal agencies, which often begins with a desktop screening to develop a prioritized portfolio of project opportunities. FEMP uses the National Renewable Energy Laboratory's REopt energy planning platform to screen potential renewable energy opportunities at a single site or across a range of sites. REopt helps organizations prioritize the most economi­cally and technically viable projects for further study and identifies the size and mix of technologies that meet the orga­nization's goals at minimum cost, along with the optimal operating strategies.

Database Dictionary for Ethiopian National Ground-Water DAtabase (ENGDA) Data Fields

USGS Publications Warehouse

Kuniansky, Eve L.; Litke, David W.; Tucci, Patrick

2007-01-01

Introduction This document describes the data fields that are used for both field forms and the Ethiopian National Ground-water Database (ENGDA) tables associated with information stored about production wells, springs, test holes, test wells, and water level or water-quality observation wells. Several different words are used in this database dictionary and in the ENGDA database to describe a narrow shaft constructed in the ground. The most general term is borehole, which is applicable to any type of hole. A well is a borehole specifically constructed to extract water from the ground; however, for this data dictionary and for the ENGDA database, the words well and borehole are used interchangeably. A production well is defined as any well used for water supply and includes hand-dug wells, small-diameter bored wells equipped with hand pumps, or large-diameter bored wells equipped with large-capacity motorized pumps. Test holes are borings made to collect information about the subsurface with continuous core or non-continuous core and/or where geophysical logs are collected. Test holes are not converted into wells. A test well is a well constructed for hydraulic testing of an aquifer in order to plan a larger ground-water production system. A water-level or water-quality observation well is a well that is used to collect information about an aquifer and not used for water supply. A spring is any naturally flowing, local, ground-water discharge site. The database dictionary is designed to help define all fields on both field data collection forms (provided in attachment 2 of this report) and for the ENGDA software screen entry forms (described in Litke, 2007). The data entered into each screen entry field are stored in relational database tables within the computer database. The organization of the database dictionary is designed based on field data collection and the field forms, because this is what the majority of people will use. After each field, however, the ENGDA database field name and relational database table is designated; along with the ENGDA screen entry form(s) and the ENGDA field form (attachment 2). The database dictionary is separated into sections. The first section, Basic Site Data Fields, describes the basic site information that is similar for all of the different types of sites. The remaining sections may be applicable for only one type of site; for example, the Well Drilling and Construction Data Fields and Lithologic Description Data Fields are applicable to boreholes and not to springs. Attachment 1 contains a table for conversion from English to metric units. Attachment 2 contains selected field forms used in conjunction with ENGDA. A separate document, 'Users Reference Manual for the Ethiopian National Ground-Water DAtabase (ENGDA),' by David W. Litke was developed as a users guide for the computer database and screen entry. This database dictionary serves as a reference for both the field forms and the computer database. Every effort has been made to have identical field names between the field forms and the screen entry forms in order to avoid confusion.

Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances

PubMed Central

Lionta, Evanthia; Spyrou, George; Vassilatis, Demetrios K.; Cournia, Zoe

2014-01-01

Structure-based drug discovery (SBDD) is becoming an essential tool in assisting fast and cost-efficient lead discovery and optimization. The application of rational, structure-based drug design is proven to be more efficient than the traditional way of drug discovery since it aims to understand the molecular basis of a disease and utilizes the knowledge of the three-dimensional structure of the biological target in the process. In this review, we focus on the principles and applications of Virtual Screening (VS) within the context of SBDD and examine different procedures ranging from the initial stages of the process that include receptor and library pre-processing, to docking, scoring and post-processing of topscoring hits. Recent improvements in structure-based virtual screening (SBVS) efficiency through ensemble docking, induced fit and consensus docking are also discussed. The review highlights advances in the field within the framework of several success studies that have led to nM inhibition directly from VS and provides recent trends in library design as well as discusses limitations of the method. Applications of SBVS in the design of substrates for engineered proteins that enable the discovery of new metabolic and signal transduction pathways and the design of inhibitors of multifunctional proteins are also reviewed. Finally, we contribute two promising VS protocols recently developed by us that aim to increase inhibitor selectivity. In the first protocol, we describe the discovery of micromolar inhibitors through SBVS designed to inhibit the mutant H1047R PI3Kα kinase. Second, we discuss a strategy for the identification of selective binders for the RXRα nuclear receptor. In this protocol, a set of target structures is constructed for ensemble docking based on binding site shape characterization and clustering, aiming to enhance the hit rate of selective inhibitors for the desired protein target through the SBVS process. PMID:25262799

Identification by Virtual Screening and In Vitro Testing of Human DOPA Decarboxylase Inhibitors

PubMed Central

Cellini, Barbara; Macchiarulo, Antonio; Giardina, Giorgio; Bossa, Francesco; Borri Voltattorni, Carla

2012-01-01

Dopa decarboxylase (DDC), a pyridoxal 5′-phosphate (PLP) enzyme responsible for the biosynthesis of dopamine and serotonin, is involved in Parkinson's disease (PD). PD is a neurodegenerative disease mainly due to a progressive loss of dopamine-producing cells in the midbrain. Co-administration of L-Dopa with peripheral DDC inhibitors (carbidopa or benserazide) is the most effective symptomatic treatment for PD. Although carbidopa and trihydroxybenzylhydrazine (the in vivo hydrolysis product of benserazide) are both powerful irreversible DDC inhibitors, they are not selective because they irreversibly bind to free PLP and PLP-enzymes, thus inducing diverse side effects. Therefore, the main goals of this study were (a) to use virtual screening to identify potential human DDC inhibitors and (b) to evaluate the reliability of our virtual-screening (VS) protocol by experimentally testing the “in vitro” activity of selected molecules. Starting from the crystal structure of the DDC-carbidopa complex, a new VS protocol, integrating pharmacophore searches and molecular docking, was developed. Analysis of 15 selected compounds, obtained by filtering the public ZINC database, yielded two molecules that bind to the active site of human DDC and behave as competitive inhibitors with Ki values ≥10 µM. By performing in silico similarity search on the latter compounds followed by a substructure search using the core of the most active compound we identified several competitive inhibitors of human DDC with Ki values in the low micromolar range, unable to bind free PLP, and predicted to not cross the blood-brain barrier. The most potent inhibitor with a Ki value of 500 nM represents a new lead compound, targeting human DDC, that may be the basis for lead optimization in the development of new DDC inhibitors. To our knowledge, a similar approach has not been reported yet in the field of DDC inhibitors discovery. PMID:22384042

Identification by virtual screening and in vitro testing of human DOPA decarboxylase inhibitors.

PubMed

Daidone, Frederick; Montioli, Riccardo; Paiardini, Alessandro; Cellini, Barbara; Macchiarulo, Antonio; Giardina, Giorgio; Bossa, Francesco; Borri Voltattorni, Carla

2012-01-01

Dopa decarboxylase (DDC), a pyridoxal 5'-phosphate (PLP) enzyme responsible for the biosynthesis of dopamine and serotonin, is involved in Parkinson's disease (PD). PD is a neurodegenerative disease mainly due to a progressive loss of dopamine-producing cells in the midbrain. Co-administration of L-Dopa with peripheral DDC inhibitors (carbidopa or benserazide) is the most effective symptomatic treatment for PD. Although carbidopa and trihydroxybenzylhydrazine (the in vivo hydrolysis product of benserazide) are both powerful irreversible DDC inhibitors, they are not selective because they irreversibly bind to free PLP and PLP-enzymes, thus inducing diverse side effects. Therefore, the main goals of this study were (a) to use virtual screening to identify potential human DDC inhibitors and (b) to evaluate the reliability of our virtual-screening (VS) protocol by experimentally testing the "in vitro" activity of selected molecules. Starting from the crystal structure of the DDC-carbidopa complex, a new VS protocol, integrating pharmacophore searches and molecular docking, was developed. Analysis of 15 selected compounds, obtained by filtering the public ZINC database, yielded two molecules that bind to the active site of human DDC and behave as competitive inhibitors with K(i) values ≥10 µM. By performing in silico similarity search on the latter compounds followed by a substructure search using the core of the most active compound we identified several competitive inhibitors of human DDC with K(i) values in the low micromolar range, unable to bind free PLP, and predicted to not cross the blood-brain barrier. The most potent inhibitor with a K(i) value of 500 nM represents a new lead compound, targeting human DDC, that may be the basis for lead optimization in the development of new DDC inhibitors. To our knowledge, a similar approach has not been reported yet in the field of DDC inhibitors discovery.

Portfolio Analysis of Renewable Energy Opportunities: Preprint

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

Richards, Allison; Deprizio, Jodi; Anderson, Kate

Time Warner Cable (TWC), now Charter Communications (CC), partnered with the National Renewable Energy Laboratory (NREL) to assess the technical and economic potential for solar photovoltaic (PV), wind, and ground-source heat-pump systems at 696 TWC facilities. NREL identified 306 sites where adding a renewable energy system would provide cost savings over the project life-cycle. In general, the top sites have some combination of high electricity rates ($0.16-$0.29/kWh), significant state incentives, and favorable net-metering policies. If all projects were implemented via third-party power purchase agreements, TWC/CC would save $37 million over 25 years and meet 10.5% of their energy consumption withmore » renewable energy. This paper describes the portfolio screening methodology used to identify and prioritize renewable energy opportunities across the TWC sites, as well as a summary of the potential cost savings that may be realized by implementing these projects. This may provide a template for other companies interested in identifying and prioritizing renewable energy opportunities across a large number of geographically dispersed sites. Following this initial portfolio analysis, NREL will be conducting in-depth analysis of project development opportunities at ten sites and evaluating off-grid solutions that may enable carbon emission reduction and grid independence at select facilities.« less

A composite docking approach for the identification and characterization of ectosteric inhibitors of cathepsin K.

PubMed

Law, Simon; Panwar, Preety; Li, Jody; Aguda, Adeleke H; Jamroz, Andrew; Guido, Rafael V C; Brömme, Dieter

2017-01-01

Cathepsin K (CatK) is a cysteine protease that plays an important role in mammalian intra- and extracellular protein turnover and is known for its unique and potent collagenase activity. Through studies on the mechanism of its collagenase activity, selective ectosteric sites were identified that are remote from the active site. Inhibitors targeting these ectosteric sites are collagenase selective and do not interfere with other proteolytic activities of the enzyme. Potential ectosteric inhibitors were identified using a computational approach to screen the druggable subset of and the entire 281,987 compounds comprising Chemical Repository library of the National Cancer Institute-Developmental Therapeutics Program (NCI-DTP). Compounds were scored based on their affinity for the ectosteric site. Here we compared the scores of three individual molecular docking methods with that of a composite score of all three methods together. The composite docking method was up to five-fold more effective at identifying potent collagenase inhibitors (IC50 < 20 μM) than the individual methods. Of 160 top compounds tested in enzymatic assays, 28 compounds revealed blocking of the collagenase activity of CatK at 100 μM. Two compounds exhibited IC50 values below 5 μM corresponding to a molar protease:inhibitor concentration of <1:12. Both compounds were subsequently tested in osteoclast bone resorption assays where the most potent inhibitor, 10-[2-[bis(2-hydroxyethyl)amino]ethyl]-7,8-diethylbenzo[g]pteridine-2,4-dione, (NSC-374902), displayed an inhibition of bone resorption with an IC50-value of approximately 300 nM and no cell toxicity effects.

A composite docking approach for the identification and characterization of ectosteric inhibitors of cathepsin K

PubMed Central

Law, Simon; Panwar, Preety; Li, Jody; Aguda, Adeleke H.; Jamroz, Andrew; Guido, Rafael V. C.

2017-01-01

Cathepsin K (CatK) is a cysteine protease that plays an important role in mammalian intra- and extracellular protein turnover and is known for its unique and potent collagenase activity. Through studies on the mechanism of its collagenase activity, selective ectosteric sites were identified that are remote from the active site. Inhibitors targeting these ectosteric sites are collagenase selective and do not interfere with other proteolytic activities of the enzyme. Potential ectosteric inhibitors were identified using a computational approach to screen the druggable subset of and the entire 281,987 compounds comprising Chemical Repository library of the National Cancer Institute-Developmental Therapeutics Program (NCI-DTP). Compounds were scored based on their affinity for the ectosteric site. Here we compared the scores of three individual molecular docking methods with that of a composite score of all three methods together. The composite docking method was up to five-fold more effective at identifying potent collagenase inhibitors (IC50 < 20 μM) than the individual methods. Of 160 top compounds tested in enzymatic assays, 28 compounds revealed blocking of the collagenase activity of CatK at 100 μM. Two compounds exhibited IC50 values below 5 μM corresponding to a molar protease:inhibitor concentration of <1:12. Both compounds were subsequently tested in osteoclast bone resorption assays where the most potent inhibitor, 10-[2-[bis(2-hydroxyethyl)amino]ethyl]-7,8-diethylbenzo[g]pteridine-2,4-dione, (NSC-374902), displayed an inhibition of bone resorption with an IC50-value of approximately 300 nM and no cell toxicity effects. PMID:29088253

Media at the Press Site for the Orion Launch

NASA Image and Video Library

2014-12-04

At NASA's Kennedy Space Center in Florida, the new countdown clock at the spaceport's Press Site is used for the first time as preparations were underway for the Orion Flight Test. The modern, multimedia display is similar to the screens seen at sporting venues. The new screen is nearly 26 feet wide by 7 feet high, a foot taller than the original clock.

Breast Cancer Screening in a Low Income Managed Care Population

DTIC Science & Technology

1998-10-01

is the only screening test to be demonstrated by prospective clinical trial to decrease cancer mortality (11-13). Its efficiency and relative safety...increase in the utilization of mammography in conjunction with clinical breast exam, the technology continues to be underutilized, especially among certain...Using familiar sites for special program activities e.g. churches, clinic sites; Developing culturally-sensitive information at the appropriate literacy

Multi-site implementation of nutrition screening and diagnosis in medical care units: Success of the More-2-Eat project.

PubMed

Keller, Heather H; Valaitis, Renata; Laur, Celia V; McNicholl, Tara; Xu, Yingying; Dubin, Joel A; Curtis, Lori; Obiorah, Suzanne; Ray, Sumantra; Bernier, Paule; Gramlich, Leah; Stickles-White, Marilee; Laporte, Manon; Bell, Jack

2018-03-22

Improving the detection and treatment of malnourished patients in hospital is needed to promote recovery. To describe the change in rates of detection and triaging of care for malnourished patients in 5 hospitals that were implementing an evidence-based nutrition care algorithm. To demonstrate that following this algorithm leads to increased detection of malnutrition and increased treatment to mitigate this condition. Sites worked towards implementing the Integrated Nutrition Pathway for Acute Care (INPAC), including screening (Canadian Nutrition Screening Tool) and triage (Subjective Global Assessment; SGA) to detect and diagnose malnourished patients. Implementation occurred over a 24-month period, including developmental (Period 1), implementation (Periods 2-5), and sustainability (Period 6) phases. Audits (n = 36) of patient health records (n = 5030) were conducted to identify nutrition care practices implemented with a variety of strategies and behaviour change techniques. All sites increased nutrition screening from Period 1, with three achieving the goal of 75% of admitted patients being screened by Period 3, and the remainder achieving a rate of 70% by end of implementation. No sites were conducting SGA at Period 1, and sites reached the goal of a 75% completion rate or referral for those identified to be at nutrition risk, by Period 3 or 4. By Period 2, 100% of patients identified as SGA C (severely malnourished) were receiving a comprehensive nutritional assessment. In Period 1, the nutrition diagnosis and documentation by the dietitian of 'malnutrition' was a modest 0.37%, increasing to over 5% of all audited health records. The overall use of any Advanced Nutrition Care practices increased from 31% during Period 1 to 63% during Period 6. The success of this multi-site study demonstrated that implementation of nutrition screening and diagnosis is feasible and leads to appropriate care. INPAC promotes efficiency in nutrition care while minimizing the risk of missing malnourished patients. Retrospectively registered ClinicalTrials.gov Identifier: NCT02800304, June 7, 2016. Copyright © 2018 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

Site Characterization Technologies for DNAPL Investigations

EPA Pesticide Factsheets

This document is intended to help managers at sites with potential or confirmed DNAPL contamination identify suitable characterization technologies, screen the technologies for potential application, learn about applications at similar sites, and...

Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network

PubMed Central

2016-01-01

Most small-molecule drug candidates fail before entering the market, frequently because of unexpected toxicity. Often, toxicity is detected only late in drug development, because many types of toxicities, especially idiosyncratic adverse drug reactions (IADRs), are particularly hard to predict and detect. Moreover, drug-induced liver injury (DILI) is the most frequent reason drugs are withdrawn from the market and causes 50% of acute liver failure cases in the United States. A common mechanism often underlies many types of drug toxicities, including both DILI and IADRs. Drugs are bioactivated by drug-metabolizing enzymes into reactive metabolites, which then conjugate to sites in proteins or DNA to form adducts. DNA adducts are often mutagenic and may alter the reading and copying of genes and their regulatory elements, causing gene dysregulation and even triggering cancer. Similarly, protein adducts can disrupt their normal biological functions and induce harmful immune responses. Unfortunately, reactive metabolites are not reliably detected by experiments, and it is also expensive to test drug candidates for potential to form DNA or protein adducts during the early stages of drug development. In contrast, computational methods have the potential to quickly screen for covalent binding potential, thereby flagging problematic molecules and reducing the total number of necessary experiments. Here, we train a deep convolution neural network—the XenoSite reactivity model—using literature data to accurately predict both sites and probability of reactivity for molecules with glutathione, cyanide, protein, and DNA. On the site level, cross-validated predictions had area under the curve (AUC) performances of 89.8% for DNA and 94.4% for protein. Furthermore, the model separated molecules electrophilically reactive with DNA and protein from nonreactive molecules with cross-validated AUC performances of 78.7% and 79.8%, respectively. On both the site- and molecule-level, the model’s performances significantly outperformed reactivity indices derived from quantum simulations that are reported in the literature. Moreover, we developed and applied a selectivity score to assess preferential reactions with the macromolecules as opposed to the common screening traps. For the entire data set of 2803 molecules, this approach yielded totals of 257 (9.2%) and 227 (8.1%) molecules predicted to be reactive only with DNA and protein, respectively, and hence those that would be missed by standard reactivity screening experiments. Site of reactivity data is an underutilized resource that can be used to not only predict if molecules are reactive, but also show where they might be modified to reduce toxicity while retaining efficacy. The XenoSite reactivity model is available at http://swami.wustl.edu/xenosite/p/reactivity. PMID:27610414

The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase

PubMed Central

Shimada, Tomohiro; Tanaka, Kan

2017-01-01

The promoter selectivity of Escherichia coli RNA polymerase (RNAP) is determined by the sigma subunit. The model prokaryote Escherichia coli K-12 contains seven species of the sigma subunit, each recognizing a specific set of promoters. For identification of the “constitutive promoters” that are recognized by each RNAP holoenzyme alone in the absence of other supporting factors, we have performed the genomic SELEX screening in vitro for their binding sites along the E. coli K-12 W3110 genome using each of the reconstituted RNAP holoenzymes and a collection of genome DNA segments of E. coli K-12. The whole set of constitutive promoters for each RNAP holoenzyme was then estimated based on the location of RNAP-binding sites. The first successful screening of the constitutive promoters was achieved for RpoD (σ70), the principal sigma for transcription of growth-related genes. As an extension, we performed in this study the screening of constitutive promoters for four minor sigma subunits, stationary-phase specific RpoS (σ38), heat-shock specific RpoH (σ32), flagellar-chemotaxis specific RpoF (σ28) and extra-cytoplasmic stress-response RpoE (σ24). The total number of constitutive promoters were: 129~179 for RpoS; 101~142 for RpoH; 34~41 for RpoF; and 77~106 for RpoE. The list of constitutive promoters were compared with that of known promoters identified in vivo under various conditions and using varieties of E. coli strains, altogether allowing the estimation of “inducible promoters” in the presence of additional supporting factors. PMID:28666008

Decreased Hospital Costs and Surgical Site Infection Incidence With a Universal Decolonization Protocol in Primary Total Joint Arthroplasty.

PubMed

Stambough, Jeffrey B; Nam, Denis; Warren, David K; Keeney, James A; Clohisy, John C; Barrack, Robert L; Nunley, Ryan M

2017-03-01

Staphylococcus aureus colonization has been identified as a key modifiable risk factor in the reduction of surgical site infections (SSI) related to elective total joint arthroplasty (TJA). We investigated the incidence of SSIs and cost-effectiveness of a universal decolonization protocol without screening consisting of nasal mupirocin and chlorhexidine before elective TJA compared to a program in which all subjects were screened for S aureus and selectively treated if positive. We reviewed 4186 primary TJAs from March 2011 through July 2015. Patients were divided into 2 cohorts based on the decolonization regimen used. Before May 2013, 1981 TJA patients were treated under a "screen and treat" program while the subsequent 2205 patients were treated under the universal protocol. We excluded the 3 months around the transition to control for treatment bias. Outcomes of interest included SSI and total hospital costs. With a universal decolonization protocol, there was a significant decrease in both the overall SSI rate (5 vs 15 cases; 0.2% vs 0.8%; P = .013) and SSIs caused by S aureus organisms (2 vs 10; 0.09% vs 0.5%; P = .01). A cost analysis accounting for the cost to administer the universal regimen demonstrated an actual savings of $717,205.59. TJA complicated by SSI costs 4.6× more to treat than that of an uncomplicated primary TJA. Our universal decolonization paradigm for elective TJA is effective in reducing the overall rate of SSIs and promoting economic gains for the health system related to the downstream savings accrued from limiting future reoperations and hospitalizations. Copyright © 2016 Elsevier Inc. All rights reserved.

Accuracy of optical spectroscopy for the detection of cervical intraepithelial neoplasia: Testing a device as an adjunct to colposcopy.

PubMed

Cantor, Scott B; Yamal, Jose-Miguel; Guillaud, Martial; Cox, Dennis D; Atkinson, E Neely; Benedet, John L; Miller, Dianne; Ehlen, Thomas; Matisic, Jasenka; van Niekerk, Dirk; Bertrand, Monique; Milbourne, Andrea; Rhodes, Helen; Malpica, Anais; Staerkel, Gregg; Nader-Eftekhari, Shahla; Adler-Storthz, Karen; Scheurer, Michael E; Basen-Engquist, Karen; Shinn, Eileen; West, Loyd A; Vlastos, Anne-Therese; Tao, Xia; Beck, J Robert; Macaulay, Calum; Follen, Michele

2011-03-01

Testing emerging technologies involves the evaluation of biologic plausibility, technical efficacy, clinical effectiveness, patient satisfaction, and cost-effectiveness. The objective of this study was to select an effective classification algorithm for optical spectroscopy as an adjunct to colposcopy and obtain preliminary estimates of its accuracy for the detection of CIN 2 or worse. We recruited 1,000 patients from screening and prevention clinics and 850 patients from colposcopy clinics at two comprehensive cancer centers and a community hospital. Optical spectroscopy was performed, and 4,864 biopsies were obtained from the sites measured, including abnormal and normal colposcopic areas. The gold standard was the histologic report of biopsies, read 2 to 3 times by histopathologists blinded to the cytologic, histopathologic, and spectroscopic results. We calculated sensitivities, specificities, receiver operating characteristic (ROC) curves, and areas under the ROC curves. We identified a cutpoint for an algorithm based on optical spectroscopy that yielded an estimated sensitivity of 1.00 [95% confidence interval (CI) = 0.92-1.00] and an estimated specificity of 0.71 [95% CI = 0.62-0.79] in a combined screening and diagnostic population. The positive and negative predictive values were 0.58 and 1.00, respectively. The area under the ROC curve was 0.85 (95% CI = 0.81-0.89). The per-patient and per-site performance were similar in the diagnostic and poorer in the screening settings. Like colposcopy, the device performs best in a diagnostic population. Alternative statistical approaches demonstrate that the analysis is robust and that spectroscopy works as well as or slightly better than colposcopy for the detection of CIN 2 to cancer. Copyright © 2010 UICC.

High-throughput screening (HTS) and hit validation to identify small molecule inhibitors with activity against NS3/4A proteases from multiple hepatitis C virus genotypes.

PubMed

Lee, Hyun; Zhu, Tian; Patel, Kavankumar; Zhang, Yan-Yan; Truong, Lena; Hevener, Kirk E; Gatuz, Joseph L; Subramanya, Gitanjali; Jeong, Hyun-Young; Uprichard, Susan L; Johnson, Michael E

2013-01-01

Development of drug-resistant mutations has been a major problem with all currently developed Hepatitis C Virus (HCV) NS3/4A inhibitors, including the two FDA approved drugs, significantly reducing the efficacy of these inhibitors. The high incidence of drug-resistance mutations and the limited utility of these inhibitors against only genotype 1 highlight the need for novel, broad-spectrum HCV therapies. Here we used high-throughput screening (HTS) to identify low molecular weight inhibitors against NS3/4A from multiple genotypes. A total of 40,967 compounds from four structurally diverse molecular libraries were screened by HTS using fluorescence-based enzymatic assays, followed by an orthogonal binding analysis using surface plasmon resonance (SPR) to eliminate false positives. A novel small molecule compound was identified with an IC50 value of 2.2 µM against the NS3/4A from genotype 1b. Mode of inhibition analysis subsequently confirmed this compound to be a competitive inhibitor with respect to the substrate, indicating direct binding to the protease active site, rather than to the allosteric binding pocket that was discovered to be the binding site of a few recently discovered small molecule inhibitors. This newly discovered inhibitor also showed promising inhibitory activity against the NS3/4As from three other HCV genotypes, as well as five common drug-resistant mutants of genotype 1b NS3/4A. The inhibitor was selective for NS3 from multiple HCV genotypes over two human serine proteases, and a whole cell lysate assay confirmed inhibitory activity in the cellular environment. This compound provides a lead for further development of potentially broader spectrum inhibitors.

Available web-based teaching resources for health care professionals on screening for oral cancer

PubMed Central

Varela-Centelles, Pablo; Insua, Angel; Warnakulasuriya, Saman; Rapidis, Alexander; Diz, Pedro; Seoane, Juan

2015-01-01

Objectives: To identify websites with adequate information on oral cancer screening for healthcare professionals (HCPs) and to assess both their quality and contents. Study Design: Websites were identified using Google and HON medical professional search engines using the terms “screening for oral cancer”. The first 100 sites retrieved by each engine were analysed using the DISCERN questionnaire (reliability), the V instrument (contents on oral cancer) and further by the Flesch-Kinkaid Reading Grade Level and the Flesch Reading Ease (readability). Results: The overall rating showed minimal shortcomings in the quality of the information in the websites. The coverage and correctness of information on “visual examination” was rated as fair/good, whereas updating of contents resulted very variable (eg: 81% for visual examination and 18.2% for molecular biomarkers). These results permitted to rank the websites housing relevant information for oral cancer. Top ranking websites were affiliated to the Oral Cancer Foundation (USA), WHO Collaborating Centre for oral cancer (UK) whose webpage is entitled “Oral Cancer Education and Research”, and the Clinical Guidelines maintained by the British Columbia Cancer Agency (Canada) and the British Dental Association (UK) respectively. Conclusions: There are web-based, HCP-addressed, resources on screening for oral cancer housing heterogeneous information both in quality and contents. The use of specific evaluation tools permits the selection of reliable websites on this topic with a potential to improve the existing educational gaps among HCPs. Key words:Oral cancer, early diagnosis, screening, secondary prevention, internet, teaching resources, continuous education. PMID:25475775

The Myth of the Normal, Average Human Brain—The ICBM Experience: (1) Subject Screening and Eligibility

PubMed Central

Mazziotta, John C.; Woods, Roger; Iacoboni, Marco; Sicotte, Nancy; Yaden, Kami; Tran, Mary; Bean, Courtney; Kaplan, Jonas; Toga, Arthur W.

2009-01-01

In the course of developing an atlas and reference system for the normal human brain throughout the human age span from structural and functional brain imaging data, the International Consortium for Brain Mapping (ICBM) developed a set of “normal” criteria for subject inclusion and the associated exclusion criteria. The approach was to minimize inclusion of subjects with any medical disorders that could affect brain structure or function. In the past two years, a group of 1,685 potential subjects responded to solicitation advertisements at one of the consortium sites (UCLA). Subjects were screened by a detailed telephone interview and then had an in-person history and physical examination. Of those who responded to the advertisement and considered themselves to be normal, only 31.6% (532 subjects) passed the telephone screening process. Of the 348 individuals who submitted to in-person history and physical examinations, only 51.7% passed these screening procedures. Thus, only 10.7% of those individuals who responded to the original advertisement qualified for imaging. The most frequent cause for exclusion in the second phase of subject screening was high blood pressure followed by abnormal signs on neurological examination. It is concluded that the majority of individuals who consider themselves normal by self-report are found not to be so by detailed historical interviews about underlying medical conditions and by thorough medical and neurological examinations. Recommendations are made with regard to the inclusion of subjects in brain imaging studies and the criteria used to select them. PMID:18775497

Discovery of d-amino acid oxidase inhibitors based on virtual screening against the lid-open enzyme conformation.

PubMed

Szilágyi, Bence; Skok, Žiga; Rácz, Anita; Frlan, Rok; Ferenczy, György G; Ilaš, Janez; Keserű, György M

2018-06-01

d-Amino acid oxidase (DAAO) inhibitors are typically small polar compounds with often suboptimal pharmacokinetic properties. Features of the native binding site limit the operational freedom of further medicinal chemistry efforts. We therefore initiated a structure based virtual screening campaign based on the X-ray structures of DAAO complexes where larger ligands shifted the loop (lid opening) covering the native binding site. The virtual screening of our in-house collection followed by the in vitro test of the best ranked compounds led to the identification of a new scaffold with micromolar IC 50 . Subsequent SAR explorations enabled us to identify submicromolar inhibitors. Docking studies supported by in vitro activity measurements suggest that compounds bind to the active site with a salt-bridge characteristic to DAAO inhibitor binding. In addition, displacement of and interaction with the loop covering the active site contributes significantly to the activity of the most potent compounds. Copyright © 2018 Elsevier Ltd. All rights reserved.

Identification of Multiple Druggable Secondary Sites by Fragment Screening against DC-SIGN.

PubMed

Aretz, Jonas; Baukmann, Hannes; Shanina, Elena; Hanske, Jonas; Wawrzinek, Robert; Zapol'skii, Viktor A; Seeberger, Peter H; Kaufmann, Dieter E; Rademacher, Christoph

2017-06-12

DC-SIGN is a cell-surface receptor for several pathogenic threats, such as HIV, Ebola virus, or Mycobacterium tuberculosis. Multiple attempts to develop inhibitors of the underlying carbohydrate-protein interactions have been undertaken in the past fifteen years. Still, drug-like DC-SIGN ligands are sparse, which is most likely due to its hydrophilic, solvent-exposed carbohydrate-binding site. Herein, we report on a parallel fragment screening against DC-SIGN applying SPR and a reporter displacement assay, which complements previous screenings using 19 F NMR spectroscopy and chemical fragment microarrays. Hit validation by SPR and 1 H- 15 N HSQC NMR spectroscopy revealed that although no fragment bound in the primary carbohydrate site, five secondary sites are available to harbor drug-like molecules. Building on key interactions of the reported fragment hits, these pockets will be targeted in future approaches to accelerate the development of DC-SIGN inhibitors. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Prevalence of Body Dysmorphic Disorder and Surgeon Diagnostic Accuracy in Facial Plastic and Oculoplastic Surgery Clinics.

PubMed

Joseph, Andrew W; Ishii, Lisa; Joseph, Shannon S; Smith, Jane I; Su, Peiyi; Bater, Kristin; Byrne, Patrick; Boahene, Kofi; Papel, Ira; Kontis, Theda; Douglas, Raymond; Nelson, Christine C; Ishii, Masaru

2017-07-01

Body dysmorphic disorder (BDD) is a relative contraindication for facial plastic surgery, but formal screening is not common in practice. The prevalence of BDD in patients seeking facial plastic surgery is not well documented. To establish the prevalence of BDD across facial plastic and oculoplastic surgery practice settings, and estimate the ability of surgeons to screen for BDD. This multicenter prospective study recruited a cohort of 597 patients who presented to academic and private facial plastic and oculoplastic surgery practices from March 2015 to February 2016. All patients were screened for BDD using the Body Dysmorphic Disorder Questionnaire (BDDQ). After each clinical encounter, surgeons independently evaluated the likelihood that a participating patient had BDD. Validated instruments were used to assess satisfaction with facial appearance including the FACE-Q, Blepharoplasty Outcomes Evaluation (BOE), Facelift Outcomes Evaluation (FOE), Rhinoplasty Outcomes Evaluation (ROE), and Skin Rejuvenation Outcomes Evaluation (SROE). Across participating practices (9 surgeons, 3 sites), a total of 597 patients were screened for BDD: 342 patients from site 1 (mean [SD] age, 44.2 [16.5] years); 158 patients, site 2 (mean [SD] age, 46.0 [16.2] years), site 3, 97 patients (mean [SD] age, 56.3 [15.5] years). Overall, 58 patients [9.7%] screened positive for BDD by the BDDQ instrument, while only 16 of 402 patients [4.0%] were clinically suspected of BDD by surgeons. A higher percentage of patients presenting for cosmetic surgery (37 of 283 patients [13.1%]) compared with those presenting for reconstructive surgery (21 of 314 patients [6.7%]) screened positive on the BDDQ (odds ratio, 2.10; 95% CI, 1.20-3.68; P = .01). Surgeons were only able to correctly identify 2 of 43 patients (4.7%) who screened positive for BDD on the BDDQ, and the positive likelihood ratio was only 1.19 (95% CI, 0.28-5.07). Patients screening positive for BDD by the BDDQ had lower satisfaction with their appearance as measured by the FACE-Q, ROE, BOE, SROE, and FOE. Body dysmorphic disorder is a relatively common condition across facial plastic and oculoplastic surgery practice settings. Patients who screen positive on the BDDQ have lower satisfaction with their facial appearance at baseline. Surgeons have a poor ability to screen for patients with BDD when compared with validated screening instruments such as the BDDQ. Routine implementation of validated BDD screening instruments may improve patient care. NA.

Two-colored fluorescence correlation spectroscopy screening for LC3-P62 interaction inhibitors.

PubMed

Tsuganezawa, Keiko; Shinohara, Yoshiyasu; Ogawa, Naoko; Tsuboi, Shun; Okada, Norihisa; Mori, Masumi; Yokoyama, Shigeyuki; Noda, Nobuo N; Inagaki, Fuyuhiko; Ohsumi, Yoshinori; Tanaka, Akiko

2013-10-01

The fluorescence correlation spectroscopy (FCS)-based competitive binding assay to screen for protein-protein interaction inhibitors is a highly sensitive method as compared with the fluorescent polarization assay used conventionally. However, the FCS assay identifies many false-positive compounds, which requires specifically designed orthogonal screenings. A two-colored application of the FCS-based screening was newly developed, and inhibitors of a protein-protein interaction, involving selective autophagy, were selected. We focused on the interaction of LC3 with the adaptor protein p62, because the interaction is crucial to degrade the specific target proteins recruited by p62. First, about 10,000 compounds were subjected to the FCS-based competitive assay using a TAMRA-labeled p62-derived probe, and 29 hit compounds were selected. Next, the obtained hits were evaluated by the second FCS assay, using an Alexa647-labeled p62-derived probe to remove the false-positive compounds, and six hit compounds inhibited the interaction. Finally, we tested all 29 compounds by surface plasmon resonance-based competitive binding assay to evaluate their inhibition of the LC3-p62 interaction and selected two inhibitors with IC50 values less than 2 µM. The two-colored FCS-based screening was shown to be effective to screen for protein-protein interaction inhibitors.