<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Susan Abbatiello</style></author><author><style face="normal" font="default" size="100%">Birgit Schilling</style></author><author><style face="normal" font="default" size="100%">D.R. Mani</style></author><author><style face="normal" font="default" size="100%">L.I. Shilling</style></author><author><style face="normal" font="default" size="100%">S.C. Hall</style></author><author><style face="normal" font="default" size="100%">B. McLean</style></author><author><style face="normal" font="default" size="100%">M. Albetolle</style></author><author><style face="normal" font="default" size="100%">S. Allen</style></author><author><style face="normal" font="default" size="100%">M. Burgess</style></author><author><style face="normal" font="default" size="100%">M.P. Cusack</style></author><author><style face="normal" font="default" size="100%">M Gosh</style></author><author><style face="normal" font="default" size="100%">V Hedrick</style></author><author><style face="normal" font="default" size="100%">J.M. Held</style></author><author><style face="normal" font="default" size="100%">H.D. Inerowicz</style></author><author><style face="normal" font="default" size="100%">A. Jackson</style></author><author><style face="normal" font="default" size="100%">H. Keshishian</style></author><author><style face="normal" font="default" size="100%">C.R. Kinsinger</style></author><author><style face="normal" font="default" size="100%">Lyssand, JS</style></author><author><style face="normal" font="default" size="100%">Makowski L</style></author><author><style face="normal" font="default" size="100%">Mesri M</style></author><author><style face="normal" font="default" size="100%">Rodriguez H</style></author><author><style face="normal" font="default" size="100%">Rudnick P</style></author><author><style face="normal" font="default" size="100%">Sadowski P</style></author><author><style face="normal" font="default" size="100%">Nell Sedransk</style></author><author><style face="normal" font="default" size="100%">Shaddox K</style></author><author><style face="normal" font="default" size="100%">Skates SJ</style></author><author><style face="normal" font="default" size="100%">Kuhn E</style></author><author><style face="normal" font="default" size="100%">Smith D</style></author><author><style face="normal" font="default" size="100%">Whiteaker, JR</style></author><author><style face="normal" font="default" size="100%">Whitwell C</style></author><author><style face="normal" font="default" size="100%">Zhang S</style></author><author><style face="normal" font="default" size="100%">Borchers CH</style></author><author><style face="normal" font="default" size="100%">Fisher SJ</style></author><author><style face="normal" font="default" size="100%">Gibson BW</style></author><author><style face="normal" font="default" size="100%">Liebler DC</style></author><author><style face="normal" font="default" size="100%">M.J. McCoss</style></author><author><style face="normal" font="default" size="100%">Neubert TA</style></author><author><style face="normal" font="default" size="100%">Paulovich AG</style></author><author><style face="normal" font="default" size="100%">Regnier FE</style></author><author><style face="normal" font="default" size="100%">Tempst, P</style></author><author><style face="normal" font="default" size="100%">Carr, SA</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular Cell Proteomics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">09/2015</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">14</style></volume><pages><style face="normal" font="default" size="100%">2357-74</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;There is an increasing need in biology and clinical medicine to robustly and reliably measure tens to hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility, and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here, we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and seven control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data, we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to subnanogram/ml sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and interlaboratory reproducibility was &amp;lt;20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy-isotope-labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an interlaboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality control measures, enables sensitive, specific, reproducible, and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.&lt;/p&gt;
</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhang K</style></author><author><style face="normal" font="default" size="100%">Hughes-Oliver JM</style></author><author><style face="normal" font="default" size="100%">Young SS</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Analysis of high-dimensional structure-activity screening datasets using the optimal bit string Tree</style></title><secondary-title><style face="normal" font="default" size="100%">Technomet</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Classification</style></keyword><keyword><style  face="normal" font="default" size="100%">Drug discovery</style></keyword><keyword><style  face="normal" font="default" size="100%">High throughput screening</style></keyword><keyword><style  face="normal" font="default" size="100%">Prediction</style></keyword><keyword><style  face="normal" font="default" size="100%">QSAR</style></keyword><keyword><style  face="normal" font="default" size="100%">Simulated annealing</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year></dates><volume><style face="normal" font="default" size="100%">55</style></volume><pages><style face="normal" font="default" size="100%">161-173</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;We propose a new classification method called the Optimal Bit String Tree (OBSTree) to identify quantitative structure-activity relationships (QSARs). The method introduces the concept of a chromosome to describe the presence/absence context of a combination of descriptors. A descriptor set and its optimal chromosome form the splitting variable. A new stochastic searching scheme that contains a weighted sampling scheme, simulated annealing, and a trimming procedure optimizes the choice of splitting variable. Simulation studies and an application to screening monoamine oxidase inhibitors show that OBSTree is advantageous in accurately and effectively identifying QSAR rules and finding different classes of active compounds. Details of the algorithm, SAS code, and simulated and real datasets are available online as supplementary materials.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Abbatiello, S.</style></author><author><style face="normal" font="default" size="100%">Feng, X.</style></author><author><style face="normal" font="default" size="100%">Sedransk, N.</style></author><author><style face="normal" font="default" size="100%">Mani, DR</style></author><author><style face="normal" font="default" size="100%">Schilling, B</style></author><author><style face="normal" font="default" size="100%">Maclean, B</style></author><author><style face="normal" font="default" size="100%">Zimmerman, LJ</style></author><author><style face="normal" font="default" size="100%">Cusack, MP</style></author><author><style face="normal" font="default" size="100%">Hall, SC</style></author><author><style face="normal" font="default" size="100%">Addona, T</style></author><author><style face="normal" font="default" size="100%">Allen, S</style></author><author><style face="normal" font="default" size="100%">Dodder, NG</style></author><author><style face="normal" font="default" size="100%">Ghosh, M</style></author><author><style face="normal" font="default" size="100%">Held, JM</style></author><author><style face="normal" font="default" size="100%">Hedrick, V</style></author><author><style face="normal" font="default" size="100%">Inerowicz, HD</style></author><author><style face="normal" font="default" size="100%">Jackson, A</style></author><author><style face="normal" font="default" size="100%">Keshishian, H</style></author><author><style face="normal" font="default" size="100%">Kim, JW</style></author><author><style face="normal" font="default" size="100%">Lyssand, JS</style></author><author><style face="normal" font="default" size="100%">Riley, CP</style></author><author><style face="normal" font="default" size="100%">Rudnick, P</style></author><author><style face="normal" font="default" size="100%">Sadowski, P</style></author><author><style face="normal" font="default" size="100%">Shaddox, K</style></author><author><style face="normal" font="default" size="100%">Smith, D</style></author><author><style face="normal" font="default" size="100%">Tomazela, D</style></author><author><style face="normal" font="default" size="100%">Wahlander, A</style></author><author><style face="normal" font="default" size="100%">Waldemarson, S</style></author><author><style face="normal" font="default" size="100%">Whitwell, CA</style></author><author><style face="normal" font="default" size="100%">You, J</style></author><author><style face="normal" font="default" size="100%">Zhang, S</style></author><author><style face="normal" font="default" size="100%">Kinsinger, CR</style></author><author><style face="normal" font="default" size="100%">Mesri, M</style></author><author><style face="normal" font="default" size="100%">Rodriguez, H</style></author><author><style face="normal" font="default" size="100%">Borchers, CH</style></author><author><style face="normal" font="default" size="100%">Buck, C</style></author><author><style face="normal" font="default" size="100%">Fisher, SJ</style></author><author><style face="normal" font="default" size="100%">Gibson, BW</style></author><author><style face="normal" font="default" size="100%">Liebler, D</style></author><author><style face="normal" font="default" size="100%">Maccoss, M</style></author><author><style face="normal" font="default" size="100%">Neubert, TA</style></author><author><style face="normal" font="default" size="100%">Paulovich, A</style></author><author><style face="normal" font="default" size="100%">Regnier, F</style></author><author><style face="normal" font="default" size="100%">Skates, SJ</style></author><author><style face="normal" font="default" size="100%">Tempst, P</style></author><author><style face="normal" font="default" size="100%">Wang, M</style></author><author><style face="normal" font="default" size="100%">Carr, SA</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS)</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular and Cellular Proteomics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2013</style></year></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">2623-2639</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation &amp;lt;0.15, peak width coefficient of variation &amp;lt;0.15, standard deviation of RT &amp;lt;0.15 min (9 s), and the RT drift &amp;lt;0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hughes-Oliver JM</style></author><author><style face="normal" font="default" size="100%">Brooks A</style></author><author><style face="normal" font="default" size="100%">Welch W</style></author><author><style face="normal" font="default" size="100%">Khaldei MG</style></author><author><style face="normal" font="default" size="100%">Hawkins DM</style></author><author><style face="normal" font="default" size="100%">Young SS</style></author><author><style face="normal" font="default" size="100%">Patil K</style></author><author><style face="normal" font="default" size="100%">Howell GW</style></author><author><style face="normal" font="default" size="100%">Ng RT</style></author><author><style face="normal" font="default" size="100%">Chu MT</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">ChemModLab: A web-based cheminromates modeling laboratory</style></title><secondary-title><style face="normal" font="default" size="100%">Cheminformatics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">61-81</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;ChemModLab, written by the ECCR @ NCSU consortium under NIH support, is a toolbox for fitting and assessing quantitative structure-activity relationships (QSARs). Its elements are: a cheminformatic front end used to supply molecular descriptors for use in modeling; a set of methods for fitting models; and methods for validating the resulting model. Compounds may be input as structures from which standard descriptors will be calculated using the freely available cheminformatic front end PowerMV; PowerMV also supports compound visualization. In addition, the user can directly input their own choices of descriptors, so the capability for comparing descriptors is effectively unlimited. The statistical methodologies comprise a comprehensive collection of approaches whose validity and utility have been accepted by experts in the fields. As far as possible, these tools are implemented in open-source software linked into the flexible R platform, giving the user the capability of applying many different QSAR modeling methods in a seamless way. As promising new QSAR methodologies emerge from the statistical and data-mining communities, they will be incorporated in the laboratory. The web site also incorporates links to public-domain data sets that can be used as test cases for proposed new modeling methods. The capabilities of ChemModLab are illustrated using a variety of biological responses, with different modeling methodologies being applied to each. These show clear differences in quality of the fitted QSAR model, and in computational requirements. The laboratory is web-based, and use is free. Researchers with new assay data, a new descriptor set, or a new modeling method may readily build QSAR models and benchmark their results against other findings. Users may also examine the diversity of the molecules identified by a QSAR model. Moreover, users have the choice of placing their data sets in a public area to facilitate communication with other researchers; or can keep them hidden to preserve confidentiality.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Beasley CM Jr</style></author><author><style face="normal" font="default" size="100%">Benson C</style></author><author><style face="normal" font="default" size="100%">Xia JQ</style></author><author><style face="normal" font="default" size="100%">Young SS</style></author><author><style face="normal" font="default" size="100%">Haber H</style></author><author><style face="normal" font="default" size="100%">Mitchell MI</style></author><author><style face="normal" font="default" size="100%">Loghin C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Systematic decrements in QTc between the first and second day of contiguous daily ECG recordings under controlled conditions</style></title><secondary-title><style face="normal" font="default" size="100%">PACE</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">ECG</style></keyword><keyword><style  face="normal" font="default" size="100%">QT interval</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">April</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">9</style></number><volume><style face="normal" font="default" size="100%">34</style></volume><pages><style face="normal" font="default" size="100%">1116-1127</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;BACKGROUND: Many thorough QT (TQT) studies use a baseline day and double delta analysis to account for potential diurnal variation in QTc. However, little is known about systematic changes in the QTc across contiguous days when normal volunteers are brought into a controlled inpatient environment.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">S. K. Kinney</style></author><author><style face="normal" font="default" size="100%">J. P. Reiter</style></author><author><style face="normal" font="default" size="100%">AP Reznek</style></author><author><style face="normal" font="default" size="100%">J Miranda</style></author><author><style face="normal" font="default" size="100%">R Jarmin</style></author><author><style face="normal" font="default" size="100%">JM Abowd</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Toward Unrestricted Public Use Business Microdata: The Synthetic Longitudinal Business Database</style></title><secondary-title><style face="normal" font="default" size="100%">International Statistical Review</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><volume><style face="normal" font="default" size="100%">79</style></volume><pages><style face="normal" font="default" size="100%"> 362-384</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">3</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Feng J.</style></author><author><style face="normal" font="default" size="100%">Sanil A</style></author><author><style face="normal" font="default" size="100%">Young SS</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PharmID: Pharmacophore identification using Gibbs sampling</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Chemical Information and Modeling</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year></dates><volume><style face="normal" font="default" size="100%">46</style></volume><pages><style face="normal" font="default" size="100%">1352-1359</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The binding of a small molecule to a protein is inherently a 3D matching problem. As crystal structures are not available for most drug targets, there is a need to be able to infer from bioassay data the key binding features of small molecules and their disposition in space, the pharmacophore. Fingerprints of 3D features and a modification of Gibbs sampling to align a set of known flexible ligands, where all compounds are active, are used to discern possible pharmacophores. A clique detection method is used to map the features back onto the binding conformations. The complete algorithm is described in detail, and it is shown that the method can find common superimposition for several test data sets. The method reproduces answers very close to the crystal structure and literature pharmacophores in the examples presented. The basic algorithm is relatively fast and can easily deal with up to 100 compounds and tens of thousands of conformations. The algorithm is also able to handle multiple binding mode problems, which means it can superimpose molecules within the same data set according to two different sets of binding features. We demonstrate the successful use of this algorithm for multiple binding modes for a set of D2 and D4 ligands.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Remlinger KS</style></author><author><style face="normal" font="default" size="100%">Hughes-Oliver JM</style></author><author><style face="normal" font="default" size="100%">Young SS</style></author><author><style face="normal" font="default" size="100%">Lam RL</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Statistical design of pools using optimal coverage and minimal collision</style></title><secondary-title><style face="normal" font="default" size="100%">Technom</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Pharmaceutical industry</style></keyword><keyword><style  face="normal" font="default" size="100%">Pooled data</style></keyword><keyword><style  face="normal" font="default" size="100%">Pooling</style></keyword><keyword><style  face="normal" font="default" size="100%">Screening</style></keyword><keyword><style  face="normal" font="default" size="100%">Throughput</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year></dates><volume><style face="normal" font="default" size="100%">48</style></volume><pages><style face="normal" font="default" size="100%">133-143</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The screening of large chemical libraries to identify new compounds can be simplified by testing compounds in pools. Two criteria for designing pools are considered: optimal coverage of the chemical space and minimal collision between compounds. Four pooling designs are applied to a public database and evaluated by determining how well the design criteria are met and whether the methods are able to find diverse active compounds. While one pool was outstanding, all designed pools outperformed randomly designed pools.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Alan Karr</style></author><author><style face="normal" font="default" size="100%">William DuMouchel</style></author><author><style face="normal" font="default" size="100%">Wen-Hua Ju</style></author><author><style face="normal" font="default" size="100%">Martin Theus</style></author><author><style face="normal" font="default" size="100%">Yehuda Vardi</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Computer intrusion: detecting masqueraders</style></title><secondary-title><style face="normal" font="default" size="100%">Statistical Science</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anomaly</style></keyword><keyword><style  face="normal" font="default" size="100%">Bayes</style></keyword><keyword><style  face="normal" font="default" size="100%">compression</style></keyword><keyword><style  face="normal" font="default" size="100%">computer security</style></keyword><keyword><style  face="normal" font="default" size="100%">high-orderMarkov</style></keyword><keyword><style  face="normal" font="default" size="100%">profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Unix</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2001</style></year></dates><number><style face="normal" font="default" size="100%">1</style></number><volume><style face="normal" font="default" size="100%">16</style></volume><pages><style face="normal" font="default" size="100%">1-17</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Masqueraders in computer intrusion detection are people who use somebody else?s computer account. We investigate a number of statistical approaches for detecting masqueraders. To evaluate them, we collected UNIX command data from 50 users and then contaminated the data with masqueraders. The experiment was blinded. We show results from six methods, including two approaches from the computer science community.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ju, W-H</style></author><author><style face="normal" font="default" size="100%">Yehuda Vardi</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A Hybrid High-Order Markov Chain Model for Computer Intrusion Detection</style></title></titles><dates><year><style  face="normal" font="default" size="100%">2001</style></year></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">277-295</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;A hybrid model based mostly on a high-order Markov chain and occasionally on a statistical-independence model is proposed for profiling command sequences of a computer user in order to identify a &quot;signature behavior&quot; for that user. Based on the model, an estimation procedure for such a signature behavior driven by maximum likelihood (ML) considerations is devised. The formal ML estimates are numerically intractable, but the ML-optimization problem can be substituted by a linear inverse problem with positivity constraint (LININPOS), for which the EM algorithm can be used as an equation solver to produce an approximate ML-estimate. The intrusion detection system works by comparing a user’s command sequence to the user’s and others’ estimated signature behaviors in real time through statistical hypothesis testing. A form of likelihood-ratio test is used to detect if a given sequence of commands is from the proclaimed user, with the alternative hypothesis being a masquerader user. Applying the model to real-life data collected from AT&amp;amp;T Labs-Research indicates that the new methodology holds some promise for intrusion detection.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Young, S.Stanley</style></author><author><style face="normal" font="default" size="100%">Jerome Sacks</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Gundertofte, Klaus</style></author><author><style face="normal" font="default" size="100%">Jørgensen, Flemming Steen</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Analysis of a Large, High-Throughput Screening Data Using Recursive Partitioning</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular Modeling and Prediction of Bioactivity</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2000</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-1-4615-4141-7_17</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer US</style></publisher><pages><style face="normal" font="default" size="100%">149-156</style></pages><isbn><style face="normal" font="default" size="100%">978-1-4613-6857-1</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;As biological drug targets multiply through the human genome project and as the number of chemical compounds available for screening becomes very large, the expense of screening every compound against every target becomes prohibitive. We need to improve the efficiency of the drug screening process so that active compounds can be found for more biological targets and turned over to medicinal chemists for atom-by-atom optimization. We create a method for analysis of the very large, complex data sets coming from high throughput screening, and then integrate the analysis with the selection of compounds for screening so that the structure-activity rules derived from an initial compound set can be used to suggest additional compounds for screening. Cycles of screening and analysis become sequential screening rather than the mass screening of all available compounds. We extend the analysis method to deal with multivariate responses. Previously, a screening campaign might screen hundreds of thousands of compounds; sequential screening can cut the number of compounds screened by up to eighty percent. Sequential screening also gives SAR rules that can be used to mathematically screen compound collections or virtual chemical libraries.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">A. F. Karr</style></author><author><style face="normal" font="default" size="100%">C.-M. Aldea</style></author><author><style face="normal" font="default" size="100%">J.D. Picka</style></author><author><style face="normal" font="default" size="100%">S. P. Shah</style></author><author><style face="normal" font="default" size="100%">S.S. Jaiswal</style></author><author><style face="normal" font="default" size="100%">T. Igusa</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Experimental and statistical study of chloride permeability of cracked high strength concrete</style></title><secondary-title><style face="normal" font="default" size="100%">ASTM Cement, Concrete and Aggregates</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2000</style></year><pub-dates><date><style  face="normal" font="default" size="100%">December</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">2</style></number><volume><style face="normal" font="default" size="100%">22</style></volume><pages><style face="normal" font="default" size="100%">000-000</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Within any cast cylinder of concrete, the coarse aggregate will tend to be inhomogeneously distributed. This variability may arise as a result of segregation caused by gravity or as a result of the wall effect that is caused by the inability of the aggregate to penetrate the walls of the mold. Using methods from image analysis, stereology, and statistics, local estimates of aggregate inhomogeniety are defined that quantify phenomena that have been qualitatively described in the past. These methods involve modification of the two-dimensional images to prepare them for analysis, as well as simple diagnostic statistics for determining the presence of a wall effect. While the techniques presented herein are developed specifically for cast cylinders, they can be generalized to other cast or cored concrete specimens.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">A. F. Karr</style></author><author><style face="normal" font="default" size="100%">S. P. Shah</style></author><author><style face="normal" font="default" size="100%">S.S. Jaiswal</style></author><author><style face="normal" font="default" size="100%">B.E. Ankenman</style></author><author><style face="normal" font="default" size="100%">J.D. Picka</style></author><author><style face="normal" font="default" size="100%">T. Igusa</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Impact of the interfacial transition zone on the chloride permeability of concrete</style></title><secondary-title><style face="normal" font="default" size="100%">Proc. 12th Engrg. Mechanics Conf</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2000</style></year></dates><pages><style face="normal" font="default" size="100%">1134-1137</style></pages><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">A. F. Karr</style></author><author><style face="normal" font="default" size="100%">S.S. Jaiswal</style></author><author><style face="normal" font="default" size="100%">T. Igusa</style></author><author><style face="normal" font="default" size="100%">J.D. Picka</style></author><author><style face="normal" font="default" size="100%">S. P. Shah</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Quantitative description of coarse aggregate volume fraction gradients</style></title><secondary-title><style face="normal" font="default" size="100%">Cement Concrete and Aggregates</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2000</style></year></dates><volume><style face="normal" font="default" size="100%">22</style></volume><pages><style face="normal" font="default" size="100%">151-159</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Within any cast cylinder of concrete, the coarse aggregate will tend to be inhomogeneously distributed. This variability may arise as a result of segregation caused by gravity or as a result of the wall effect that is caused by the inability of the aggregate to penetrate the walls of the mold. Using methods from image analysis, stereology, and statistics, local estimates of aggregate inhomogeniety are defined that quantify phenomena that have been qualitatively described in the past. These methods involve modification of the two-dimensional images to prepare them for analysis, as well as simple diagnostic statistics for determining the presence of a wall effect. While the techniques presented herein are developed specifically for cast cylinders, they can be generalized to other cast or cored concrete specimens.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">A. F. Karr</style></author><author><style face="normal" font="default" size="100%">S.S. Jaiswal</style></author><author><style face="normal" font="default" size="100%">J.D. Picka</style></author><author><style face="normal" font="default" size="100%">T. Igusa</style></author><author><style face="normal" font="default" size="100%">S. P. Shah</style></author><author><style face="normal" font="default" size="100%">B.E. Ankenman</style></author><author><style face="normal" font="default" size="100%">P. Styer</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Statistical studies of the conductivity of concrete using ASTM C1202?94</style></title><secondary-title><style face="normal" font="default" size="100%">Concrete Science and Engineering</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2000</style></year></dates><volume><style face="normal" font="default" size="100%">2</style></volume><pages><style face="normal" font="default" size="100%">97-105</style></pages><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">A. F. Karr</style></author><author><style face="normal" font="default" size="100%">C.-M. Aldea</style></author><author><style face="normal" font="default" size="100%">S.S. Jaiswal</style></author><author><style face="normal" font="default" size="100%">B.E. Ankenman</style></author><author><style face="normal" font="default" size="100%">J.D. Picka</style></author><author><style face="normal" font="default" size="100%">T. Igusa</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Water permeability of cracked concrete</style></title><secondary-title><style face="normal" font="default" size="100%">Proc. 12th Engrg. Mechanics Conf</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2000</style></year></dates><pages><style face="normal" font="default" size="100%">1158?1162</style></pages><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Valerie S. L. Williams</style></author><author><style face="normal" font="default" size="100%">Lyle V. Jones</style></author><author><style face="normal" font="default" size="100%">John W. Tukey</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Controlling error in multiple comparisons, with special attention to the national assessment of educational progress</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Educational and Behavioral Statistics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">1999</style></year></dates><volume><style face="normal" font="default" size="100%">24</style></volume><pages><style face="normal" font="default" size="100%">42–69</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Three alternative procedures to adjust significance levels for multiplicity are the traditional Bonferroni technique, a sequential Bonferroni technique devel-oped by Hochberg (1988), and a sequential approach for controlling the false discovery rate proposed by Benjamini and Hochberg (1995). These procedures are illustrated and compared using examples from the National Assessment of Educational Progress (NAEP). A prominent advantage of the Benjamini and Hochberg (B-H) procedure, as demonstrated in these examples, is the greater invariance of statistical significance for given comparisons over alternative family sizes. Simulation studies show that all three procedures maintain a false discovery rate bounded above, often grossly, by ct (or c&amp;nbsp;/2). For both uncorre-lated and pairwise families of comparisons, the B-H technique is shown to have greater power than the Hochberg or Bonferroni procedures, and its power remains relatively stable as the number of comparisons becomes large, giving it an increasing advantage when many comparisons are involved. We recommend that results from NAEP State Assessments be reported using the B-H technique rather than the Bonferroni procedure. Two questions often asked about each of a set of observed comparisons are: (a) should we be confident about the direction or the sign of the corresponding underlying population comparison, and (b) for what interval of values should we be confident that it contains the value for the population comparison?&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>10</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Boyce, D. E.</style></author><author><style face="normal" font="default" size="100%">Lee, D.-H.</style></author><author><style face="normal" font="default" size="100%">Janson, B.N.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Variational inequality Model of Ideal Dynamic User-Optimal Route Choice</style></title><secondary-title><style face="normal" font="default" size="100%">Transportation Networks: Recent Methodological Advances. Selected Proceedings of the 4th EURO Transportation Meeting</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Advanced traffic management systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Advanced Traveler Information Systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Links (Networks)</style></keyword><keyword><style  face="normal" font="default" size="100%">Route choice</style></keyword><keyword><style  face="normal" font="default" size="100%">Variational inequalities (Mathematics)</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1999</style></year></dates><pub-location><style face="normal" font="default" size="100%">Newcastle, England</style></pub-location><pages><style face="normal" font="default" size="100%">289-302</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;An ideal dynamic user-optimal (DUO) route choice model is described for predicting dynamic traffic conditions, as required for off-line evaluation of Advanced Traffic Management Systems and Advanced Traveler Information Systems. The model is formulated as a variational inequality (VI), a general way of describing a dynamic network equilibrium. Although route-based VI models have an intuitive interpretation, their computational complexity makes them intractable for real applications. Consequently, the proposed model is formulated as a link-based variational inequality for use in large-scale implementations. Using the diagonalization technique with discrete time intervals, the model is solved to a specified level of convergence. Computational results for a real, large-scale traffic network are presented.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">M. Schonlau</style></author><author><style face="normal" font="default" size="100%">Welch, William J.</style></author><author><style face="normal" font="default" size="100%">Jones, Donald R.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Global versus Local Search in Constrained Optimization of Computer Models</style></title><secondary-title><style face="normal" font="default" size="100%">Lecture Notes-Monograph Series</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bayesian global optimization</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer code</style></keyword><keyword><style  face="normal" font="default" size="100%">sequential design</style></keyword><keyword><style  face="normal" font="default" size="100%">Stochastic process</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">1998</style></year></dates><volume><style face="normal" font="default" size="100%">34</style></volume><pages><style face="normal" font="default" size="100%">11-25</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Engineering systems are now frequently optimized via computer models. The input-output relationships in these models are often highly nonlinear deterministic functions that are expensive to compute. Thus, when searching for the global optimum, it is desirable to minimize the number of function evaluations. Bayesian global optimization methods are well-suited to this task because they make use of all previous evaluations in selecting the next search point. A statistical model is fit to the sampled points which allows predictions to be made elsewhere, along with a measure of possible prediction error (uncertainty). The next point is chosen to maximize a criterion that balances searching where the predicted value of the function is good (local search) with searching where the uncertainty of prediction is large (global search). We extend this methodology in several ways. First, we introduce a parameter that controls the local-global balance. Secondly, we propose a method for dealing with nonlinear inequality constraints from additional response variables. Lastly, we adapt the sequential algorithm to proceed in stages rather than one point at a time. The extensions are illustrated using a shape optimization problem from the automotive industry.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>5</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Boyce, D. E.</style></author><author><style face="normal" font="default" size="100%">Lee, D.-H.</style></author><author><style face="normal" font="default" size="100%">Janson, B.N.</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">Beckmann, Martin J.</style></author><author><style face="normal" font="default" size="100%">Johannsson, Börje</style></author><author><style face="normal" font="default" size="100%">Snickars, Folke</style></author><author><style face="normal" font="default" size="100%">Thord, Roland</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Roadway Incident Analysis with a Dynamic User-Optimal Route Choice Model</style></title><secondary-title><style face="normal" font="default" size="100%">Knowledge and Networks in a Dynamic Economy</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">1998</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1007/978-3-642-60318-1_21</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Springer Berlin Heidelberg</style></publisher><pages><style face="normal" font="default" size="100%">371-390</style></pages><isbn><style face="normal" font="default" size="100%">978-3-642-64350-7</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The transportation system conveys interdependencies. When analysing the costs and benefits of transport investment projects, it is therefore necessary to address the question of linkages among projects. Such linkages can occur in terms of economies of scale in arising from the combination of projects during the construction phase. Intelligent Transportation Systems (ITS), also known as Intelligent Vehicle Highway Systems (IVHS), are applying advanced technologies (such as navigation, automobile, computer science, telecommunication, electronic engineering, automatic information collection and processing) in an effort to bring revolutionary improvements in traffic safety, network capacity utilization, vehicle emission reductions, travel time and fuel consumption savings, etc. Within the framework of ITS, Advanced Traffic Management Systems (ATMS) and Advanced Traveler Information Systems (ATIS) both aim to manage and predict traffic congestion and provide historical and real time network-wide traffic information to support drivers’ route choice decisions. To enable ATMS/ATIS to achieve the above described goals, traffic flow prediction models are needed for system operation and evaluation. Linkages may also arise in supply through interaction among network components, or among the producers of transportation services. Linkages may also emerge in demand through the creation of new opportunities for interaction.&lt;/p&gt;
</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">S. Jaiswal</style></author><author><style face="normal" font="default" size="100%">T. Igusa</style></author><author><style face="normal" font="default" size="100%">T. Styer</style></author><author><style face="normal" font="default" size="100%">A. F. Karr</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Influence of microstructure and fracture on the transport properties in cement-based materials</style></title><secondary-title><style face="normal" font="default" size="100%">Brittle Matrix Composites - International Symposium</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">1997</style></year></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">199-220</style></pages><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">K. Wang</style></author><author><style face="normal" font="default" size="100%">D.C. Jansen</style></author><author><style face="normal" font="default" size="100%">S. P. Shah</style></author><author><style face="normal" font="default" size="100%">A. F. Karr</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Permeability study of cracked concrete</style></title><secondary-title><style face="normal" font="default" size="100%">Cement Concrete Res.</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">1997</style></year></dates><volume><style face="normal" font="default" size="100%">27</style></volume><pages><style face="normal" font="default" size="100%">381-393</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Cracks in concrete generally interconnect flow paths and increase concrete permeability. The increase in concrete permeability due to the progression of cracks allows more water or aggressive chemical ions to penetrate into the concrete, facilitating deterioration. The present work studies the relationship between crack characteristics and concrete permeability. In this study, feedback controlled splitting tests are introduced to generate crack width-controlled concrete specimens. Sequential crack patterns with different crack widths are viewed under a microscope. The permeability of cracked concrete is evaluated by water permeability tests. The preliminary results indicate that crack openings generally accelerate water flow rate in concrete. When a specimen is loaded to have a crack opening displacement smaller than 50 microns prior to unloading, the crack opening has little effect on concrete permeability. When the crack opening displacement increases from 50 microns to about 200 microns, concrete permeability increases rapidly. After the crack opening displacement reaches 200 microns, the rate of water permeability increases steadily. The present research may provide insight into developing design criteria for a durable concrete and in predicting service life of a concrete structure.&lt;/p&gt;
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