Multisensory Integration Strategy for Modality-Specific Loss of Inhibition Control in Older Adults.

PubMed

Lee, Ahreum; Ryu, Hokyoung; Kim, Jae-Kwan; Jeong, Eunju

2018-04-11

Older adults are known to have lesser cognitive control capability and greater susceptibility to distraction than young adults. Previous studies have reported age-related problems in selective attention and inhibitory control, yielding mixed results depending on modality and context in which stimuli and tasks were presented. The purpose of the study was to empirically demonstrate a modality-specific loss of inhibitory control in processing audio-visual information with ageing. A group of 30 young adults (mean age = 25.23, Standar Desviation (SD) = 1.86) and 22 older adults (mean age = 55.91, SD = 4.92) performed the audio-visual contour identification task (AV-CIT). We compared performance of visual/auditory identification (Uni-V, Uni-A) with that of visual/auditory identification in the presence of distraction in counterpart modality (Multi-V, Multi-A). The findings showed a modality-specific effect on inhibitory control. Uni-V performance was significantly better than Multi-V, indicating that auditory distraction significantly hampered visual target identification. However, Multi-A performance was significantly enhanced compared to Uni-A, indicating that auditory target performance was significantly enhanced by visual distraction. Additional analysis showed an age-specific effect on enhancement between Uni-A and Multi-A depending on the level of visual inhibition. Together, our findings indicated that the loss of visual inhibitory control was beneficial for the auditory target identification presented in a multimodal context in older adults. A likely multisensory information processing strategy in the older adults was further discussed in relation to aged cognition.

Identification of ground targets from airborne platforms

NASA Astrophysics Data System (ADS)

Doe, Josh; Boettcher, Evelyn; Miller, Brian

2009-05-01

The US Army RDECOM CERDEC Night Vision and Electronic Sensors Directorate (NVESD) sensor performance models predict the ability of soldiers to perform a specified military discrimination task using an EO/IR sensor system. Increasingly EO/IR systems are being used on manned and un-manned aircraft for surveillance and target acquisition tasks. In response to this emerging requirement, the NVESD Modeling and Simulation division has been tasked to compare target identification performance between ground-to-ground and air-to-ground platforms for both IR and visible spectra for a set of wheeled utility vehicles. To measure performance, several forced choice experiments were designed and administered and the results analyzed. This paper describes these experiments and reports the results as well as the NVTherm model calibration factors derived for the infrared imagery.

ERPs reveal subliminal processing of fearful faces.

PubMed

Kiss, Monika; Eimer, Martin

2008-03-01

To investigate whether facial expression is processed in the absence of conscious awareness, ERPs were recorded in a task in which participants had to identify the expression of masked fearful and neutral target faces. On supraliminal trials (200 ms target duration), in which identification performance was high, a sustained positivity to fearful versus neutral target faces started 140 ms after target face onset. On subliminal trials (8 ms target duration), identification performance was at chance level, but ERPs still showed systematic fear-specific effects. An early positivity to fearful target faces was present but smaller than on supraliminal trials. A subsequent enhanced N2 to fearful faces was only present for subliminal trials. In contrast, a P3 enhancement to fearful faces was observed on supraliminal but not subliminal trials. Results demonstrate rapid emotional expression processing in the absence of awareness.

ERPs reveal subliminal processing of fearful faces

PubMed Central

Kiss, Monika; Eimer, Martin

2008-01-01

To investigate whether facial expression is processed in the absence of conscious awareness, ERPs were recorded in a task where participants had to identify the expression of masked fearful and neutral target faces. On supraliminal trials (200 ms target duration), where identification performance was high, a sustained positivity to fearful versus neutral target faces started 140 ms after target face onset. On subliminal trials (8 ms target duration), identification performance was at chance level, but ERPs still showed systematic fear-specific effects. An early positivity to fearful target faces was present but smaller than on supraliminal trials. A subsequent enhanced N2 to fearful faces was only present for subliminal trials. In contrast, a P3 enhancement to fearful faces was observed on supraliminal but not subliminal trials. Results demonstrate rapid emotional expression processing in the absence of awareness. PMID:17995905

Plant microRNA-Target Interaction Identification Model Based on the Integration of Prediction Tools and Support Vector Machine

PubMed Central

Meng, Jun; Shi, Lin; Luan, Yushi

2014-01-01

Background Confident identification of microRNA-target interactions is significant for studying the function of microRNA (miRNA). Although some computational miRNA target prediction methods have been proposed for plants, results of various methods tend to be inconsistent and usually lead to more false positive. To address these issues, we developed an integrated model for identifying plant miRNA–target interactions. Results Three online miRNA target prediction toolkits and machine learning algorithms were integrated to identify and analyze Arabidopsis thaliana miRNA-target interactions. Principle component analysis (PCA) feature extraction and self-training technology were introduced to improve the performance. Results showed that the proposed model outperformed the previously existing methods. The results were validated by using degradome sequencing supported Arabidopsis thaliana miRNA-target interactions. The proposed model constructed on Arabidopsis thaliana was run over Oryza sativa and Vitis vinifera to demonstrate that our model is effective for other plant species. Conclusions The integrated model of online predictors and local PCA-SVM classifier gained credible and high quality miRNA-target interactions. The supervised learning algorithm of PCA-SVM classifier was employed in plant miRNA target identification for the first time. Its performance can be substantially improved if more experimentally proved training samples are provided. PMID:25051153

Sleep and eyewitness memory: Fewer false identifications after sleep when the target is absent from the lineup.

PubMed

Stepan, Michelle E; Dehnke, Taylor M; Fenn, Kimberly M

2017-01-01

Inaccurate eyewitness identifications are the leading cause of known false convictions in the United States. Moreover, improving eyewitness memory is difficult and often unsuccessful. Sleep consistently strengthens and protects memory from interference, particularly when a recall test is used. However, the effect of sleep on recognition memory is more equivocal. Eyewitness identification tests are often recognition based, thus leaving open the question of how sleep affects recognition performance in an eyewitness context. In the current study, we investigated the effect of sleep on eyewitness memory. Participants watched a video of a mock-crime and attempted to identify the perpetrator from a simultaneous lineup after a 12-hour retention interval that either spanned a waking day or night of sleep. In Experiment 1, we used a target-present lineup and, in Experiment 2, we used a target-absent lineup in order to investigate correct and false identifications, respectively. Sleep reduced false identifications in the target-absent lineup (Experiment 2) but had no effect on correct identifications in the target-present lineup (Experiment 1). These results are discussed with respect to memory strength and decision making strategies.

Sleep and eyewitness memory: Fewer false identifications after sleep when the target is absent from the lineup

PubMed Central

Dehnke, Taylor M.; Fenn, Kimberly M.

2017-01-01

Inaccurate eyewitness identifications are the leading cause of known false convictions in the United States. Moreover, improving eyewitness memory is difficult and often unsuccessful. Sleep consistently strengthens and protects memory from interference, particularly when a recall test is used. However, the effect of sleep on recognition memory is more equivocal. Eyewitness identification tests are often recognition based, thus leaving open the question of how sleep affects recognition performance in an eyewitness context. In the current study, we investigated the effect of sleep on eyewitness memory. Participants watched a video of a mock-crime and attempted to identify the perpetrator from a simultaneous lineup after a 12-hour retention interval that either spanned a waking day or night of sleep. In Experiment 1, we used a target-present lineup and, in Experiment 2, we used a target-absent lineup in order to investigate correct and false identifications, respectively. Sleep reduced false identifications in the target-absent lineup (Experiment 2) but had no effect on correct identifications in the target-present lineup (Experiment 1). These results are discussed with respect to memory strength and decision making strategies. PMID:28877169

NCTR using a polarization-agile coherent radar system

NASA Astrophysics Data System (ADS)

Walton, E. K.; Moffatt, D. L.; Garber, F. D.; Kamis, A.; Lai, C. Y.

1986-01-01

This report describes the results of the first year of a research project performed by the Ohio State University ElectroScience Laboratory (OSU/ESL) for the Naval Weapons Center (NWC). The goal of this project is to explore the use of the polarization properties of the signal scattered from a radar target for the purpose of radar target identification. Various radar target identification algorithms were applied to the case of a full polarization coherent radar system, and were tested using a specific data base and noise model. The data base used to test the performance of the radar target identification algorithms developed here is a unique set of measurements made on scale models of aircraft. Measurements were made using the OSU/ESL Compact Radar Measurement Range. The range was operated in a broad-band (1-12 GHZ) mode and the full polarization matrix was measured. Calibrated values (amplitude and phase) of the RCS for the three polarization states were thus available. The polarization states are listed below.

Multisensory Integration Strategy for Modality-Specific Loss of Inhibition Control in Older Adults

PubMed Central

Ryu, Hokyoung; Kim, Jae-Kwan; Jeong, Eunju

2018-01-01

Older adults are known to have lesser cognitive control capability and greater susceptibility to distraction than young adults. Previous studies have reported age-related problems in selective attention and inhibitory control, yielding mixed results depending on modality and context in which stimuli and tasks were presented. The purpose of the study was to empirically demonstrate a modality-specific loss of inhibitory control in processing audio-visual information with ageing. A group of 30 young adults (mean age = 25.23, Standard Deviation (SD) = 1.86) and 22 older adults (mean age = 55.91, SD = 4.92) performed the audio-visual contour identification task (AV-CIT). We compared performance of visual/auditory identification (Uni-V, Uni-A) with that of visual/auditory identification in the presence of distraction in counterpart modality (Multi-V, Multi-A). The findings showed a modality-specific effect on inhibitory control. Uni-V performance was significantly better than Multi-V, indicating that auditory distraction significantly hampered visual target identification. However, Multi-A performance was significantly enhanced compared to Uni-A, indicating that auditory target performance was significantly enhanced by visual distraction. Additional analysis showed an age-specific effect on enhancement between Uni-A and Multi-A depending on the level of visual inhibition. Together, our findings indicated that the loss of visual inhibitory control was beneficial for the auditory target identification presented in a multimodal context in older adults. A likely multisensory information processing strategy in the older adults was further discussed in relation to aged cognition. PMID:29641462

Improved Targeting Through Collaborative Decision-Making and Brain Computer Interfaces

NASA Technical Reports Server (NTRS)

Stoica, Adrian; Barrero, David F.; McDonald-Maier, Klaus

2013-01-01

This paper reports a first step toward a brain-computer interface (BCI) for collaborative targeting. Specifically, we explore, from a broad perspective, how the collaboration of a group of people can increase the performance on a simple target identification task. To this end, we requested a group of people to identify the location and color of a sequence of targets appearing on the screen and measured the time and accuracy of the response. The individual results are compared to a collective identification result determined by simple majority voting, with random choice in case of drawn. The results are promising, as the identification becomes significantly more reliable even with this simple voting and a small number of people (either odd or even number) involved in the decision. In addition, the paper briefly analyzes the role of brain-computer interfaces in collaborative targeting, extending the targeting task by using a BCI instead of a mechanical response.

Modeling and performance of HF/OTH (High-Frequency/Over-the-Horizon) radar target identification systems

NASA Astrophysics Data System (ADS)

Strausberger, Donald J.

Several Radar Target Identification (RTI) techniques have been developed at The Ohio State University in recent years. Using the ElectroScience Laboratory compact range a large database of coherent RCS measurement has been constructed for several types of targets (aircraft, ships, and ground vehicles) at a variety of polarizations, aspect angles, and frequency bands. This extensive database has been used to analyze the performance of several different classification algorithms through the use of computer simulations. In order to optimize classification performance, it was concluded that the radar frequency range should lie in the Rayleigh-resonance frequency range, where the wavelength is on the order of or larger than the target size. For aircraft and ships with general dimensions on the order of 10 meters to 100 meters it is apparent that the High Frequency (HF) band provides optimal classification performance. Since existing HF radars are currently being used for detection and tracking or aircraft and ships of these dimensions, it is natural to further investigate the possibility of using these existing radars as the measurement devices in a radar target classification system.

Snapshot spectral and polarimetric imaging; target identification with multispectral video

NASA Astrophysics Data System (ADS)

Bartlett, Brent D.; Rodriguez, Mikel D.

2013-05-01

As the number of pixels continue to grow in consumer and scientific imaging devices, it has become feasible to collect the incident light field. In this paper, an imaging device developed around light field imaging is used to collect multispectral and polarimetric imagery in a snapshot fashion. The sensor is described and a video data set is shown highlighting the advantage of snapshot spectral imaging. Several novel computer vision approaches are applied to the video cubes to perform scene characterization and target identification. It is shown how the addition of spectral and polarimetric data to the video stream allows for multi-target identification and tracking not possible with traditional RGB video collection.

Device for detection and identification of carbon- and nitrogen-containing materials

DOEpatents

Karev, Alexander Ivanovich; Raevsky, Valery Georgievich; Dzhilavyan, Leonid Zavenovich; Laptev, Valery Dmitrievich; Pakhomov, Nikolay Ivanovich; Shvedunov, Vasily Ivanovich; Rykalin, Vladimir Ivanovich; Brothers, Louis Joseph; Wilhide, Larry K

2014-03-25

A device for detection and identification of carbon- and nitrogen-containing materials is described. In particular, the device performs the detection and identification of carbon- and nitrogen-containing materials by photo-nuclear detection. The device may comprise a race-track microtron, a breaking target, and a water-filled Cherenkov radiation counter.

Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server.

PubMed

Lee, Kyoungyeul; Lee, Minho; Kim, Dongsup

2017-12-28

The identification of target molecules is important for understanding the mechanism of "target deconvolution" in phenotypic screening and "polypharmacology" of drugs. Because conventional methods of identifying targets require time and cost, in-silico target identification has been considered an alternative solution. One of the well-known in-silico methods of identifying targets involves structure activity relationships (SARs). SARs have advantages such as low computational cost and high feasibility; however, the data dependency in the SAR approach causes imbalance of active data and ambiguity of inactive data throughout targets. We developed a ligand-based virtual screening model comprising 1121 target SAR models built using a random forest algorithm. The performance of each target model was tested by employing the ROC curve and the mean score using an internal five-fold cross validation. Moreover, recall rates for top-k targets were calculated to assess the performance of target ranking. A benchmark model using an optimized sampling method and parameters was examined via external validation set. The result shows recall rates of 67.6% and 73.9% for top-11 (1% of the total targets) and top-33, respectively. We provide a website for users to search the top-k targets for query ligands available publicly at http://rfqsar.kaist.ac.kr . The target models that we built can be used for both predicting the activity of ligands toward each target and ranking candidate targets for a query ligand using a unified scoring scheme. The scores are additionally fitted to the probability so that users can estimate how likely a ligand-target interaction is active. The user interface of our web site is user friendly and intuitive, offering useful information and cross references.

Proposed New Vision Standards for the 1980’s and Beyond: Contrast Sensitivity

DTIC Science & Technology

1981-09-01

spatial frequency, visual acuity, target aquistion, visual filters, spatial filtering, target detection, recognitio identification, eye charts, workload...visual standards, as well as other performance criteria, are required to be thown relevant to "real-world" performance before acceptance. On the sur- face

Stereotype Threat in Classroom Settings: The Interactive Effect of Domain Identification, Task Difficulty and Stereotype Threat on Female Students' Maths Performance

ERIC Educational Resources Information Center

Keller, Johannes

2007-01-01

Background: Stereotype threat research revealed that negative stereotypes can disrupt the performance of persons targeted by such stereotypes. This paper contributes to stereotype threat research by providing evidence that domain identification and the difficulty level of test items moderate stereotype threat effects on female students' maths…

A Camera-Based Target Detection and Positioning UAV System for Search and Rescue (SAR) Purposes

PubMed Central

Sun, Jingxuan; Li, Boyang; Jiang, Yifan; Wen, Chih-yung

2016-01-01

Wilderness search and rescue entails performing a wide-range of work in complex environments and large regions. Given the concerns inherent in large regions due to limited rescue distribution, unmanned aerial vehicle (UAV)-based frameworks are a promising platform for providing aerial imaging. In recent years, technological advances in areas such as micro-technology, sensors and navigation have influenced the various applications of UAVs. In this study, an all-in-one camera-based target detection and positioning system is developed and integrated into a fully autonomous fixed-wing UAV. The system presented in this paper is capable of on-board, real-time target identification, post-target identification and location and aerial image collection for further mapping applications. Its performance is examined using several simulated search and rescue missions, and the test results demonstrate its reliability and efficiency. PMID:27792156

A Camera-Based Target Detection and Positioning UAV System for Search and Rescue (SAR) Purposes.

PubMed

Sun, Jingxuan; Li, Boyang; Jiang, Yifan; Wen, Chih-Yung

2016-10-25

Wilderness search and rescue entails performing a wide-range of work in complex environments and large regions. Given the concerns inherent in large regions due to limited rescue distribution, unmanned aerial vehicle (UAV)-based frameworks are a promising platform for providing aerial imaging. In recent years, technological advances in areas such as micro-technology, sensors and navigation have influenced the various applications of UAVs. In this study, an all-in-one camera-based target detection and positioning system is developed and integrated into a fully autonomous fixed-wing UAV. The system presented in this paper is capable of on-board, real-time target identification, post-target identification and location and aerial image collection for further mapping applications. Its performance is examined using several simulated search and rescue missions, and the test results demonstrate its reliability and efficiency.

The role of driver age in performance and attention allocation effects of roadway sign count, format and familiarity.

PubMed

Zahabi, Maryam; Machado, Patricia; Pankok, Carl; Lau, Mei Ying; Liao, Yi-Fan; Hummer, Joseph; Rasdorf, William; Kaber, David B

2017-09-01

White-on-blue logo signs are used to inform drivers of food, gas, lodging, and attraction businesses at highway interchanges. In this study, 60 drivers were asked to look for food and attraction targets on logo signs while driving in a realistic freeway simulation. The objective of the study was to quantify effects of the number of sign panels (six vs. nine), logo familiarity (familiar vs. unfamiliar), logo format (text vs. pictorial), and driver age (young, middle, and elderly) on performance, attention allocation and target identification accuracy. Results revealed elderly drivers to exhibit worse performance in comparison to middle-age and young groups even though they adopted a more conservative driving strategy. There was no significant effect of the number of panels, logo familiarity, and logo format on driver performance or attention allocation. In target identification, drivers were more accurate with familiar or text-based panels appearing in six-panel signs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Driver landmark and traffic sign identification in early Alzheimer's disease.

PubMed

Uc, E Y; Rizzo, M; Anderson, S W; Shi, Q; Dawson, J D

2005-06-01

To assess visual search and recognition of roadside targets and safety errors during a landmark and traffic sign identification task in drivers with Alzheimer's disease. 33 drivers with probable Alzheimer's disease of mild severity and 137 neurologically normal older adults underwent a battery of visual and cognitive tests and were asked to report detection of specific landmarks and traffic signs along a segment of an experimental drive. The drivers with mild Alzheimer's disease identified significantly fewer landmarks and traffic signs and made more at-fault safety errors during the task than control subjects. Roadside target identification performance and safety errors were predicted by scores on standardised tests of visual and cognitive function. Drivers with Alzheimer's disease are impaired in a task of visual search and recognition of roadside targets; the demands of these targets on visual perception, attention, executive functions, and memory probably increase the cognitive load, worsening driving safety.

Cross-domain latent space projection for person re-identification

NASA Astrophysics Data System (ADS)

Pu, Nan; Wu, Song; Qian, Li; Xiao, Guoqiang

2018-04-01

In this paper, we research the problem of person re-identification and propose a cross-domain latent space projection (CDLSP) method to address the problems of the absence or insufficient labeled data in the target domain. Under the assumption that the visual features in the source domain and target domain share the similar geometric structure, we transform the visual features from source domain and target domain to a common latent space by optimizing the object function defined in the manifold alignment method. Moreover, the proposed object function takes into account the specific knowledge in the re-id with the aim to improve the performance of re-id under complex situations. Extensive experiments conducted on four benchmark datasets show the proposed CDLSP outperforms or is competitive with stateof- the-art methods for person re-identification.

Identification of active sources inside cavities using the equivalent source method-based free-field recovery technique

NASA Astrophysics Data System (ADS)

Bi, Chuan-Xing; Hu, Ding-Yu; Zhang, Yong-Bin; Jing, Wen-Qian

2015-06-01

In previous studies, an equivalent source method (ESM)-based technique for recovering the free sound field in a noisy environment has been successfully applied to exterior problems. In order to evaluate its performance when applied to a more general noisy environment, that technique is used to identify active sources inside cavities where the sound field is composed of the field radiated by active sources and that reflected by walls. A patch approach with two semi-closed surfaces covering the target active sources is presented to perform the measurements, and the field that would be radiated by these target active sources into free space is extracted from the mixed field by using the proposed technique, which will be further used as the input of nearfield acoustic holography for source identification. Simulation and experimental results validate the effectiveness of the proposed technique for source identification in cavities, and show the feasibility of performing the measurements with a double layer planar array.

Detection, recognition, identification, and tracking of military vehicles using biomimetic intelligence

NASA Astrophysics Data System (ADS)

Pace, Paul W.; Sutherland, John

2001-10-01

This project is aimed at analyzing EO/IR images to provide automatic target detection/recognition/identification (ATR/D/I) of militarily relevant land targets. An increase in performance was accomplished using a biomimetic intelligence system functioning on low-cost, commercially available processing chips. Biomimetic intelligence has demonstrated advanced capabilities in the areas of hand- printed character recognition, real-time detection/identification of multiple faces in full 3D perspectives in cluttered environments, advanced capabilities in classification of ground-based military vehicles from SAR, and real-time ATR/D/I of ground-based military vehicles from EO/IR/HRR data in cluttered environments. The investigation applied these tools to real data sets and examined the parameters such as the minimum resolution for target recognition, the effect of target size, rotation, line-of-sight changes, contrast, partial obscuring, background clutter etc. The results demonstrated a real-time ATR/D/I capability against a subset of militarily relevant land targets operating in a realistic scenario. Typical results on the initial EO/IR data indicate probabilities of correct classification of resolved targets to be greater than 95 percent.

Identification and Therapeutic Targeting of Paracrine Senescence Factors in the Prostate Tumor Microenvironment

DTIC Science & Technology

2011-03-01

UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING...leading cause of cancer death in men in the United States - could be prevented with more effective treatments. Overcoming tumor cell resistance to...as described in prior reports. Recent work has focused on identification of possible functional effects of altered STC1 levels in the prostate tumor

Evidence for Deficits in the Temporal Attention Span of Poor Readers

PubMed Central

Visser, Troy A. W.

2014-01-01

Background While poor reading is often associated with phonological deficits, many studies suggest that visual processing might also be impaired. In particular, recent research has indicated that poor readers show impaired spatial visual attention spans in partial and whole report tasks. Given the similarities between competition-based accounts for reduced visual attention span and similar explanations for impairments in sequential object processing, the present work examined whether poor readers show deficits in their “temporal attention span” – that is, their ability to rapidly and accurately process sequences of consecutive target items. Methodology/Principal Findings Poor and normal readers monitored a sequential stream of visual items for two (TT condition) or three (TTT condition) consecutive target digits. Target identification was examined using both unconditional and conditional measures of accuracy in order to gauge the overall likelihood of identifying a target and the likelihood of identifying a target given successful identification of previous items. Compared to normal readers, poor readers showed small but consistent deficits in identification across targets whether unconditional or conditional accuracy was used. Additionally, in the TTT condition, final-target conditional accuracy was poorer than unconditional accuracy, particularly for poor readers, suggesting a substantial cost arising from processing the previous two targets that was not present in normal readers. Conclusions/Significance Mirroring the differences found between poor and normal readers in spatial visual attention span, the present findings suggest two principal differences between the temporal attention spans of poor and normal readers. First, the consistent pattern of reduced performance across targets suggests increased competition amongst items within the same span for poor readers. Second, the steeper decline in final target performance amongst poor readers in the TTT condition suggests a reduction in the extent of their temporal attention span. PMID:24651313

Evidence for deficits in the temporal attention span of poor readers.

PubMed

Visser, Troy A W

2014-01-01

While poor reading is often associated with phonological deficits, many studies suggest that visual processing might also be impaired. In particular, recent research has indicated that poor readers show impaired spatial visual attention spans in partial and whole report tasks. Given the similarities between competition-based accounts for reduced visual attention span and similar explanations for impairments in sequential object processing, the present work examined whether poor readers show deficits in their "temporal attention span"--that is, their ability to rapidly and accurately process sequences of consecutive target items. Poor and normal readers monitored a sequential stream of visual items for two (TT condition) or three (TTT condition) consecutive target digits. Target identification was examined using both unconditional and conditional measures of accuracy in order to gauge the overall likelihood of identifying a target and the likelihood of identifying a target given successful identification of previous items. Compared to normal readers, poor readers showed small but consistent deficits in identification across targets whether unconditional or conditional accuracy was used. Additionally, in the TTT condition, final-target conditional accuracy was poorer than unconditional accuracy, particularly for poor readers, suggesting a substantial cost arising from processing the previous two targets that was not present in normal readers. Mirroring the differences found between poor and normal readers in spatial visual attention span, the present findings suggest two principal differences between the temporal attention spans of poor and normal readers. First, the consistent pattern of reduced performance across targets suggests increased competition amongst items within the same span for poor readers. Second, the steeper decline in final target performance amongst poor readers in the TTT condition suggests a reduction in the extent of their temporal attention span.

Genome-wide identification of microRNA targets in the neglected disease pathogens of the genus Echinococcus.

PubMed

Macchiaroli, Natalia; Maldonado, Lucas L; Zarowiecki, Magdalena; Cucher, Marcela; Gismondi, María Inés; Kamenetzky, Laura; Rosenzvit, Mara Cecilia

2017-06-01

MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in biological processes such as development. MiRNAs silence target mRNAs by binding to complementary sequences in the 3'untranslated regions (3'UTRs). The parasitic helminths of the genus Echinococcus are the causative agents of echinococcosis, a zoonotic neglected disease. In previous work, we performed a comprehensive identification and characterization of Echinococcus miRNAs. However, current knowledge about their targets is limited. Since target prediction algorithms rely on complementarity between 3'UTRs and miRNA sequences, a major limitation is the lack of accurate sequence information of 3'UTR for most species including parasitic helminths. We performed RNA-seq and developed a pipeline that integrates the transcriptomic data with available genomic data of this parasite in order to identify 3'UTRs of Echinococcus canadensis. The high confidence set of 3'UTRs obtained allowed the prediction of miRNA targets in Echinococcus through a bioinformatic approach. We performed for the first time a comparative analysis of miRNA targets in Echinococcus and Taenia. We found that many evolutionarily conserved target sites in Echinococcus and Taenia may be functional and under selective pressure. Signaling pathways such as MAPK and Wnt were among the most represented pathways indicating miRNA roles in parasite growth and development. Genome-wide identification and characterization of miRNA target genes in Echinococcus provide valuable information to guide experimental studies in order to understand miRNA functions in the parasites biology. miRNAs involved in essential functions, especially those being absent in the host or showing sequence divergence with respect to host orthologs, might be considered as novel therapeutic targets for echinococcosis control. Copyright © 2017 Elsevier B.V. All rights reserved.

Performance analysis and prediction in triathlon.

PubMed

Ofoghi, Bahadorreza; Zeleznikow, John; Macmahon, Clare; Rehula, Jan; Dwyer, Dan B

2016-01-01

Performance in triathlon is dependent upon factors that include somatotype, physiological capacity, technical proficiency and race strategy. Given the multidisciplinary nature of triathlon and the interaction between each of the three race components, the identification of target split times that can be used to inform the design of training plans and race pacing strategies is a complex task. The present study uses machine learning techniques to analyse a large database of performances in Olympic distance triathlons (2008-2012). The analysis reveals patterns of performance in five components of triathlon (three race "legs" and two transitions) and the complex relationships between performance in each component and overall performance in a race. The results provide three perspectives on the relationship between performance in each component of triathlon and the final placing in a race. These perspectives allow the identification of target split times that are required to achieve a certain final place in a race and the opportunity to make evidence-based decisions about race tactics in order to optimise performance.

Target identification using Zernike moments and neural networks

NASA Astrophysics Data System (ADS)

Azimi-Sadjadi, Mahmood R.; Jamshidi, Arta A.; Nevis, Andrew J.

2001-10-01

The development of an underwater target identification algorithm capable of identifying various types of underwater targets, such as mines, under different environmental conditions pose many technical problems. Some of the contributing factors are: targets have diverse sizes, shapes and reflectivity properties. Target emplacement environment is variable; targets may be proud or partially buried. Environmental properties vary significantly from one location to another. Bottom features such as sand, rocks, corals, and vegetation can conceal a target whether it is partially buried or proud. Competing clutter with responses that closely resemble those of the targets may lead to false positives. All the problems mentioned above contribute to overly difficult and challenging conditions that could lead to unreliable algorithm performance with existing methods. In this paper, we developed and tested a shape-dependent feature extraction scheme that provides features invariant to rotation, size scaling and translation; properties that are extremely useful for any target classification problem. The developed schemes were tested on an electro-optical imagery data set collected under different environmental conditions with variable background, range and target types. The electro-optic data set was collected using a Laser Line Scan (LLS) sensor by the Coastal Systems Station (CSS), located in Panama City, Florida. The performance of the developed scheme and its robustness to distortion, rotation, scaling and translation was also studied.

Fostering group identification and creativity in diverse groups: the role of individuation and self-verification.

PubMed

Swann, William B; Kwan, Virginia S Y; Polzer, Jeffrey T; Milton, Laurie P

2003-11-01

A longitudinal study examined the interplay of identity negotiation processes and diversity in small groups of master's of business administration (MBA) students. When perceivers formed relatively positive impressions of other group members, higher diversity predicted more individuation of targets. When perceivers formed relatively neutral impressions of other group members, however, higher diversity predicted less individuation of targets. Individuation at the outset of the semester predicted self-verification effects several weeks later, and self-verification, in turn, predicted group identification and creative task performance. The authors conclude that contrary to self-categorization theory, fostering individuation and self-verification in diverse groups may maximize group identification and productivity.

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets.

PubMed

Savitski, Mikhail M; Wilhelm, Mathias; Hahne, Hannes; Kuster, Bernhard; Bantscheff, Marcus

2015-09-01

Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there are strong differences in opinion regarding the conceptual validity of a protein FDR and no consensus regarding the methodology for protein FDR determination. There are also limitations inherent to the widely used classic target-decoy strategy that particularly show when analyzing very large data sets and that lead to a strong over-representation of decoy identifications. In this study, we investigated the merits of the classic, as well as a novel target-decoy-based protein FDR estimation approach, taking advantage of a heterogeneous data collection comprised of ∼19,000 LC-MS/MS runs deposited in ProteomicsDB (https://www.proteomicsdb.org). The "picked" protein FDR approach treats target and decoy sequences of the same protein as a pair rather than as individual entities and chooses either the target or the decoy sequence depending on which receives the highest score. We investigated the performance of this approach in combination with q-value based peptide scoring to normalize sample-, instrument-, and search engine-specific differences. The "picked" target-decoy strategy performed best when protein scoring was based on the best peptide q-value for each protein yielding a stable number of true positive protein identifications over a wide range of q-value thresholds. We show that this simple and unbiased strategy eliminates a conceptual issue in the commonly used "classic" protein FDR approach that causes overprediction of false-positive protein identification in large data sets. The approach scales from small to very large data sets without losing performance, consistently increases the number of true-positive protein identifications and is readily implemented in proteomics analysis software. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Optical Quality, Threshold Target Identification, and Military Target Task Performance After Advanced Keratorefractive Surgery

DTIC Science & Technology

2012-05-01

undergo wavefront-guided (WFG) photorefractive keratectomy ( PRK ), WFG laser in situ keratomileusis ( LASIK ), wavefront optimized (WFO) PRK or WFO...Military, Refractive Surgery, PRK , LASIK , Night Vision, Wavefront Optimized, Wavefront Guided, Visual Performance, Quality of Vision, Outcomes...military. In a prospective, randomized treatment trial we will enroll 224 nearsighted soldiers to WFG photorefractive keratectomy ( PRK ), WFG LASIK , WFO PRK

Optical Quality and Threshold Target Identification and Military Target Task Performance after Advanced Keratorefractive Surgery

DTIC Science & Technology

2013-05-01

and Sensors Directorate. • Study participants and physicians select treatment: PRK or LASIK . WFG vs . WFO treatment modality is randomized. The...to undergo wavefront-guided (WFG) photorefractive keratectomy ( PRK ), WFG laser in situ keratomileusis ( LASIK ), wavefront optimized (WFO) PRK or WFO...TERMS Military, Refractive Surgery, PRK , LASIK , Night Vision, Wavefront Optimized, Wavefront Guided, Visual Performance, Quality of Vision, Outcomes

Optical Quality, Threshold Target Identification and Military Target Task Performance After Advanced Keratorefractive Surgery

DTIC Science & Technology

2010-05-01

PRK vs . LASIK ) will no longer randomized but rather the patient a...commercial workstation & software. Analysis will determine the effect on visual performance of the different treatments (WFO PRK vs . WFO LASIK vs . WFG PRK ...Overall objective. To determine the effect of two types of wavefront modalities (WFG vs . WFO) and two types of refractive surgery ( PRK vs . LASIK )

Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing.

PubMed

Lim, Hansaim; Poleksic, Aleksandar; Yao, Yuan; Tong, Hanghang; He, Di; Zhuang, Luke; Meng, Patrick; Xie, Lei

2016-10-01

Target-based screening is one of the major approaches in drug discovery. Besides the intended target, unexpected drug off-target interactions often occur, and many of them have not been recognized and characterized. The off-target interactions can be responsible for either therapeutic or side effects. Thus, identifying the genome-wide off-targets of lead compounds or existing drugs will be critical for designing effective and safe drugs, and providing new opportunities for drug repurposing. Although many computational methods have been developed to predict drug-target interactions, they are either less accurate than the one that we are proposing here or computationally too intensive, thereby limiting their capability for large-scale off-target identification. In addition, the performances of most machine learning based algorithms have been mainly evaluated to predict off-target interactions in the same gene family for hundreds of chemicals. It is not clear how these algorithms perform in terms of detecting off-targets across gene families on a proteome scale. Here, we are presenting a fast and accurate off-target prediction method, REMAP, which is based on a dual regularized one-class collaborative filtering algorithm, to explore continuous chemical space, protein space, and their interactome on a large scale. When tested in a reliable, extensive, and cross-gene family benchmark, REMAP outperforms the state-of-the-art methods. Furthermore, REMAP is highly scalable. It can screen a dataset of 200 thousands chemicals against 20 thousands proteins within 2 hours. Using the reconstructed genome-wide target profile as the fingerprint of a chemical compound, we predicted that seven FDA-approved drugs can be repurposed as novel anti-cancer therapies. The anti-cancer activity of six of them is supported by experimental evidences. Thus, REMAP is a valuable addition to the existing in silico toolbox for drug target identification, drug repurposing, phenotypic screening, and side effect prediction. The software and benchmark are available at https://github.com/hansaimlim/REMAP.

Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing

PubMed Central

Poleksic, Aleksandar; Yao, Yuan; Tong, Hanghang; Meng, Patrick; Xie, Lei

2016-01-01

Target-based screening is one of the major approaches in drug discovery. Besides the intended target, unexpected drug off-target interactions often occur, and many of them have not been recognized and characterized. The off-target interactions can be responsible for either therapeutic or side effects. Thus, identifying the genome-wide off-targets of lead compounds or existing drugs will be critical for designing effective and safe drugs, and providing new opportunities for drug repurposing. Although many computational methods have been developed to predict drug-target interactions, they are either less accurate than the one that we are proposing here or computationally too intensive, thereby limiting their capability for large-scale off-target identification. In addition, the performances of most machine learning based algorithms have been mainly evaluated to predict off-target interactions in the same gene family for hundreds of chemicals. It is not clear how these algorithms perform in terms of detecting off-targets across gene families on a proteome scale. Here, we are presenting a fast and accurate off-target prediction method, REMAP, which is based on a dual regularized one-class collaborative filtering algorithm, to explore continuous chemical space, protein space, and their interactome on a large scale. When tested in a reliable, extensive, and cross-gene family benchmark, REMAP outperforms the state-of-the-art methods. Furthermore, REMAP is highly scalable. It can screen a dataset of 200 thousands chemicals against 20 thousands proteins within 2 hours. Using the reconstructed genome-wide target profile as the fingerprint of a chemical compound, we predicted that seven FDA-approved drugs can be repurposed as novel anti-cancer therapies. The anti-cancer activity of six of them is supported by experimental evidences. Thus, REMAP is a valuable addition to the existing in silico toolbox for drug target identification, drug repurposing, phenotypic screening, and side effect prediction. The software and benchmark are available at https://github.com/hansaimlim/REMAP. PMID:27716836

Mistaken identity of a PCR target proposed for identification of Mycoplasma bovis and the effect of sequence variation on assay performance

USDA-ARS?s Scientific Manuscript database

Background. Mycoplasma bovis is an important cause of disease in cattle and has recently emerged as a primary disease agent in bison. Because the bacterium requires specialized growth conditions many diagnostic laboratories use PCR to replace or complement traditional isolation and identification ...

Auditory Emotional Cues Enhance Visual Perception

ERIC Educational Resources Information Center

Zeelenberg, Rene; Bocanegra, Bruno R.

2010-01-01

Recent studies show that emotional stimuli impair performance to subsequently presented neutral stimuli. Here we show a cross-modal perceptual enhancement caused by emotional cues. Auditory cue words were followed by a visually presented neutral target word. Two-alternative forced-choice identification of the visual target was improved by…

New support vector machine-based method for microRNA target prediction.

PubMed

Li, L; Gao, Q; Mao, X; Cao, Y

2014-06-09

MicroRNA (miRNA) plays important roles in cell differentiation, proliferation, growth, mobility, and apoptosis. An accurate list of precise target genes is necessary in order to fully understand the importance of miRNAs in animal development and disease. Several computational methods have been proposed for miRNA target-gene identification. However, these methods still have limitations with respect to their sensitivity and accuracy. Thus, we developed a new miRNA target-prediction method based on the support vector machine (SVM) model. The model supplies information of two binding sites (primary and secondary) for a radial basis function kernel as a similarity measure for SVM features. The information is categorized based on structural, thermodynamic, and sequence conservation. Using high-confidence datasets selected from public miRNA target databases, we obtained a human miRNA target SVM classifier model with high performance and provided an efficient tool for human miRNA target gene identification. Experiments have shown that our method is a reliable tool for miRNA target-gene prediction, and a successful application of an SVM classifier. Compared with other methods, the method proposed here improves the sensitivity and accuracy of miRNA prediction. Its performance can be further improved by providing more training examples.

Utilization of volume correlation filters for underwater mine identification in LIDAR imagery

NASA Astrophysics Data System (ADS)

Walls, Bradley

2008-04-01

Underwater mine identification persists as a critical technology pursued aggressively by the Navy for fleet protection. As such, new and improved techniques must continue to be developed in order to provide measurable increases in mine identification performance and noticeable reductions in false alarm rates. In this paper we show how recent advances in the Volume Correlation Filter (VCF) developed for ground based LIDAR systems can be adapted to identify targets in underwater LIDAR imagery. Current automated target recognition (ATR) algorithms for underwater mine identification employ spatial based three-dimensional (3D) shape fitting of models to LIDAR data to identify common mine shapes consisting of the box, cylinder, hemisphere, truncated cone, wedge, and annulus. VCFs provide a promising alternative to these spatial techniques by correlating 3D models against the 3D rendered LIDAR data.

A comparison of machine learning techniques for detection of drug target articles.

PubMed

Danger, Roxana; Segura-Bedmar, Isabel; Martínez, Paloma; Rosso, Paolo

2010-12-01

Important progress in treating diseases has been possible thanks to the identification of drug targets. Drug targets are the molecular structures whose abnormal activity, associated to a disease, can be modified by drugs, improving the health of patients. Pharmaceutical industry needs to give priority to their identification and validation in order to reduce the long and costly drug development times. In the last two decades, our knowledge about drugs, their mechanisms of action and drug targets has rapidly increased. Nevertheless, most of this knowledge is hidden in millions of medical articles and textbooks. Extracting knowledge from this large amount of unstructured information is a laborious job, even for human experts. Drug target articles identification, a crucial first step toward the automatic extraction of information from texts, constitutes the aim of this paper. A comparison of several machine learning techniques has been performed in order to obtain a satisfactory classifier for detecting drug target articles using semantic information from biomedical resources such as the Unified Medical Language System. The best result has been achieved by a Fuzzy Lattice Reasoning classifier, which reaches 98% of ROC area measure. Copyright © 2010 Elsevier Inc. All rights reserved.

Optical Quality, Threshold Target Identification, and Military Target Task Performance After Advanced Keratorefractive Surgery

DTIC Science & Technology

2011-05-01

WFG) photorefractive keratectomy (PRK), WFG laser in situ keratomileusis ( LASIK ), wavefront optimized (WFO) PRK or WFO LASIK (56 in each group...design will enable comparison to preoperative performance as well as comparisons between treatment groups. Military, Refractive Surgery, PRK, LASIK ...randomized treatment trial we will enroll 224 nearsighted soldiers to WFG photorefractive keratectomy (PRK), WFG LASIK , WFO PRK or WFO LASIK (56 in

Tactile Cueing for Target Acquisition and Identification

DTIC Science & Technology

2005-09-01

method of coding tactile information, and the method of presenting elevation information were studied. Results: Subjects were divided into video game experienced...VGP) subjects and non- video game (NVGP) experienced subjects. VGPs showed a significantly lower’ target acquisition time with the 12...that video game players performed better with the highest level of tactile resolution, while non- video game players performed better with simpler pattern and a lower resolution display.

Building Face Composites Can Harm Lineup Identification Performance

ERIC Educational Resources Information Center

Wells, Gary L.; Charman, Steve D.; Olson, Elizabeth A.

2005-01-01

Face composite programs permit eyewitnesses to build likenesses of target faces by selecting facial features and combining them into an intact face. Research has shown that these composites are generally poor likenesses of the target face. Two experiments tested the proposition that this composite-building process could harm the builder's memory…

Postidentification Feedback Affects Subsequent Eyewitness Identification Performance

ERIC Educational Resources Information Center

Palmer, Matthew A.; Brewer, Neil; Weber, Nathan

2010-01-01

Eyewitnesses sometimes view more than one lineup during an investigation. We investigated the effects of postidentification feedback following one lineup on responses to a second lineup. Witnesses (N = 621) viewed a mock crime and, later, attempted to identify the culprit from an initial (target-absent) lineup and a second (target-present or…

Department of Defense Chemical, Biological, Radiological, and Nuclear Defense Program. FY2003-2005 Performance Plan

DTIC Science & Technology

2004-05-01

Agents (NTAs) Compare the direct effects of PAF on smooth muscle, hematic constituents, and lung to determine role in toxicity. Continue to...baselined. Long Range Biometric Target ID System Explore technologies for a long range biometric target identification system. 3.5.1.6

Signal detection theory applied to three visual search tasks--identification, yes/no detection and localization.

PubMed

Cameron, E Leslie; Tai, Joanna C; Eckstein, Miguel P; Carrasco, Marisa

2004-01-01

Adding distracters to a display impairs performance on visual tasks (i.e. the set-size effect). While keeping the display characteristics constant, we investigated this effect in three tasks: 2 target identification, yes-no detection with 2 targets, and 8-alternative localization. A Signal Detection Theory (SDT) model, tailored for each task, accounts for the set-size effects observed in identification and localization tasks, and slightly under-predicts the set-size effect in a detection task. Given that sensitivity varies as a function of spatial frequency (SF), we measured performance in each of these three tasks in neutral and peripheral precue conditions for each of six spatial frequencies (0.5-12 cpd). For all spatial frequencies tested, performance on the three tasks decreased as set size increased in the neutral precue condition, and the peripheral precue reduced the effect. Larger set-size effects were observed at low SFs in the identification and localization tasks. This effect can be described using the SDT model, but was not predicted by it. For each of these tasks we also established the extent to which covert attention modulates performance across a range of set sizes. A peripheral precue substantially diminished the set-size effect and improved performance, even at set size 1. These results provide support for distracter exclusion, and suggest that signal enhancement may also be a mechanism by which covert attention can impose its effect.

The relation between resource limitations and optional conceptual processing by children and adults.

PubMed

Ackerman, B P; Spiker, K; Bailey, K

1989-10-01

In some situations children fail to perform optional conceptual processing that they are able to perform. The purpose of the 4 experiments was to determine if the difficulty of word identification affects optional conceptual processing by second/third graders, fifth graders, and college students in a cued recall task. Conceptual processing was manipulated by presenting Hard (e.g., hawk eagle canary) or Easy (river lake canary) word triplets that varied in the contrastive processing necessary to identify the "odd" target word (canary). The orienting activity also varied: for the Oddity Choice activity, contrastive processing was obligatory because the subject had to identify the target; for the Read activity, contrastive processing was optional because the experimenter identified the target. A recall advantage for the Hard over the Easy triplets was the measure of contrastive processing. Finally, the difficulty of word identification varied in that the subjects read the stimuli or the experimenter read the stimuli, and all the words were degraded, only the nontarget words were degraded, or all the words were intact. The results established that contrastive processing facilitates recall, and that word identification difficulty may limit the extent of optional contrastive processing.

Choking under the pressure of a positive stereotype: gender identification and self-consciousness moderate men's math test performance.

PubMed

Tagler, Michael J

2012-01-01

Choking under pressure occurs when an individual underperforms due to situational pressure. The present study examined whether being the target of a positive social stereotype regarding math ability causes choking among men. Gender identification and self-consciousness were hypothesized to moderate the effect of math-gender stereotypes on men's math test performance. Men high in self-consciousness but low in gender identification significantly underperformed when exposed to gender-relevant test instructions. No significant effects were found under a gender-irrelevant condition. These findings are discussed in the contexts of research on stereotype threat, stereotype lift, and choking under pressure.

Rapid Identification of Mycobacteria and Drug-Resistant Mycobacterium tuberculosis by Use of a Single Multiplex PCR and DNA Sequencing

PubMed Central

Pérez-Osorio, Ailyn C.; Boyle, David S.; Ingham, Zachary K.; Ostash, Alla; Gautom, Romesh K.; Colombel, Craig; Houze, Yolanda

2012-01-01

Tuberculosis (TB) remains a significant global health problem for which rapid diagnosis is critical to both treatment and control. This report describes a multiplex PCR method, the Mycobacterial IDentification and Drug Resistance Screen (MID-DRS) assay, which allows identification of members of the Mycobacterium tuberculosis complex (MTBC) and the simultaneous amplification of targets for sequencing-based drug resistance screening of rifampin-resistant (rifampinr), isoniazidr, and pyrazinamider TB. Additionally, the same multiplex reaction amplifies a specific 16S rRNA gene target for rapid identification of M. avium complex (MAC) and a region of the heat shock protein 65 gene (hsp65) for further DNA sequencing-based confirmation or identification of other mycobacterial species. Comparison of preliminary results generated with MID-DRS versus culture-based methods for a total of 188 bacterial isolates demonstrated MID-DRS sensitivity and specificity as 100% and 96.8% for MTBC identification; 100% and 98.3% for MAC identification; 97.4% and 98.7% for rifampinr TB identification; 60.6% and 100% for isoniazidr TB identification; and 75.0% and 98.1% for pyrazinamider TB identification. The performance of the MID-DRS was also tested on acid-fast-bacterium (AFB)-positive clinical specimens, resulting in sensitivity and specificity of 100% and 78.6% for detection of MTBC and 100% and 97.8% for detection of MAC. In conclusion, use of the MID-DRS reduces the time necessary for initial identification and drug resistance screening of TB specimens to as little as 2 days. Since all targets needed for completing the assay are included in a single PCR amplification step, assay costs, preparation time, and risks due to user errors are also reduced. PMID:22162548

Experiment research on infrared targets signature in mid and long IR spectral bands

NASA Astrophysics Data System (ADS)

Wang, Chensheng; Hong, Pu; Lei, Bo; Yue, Song; Zhang, Zhijie; Ren, Tingting

2013-09-01

Since the infrared imaging system has played a significant role in the military self-defense system and fire control system, the radiation signature of IR target becomes an important topic in IR imaging application technology. IR target signature can be applied in target identification, especially for small and dim targets, as well as the target IR thermal design. To research and analyze the targets IR signature systematically, a practical and experimental project is processed under different backgrounds and conditions. An infrared radiation acquisition system based on a MWIR cooled thermal imager and a LWIR cooled thermal imager is developed to capture the digital infrared images. Furthermore, some instruments are introduced to provide other parameters. According to the original image data and the related parameters in a certain scene, the IR signature of interested target scene can be calculated. Different background and targets are measured with this approach, and a comparison experiment analysis shall be presented in this paper as an example. This practical experiment has proved the validation of this research work, and it is useful in detection performance evaluation and further target identification research.

EOID Model Validation and Performance Prediction

DTIC Science & Technology

2002-09-30

Our long-term goal is to accurately predict the capability of the current generation of laser-based underwater imaging sensors to perform Electro ... Optic Identification (EOID) against relevant targets in a variety of realistic environmental conditions. The two most prominent technologies in this area

Embodied memory allows accurate and stable perception of hidden objects despite orientation change.

PubMed

Pan, Jing Samantha; Bingham, Ned; Bingham, Geoffrey P

2017-07-01

Rotating a scene in a frontoparallel plane (rolling) yields a change in orientation of constituent images. When using only information provided by static images to perceive a scene after orientation change, identification performance typically decreases (Rock & Heimer, 1957). However, rolling generates optic flow information that relates the discrete, static images (before and after the change) and forms an embodied memory that aids recognition. The embodied memory hypothesis predicts that upon detecting a continuous spatial transformation of image structure, or in other words, seeing the continuous rolling process and objects undergoing rolling observers should accurately perceive objects during and after motion. Thus, in this case, orientation change should not affect performance. We tested this hypothesis in three experiments and found that (a) using combined optic flow and image structure, participants identified locations of previously perceived but currently occluded targets with great accuracy and stability (Experiment 1); (b) using combined optic flow and image structure information, participants identified hidden targets equally well with or without 30° orientation changes (Experiment 2); and (c) when the rolling was unseen, identification of hidden targets after orientation change became worse (Experiment 3). Furthermore, when rolling was unseen, although target identification was better when participants were told about the orientation change than when they were not told, performance was still worse than when there was no orientation change. Therefore, combined optic flow and image structure information, not mere knowledge about the rolling, enables accurate and stable perception despite orientation change. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Improving the Performance of an Auditory Brain-Computer Interface Using Virtual Sound Sources by Shortening Stimulus Onset Asynchrony

PubMed Central

Sugi, Miho; Hagimoto, Yutaka; Nambu, Isao; Gonzalez, Alejandro; Takei, Yoshinori; Yano, Shohei; Hokari, Haruhide; Wada, Yasuhiro

2018-01-01

Recently, a brain-computer interface (BCI) using virtual sound sources has been proposed for estimating user intention via electroencephalogram (EEG) in an oddball task. However, its performance is still insufficient for practical use. In this study, we examine the impact that shortening the stimulus onset asynchrony (SOA) has on this auditory BCI. While very short SOA might improve its performance, sound perception and task performance become difficult, and event-related potentials (ERPs) may not be induced if the SOA is too short. Therefore, we carried out behavioral and EEG experiments to determine the optimal SOA. In the experiments, participants were instructed to direct attention to one of six virtual sounds (target direction). We used eight different SOA conditions: 200, 300, 400, 500, 600, 700, 800, and 1,100 ms. In the behavioral experiment, we recorded participant behavioral responses to target direction and evaluated recognition performance of the stimuli. In all SOA conditions, recognition accuracy was over 85%, indicating that participants could recognize the target stimuli correctly. Next, using a silent counting task in the EEG experiment, we found significant differences between target and non-target sound directions in all but the 200-ms SOA condition. When we calculated an identification accuracy using Fisher discriminant analysis (FDA), the SOA could be shortened by 400 ms without decreasing the identification accuracies. Thus, improvements in performance (evaluated by BCI utility) could be achieved. On average, higher BCI utilities were obtained in the 400 and 500-ms SOA conditions. Thus, auditory BCI performance can be optimized for both behavioral and neurophysiological responses by shortening the SOA. PMID:29535602

Mistaken identity of an open reading frame proposed for PCR-based identification of Mycoplasma bovis and the effect of polymorphisms and insertions on assay performance

USDA-ARS?s Scientific Manuscript database

Mycoplasma bovis is an important cause of disease in cattle and bison. Because the bacterium requires specialized growth conditions many diagnostic laboratories routinely use PCR to replace or complement conventional isolation and identification methods. A frequently used target of such assays is th...

Reduced-order model for underwater target identification using proper orthogonal decomposition

NASA Astrophysics Data System (ADS)

Ramesh, Sai Sudha; Lim, Kian Meng

2017-03-01

Research on underwater acoustics has seen major development over the past decade due to its widespread applications in domains such as underwater communication/navigation (SONAR), seismic exploration and oceanography. In particular, acoustic signatures from partially or fully buried targets can be used in the identification of buried mines for mine counter measures (MCM). Although there exist several techniques to identify target properties based on SONAR images and acoustic signatures, these methods first employ a feature extraction method to represent the dominant characteristics of a data set, followed by the use of an appropriate classifier based on neural networks or the relevance vector machine. The aim of the present study is to demonstrate the applications of proper orthogonal decomposition (POD) technique in capturing dominant features of a set of scattered pressure signals, and subsequent use of the POD modes and coefficients in the identification of partially buried underwater target parameters such as its location, size and material density. Several numerical examples are presented to demonstrate the performance of the system identification method based on POD. Although the present study is based on 2D acoustic model, the method can be easily extended to 3D models and thereby enables cost-effective representations of large-scale data.

Working memory-driven attention improves spatial resolution: Support for perceptual enhancement.

PubMed

Pan, Yi; Luo, Qianying; Cheng, Min

2016-08-01

Previous research has indicated that attention can be biased toward those stimuli matching the contents of working memory and thereby facilitates visual processing at the location of the memory-matching stimuli. However, whether this working memory-driven attentional modulation takes place on early perceptual processes remains unclear. Our present results showed that working memory-driven attention improved identification of a brief Landolt target presented alone in the visual field. Because the suprathreshold target appeared without any external noise added (i.e., no distractors or masks), the results suggest that working memory-driven attention enhances the target signal at early perceptual stages of visual processing. Furthermore, given that performance in the Landolt target identification task indexes spatial resolution, this attentional facilitation indicates that working memory-driven attention can boost early perceptual processing via enhancement of spatial resolution at the attended location.

Concept development and needs identification for INFLO : report on stakeholder input on transformative goals, performance measures and high level user needs for INFLO.

DOT National Transportation Integrated Search

2012-04-01

The purpose of this report is to document the stakeholder input received at the February 8, 2012, stakeholder workshop at the Hall of States in Washington, D.C. on goals, performance measures, transformative performance targets, and high-level user n...

Millimeter wave sensor requirements for maritime small craft identification

NASA Astrophysics Data System (ADS)

Krapels, Keith; Driggers, Ronald G.; Garcia, Jose; Boettcher, Evelyn; Prather, Dennis; Schuetz, Chrisopher; Samluk, Jesse; Stein, Lee; Kiser, William; Visnansky, Andrew; Grata, Jeremy; Wikner, David; Harris, Russ

2009-09-01

Passive millimeter wave (mmW) imagers have improved in terms of resolution sensitivity and frame rate. Currently, the Office of Naval Research (ONR), along with the US Army Research, Development and Engineering Command, Communications Electronics Research Development and Engineering Center (RDECOM CERDEC) Night Vision and Electronic Sensor Directorate (NVESD), are investigating the current state-of-the-art of mmW imaging systems. The focus of this study was the performance of mmW imaging systems for the task of small watercraft / boat identification field performance. First mmW signatures were collected. This consisted of a set of eight small watercrafts; at 5 different aspects, during the daylight hours over a 48 hour period in the spring of 2008. Target characteristics were measured and characteristic dimension, signatures, and Root Sum Squared of Target's Temperature (RRSΔT) tabulated. Then an eight-alternative, forced choice (8AFC) human perception experiment was developed and conducted at NVESD. The ability of observers to discriminate between small watercraft was quantified. Next, the task difficulty criterion, V50, was quantified by applying this data to NVESD's target acquisition models using the Targeting Task Performance (TTP) metric. These parameters can be used to evaluate sensor field performance for Anti-Terrorism / Force Protection (AT/FP) and navigation tasks for the U.S. Navy, as well as for design and evaluation of imaging passive mmW sensors for both the U.S. Navy and U.S. Coast Guard.

Aided speech recognition in single-talker competition by elderly hearing-impaired listeners

NASA Astrophysics Data System (ADS)

Coughlin, Maureen; Humes, Larry

2004-05-01

This study examined the speech-identification performance in one-talker interference conditions that increased in complexity while audibility was ensured over a wide bandwidth (200-4000 Hz). Factorial combinations of three independent variables were used to vary the amount of informational masking. These variables were: (1) competition playback direction (forward or reverse); (2) gender match between target and competition talkers (same or different); and (3) target talker uncertainty (one of three possible talkers from trial to trial). Four groups of listeners, two elderly hearing-impaired groups differing in age (65-74 and 75-84 years) and two young normal-hearing groups, were tested. One of the groups of young normal-hearing listeners was tested under acoustically equivalent test conditions and one was tested under perceptually equivalent test conditions. The effect of each independent variable on speech-identification performance and informational masking was generally consistent with expectations. Group differences in the observed informational masking were most pronounced for the oldest group of hearing-impaired listeners. The eight measures of speech-identification performance were found to be strongly correlated with one another, and individual differences in speech understanding performance among the elderly were found to be associated with age and level of education. [Work supported, in part, by NIA.

Does a Flatter General Gradient of Visual Attention Explain Peripheral Advantages and Central Deficits in Deaf Adults?

PubMed Central

Samar, Vincent J.; Berger, Lauren

2017-01-01

Individuals deaf from early age often outperform hearing individuals in the visual periphery on attention-dependent dorsal stream tasks (e.g., spatial localization or movement detection), but sometimes show central visual attention deficits, usually on ventral stream object identification tasks. It has been proposed that early deafness adaptively redirects attentional resources from central to peripheral vision to monitor extrapersonal space in the absence of auditory cues, producing a more evenly distributed attention gradient across visual space. However, little direct evidence exists that peripheral advantages are functionally tied to central deficits, rather than determined by independent mechanisms, and previous studies using several attention tasks typically report peripheral advantages or central deficits, not both. To test the general altered attentional gradient proposal, we employed a novel divided attention paradigm that measured target localization performance along a gradient from parafoveal to peripheral locations, independent of concurrent central object identification performance in prelingually deaf and hearing groups who differed in access to auditory input. Deaf participants without cochlear implants (No-CI), with cochlear implants (CI), and hearing participants identified vehicles presented centrally, and concurrently reported the location of parafoveal (1.4°) and peripheral (13.3°) targets among distractors. No-CI participants but not CI participants showed a central identification accuracy deficit. However, all groups displayed equivalent target localization accuracy at peripheral and parafoveal locations and nearly parallel parafoveal-peripheral gradients. Furthermore, the No-CI group’s central identification deficit remained after statistically controlling peripheral performance; conversely, the parafoveal and peripheral group performance equivalencies remained after controlling central identification accuracy. These results suggest that, in the absence of auditory input, reduced central attentional capacity is not necessarily associated with enhanced peripheral attentional capacity or with flattening of a general attention gradient. Our findings converge with earlier studies suggesting that a general graded trade-off of attentional resources across the visual field does not adequately explain the complex task-dependent spatial distribution of deaf-hearing performance differences reported in the literature. Rather, growing evidence suggests that the spatial distribution of attention-mediated performance in deaf people is determined by sophisticated cross-modal plasticity mechanisms that recruit specific sensory and polymodal cortex to achieve specific compensatory processing goals. PMID:28559861

Comparison of the development of performance skills in ultrasound-guided regional anesthesia simulations with different phantom models.

PubMed

Liu, Yang; Glass, Nancy L; Glover, Chris D; Power, Robert W; Watcha, Mehernoor F

2013-12-01

Ultrasound-guided regional anesthesia (UGRA) skills are traditionally obtained by supervised performance on patients, but practice on phantom models improves success. Currently available models are expensive or use perishable products, for example, olive-in-chicken breasts (OCB). We constructed 2 inexpensive phantom (transparent and opaque) models with readily available nonperishable products and compared the process of learning UGRA skills by novice practitioners on these models with the OCB model. Three experts first established criteria for a satisfactory completion of the simulated UGRA task in the 3 models. Thirty-six novice trainees (<20 previous UGRA experience) were randomly assigned to perform a UGRA task on 1 of 3 models-the transparent, opaque, and OCB models, where the hyperechoic target was identified, a needle was advanced to it under ultrasound guidance, fluid was injected, and images were saved. We recorded the errors during task completion, number of attempts and needle passes, and the time for target identification and needle placement until the predetermined benchmark of 3 consecutive successful UGRA simulations was accomplished. The number of errors, needle passes, and time for task completion per attempt progressively decreased in all 3 groups. However, failure to identify the target and to visualize the needle on the ultrasound image occurred more frequently with the OCB model. The time to complete simulator training was shortest with the transparent model, owing to shorter target identification times. However, trainees were less likely to agree strongly that this model was realistic for teaching UGRA skills. Training on inexpensive synthetic simulation models with no perishable products permits learning of UGRA skills by novices. The OCB model has disadvantages of containing potentially infective material, requires refrigeration, cannot be used after multiple needle punctures, and is associated with more failures during simulated UGRA. Direct visualization of the target in the transparent model allows the trainee to focus on needle insertion skills, but the opaque model may be more realistic for learning target identification skills required when UGRA is performed on real patients in the operating room.

Visual Search in the Real World: Color Vision Deficiency Affects Peripheral Guidance, but Leaves Foveal Verification Largely Unaffected.

PubMed

Kugler, Günter; 't Hart, Bernard M; Kohlbecher, Stefan; Bartl, Klaus; Schumann, Frank; Einhäuser, Wolfgang; Schneider, Erich

2015-01-01

People with color vision deficiencies report numerous limitations in daily life, restricting, for example, their access to some professions. However, they use basic color terms systematically and in a similar manner as people with normal color vision. We hypothesize that a possible explanation for this discrepancy between color perception and behavioral consequences might be found in the gaze behavior of people with color vision deficiency. A group of participants with color vision deficiencies and a control group performed several search tasks in a naturalistic setting on a lawn. All participants wore a mobile eye-tracking-driven camera with a high foveal image resolution (EyeSeeCam). Search performance as well as fixations of objects of different colors were examined. Search performance was similar in both groups in a color-unrelated search task as well as in a search for yellow targets. While searching for red targets, participants with color vision deficiencies exhibited a strongly degraded performance. This was closely matched by the number of fixations on red objects shown by the two groups. Importantly, once they fixated a target, participants with color vision deficiencies exhibited only few identification errors. In contrast to controls, participants with color vision deficiencies are not able to enhance their search for red targets on a (green) lawn by an efficient guiding mechanism. The data indicate that the impaired guiding is the main influence on search performance, while foveal identification (verification) is largely unaffected by the color vision deficiency.

The impact of emotion on perception: bias or enhanced processing?

PubMed

Zeelenberg, René; Wagenmakers, Eric-Jan; Rotteveel, Mark

2006-04-01

Recent studies have shown that emotionally significant stimuli are often better identified than neutral stimuli. It is not clear, however, whether these results are due to enhanced perceptual processing or to a bias favoring the identification of emotionally significant stimuli over neutral stimuli. The present study used a two-alternative forced-choice perceptual identification task to disentangle the effects of bias and enhanced processing. We found that emotionally significant targets were better identified than neutral targets. In contrast, the emotional significance of the foil alternative had no effect on performance. The present results support the hypothesis that perceptual encoding of emotionally significant stimuli is enhanced.

Targeting Anti-Cancer Active Compounds: Affinity-Based Chromatographic Assays

PubMed Central

de Moraes, Marcela Cristina; Cardoso, Carmen Lucia; Seidl, Claudia; Moaddel, Ruin; Cass, Quezia Bezerra

2016-01-01

Affinity-based chromatography assays encompass the use of solid supports containing immobilized biological targets to monitor binding events in the isolation , identification and/or characterization of bioactive compounds. This powerful bioanalytical technique allows the screening of potential binders through fast analyses that can be directly performed using isolated substances or complex matrices. An overview of the recent researches in frontal and zonal affinity-based chromatography screening assays, which has been used as a tool in the identification and characterization of new anti-cancer agents, is discussed. In addition, a critical evaluation of the recently emerged ligands fishing assays in complex mixtures is also discussed. PMID:27306095

Microfluidic droplet enrichment for targeted sequencing

PubMed Central

Eastburn, Dennis J.; Huang, Yong; Pellegrino, Maurizio; Sciambi, Adam; Ptáček, Louis J.; Abate, Adam R.

2015-01-01

Targeted sequence enrichment enables better identification of genetic variation by providing increased sequencing coverage for genomic regions of interest. Here, we report the development of a new target enrichment technology that is highly differentiated from other approaches currently in use. Our method, MESA (Microfluidic droplet Enrichment for Sequence Analysis), isolates genomic DNA fragments in microfluidic droplets and performs TaqMan PCR reactions to identify droplets containing a desired target sequence. The TaqMan positive droplets are subsequently recovered via dielectrophoretic sorting, and the TaqMan amplicons are removed enzymatically prior to sequencing. We demonstrated the utility of this approach by generating an average 31.6-fold sequence enrichment across 250 kb of targeted genomic DNA from five unique genomic loci. Significantly, this enrichment enabled a more comprehensive identification of genetic polymorphisms within the targeted loci. MESA requires low amounts of input DNA, minimal prior locus sequence information and enriches the target region without PCR bias or artifacts. These features make it well suited for the study of genetic variation in a number of research and diagnostic applications. PMID:25873629

Automatic Target Recognition Based on Cross-Plot

PubMed Central

Wong, Kelvin Kian Loong; Abbott, Derek

2011-01-01

Automatic target recognition that relies on rapid feature extraction of real-time target from photo-realistic imaging will enable efficient identification of target patterns. To achieve this objective, Cross-plots of binary patterns are explored as potential signatures for the observed target by high-speed capture of the crucial spatial features using minimal computational resources. Target recognition was implemented based on the proposed pattern recognition concept and tested rigorously for its precision and recall performance. We conclude that Cross-plotting is able to produce a digital fingerprint of a target that correlates efficiently and effectively to signatures of patterns having its identity in a target repository. PMID:21980508

Identification-While-Scanning of a Multi-Aircraft Formation Based on Sparse Recovery for Narrowband Radar.

PubMed

Jiang, Yuan; Xu, Jia; Peng, Shi-Bao; Mao, Er-Ke; Long, Teng; Peng, Ying-Ning

2016-11-23

It is known that the identification performance of a multi-aircraft formation (MAF) of narrowband radar mainly depends on the time on target (TOT). To realize the identification task in one rotated scan with limited TOT, the paper proposes a novel identification-while-scanning (IWS) method based on sparse recovery to maintain high rotating speed and super-resolution for MAF identification, simultaneously. First, a multiple chirp signal model is established for MAF in a single scan, where different aircraft may have different Doppler centers and Doppler rates. Second, based on the sparsity of MAF in the Doppler parameter space, a novel hierarchical basis pursuit (HBP) method is proposed to obtain satisfactory sparse recovery performance as well as high computational efficiency. Furthermore, the parameter estimation performance of the proposed IWS identification method is analyzed with respect to recovery condition, signal-to-noise ratio and TOT. It is shown that an MAF can be effectively identified via HBP with a TOT of only about one hundred microseconds for IWS applications. Finally, some numerical experiment results are provided to demonstrate the effectiveness of the proposed method based on both simulated and real measured data.

Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification

PubMed Central

Ballester, Pedro J.; Mangold, Martina; Howard, Nigel I.; Robinson, Richard L. Marchese; Abell, Chris; Blumberger, Jochen; Mitchell, John B. O.

2012-01-01

One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated Ki ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification. PMID:22933186

Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification.

PubMed

Ballester, Pedro J; Mangold, Martina; Howard, Nigel I; Robinson, Richard L Marchese; Abell, Chris; Blumberger, Jochen; Mitchell, John B O

2012-12-07

One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated K(i) ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification.

Lineup identification by children: effects of clothing bias.

PubMed

Freire, Alejo; Lee, Kang; Williamson, Karen S; Stuart, Sarah J E; Lindsay, R C L

2004-06-01

This study examined effects of clothing cues on children's identification accuracy from lineups. Four- to 14-year-olds (n = 228) saw 12 video clips of individuals, each wearing a distinctly colored shirt. After watching each clip children were presented with a target-present or target-absent photo lineup. Three clothing conditions were included. In 2 conditions all lineup members wore the same colored shirt; in the third, biased condition, the shirt color of only one individual matched that seen in the preceding clip (the target in target-present trials and the replacement in target-absent trials). Correct identifications of the target in target-present trials were most frequent in the biased condition, whereas in target-absent trials the biased condition led to more false identifications of the target replacement. Older children were more accurate than younger children, both in choosing the target from target-present lineups and rejecting target-absent lineups. These findings suggest that a simple clothing cue such as shirt color can have a significant impact on children's lineup identification accuracy.

Lineup Identification by Children: Effects of Clothing Bias

PubMed Central

Freire, Alejo; Lee, Kang; Williamson, Karen S.; Stuart, Sarah J. E.; Lindsay, R. C. L.

2008-01-01

This study examined effects of clothing cues on children's identification accuracy from lineups. Four- to 14-year-olds (n = 228) saw 12 video clips of individuals, each wearing a distinctly colored shirt. After watching each clip children were presented with a target-present or target-absent photo lineup. Three clothing conditions were included. In 2 conditions all lineup members wore the same colored shirt; in the third, biased condition, the shirt color of only one individual matched that seen in the preceding clip (the target in target-present trials and the replacement in target-absent trials). Correct identifications of the target in target-present trials were most frequent in the biased condition, whereas in target-absent trials the biased condition led to more false identifications of the target replacement. Older children were more accurate than younger children, both in choosing the target from target-present lineups and rejecting target-absent lineups. These findings suggest that a simple clothing cue such as shirt color can have a significant impact on children's lineup identification accuracy. PMID:15264450

Autonomous target tracking of UAVs based on low-power neural network hardware

NASA Astrophysics Data System (ADS)

Yang, Wei; Jin, Zhanpeng; Thiem, Clare; Wysocki, Bryant; Shen, Dan; Chen, Genshe

2014-05-01

Detecting and identifying targets in unmanned aerial vehicle (UAV) images and videos have been challenging problems due to various types of image distortion. Moreover, the significantly high processing overhead of existing image/video processing techniques and the limited computing resources available on UAVs force most of the processing tasks to be performed by the ground control station (GCS) in an off-line manner. In order to achieve fast and autonomous target identification on UAVs, it is thus imperative to investigate novel processing paradigms that can fulfill the real-time processing requirements, while fitting the size, weight, and power (SWaP) constrained environment. In this paper, we present a new autonomous target identification approach on UAVs, leveraging the emerging neuromorphic hardware which is capable of massively parallel pattern recognition processing and demands only a limited level of power consumption. A proof-of-concept prototype was developed based on a micro-UAV platform (Parrot AR Drone) and the CogniMemTMneural network chip, for processing the video data acquired from a UAV camera on the y. The aim of this study was to demonstrate the feasibility and potential of incorporating emerging neuromorphic hardware into next-generation UAVs and their superior performance and power advantages towards the real-time, autonomous target tracking.

Fred Hutchinson Cancer Research Center (FHCRC1): Identification of Candidate Therapeutic Targets in Head and Neck Cancer Using Functional Kinomics | Office of Cancer Genomics

Cancer.gov

Kinome-wide siRNA screens targeting 713 human (MISSION® siRNA Human Gene Family Set, Sigma) were performed with viability as the phenotypic endpoint on five HNSCC lines: JHU-019; PCI15A and 15B; UM-SCC14A and 14C. Read the abstract

Fred Hutchinson Cancer Research Center (FHCRC-1): Identification of Candidate Therapeutic Targets in Head and Neck Cancer Using Functional Kinomics | Office of Cancer Genomics

Cancer.gov

Kinome-wide siRNA screens targeting 713 human (MISSION® siRNA Human Gene Family Set, Sigma) were performed with viability as the phenotypic endpoint on five HNSCC lines: JHU-019; PCI15A and 15B; UM-SCC14A and 14C. Read the abstract

Cancer Transcriptome Dataset Analysis: Comparing Methods of Pathway and Gene Regulatory Network-Based Cluster Identification.

PubMed

Nam, Seungyoon

2017-04-01

Cancer transcriptome analysis is one of the leading areas of Big Data science, biomarker, and pharmaceutical discovery, not to forget personalized medicine. Yet, cancer transcriptomics and postgenomic medicine require innovation in bioinformatics as well as comparison of the performance of available algorithms. In this data analytics context, the value of network generation and algorithms has been widely underscored for addressing the salient questions in cancer pathogenesis. Analysis of cancer trancriptome often results in complicated networks where identification of network modularity remains critical, for example, in delineating the "druggable" molecular targets. Network clustering is useful, but depends on the network topology in and of itself. Notably, the performance of different network-generating tools for network cluster (NC) identification has been little investigated to date. Hence, using gastric cancer (GC) transcriptomic datasets, we compared two algorithms for generating pathway versus gene regulatory network-based NCs, showing that the pathway-based approach better agrees with a reference set of cancer-functional contexts. Finally, by applying pathway-based NC identification to GC transcriptome datasets, we describe cancer NCs that associate with candidate therapeutic targets and biomarkers in GC. These observations collectively inform future research on cancer transcriptomics, drug discovery, and rational development of new analysis tools for optimal harnessing of omics data.

Modeling of video compression effects on target acquisition performance

NASA Astrophysics Data System (ADS)

Cha, Jae H.; Preece, Bradley; Espinola, Richard L.

2009-05-01

The effect of video compression on image quality was investigated from the perspective of target acquisition performance modeling. Human perception tests were conducted recently at the U.S. Army RDECOM CERDEC NVESD, measuring identification (ID) performance on simulated military vehicle targets at various ranges. These videos were compressed with different quality and/or quantization levels utilizing motion JPEG, motion JPEG2000, and MPEG-4 encoding. To model the degradation on task performance, the loss in image quality is fit to an equivalent Gaussian MTF scaled by the Structural Similarity Image Metric (SSIM). Residual compression artifacts are treated as 3-D spatio-temporal noise. This 3-D noise is found by taking the difference of the uncompressed frame, with the estimated equivalent blur applied, and the corresponding compressed frame. Results show good agreement between the experimental data and the model prediction. This method has led to a predictive performance model for video compression by correlating various compression levels to particular blur and noise input parameters for NVESD target acquisition performance model suite.

Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants.

PubMed

Meng, Yijun; Shao, Chaogang; Wang, Huizhong; Jin, Yongfeng

2012-05-21

MicroRNAs (miRNAs) play an essential role in gene regulation in plants. At the same time, the expression of miRNA genes is also tightly controlled. Recently, a novel mechanism called "target mimicry" was discovered, providing another layer for modulating miRNA activities. However, except for the artificial target mimics manipulated for functional studies on certain miRNA genes, only one example, IPS1 (Induced by Phosphate Starvation 1)-miR399 was experimentally confirmed in planta. To date, few analyses for comprehensive identification of natural target mimics have been performed in plants. Thus, limited evidences are available to provide detailed information for interrogating the questionable issue whether target mimicry was widespread in planta, and implicated in certain biological processes. In this study, genome-wide computational prediction of endogenous miRNA mimics was performed in Arabidopsis and rice, and dozens of target mimics were identified. In contrast to a recent report, the densities of target mimic sites were found to be much higher within the untranslated regions (UTRs) when compared to those within the coding sequences (CDSs) in both plants. Some novel sequence characteristics were observed for the miRNAs that were potentially regulated by the target mimics. GO (Gene Ontology) term enrichment analysis revealed some functional insights into the predicted mimics. After degradome sequencing data-based identification of miRNA targets, the regulatory networks constituted by target mimics, miRNAs and their downstream targets were constructed, and some intriguing subnetworks were further exploited. These results together suggest that target mimicry may be widely implicated in regulating miRNA activities in planta, and we hope this study could expand the current understanding of miRNA-involved regulatory networks.

Remote sensing based on hyperspectral data analysis

NASA Astrophysics Data System (ADS)

Sharifahmadian, Ershad

In remote sensing, accurate identification of far objects, especially concealed objects is difficult. In this study, to improve object detection from a distance, the hyperspecral imaging and wideband technology are employed with the emphasis on wideband radar. As the wideband data includes a broad range of frequencies, it can reveal information about both the surface of the object and its content. Two main contributions are made in this study: 1) Developing concept of return loss for target detection: Unlike typical radar detection methods which uses radar cross section to detect an object, it is possible to enhance the process of detection and identification of concealed targets using the wideband radar based on the electromagnetic characteristics --conductivity, permeability, permittivity, and return loss-- of materials. During the identification process, collected wideband data is evaluated with information from wideband signature library which has already been built. In fact, several classes (e.g. metal, wood, etc.) and subclasses (ex. metals with high conductivity) have been defined based on their electromagnetic characteristics. Materials in a scene are then classified based on these classes. As an example, materials with high electrical conductivity can be conveniently detected. In fact, increasing relative conductivity leads to a reduction in the return loss. Therefore, metals with high conductivity (ex. copper) shows stronger radar reflections compared with metals with low conductivity (ex. stainless steel). Thus, it is possible to appropriately discriminate copper from stainless steel. 2) Target recognition techniques: To detect and identify targets, several techniques have been proposed, in particular the Multi-Spectral Wideband Radar Image (MSWRI) which is able to localize and identify concealed targets. The MSWRI is based on the theory of robust capon beamformer. During identification process, information from wideband signature library is utilized. The WB signature library includes such parameters as conductivity, permeability, permittivity, and return loss at different frequencies for possible materials related to a target. In the MSWRI approach, identification procedure is performed by calculating the RLs at different selected frequencies. Based on similarity of the calculated RLs and RL from WB signature library, targets are detected and identified. Based on the simulation and experimental results, it is concluded that the MSWRI technique is a promising approach for standoff target detection.

Infrared detection, recognition and identification of handheld objects

NASA Astrophysics Data System (ADS)

Adomeit, Uwe

2012-10-01

A main criterion for comparison and selection of thermal imagers for military applications is their nominal range performance. This nominal range performance is calculated for a defined task and standardized target and environmental conditions. The only standardization available to date is STANAG 4347. The target defined there is based on a main battle tank in front view. Because of modified military requirements, this target is no longer up-to-date. Today, different topics of interest are of interest, especially differentiation between friend and foe and identification of humans. There is no direct way to differentiate between friend and foe in asymmetric scenarios, but one clue can be that someone is carrying a weapon. This clue can be transformed in the observer tasks detection: a person is carrying or is not carrying an object, recognition: the object is a long / medium / short range weapon or civil equipment and identification: the object can be named (e. g. AK-47, M-4, G36, RPG7, Axe, Shovel etc.). These tasks can be assessed experimentally and from the results of such an assessment, a standard target for handheld objects may be derived. For a first assessment, a human carrying 13 different handheld objects in front of his chest was recorded at four different ranges with an IR-dual-band camera. From the recorded data, a perception experiment was prepared. It was conducted with 17 observers in a 13-alternative forced choice, unlimited observation time arrangement. The results of the test together with Minimum Temperature Difference Perceived measurements of the camera and temperature difference and critical dimension derived from the recorded imagery allowed defining a first standard target according to the above tasks. This standard target consist of 2.5 / 3.5 / 5 DRI line pairs on target, 0.24 m critical size and 1 K temperature difference. The values are preliminary and have to be refined in the future. Necessary are different aspect angles, different carriage and movement.

OPTICAL correlation identification technology applied in underwater laser imaging target identification

NASA Astrophysics Data System (ADS)

Yao, Guang-tao; Zhang, Xiao-hui; Ge, Wei-long

2012-01-01

The underwater laser imaging detection is an effective method of detecting short distance target underwater as an important complement of sonar detection. With the development of underwater laser imaging technology and underwater vehicle technology, the underwater automatic target identification has gotten more and more attention, and is a research difficulty in the area of underwater optical imaging information processing. Today, underwater automatic target identification based on optical imaging is usually realized with the method of digital circuit software programming. The algorithm realization and control of this method is very flexible. However, the optical imaging information is 2D image even 3D image, the amount of imaging processing information is abundant, so the electronic hardware with pure digital algorithm will need long identification time and is hard to meet the demands of real-time identification. If adopt computer parallel processing, the identification speed can be improved, but it will increase complexity, size and power consumption. This paper attempts to apply optical correlation identification technology to realize underwater automatic target identification. The optics correlation identification technology utilizes the Fourier transform characteristic of Fourier lens which can accomplish Fourier transform of image information in the level of nanosecond, and optical space interconnection calculation has the features of parallel, high speed, large capacity and high resolution, combines the flexibility of calculation and control of digital circuit method to realize optoelectronic hybrid identification mode. We reduce theoretical formulation of correlation identification and analyze the principle of optical correlation identification, and write MATLAB simulation program. We adopt single frame image obtained in underwater range gating laser imaging to identify, and through identifying and locating the different positions of target, we can improve the speed and orientation efficiency of target identification effectively, and validate the feasibility of this method primarily.

Identification of Optimal Epitopes for Plasmodium falciparum Rapid Diagnostic Tests That Target Histidine-Rich Proteins 2 and 3

PubMed Central

Lee, Nelson; Gatton, Michelle L.; Pelecanos, Anita; Bubb, Martin; Gonzalez, Iveth; Bell, David; Cheng, Qin

2012-01-01

Rapid diagnostic tests (RDTs) represent important tools to diagnose malaria infection. To improve understanding of the variable performance of RDTs that detect the major target in Plasmodium falciparum, namely, histidine-rich protein 2 (HRP2), and to inform the design of better tests, we undertook detailed mapping of the epitopes recognized by eight HRP-specific monoclonal antibodies (MAbs). To investigate the geographic skewing of this polymorphic protein, we analyzed the distribution of these epitopes in parasites from geographically diverse areas. To identify an ideal amino acid motif for a MAb to target in HRP2 and in the related protein HRP3, we used a purpose-designed script to perform bioinformatic analysis of 448 distinct gene sequences from pfhrp2 and from 99 sequences from the closely related gene pfhrp3. The frequency and distribution of these motifs were also compared to the MAb epitopes. Heat stability testing of MAbs immobilized on nitrocellulose membranes was also performed. Results of these experiments enabled the identification of MAbs with the most desirable characteristics for inclusion in RDTs, including copy number and coverage of target epitopes, geographic skewing, heat stability, and match with the most abundant amino acid motifs identified. This study therefore informs the selection of MAbs to include in malaria RDTs as well as in the generation of improved MAbs that should improve the performance of HRP-detecting malaria RDTs. PMID:22259210

Naturalistic distraction and driving safety in older drivers.

PubMed

Aksan, Nazan; Dawson, Jeffrey D; Emerson, Jamie L; Yu, Lixi; Uc, Ergun Y; Anderson, Steven W; Rizzo, Matthew

2013-08-01

In this study, we aimed to quantify and compare performance of middle-aged and older drivers during a naturalistic distraction paradigm (visual search for roadside targets) and to predict older drivers performance given functioning in visual, motor, and cognitive domains. Distracted driving can imperil healthy adults and may disproportionally affect the safety of older drivers with visual, motor, and cognitive decline. A total of 203 drivers, 120 healthy older (61 men and 59 women, ages 65 years and older) and 83 middle-aged drivers (38 men and 45 women, ages 40 to 64 years), participated in an on-road test in an instrumented vehicle. Outcome measures included performance in roadside target identification (traffic signs and restaurants) and concurrent driver safety. Differences in visual, motor, and cognitive functioning served as predictors. Older drivers identified fewer landmarks and drove slower but committed more safety errors than did middle-aged drivers. Greater familiarity with local roads benefited performance of middle-aged but not older drivers.Visual cognition predicted both traffic sign identification and safety errors, and executive function predicted traffic sign identification over and above vision. Older adults are susceptible to driving safety errors while distracted by common secondary visual search tasks that are inherent to driving. The findings underscore that age-related cognitive decline affects older drivers' management of driving tasks at multiple levels and can help inform the design of on-road tests and interventions for older drivers.

Identification of chemogenomic features from drug–target interaction networks using interpretable classifiers

PubMed Central

Tabei, Yasuo; Pauwels, Edouard; Stoven, Véronique; Takemoto, Kazuhiro; Yamanishi, Yoshihiro

2012-01-01

Motivation: Drug effects are mainly caused by the interactions between drug molecules and their target proteins including primary targets and off-targets. Identification of the molecular mechanisms behind overall drug–target interactions is crucial in the drug design process. Results: We develop a classifier-based approach to identify chemogenomic features (the underlying associations between drug chemical substructures and protein domains) that are involved in drug–target interaction networks. We propose a novel algorithm for extracting informative chemogenomic features by using L1 regularized classifiers over the tensor product space of possible drug–target pairs. It is shown that the proposed method can extract a very limited number of chemogenomic features without loosing the performance of predicting drug–target interactions and the extracted features are biologically meaningful. The extracted substructure–domain association network enables us to suggest ligand chemical fragments specific for each protein domain and ligand core substructures important for a wide range of protein families. Availability: Softwares are available at the supplemental website. Contact: yamanishi@bioreg.kyushu-u.ac.jp Supplementary Information: Datasets and all results are available at http://cbio.ensmp.fr/~yyamanishi/l1binary/ . PMID:22962471

Target Acquisition: Human Observer Performance Studies and TARGAC Model Validation

DTIC Science & Technology

1994-06-01

complete Scenario I run were displayed on a monitor. A transparent sheet was attached to the face of the monitor, the approach route was sketched on...track, passed a mark on the monitor face , the target was at a stop-sign location. The IRIG-B time of that instance was noted, and, since the distance of...route right 100- 80- 60 - 40 C.) 20 [- ion, A20 recognitio 0 0 . identification,C.) . 1I . I - - -• , 4) 1000 2000 3000 4000 SP Target G Q Target I0

Visual Search in the Real World: Color Vision Deficiency Affects Peripheral Guidance, but Leaves Foveal Verification Largely Unaffected

PubMed Central

Kugler, Günter; 't Hart, Bernard M.; Kohlbecher, Stefan; Bartl, Klaus; Schumann, Frank; Einhäuser, Wolfgang; Schneider, Erich

2015-01-01

Background: People with color vision deficiencies report numerous limitations in daily life, restricting, for example, their access to some professions. However, they use basic color terms systematically and in a similar manner as people with normal color vision. We hypothesize that a possible explanation for this discrepancy between color perception and behavioral consequences might be found in the gaze behavior of people with color vision deficiency. Methods: A group of participants with color vision deficiencies and a control group performed several search tasks in a naturalistic setting on a lawn. All participants wore a mobile eye-tracking-driven camera with a high foveal image resolution (EyeSeeCam). Search performance as well as fixations of objects of different colors were examined. Results: Search performance was similar in both groups in a color-unrelated search task as well as in a search for yellow targets. While searching for red targets, participants with color vision deficiencies exhibited a strongly degraded performance. This was closely matched by the number of fixations on red objects shown by the two groups. Importantly, once they fixated a target, participants with color vision deficiencies exhibited only few identification errors. Conclusions: In contrast to controls, participants with color vision deficiencies are not able to enhance their search for red targets on a (green) lawn by an efficient guiding mechanism. The data indicate that the impaired guiding is the main influence on search performance, while foveal identification (verification) is largely unaffected by the color vision deficiency. PMID:26733851

Hit identification and optimization in virtual screening: practical recommendations based on a critical literature analysis.

PubMed

Zhu, Tian; Cao, Shuyi; Su, Pin-Chih; Patel, Ram; Shah, Darshan; Chokshi, Heta B; Szukala, Richard; Johnson, Michael E; Hevener, Kirk E

2013-09-12

A critical analysis of virtual screening results published between 2007 and 2011 was performed. The activity of reported hit compounds from over 400 studies was compared to their hit identification criteria. Hit rates and ligand efficiencies were calculated to assist in these analyses, and the results were compared with factors such as the size of the virtual library and the number of compounds tested. A series of promiscuity, druglike, and ADMET filters were applied to the reported hits to assess the quality of compounds reported, and a careful analysis of a subset of the studies that presented hit optimization was performed. These data allowed us to make several practical recommendations with respect to selection of compounds for experimental testing, definition of hit identification criteria, and general virtual screening hit criteria to allow for realistic hit optimization. A key recommendation is the use of size-targeted ligand efficiency values as hit identification criteria.

UAV-borne X-band radar for MAV collision avoidance

NASA Astrophysics Data System (ADS)

Moses, Allistair A.; Rutherford, Matthew J.; Kontitsis, Michail; Valavanis, Kimon P.

2011-05-01

Increased use of Miniature (Unmanned) Aerial Vehicles (MAVs) is coincidentally accompanied by a notable lack of sensors suitable for enabling further increases in levels of autonomy and consequently, integration into the National Airspace System (NAS). The majority of available sensors suitable for MAV integration are based on infrared detectors, focal plane arrays, optical and ultrasonic rangefinders, etc. These sensors are generally not able to detect or identify other MAV-sized targets and, when detection is possible, considerable computational power is typically required for successful identification. Furthermore, performance of visual-range optical sensor systems can suffer greatly when operating in the conditions that are typically encountered during search and rescue, surveillance, combat, and most common MAV applications. However, the addition of a miniature radar system can, in consort with other sensors, provide comprehensive target detection and identification capabilities for MAVs. This trend is observed in manned aviation where radar systems are the primary detection and identification sensor system. Within this document a miniature, lightweight X-Band radar system for use on a miniature (710mm rotor diameter) rotorcraft is described. We present analyses of the performance of the system in a realistic scenario with two MAVs. Additionally, an analysis of MAV navigation and collision avoidance behaviors is performed to determine the effect of integrating radar systems into MAV-class vehicles.

Isolation of Mycobacterium massiliense from a corneal biopsy in India.

PubMed

Kulandai, Lily Therese; Lakshmipathy, Dhanurekha; Ramasubban, Gayathri; Rao, Madhavan Hajib Narahari

2014-12-01

Rapidly growing mycobacteria (RGM) are ubiquitous and are usually considered as saprophytes, and have been recovered from the environment, particularly in dust, watery soil and water distribution systems. However, Mycobacterium massiliense is a rare causative agent of ocular infection. We report a case of M. massiliense in a 44-year-old female with signs and symptoms of a corneal ulcer. We carried out PCR-based DNA sequencing targeting the hsp 65 gene for the identification of M. massiliense . To confirm the identification, we also performed PCR-based RFLP targeting the hsp65 gene and PCR-based DNA sequencing targeting the internal transcribed spacer region, which showed 97 % nucleotide identity with M. massiliense . To the best of our knowledge, this is the first study in India to report the detection of M. massiliense from a corneal biopsy.

Building face composites can harm lineup identification performance.

PubMed

Wells, Gary L; Charman, Steve D; Olson, Elizabeth A

2005-09-01

Face composite programs permit eyewitnesses to build likenesses of target faces by selecting facial features and combining them into an intact face. Research has shown that these composites are generally poor likenesses of the target face. Two experiments tested the proposition that this composite-building process could harm the builder's memory for the face. In Experiment 1 (n = 150), the authors used 50 different faces and found that the building of a composite reduced the chances that the person could later identify the original face from a lineup when compared with no composite control conditions or with yoked composite-exposure control conditions. In Experiment 2 (n = 200), the authors found that this effect generalized to a simulated-crime video, but mistaken identifications from target-absent lineups were not inflated by composite building. Copyright 2005 APA, all rights reserved.

Network-assisted target identification for haploinsufficiency and homozygous profiling screens

PubMed Central

Wang, Sheng

2017-01-01

Chemical genomic screens have recently emerged as a systematic approach to drug discovery on a genome-wide scale. Drug target identification and elucidation of the mechanism of action (MoA) of hits from these noisy high-throughput screens remain difficult. Here, we present GIT (Genetic Interaction Network-Assisted Target Identification), a network analysis method for drug target identification in haploinsufficiency profiling (HIP) and homozygous profiling (HOP) screens. With the drug-induced phenotypic fitness defect of the deletion of a gene, GIT also incorporates the fitness defects of the gene’s neighbors in the genetic interaction network. On three genome-scale yeast chemical genomic screens, GIT substantially outperforms previous scoring methods on target identification on HIP and HOP assays, respectively. Finally, we showed that by combining HIP and HOP assays, GIT further boosts target identification and reveals potential drug’s mechanism of action. PMID:28574983

The confidence-accuracy relationship in eyewitness identification: effects of lineup instructions, foil similarity, and target-absent base rates.

PubMed

Brewer, Neil; Wells, Gary L

2006-03-01

Discriminating accurate from mistaken eyewitness identifications is a major issue facing criminal justice systems. This study examined whether eyewitness confidence assists such decisions under a variety of conditions using a confidence-accuracy (CA) calibration approach. Participants (N = 1,200) viewed a simulated crime and attempted 2 separate identifications from 8-person target-present or target-absent lineups. Confidence and accuracy were calibrated for choosers (but not nonchoosers) for both targets under all conditions. Lower overconfidence was associated with higher diagnosticity, lower target-absent base rates, and shorter identification latencies. Although researchers agree that courtroom expressions of confidence are uninformative, our findings indicate that confidence assessments obtained immediately after a positive identification can provide a useful guide for investigators about the likely accuracy of an identification.

Perceptual context and individual differences in the language proficiency of preschool children.

PubMed

Banai, Karen; Yifat, Rachel

2016-02-01

Although the contribution of perceptual processes to language skills during infancy is well recognized, the role of perception in linguistic processing beyond infancy is not well understood. In the experiments reported here, we asked whether manipulating the perceptual context in which stimuli are presented across trials influences how preschool children perform visual (shape-size identification; Experiment 1) and auditory (syllable identification; Experiment 2) tasks. Another goal was to determine whether the sensitivity to perceptual context can explain part of the variance in oral language skills in typically developing preschool children. Perceptual context was manipulated by changing the relative frequency with which target visual (Experiment 1) and auditory (Experiment 2) stimuli were presented in arrays of fixed size, and identification of the target stimuli was tested. Oral language skills were assessed using vocabulary, word definition, and phonological awareness tasks. Changes in perceptual context influenced the performance of the majority of children on both identification tasks. Sensitivity to perceptual context accounted for 7% to 15% of the variance in language scores. We suggest that context effects are an outcome of a statistical learning process. Therefore, the current findings demonstrate that statistical learning can facilitate both visual and auditory identification processes in preschool children. Furthermore, consistent with previous findings in infants and in older children and adults, individual differences in statistical learning were found to be associated with individual differences in language skills of preschool children. Copyright © 2015 Elsevier Inc. All rights reserved.

Department of Defense Chemical and Biological Defense Program. FY2004-2006 Performance Plan

DTIC Science & Technology

2005-03-01

Agents (NTAs) Compare the direct effects of PAF on smooth muscle, hematic constituents, and lung to determine role in toxicity. Continue to identify...Range Biometric Target ID System Explore technologies for a long range biometric target identification system. Air Containment Monitoring System...Continue development of systems for contained air monitoring for chemical agents.Long Range Biometric Air Containment Monitoring System Continued

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

PubMed Central

2014-01-01

Background Non-coding sequences such as microRNAs have important roles in disease processes. Computational microRNA target identification (CMTI) is becoming increasingly important since traditional experimental methods for target identification pose many difficulties. These methods are time-consuming, costly, and often need guidance from computational methods to narrow down candidate genes anyway. However, most CMTI methods are computationally demanding, since they need to handle not only several million query microRNA and reference RNA pairs, but also several million nucleotide comparisons within each given pair. Thus, the need to perform microRNA identification at such large scale has increased the demand for parallel computing. Methods Although most CMTI programs (e.g., the miRanda algorithm) are based on a modified Smith-Waterman (SW) algorithm, the existing parallel SW implementations (e.g., CUDASW++ 2.0/3.0, SWIPE) are unable to meet this demand in CMTI tasks. We present CUDA-miRanda, a fast microRNA target identification algorithm that takes advantage of massively parallel computing on Graphics Processing Units (GPU) using NVIDIA's Compute Unified Device Architecture (CUDA). CUDA-miRanda specifically focuses on the local alignment of short (i.e., ≤ 32 nucleotides) sequences against longer reference sequences (e.g., 20K nucleotides). Moreover, the proposed algorithm is able to report multiple alignments (up to 191 top scores) and the corresponding traceback sequences for any given (query sequence, reference sequence) pair. Results Speeds over 5.36 Giga Cell Updates Per Second (GCUPs) are achieved on a server with 4 NVIDIA Tesla M2090 GPUs. Compared to the original miRanda algorithm, which is evaluated on an Intel Xeon E5620@2.4 GHz CPU, the experimental results show up to 166 times performance gains in terms of execution time. In addition, we have verified that the exact same targets were predicted in both CUDA-miRanda and the original miRanda implementations through multiple test datasets. Conclusions We offer a GPU-based alternative to high performance compute (HPC) that can be developed locally at a relatively small cost. The community of GPU developers in the biomedical research community, particularly for genome analysis, is still growing. With increasing shared resources, this community will be able to advance CMTI in a very significant manner. Our source code is available at https://sourceforge.net/projects/cudamiranda/. PMID:25077821

Research and development on performance models of thermal imaging systems

NASA Astrophysics Data System (ADS)

Wang, Ji-hui; Jin, Wei-qi; Wang, Xia; Cheng, Yi-nan

2009-07-01

Traditional ACQUIRE models perform the discrimination tasks of detection (target orientation, recognition and identification) for military target based upon minimum resolvable temperature difference (MRTD) and Johnson criteria for thermal imaging systems (TIS). Johnson criteria is generally pessimistic for performance predict of sampled imager with the development of focal plane array (FPA) detectors and digital image process technology. Triangle orientation discrimination threshold (TOD) model, minimum temperature difference perceived (MTDP)/ thermal range model (TRM3) Model and target task performance (TTP) metric have been developed to predict the performance of sampled imager, especially TTP metric can provides better accuracy than the Johnson criteria. In this paper, the performance models above are described; channel width metrics have been presented to describe the synthesis performance including modulate translate function (MTF) channel width for high signal noise to ration (SNR) optoelectronic imaging systems and MRTD channel width for low SNR TIS; the under resolvable questions for performance assessment of TIS are indicated; last, the development direction of performance models for TIS are discussed.

Simultaneous screening of targeted and non-targeted contaminants using an LC-QTOF-MS system and automated MS/MS library searching.

PubMed

Herrera-Lopez, S; Hernando, M D; García-Calvo, E; Fernández-Alba, A R; Ulaszewska, M M

2014-09-01

Simultaneous high-resolution full-scan and tandem mass spectrometry (MS/MS) analysis using time of flight mass spectrometry brings an answer for increasing demand of retrospective and non-targeted data analysis. Such analysis combined with spectral library searching is a promising tool for targeted and untargeted screening of small molecules. Despite considerable extension of the panel of compounds of tandem mass spectral libraries, the heterogeneity of spectral data poses a major challenge against the effective usage of spectral libraries. Performance evaluation of available LC-MS/MS libraries will significantly increase credibility in the search results. The present work was aimed to evaluate fluctuation of MS/MS pattern, in the peak intensities distribution together with mass accuracy measurements, and in consequence, performance compliant with ion ratio and mass error criteria as principles in identification processes for targeted and untargeted contaminants at trace levels. Matrix effect and ultra-trace levels of concentration (from 50 ng l(-1) to 1000 ng l(-1) were evaluated as potential source of inaccuracy in the performance of spectral matching. Matrix-matched samples and real samples were screened for proof of applicability. By manual review of data and application of ion ratio and ppm error criteria, false negatives were obtained; this number diminished when in-house library was used, while with on-line MS/MS databases 100% of positive samples were found. In our experience, intensity of peaks across spectra was highly correlated to the concentration effect and matrix complexity. In turn, analysis of spectra acquired at trace concentrations and in different matrices results in better performance in providing correct and reliable identification. Copyright © 2014 John Wiley & Sons, Ltd.

RISC RNA sequencing for context-specific identification of in vivo miR targets

PubMed Central

Matkovich, Scot J; Van Booven, Derek J; Eschenbacher, William H; Dorn, Gerald W

2010-01-01

Rationale MicroRNAs (miRs) are expanding our understanding of cardiac disease and have the potential to transform cardiovascular therapeutics. One miR can target hundreds of individual mRNAs, but existing methodologies are not sufficient to accurately and comprehensively identify these mRNA targets in vivo. Objective To develop methods permitting identification of in vivo miR targets in an unbiased manner, using massively parallel sequencing of mouse cardiac transcriptomes in combination with sequencing of mRNA associated with mouse cardiac RNA-induced silencing complexes (RISCs). Methods and Results We optimized techniques for expression profiling small amounts of RNA without introducing amplification bias, and applied this to anti-Argonaute 2 immunoprecipitated RISCs (RISC-Seq) from mouse hearts. By comparing RNA-sequencing results of cardiac RISC and transcriptome from the same individual hearts, we defined 1,645 mRNAs consistently targeted to mouse cardiac RISCs. We employed this approach in hearts overexpressing miRs from Myh6 promoter-driven precursors (programmed RISC-Seq) to identify 209 in vivo targets of miR-133a and 81 in vivo targets of miR-499. Consistent with the fact that miR-133a and miR-499 have widely differing ‘seed’ sequences and belong to different miR families, only 6 targets were common to miR-133a- and miR-499-programmed hearts. Conclusions RISC-sequencing is a highly sensitive method for general RISC profiling and individual miR target identification in biological context, and is applicable to any tissue and any disease state. Summary MicroRNAs (miRs) are key regulators of mRNA translation in health and disease. While bioinformatic predictions suggest that a single miR may target hundreds of mRNAs, the number of experimentally verified targets of miRs is low. To enable comprehensive, unbiased examination of miR targets, we have performed deep RNA sequencing of cardiac transcriptomes in parallel with cardiac RNA-induced silencing complex (RISC)-associated RNAs (the RISCome), called RISC sequencing. We developed methods that did not require cross-linking of RNAs to RISCs or amplification of mRNA prior to sequencing, making it possible to rapidly perform RISC sequencing from intact tissue while avoiding amplification bias. Comparison of RISCome with transcriptome expression defined the degree of RISC enrichment for each mRNA. The majority of the mRNAs enriched in wild-type cardiac RISComes compared to transcriptomes were bioinformatically predicted to be targets of at least 1 of 139 cardiac-expressed miRs. Programming cardiomyocyte RISCs via transgenic overexpression in adult hearts of miR-133a or miR-499, two miRs that contain entirely different ‘seed’ sequences, elicited differing profiles of RISC-targeted mRNAs. Thus, RISC sequencing represents a highly sensitive method for general RISC profiling and individual miR target identification in biological context. PMID:21030712

BP network identification technology of infrared polarization based on fuzzy c-means clustering

NASA Astrophysics Data System (ADS)

Zeng, Haifang; Gu, Guohua; He, Weiji; Chen, Qian; Yang, Wei

2011-08-01

Infrared detection system is frequently employed on surveillance operations and reconnaissance mission to detect particular targets of interest in both civilian and military communities. By incorporating the polarization of light as supplementary information, the target discrimination performance could be enhanced. So this paper proposed an infrared target identification method which is based on fuzzy theory and neural network with polarization properties of targets. The paper utilizes polarization degree and light intensity to advance the unsupervised KFCM (kernel fuzzy C-Means) clustering method. And establish different material pol1arization properties database. In the built network, the system can feedback output corresponding material types of probability distribution toward any input polarized degree such as 10° 15°, 20°, 25°, 30°. KFCM, which has stronger robustness and accuracy than FCM, introduces kernel idea and gives the noise points and invalid value different but intuitively reasonable weights. Because of differences in characterization of material properties, there will be some conflicts in classification results. And D - S evidence theory was used in the combination of the polarization and intensity information. Related results show KFCM clustering precision and operation rate are higher than that of the FCM clustering method. The artificial neural network method realizes material identification, which reasonable solved the problems of complexity in environmental information of infrared polarization, and improperness of background knowledge and inference rule. This method of polarization identification is fast in speed, good in self-adaption and high in resolution.

Comparison of conventional ultrasonography and ultrasonography-computed tomography fusion imaging for target identification using digital/real hybrid phantoms: a preliminary study.

PubMed

Soyama, Takeshi; Sakuhara, Yusuke; Kudo, Kohsuke; Abo, Daisuke; Wang, Jeff; Ito, Yoichi M; Hasegawa, Yu; Shirato, Hiroki

2016-07-01

This preliminary study compared ultrasonography-computed tomography (US-CT) fusion imaging and conventional ultrasonography (US) for accuracy and time required for target identification using a combination of real phantoms and sets of digitally modified computed tomography (CT) images (digital/real hybrid phantoms). In this randomized prospective study, 27 spheres visible on B-mode US were placed at depths of 3.5, 8.5, and 13.5 cm (nine spheres each). All 27 spheres were digitally erased from the CT images, and a radiopaque sphere was digitally placed at each of the 27 locations to create 27 different sets of CT images. Twenty clinicians were instructed to identify the sphere target using US alone and fusion imaging. The accuracy of target identification of the two methods was compared using McNemar's test. The mean time required for target identification and error distances were compared using paired t tests. At all three depths, target identification was more accurate and the mean time required for target identification was significantly less with US-CT fusion imaging than with US alone, and the mean error distances were also shorter with US-CT fusion imaging. US-CT fusion imaging was superior to US alone in terms of accurate and rapid identification of target lesions.

Light Video Game Play is Associated with Enhanced Visual Processing of Rapid Serial Visual Presentation Targets.

PubMed

Howard, Christina J; Wilding, Robert; Guest, Duncan

2017-02-01

There is mixed evidence that video game players (VGPs) may demonstrate better performance in perceptual and attentional tasks than non-VGPs (NVGPs). The rapid serial visual presentation task is one such case, where observers respond to two successive targets embedded within a stream of serially presented items. We tested light VGPs (LVGPs) and NVGPs on this task. LVGPs were better at correct identification of second targets whether they were also attempting to respond to the first target. This performance benefit seen for LVGPs suggests enhanced visual processing for briefly presented stimuli even with only very moderate game play. Observers were less accurate at discriminating the orientation of a second target within the stream if it occurred shortly after presentation of the first target, that is to say, they were subject to the attentional blink (AB). We find no evidence for any reduction in AB in LVGPs compared with NVGPs.

In Vitro Evaluation of Molecular Tumor Targets in Nuclear Medicine: Immunohistochemistry Is One Option, but Under Which Conditions?

PubMed

Reubi, Jean Claude

2017-12-01

The identification of new molecular targets for diagnostic and therapeutic applications using in vitro methods is an important challenge in nuclear medicine. One such method is immunohistochemistry, increasingly popular because it is easy to perform. This review presents the case for conducting receptor immunohistochemistry to evaluate potential molecular targets in human tumor tissue sections. The focus is on the immunohistochemistry of G-protein-coupled receptors, one of the largest families of cell surface proteins, representing a major class of drug targets and thus playing an important role in nuclear medicine. This review identifies common pitfalls and challenges and provides guidelines on performing such immunohistochemical studies. An appropriate validation of the target is a prerequisite for developing robust and informative new molecular probes. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

PubMed

Yang, Chia-Chun; Andrews, Erik H; Chen, Min-Hsuan; Wang, Wan-Yu; Chen, Jeremy J W; Gerstein, Mark; Liu, Chun-Chi; Cheng, Chao

2016-08-12

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the characteristic binding profiles and the density plot of normalized regulatory scores. The iTAR web server is a useful tool in identifying TF target genes from ChIP-seq/ChIP-chip data and discovering biological insights.

Comparative genome analysis identifies novel nucleic acid diagnostic targets for use in the specific detection of Haemophilus influenzae.

PubMed

Coughlan, Helena; Reddington, Kate; Tuite, Nina; Boo, Teck Wee; Cormican, Martin; Barrett, Louise; Smith, Terry J; Clancy, Eoin; Barry, Thomas

2015-10-01

Haemophilus influenzae is recognised as an important human pathogen associated with invasive infections, including bloodstream infection and meningitis. Currently used molecular-based diagnostic assays lack specificity in correctly detecting and identifying H. influenzae. As such, there is a need to develop novel diagnostic assays for the specific identification of H. influenzae. Whole genome comparative analysis was performed to identify putative diagnostic targets, which are unique in nucleotide sequence to H. influenzae. From this analysis, we identified 2H. influenzae putative diagnostic targets, phoB and pstA, for use in real-time PCR diagnostic assays. Real-time PCR diagnostic assays using these targets were designed and optimised to specifically detect and identify all 55H. influenzae strains tested. These novel rapid assays can be applied to the specific detection and identification of H. influenzae for use in epidemiological studies and could also enable improved monitoring of invasive disease caused by these bacteria. Copyright © 2015 Elsevier Inc. All rights reserved.

Fast identification of dermatophytes by MALDI-TOF/MS using direct transfer of fungal cells on ground steel target plates.

PubMed

da Cunha, Keith C; Riat, Arnaud; Normand, Anne-Cecile; Bosshard, Philipp P; de Almeida, Margarete T G; Piarroux, Renaud; Schrenzel, Jacques; Fontao, Lionel

2018-05-15

Dermatophytes cause human infections limited to keratinized tissues. We showed that the direct transfer method allows reliable identification of non-dermatophytes mould and yeast by MALDI-TOF/MS. We aimed at assessing whether the direct transfer method can be used for dermatophytes and whether an own mass spectra library would be superior to the Bruker library. We used the Bruker Biotyper to build a dermatophyte mass spectra library and assessed its performance by 1/ testing a panel of mass spectrum produced with strains genotypically identified and, 2/ comparing MALDI-TOF/MS identification to morphology-based methods. Identification of dermatophytes using the Bruker library is poor. Our library provided 97% concordance between ITS sequencing and MALDI-TOF/MS analysis with a panel of 1104 spectra corresponding to 276 strains. Direct transfer method using unpolished target plates allowed proper identification of 85% of dermatophytes clinical isolates most of which were common dermatophytes. A homemade dermatophyte MSP library is a prerequisite for accurate identification of species absent in the Bruker library but it also improves identification of species already listed in the database. The direct deposit method can be used to identify the most commonly found dermatophytes such as T. rubrum and T. interdigitale/mentagrophytes by MALDI-TOF/MS. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Passive RFID Rotation Dimension Reduction via Aggregation

NASA Astrophysics Data System (ADS)

Matthews, Eric

Radio Frequency IDentification (RFID) has applications in object identification, position, and orientation tracking. RFID technology can be applied in hospitals for patient and equipment tracking, stores and warehouses for product tracking, robots for self-localisation, tracking hazardous materials, or locating any other desired object. Efficient and accurate algorithms that perform localisation are required to extract meaningful data beyond simple identification. A Received Signal Strength Indicator (RSSI) is the strength of a received radio frequency signal used to localise passive and active RFID tags. Many factors affect RSSI such as reflections, tag rotation in 3D space, and obstacles blocking line-of-sight. LANDMARC is a statistical method for estimating tag location based on a target tag's similarity to surrounding reference tags. LANDMARC does not take into account the rotation of the target tag. By either aggregating multiple reference tag positions at various rotations, or by determining a rotation value for a newly read tag, we can perform an expected value calculation based on a comparison to the k-most similar training samples via an algorithm called K-Nearest Neighbours (KNN) more accurately. By choosing the average as the aggregation function, we improve the relative accuracy of single-rotation LANDMARC localisation by 10%, and any-rotation localisation by 20%.

A target and nontarget strategy for identification or characterization of the chemical ingredients in Chinese herb preparation Shuang-Huang-Lian oral liquid by ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry.

PubMed

Zhang, Feng-Xiang; Li, Min; Yao, Zhi-Hong; Li, Chang; Qiao, Li-Rui; Shen, Xiu-Yu; Yu, Kate; Dai, Yi; Yao, Xin-Sheng

2018-03-01

A target and nontarget strategy based on in-house chemical components library was developed for rapid and comprehensive analysis of complicated components from traditional Chinese medicine preparation Shuang-Huang-Lian oral liquid. The sample was analyzed by ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry using generic acquisition parameters. Automated detection and data filtering were performed on the UNIFI™ software and the detected peaks were evaluated against an in-house library. As a result, a total of 170 chemical components (110 target compounds and 60 nontarget ones) were identified or tentatively characterized, including 54 flavonoids, 30 phenylethanoid glycosides, 16 iridoid glycosides, 14 lignans, 32 organic acids, 19 triterpenoid saponins and five other types of compounds. Among them, 44 compounds were further confirmed by comparison with reference standards. It was demonstrated that this systematical approach could be successfully applied for rapid identification of multiple compounds in traditional Chinese medicine and its preparations. Furthermore, this work established the foundation for the further investigation on the metabolic fates of multiple ingredients in Shuang-Huang-Lian oral liquid. Copyright © 2017 John Wiley & Sons, Ltd.

Charged Particle Identification for Prefragmentation Studies

NASA Astrophysics Data System (ADS)

Hu, Jonathan; MoNA Collaboration

2017-09-01

Projectile fragmentation refers to high energy (>50 MeV/u) heavy ion beams on production targets to generate intermediate mass and target fragments at facilities like the NSCL, FRIB, GSI, GANIL and RIKEN. The resulting secondary beams can then be isolated by fragment separators like the NCSL's A1900 and that secondary beam then used on reaction targets for a variety of experiments. Predictions of beam intensities for experiment planning depend on models and data. The MoNA Collaboration performed an experiment at the NSCL in which a 48Ca primary beam was used with a 9Be target to produce a 32Mg secondary beam with energy 86 MeV/u that was incident on a second target of 9Be. By characterizing the energy distributions of final fragments of neon, sodium, and fluorine in coincidence with neutrons created both by prefragmentation processes and reaction mechanisms, we are able to extract information about prefragmentation dynamics. The identification of charged fragments is a multi-step process crucial to this analysis. This work is supported by the National Science Foundation under Grant No. PHY-1613429.

Collaborative identification method for sea battlefield target based on deep convolutional neural networks

NASA Astrophysics Data System (ADS)

Zheng, Guangdi; Pan, Mingbo; Liu, Wei; Wu, Xuetong

2018-03-01

The target identification of the sea battlefield is the prerequisite for the judgment of the enemy in the modern naval battle. In this paper, a collaborative identification method based on convolution neural network is proposed to identify the typical targets of sea battlefields. Different from the traditional single-input/single-output identification method, the proposed method constructs a multi-input/single-output co-identification architecture based on optimized convolution neural network and weighted D-S evidence theory. The simulation results show that

Nuclear Security: Target Analysis-rev

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

Singh, Surinder Paul; Gibbs, Philip W.; Bultz, Garl A.

2014-03-01

The objectives of this presentation are to understand target identification, including roll-up and protracted theft; evaluate target identification in the SNRI; recognize the target characteristics and consequence levels; and understand graded safeguards.

Reducing time to identification of aerobic bacteria and fastidious micro-organisms in positive blood cultures.

PubMed

Intra, J; Sala, M R; Falbo, R; Cappellini, F; Brambilla, P

2016-12-01

Rapid and early identification of micro-organisms in blood has a key role in the diagnosis of a febrile patient, in particular, in guiding the clinician to define the correct antibiotic therapy. This study presents a simple and very fast method with high performances for identifying bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after only 4 h of incubation. We used early bacterial growth on PolyViteX chocolate agar plates inoculated with five drops of blood-broth medium deposited in the same point and spread with a sterile loop, followed by a direct transfer procedure on MALDI-TOF MS target slides without additional modification. Ninety-nine percentage of aerobic bacteria were correctly identified from 600 monomicrobial-positive blood cultures. This procedure allowed obtaining the correct identification of fastidious pathogens, such as Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae that need complex nutritional and environmental requirements in order to grow. Compared to the traditional pathogen identification from blood cultures that takes over 24 h, the reliability of results, rapid performance and suitability of this protocol allowed a more rapid administration of optimal antimicrobial treatment in the patients. Bloodstream infections are serious conditions with a high mortality and morbidity rate. Rapid identification of pathogens and appropriate antimicrobial therapy have a key role for successful patient outcome. In this work, we developed a rapid, simplified, accurate, and efficient method, reaching 99 % identification of aerobic bacteria from monomicrobial-positive blood cultures by using early growth on enriched medium, direct transfer to target plate without additional procedures, matrix-assisted laser desorption ionization-time of flight mass spectrometry and SARAMIS database. The application of this protocol allows to anticipate appropriate antibiotic therapy. © 2016 The Society for Applied Microbiology.

Allocation of attention during pursuit of large objects is no different than during fixation.

PubMed

Watamaniuk, Scott N J; Heinen, Stephen J

2015-01-01

Attention allocation during pursuit of a spot is usually characterized as asymmetric with more attention placed ahead of the target than behind it. However, attention is symmetrically allocated across larger pursuit stimuli. An unresolved issue is how tightly attention is constrained on large stimuli during pursuit. Although some work shows it is tightly locked to the fovea, other work shows it is allocated flexibly. To investigate this, we had observers perform a character identification task on large pursuit stimuli composed of arrays of five, nine, or 15 characters spaced between 0.6° and 4.0° apart. Initially, the characters were identical, but at a random time, they all changed briefly, rendering one of them unique. Observers identified the unique character. Consistent with previous literature, attention appeared narrow and symmetric around the pursuit target for tightly spaced (0.6°) characters. Increasing spacing dramatically expanded the attention scope, presumably by mitigating crowding. However, when we controlled for crowding, performance was limited by set size, suffering more for eccentric targets. Interestingly, the same limitations on attention allocation were observed with stationary and pursued stimuli-evidence that attention operates similarly during fixation and pursuit of a stimulus that extends into the periphery. The results suggest that attention is flexibly allocated during pursuit, but performance is limited by crowding and set size. In addition, performing the identification task did not hurt pursuit performance, further evidence that pursuit of large stimuli is relatively inattentive.

Naturalistic distraction and driving safety in older drivers

PubMed Central

Aksan, Nazan; Dawson, Jeffrey D.; Emerson, Jamie L.; Yu, Lixi; Uc, Ergun Y.; Anderson, Steven W.; Rizzo, Matthew

2013-01-01

Objective This study aimed to quantify and compare performance of middle-aged and older drivers during a naturalistic distraction paradigm (visual search for roadside targets) and predict older driver performance given functioning in visual, motor, and cognitive domains. Background Distracted driving can imperil healthy adults and may disproportionally affect the safety of older drivers with visual, motor, and cognitive decline. Methods Two hundred and three drivers, 120 healthy older (61 men and 59 women, ages 65 years or greater) and 83 middle-aged drivers (38 men and 45 women, ages 40–64 years), participated in an on-road test in an instrumented vehicle. Outcome measures included performance in roadside target identification (traffic signs and restaurants) and concurrent driver safety. Differences in visual, motor, and cognitive functioning served as predictors. Results Older drivers identified fewer landmarks and drove slower but committed more safety errors than middle-aged drivers. Greater familiarity with local roads benefited performance of middle-aged but not older drivers. Visual cognition predicted both traffic sign identification and safety errors while executive function predicted traffic sign identification over and above vision. Conclusion Older adults are susceptible to driving safety errors while distracted by common secondary visual search tasks that are inherent to driving. The findings underscore that age-related cognitive decline affects older driver management of driving tasks at multiple levels, and can help inform the design of on-road tests and interventions for older drivers. PMID:23964422

An Optically Implemented Kalman Filter Algorithm.

DTIC Science & Technology

1983-12-01

8b. OFFICE SYMOOL 9. PROCUREMENT INSTRUMENT IDENTIFICATION NUMBER 8c. ADDRESS (City, State and ZIP Code ) 10. SOURCE OF FUNDING NOS.______ PROGRAM...are completely speci- fied for the correlation stage to perform the required corre- lation in real time, and the filter stage to perform the lin- ear...performance analy- ses indicated an enhanced ability of the nonadaptive filter to track a realistic distant point source target with an error standard

Automatic identification of bird targets with radar via patterns produced by wing flapping.

PubMed

Zaugg, Serge; Saporta, Gilbert; van Loon, Emiel; Schmaljohann, Heiko; Liechti, Felix

2008-09-06

Bird identification with radar is important for bird migration research, environmental impact assessments (e.g. wind farms), aircraft security and radar meteorology. In a study on bird migration, radar signals from birds, insects and ground clutter were recorded. Signals from birds show a typical pattern due to wing flapping. The data were labelled by experts into the four classes BIRD, INSECT, CLUTTER and UFO (unidentifiable signals). We present a classification algorithm aimed at automatic recognition of bird targets. Variables related to signal intensity and wing flapping pattern were extracted (via continuous wavelet transform). We used support vector classifiers to build predictive models. We estimated classification performance via cross validation on four datasets. When data from the same dataset were used for training and testing the classifier, the classification performance was extremely to moderately high. When data from one dataset were used for training and the three remaining datasets were used as test sets, the performance was lower but still extremely to moderately high. This shows that the method generalizes well across different locations or times. Our method provides a substantial gain of time when birds must be identified in large collections of radar signals and it represents the first substantial step in developing a real time bird identification radar system. We provide some guidelines and ideas for future research.

Modeling of 1.5 μm range gated imaging for small surface vessel identification

NASA Astrophysics Data System (ADS)

Espinola, Richard L.; Steinvall, Ove; Elmquist, Magnus; Karlsson, Kjell

2010-10-01

Within the framework of the NATO group (NATO SET-132/RTG-72) on imaging ladars, a test was performed to collect simultaneous multi-mode LADAR signatures of maritime objects entering and leaving San Diego Harbor. Beside ladars, passive sensors were also employed during the test which occurred during April 2009 from Point Loma and the harbor in San Diego. This paper will report on 1.5 μm gated imaging on a number of small civilian surface vessels with the aim to present human perception experimental results and comparisons with sensor performance models developed by US Army RDECOM CERDEC NVESD. We use controlled human perception tests to measure target identification performance and compare the experimental results with model predictions.

Optimization of a chemical identification algorithm

NASA Astrophysics Data System (ADS)

Chyba, Thomas H.; Fisk, Brian; Gunning, Christin; Farley, Kevin; Polizzi, Amber; Baughman, David; Simpson, Steven; Slamani, Mohamed-Adel; Almassy, Robert; Da Re, Ryan; Li, Eunice; MacDonald, Steve; Slamani, Ahmed; Mitchell, Scott A.; Pendell-Jones, Jay; Reed, Timothy L.; Emge, Darren

2010-04-01

A procedure to evaluate and optimize the performance of a chemical identification algorithm is presented. The Joint Contaminated Surface Detector (JCSD) employs Raman spectroscopy to detect and identify surface chemical contamination. JCSD measurements of chemical warfare agents, simulants, toxic industrial chemicals, interferents and bare surface backgrounds were made in the laboratory and under realistic field conditions. A test data suite, developed from these measurements, is used to benchmark algorithm performance throughout the improvement process. In any one measurement, one of many possible targets can be present along with interferents and surfaces. The detection results are expressed as a 2-category classification problem so that Receiver Operating Characteristic (ROC) techniques can be applied. The limitations of applying this framework to chemical detection problems are discussed along with means to mitigate them. Algorithmic performance is optimized globally using robust Design of Experiments and Taguchi techniques. These methods require figures of merit to trade off between false alarms and detection probability. Several figures of merit, including the Matthews Correlation Coefficient and the Taguchi Signal-to-Noise Ratio are compared. Following the optimization of global parameters which govern the algorithm behavior across all target chemicals, ROC techniques are employed to optimize chemical-specific parameters to further improve performance.

Evaluation of eye metrics as a detector of fatigue.

PubMed

McKinley, R Andy; McIntire, Lindsey K; Schmidt, Regina; Repperger, Daniel W; Caldwell, John A

2011-08-01

This study evaluated oculometrics as a detector of fatigue in Air Force-relevant tasks after sleep deprivation. Using the metrics of total eye closure duration (PERCLOS) and approximate entropy (ApEn), the relation between these eye metrics and fatigue-induced performance decrements was investigated. One damaging effect to the successful outcome of operational military missions is that attributed to sleep deprivation-induced fatigue. Consequently, there is interest in the development of reliable monitoring devices that can assess when an operator is overly fatigued. Ten civilian participants volunteered to serve in this study. Each was trained on three performance tasks: target identification, unmanned aerial vehicle landing, and the psychomotor vigilance task (PVT). Experimental testing began after 14 hr awake and continued every 2 hr until 28 hr of sleep deprivation was reached. Performance on the PVT and target identification tasks declined significantly as the level of sleep deprivation increased.These performance declines were paralleled more closely by changes in the ApEn compared to the PERCLOS measure. The results provide evidence that the ApEn eye metric can be used to detect fatigue in relevant military aviation tasks. Military and commercial operators could benefit from an alertness monitoring device.

MALDI-TOF MS identification of anaerobic bacteria: assessment of pre-analytical variables and specimen preparation techniques.

PubMed

Hsu, Yen-Michael S; Burnham, Carey-Ann D

2014-06-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a tool for identifying clinically relevant anaerobes. We evaluated the analytical performance characteristics of the Bruker Microflex with Biotyper 3.0 software system for identification of anaerobes and examined the impact of direct formic acid (FA) treatment and other pre-analytical factors on MALDI-TOF MS performance. A collection of 101 anaerobic bacteria were evaluated, including Clostridium spp., Propionibacterium spp., Fusobacterium spp., Bacteroides spp., and other anaerobic bacterial of clinical relevance. The results of our study indicate that an on-target extraction with 100% FA improves the rate of accurate identification without introducing misidentification (P<0.05). In addition, we modify the reporting cutoffs for the Biotyper "score" yielding acceptable identification. We found that a score of ≥1.700 can maximize the rate of identification. Of interest, MALDI-TOF MS can correctly identify anaerobes grown in suboptimal conditions, such as on selective culture media and following oxygen exposure. In conclusion, we report on a number of simple and cost-effective pre- and post-analytical modifications could enhance MALDI-TOF MS identification for anaerobic bacteria. Copyright © 2014 Elsevier Inc. All rights reserved.

Performance of resonant radar target identification algorithms using intra-class weighting functions

NASA Astrophysics Data System (ADS)

Mustafa, A.

The use of calibrated resonant-region radar cross section (RCS) measurements of targets for the classification of large aircraft is discussed. Errors in the RCS estimate of full scale aircraft flying over an ocean, introduced by the ionospheric variability and the sea conditions were studied. The Weighted Target Representative (WTR) classification algorithm was developed, implemented, tested and compared with the nearest neighbor (NN) algorithm. The WTR-algorithm has a low sensitivity to the uncertainty in the aspect angle of the unknown target returns. In addition, this algorithm was based on the development of a new catalog of representative data which reduces the storage requirements and increases the computational efficiency of the classification system compared to the NN-algorithm. Experiments were designed to study and evaluate the characteristics of the WTR- and the NN-algorithms, investigate the classifiability of targets and study the relative behavior of the number of misclassifications as a function of the target backscatter features. The classification results and statistics were shown in the form of performance curves, performance tables and confusion tables.

Hit Identification and Optimization in Virtual Screening: Practical Recommendations Based Upon a Critical Literature Analysis

PubMed Central

Zhu, Tian; Cao, Shuyi; Su, Pin-Chih; Patel, Ram; Shah, Darshan; Chokshi, Heta B.; Szukala, Richard; Johnson, Michael E.; Hevener, Kirk E.

2013-01-01

A critical analysis of virtual screening results published between 2007 and 2011 was performed. The activity of reported hit compounds from over 400 studies was compared to their hit identification criteria. Hit rates and ligand efficiencies were calculated to assist in these analyses and the results were compared with factors such as the size of the virtual library and the number of compounds tested. A series of promiscuity, drug-like, and ADMET filters were applied to the reported hits to assess the quality of compounds reported and a careful analysis of a subset of the studies which presented hit optimization was performed. This data allowed us to make several practical recommendations with respect to selection of compounds for experimental testing, defining hit identification criteria, and general virtual screening hit criteria to allow for realistic hit optimization. A key recommendation is the use of size-targeted ligand efficiency values as hit identification criteria. PMID:23688234

Fast and Confident: Postdicting Eyewitness Identification Accuracy in a Field Study

ERIC Educational Resources Information Center

Sauerland, Melanie; Sporer, Siegfried L.

2009-01-01

The combined postdictive value of postdecision confidence, decision time, and Remember-Know-Familiar (RKF) judgments as markers of identification accuracy was evaluated with 10 targets and 720 participants. In a pedestrian area, passers-by were asked for directions. Identifications were made from target-absent or target-present lineups. Fast…

Target identification for small bioactive molecules: finding the needle in the haystack.

PubMed

Ziegler, Slava; Pries, Verena; Hedberg, Christian; Waldmann, Herbert

2013-03-04

Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Target Identification Support and Location Support Among Teams of Unmanned Systems Operators

DTIC Science & Technology

2008-12-01

effectiveness and performance, many studies have highlighted the importance of attending to team process (Campion, Medsker, & Higgs, 1993, Campion, Papper ...work groups. Personnel Psychology, 46, 823-850. Campion, M., Papper , E., & Medsker, G., 1996: Relations between work team characteristics and

EOID System Model Validation, Metrics, and Synthetic Clutter Generation

DTIC Science & Technology

2003-09-30

Our long-term goal is to accurately predict the capability of the current generation of laser-based underwater imaging sensors to perform Electro ... Optic Identification (EOID) against relevant targets in a variety of realistic environmental conditions. The models will predict the impact of

Identification of Mucorales From Clinical Specimens: A 4-Year Experience in a Single Institution

PubMed Central

Yang, Mina; Lee, Jang Ho; Kim, Young-Kwon; Ki, Chang-Seok

2016-01-01

Mucormycosis, a fatal opportunistic infection in immunocompromised hosts, is caused by fungi belonging to the order Mucorales. Early diagnosis based on exact identification and multidisciplinary treatments is critical. However, identification of Mucorales fungi is difficult and often delayed, resulting in poor prognosis. This study aimed to compare the results of phenotypic and molecular identification of 12 Mucorales isolates collected from 4-yr-accumulated data. All isolates were identified on the basis of phenotypic characteristics such as growth rate, colony morphology, and reproductive structures. PCR and direct sequencing were performed to target internal transcribed spacer (ITS) and/or D1/D2 regions. Target DNA sequencing identified five Lichtheimia isolates, two Rhizopus microsporus isolates, two Rhizomucor pusillus isolates, one Cunninghamella bertholletiae isolate, one Mucor fragilis isolate, and one Syncephalastrum racemosum isolate. Five of the 12 (41.7%) isolates were incorrectly identified on the basis of phenotypic identification. DNA sequencing showed that of these five isolates, two were Lichtheimia isolates, one was Mucor isolate, one was Rhizomucor isolate, and one was Rhizopus microspores. All the isolates were identified at the species level by ITS and/or D1/D2 analyses. Phenotypic differentiation and identification of Mucorales is difficult because different Mucorales share similar morphology. Our results indicate that the molecular methods employed in this study are valuable for identifying Mucorales. PMID:26522761

Identification of mucorales from clinical specimens: a 4-year experience in a single institution.

PubMed

Yang, Mina; Lee, Jang Ho; Kim, Young Kwon; Ki, Chang Seok; Huh, Hee Jae; Lee, Nam Yong

2016-01-01

Mucormycosis, a fatal opportunistic infection in immunocompromised hosts, is caused by fungi belonging to the order Mucorales. Early diagnosis based on exact identification and multidisciplinary treatments is critical. However, identification of Mucorales fungi is difficult and often delayed, resulting in poor prognosis. This study aimed to compare the results of phenotypic and molecular identification of 12 Mucorales isolates collected from 4-yr-accumulated data. All isolates were identified on the basis of phenotypic characteristics such as growth rate, colony morphology, and reproductive structures. PCR and direct sequencing were performed to target internal transcribed spacer (ITS) and/or D1/D2 regions. Target DNA sequencing identified five Lichtheimia isolates, two Rhizopus microsporus isolates, two Rhizomucor pusillus isolates, one Cunninghamella bertholletiae isolate, one Mucor fragilis isolate, and one Syncephalastrum racemosum isolate. Five of the 12 (41.7%) isolates were incorrectly identified on the basis of phenotypic identification. DNA sequencing showed that of these five isolates, two were Lichtheimia isolates, one was Mucor isolate, one was Rhizomucor isolate, and one was Rhizopus microspores. All the isolates were identified at the species level by ITS and/or D1/D2 analyses. Phenotypic differentiation and identification of Mucorales is difficult because different Mucorales share similar morphology. Our results indicate that the molecular methods employed in this study are valuable for identifying Mucorales.

Development of a real-time PCR assay for the detection and identification of Staphylococcus capitis, Staphylococcus haemolyticus and Staphylococcus warneri.

PubMed

Iwase, Tadayuki; Seki, Keiko; Shinji, Hitomi; Mizunoe, Yoshimitsu; Masuda, Shogo

2007-10-01

Staphylococcus capitis, Staphylococcus haemolyticus and Staphylococcus warneri are coagulase-negative staphylococci. Each species has different characteristics, and a difference in pathology is also seen in compromised hosts. Therefore, the development of a species-specific simple detection method for the identification of these staphylococci is important. Here, a species-specific real-time PCR assay is reported that targets the superoxide dismutase A-encoding gene of these bacteria. Primers were designed with a base that was non-complementary with regard to the other bacteria. This base was at the 3' end of the primer (3' mismatch primer) and conferred high specificity. These primers were then evaluated using real-time PCR. They reacted only with the target bacterium. In addition, stable quantitative reactions were observed when experiments were performed using genomic DNA extracted from varying numbers of staphylococci cells (10(1)-10(7) cells). These results indicate that this method is useful for the identification and quantitative analysis of S. capitis, S. haemolyticus and S. warneri.

Age differences in accuracy and choosing in eyewitness identification and face recognition.

PubMed

Searcy, J H; Bartlett, J C; Memon, A

1999-05-01

Studies of aging and face recognition show age-related increases in false recognitions of new faces. To explore implications of this false alarm effect, we had young and senior adults perform (1) three eye-witness identification tasks, using both target present and target absent lineups, and (2) and old/new recognition task in which a study list of faces was followed by a test including old and new faces, along with conjunctions of old faces. Compared with the young, seniors had lower accuracy and higher choosing rates on the lineups, and they also falsely recognized more new faces on the recognition test. However, after screening for perceptual processing deficits, there was no age difference in false recognition of conjunctions, or in discriminating old faces from conjunctions. We conclude that the false alarm effect generalizes to lineup identification, but does not extend to conjunction faces. The findings are consistent with age-related deficits in recollection of context and relative age invariance in perceptual integrative processes underlying the experience of familiarity.

Identification of tissue-specific targeting peptide

NASA Astrophysics Data System (ADS)

Jung, Eunkyoung; Lee, Nam Kyung; Kang, Sang-Kee; Choi, Seung-Hoon; Kim, Daejin; Park, Kisoo; Choi, Kihang; Choi, Yun-Jaie; Jung, Dong Hyun

2012-11-01

Using phage display technique, we identified tissue-targeting peptide sets that recognize specific tissues (bone-marrow dendritic cell, kidney, liver, lung, spleen and visceral adipose tissue). In order to rapidly evaluate tissue-specific targeting peptides, we performed machine learning studies for predicting the tissue-specific targeting activity of peptides on the basis of peptide sequence information using four machine learning models and isolated the groups of peptides capable of mediating selective targeting to specific tissues. As a representative liver-specific targeting sequence, the peptide "DKNLQLH" was selected by the sequence similarity analysis. This peptide has a high degree of homology with protein ligands which can interact with corresponding membrane counterparts. We anticipate that our models will be applicable to the prediction of tissue-specific targeting peptides which can recognize the endothelial markers of target tissues.

Effects of postidentification feedback on eyewitness identification and nonidentification confidence.

PubMed

Semmler, Carolyn; Brewer, Neil; Wells, Gary L

2004-04-01

Two experiments investigated new dimensions of the effect of confirming feedback on eyewitness identification confidence using target-absent and target-present lineups and (previously unused) unbiased witness instructions (i.e., "offender not present" option highlighted). In Experiment 1, participants viewed a crime video and were later asked to try to identify the thief from an 8-person target-absent photo array. Feedback inflated witness confidence for both mistaken identifications and correct lineup rejections. With target-present lineups in Experiment 2, feedback inflated confidence for correct and mistaken identifications and lineup rejections. Although feedback had no influence on the confidence-accuracy correlation, it produced clear overconfidence. Confidence inflation varied with the confidence measure reference point (i.e., retrospective vs. current confidence) and identification response latency.

Multiple-target tracking implementation in the ebCMOS camera system: the LUSIPHER prototype

NASA Astrophysics Data System (ADS)

Doan, Quang Tuyen; Barbier, Remi; Dominjon, Agnes; Cajgfinger, Thomas; Guerin, Cyrille

2012-06-01

The domain of the low light imaging systems progresses very fast, thanks to detection and electronic multiplication technology evolution, such as the emCCD (electron multiplying CCD) or the ebCMOS (electron bombarded CMOS). We present an ebCMOS camera system that is able to track every 2 ms more than 2000 targets with a mean number of photons per target lower than two. The point light sources (targets) are spots generated by a microlens array (Shack-Hartmann) used in adaptive optics. The Multiple-Target-Tracking designed and implemented on a rugged workstation is described. The results and the performances of the system on the identification and tracking are presented and discussed.

Decision time and confidence predict choosers' identification performance in photographic showups

PubMed Central

Sagana, Anna; Sporer, Siegfried L.; Wixted, John T.

2018-01-01

In vast contrast to the multitude of lineup studies that report on the link between decision time, confidence, and identification accuracy, only a few studies looked at these associations for showups, with results varying widely across studies. We therefore set out to test the individual and combined value of decision time and post-decision confidence for diagnosing the accuracy of positive showup decisions using confidence-accuracy characteristic curves and Bayesian analyses. Three-hundred-eighty-four participants viewed a stimulus event and were subsequently presented with two showups which could be target-present or target-absent. As expected, we found a negative decision time-accuracy and a positive post-decision confidence-accuracy correlation for showup selections. Confidence-accuracy characteristic curves demonstrated the expected additive effect of combining both postdictors. Likewise, Bayesian analyses, taking into account all possible target-presence base rate values showed that fast and confident identification decisions were more diagnostic than slow or less confident decisions, with the combination of both being most diagnostic for postdicting accurate and inaccurate decisions. The postdictive value of decision time and post-decision confidence was higher when the prior probability that the suspect is the perpetrator was high compared to when the prior probability that the suspect is the perpetrator was low. The frequent use of showups in practice emphasizes the importance of these findings for court proceedings. Overall, these findings support the idea that courts should have most trust in showup identifications that were made fast and confidently, and least in showup identifications that were made slowly and with low confidence. PMID:29346394

Decision time and confidence predict choosers' identification performance in photographic showups.

PubMed

Sauerland, Melanie; Sagana, Anna; Sporer, Siegfried L; Wixted, John T

2018-01-01

In vast contrast to the multitude of lineup studies that report on the link between decision time, confidence, and identification accuracy, only a few studies looked at these associations for showups, with results varying widely across studies. We therefore set out to test the individual and combined value of decision time and post-decision confidence for diagnosing the accuracy of positive showup decisions using confidence-accuracy characteristic curves and Bayesian analyses. Three-hundred-eighty-four participants viewed a stimulus event and were subsequently presented with two showups which could be target-present or target-absent. As expected, we found a negative decision time-accuracy and a positive post-decision confidence-accuracy correlation for showup selections. Confidence-accuracy characteristic curves demonstrated the expected additive effect of combining both postdictors. Likewise, Bayesian analyses, taking into account all possible target-presence base rate values showed that fast and confident identification decisions were more diagnostic than slow or less confident decisions, with the combination of both being most diagnostic for postdicting accurate and inaccurate decisions. The postdictive value of decision time and post-decision confidence was higher when the prior probability that the suspect is the perpetrator was high compared to when the prior probability that the suspect is the perpetrator was low. The frequent use of showups in practice emphasizes the importance of these findings for court proceedings. Overall, these findings support the idea that courts should have most trust in showup identifications that were made fast and confidently, and least in showup identifications that were made slowly and with low confidence.

Slowing down after a mild traumatic brain injury: a strategy to improve cognitive task performance?

PubMed

Ozen, Lana J; Fernandes, Myra A

2012-01-01

Long-term persistent attention and memory difficulties following a mild traumatic brain injury (TBI) often go undetected on standard neuropsychological tests, despite complaints by mild TBI individuals. We conducted a visual Repetition Detection working memory task to digits, in which we manipulated task difficulty by increasing cognitive load, to identify subtle deficits long after a mild TBI. Twenty-six undergraduate students with a self-report of one mild TBI, which occurred at least 6 months prior, and 31 non-head-injured controls took part in the study. Participants were not informed until study completion that the study's purpose was to examine cognitive changes following a mild TBI, to reduce the influence of "diagnosis threat" on performance. Neuropsychological tasks did not differentiate the groups, though mild TBI participants reported higher state anxiety levels. On our working memory task, the mild TBI group took significantly longer to accurately detect repeated targets on our task, suggesting that slowed information processing is a long-term consequence of mild TBI. Accuracy was comparable in the low-load condition and, unexpectedly, mild TBI performance surpassed that of controls in the high-load condition. Temporal analysis of target identification suggested a strategy difference between groups: mild TBI participants made a significantly greater number of accurate responses following the target's offset, and significantly fewer erroneous distracter responses prior to target onset, compared with controls. Results suggest that long after a mild TBI, high-functioning young adults invoke a strategy of delaying their identification of targets in order to maintain, and facilitate, accuracy on cognitively demanding tasks. © The Author 2011. Published by Oxford University Press. All rights reserved.

Social judgment of abortion: a black-sheep effect in a Catholic sheepfold.

PubMed

Bègue, L

2001-10-01

French Catholic participants (N = 340) with high or low religious identification read 1 of 8 scenarios presented as an interview with a female target 2 months after she had had an abortion. The experimental device varied situational pressure (pressure vs. no pressure), the target's religious social identity (Catholic vs. neutral), and the consequences of abortion for the target (positive vs. negative). The participants then rated the acceptability of the target's decision. The participants judged abortion more negatively in the no-pressure condition. Moreover, the participants with high religious identification judged abortion more negatively than did those with low religious identification. In partial support of a black-sheep effect, the participants with high religious identification judged the Catholic target more negatively than they judged the neutral one in some conditions (pressure, negative consequences). In other conditions (no pressure, both positive and negative consequences), the participants with low religious identification judged the Catholic target more positively than they judged the neutral one.

Cue combination in a combined feature contrast detection and figure identification task.

PubMed

Meinhardt, Günter; Persike, Malte; Mesenholl, Björn; Hagemann, Cordula

2006-11-01

Target figures defined by feature contrast in spatial frequency, orientation or both cues had to be detected in Gabor random fields and their shape had to be identified in a dual task paradigm. Performance improved with increasing feature contrast and was strongly correlated among both tasks. Subjects performed significantly better with combined cues than with single cues. The improvement due to cue summation was stronger than predicted by the assumption of independent feature specific mechanisms, and increased with the performance level achieved with single cues until it was limited by ceiling effects. Further, cue summation was also strongly correlated among tasks: when there was benefit due to the additional cue in feature contrast detection, there was also benefit in figure identification. For the same performance level achieved with single cues, cue summation was generally larger in figure identification than in feature contrast detection, indicating more benefit when processes of shape and surface formation are involved. Our results suggest that cue combination improves spatial form completion and figure-ground segregation in noisy environments, and therefore leads to more stable object vision.

Performance Characteristics of Compact Mobile LIFS (Laser-Induced Fluorescence Spectrum) Lidar

NASA Astrophysics Data System (ADS)

Tomida, Takayuki; Nishizawa, Naoto; Sakurai, Kosuke; Suganumata, Hikaru; Tsukada, Shodai; Song, Sung-Moo; Park, Ho-Dong; Saito, Yasunori

2016-06-01

We developed a compact but versatile laser-induced fluorescence spectrum (LIFS) lidar that has potential use for material or aerosol identification outside experimental rooms. The compactness and mobility of the LIFS lidar means observations can be more freely conducted at any place and any time. Its performance characteristics were validated by threedimensional fluorescence imaging of targets and remote detection of quasi bio/organic aerosols.

Non-Cooperative Target Recognition by Means of Singular Value Decomposition Applied to Radar High Resolution Range Profiles †

PubMed Central

López-Rodríguez, Patricia; Escot-Bocanegra, David; Fernández-Recio, Raúl; Bravo, Ignacio

2015-01-01

Radar high resolution range profiles are widely used among the target recognition community for the detection and identification of flying targets. In this paper, singular value decomposition is applied to extract the relevant information and to model each aircraft as a subspace. The identification algorithm is based on angle between subspaces and takes place in a transformed domain. In order to have a wide database of radar signatures and evaluate the performance, simulated range profiles are used as the recognition database while the test samples comprise data of actual range profiles collected in a measurement campaign. Thanks to the modeling of aircraft as subspaces only the valuable information of each target is used in the recognition process. Thus, one of the main advantages of using singular value decomposition, is that it helps to overcome the notable dissimilarities found in the shape and signal-to-noise ratio between actual and simulated profiles due to their difference in nature. Despite these differences, the recognition rates obtained with the algorithm are quite promising. PMID:25551484

Dissociating emotion-induced blindness and hypervision.

PubMed

Bocanegra, Bruno R; Zeelenberg, René

2009-12-01

Previous findings suggest that emotional stimuli sometimes improve (emotion-induced hypervision) and sometimes impair (emotion-induced blindness) the visual perception of subsequent neutral stimuli. We hypothesized that these differential carryover effects might be due to 2 distinct emotional influences in visual processing. On the one hand, emotional stimuli trigger a general enhancement in the efficiency of visual processing that can carry over onto other stimuli. On the other hand, emotional stimuli benefit from a stimulus-specific enhancement in later attentional processing at the expense of competing visual stimuli. We investigated whether detrimental (blindness) and beneficial (hypervision) carryover effects of emotion in perception can be dissociated within a single experimental paradigm. In 2 experiments, we manipulated the temporal competition for attention between an emotional cue word and a subsequent neutral target word by varying cue-target interstimulus interval (ISI) and cue visibility. Interestingly, emotional cues impaired target identification at short ISIs but improved target identification when competition was diminished by either increasing ISI or reducing cue visibility, suggesting that emotional significance of stimuli can improve and impair visual performance through distinct perceptual mechanisms.

Exploring the Process of Energy Generation in Pathophysiology by Targeted Metabolomics: Performance of a Simple and Quantitative Method.

PubMed

Riera-Borrull, Marta; Rodríguez-Gallego, Esther; Hernández-Aguilera, Anna; Luciano, Fedra; Ras, Rosa; Cuyàs, Elisabet; Camps, Jordi; Segura-Carretero, Antonio; Menendez, Javier A; Joven, Jorge; Fernández-Arroyo, Salvador

2016-01-01

Abnormalities in mitochondrial metabolism and regulation of energy balance contribute to human diseases. The consequences of high fat and other nutrient intake, and the resulting acquired mitochondrial dysfunction, are essential to fully understand common disorders, including obesity, cancer, and atherosclerosis. To simultaneously and noninvasively measure and quantify indirect markers of mitochondrial function, we have developed a method based on gas chromatography coupled to quadrupole-time of flight mass spectrometry and an electron ionization interface, and validated the system using plasma from patients with peripheral artery disease, human cancer cells, and mouse tissues. This approach was used to increase sensibility in the measurement of a wide dynamic range and chemical diversity of multiple intermediate metabolites used in energy metabolism. We demonstrate that our targeted metabolomics method allows for quick and accurate identification and quantification of molecules, including the measurement of small yet significant biological changes in experimental samples. The apparently low process variability required for its performance in plasma, cell lysates, and tissues allowed a rapid identification of correlations between interconnected pathways. Our results suggest that delineating the process of energy generation by targeted metabolomics can be a valid surrogate for predicting mitochondrial dysfunction in biological samples. Importantly, when used in plasma, targeted metabolomics should be viewed as a robust and noninvasive source of biomarkers in specific pathophysiological scenarios.

Exploring the Process of Energy Generation in Pathophysiology by Targeted Metabolomics: Performance of a Simple and Quantitative Method

NASA Astrophysics Data System (ADS)

Riera-Borrull, Marta; Rodríguez-Gallego, Esther; Hernández-Aguilera, Anna; Luciano, Fedra; Ras, Rosa; Cuyàs, Elisabet; Camps, Jordi; Segura-Carretero, Antonio; Menendez, Javier A.; Joven, Jorge; Fernández-Arroyo, Salvador

2016-01-01

Abnormalities in mitochondrial metabolism and regulation of energy balance contribute to human diseases. The consequences of high fat and other nutrient intake, and the resulting acquired mitochondrial dysfunction, are essential to fully understand common disorders, including obesity, cancer, and atherosclerosis. To simultaneously and noninvasively measure and quantify indirect markers of mitochondrial function, we have developed a method based on gas chromatography coupled to quadrupole-time of flight mass spectrometry and an electron ionization interface, and validated the system using plasma from patients with peripheral artery disease, human cancer cells, and mouse tissues. This approach was used to increase sensibility in the measurement of a wide dynamic range and chemical diversity of multiple intermediate metabolites used in energy metabolism. We demonstrate that our targeted metabolomics method allows for quick and accurate identification and quantification of molecules, including the measurement of small yet significant biological changes in experimental samples. The apparently low process variability required for its performance in plasma, cell lysates, and tissues allowed a rapid identification of correlations between interconnected pathways. Our results suggest that delineating the process of energy generation by targeted metabolomics can be a valid surrogate for predicting mitochondrial dysfunction in biological samples. Importantly, when used in plasma, targeted metabolomics should be viewed as a robust and noninvasive source of biomarkers in specific pathophysiological scenarios.

Comprehensive identification and structural characterization of target components from Gelsemium elegans by high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry based on accurate mass databases combined with MS/MS spectra.

PubMed

Liu, Yan-Chun; Xiao, Sa; Yang, Kun; Ling, Li; Sun, Zhi-Liang; Liu, Zhao-Ying

2017-06-01

This study reports an applicable analytical strategy of comprehensive identification and structure characterization of target components from Gelsemium elegans by using high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QqTOF MS) based on the use of accurate mass databases combined with MS/MS spectra. The databases created included accurate masses and elemental compositions of 204 components from Gelsemium and their structural data. The accurate MS and MS/MS spectra were acquired through data-dependent auto MS/MS mode followed by an extraction of the potential compounds from the LC-QqTOF MS raw data of the sample. The same was matched using the databases to search for targeted components in the sample. The structures for detected components were tentatively characterized by manually interpreting the accurate MS/MS spectra for the first time. A total of 57 components have been successfully detected and structurally characterized from the crude extracts of G. elegans, but has failed to differentiate some isomers. This analytical strategy is generic and efficient, avoids isolation and purification procedures, enables a comprehensive structure characterization of target components of Gelsemium and would be widely applicable for complicated mixtures that are derived from Gelsemium preparations. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Application of infrared uncooled cameras in surveillance systems

NASA Astrophysics Data System (ADS)

Dulski, R.; Bareła, J.; Trzaskawka, P.; PiÄ tkowski, T.

2013-10-01

The recent necessity to protect military bases, convoys and patrols gave serious impact to the development of multisensor security systems for perimeter protection. One of the most important devices used in such systems are IR cameras. The paper discusses technical possibilities and limitations to use uncooled IR camera in a multi-sensor surveillance system for perimeter protection. Effective ranges of detection depend on the class of the sensor used and the observed scene itself. Application of IR camera increases the probability of intruder detection regardless of the time of day or weather conditions. It also simultaneously decreased the false alarm rate produced by the surveillance system. The role of IR cameras in the system was discussed as well as technical possibilities to detect human being. Comparison of commercially available IR cameras, capable to achieve desired ranges was done. The required spatial resolution for detection, recognition and identification was calculated. The simulation of detection ranges was done using a new model for predicting target acquisition performance which uses the Targeting Task Performance (TTP) metric. Like its predecessor, the Johnson criteria, the new model bounds the range performance with image quality. The scope of presented analysis is limited to the estimation of detection, recognition and identification ranges for typical thermal cameras with uncooled microbolometer focal plane arrays. This type of cameras is most widely used in security systems because of competitive price to performance ratio. Detection, recognition and identification range calculations were made, and the appropriate results for the devices with selected technical specifications were compared and discussed.

Effect of attention on the detection and identification of masked spatial patterns.

PubMed

Põder, Endel

2005-01-01

The effect of attention on the detection and identification of vertically and horizontally oriented Gabor patterns in the condition of simultaneous masking with obliquely oriented Gabors was studied. Attention was manipulated by varying the set size in a visual-search experiment. In the first experiment, small target Gabors were presented on the background of larger masking Gabors. In the detection task, the effect of set size was as predicted by unlimited-capacity signal detection theory. In the orientation identification task, increasing the set size from 1 to 8 resulted in a much larger decline in performance. The results of the additional experiments suggest that attention can reduce the crowding effect of maskers.

Identification of New Drug Targets in Multi-Drug Resistant Bacterial Infections

DTIC Science & Technology

2012-10-01

readout from malachite green, which detects the presence of inorganic phosphate with a simple color change. We have performed preliminary tests, however...SK requires ATP as a co-factor, which substantially increases the background by reacting with the malachite green. For the coupled reaction of SK

Advancements in robust algorithm formulation for speaker identification of whispered speech

NASA Astrophysics Data System (ADS)

Fan, Xing

Whispered speech is an alternative speech production mode from neutral speech, which is used by talkers intentionally in natural conversational scenarios to protect privacy and to avoid certain content from being overheard/made public. Due to the profound differences between whispered and neutral speech in production mechanism and the absence of whispered adaptation data, the performance of speaker identification systems trained with neutral speech degrades significantly. This dissertation therefore focuses on developing a robust closed-set speaker recognition system for whispered speech by using no or limited whispered adaptation data from non-target speakers. This dissertation proposes the concept of "High''/"Low'' performance whispered data for the purpose of speaker identification. A variety of acoustic properties are identified that contribute to the quality of whispered data. An acoustic analysis is also conducted to compare the phoneme/speaker dependency of the differences between whispered and neutral data in the feature domain. The observations from those acoustic analysis are new in this area and also serve as a guidance for developing robust speaker identification systems for whispered speech. This dissertation further proposes two systems for speaker identification of whispered speech. One system focuses on front-end processing. A two-dimensional feature space is proposed to search for "Low''-quality performance based whispered utterances and separate feature mapping functions are applied to vowels and consonants respectively in order to retain the speaker's information shared between whispered and neutral speech. The other system focuses on speech-mode-independent model training. The proposed method generates pseudo whispered features from neutral features by using the statistical information contained in a whispered Universal Background model (UBM) trained from extra collected whispered data from non-target speakers. Four modeling methods are proposed for the transformation estimation in order to generate the pseudo whispered features. Both of the above two systems demonstrate a significant improvement over the baseline system on the evaluation data. This dissertation has therefore contributed to providing a scientific understanding of the differences between whispered and neutral speech as well as improved front-end processing and modeling method for speaker identification of whispered speech. Such advancements will ultimately contribute to improve the robustness of speech processing systems.

Enhanced terahertz imaging system performance analysis and design tool for concealed weapon identification

NASA Astrophysics Data System (ADS)

Murrill, Steven R.; Franck, Charmaine C.; Espinola, Richard L.; Petkie, Douglas T.; De Lucia, Frank C.; Jacobs, Eddie L.

2011-11-01

The U.S. Army Research Laboratory (ARL) and the U.S. Army Night Vision and Electronic Sensors Directorate (NVESD) have developed a terahertz-band imaging system performance model/tool for detection and identification of concealed weaponry. The details of the MATLAB-based model which accounts for the effects of all critical sensor and display components, and for the effects of atmospheric attenuation, concealment material attenuation, and active illumination, were reported on at the 2005 SPIE Europe Security & Defence Symposium (Brugge). An advanced version of the base model that accounts for both the dramatic impact that target and background orientation can have on target observability as related to specular and Lambertian reflections captured by an active-illumination-based imaging system, and for the impact of target and background thermal emission, was reported on at the 2007 SPIE Defense and Security Symposium (Orlando). This paper will provide a comprehensive review of an enhanced, user-friendly, Windows-executable, terahertz-band imaging system performance analysis and design tool that now includes additional features such as a MODTRAN-based atmospheric attenuation calculator and advanced system architecture configuration inputs that allow for straightforward performance analysis of active or passive systems based on scanning (single- or line-array detector element(s)) or staring (focal-plane-array detector elements) imaging architectures. This newly enhanced THz imaging system design tool is an extension of the advanced THz imaging system performance model that was developed under the Defense Advanced Research Project Agency's (DARPA) Terahertz Imaging Focal-Plane Technology (TIFT) program. This paper will also provide example system component (active-illumination source and detector) trade-study analyses using the new features of this user-friendly THz imaging system performance analysis and design tool.

Does methodology matter in eyewitness identification research? The effect of live versus video exposure on eyewitness identification accuracy.

PubMed

Pozzulo, Joanna D; Crescini, Charmagne; Panton, Tasha

2008-01-01

The present study examined the effect of mode of target exposure (live versus video) on eyewitness identification accuracy. Adult participants (N=104) were exposed to a staged crime that they witnessed either live or on videotape. Participants were then asked to rate their stress and arousal levels prior to being presented with either a target-present or -absent simultaneous lineup. Across target-present and -absent lineups, mode of target exposure did not have a significant effect on identification accuracy. However, mode of target exposure was found to have a significant effect on stress and arousal levels. Participants who witnessed the crime live had higher levels of stress and arousal than those who were exposed to the videotaped crime. A higher level of arousal was significantly related to poorer identification accuracy for those in the video condition. For participants in the live condition however, stress and arousal had no effect on eyewitness identification accuracy. Implications of these findings in regards to the generalizability of laboratory-based research on eyewitness testimony to real-life crime are discussed.

Identification of Direct Target Genes Using Joint Sequence and Expression Likelihood with Application to DAF-16

PubMed Central

Yu, Ron X.; Liu, Jie; True, Nick; Wang, Wei

2008-01-01

A major challenge in the post-genome era is to reconstruct regulatory networks from the biological knowledge accumulated up to date. The development of tools for identifying direct target genes of transcription factors (TFs) is critical to this endeavor. Given a set of microarray experiments, a probabilistic model called TRANSMODIS has been developed which can infer the direct targets of a TF by integrating sequence motif, gene expression and ChIP-chip data. The performance of TRANSMODIS was first validated on a set of transcription factor perturbation experiments (TFPEs) involving Pho4p, a well studied TF in Saccharomyces cerevisiae. TRANSMODIS removed elements of arbitrariness in manual target gene selection process and produced results that concur with one's intuition. TRANSMODIS was further validated on a genome-wide scale by comparing it with two other methods in Saccharomyces cerevisiae. The usefulness of TRANSMODIS was then demonstrated by applying it to the identification of direct targets of DAF-16, a critical TF regulating ageing in Caenorhabditis elegans. We found that 189 genes were tightly regulated by DAF-16. In addition, DAF-16 has differential preference for motifs when acting as an activator or repressor, which awaits experimental verification. TRANSMODIS is computationally efficient and robust, making it a useful probabilistic framework for finding immediate targets. PMID:18350157

Retrospective Cost Adaptive Control with Concurrent Closed-Loop Identification

NASA Astrophysics Data System (ADS)

Sobolic, Frantisek M.

Retrospective cost adaptive control (RCAC) is a discrete-time direct adaptive control algorithm for stabilization, command following, and disturbance rejection. RCAC is known to work on systems given minimal modeling information which is the leading numerator coefficient and any nonminimum-phase (NMP) zeros of the plant transfer function. This information is normally needed a priori and is key in the development of the filter, also known as the target model, within the retrospective performance variable. A novel approach to alleviate the need for prior modeling of both the leading coefficient of the plant transfer function as well as any NMP zeros is developed. The extension to the RCAC algorithm is the use of concurrent optimization of both the target model and the controller coefficients. Concurrent optimization of the target model and controller coefficients is a quadratic optimization problem in the target model and controller coefficients separately. However, this optimization problem is not convex as a joint function of both variables, and therefore nonconvex optimization methods are needed. Finally, insights within RCAC that include intercalated injection between the controller numerator and the denominator, unveil the workings of RCAC fitting a specific closed-loop transfer function to the target model. We exploit this interpretation by investigating several closed-loop identification architectures in order to extract this information for use in the target model.

Spectral imaging of chemical compounds using multivariate optically enhanced filters integrated with InGaAs VGA cameras

NASA Astrophysics Data System (ADS)

Priore, Ryan J.; Jacksen, Niels

2016-05-01

Infrared hyperspectral imagers (HSI) have been fielded for the detection of hazardous chemical and biological compounds, tag detection (friend versus foe detection) and other defense critical sensing missions over the last two decades. Low Size/Weight/Power/Cost (SWaPc) methods of identification of chemical compounds spectroscopy has been a long term goal for hand held applications. We describe a new HSI concept for low cost / high performance InGaAs SWIR camera chemical identification for military, security, industrial and commercial end user applications. Multivariate Optical Elements (MOEs) are thin-film devices that encode a broadband, spectroscopic pattern allowing a simple broadband detector to generate a highly sensitive and specific detection for a target analyte. MOEs can be matched 1:1 to a discrete analyte or class prediction. Additionally, MOE filter sets are capable of sensing an orthogonal projection of the original sparse spectroscopic space enabling a small set of MOEs to discriminate a multitude of target analytes. This paper identifies algorithms and broadband optical filter designs that have been demonstrated to identify chemical compounds using high performance InGaAs VGA detectors. It shows how some of the initial models have been reduced to simple spectral designs and tested to produce positive identification of such chemicals. We also are developing pixilated MOE compressed detection sensors for the detection of a multitude of chemical targets in challenging backgrounds/environments for both commercial and defense/security applications. This MOE based, real-time HSI sensor will exhibit superior sensitivity and specificity as compared to currently fielded HSI systems.

Detergent Lysis of Animal Tissues for Immunoprecipitation.

PubMed

DeCaprio, James; Kohl, Thomas O

2017-12-01

This protocol details protein extraction from mouse tissues for immunoprecipitation purposes and has been applied for the performance of large-scale immunoprecipitations of target proteins from various tissues for the identification of associated proteins by mass spectroscopy. The key factors in performing a successful immunoprecipitation directly relate to the abundance of target protein in a particular tissue type and whether or not the embryonic, newborn, or adult mouse-derived tissues contain fibrous and other insoluble material. Several tissue types, including lung and liver as well as carcinomas, contain significant amounts of fibrous tissue that can interfere with an immunoprecipitation. © 2017 Cold Spring Harbor Laboratory Press.

Strategic relatedness in mergers and financial performance: the case of the health maintenance organization industry in the United States.

PubMed

Weech-Maldonado, Robert

2002-11-01

Knowledge and identification of strategic factors associated with favourable post-acquisition performance can be of benefit to both managers and shareholders. From a management perspective, the identification of contextual factors that can influence postmerger performance is 'strategic' in nature, and should be considered in the analysis of future acquisitions. Within the context of the health maintenance organization (HMO) industry, this study examines the impact of strategic relatedness on postmerger financial performance. Strategic relatedness is conceptualized as similarity between the acquirer and target HMOs in terms of operational efficiency, marketing orientation, organizational structure and profit orientation. Regression analysis showed that similarity in operational efficiency and similarity in HMO structure were associated with better postmerger financial performance. However, marketing orientation similarity and profit orientation similarity were not significantly related to postmerger performance. This finding suggests that HMO mergers involving firms with similar strategic orientations and similar approaches to the delivery of care have greater strategic fit and experience better financial performance.

Local structure preserving sparse coding for infrared target recognition

PubMed Central

Han, Jing; Yue, Jiang; Zhang, Yi; Bai, Lianfa

2017-01-01

Sparse coding performs well in image classification. However, robust target recognition requires a lot of comprehensive template images and the sparse learning process is complex. We incorporate sparsity into a template matching concept to construct a local sparse structure matching (LSSM) model for general infrared target recognition. A local structure preserving sparse coding (LSPSc) formulation is proposed to simultaneously preserve the local sparse and structural information of objects. By adding a spatial local structure constraint into the classical sparse coding algorithm, LSPSc can improve the stability of sparse representation for targets and inhibit background interference in infrared images. Furthermore, a kernel LSPSc (K-LSPSc) formulation is proposed, which extends LSPSc to the kernel space to weaken the influence of the linear structure constraint in nonlinear natural data. Because of the anti-interference and fault-tolerant capabilities, both LSPSc- and K-LSPSc-based LSSM can implement target identification based on a simple template set, which just needs several images containing enough local sparse structures to learn a sufficient sparse structure dictionary of a target class. Specifically, this LSSM approach has stable performance in the target detection with scene, shape and occlusions variations. High performance is demonstrated on several datasets, indicating robust infrared target recognition in diverse environments and imaging conditions. PMID:28323824

Construction of a directed hammerhead ribozyme library: towards the identification of optimal target sites for antisense-mediated gene inhibition.

PubMed Central

Pierce, M L; Ruffner, D E

1998-01-01

Antisense-mediated gene inhibition uses short complementary DNA or RNA oligonucleotides to block expression of any mRNA of interest. A key parameter in the success or failure of an antisense therapy is the identification of a suitable target site on the chosen mRNA. Ultimately, the accessibility of the target to the antisense agent determines target suitability. Since accessibility is a function of many complex factors, it is currently beyond our ability to predict. Consequently, identification of the most effective target(s) requires examination of every site. Towards this goal, we describe a method to construct directed ribozyme libraries against any chosen mRNA. The library contains nearly equal amounts of ribozymes targeting every site on the chosen transcript and the library only contains ribozymes capable of binding to that transcript. Expression of the ribozyme library in cultured cells should allow identification of optimal target sites under natural conditions, subject to the complexities of a fully functional cell. Optimal target sites identified in this manner should be the most effective sites for therapeutic intervention. PMID:9801305

Target detection cycle criteria when using the targeting task performance metric

NASA Astrophysics Data System (ADS)

Hixson, Jonathan G.; Jacobs, Eddie L.; Vollmerhausen, Richard H.

2004-12-01

The US Army RDECOM CERDEC Night Vision and Electronic Sensors Directorate of the US Army (NVESD) has developed a new target acquisition metric to better predict the performance of modern electro-optical imagers. The TTP metric replaces the Johnson criteria. One problem with transitioning to the new model is that the difficulty of searching in a terrain has traditionally been quantified by an "N50." The N50 is the number of Johnson criteria cycles needed for the observer to detect the target half the time, assuming that the observer is not time limited. In order to make use of this empirical data base, a conversion must be found relating Johnson cycles for detection to TTP cycles for detection. This paper describes how that relationship is established. We have found that the relationship between Johnson and TTP is 1:2.7 for the recognition and identification tasks.

GEPSI: A Gene Expression Profile Similarity-Based Identification Method of Bioactive Components in Traditional Chinese Medicine Formula.

PubMed

Zhang, Baixia; He, Shuaibing; Lv, Chenyang; Zhang, Yanling; Wang, Yun

2018-01-01

The identification of bioactive components in traditional Chinese medicine (TCM) is an important part of the TCM material foundation research. Recently, molecular docking technology has been extensively used for the identification of TCM bioactive components. However, target proteins that are used in molecular docking may not be the actual TCM target. For this reason, the bioactive components would likely be omitted or incorrect. To address this problem, this study proposed the GEPSI method that identified the target proteins of TCM based on the similarity of gene expression profiles. The similarity of the gene expression profiles affected by TCM and small molecular drugs was calculated. The pharmacological action of TCM may be similar to that of small molecule drugs that have a high similarity score. Indeed, the target proteins of the small molecule drugs could be considered TCM targets. Thus, we identified the bioactive components of a TCM by molecular docking and verified the reliability of this method by a literature investigation. Using the target proteins that TCM actually affected as targets, the identification of the bioactive components was more accurate. This study provides a fast and effective method for the identification of TCM bioactive components.

GEPSI: A Gene Expression Profile Similarity-Based Identification Method of Bioactive Components in Traditional Chinese Medicine Formula

PubMed Central

Zhang, Baixia; He, Shuaibing; Lv, Chenyang; Zhang, Yanling

2018-01-01

The identification of bioactive components in traditional Chinese medicine (TCM) is an important part of the TCM material foundation research. Recently, molecular docking technology has been extensively used for the identification of TCM bioactive components. However, target proteins that are used in molecular docking may not be the actual TCM target. For this reason, the bioactive components would likely be omitted or incorrect. To address this problem, this study proposed the GEPSI method that identified the target proteins of TCM based on the similarity of gene expression profiles. The similarity of the gene expression profiles affected by TCM and small molecular drugs was calculated. The pharmacological action of TCM may be similar to that of small molecule drugs that have a high similarity score. Indeed, the target proteins of the small molecule drugs could be considered TCM targets. Thus, we identified the bioactive components of a TCM by molecular docking and verified the reliability of this method by a literature investigation. Using the target proteins that TCM actually affected as targets, the identification of the bioactive components was more accurate. This study provides a fast and effective method for the identification of TCM bioactive components. PMID:29692857

Identification of Vibrio parahaemolyticus Strains at the Species Level by PCR Targeted to the toxR Gene

PubMed Central

Kim, Yung Bu; Okuda, Jun; Matsumoto, Chiho; Takahashi, Naoki; Hashimoto, Satoru; Nishibuchi, Mitsuaki

1999-01-01

The DNA colony hybridization test with the polynucleotide probe for Vibrio parahaemolyticus toxR gene was performed. All 373 strains of V. parahaemolyticus gave positive results, and the strains belonging to four other Vibrio species including Vibrio alginolyticus gave weakly positive results, suggesting that toxR sequence variation may reflect the phylogenetic relationships of Vibrio species. We then established a toxR-targeted PCR protocol for the specific detection of V. parahaemolyticus. PMID:10074546

Uridine monophosphate kinase as potential target for tuberculosis: from target to lead identification.

PubMed

Arvind, Akanksha; Jain, Vaibhav; Saravanan, Parameswaran; Mohan, C Gopi

2013-12-01

Mycobacterium tuberculosis (Mtb) is a causative agent of tuberculosis (TB) disease, which has affected approximately 2 billion people worldwide. Due to the emergence of resistance towards the existing drugs, discovery of new anti-TB drugs is an important global healthcare challenge. To address this problem, there is an urgent need to identify new drug targets in Mtb. In the present study, the subtractive genomics approach has been employed for the identification of new drug targets against TB. Screening the Mtb proteome using the Database of Essential Genes (DEG) and human proteome resulted in the identification of 60 key proteins which have no eukaryotic counterparts. Critical analysis of these proteins using Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways database revealed uridine monophosphate kinase (UMPK) enzyme as a potential drug target for developing novel anti-TB drugs. Homology model of Mtb-UMPK was constructed for the first time on the basis of the crystal structure of E. coli-UMPK, in order to understand its structure-function relationships, and which would in turn facilitate to perform structure-based inhibitor design. Furthermore, the structural similarity search was carried out using physiological inhibitor UTP of Mtb-UMPK to virtually screen ZINC database. Retrieved hits were further screened by implementing several filters like ADME and toxicity followed by molecular docking. Finally, on the basis of the Glide docking score and the mode of binding, 6 putative leads were identified as inhibitors of this enzyme which can potentially emerge as future drugs for the treatment of TB.

Unveiling the identity of distant targets through advanced Raman-laser-induced breakdown spectroscopy data fusion strategies.

PubMed

Moros, Javier; Javier Laserna, J

2015-03-01

Data fusion is the process of combining data gathered from two or more sensors to produce a more specific, comprehensive and unified dataset of the inspected target. On this basis, much has been said about the possible benefits resulting from the use of molecular and atomic information for the detection of explosives. The orthogonal nature of the spectral and compositional information provided by Raman spectroscopy and laser-induced breakdown spectroscopy (LIBS) makes them suitable candidates for an optimal combination of their data, thus achieving inferences that are not feasible using a single sensor. The present manuscript evaluates several architectures for the combination of spectral outputs from these two sensors in order to compare the benefits and drawbacks of data fusion for improving the overall identification performance. From the simple assembling (concatenation or addition) of Raman and LIBS spectra to signals' processing on the basis of linear algebra (either the outer product or the outer sum), different identification patterns of several compounds (explosives, potential confusants and supports) have been built. The efficiency on target differentiation by using each of the architectures has been evaluated by comparing the identification yield obtained for all the inspected targets from correlation and similarity measurements. Additionally, a specific code integrated by several of these patterns to identify each compound has also been evaluated. This approach permits to obtain a better knowledge about the identity of an interrogated target, mainly in those decisive cases in which LIBS or Raman cannot be effective separately to reach a decision. Copyright © 2014 Elsevier B.V. All rights reserved.

Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation

PubMed Central

Qian, Jiang; Esumi, Noriko; Chen, Yangjian; Wang, Qingliang; Chowers, Itay; Zack, Donald J.

2005-01-01

Identification of tissue-specific gene regulatory networks can yield insights into the molecular basis of a tissue's development, function and pathology. Here, we present a computational approach designed to identify potential regulatory target genes of photoreceptor cell-specific transcription factors (TFs). The approach is based on the hypothesis that genes related to the retina in terms of expression, disease and/or function are more likely to be the targets of retina-specific TFs than other genes. A list of genes that are preferentially expressed in retina was obtained by integrating expressed sequence tag, SAGE and microarray datasets. The regulatory targets of retina-specific TFs are enriched in this set of retina-related genes. A Bayesian approach was employed to integrate information about binding site location relative to a gene's transcription start site. Our method was applied to three retina-specific TFs, CRX, NRL and NR2E3, and a number of potential targets were predicted. To experimentally assess the validity of the bioinformatic predictions, mobility shift, transient transfection and chromatin immunoprecipitation assays were performed with five predicted CRX targets, and the results were suggestive of CRX regulation in 5/5, 3/5 and 4/5 cases, respectively. Together, these experiments strongly suggest that RP1, GUCY2D, ABCA4 are novel targets of CRX. PMID:15967807

Approximate Arithmetic Training Improves Informal Math Performance in Low Achieving Preschoolers

PubMed Central

Szkudlarek, Emily; Brannon, Elizabeth M.

2018-01-01

Recent studies suggest that practice with approximate and non-symbolic arithmetic problems improves the math performance of adults, school aged children, and preschoolers. However, the relative effectiveness of approximate arithmetic training compared to available educational games, and the type of math skills that approximate arithmetic targets are unknown. The present study was designed to (1) compare the effectiveness of approximate arithmetic training to two commercially available numeral and letter identification tablet applications and (2) to examine the specific type of math skills that benefit from approximate arithmetic training. Preschool children (n = 158) were pseudo-randomly assigned to one of three conditions: approximate arithmetic, letter identification, or numeral identification. All children were trained for 10 short sessions and given pre and post tests of informal and formal math, executive function, short term memory, vocabulary, alphabet knowledge, and number word knowledge. We found a significant interaction between initial math performance and training condition, such that children with low pretest math performance benefited from approximate arithmetic training, and children with high pretest math performance benefited from symbol identification training. This effect was restricted to informal, and not formal, math problems. There were also effects of gender, socio-economic status, and age on post-test informal math score after intervention. A median split on pretest math ability indicated that children in the low half of math scores in the approximate arithmetic training condition performed significantly better than children in the letter identification training condition on post-test informal math problems when controlling for pretest, age, gender, and socio-economic status. Our results support the conclusion that approximate arithmetic training may be especially effective for children with low math skills, and that approximate arithmetic training improves early informal, but not formal, math skills. PMID:29867624

Approximate Arithmetic Training Improves Informal Math Performance in Low Achieving Preschoolers.

PubMed

Szkudlarek, Emily; Brannon, Elizabeth M

2018-01-01

Recent studies suggest that practice with approximate and non-symbolic arithmetic problems improves the math performance of adults, school aged children, and preschoolers. However, the relative effectiveness of approximate arithmetic training compared to available educational games, and the type of math skills that approximate arithmetic targets are unknown. The present study was designed to (1) compare the effectiveness of approximate arithmetic training to two commercially available numeral and letter identification tablet applications and (2) to examine the specific type of math skills that benefit from approximate arithmetic training. Preschool children ( n = 158) were pseudo-randomly assigned to one of three conditions: approximate arithmetic, letter identification, or numeral identification. All children were trained for 10 short sessions and given pre and post tests of informal and formal math, executive function, short term memory, vocabulary, alphabet knowledge, and number word knowledge. We found a significant interaction between initial math performance and training condition, such that children with low pretest math performance benefited from approximate arithmetic training, and children with high pretest math performance benefited from symbol identification training. This effect was restricted to informal, and not formal, math problems. There were also effects of gender, socio-economic status, and age on post-test informal math score after intervention. A median split on pretest math ability indicated that children in the low half of math scores in the approximate arithmetic training condition performed significantly better than children in the letter identification training condition on post-test informal math problems when controlling for pretest, age, gender, and socio-economic status. Our results support the conclusion that approximate arithmetic training may be especially effective for children with low math skills, and that approximate arithmetic training improves early informal, but not formal, math skills.

Constraints in distortion-invariant target recognition system simulation

NASA Astrophysics Data System (ADS)

Iftekharuddin, Khan M.; Razzaque, Md A.

2000-11-01

Automatic target recognition (ATR) is a mature but active research area. In an earlier paper, we proposed a novel ATR approach for recognition of targets varying in fine details, rotation, and translation using a Learning Vector Quantization (LVQ) Neural Network (NN). The proposed approach performed segmentation of multiple objects and the identification of the objects using LVQNN. In this current paper, we extend the previous approach for recognition of targets varying in rotation, translation, scale, and combination of all three distortions. We obtain the analytical results of the system level design to show that the approach performs well with some constraints. The first constraint determines the size of the input images and input filters. The second constraint shows the limits on amount of rotation, translation, and scale of input objects. We present the simulation verification of the constraints using DARPA's Moving and Stationary Target Recognition (MSTAR) images with different depression and pose angles. The simulation results using MSTAR images verify the analytical constraints of the system level design.

Phage display biopanning and isolation of target-unrelated peptides: in search of nonspecific binders hidden in a combinatorial library.

PubMed

Bakhshinejad, Babak; Zade, Hesam Motaleb; Shekarabi, Hosna Sadat Zahed; Neman, Sara

2016-12-01

Phage display is known as a powerful methodology for the identification of targeting ligands that specifically bind to a variety of targets. The high-throughput screening of phage display combinatorial peptide libraries is performed through the affinity selection method of biopanning. Although phage display selection has proven very successful in the discovery of numerous high-affinity target-binding peptides with potential application in drug discovery and delivery, the enrichment of false-positive target-unrelated peptides (TUPs) without any actual affinity towards the target remains a major problem of library screening. Selection-related TUPs may emerge because of binding to the components of the screening system rather than the target. Propagation-related TUPs may arise as a result of faster growth rate of some phage clones enabling them to outcompete slow-propagating clones. Amplification of the library between rounds of biopanning makes a significant contribution to the selection of phage clones with propagation advantage. Distinguishing nonspecific TUPs from true target binders is of particular importance for the translation of biopanning findings from basic research to clinical applications. Different experimental and in silico approaches are applied to assess the specificity of phage display-derived peptides towards the target. Bioinformatic tools are playing a rapidly growing role in the analysis of biopanning data and identification of target-irrelevant TUPs. Recent progress in the introduction of efficient strategies for TUP detection holds enormous promise for the discovery of clinically relevant cell- and tissue-homing peptides and paves the way for the development of novel targeted diagnostic and therapeutic platforms in pharmaceutical areas.

Blended shared control utilizing online identification : Regulating grasping forces of a surrogate surgical grasper.

PubMed

Stephens, Trevor K; Kong, Nathan J; Dockter, Rodney L; O'Neill, John J; Sweet, Robert M; Kowalewski, Timothy M

2018-06-01

Surgical robots are increasingly common, yet routine tasks such as tissue grasping remain potentially harmful with high occurrences of tissue crush injury due to the lack of force feedback from the grasper. This work aims to investigate whether a blended shared control framework which utilizes real-time identification of the object being grasped as part of the feedback may help address the prevalence of tissue crush injury in robotic surgeries. This work tests the proposed shared control framework and tissue identification algorithm on a custom surrogate surgical robotic grasping setup. This scheme utilizes identification of the object being grasped as part of the feedback to regulate to a desired force. The blended shared control is arbitrated between human and an implicit force controller based on a computed confidence in the identification of the grasped object. The online identification is performed using least squares based on a nonlinear tissue model. Testing was performed on five silicone tissue surrogates. Twenty grasps were conducted, with half of the grasps performed under manual control and half of the grasps performed with the proposed blended shared control, to test the efficacy of the control scheme. The identification method resulted in an average of 95% accuracy across all time samples of all tissue grasps using a full leave-grasp-out cross-validation. There was an average convergence time of [Formula: see text] ms across all training grasps for all tissue surrogates. Additionally, there was a reduction in peak forces induced during grasping for all tissue surrogates when applying blended shared control online. The blended shared control using online identification more successfully regulated grasping forces to the desired target force when compared with manual control. The preliminary work on this surrogate setup for surgical grasping merits further investigation on real surgical tools and with real human tissues.

Novel toggle-rate based energy-efficient scheme for heavy load real-time IM-DD OFDM-PON with ONU LLID identification in time-domain using amplitude decision.

PubMed

Qin, Youxiang; Zhang, Junjie

2017-07-10

A novel low complexity and energy-efficient scheme by controlling the toggle-rate of ONU with time-domain amplitude identification is proposed for a heavy load downlink in an intensity-modulation and direct-detection orthogonal frequency division multiplexing passive optical network (IM-DD OFDM-PON). In a conventional OFDM-PON downlink, all ONUs have to perform demodulation for all the OFDM frames in a broadcast way no matter whether the frames are targeted to or not, which causes a huge energy waste. However, in our scheme, the optical network unit (ONU) logical link identifications (LLIDs) are inserted into each downlink OFDM frame in time-domain at the optical line terminal (OLT) side. At the ONU side, the LLID is obtained with a low complexity and high precision amplitude identification method. The ONU sets the toggle-rate of demodulation module to zero when the frames are not targeted to, which avoids unnecessary digital signal processing (DSP) energy consumption. Compared with the sleep-mode methods consisting of clock recovery and synchronization, toggle-rate shows its advantage in fast changing, which is more suitable for the heavy load scenarios. Moreover, for the first time to our knowledge, the characteristics of the proposed scheme are investigated in a real-time IM-DD OFDM system, which performs well at the received optical power as low as -21dBm. The experimental results show that 25.1% energy consumption can be saved in the receiver compared to the conventional configurations.

Rapid polymerase chain reaction-based screening assay for bacterial biothreat agents.

PubMed

Yang, Samuel; Rothman, Richard E; Hardick, Justin; Kuroki, Marcos; Hardick, Andrew; Doshi, Vishal; Ramachandran, Padmini; Gaydos, Charlotte A

2008-04-01

To design and evaluate a rapid polymerase chain reaction (PCR)-based assay for detecting Eubacteria and performing early screening for selected Class A biothreat bacterial pathogens. The authors designed a two-step PCR-based algorithm consisting of an initial broad-based universal detection step, followed by specific pathogen identification targeted for identification of the Class A bacterial biothreat agents. A region in the bacterial 16S rRNA gene containing a highly variable sequence flanked by clusters of conserved sequences was chosen as the target for the PCR assay design. A previously described highly conserved region located within the 16S rRNA amplicon was selected as the universal probe (UniProbe, Integrated DNA Technology, Coralville, IA). Pathogen-specific TaqMan probes were designed for Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Performance of the assay was assessed using genomic DNA extracted from the aforementioned biothreat-related organisms (inactivated or surrogate) and other common bacteria. The UniProbe detected the presence of all tested Eubacteria (31/31) with high analytical sensitivity. The biothreat-specific probes accurately identified organisms down to the closely related species and genus level, but were unable to discriminate between very close surrogates, such as Yersinia philomiragia and Bacillus cereus. A simple, two-step PCR-based assay proved capable of both universal bacterial detection and identification of select Class A bacterial biothreat and biothreat-related pathogens. Although this assay requires confirmatory testing for definitive species identification, the method has great potential for use in ED-based settings for rapid diagnosis in cases of suspected Category A bacterial biothreat agents.

Cerebellar Patients Demonstrate Preserved Implicit Knowledge of Association Strengths in Musical Sequences

ERIC Educational Resources Information Center

Tillmann, Barbara; Justus, Timothy; Bigand, Emmanuel

2008-01-01

Recent findings suggest the involvement of the cerebellum in perceptual and cognitive tasks. Our study investigated whether cerebellar patients show musical priming based on implicit knowledge of tonal-harmonic music. Participants performed speeded phoneme identification on sung target chords, which were either related or less-related to prime…

Relieving the attentional blink in the amblyopic brain with video games.

PubMed

Li, Roger W; Ngo, Charlie V; Levi, Dennis M

2015-02-26

Video game play induces a generalized recovery of a range of spatial visual functions in the amblyopic brain. Here we ask whether video game play also alters temporal processing in the amblyopic brain. When visual targets are presented in rapid succession, correct identification of the first target (T1) can interfere with identification of the second (T2). This is known as the "attentional blink". We measured the attentional blink in each eye of adults with amblyopia before and after 40 hours of active video game play, using a rapid serial visual presentation technique. After videogame play, we observed a ~40% reduction in the attentional blink (identifying T2 200 ms after T1) seen through the amblyopic eye and this improvement in performance transferred substantially to the untrained fellow sound eye. Our experiments show that the enhanced performance cannot be simply explained by eye patching alone, or to improved visual acuity, but is specific to videogame experience. Thus, videogame training might have important therapeutic applications for amblyopia and other visual brain disorders.

The aging eyewitness: effects of age on face, delay, and source-memory ability.

PubMed

Memon, Amina; Bartlett, James; Rose, Rachel; Gray, Colin

2003-11-01

As a way to examine the nature of age-related differences in lineup identification accuracy, young (16-33 years) and older (60-82 years) witnesses viewed two similar videotaped incidents, one involving a young perpetrator and the other involving an older perpetrator. The incidents were followed by two separate lineups, one for the younger perpetrator and one for the older perpetrator. When the test delay was short (35 min), the young and older witnesses performed similarly on the lineups, but when the tests were delayed by 1 week, the older witnesses were substantially less accurate. When the target was absent from the lineups, the older witnesses made more false alarm errors, particularly when the faces were young. When the target was present in the lineups, correct identifications by both young and older witnesses were positively correlated with a measure of source recollection derived from a separate face-recognition task. Older witnesses scored poorly on this measure, suggesting that source-recollection deficits are partially responsible for age-related differences in performance on the lineup task.

Passive Fingerprinting Of Computer Network Reconnaissance Tools

DTIC Science & Technology

2009-09-01

v6 for version 6 MITM : Man-In-The-Middle Attack MSS: Maximum Segment Size NOP: No Operation Performed NPS: Naval Postgraduate School OS...specific, or man-in-the- middle ( MITM ) attacks. Depending on the attacker’s position to access the targeted network, the attacker may be able to...identification numbers. Both are ordinarily supposed to be initialized as a random number to make it difficult for an attacker to perform an injection MITM

Examination of the mGluR mTOR Pathway for the Identification of Potential Therapeutic Targets To Treat Fragile X

DTIC Science & Technology

2016-11-01

Introduction Fragile X syndrome is the leading cause of intellectual disability resulting from a single gene mutation...performance, which measures motor learning and coordination. Treatment with metformin did not significantly affect performance in the rotarod task (Fig 5...marble burying, novel object recognition, object place memory, and reversal learning in the water Y maze (data not shown). It has been previously

Forecasting the ocean optical environment in support of Navy mine warfare operations

NASA Astrophysics Data System (ADS)

Ladner, S. D.; Arnone, R.; Jolliff, J.; Casey, B.; Matulewski, K.

2012-06-01

A 3D ocean optical forecast system called TODS (Tactical Ocean Data System) has been developed to determine the performance of underwater LIDAR detection/identification systems. TODS fuses optical measurements from gliders, surface satellite optical properties, and 3D ocean forecast circulation models to extend the 2-dimensional surface satellite optics into a 3-dimensional optical volume including subsurface optical layers of beam attenuation coefficient (c) and diver visibility. Optical 3D nowcast and forecasts are combined with electro-optical identification (EOID) models to determine the underwater LIDAR imaging performance field used to identify subsurface mine threats in rapidly changing coastal regions. TODS was validated during a recent mine warfare exercise with Helicopter Mine Countermeasures Squadron (HM-14). Results include the uncertainties in the optical forecast and lidar performance and sensor tow height predictions that are based on visual detection and identification metrics using actual mine target images from the EOID system. TODS is a new capability of coupling the 3D optical environment and EOID system performance and is proving important for the MIW community as both a tactical decision aid and for use in operational planning, improving timeliness and efficiency in clearance operations.

Context cue focality influences strategic prospective memory monitoring.

PubMed

Hunter Ball, B; Bugg, Julie M

2018-02-12

Monitoring the environment for the occurrence of prospective memory (PM) targets is a resource-demanding process that produces cost (e.g., slower responding) to ongoing activities. However, research suggests that individuals are able to monitor strategically by using contextual cues to reduce monitoring in contexts in which PM targets are not expected to occur. In the current study, we investigated the processes supporting context identification (i.e., determining whether or not the context is appropriate for monitoring) by testing the context cue focality hypothesis. This hypothesis predicts that the ability to monitor strategically depends on whether the ongoing task orients attention to the contextual cues that are available to guide monitoring. In Experiment 1, participants performed an ongoing lexical decision task and were told that PM targets (TOR syllable) would only occur in word trials (focal context cue condition) or in items starting with consonants (nonfocal context cue condition). In Experiment 2, participants performed an ongoing first letter judgment (consonant/vowel) task and were told that PM targets would only occur in items starting with consonants (focal context cue condition) or in word trials (nonfocal context cue condition). Consistent with the context cue focality hypothesis, strategic monitoring was only observed during focal context cue conditions in which the type of ongoing task processing automatically oriented attention to the relevant features of the contextual cue. These findings suggest that strategic monitoring is dependent on limited-capacity processing resources and may be relatively limited when the attentional demands of context identification are sufficiently high.

Selecting among competing models of electro-optic, infrared camera system range performance

USGS Publications Warehouse

Nichols, Jonathan M.; Hines, James E.; Nichols, James D.

2013-01-01

Range performance is often the key requirement around which electro-optical and infrared camera systems are designed. This work presents an objective framework for evaluating competing range performance models. Model selection based on the Akaike’s Information Criterion (AIC) is presented for the type of data collected during a typical human observer and target identification experiment. These methods are then demonstrated on observer responses to both visible and infrared imagery in which one of three maritime targets was placed at various ranges. We compare the performance of a number of different models, including those appearing previously in the literature. We conclude that our model-based approach offers substantial improvements over the traditional approach to inference, including increased precision and the ability to make predictions for some distances other than the specific set for which experimental trials were conducted.

How visual cues for when to listen aid selective auditory attention.

PubMed

Varghese, Lenny A; Ozmeral, Erol J; Best, Virginia; Shinn-Cunningham, Barbara G

2012-06-01

Visual cues are known to aid auditory processing when they provide direct information about signal content, as in lip reading. However, some studies hint that visual cues also aid auditory perception by guiding attention to the target in a mixture of similar sounds. The current study directly tests this idea for complex, nonspeech auditory signals, using a visual cue providing only timing information about the target. Listeners were asked to identify a target zebra finch bird song played at a random time within a longer, competing masker. Two different maskers were used: noise and a chorus of competing bird songs. On half of all trials, a visual cue indicated the timing of the target within the masker. For the noise masker, the visual cue did not affect performance when target and masker were from the same location, but improved performance when target and masker were in different locations. In contrast, for the chorus masker, visual cues improved performance only when target and masker were perceived as coming from the same direction. These results suggest that simple visual cues for when to listen improve target identification by enhancing sounds near the threshold of audibility when the target is energetically masked and by enhancing segregation when it is difficult to direct selective attention to the target. Visual cues help little when target and masker already differ in attributes that enable listeners to engage selective auditory attention effectively, including differences in spectrotemporal structure and in perceived location.

Distinct Leishmania Species Infecting Wild Caviomorph Rodents (Rodentia: Hystricognathi) from Brazil

PubMed Central

Cássia-Pires, Renata; Boité, Mariana C.; D'Andrea, Paulo S.; Herrera, Heitor M.; Cupolillo, Elisa; Jansen, Ana Maria; Roque, André Luiz R.

2014-01-01

Background Caviomorph rodents, some of the oldest Leishmania spp. hosts, are widely dispersed in Brazil. Despite both experimental and field studies having suggested that these rodents are potential reservoirs of Leishmania parasites, not more than 88 specimens were analyzed in the few studies of natural infection. Our hypothesis was that caviomorph rodents are inserted in the transmission cycles of Leishmania in different regions, more so than is currently recognized. Methodology We investigated the Leishmania infection in spleen fragments of 373 caviomorph rodents from 20 different species collected in five Brazilian biomes in a period of 13 years. PCR reactions targeting kDNA of Leishmania sp. were used to diagnose infection, while Leishmania species identification was performed by DNA sequencing of the amplified products obtained in the HSP70 (234) targeting. Serology by IFAT was performed on the available serum of these rodents. Principal findings In 13 caviomorph rodents, DNA sequencing analyses allowed the identification of 4 species of the subgenus L. (Viannia): L. shawi, L. guyanensis, L. naiffi, and L. braziliensis; and 1 species of the subgenus L. (Leishmania): L. infantum. These include the description of parasite species in areas not previously included in their known distribution: L. shawi in Thrichomys inermis from Northeastern Brazil and L. naiffi in T. fosteri from Western Brazil. From the four other positive rodents, two were positive for HSP70 (234) targeting but did not generate sequences that enabled the species identification, and another two were positive only in kDNA targeting. Conclusions/Significance The infection rate demonstrated by the serology (51.3%) points out that the natural Leishmania infection in caviomorph rodents is much higher than that observed in the molecular diagnosis (4.6%), highlighting that, in terms of the host species responsible for maintaining Leishmania species in the wild, our current knowledge represents only the “tip of the iceberg.” PMID:25503973

The effects of stimulus-driven competition and task set on involuntary attention

PubMed Central

Han, Suk Won; Marois, René

2014-01-01

It is well established that involuntary attention—the exogenous capture of attention by salient but task-irrelevant stimuli—can strongly modulate target detection and discrimination performance. There is an ongoing debate, however, about how involuntary attention affects target performance. Some studies suggest that it results from enhanced perception of the target, whereas others indicate instead that it affects decisional stages of information processing. From a review of these studies, we hypothesized that the presence of distractors and task sets are key factors in determining the effect of involuntary attention on target perception. Consistent with this hypothesis, here we found that noninformative cues summoning involuntary attention affected perceptual identification of a target when distractors were present. This cuing effect could not be attributed to reduced target location uncertainty or decision bias. The only condition under which involuntary attention improved target perception in the absence of distractors occurred when observers did not adopt a task set to focus attention on the target location. We conclude that the perceptual effects of involuntary attention depend on distractor interference and the adoption of a task set to resolve such stimulus competition. PMID:24970921

Camera calibration: active versus passive targets

NASA Astrophysics Data System (ADS)

Schmalz, Christoph; Forster, Frank; Angelopoulou, Elli

2011-11-01

Traditionally, most camera calibrations rely on a planar target with well-known marks. However, the localization error of the marks in the image is a source of inaccuracy. We propose the use of high-resolution digital displays as active calibration targets to obtain more accurate calibration results for all types of cameras. The display shows a series of coded patterns to generate correspondences between world points and image points. This has several advantages. No special calibration hardware is necessary because suitable displays are practically ubiquitious. The method is fully automatic, and no identification of marks is necessary. For a coding scheme based on phase shifting, the localization accuracy is approximately independent of the camera's focus settings. Most importantly, higher accuracy can be achieved compared to passive targets, such as printed checkerboards. A rigorous evaluation is performed to substantiate this claim. Our active target method is compared to standard calibrations using a checkerboard target. We perform camera, calibrations with different combinations of displays, cameras, and lenses, as well as with simulated images and find markedly lower reprojection errors when using active targets. For example, in a stereo reconstruction task, the accuracy of a system calibrated with an active target is five times better.

Feasibility of CRISPR-Cas9-Based In Vitro Drug Target Identification for Personalized Prostate Cancer Medicine

DTIC Science & Technology

2017-09-01

AWARD NUMBER: W81XWH-16-1-0502 TITLE: Feasibility of CRISPR -Cas9-Based In Vitro Drug Target Identification for Personalized Prostate Cancer Medicine...CONTRACT NUMBER Feasibility of CRISPR -Cas9-Based In Vitro Drug Target Identification for Personalized Prostate Cancer Medicine 5b. GRANT NUMBER...Approved for Public Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT This study tests the feasibility of using CRISPR -Cas9 to

Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data.

PubMed

Jayaswal, Vivek; Lutherborrow, Mark; Ma, David D F; Hwa Yang, Yee

2009-05-01

Over the past decade, a class of small RNA molecules called microRNAs (miRNAs) has been shown to regulate gene expression at the post-transcription stage. While early work focused on the identification of miRNAs using a combination of experimental and computational techniques, subsequent studies have focused on identification of miRNA-target mRNA pairs as each miRNA can have hundreds of mRNA targets. The experimental validation of some miRNAs as oncogenic has provided further motivation for research in this area. In this article we propose an odds-ratio (OR) statistic for identification of regulatory miRNAs. It is based on integrative analysis of matched miRNA and mRNA time-course microarray data. The OR-statistic was used for (i) identification of miRNAs with regulatory potential, (ii) identification of miRNA-target mRNA pairs and (iii) identification of time lags between changes in miRNA expression and those of its target mRNAs. We applied the OR-statistic to a cancer data set and identified a small set of miRNAs that were negatively correlated to mRNAs. A literature survey revealed that some of the miRNAs that were predicted to be regulatory, were indeed oncogenic or tumor suppressors. Finally, some of the predicted miRNA targets have been shown to be experimentally valid.

Ground target recognition using rectangle estimation.

PubMed

Grönwall, Christina; Gustafsson, Fredrik; Millnert, Mille

2006-11-01

We propose a ground target recognition method based on 3-D laser radar data. The method handles general 3-D scattered data. It is based on the fact that man-made objects of complex shape can be decomposed to a set of rectangles. The ground target recognition method consists of four steps; 3-D size and orientation estimation, target segmentation into parts of approximately rectangular shape, identification of segments that represent the target's functional/main parts, and target matching with CAD models. The core in this approach is rectangle estimation. The performance of the rectangle estimation method is evaluated statistically using Monte Carlo simulations. A case study on tank recognition is shown, where 3-D data from four fundamentally different types of laser radar systems are used. Although the approach is tested on rather few examples, we believe that the approach is promising.

Identification and Expression Analyses of miRNAs from Two Contrasting Flower Color Cultivars of Canna by Deep Sequencing.

PubMed

Roy, Sribash; Tripathi, Abhinandan Mani; Yadav, Amrita; Mishra, Parneeta; Nautiyal, Chandra Shekhar

2016-01-01

miRNAs are endogenous small RNA (sRNA) that play critical roles in plant development processes. Canna is an ornamental plant belonging to family Cannaceae. Here, we report for the first time the identification and differential expression of miRNAs in two contrasting flower color cultivars of Canna, Tropical sunrise and Red president. A total of 313 known miRNAs belonging to 78 miRNA families were identified from both the cultivars. Thirty one miRNAs (17 miRNA families) were specific to Tropical sunrise and 43 miRNAs (10 miRNA families) were specific to Red president. Thirty two and 18 putative new miRNAs were identified from Tropical sunrise and Red president, respectively. One hundred and nine miRNAs were differentially expressed in the two cultivars targeting 1343 genes. Among these, 16 miRNAs families targeting 60 genes were involved in flower development related traits and five miRNA families targeting five genes were involved in phenyl propanoid and pigment metabolic processes. We further validated the expression analysis of a few miRNA and their target genes by qRT-PCR. Transcription factors were the major miRNA targets identified. Target validation of a few randomly selected miRNAs by RLM-RACE was performed but was successful with only miR162. These findings will help in understanding flower development processes, particularly the color development in Canna.

The effect of normal aging and age-related macular degeneration on perceptual learning.

PubMed

Astle, Andrew T; Blighe, Alan J; Webb, Ben S; McGraw, Paul V

2015-01-01

We investigated whether perceptual learning could be used to improve peripheral word identification speed. The relationship between the magnitude of learning and age was established in normal participants to determine whether perceptual learning effects are age invariant. We then investigated whether training could lead to improvements in patients with age-related macular degeneration (AMD). Twenty-eight participants with normal vision and five participants with AMD trained on a word identification task. They were required to identify three-letter words, presented 10° from fixation. To standardize crowding across each of the letters that made up the word, words were flanked laterally by randomly chosen letters. Word identification performance was measured psychophysically using a staircase procedure. Significant improvements in peripheral word identification speed were demonstrated following training (71% ± 18%). Initial task performance was correlated with age, with older participants having poorer performance. However, older adults learned more rapidly such that, following training, they reached the same level of performance as their younger counterparts. As a function of number of trials completed, patients with AMD learned at an equivalent rate as age-matched participants with normal vision. Improvements in word identification speed were maintained at least 6 months after training. We have demonstrated that temporal aspects of word recognition can be improved in peripheral vision with training across a range of ages and these learned improvements are relatively enduring. However, training targeted at other bottlenecks to peripheral reading ability, such as visual crowding, may need to be incorporated to optimize this approach.

The effect of normal aging and age-related macular degeneration on perceptual learning

PubMed Central

Astle, Andrew T.; Blighe, Alan J.; Webb, Ben S.; McGraw, Paul V.

2015-01-01

We investigated whether perceptual learning could be used to improve peripheral word identification speed. The relationship between the magnitude of learning and age was established in normal participants to determine whether perceptual learning effects are age invariant. We then investigated whether training could lead to improvements in patients with age-related macular degeneration (AMD). Twenty-eight participants with normal vision and five participants with AMD trained on a word identification task. They were required to identify three-letter words, presented 10° from fixation. To standardize crowding across each of the letters that made up the word, words were flanked laterally by randomly chosen letters. Word identification performance was measured psychophysically using a staircase procedure. Significant improvements in peripheral word identification speed were demonstrated following training (71% ± 18%). Initial task performance was correlated with age, with older participants having poorer performance. However, older adults learned more rapidly such that, following training, they reached the same level of performance as their younger counterparts. As a function of number of trials completed, patients with AMD learned at an equivalent rate as age-matched participants with normal vision. Improvements in word identification speed were maintained at least 6 months after training. We have demonstrated that temporal aspects of word recognition can be improved in peripheral vision with training across a range of ages and these learned improvements are relatively enduring. However, training targeted at other bottlenecks to peripheral reading ability, such as visual crowding, may need to be incorporated to optimize this approach. PMID:26605694

C-mii: a tool for plant miRNA and target identification.

PubMed

Numnark, Somrak; Mhuantong, Wuttichai; Ingsriswang, Supawadee; Wichadakul, Duangdao

2012-01-01

MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce. To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management. C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms.

C-mii: a tool for plant miRNA and target identification

PubMed Central

2012-01-01

Background MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce. Results To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management. Conclusions C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms. PMID:23281648

Development of a rapid and simplified protocol for direct bacterial identification from positive blood cultures by using matrix assisted laser desorption ionization time-of- flight mass spectrometry.

PubMed

Jakovljev, Aleksandra; Bergh, Kåre

2015-11-06

Bloodstream infections represent serious conditions carrying a high mortality and morbidity rate. Rapid identification of microorganisms and prompt institution of adequate antimicrobial therapy is of utmost importance for a successful outcome. Aiming at the development of a rapid, simplified and efficient protocol, we developed and compared two in-house preparatory methods for the direct identification of bacteria from positive blood culture flasks (BD BACTEC FX system) by using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF MS). Both methods employed saponin and distilled water for erythrocyte lysis. In method A the cellular pellet was overlaid with formic acid on the MALDI TOF target plate for protein extraction, whereas in method B the pellet was exposed to formic acid followed by acetonitrile prior to placing on the target plate. Best results were obtained by method A. Direct identification was achieved for 81.9 % and 65.8 % (50.3 % and 26.2 % with scores >2.0) of organisms by method A and method B, respectively. Overall concordance with final identification was 100 % to genus and 97.9 % to species level. By applying a lower cut-off score value, the levels of identification obtained by method A and method B increased to 89.3 % and 77.8 % of organisms (81.9 % and 65.8 % identified with scores >1.7), respectively. Using the lowered score criteria, concordance with final results was obtained for 99.3 % of genus and 96.6 % of species identifications. The reliability of results, rapid performance (approximately 25 min) and applicability of in-house method A have contributed to implementation of this robust and cost-effective method in our laboratory.

Probability of identification: a statistical model for the validation of qualitative botanical identification methods.

PubMed

LaBudde, Robert A; Harnly, James M

2012-01-01

A qualitative botanical identification method (BIM) is an analytical procedure that returns a binary result (1 = Identified, 0 = Not Identified). A BIM may be used by a buyer, manufacturer, or regulator to determine whether a botanical material being tested is the same as the target (desired) material, or whether it contains excessive nontarget (undesirable) material. The report describes the development and validation of studies for a BIM based on the proportion of replicates identified, or probability of identification (POI), as the basic observed statistic. The statistical procedures proposed for data analysis follow closely those of the probability of detection, and harmonize the statistical concepts and parameters between quantitative and qualitative method validation. Use of POI statistics also harmonizes statistical concepts for botanical, microbiological, toxin, and other analyte identification methods that produce binary results. The POI statistical model provides a tool for graphical representation of response curves for qualitative methods, reporting of descriptive statistics, and application of performance requirements. Single collaborator and multicollaborative study examples are given.

Attitude identification for SCOLE using two infrared cameras

NASA Technical Reports Server (NTRS)

Shenhar, Joram

1991-01-01

An algorithm is presented that incorporates real time data from two infrared cameras and computes the attitude parameters of the Spacecraft COntrol Lab Experiment (SCOLE), a lab apparatus representing an offset feed antenna attached to the Space Shuttle by a flexible mast. The algorithm uses camera position data of three miniature light emitting diodes (LEDs), mounted on the SCOLE platform, permitting arbitrary camera placement and an on-line attitude extraction. The continuous nature of the algorithm allows identification of the placement of the two cameras with respect to some initial position of the three reference LEDs, followed by on-line six degrees of freedom attitude tracking, regardless of the attitude time history. A description is provided of the algorithm in the camera identification mode as well as the mode of target tracking. Experimental data from a reduced size SCOLE-like lab model, reflecting the performance of the camera identification and the tracking processes, are presented. Computer code for camera placement identification and SCOLE attitude tracking is listed.

Individual differences in selective attention predict speech identification at a cocktail party.

PubMed

Oberfeld, Daniel; Klöckner-Nowotny, Felicitas

2016-08-31

Listeners with normal hearing show considerable individual differences in speech understanding when competing speakers are present, as in a crowded restaurant. Here, we show that one source of this variance are individual differences in the ability to focus selective attention on a target stimulus in the presence of distractors. In 50 young normal-hearing listeners, the performance in tasks measuring auditory and visual selective attention was associated with sentence identification in the presence of spatially separated competing speakers. Together, the measures of selective attention explained a similar proportion of variance as the binaural sensitivity for the acoustic temporal fine structure. Working memory span, age, and audiometric thresholds showed no significant association with speech understanding. These results suggest that a reduced ability to focus attention on a target is one reason why some listeners with normal hearing sensitivity have difficulty communicating in situations with background noise.

Priming in implicit memory tasks: prior study causes enhanced discriminability, not only bias.

PubMed

Zeelenberg, René; Wagenmakers, Eric-Jan M; Raaijmakers, Jeroen G W

2002-03-01

R. Ratcliff and G. McKoon (1995, 1996, 1997; R. Ratcliff, D. Allbritton, & G. McKoon, 1997) have argued that repetition priming effects are solely due to bias. They showed that prior study of the target resulted in a benefit in a later implicit memory task. However, prior study of a stimulus similar to the target resulted in a cost. The present study, using a 2-alternative forced-choice procedure, investigated the effect of prior study in an unbiased condition: Both alternatives were studied prior to their presentation in an implicit memory task. Contrary to a pure bias interpretation of priming, consistent evidence was obtained in 3 implicit memory tasks (word fragment completion, auditory word identification, and picture identification) that performance was better when both alternatives were studied than when neither alternative was studied. These results show that prior study results in enhanced discriminability, not only bias.

Photonics: From target recognition to lesion detection

NASA Technical Reports Server (NTRS)

Henry, E. Michael

1994-01-01

Since 1989, Martin Marietta has invested in the development of an innovative concept for robust real-time pattern recognition for any two-dimensioanal sensor. This concept has been tested in simulation, and in laboratory and field hardware, for a number of DOD and commercial uses from automatic target recognition to manufacturing inspection. We have now joined Rose Health Care Systems in developing its use for medical diagnostics. The concept is based on determining regions of interest by using optical Fourier bandpassing as a scene segmentation technique, enhancing those regions using wavelet filters, passing the enhanced regions to a neural network for analysis and initial pattern identification, and following this initial identification with confirmation by optical correlation. The optical scene segmentation and pattern confirmation are performed by the same optical module. The neural network is a recursive error minimization network with a small number of connections and nodes that rapidly converges to a global minimum.

Neuromorphic Optical Signal Processing and Image Understanding for Automated Target Recognition

DTIC Science & Technology

1989-12-01

34 Stochastic Learning Machine " Neuromorphic Target Identification * Cognitive Networks 3. Conclusions ..... ................ .. 12 4. Publications...16 5. References ...... ................... . 17 6. Appendices ....... .................. 18 I. Optoelectronic Neural Networks and...Learning Machines. II. Stochastic Optical Learning Machine. III. Learning Network for Extrapolation AccesFon For and Radar Target Identification

Biased lineup instructions and face identification from video images.

PubMed

Thompson, W Burt; Johnson, Jaime

2008-01-01

Previous eyewitness memory research has shown that biased lineup instructions reduce identification accuracy, primarily by increasing false-positive identifications in target-absent lineups. Because some attempts at identification do not rely on a witness's memory of the perpetrator but instead involve matching photos to images on surveillance video, the authors investigated the effects of biased instructions on identification accuracy in a matching task. In Experiment 1, biased instructions did not affect the overall accuracy of participants who used video images as an identification aid, but nearly all correct decisions occurred with target-present photo spreads. Both biased and unbiased instructions resulted in high false-positive rates. In Experiment 2, which focused on video-photo matching accuracy with target-absent photo spreads, unbiased instructions led to more correct responses (i.e., fewer false positives). These findings suggest that investigators should not relax precautions against biased instructions when people attempt to match photos to an unfamiliar person recorded on video.

A new disaster victim identification management strategy targeting "near identification-threshold" cases: Experiences from the Boxing Day tsunami.

PubMed

Wright, Kirsty; Mundorff, Amy; Chaseling, Janet; Forrest, Alexander; Maguire, Christopher; Crane, Denis I

2015-05-01

The international disaster victim identification (DVI) response to the Boxing Day tsunami, led by the Royal Thai Police in Phuket, Thailand, was one of the largest and most complex in DVI history. Referred to as the Thai Tsunami Victim Identification operation, the group comprised a multi-national, multi-agency, and multi-disciplinary team. The traditional DVI approach proved successful in identifying a large number of victims quickly. However, the team struggled to identify certain victims due to incomplete or poor quality ante-mortem and post-mortem data. In response to these challenges, a new 'near-threshold' DVI management strategy was implemented to target presumptive identifications and improve operational efficiency. The strategy was implemented by the DNA Team, therefore DNA kinship matches that just failed to reach the reporting threshold of 99.9% were prioritized, however the same approach could be taken by targeting, for example, cases with partial fingerprint matches. The presumptive DNA identifications were progressively filtered through the Investigation, Dental and Fingerprint Teams to add additional information necessary to either strengthen or conclusively exclude the identification. Over a five-month period 111 victims from ten countries were identified using this targeted approach. The new identifications comprised 87 adults, 24 children and included 97 Thai locals. New data from the Fingerprint Team established nearly 60% of the total near-threshold identifications and the combined DNA/Physical method was responsible for over 30%. Implementing the new strategy, targeting near-threshold cases, had positive management implications. The process initiated additional ante-mortem information collections, and established a much-needed, distinct "end-point" for unresolved cases. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Implementation of statistical process control for proteomic experiments via LC MS/MS.

PubMed

Bereman, Michael S; Johnson, Richard; Bollinger, James; Boss, Yuval; Shulman, Nick; MacLean, Brendan; Hoofnagle, Andrew N; MacCoss, Michael J

2014-04-01

Statistical process control (SPC) is a robust set of tools that aids in the visualization, detection, and identification of assignable causes of variation in any process that creates products, services, or information. A tool has been developed termed Statistical Process Control in Proteomics (SProCoP) which implements aspects of SPC (e.g., control charts and Pareto analysis) into the Skyline proteomics software. It monitors five quality control metrics in a shotgun or targeted proteomic workflow. None of these metrics require peptide identification. The source code, written in the R statistical language, runs directly from the Skyline interface, which supports the use of raw data files from several of the mass spectrometry vendors. It provides real time evaluation of the chromatographic performance (e.g., retention time reproducibility, peak asymmetry, and resolution), and mass spectrometric performance (targeted peptide ion intensity and mass measurement accuracy for high resolving power instruments) via control charts. Thresholds are experiment- and instrument-specific and are determined empirically from user-defined quality control standards that enable the separation of random noise and systematic error. Finally, Pareto analysis provides a summary of performance metrics and guides the user to metrics with high variance. The utility of these charts to evaluate proteomic experiments is illustrated in two case studies.

Parallel Analysis of 124 Universal SNPs for Human Identification by Targeted Semiconductor Sequencing

PubMed Central

Zhang, Suhua; Bian, Yingnan; Zhang, Zheren; Zheng, Hancheng; Wang, Zheng; Zha, Lagabaiyila; Cai, Jifeng; Gao, Yuzhen; Ji, Chaoneng; Hou, Yiping; Li, Chengtao

2015-01-01

SNPs, abundant in human genome with lower mutation rate, are attractive to genetic application like forensic, anthropological and evolutionary studies. Universal SNPs showing little allelic frequency variation among populations while remaining highly informative for human identification were obtained from previous studies. However, genotyping tools target only dozens of markers simultaneously, limiting their applications. Here, 124 SNPs were simultaneous tested using Ampliseq technology with Ion Torrent PGM platform. Concordance study was performed with 2 reference samples of 9947A and 9948 between NGS and Sanger sequencing. Full concordance were obtained except genotype of rs576261 with 9947A. Parameter of FMAR (%) was introduced for NGS data analysis for the first time, evaluating allelic performance, sensitivity testing and mixture testing. FMAR values for accurate heterozygotes should be range from 50% to 60%, for homozygotes or Y-SNP should be above 90%. SNPs of rs7520386, rs4530059, rs214955, rs1523537, rs2342747, rs576261 and rs12997453 were recognized as poorly performing loci, either with allelic imbalance or with lower coverage. Sensitivity testing demonstrated that with DNA range from 10 ng-0.5 ng, all correct genotypes were obtained. For mixture testing, a clear linear correlation (R2 = 0.9429) between the excepted FMAR and observed FMAR values of mixtures was observed. PMID:26691610

Identification of small molecule compounds targeting the interaction of HIV-1 Vif and human APOBEC3G by virtual screening and biological evaluation.

PubMed

Ma, Ling; Zhang, Zhixin; Liu, Zhenlong; Pan, Qinghua; Wang, Jing; Li, Xiaoyu; Guo, Fei; Liang, Chen; Hu, Laixing; Zhou, Jinming; Cen, Shan

2018-05-23

Human APOBEC3G (hA3G) is a restriction factor that inhibits human immunodeficiency 1 virus (HIV-1) replication. The virally encoded protein Vif binds to hA3G and induces its degradation, thereby counteracting the antiviral activity of hA3G. Vif-mediated hA3G degradation clearly represents a potential target for anti-HIV drug development. Herein, we have performed virtual screening to discover small molecule inhibitors that target the binding interface of the Vif/hA3G complex. Subsequent biochemical studies have led to the identification of a small molecule inhibitor, IMB-301 that binds to hA3G, interrupts the hA3G-Vif interaction and inhibits Vif-mediated degradation of hA3G. As a result, IMB-301 strongly inhibits HIV-1 replication in a hA3G-dependent manner. Our study further demonstrates the feasibility of inhibiting HIV replication by abrogating the Vif-hA3G interaction with small molecules.

Genome-Wide Identification of CBX2 Targets: Insights in the Human Sex Development Network

PubMed Central

Eid, Wassim; Opitz, Lennart

2015-01-01

Chromobox homolog 2 (CBX2) is a chromatin modifier that plays an important role in sexual development and its disorders (disorders of sex development [DSD]), yet the exact rank and function of human CBX2 in this pathway remains unclear. Here, we performed large-scale mapping and analysis of in vivo target loci of the protein CBX2 in Sertoli-like NT-2D1 cells, using the DNA adenine methyltransferase identification technique. We identified close to 1600 direct targets for CBX2. Intriguingly, validation of selected candidate genes using qRT-PCR in cells overexpressing CBX2 or in which CBX2 has been knocked down indicated that several CBX2-responsive genes encode proteins that are involved in DSD. We further validated these effects on the candidate genes using a mutated CBX2 causing DSD in human patient. Overall, our findings suggest that CBX2 role in the sex development cascade is to stimulate the male pathway and concurrently inhibit the female pathway. These data provide fundamental insights into potential etiology of DSD. PMID:25569159

Identification of non-volatile compounds and their migration from hot melt adhesives used in food packaging materials characterized by ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry.

PubMed

Vera, Paula; Canellas, Elena; Nerín, Cristina

2013-05-01

The identification of unknown non-volatile migrant compounds from adhesives used in food contact materials is a very challenging task because of the number of possible compounds involved, given that adhesives are complex mixtures of chemicals. The use of ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-MS/QTOF) is shown to be a successful tool for identifying non-targeted migrant compounds from two hot melt adhesives used in food packaging laminates. Out of the seven migrants identified and quantified, five were amides and one was a compound classified in Class II of the Cramer toxicity. None of the migration values exceeded the recommended Cramer exposure values.

Targeted next-generation sequencing at copy-number breakpoints for personalized analysis of rearranged ends in solid tumors.

PubMed

Kim, Hyun-Kyoung; Park, Won Cheol; Lee, Kwang Man; Hwang, Hai-Li; Park, Seong-Yeol; Sorn, Sungbin; Chandra, Vishal; Kim, Kwang Gi; Yoon, Woong-Bae; Bae, Joon Seol; Shin, Hyoung Doo; Shin, Jong-Yeon; Seoh, Ju-Young; Kim, Jong-Il; Hong, Kyeong-Man

2014-01-01

The concept of the utilization of rearranged ends for development of personalized biomarkers has attracted much attention owing to its clinical applicability. Although targeted next-generation sequencing (NGS) for recurrent rearrangements has been successful in hematologic malignancies, its application to solid tumors is problematic due to the paucity of recurrent translocations. However, copy-number breakpoints (CNBs), which are abundant in solid tumors, can be utilized for identification of rearranged ends. As a proof of concept, we performed targeted next-generation sequencing at copy-number breakpoints (TNGS-CNB) in nine colon cancer cases including seven primary cancers and two cell lines, COLO205 and SW620. For deduction of CNBs, we developed a novel competitive single-nucleotide polymorphism (cSNP) microarray method entailing CNB-region refinement by competitor DNA. Using TNGS-CNB, 19 specific rearrangements out of 91 CNBs (20.9%) were identified, and two polymerase chain reaction (PCR)-amplifiable rearrangements were obtained in six cases (66.7%). And significantly, TNGS-CNB, with its high positive identification rate (82.6%) of PCR-amplifiable rearrangements at candidate sites (19/23), just from filtering of aligned sequences, requires little effort for validation. Our results indicate that TNGS-CNB, with its utility for identification of rearrangements in solid tumors, can be successfully applied in the clinical laboratory for cancer-relapse and therapy-response monitoring.

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

PubMed Central

Savitski, Mikhail M.; Wilhelm, Mathias; Hahne, Hannes; Kuster, Bernhard; Bantscheff, Marcus

2015-01-01

Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there are strong differences in opinion regarding the conceptual validity of a protein FDR and no consensus regarding the methodology for protein FDR determination. There are also limitations inherent to the widely used classic target–decoy strategy that particularly show when analyzing very large data sets and that lead to a strong over-representation of decoy identifications. In this study, we investigated the merits of the classic, as well as a novel target–decoy-based protein FDR estimation approach, taking advantage of a heterogeneous data collection comprised of ∼19,000 LC-MS/MS runs deposited in ProteomicsDB (https://www.proteomicsdb.org). The “picked” protein FDR approach treats target and decoy sequences of the same protein as a pair rather than as individual entities and chooses either the target or the decoy sequence depending on which receives the highest score. We investigated the performance of this approach in combination with q-value based peptide scoring to normalize sample-, instrument-, and search engine-specific differences. The “picked” target–decoy strategy performed best when protein scoring was based on the best peptide q-value for each protein yielding a stable number of true positive protein identifications over a wide range of q-value thresholds. We show that this simple and unbiased strategy eliminates a conceptual issue in the commonly used “classic” protein FDR approach that causes overprediction of false-positive protein identification in large data sets. The approach scales from small to very large data sets without losing performance, consistently increases the number of true-positive protein identifications and is readily implemented in proteomics analysis software. PMID:25987413

Detection and Identification of Multiple Stationary Human Targets Via Bio-Radar Based on the Cross-Correlation Method

PubMed Central

Zhang, Yang; Chen, Fuming; Xue, Huijun; Li, Zhao; An, Qiang; Wang, Jianqi; Zhang, Yang

2016-01-01

Ultra-wideband (UWB) radar has been widely used for detecting human physiological signals (respiration, movement, etc.) in the fields of rescue, security, and medicine owing to its high penetrability and range resolution. In these applications, especially in rescue after disaster (earthquake, collapse, mine accident, etc.), the presence, number, and location of the trapped victims to be detected and rescued are the key issues of concern. Ample research has been done on the first issue, whereas the identification and localization of multi-targets remains a challenge. False positive and negative identification results are two common problems associated with the detection of multiple stationary human targets. This is mainly because the energy of the signal reflected from the target close to the receiving antenna is considerably stronger than those of the targets at further range, often leading to missing or false recognition if the identification method is based on the energy of the respiratory signal. Therefore, a novel method based on cross-correlation is proposed in this paper that is based on the relativity and periodicity of the signals, rather than on the energy. The validity of this method is confirmed through experiments using different scenarios; the results indicate a discernible improvement in the detection precision and identification of the multiple stationary targets. PMID:27801795

Strategies for target identification of antimicrobial natural products.

PubMed

Farha, Maya A; Brown, Eric D

2016-05-04

Covering: 2000 to 2015Despite a pervasive decline in natural product research at many pharmaceutical companies over the last two decades, natural products have undeniably been a prolific and unsurpassed source for new lead antibacterial compounds. Due to their inherent complexity, natural extracts face several hurdles in high-throughout discovery programs, including target identification. Target identification and validation is a crucial process for advancing hits through the discovery pipeline, but has remained a major bottleneck. In the case of natural products, extremely low yields and limited compound supply further impede the process. Here, we review the wealth of target identification strategies that have been proposed and implemented for the characterization of novel antibacterials. Traditionally, these have included genomic and biochemical-based approaches, which, in recent years, have been improved with modern-day technology and better honed for natural product discovery. Further, we discuss the more recent innovative approaches for uncovering the target of new antibacterial natural products, which have resulted from modern advances in chemical biology tools. Finally, we present unique screening platforms implemented to streamline the process of target identification. The different innovative methods to respond to the challenge of characterizing the mode of action for antibacterial natural products have cumulatively built useful frameworks that may advocate a renovated interest in natural product drug discovery programs.

Detection and Identification of Multiple Stationary Human Targets Via Bio-Radar Based on the Cross-Correlation Method.

PubMed

Zhang, Yang; Chen, Fuming; Xue, Huijun; Li, Zhao; An, Qiang; Wang, Jianqi; Zhang, Yang

2016-10-27

Ultra-wideband (UWB) radar has been widely used for detecting human physiological signals (respiration, movement, etc.) in the fields of rescue, security, and medicine owing to its high penetrability and range resolution. In these applications, especially in rescue after disaster (earthquake, collapse, mine accident, etc.), the presence, number, and location of the trapped victims to be detected and rescued are the key issues of concern. Ample research has been done on the first issue, whereas the identification and localization of multi-targets remains a challenge. False positive and negative identification results are two common problems associated with the detection of multiple stationary human targets. This is mainly because the energy of the signal reflected from the target close to the receiving antenna is considerably stronger than those of the targets at further range, often leading to missing or false recognition if the identification method is based on the energy of the respiratory signal. Therefore, a novel method based on cross-correlation is proposed in this paper that is based on the relativity and periodicity of the signals, rather than on the energy. The validity of this method is confirmed through experiments using different scenarios; the results indicate a discernible improvement in the detection precision and identification of the multiple stationary targets.

Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics

PubMed Central

Radonić, Aleksandar; Kocak Tufan, Zeliha; Domingo, Cristina

2017-01-01

Background We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. Methodology An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. Principal findings The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1–10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours. Conclusions Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring. PMID:29155823

Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics.

PubMed

Brinkmann, Annika; Ergünay, Koray; Radonić, Aleksandar; Kocak Tufan, Zeliha; Domingo, Cristina; Nitsche, Andreas

2017-11-01

We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours. Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.

Neural Network Target Identification System for False Alarm Reduction

NASA Technical Reports Server (NTRS)

Ye, David; Edens, Weston; Lu, Thomas T.; Chao, Tien-Hsin

2009-01-01

A multi-stage automated target recognition (ATR) system has been designed to perform computer vision tasks with adequate proficiency in mimicking human vision. The system is able to detect, identify, and track targets of interest. Potential regions of interest (ROIs) are first identified by the detection stage using an Optimum Trade-off Maximum Average Correlation Height (OT-MACH) filter combined with a wavelet transform. False positives are then eliminated by the verification stage using feature extraction methods in conjunction with neural networks. Feature extraction transforms the ROIs using filtering and binning algorithms to create feature vectors. A feed forward back propagation neural network (NN) is then trained to classify each feature vector and remove false positives. This paper discusses the test of the system performance and parameter optimizations process which adapts the system to various targets and datasets. The test results show that the system was successful in substantially reducing the false positive rate when tested on a sonar image dataset.

Rapid identification of a novel complex I MT-ND3 m.10134C>A mutation in a Leigh syndrome patient.

PubMed

Miller, David K; Menezes, Minal J; Simons, Cas; Riley, Lisa G; Cooper, Sandra T; Grimmond, Sean M; Thorburn, David R; Christodoulou, John; Taft, Ryan J

2014-01-01

Leigh syndrome (LS) is a rare progressive multi-system neurodegenerative disorder, the genetics of which is frequently difficult to resolve. Rapid determination of the genetic etiology of LS in a 5-year-old girl facilitated inclusion in Edison Pharmaceutical's phase 2B clinical trial of EPI-743. SNP-arrays and high-coverage whole exome sequencing were performed on the proband, both parents and three unaffected siblings. Subsequent multi-tissue targeted high-depth mitochondrial sequencing was performed using custom long-range PCR amplicons. Tissue-specific mutant load was also assessed by qPCR. Complex I was interrogated by spectrophotometric enzyme assays and Western Blot. No putatively causal mutations were identified in nuclear-encoded genes. Analysis of low-coverage off-target mitochondrial reads revealed a previously unreported mitochondrial mutation in the proband in MT-ND3 (m.10134C>A, p.Q26K), a Complex I mitochondrial gene previously associated with LS. Targeted investigations demonstrated that this mutation was 1% heteroplasmic in the mother's blood and homoplasmic in the proband's blood, fibroblasts, liver and muscle. Enzyme assays revealed decreased Complex I activity. The identification of this novel LS MT-ND3 variant, the genomics of which was accomplished in less than 3.5 weeks, indicates that rapid genomic approaches may prove useful in time-sensitive cases with an unresolved genetic diagnosis.

Visual Search of Experts in Medical Image Reading: The Effect of Training, Target Prevalence, and Expert Knowledge

PubMed Central

Nakashima, Ryoichi; Kobayashi, Kazufumi; Maeda, Eriko; Yoshikawa, Takeharu; Yokosawa, Kazuhiko

2013-01-01

The aims of this study are (a) To determine the effect of training on the multiple-target lesion search performance; and (b) To examine the effect of target prevalence on the performance of radiologists and novices. We conducted four sessions of 500 trials in a lesion search on a medical image task in which participants searched for three different target lesions. Participants were 10 radiologists and novices. In each session, the prevalence of the different target lesions varied from low (2%) to high (40%). The sensitivity of novices was higher in the later sessions than in the first session, whereas there were no differences among sessions in radiologists. The improvement on sensitivity of novices was largely due to attenuations of false alarm (FA) errors. In addition, miss rates of the three targets did not differ in data of novices, whereas radiologists produced a higher miss rate for the highest prevalence target lesion (non-serious lesion) than for the other two lesions (serious lesions). The conclusions are (a) The training for the multiple-target lesion search task can be effective to reduce FA errors; and (b) The prevalence effect on lesion search can be attenuated by the multiple-target identification and the knowledge about seriousness of lesions. This suggests that acquired knowledge about normal cases and serious lesions is an important aspect of a radiologists’ skill in searching for medical lesions and their high performance levels. PMID:23576997

Visual search of experts in medical image reading: the effect of training, target prevalence, and expert knowledge.

PubMed

Nakashima, Ryoichi; Kobayashi, Kazufumi; Maeda, Eriko; Yoshikawa, Takeharu; Yokosawa, Kazuhiko

2013-01-01

The aims of this study are (a) To determine the effect of training on the multiple-target lesion search performance; and (b) To examine the effect of target prevalence on the performance of radiologists and novices. We conducted four sessions of 500 trials in a lesion search on a medical image task in which participants searched for three different target lesions. Participants were 10 radiologists and novices. In each session, the prevalence of the different target lesions varied from low (2%) to high (40%). The sensitivity of novices was higher in the later sessions than in the first session, whereas there were no differences among sessions in radiologists. The improvement on sensitivity of novices was largely due to attenuations of false alarm (FA) errors. In addition, miss rates of the three targets did not differ in data of novices, whereas radiologists produced a higher miss rate for the highest prevalence target lesion (non-serious lesion) than for the other two lesions (serious lesions). The conclusions are (a) The training for the multiple-target lesion search task can be effective to reduce FA errors; and (b) The prevalence effect on lesion search can be attenuated by the multiple-target identification and the knowledge about seriousness of lesions. This suggests that acquired knowledge about normal cases and serious lesions is an important aspect of a radiologists' skill in searching for medical lesions and their high performance levels.

Active imaging system performance model for target acquisition

NASA Astrophysics Data System (ADS)

Espinola, Richard L.; Teaney, Brian; Nguyen, Quang; Jacobs, Eddie L.; Halford, Carl E.; Tofsted, David H.

2007-04-01

The U.S. Army RDECOM CERDEC Night Vision & Electronic Sensors Directorate has developed a laser-range-gated imaging system performance model for the detection, recognition, and identification of vehicle targets. The model is based on the established US Army RDECOM CERDEC NVESD sensor performance models of the human system response through an imaging system. The Java-based model, called NVLRG, accounts for the effect of active illumination, atmospheric attenuation, and turbulence effects relevant to LRG imagers, such as speckle and scintillation, and for the critical sensor and display components. This model can be used to assess the performance of recently proposed active SWIR systems through various trade studies. This paper will describe the NVLRG model in detail, discuss the validation of recent model components, present initial trade study results, and outline plans to validate and calibrate the end-to-end model with field data through human perception testing.

Performance Evaluation of the Verigene Gram-Positive and Gram-Negative Blood Culture Test for Direct Identification of Bacteria and Their Resistance Determinants from Positive Blood Cultures in Hong Kong

PubMed Central

Siu, Gilman K. H.; Chen, Jonathan H. K.; Ng, T. K.; Lee, Rodney A.; Fung, Kitty S. C.; To, Sabrina W. C.; Wong, Barry K. C.; Cheung, Sherman; Wong, Ivan W. F.; Tam, Marble M. P.; Lee, Swing S. W.; Yam, W. C.

2015-01-01

Background A multicenter study was conducted to evaluate the diagnostic performance and the time to identifcation of the Verigene Blood Culture Test, the BC-GP and BC-GN assays, to identify both Gram-positive and Gram-negative bacteria and their drug resistance determinants directly from positive blood cultures collected in Hong Kong. Methods and Results A total of 364 blood cultures were prospectively collected from four public hospitals, in which 114 and 250 cultures yielded Gram-positive and Gram-negative bacteria, and were tested with the BC-GP and BC-GN assay respectively. The overall identification agreement for Gram-positive and Gram-negative bacteria were 89.6% and 90.5% in monomicrobial cultures and 62.5% and 53.6% in polymicrobial cultures, respectively. The sensitivities for most genus/species achieved at least 80% except Enterococcus spp. (60%), K.oxytoca (0%), K.pneumoniae (69.2%), whereas the specificities for all targets ranged from 98.9% to 100%. Of note, 50% (7/14) cultures containing K.pneumoniae that were missed by the BC-GN assay were subsequently identified as K.variicola. Approximately 5.5% (20/364) cultures contained non-target organisms, of which Aeromonas spp. accounted for 25% and are of particular concern. For drug resistance determination, the Verigene test showed 100% sensitivity for identification of MRSA, VRE and carbapenem resistant Acinetobacter, and 84.4% for ESBL-producing Enterobacteriaceae based on the positive detection of mecA, vanA, bla OXA and bla CTXM respectively. Conclusion Overall, the Verigene test provided acceptable accuracy for identification of bacteria and resistance markers with a range of turnaround time 40.5 to 99.2 h faster than conventional methods in our region. PMID:26431434

PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies.

PubMed

Jeon, Jouhyun; Arnold, Roland; Singh, Fateh; Teyra, Joan; Braun, Tatjana; Kim, Philip M

2016-04-01

The identification of structured units in a protein sequence is an important first step for most biochemical studies. Importantly for this study, the identification of stable structured region is a crucial first step to generate novel synthetic antibodies. While many approaches to find domains or predict structured regions exist, important limitations remain, such as the optimization of domain boundaries and the lack of identification of non-domain structured units. Moreover, no integrated tool exists to find and optimize structural domains within protein sequences. Here, we describe a new tool, PAT ( http://www.kimlab.org/software/pat ) that can efficiently identify both domains (with optimized boundaries) and non-domain putative structured units. PAT automatically analyzes various structural properties, evaluates the folding stability, and reports possible structural domains in a given protein sequence. For reliability evaluation of PAT, we applied PAT to identify antibody target molecules based on the notion that soluble and well-defined protein secondary and tertiary structures are appropriate target molecules for synthetic antibodies. PAT is an efficient and sensitive tool to identify structured units. A performance analysis shows that PAT can characterize structurally well-defined regions in a given sequence and outperforms other efforts to define reliable boundaries of domains. Specially, PAT successfully identifies experimentally confirmed target molecules for antibody generation. PAT also offers the pre-calculated results of 20,210 human proteins to accelerate common queries. PAT can therefore help to investigate large-scale structured domains and improve the success rate for synthetic antibody generation.

Appearance-change instruction effects on eyewitness lineup identification accuracy are not moderated by amount of appearance change.

PubMed

Molinaro, Peter F; Arndorfer, Andrea; Charman, Steve D

2013-12-01

Instructing witnesses that a criminal may have changed appearance prior to showing them a lineup has been shown to increase false identifications without increasing correct identifications (S. D. Charman & G. L. Wells, 2007, Is the appearance-change instruction a good idea? Law and Human Behavior, Vol. 31, pp. 3-22). However, the generalizability of the effects of this appearance-change instruction (ACI) is unknown, and there are reasons to believe that the instruction's effects may be moderated by the amount of appearance change the criminal has actually undergone. The current study tested this hypothesis. Undergraduate students (N = 315) were exposed to a series of target faces and lineups, some of which contained the target and some of which did not, and made identification decisions. Half of the participants received a standard ACI prior to each lineup; the other half did not. The targets varied with respect to the amount to which their appearance had changed. Results indicated that the ACI inflated false identifications without inflating correct identifications, and that these effects did not depend on the amount of appearance change the target had undergone. Current recommendations to administer the ACI seem to be unfounded and may be harmful to the reliability of identification evidence. (c) 2013 APA, all rights reserved

Advances in identification and validation of protein targets of natural products without chemical modification.

PubMed

Chang, J; Kim, Y; Kwon, H J

2016-05-04

Covering: up to February 2016Identification of the target proteins of natural products is pivotal to understanding the mechanisms of action to develop natural products for use as molecular probes and potential therapeutic drugs. Affinity chromatography of immobilized natural products has been conventionally used to identify target proteins, and has yielded good results. However, this method has limitations, in that labeling or tagging for immobilization and affinity purification often result in reduced or altered activity of the natural product. New strategies have recently been developed and applied to identify the target proteins of natural products and synthetic small molecules without chemical modification of the natural product. These direct and indirect methods for target identification of label-free natural products include drug affinity responsive target stability (DARTS), stability of proteins from rates of oxidation (SPROX), cellular thermal shift assay (CETSA), thermal proteome profiling (TPP), and bioinformatics-based analysis of connectivity. This review focuses on and reports case studies of the latest advances in target protein identification methods for label-free natural products. The integration of newly developed technologies will provide new insights and highlight the value of natural products for use as biological probes and new drug candidates.

Target-decoy Based False Discovery Rate Estimation for Large-scale Metabolite Identification.

PubMed

Wang, Xusheng; Jones, Drew R; Shaw, Timothy I; Cho, Ji-Hoon; Wang, Yuanyuan; Tan, Haiyan; Xie, Boer; Zhou, Suiping; Li, Yuxin; Peng, Junmin

2018-05-23

Metabolite identification is a crucial step in mass spectrometry (MS)-based metabolomics. However, it is still challenging to assess the confidence of assigned metabolites. In this study, we report a novel method for estimating false discovery rate (FDR) of metabolite assignment with a target-decoy strategy, in which the decoys are generated through violating the octet rule of chemistry by adding small odd numbers of hydrogen atoms. The target-decoy strategy was integrated into JUMPm, an automated metabolite identification pipeline for large-scale MS analysis, and was also evaluated with two other metabolomics tools, mzMatch and mzMine 2. The reliability of FDR calculation was examined by false datasets, which were simulated by altering MS1 or MS2 spectra. Finally, we used the JUMPm pipeline coupled with the target-decoy strategy to process unlabeled and stable-isotope labeled metabolomic datasets. The results demonstrate that the target-decoy strategy is a simple and effective method for evaluating the confidence of high-throughput metabolite identification.

Is facial skin tone sufficient to produce a cross-racial identification effect?

PubMed

Alley, T R; Schultheis, J A

2001-06-01

Research clearly supports the existence of an other race effect for human faces whereby own-race faces are more accurately perceived and recognized. Why this occurs remains unclear. A computerized program (Mac-a-Mug Pro) for face composition was used to create pairs of target and distractor faces that differed only in skin tone. The six target faces were rated on honesty and aggressiveness by 72 university students, with just one 'Black' and one 'White' face viewed by each student. One week later, they attempted to identify these faces in four lineups: two with target-present and two with target-absent. The order of presentation of targets, lineups, and faces within lineups was varied. Own-race identification was slightly better than cross-racial identification. There was no significant difference in the confidence of responses to own- versus other-race faces. These results indicate that neither morphological variation nor differential confidence is necessary for a cross-racial identification effect.

Autistic traits and social anxiety predict differential performance on social cognitive tasks in typically developing young adults

PubMed Central

Burk, Joshua A.; Fleckenstein, Katarina; Kozikowski, C. Teal

2018-01-01

The current work examined the unique contribution that autistic traits and social anxiety have on tasks examining attention and emotion processing. In Study 1, 119 typically-developing college students completed a flanker task assessing the control of attention to target faces and away from distracting faces during emotion identification. In Study 2, 208 typically-developing college students performed a visual search task which required identification of whether a series of 8 or 16 emotional faces depicted the same or different emotions. Participants with more self-reported autistic traits performed more slowly on the flanker task in Study 1 than those with fewer autistic traits when stimuli depicted complex emotions. In Study 2, participants higher in social anxiety performed less accurately on trials showing all complex faces; participants with autistic traits showed no differences. These studies suggest that traits related to autism and to social anxiety differentially impact social cognitive processing. PMID:29596523

Identification of (antioxidative) plants in herbal pharmaceutical preparations and dietary supplements.

PubMed

Deconinck, Eric; Custers, Deborah; De Beer, Jacques Omer

2015-01-01

The standard procedures for the identification, authentication, and quality control of medicinal plants and herbs are nowadays limited to pure herbal products. No guidelines or procedures, describing the detection or identification of a targeted plant or herb in pharmaceutical preparations or dietary supplements, can be found. In these products the targeted plant is often present together with other components of herbal or synthetic origin. This chapter describes a strategy for the fast development of a chromatographic fingerprint approach that allows the identification of a targeted plant in herbal preparations and dietary supplements. The strategy consists of a standard chromatographic gradient that is tested for the targeted plant with different extraction solvents and different mobile phases. From the results obtained, the optimal fingerprint is selected. Subsequently the samples are analyzed according to the selected methodological parameters, and the obtained fingerprints can be compared with the one obtained for the pure herbal product or a standard preparation. Calculation of the dissimilarity between these fingerprints will result in a probability of presence of the targeted plant. Optionally mass spectrometry can be used to improve specificity, to confirm identification, or to identify molecules with a potential medicinal or antioxidant activity.

Multisensor data fusion for integrated maritime surveillance

NASA Astrophysics Data System (ADS)

Premji, A.; Ponsford, A. M.

1995-01-01

A prototype Integrated Coastal Surveillance system has been developed on Canada's East Coast to provide effective surveillance out to and beyond the 200 nautical mile Exclusive Economic Zone. The system has been designed to protect Canada's natural resources, and to monitor and control the coastline for smuggling, drug trafficking, and similar illegal activity. This paper describes the Multiple Sensor - Multiple Target data fusion system that has been developed. The fusion processor has been developed around the celebrated Multiple Hypothesis Tracking algorithm which accommodates multiple targets, new targets, false alarms, and missed detections. This processor performs four major functions: plot-to-track association to form individual radar tracks; fusion of radar tracks with secondary sensor reports; track identification and tagging using secondary reports; and track level fusion to form common tracks. Radar data from coherent and non-coherent radars has been used to evaluate the performance of the processor. This paper presents preliminary results.

Natural Iminosugar (+)-Lentiginosine Inhibits ATPase and Chaperone Activity of Hsp90

PubMed Central

Dal Piaz, Fabrizio; Vassallo, Antonio; Chini, Maria Giovanna; Cordero, Franca M.; Cardona, Francesca; Pisano, Claudio; Bifulco, Giuseppe; De Tommasi, Nunziatina; Brandi, Alberto

2012-01-01

Heat shock protein 90 (Hsp90) is a significant target in the development of rational cancer therapy due to its role at the crossroads of multiple signaling pathways associated with cell proliferation and cell viability. The relevance of Hsp90 as a therapeutic target for numerous diseases states has prompted the identification and optimization of novel Hsp90 inhibitors as an emerging therapeutic strategy. We performed a screening aimed to identify novel Hsp90 inhibitors among several natural compounds and we focused on the iminosugar (+)-lentiginosine, a natural amyloglucosidases inhibitor, for its peculiar bioactivity profile. Characterization of Hsp90 inhibition was performed using a panel of chemical and biological approaches, including limited proteolysis, biochemical and cellular assays. Our result suggested that the middle domain of Hsp90, as opposed to its ATP-binding pocket, is a promising binding site for new classes of Hsp90 inhibitors with multi-target anti-cancer potential. PMID:22916240

Interactions between facial emotion and identity in face processing: evidence based on redundancy gains.

PubMed

Yankouskaya, Alla; Booth, David A; Humphreys, Glyn

2012-11-01

Interactions between the processing of emotion expression and form-based information from faces (facial identity) were investigated using the redundant-target paradigm, in which we specifically tested whether identity and emotional expression are integrated in a superadditive manner (Miller, Cognitive Psychology 14:247-279, 1982). In Experiments 1 and 2, participants performed emotion and face identity judgments on faces with sad or angry emotional expressions. Responses to redundant targets were faster than responses to either single target when a universal emotion was conveyed, and performance violated the predictions from a model assuming independent processing of emotion and face identity. Experiment 4 showed that these effects were not modulated by varying interstimulus and nontarget contingencies, and Experiment 5 demonstrated that the redundancy gains were eliminated when faces were inverted. Taken together, these results suggest that the identification of emotion and facial identity interact in face processing.

In silico re-identification of properties of drug target proteins.

PubMed

Kim, Baeksoo; Jo, Jihoon; Han, Jonghyun; Park, Chungoo; Lee, Hyunju

2017-05-31

Computational approaches in the identification of drug targets are expected to reduce time and effort in drug development. Advances in genomics and proteomics provide the opportunity to uncover properties of druggable genomes. Although several studies have been conducted for distinguishing drug targets from non-drug targets, they mainly focus on the sequences and functional roles of proteins. Many other properties of proteins have not been fully investigated. Using the DrugBank (version 3.0) database containing nearly 6,816 drug entries including 760 FDA-approved drugs and 1822 of their targets and human UniProt/Swiss-Prot databases, we defined 1578 non-redundant drug target and 17,575 non-drug target proteins. To select these non-redundant protein datasets, we built four datasets (A, B, C, and D) by considering clustering of paralogous proteins. We first reassessed the widely used properties of drug target proteins. We confirmed and extended that drug target proteins (1) are likely to have more hydrophobic, less polar, less PEST sequences, and more signal peptide sequences higher and (2) are more involved in enzyme catalysis, oxidation and reduction in cellular respiration, and operational genes. In this study, we proposed new properties (essentiality, expression pattern, PTMs, and solvent accessibility) for effectively identifying drug target proteins. We found that (1) drug targetability and protein essentiality are decoupled, (2) druggability of proteins has high expression level and tissue specificity, and (3) functional post-translational modification residues are enriched in drug target proteins. In addition, to predict the drug targetability of proteins, we exploited two machine learning methods (Support Vector Machine and Random Forest). When we predicted drug targets by combining previously known protein properties and proposed new properties, an F-score of 0.8307 was obtained. When the newly proposed properties are integrated, the prediction performance is improved and these properties are related to drug targets. We believe that our study will provide a new aspect in inferring drug-target interactions.

Rapid screening, identification, and purification of neuraminidase inhibitors from Lithospermum erythrorhizon Sieb.et Zucc. by ultrafiltration with HPLC-ESI-TOF-MS combined with semipreparative HPLC.

PubMed

Zhang, Minmin; Zhao, Hengqiang; Zhao, Zhiguo; Yan, Huijiao; Lv, Ruimin; Cui, Li; Yuan, Jinpeng; Wang, Daijie; Geng, Yanling; Liu, Daicheng; Wang, Xiao

2016-06-01

We put forward an efficient strategy based on bioassay guidance for the rapid screening, identification, and purification of the neuraminidase inhibitors from traditional Chinese medicines, and apply to the discovery of anti-influenza components from Lithospermiun erythrorhizon Sieb.et Zucc. Ultrafiltration with high-performance liquid chromatography and electrospray ionization time-of-flight mass spectrometry was employed for the rapid screening and preliminarily identification of anti-influenza components from Zicao. Semipreparative high-performance liquid chromatography was used for the rapid separation and purification of the target compounds. NMR spectroscopy, mass spectrometry, and UV spectroscopy were used for further structural identification, and the activity of the compounds was verified by in vitro assay. Five compounds were found to have neuraminidase inhibitory activity by this method. Subsequently, the five compounds were separated by semipreparative high-performance liquid chromatography with the purity over 98% for all of them by high-performance liquid chromatography test. Combined with the NMR spectroscopy, mass spectrometry, and UV spectroscopy data, they were identified as alkannin, acetylalkannin, isobutyrylalkannin, β,β-dimethylacryloylalkannin and isovalerylalkannin. The in vitro assay showed that all five compounds had good neuraminidase inhibitory activities. These results suggested that the method is highly efficient, and it can provide platform and methodology supports for the rapid discovery of anti-influenza active ingredients from complex Chinese herbal medicines. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of Mycology Laboratory Proficiency Testing

PubMed Central

Reilly, Andrew A.; Salkin, Ira F.; McGinnis, Michael R.; Gromadzki, Sally; Pasarell, Lester; Kemna, Maggi; Higgins, Nancy; Salfinger, Max

1999-01-01

Changes over the last decade in overt proficiency testing (OPT) regulations have been ostensibly directed at improving laboratory performance on patient samples. However, the overt (unblinded) format of the tests and regulatory penalties associated with incorrect values allow and encourage laboratorians to take extra precautions with OPT analytes. As a result OPT may measure optimal laboratory performance instead of the intended target of typical performance attained during routine patient testing. This study addresses this issue by evaluating medical mycology OPT and comparing its fungal specimen identification error rates to those obtained in a covert (blinded) proficiency testing (CPT) program. Identifications from 188 laboratories participating in the New York State mycology OPT from 1982 to 1994 were compared with the identifications of the same fungi recovered from patient specimens in 1989 and 1994 as part of the routine procedures of 88 of these laboratories. The consistency in the identification of OPT specimens was sufficient to make accurate predictions of OPT error rates. However, while the error rates in OPT and CPT were similar for Candida albicans, significantly higher error rates were found in CPT for Candida tropicalis, Candida glabrata, and other common pathogenic fungi. These differences may, in part, be due to OPT’s use of ideal organism representatives cultured under optimum growth conditions. This difference, as well as the organism-dependent error rate differences, reflects the limitations of OPT as a means of assessing the quality of routine laboratory performance in medical mycology. PMID:10364601

Defining the uncertainty of electro-optical identification system performance estimates using a 3D optical environment derived from satellite

NASA Astrophysics Data System (ADS)

Ladner, S. D.; Arnone, R.; Casey, B.; Weidemann, A.; Gray, D.; Shulman, I.; Mahoney, K.; Giddings, T.; Shirron, J.

2009-05-01

Current United States Navy Mine-Counter-Measure (MCM) operations primarily use electro-optical identification (EOID) sensors to identify underwater targets after detection via acoustic sensors. These EOID sensors which are based on laser underwater imaging by design work best in "clear" waters and are limited in coastal waters especially with strong optical layers. Optical properties and in particular scattering and absorption play an important role on systems performance. Surface optical properties alone from satellite are not adequate to determine how well a system will perform at depth due to the existence of optical layers. The spatial and temporal characteristics of the 3d optical variability of the coastal waters along with strength and location of subsurface optical layers maximize chances of identifying underwater targets by exploiting optimum sensor deployment. Advanced methods have been developed to fuse the optical measurements from gliders, optical properties from "surface" satellite snapshot and 3-D ocean circulation models to extend the two-dimensional (2-D) surface satellite optical image into a three-dimensional (3-D) optical volume with subsurface optical layers. Modifications were made to an EOID performance model to integrate a 3-D optical volume covering an entire region of interest as input and derive system performance field. These enhancements extend present capability based on glider optics and EOID sensor models to estimate the system's "image quality". This only yields system performance information for a single glider profile location in a very large operational region. Finally, we define the uncertainty of the system performance by coupling the EOID performance model with the 3-D optical volume uncertainties. Knowing the ensemble spread of EOID performance field provides a new and unique capability for tactical decision makers and Navy Operations.

Stereotype threat in classroom settings: the interactive effect of domain identification, task difficulty and stereotype threat on female students' maths performance.

PubMed

Keller, Johannes

2007-06-01

Stereotype threat research revealed that negative stereotypes can disrupt the performance of persons targeted by such stereotypes. This paper contributes to stereotype threat research by providing evidence that domain identification and the difficulty level of test items moderate stereotype threat effects on female students' maths performance. The study was designed to test theoretical ideas derived from stereotype threat theory and assumptions outlined in the Yerkes-Dodson law proposing a nonlinear relationship between arousal, task difficulty and performance. Participants were 108 high school students attending secondary schools. Participants worked on a test comprising maths problems of different difficulty levels. Half of the participants learned that the test had been shown to produce gender differences (stereotype threat). The other half learned that the test had been shown not to produce gender differences (no threat). The degree to which participants identify with the domain of maths was included as a quasi-experimental factor. Maths-identified female students showed performance decrements under conditions of stereotype threat. Moreover, the stereotype threat manipulation had different effects on low and high domain identifiers' performance depending on test item difficulty. On difficult items, low identifiers showed higher performance under threat (vs. no threat) whereas the reverse was true in high identifiers. This interaction effect did not emerge on easy items. Domain identification and test item difficulty are two important factors that need to be considered in the attempt to understand the impact of stereotype threat on performance.

ARI Image Interpretation Research: 1970-1980

DTIC Science & Technology

1980-07-01

28 3. Index marks on data base stereo pair ... .......... .. 41 4. Identification learning curves for three methods used by interpreters of high...it may be impractical in operational units (but not in the school). Team consensus feedback can increase target identification proficiency and...in target identification can be provided with a minimum of instructor participation using operational imagery as the basic instructional material

The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers

PubMed Central

Sahl, Jason W.; Vazquez, Adam J.; Hall, Carina M.; Busch, Joseph D.; Tuanyok, Apichai; Mayo, Mark; Schupp, James M.; Lummis, Madeline; Pearson, Talima; Shippy, Kenzie; Allender, Christopher J.; Theobald, Vanessa; Hutcheson, Alex; Korlach, Jonas; LiPuma, John J.; Ladner, Jason; Lovett, Sean; Koroleva, Galina; Palacios, Gustavo; Limmathurotsakul, Direk; Wuthiekanun, Vanaporn; Wongsuwan, Gumphol; Currie, Bart J.

2016-01-01

ABSTRACT Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives. PMID:27651357

Genome-wide identification of Hami melon miRNAs with putative roles during fruit development

PubMed Central

Wang, Guangzhi; Ma, Xinli; Li, Meihua; Wu, Haibo; Fu, Qiushi; Zhang, Yi; Yi, Hongping

2017-01-01

MicroRNAs represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Hami melon is famous for its attractive flavor and excellent nutritional value, however, the mechanisms underlying the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the roles of miRNAs during Hami melon fruit development. Two batches of flesh samples were collected at four fruit development stages. Small RNA sequencing yielded a total of 54,553,424 raw reads from eight libraries. 113 conserved miRNAs belonging to 30 miRNA families and nine novel miRNAs comprising nine miRNA families were identified. The expression of 42 conserved miRNAs and three Hami melon-specific miRNAs significantly changed during fruit development. Furthermore, 484 and 124 melon genes were predicted as putative targets of 29 conserved and nine Hami melon-specific miRNA families, respectively. GO enrichment analysis were performed on target genes, “transcription, DNA-dependent”, “rRNA processing”, “oxidation reduction”, “signal transduction”, “regulation of transcription, DNA-dependent”, and “metabolic process” were the over-represented biological process terms. Cleavage sites of six target genes were validated using 5’ RACE. Our results present a comprehensive set of identification and characterization of Hami melon fruit miRNAs and their potential targets, which provide valuable basis towards understanding the regulatory mechanisms in programmed process of normal Hami fruit development and ripening. Specific miRNAs could be selected for further research and applications in breeding practices. PMID:28742088

Quantitative targeted and retrospective data analysis of relevant pesticides, antibiotics and mycotoxins in bakery products by liquid chromatography-single-stage Orbitrap mass spectrometry.

PubMed

De Dominicis, Emiliano; Commissati, Italo; Gritti, Elisa; Catellani, Dante; Suman, Michele

2015-01-01

In addition to 'traditional' multi-residue and multi-contaminant multiple reaction monitoring (MRM) mass spectrometric techniques devoted to quantifying a list of targeted compounds, the global food industry requires non-targeted methods capable of detecting other possible potentially hazardous compounds. Ultra-high-performance liquid chromatography combined with a single-stage Orbitrap high-resolution mass spectrometer (UHPLC-HRMS Exactive™-Orbitrap Technology) was successfully exploited for the complete selective and quantitative determination of 33 target compounds within three major cross categories (pesticides, antibiotics and mycotoxins) in bakery matrices (specifically milk, wheat flour and mini-cakes). Resolution was set at 50 000 full width at half maximum (FWHM) to achieve the right compromise between an adequate scan speed and selectivity, allowing for the limitations related to the necessary generic sample preparation approach. An exact mass with tolerance of 5 ppm and minimum peak threshold of 10 000 units were fixed as the main identification conditions, including retention time and isotopic pattern as additional criteria devoted to greatly reducing the risk of false-positive findings. The full validation for all the target analytes was performed: linearity, intermediate repeatability and recovery (28 analytes within 70-120%) were positively assessed; furthermore, limits of quantification between 5 and 100 µg kg(-1) (with most of the analytes having a limit of detection below 6 µg kg(-1)) indicate good performance, which is compatible with almost all the regulatory needs. Naturally contaminated and fortified mini-cakes, prepared through combined use of industrial and pilot plant production lines, were analysed at two different concentration levels, obtaining good overall quantitative results and providing preliminary indications of the potential of full-scan HRMS cluster analysis. The effectiveness of this analytical approach was also tested in terms of the formulation of hypotheses for the identification of other analytes not initially targeted which can have toxicological implications (e.g. 3-acetyl-deoxynivalenol and deoxynivalenol-3-glucoside), opening a window on retrospective investigation perspectives in food safety laboratories.

Hyperspectral material identification on radiance data using single-atmosphere or multiple-atmosphere modeling

NASA Astrophysics Data System (ADS)

Mariano, Adrian V.; Grossmann, John M.

2010-11-01

Reflectance-domain methods convert hyperspectral data from radiance to reflectance using an atmospheric compensation model. Material detection and identification are performed by comparing the compensated data to target reflectance spectra. We introduce two radiance-domain approaches, Single atmosphere Adaptive Cosine Estimator (SACE) and Multiple atmosphere ACE (MACE) in which the target reflectance spectra are instead converted into sensor-reaching radiance using physics-based models. For SACE, known illumination and atmospheric conditions are incorporated in a single atmospheric model. For MACE the conditions are unknown so the algorithm uses many atmospheric models to cover the range of environmental variability, and it approximates the result using a subspace model. This approach is sometimes called the invariant method, and requires the choice of a subspace dimension for the model. We compare these two radiance-domain approaches to a Reflectance-domain ACE (RACE) approach on a HYDICE image featuring concealed materials. All three algorithms use the ACE detector, and all three techniques are able to detect most of the hidden materials in the imagery. For MACE we observe a strong dependence on the choice of the material subspace dimension. Increasing this value can lead to a decline in performance.

Application of characteristic ion filtering with ultra-high performance liquid chromatography quadrupole time of flight tandem mass spectrometry for rapid detection and identification of chemical profiling in Eucommia ulmoides Oliv.

PubMed

He, Mingzhen; Jia, Jia; Li, Junmao; Wu, Bei; Huang, Wenping; Liu, Mi; Li, Yan; Yang, Shilin; Ouyang, Hui; Feng, Yulin

2018-06-15

Efficient targeted identification of chemical constituents from traditional Chinese medicine is still a major challenge. In this study, we used a characteristic ion filtering strategy to characterize compounds of Eucommia ulmoides Oliv. by ultra-high performance liquid chromatography quadrupole time of flight tandem mass spectrometry (UHPLC-ESI-Q-TOF-MS/MS). By using the ion filtering approach, target constituents of Eucommia ulmoides Oliv. were easily tentatively identified from the enormous LC/MS data set. The strategy consisted of the following three steps: 1) To establishing a characteristic ion database by diagnostic product ions or neutral loss fragments; 2) To evaluate the structural information of the compounds by high-resolution diagnostic characteristic ion filtering; 3) To confirm the different classes by chemical profiling according to their MS/MS spectra. In this study, characteristic ions are summarized as five major groups of compounds in Eucommia ulmoides Oliv. In total, 113 compounds were tentatively identified, including 23 potentially novel compounds. The results form a foundation for the quality control and chemical basis of Eucommia ulmoides Oliv. Copyright © 2018 Elsevier B.V. All rights reserved.

Simple Real-Time PCR and Amplicon Sequencing Method for Identification of Plasmodium Species in Human Whole Blood.

PubMed

Lefterova, Martina I; Budvytiene, Indre; Sandlund, Johanna; Färnert, Anna; Banaei, Niaz

2015-07-01

Malaria is the leading identifiable cause of fever in returning travelers. Accurate Plasmodium species identification has therapy implications for P. vivax and P. ovale, which have dormant liver stages requiring primaquine. Compared to microscopy, nucleic acid tests have improved specificity for species identification and higher sensitivity for mixed infections. Here, we describe a SYBR green-based real-time PCR assay for Plasmodium species identification from whole blood, which uses a panel of reactions to detect species-specific non-18S rRNA gene targets. A pan-Plasmodium 18S rRNA target is also amplified to allow species identification or confirmation by sequencing if necessary. An evaluation of assay accuracy, performed on 76 clinical samples (56 positives using thin smear microscopy as the reference method and 20 negatives), demonstrated clinical sensitivities of 95.2% for P. falciparum (20/21 positives detected) and 100% for the Plasmodium genus (52/52), P. vivax (20/20), P. ovale (9/9), and P. malariae (6/6). The sensitivity of the P. knowlesi-specific PCR was evaluated using spiked whole blood samples (100% [10/10 detected]). The specificities of the real-time PCR primers were 94.2% for P. vivax (49/52) and 100% for P. falciparum (51/51), P. ovale (62/62), P. malariae (69/69), and P. knowlesi (52/52). Thirty-three specimens were used to test species identification by sequencing the pan-Plasmodium 18S rRNA PCR product, with correct identification in all cases. The real-time PCR assay also identified two samples with mixed P. falciparum and P. ovale infection, which was confirmed by sequencing. The assay described here can be integrated into a malaria testing algorithm in low-prevalence areas, allowing definitive Plasmodium species identification shortly after malaria diagnosis by microscopy. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

High-speed counter-current chromatography coupled online to high performance liquid chromatography-diode array detector-mass spectrometry for purification, analysis and identification of target compounds from natural products.

PubMed

Liang, Xuejuan; Zhang, Yuping; Chen, Wei; Cai, Ping; Zhang, Shuihan; Chen, Xiaoqin; Shi, Shuyun

2015-03-13

A challenge in coupling high-speed counter-current chromatography (HSCCC) online with high performance liquid chromatography (HPLC) for purity analysis was their time incompatibility. Consequently, HSCCC-HPLC was conducted by either controlling HPLC analysis time and HSCCC flow rate or using stop-and-go scheme. For natural products containing compounds with a wide range of polarities, the former would optimize experimental conditions, while the latter required more time. Here, a novel HSCCC-HPLC-diode array detector-mass spectrometry (HSCCC-HPLC-DAD-MS) was developed for undisrupted purification, analysis and identification of multi-compounds from natural products. Two six-port injection valves and a six-port switching valve were used as interface for collecting key HSCCC effluents alternatively for HPLC-DAD-MS analysis and identification. The ethyl acetate extract of Malus doumeri was performed on the hyphenated system to verify its efficacy. Five main flavonoids, 3-hydroxyphloridzin (1), phloridzin (2), 4',6'-dihydroxyhydrochalcone-2'-O-β-D-glucopyranoside (3, first found in M. doumeri), phloretin (4), and chrysin (5), were purified with purities over 99% by extrusion elution and/or stepwise elution mode in two-step HSCCC, and 25mM ammonium acetate solution was selected instead of water to depress emulsification in the first HSCCC. The online system shortened manipulation time largely compared with off-line analysis procedure and stop-and-go scheme. The results indicated that the present method could serve as a simple, rapid and effective way to achieve target compounds with high purity from natural products. Copyright © 2015 Elsevier B.V. All rights reserved.

Simulation of target interpretation based on infrared image features and psychology principle

NASA Astrophysics Data System (ADS)

Lin, Wei; Chen, Yu-hua; Gao, Hong-sheng; Wang, Zhan-feng; Wang, Ji-jun; Su, Rong-hua; Huang, Yan-ping

2009-07-01

It's an important and complicated process in target interpretation that target features extraction and identification, which effect psychosensorial quantity of interpretation person to target infrared image directly, and decide target viability finally. Using statistical decision theory and psychology principle, designing four psychophysical experiment, the interpretation model of the infrared target is established. The model can get target detection probability by calculating four features similarity degree between target region and background region, which were plotted out on the infrared image. With the verification of a great deal target interpretation in practice, the model can simulate target interpretation and detection process effectively, get the result of target interpretation impersonality, which can provide technique support for target extraction, identification and decision-making.

A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data.

PubMed

Demidov, German; Simakova, Tamara; Vnuchkova, Julia; Bragin, Anton

2016-10-22

Multiplex polymerase chain reaction (PCR) is a common enrichment technique for targeted massive parallel sequencing (MPS) protocols. MPS is widely used in biomedical research and clinical diagnostics as the fast and accurate tool for the detection of short genetic variations. However, identification of larger variations such as structure variants and copy number variations (CNV) is still being a challenge for targeted MPS. Some approaches and tools for structural variants detection were proposed, but they have limitations and often require datasets of certain type, size and expected number of amplicons affected by CNVs. In the paper, we describe novel algorithm for high-resolution germinal CNV detection in the PCR-enriched targeted sequencing data and present accompanying tool. We have developed a machine learning algorithm for the detection of large duplications and deletions in the targeted sequencing data generated with PCR-based enrichment step. We have performed verification studies and established the algorithm's sensitivity and specificity. We have compared developed tool with other available methods applicable for the described data and revealed its higher performance. We showed that our method has high specificity and sensitivity for high-resolution copy number detection in targeted sequencing data using large cohort of samples.

Unmasking Upstream Gene Expression Regulators with miRNA-corrected mRNA Data

PubMed Central

Bollmann, Stephanie; Bu, Dengpan; Wang, Jiaqi; Bionaz, Massimo

2015-01-01

Expressed micro-RNA (miRNA) affects messenger RNA (mRNA) abundance, hindering the accuracy of upstream regulator analysis. Our objective was to provide an algorithm to correct such bias. Large mRNA and miRNA analyses were performed on RNA extracted from bovine liver and mammary tissue. Using four levels of target scores from TargetScan (all miRNA:mRNA target gene pairs or only the top 25%, 50%, or 75%). Using four levels of target scores from TargetScan (all miRNA:mRNA target gene pairs or only the top 25%, 50%, or 75%) and four levels of the magnitude of miRNA effect (ME) on mRNA expression (30%, 50%, 75%, and 83% mRNA reduction), we generated 17 different datasets (including the original dataset). For each dataset, we performed upstream regulator analysis using two bioinformatics tools. We detected an increased effect on the upstream regulator analysis with larger miRNA:mRNA pair bins and higher ME. The miRNA correction allowed identification of several upstream regulators not present in the analysis of the original dataset. Thus, the proposed algorithm improved the prediction of upstream regulators. PMID:27279737

Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic.

PubMed

Gu, Jinghua; Xuan, Jianhua; Riggins, Rebecca B; Chen, Li; Wang, Yue; Clarke, Robert

2012-08-01

Identification of transcriptional regulatory networks (TRNs) is of significant importance in computational biology for cancer research, providing a critical building block to unravel disease pathways. However, existing methods for TRN identification suffer from the inclusion of excessive 'noise' in microarray data and false-positives in binding data, especially when applied to human tumor-derived cell line studies. More robust methods that can counteract the imperfection of data sources are therefore needed for reliable identification of TRNs in this context. In this article, we propose to establish a link between the quality of one target gene to represent its regulator and the uncertainty of its expression to represent other target genes. Specifically, an outlier sum statistic was used to measure the aggregated evidence for regulation events between target genes and their corresponding transcription factors. A Gibbs sampling method was then developed to estimate the marginal distribution of the outlier sum statistic, hence, to uncover underlying regulatory relationships. To evaluate the effectiveness of our proposed method, we compared its performance with that of an existing sampling-based method using both simulation data and yeast cell cycle data. The experimental results show that our method consistently outperforms the competing method in different settings of signal-to-noise ratio and network topology, indicating its robustness for biological applications. Finally, we applied our method to breast cancer cell line data and demonstrated its ability to extract biologically meaningful regulatory modules related to estrogen signaling and action in breast cancer. The Gibbs sampler MATLAB package is freely available at http://www.cbil.ece.vt.edu/software.htm. xuan@vt.edu Supplementary data are available at Bioinformatics online.

Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic

PubMed Central

Gu, Jinghua; Xuan, Jianhua; Riggins, Rebecca B.; Chen, Li; Wang, Yue; Clarke, Robert

2012-01-01

Motivation: Identification of transcriptional regulatory networks (TRNs) is of significant importance in computational biology for cancer research, providing a critical building block to unravel disease pathways. However, existing methods for TRN identification suffer from the inclusion of excessive ‘noise’ in microarray data and false-positives in binding data, especially when applied to human tumor-derived cell line studies. More robust methods that can counteract the imperfection of data sources are therefore needed for reliable identification of TRNs in this context. Results: In this article, we propose to establish a link between the quality of one target gene to represent its regulator and the uncertainty of its expression to represent other target genes. Specifically, an outlier sum statistic was used to measure the aggregated evidence for regulation events between target genes and their corresponding transcription factors. A Gibbs sampling method was then developed to estimate the marginal distribution of the outlier sum statistic, hence, to uncover underlying regulatory relationships. To evaluate the effectiveness of our proposed method, we compared its performance with that of an existing sampling-based method using both simulation data and yeast cell cycle data. The experimental results show that our method consistently outperforms the competing method in different settings of signal-to-noise ratio and network topology, indicating its robustness for biological applications. Finally, we applied our method to breast cancer cell line data and demonstrated its ability to extract biologically meaningful regulatory modules related to estrogen signaling and action in breast cancer. Availability and implementation: The Gibbs sampler MATLAB package is freely available at http://www.cbil.ece.vt.edu/software.htm. Contact: xuan@vt.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22595208

The effects of platform motion and target orientation on the performance of trackball manipulation.

PubMed

Yau, Yi-Jan; Chao, Chin-Jung; Feng, Wen-Yang; Hwang, Sheue-Ling

2011-08-01

The trackball has been widely employed as a control/command input device on moving vehicles, but few studies have explored the effects of platform motion on its manipulation. Fewer still have considered this issue in designing the user interface and the arrangement of console location and orientation simultaneously. This work describes an experiment carried out to investigate the performance of trackball users on a simple point-and-click task in a motion simulator. By varying the orientation of onscreen targets, the effect of cursor movement direction on performance is investigated. The results indicate that the platform motion and target orientation both significantly affect the time required to point and click, but not the accuracy of target selection. The movement times were considerably longer under rolling and pitching motions and for targets located along the diagonal axes of the interface. Subjective evaluations carried out by the participants agree with these objective results. These findings could be used to optimise console and graphical menu design for use on maritime vessels. STATEMENT OF RELEVANCE: In military situations, matters of life or death may be decided in milliseconds. Any delay or error in classification and identification will thus affect the safety of the ship and its crew. This study demonstrates that performance of manipulating a trackball is affected by the platform motion and target orientation. The results of the present study can guide the arrangement of consoles and the design of trackball-based graphical user interfaces on maritime vessels.

Identifying MicroRNAs and Transcript Targets in Jatropha Seeds

PubMed Central

Galli, Vanessa; Guzman, Frank; de Oliveira, Luiz F. V.; Loss-Morais, Guilherme; Körbes, Ana P.; Silva, Sérgio D. A.; Margis-Pinheiro, Márcia M. A. N.; Margis, Rogério

2014-01-01

MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received significant attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library of mature seeds and three mRNA libraries from three different seed development stages were generated by deep sequencing to identify and characterize the miRNAs and pre-miRNAs of J. curcas. Computational analysis was used for the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs) as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense, and lipid metabolism. Some pre-miRNA and miRNA targets vary in abundance between the three stages of seed development. A search for sequences that produce siRNA was performed, and the results indicated that J. curcas siRNAs play a role in nuclear functions, transport, catalytic processes and disease resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing, and it contributes to a functional understanding of these miRNAs. PMID:24551031

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

PubMed Central

Euskirchen, Ghia M.; Rozowsky, Joel S.; Wei, Chia-Lin; Lee, Wah Heng; Zhang, Zhengdong D.; Hartman, Stephen; Emanuelsson, Olof; Stolc, Viktor; Weissman, Sherman; Gerstein, Mark B.; Ruan, Yijun; Snyder, Michael

2007-01-01

Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding regions in mammalian cells using two different ChIP schemes: ChIP with DNA microarray analysis (ChIP-chip) and ChIP with DNA sequencing (ChIP-PET). We first investigated parameters central to obtaining robust ChIP-chip data sets by analyzing STAT1 targets in the ENCODE regions of the human genome, and then compared ChIP-chip to ChIP-PET. We devised methods for scoring and comparing results among various tiling arrays and examined parameters such as DNA microarray format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides ≥50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When target identification was evaluated as a function of array number, 80%–86% of targets were identified with three or more arrays. Comparison of ChIP-chip with ChIP-PET revealed strong agreement for the highest ranked targets with less overlap for the low ranked targets. With advantages and disadvantages unique to each approach, we found that ChIP-chip and ChIP-PET are frequently complementary in their relative abilities to detect STAT1 targets for the lower ranked targets; each method detected validated targets that were missed by the other method. The most comprehensive list of STAT1 binding regions is obtained by merging results from ChIP-chip and ChIP-sequencing. Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies. PMID:17568005

An Investigation of the Use of Real-time Image Mosaicing for Facilitating Global Spatial Awareness in Visual Search

NASA Astrophysics Data System (ADS)

Soung Yee, Anthony

Three experiments have been completed to investigate whether and how a software technique called real-time image mosaicing applied to a restricted field of view (FOV) might influence target detection and path integration performance in simulated aerial search scenarios, representing local and global spatial awareness tasks respectively. The mosaiced FOV (mFOV) was compared to single FOV (sFOV) and one with double the single size (dFOV). In addition to advancing our understanding of visual information in mosaicing, the present study examines the advantages and limitations of a number of metrics used to evaluate performance in path integration tasks, with particular attention paid to measuring performance in identifying complex routes. The highlights of the results are summarized as follows, according to Experiments 1 through 3 respectively. 1. A novel response method for evaluating route identification performance was developed. The surmised benefits of the mFOV relative to sFOV and dFOV revealed no significant differences in performance for the relatively simple route shapes tested. Compared to the mFOV and dFOV conditions, target detection performance in the local task was found to be superior in the sFOV condition. 2. In order to appropriately quantify the observed differences in complex route selections made by the participants, a novel analysis method was developed using the Thurstonian Paired Comparisons Method. 3. To investigate the effect of display size and elevation angle (EA) in a complex route environment, a 2x3 experiment was conducted for the two spatial tasks, at a height selected from Experiment 2. Although no significant differences were found in the target detection task, contrasts in the Paired Comparisons Method results revealed that route identification performance were as hypothesised: mFOV > dFOV > sFOV for EA = 90°. Results were similar for EA = 45°, but with mFOV being no different than dFOV. As hypothesised, EA was found to have an effect on route selection performance, with a top down view performing better than an angled view for the mFOV and sFOV conditions.

Performance characterization of a combined material identification and screening algorithm

NASA Astrophysics Data System (ADS)

Green, Robert L.; Hargreaves, Michael D.; Gardner, Craig M.

2013-05-01

Portable analytical devices based on a gamut of technologies (Infrared, Raman, X-Ray Fluorescence, Mass Spectrometry, etc.) are now widely available. These tools have seen increasing adoption for field-based assessment by diverse users including military, emergency response, and law enforcement. Frequently, end-users of portable devices are non-scientists who rely on embedded software and the associated algorithms to convert collected data into actionable information. Two classes of problems commonly encountered in field applications are identification and screening. Identification algorithms are designed to scour a library of known materials and determine whether the unknown measurement is consistent with a stored response (or combination of stored responses). Such algorithms can be used to identify a material from many thousands of possible candidates. Screening algorithms evaluate whether at least a subset of features in an unknown measurement correspond to one or more specific substances of interest and are typically configured to detect from a small list potential target analytes. Thus, screening algorithms are much less broadly applicable than identification algorithms; however, they typically provide higher detection rates which makes them attractive for specific applications such as chemical warfare agent or narcotics detection. This paper will present an overview and performance characterization of a combined identification/screening algorithm that has recently been developed. It will be shown that the combined algorithm provides enhanced detection capability more typical of screening algorithms while maintaining a broad identification capability. Additionally, we will highlight how this approach can enable users to incorporate situational awareness during a response.

Detection and identification of human targets in radar data

NASA Astrophysics Data System (ADS)

Gürbüz, Sevgi Z.; Melvin, William L.; Williams, Douglas B.

2007-04-01

Radar offers unique advantages over other sensors, such as visual or seismic sensors, for human target detection. Many situations, especially military applications, prevent the placement of video cameras or implantment seismic sensors in the area being observed, because of security or other threats. However, radar can operate far away from potential targets, and functions during daytime as well as nighttime, in virtually all weather conditions. In this paper, we examine the problem of human target detection and identification using single-channel, airborne, synthetic aperture radar (SAR). Human targets are differentiated from other detected slow-moving targets by analyzing the spectrogram of each potential target. Human spectrograms are unique, and can be used not just to identify targets as human, but also to determine features about the human target being observed, such as size, gender, action, and speed. A 12-point human model, together with kinematic equations of motion for each body part, is used to calculate the expected target return and spectrogram. A MATLAB simulation environment is developed including ground clutter, human and non-human targets for the testing of spectrogram-based detection and identification algorithms. Simulations show that spectrograms have some ability to detect and identify human targets in low noise. An example gender discrimination system correctly detected 83.97% of males and 91.11% of females. The problems and limitations of spectrogram-based methods in high clutter environments are discussed. The SNR loss inherent to spectrogram-based methods is quantified. An alternate detection and identification method that will be used as a basis for future work is proposed.

Identification of Enterobacteriaceae by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using the VITEK MS system.

PubMed

Richter, S S; Sercia, L; Branda, J A; Burnham, C-A D; Bythrow, M; Ferraro, M J; Garner, O B; Ginocchio, C C; Jennemann, R; Lewinski, M A; Manji, R; Mochon, A B; Rychert, J A; Westblade, L F; Procop, G W

2013-12-01

This multicenter study evaluated the accuracy of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry identifications from the VITEK MS system (bioMérieux, Marcy l'Etoile, France) for Enterobacteriaceae typically encountered in the clinical laboratory. Enterobacteriaceae isolates (n = 965) representing 17 genera and 40 species were analyzed on the VITEK MS system (database v2.0), in accordance with the manufacturer's instructions. Colony growth (≤72 h) was applied directly to the target slide. Matrix solution (α-cyano-4-hydroxycinnamic acid) was added and allowed to dry before mass spectrometry analysis. On the basis of the confidence level, the VITEK MS system provided a species, genus only, or no identification for each isolate. The accuracy of the mass spectrometric identification was compared to 16S rRNA gene sequencing performed at MIDI Labs (Newark, DE). Supplemental phenotypic testing was performed at bioMérieux when necessary. The VITEK MS result agreed with the reference method identification for 96.7% of the 965 isolates tested, with 83.8% correct to the species level and 12.8% limited to a genus-level identification. There was no identification for 1.7% of the isolates. The VITEK MS system misidentified 7 isolates (0.7 %) as different genera. Three Pantoea agglomerans isolates were misidentified as Enterobacter spp. and single isolates of Enterobacter cancerogenus, Escherichia hermannii, Hafnia alvei, and Raoultella ornithinolytica were misidentified as Klebsiella oxytoca, Citrobacter koseri, Obesumbacterium proteus, and Enterobacter aerogenes, respectively. Eight isolates (0.8 %) were misidentified as a different species in the correct genus. The VITEK MS system provides reliable mass spectrometric identifications for Enterobacteriaceae.

Feature Transformation Detection Method with Best Spectral Band Selection Process for Hyper-spectral Imaging

NASA Astrophysics Data System (ADS)

Chen, Hai-Wen; McGurr, Mike; Brickhouse, Mark

2015-11-01

We present a newly developed feature transformation (FT) detection method for hyper-spectral imagery (HSI) sensors. In essence, the FT method, by transforming the original features (spectral bands) to a different feature domain, may considerably increase the statistical separation between the target and background probability density functions, and thus may significantly improve the target detection and identification performance, as evidenced by the test results in this paper. We show that by differentiating the original spectral, one can completely separate targets from the background using a single spectral band, leading to perfect detection results. In addition, we have proposed an automated best spectral band selection process with a double-threshold scheme that can rank the available spectral bands from the best to the worst for target detection. Finally, we have also proposed an automated cross-spectrum fusion process to further improve the detection performance in lower spectral range (<1000 nm) by selecting the best spectral band pair with multivariate analysis. Promising detection performance has been achieved using a small background material signature library for concept-proving, and has then been further evaluated and verified using a real background HSI scene collected by a HYDICE sensor.

Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization

PubMed Central

Girard, Laurie D.; Boissinot, Karel; Peytavi, Régis; Boissinot, Maurice; Bergeron, Michel G.

2014-01-01

The combination of molecular diagnostic technologies is increasingly used to overcome limitations on sensitivity, specificity or multiplexing capabilities, and provide efficient lab-on-chip devices. Two such techniques, PCR amplification and microarray hybridization are used serially to take advantage of the high sensitivity and specificity of the former combined with high multiplexing capacities of the latter. These methods are usually performed in different buffers and reaction chambers. However, these elaborate methods have a high complexity cost related to reagent requirements, liquid storage and the number of reaction chambers to integrate into automated devices. Furthermore, microarray hybridizations have a sequence dependent efficiency not always predictable. In this work, we have developed the concept of a structured oligonucleotide probe which is activated by cleavage from polymerase exonuclease activity. This technology is called SCISSOHR for Structured Cleavage Induced Single-Stranded Oligonucleotide Hybridization Reaction. The SCISSOHR probes enable indexing the target sequence to a tag sequence. The SCISSOHR technology also allows the combination of nucleic acid amplification and microarray hybridization in a single vessel in presence of the PCR buffer only. The SCISSOHR technology uses an amplification probe that is irreversibly modified in presence of the target, releasing a single-stranded DNA tag for microarray hybridization. Each tag is composed of a 3-nucleotidesequence-dependent segment and a unique “target sequence-independent” 14-nucleotide segment allowing for optimal hybridization with minimal cross-hybridization. We evaluated the performance of five (5) PCR buffers to support microarray hybridization, compared to a conventional hybridization buffer. Finally, as a proof of concept, we developed a multiplexed assay for the amplification, detection, and identification of three (3) DNA targets. This new technology will facilitate the design of lab-on-chip microfluidic devices, while also reducing consumable costs. At term, it will allow the cost-effective automation of highly multiplexed assays for detection and identification of genetic targets. PMID:25489607

Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization.

PubMed

Girard, Laurie D; Boissinot, Karel; Peytavi, Régis; Boissinot, Maurice; Bergeron, Michel G

2015-02-07

The combination of molecular diagnostic technologies is increasingly used to overcome limitations on sensitivity, specificity or multiplexing capabilities, and provide efficient lab-on-chip devices. Two such techniques, PCR amplification and microarray hybridization are used serially to take advantage of the high sensitivity and specificity of the former combined with high multiplexing capacities of the latter. These methods are usually performed in different buffers and reaction chambers. However, these elaborate methods have high complexity and cost related to reagent requirements, liquid storage and the number of reaction chambers to integrate into automated devices. Furthermore, microarray hybridizations have a sequence dependent efficiency not always predictable. In this work, we have developed the concept of a structured oligonucleotide probe which is activated by cleavage from polymerase exonuclease activity. This technology is called SCISSOHR for Structured Cleavage Induced Single-Stranded Oligonucleotide Hybridization Reaction. The SCISSOHR probes enable indexing the target sequence to a tag sequence. The SCISSOHR technology also allows the combination of nucleic acid amplification and microarray hybridization in a single vessel in presence of the PCR buffer only. The SCISSOHR technology uses an amplification probe that is irreversibly modified in presence of the target, releasing a single-stranded DNA tag for microarray hybridization. Each tag is composed of a 3-nucleotide sequence-dependent segment and a unique "target sequence-independent" 14-nucleotide segment allowing for optimal hybridization with minimal cross-hybridization. We evaluated the performance of five (5) PCR buffers to support microarray hybridization, compared to a conventional hybridization buffer. Finally, as a proof of concept, we developed a multiplexed assay for the amplification, detection, and identification of three (3) DNA targets. This new technology will facilitate the design of lab-on-chip microfluidic devices, while also reducing consumable costs. At term, it will allow the cost-effective automation of highly multiplexed assays for detection and identification of genetic targets.

Combined effects of expectations and visual uncertainty upon detection and identification of a target in the fog.

PubMed

Quétard, Boris; Quinton, Jean-Charles; Colomb, Michèle; Pezzulo, Giovanni; Barca, Laura; Izaute, Marie; Appadoo, Owen Kevin; Mermillod, Martial

2015-09-01

Detecting a pedestrian while driving in the fog is one situation where the prior expectation about the target presence is integrated with the noisy visual input. We focus on how these sources of information influence the oculomotor behavior and are integrated within an underlying decision-making process. The participants had to judge whether high-/low-density fog scenes displayed on a computer screen contained a pedestrian or a deer by executing a mouse movement toward the response button (mouse-tracking). A variable road sign was added on the scene to manipulate expectations about target identity. We then analyzed the timing and amplitude of the deviation of mouse trajectories toward the incorrect response and, using an eye tracker, the detection time (before fixating the target) and the identification time (fixations on the target). Results revealed that expectation of the correct target results in earlier decisions with less deviation toward the alternative response, this effect being partially explained by the facilitation of target identification.

How variations in distance affect eyewitness reports and identification accuracy.

PubMed

Lindsay, R C L; Semmler, Carolyn; Weber, Nathan; Brewer, Neil; Lindsay, Marilyn R

2008-12-01

Witnesses observe crimes at various distances and the courts have to interpret their testimony given the likely quality of witnesses' views of events. We examined how accurately witnesses judged the distance between themselves and a target person, and how distance affected description accuracy, choosing behavior, and identification test accuracy. Over 1,300 participants were approached during normal daily activities, and asked to observe a target person at one of a number of possible distances. Under a Perception, Immediate Memory, or Delayed Memory condition, witnesses provided a brief description of the target, estimated the distance to the target, and then examined a 6-person target-present or target-absent lineup to see if they could identify the target. Errors in distance judgments were often substantial. Description accuracy was mediocre and did not vary systematically with distance. Identification choosing rates were not affected by distance, but decision accuracy declined with distance. Contrary to previous research, a 15-m viewing distance was not critical for discriminating accurate from inaccurate decisions.

Virtual reality, ultrasound-guided liver biopsy simulator: development and performance discrimination.

PubMed

Johnson, S J; Hunt, C M; Woolnough, H M; Crawshaw, M; Kilkenny, C; Gould, D A; England, A; Sinha, A; Villard, P F

2012-05-01

The aim of this article was to identify and prospectively investigate simulated ultrasound-guided targeted liver biopsy performance metrics as differentiators between levels of expertise in interventional radiology. Task analysis produced detailed procedural step documentation allowing identification of critical procedure steps and performance metrics for use in a virtual reality ultrasound-guided targeted liver biopsy procedure. Consultant (n=14; male=11, female=3) and trainee (n=26; male=19, female=7) scores on the performance metrics were compared. Ethical approval was granted by the Liverpool Research Ethics Committee (UK). Independent t-tests and analysis of variance (ANOVA) investigated differences between groups. Independent t-tests revealed significant differences between trainees and consultants on three performance metrics: targeting, p=0.018, t=-2.487 (-2.040 to -0.207); probe usage time, p = 0.040, t=2.132 (11.064 to 427.983); mean needle length in beam, p=0.029, t=-2.272 (-0.028 to -0.002). ANOVA reported significant differences across years of experience (0-1, 1-2, 3+ years) on seven performance metrics: no-go area touched, p=0.012; targeting, p=0.025; length of session, p=0.024; probe usage time, p=0.025; total needle distance moved, p=0.038; number of skin contacts, p<0.001; total time in no-go area, p=0.008. More experienced participants consistently received better performance scores on all 19 performance metrics. It is possible to measure and monitor performance using simulation, with performance metrics providing feedback on skill level and differentiating levels of expertise. However, a transfer of training study is required.

Are multiple-trial experiments appropriate for eyewitness identification studies? Accuracy, choosing, and confidence across trials.

PubMed

Mansour, J K; Beaudry, J L; Lindsay, R C L

2017-12-01

Eyewitness identification experiments typically involve a single trial: A participant views an event and subsequently makes a lineup decision. As compared to this single-trial paradigm, multiple-trial designs are more efficient, but significantly reduce ecological validity and may affect the strategies that participants use to make lineup decisions. We examined the effects of a number of forensically relevant variables (i.e., memory strength, type of disguise, degree of disguise, and lineup type) on eyewitness accuracy, choosing, and confidence across 12 target-present and 12 target-absent lineup trials (N = 349; 8,376 lineup decisions). The rates of correct rejections and choosing (across both target-present and target-absent lineups) did not vary across the 24 trials, as reflected by main effects or interactions with trial number. Trial number had a significant but trivial quadratic effect on correct identifications (OR = 0.99) and interacted significantly, but again trivially, with disguise type (OR = 1.00). Trial number did not significantly influence participants' confidence in correct identifications, confidence in correct rejections, or confidence in target-absent selections. Thus, multiple-trial designs appear to have minimal effects on eyewitness accuracy, choosing, and confidence. Researchers should thus consider using multiple-trial designs for conducting eyewitness identification experiments.

Long-term memory for temporal structure: evidence form the identification of well-known and novel songs.

PubMed

Schulkind, M D

1999-09-01

In three experiments, long-term memory for temporal structure was examined by having participants identify both well-known (e.g., "I've Been Working on the Railroad") and novel songs. The target songs were subjected to a number of rhythmic alterations, to assess the importance of four critical features of identification performance. The four critical features were meter, phrasing, rhythmic contour (ordinal scaling of note durations), and the ratio of successive durations. In contrast with previous work, the unaltered version of each song was identified significantly better than any altered version. This indicates that rhythm is stored in long-term memory. Furthermore, the results demonstrated that all four critical features play a role in the identification of songs. These results held for both well-known and novel tunes.

Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

PubMed Central

Wang, Jigang; Zhang, Chong-Jing; Zhang, Jianbin; He, Yingke; Lee, Yew Mun; Chen, Songbi; Lim, Teck Kwang; Ng, Shukie; Shen, Han-Ming; Lin, Qingsong

2015-01-01

Target-identification and understanding of mechanism-of-action (MOA) are challenging for development of small-molecule probes and their application in biology and drug discovery. For example, although aspirin has been widely used for more than 100 years, its molecular targets have not been fully characterized. To cope with this challenge, we developed a novel technique called quantitative acid-cleavable activity-based protein profiling (QA-ABPP) with combination of the following two parts: (i) activity-based protein profiling (ABPP) and iTRAQ™ quantitative proteomics for identification of target proteins and (ii) acid-cleavable linker-based ABPP for identification of peptides with specific binding sites. It is known that reaction of aspirin with its target proteins leads to acetylation. We thus applied the above technique using aspirin-based probes in human cancer HCT116 cells. We identified 1110 target proteins and 2775 peptides with exact acetylation sites. By correlating these two sets of data, 523 proteins were identified as targets of aspirin. We used various biological assays to validate the effects of aspirin on inhibition of protein synthesis and induction of autophagy which were elicited from the pathway analysis of Aspirin target profile. This technique is widely applicable for target identification in the field of drug discovery and biology, especially for the covalent drugs. PMID:25600173

Open Targets: a platform for therapeutic target identification and validation

PubMed Central

Koscielny, Gautier; An, Peter; Carvalho-Silva, Denise; Cham, Jennifer A.; Fumis, Luca; Gasparyan, Rippa; Hasan, Samiul; Karamanis, Nikiforos; Maguire, Michael; Papa, Eliseo; Pierleoni, Andrea; Pignatelli, Miguel; Platt, Theo; Rowland, Francis; Wankar, Priyanka; Bento, A. Patrícia; Burdett, Tony; Fabregat, Antonio; Forbes, Simon; Gaulton, Anna; Gonzalez, Cristina Yenyxe; Hermjakob, Henning; Hersey, Anne; Jupe, Steven; Kafkas, Şenay; Keays, Maria; Leroy, Catherine; Lopez, Francisco-Javier; Magarinos, Maria Paula; Malone, James; McEntyre, Johanna; Munoz-Pomer Fuentes, Alfonso; O'Donovan, Claire; Papatheodorou, Irene; Parkinson, Helen; Palka, Barbara; Paschall, Justin; Petryszak, Robert; Pratanwanich, Naruemon; Sarntivijal, Sirarat; Saunders, Gary; Sidiropoulos, Konstantinos; Smith, Thomas; Sondka, Zbyslaw; Stegle, Oliver; Tang, Y. Amy; Turner, Edward; Vaughan, Brendan; Vrousgou, Olga; Watkins, Xavier; Martin, Maria-Jesus; Sanseau, Philippe; Vamathevan, Jessica; Birney, Ewan; Barrett, Jeffrey; Dunham, Ian

2017-01-01

We have designed and developed a data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources. The platform provides either a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease. Users can easily transition between these target- and disease-centric workflows. The Open Targets Validation Platform is accessible at https://www.targetvalidation.org. PMID:27899665

Identification of testis-specific male contraceptive targets: insights from transcriptional profiling of the cycle of the rat seminiferous epithelium and purified testicular cells.

PubMed

Johnston, Daniel S; Jelinsky, Scott A; Zhi, Yu; Finger, Joshua N; Kopf, Gregory S; Wright, William W

2007-12-01

In an effort to identify novel targets for the development of nonhormonal male contraceptives, genome-wide transcriptional profiling of the rat testis was performed. Specifically, enzymatically purified spermatogonia plus early spermatocyctes, pachytene spermatocytes, round spermatids, and Sertoli cells was analyzed along with microdissected rat seminiferous tubules at stages I, II-III, IV-V, VI, VIIa,b, VIIc,d, VIII, IX- XI, XII, XIII-XIV of the cycle of the seminiferous epithelium using RAE 230_2.0 microarrays. The combined analysis of these studies identified 16,971 expressed probe sets on the array. How these expression data, combined with additional bioinformatic data analysis and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) analysis, led to the identification of 58 genes that have 1000-fold higher expression transcriptionally in the testis when compared to over 20 other nonreproductive tissues is described. The products of these genes may play important roles in testicular and/or sperm function, and further investigation on their utility as nonhormonal contraceptive targets is warranted. Moreover, these microarray data have been used to expedite the identification of a mutation in RIKEN cDNA 2410004F06 gene as likely being responsible for spermatogenic failure in a line of infertile mice generated by N-ethyl-N-nitrosourea (ENU) mutagenesis. The microarray data and the qRT-PCR data described are available in the Mammalian Reproductive Genetics database (http://mrg.genetics.washington.edu/).

Lasers' spectral and temporal profile can affect visual glare disability.

PubMed

Beer, Jeremy M A; Freeman, David A

2012-12-01

Experiments measured the effects of laser glare on visual orientation and motion perception. Laser stimuli were varied according to spectral composition and temporal presentation as subjects identified targets' tilt (Experiment 1) and movement (Experiment 2). The objective was to determine whether the glare parameters would alter visual disruption. Three spectral profiles (monochromatic Green vs. polychromatic White vs. alternating Red-Green) were used to produce a ring of laser glare surrounding a target. Two experiments were performed to measure the minimum contrast required to report target orientation or motion direction. The temporal glare profile was also varied: the ring was illuminated either continuously or discontinuously. Time-averaged luminance of the glare stimuli was matched across all conditions. In both experiments, threshold (deltaL) values were approximately 0.15 log units higher in monochromatic Green than in polychromatic White conditions. In Experiment 2 (motion identification), thresholds were approximately 0.17 log units higher in rapidly flashing (6, 10, or 14 Hz) than in continuous exposure conditions. Monochromatic extended-source laser glare disrupted orientation and motion identification more than polychromatic glare. In the motion task, pulse trains faster than 6 Hz (but below flicker fusion) elevated thresholds more than continuous glare with the same time-averaged luminance. Under these conditions, alternating the wavelength of monochromatic glare over time did not aggravate disability relative to green-only glare. Repetitively flashing monochromatic laser glare induced occasional episodes of impaired motion identification, perhaps resulting from cognitive interference. Interference speckle might play a role in aggravating monochromatic glare effects.

Optimization of a Multi-Stage ATR System for Small Target Identification

NASA Technical Reports Server (NTRS)

Lin, Tsung-Han; Lu, Thomas; Braun, Henry; Edens, Western; Zhang, Yuhan; Chao, Tien- Hsin; Assad, Christopher; Huntsberger, Terrance

2010-01-01

An Automated Target Recognition system (ATR) was developed to locate and target small object in images and videos. The data is preprocessed and sent to a grayscale optical correlator (GOC) filter to identify possible regionsof- interest (ROIs). Next, features are extracted from ROIs based on Principal Component Analysis (PCA) and sent to neural network (NN) to be classified. The features are analyzed by the NN classifier indicating if each ROI contains the desired target or not. The ATR system was found useful in identifying small boats in open sea. However, due to "noisy background," such as weather conditions, background buildings, or water wakes, some false targets are mis-classified. Feedforward backpropagation and Radial Basis neural networks are optimized for generalization of representative features to reduce false-alarm rate. The neural networks are compared for their performance in classification accuracy, classifying time, and training time.

Two-dimensional hidden semantic information model for target saliency detection and eyetracking identification

NASA Astrophysics Data System (ADS)

Wan, Weibing; Yuan, Lingfeng; Zhao, Qunfei; Fang, Tao

2018-01-01

Saliency detection has been applied to the target acquisition case. This paper proposes a two-dimensional hidden Markov model (2D-HMM) that exploits the hidden semantic information of an image to detect its salient regions. A spatial pyramid histogram of oriented gradient descriptors is used to extract features. After encoding the image by a learned dictionary, the 2D-Viterbi algorithm is applied to infer the saliency map. This model can predict fixation of the targets and further creates robust and effective depictions of the targets' change in posture and viewpoint. To validate the model with a human visual search mechanism, two eyetrack experiments are employed to train our model directly from eye movement data. The results show that our model achieves better performance than visual attention. Moreover, it indicates the plausibility of utilizing visual track data to identify targets.

Identification accuracy of children versus adults: a meta-analysis.

PubMed

Pozzulo, J D; Lindsay, R C

1998-10-01

Identification accuracy of children and adults was examined in a meta-analysis. Preschoolers (M = 4 years) were less likely than adults to make correct identifications. Children over the age of 5 did not differ significantly from adults with regard to correct identification rate. Children of all ages examined were less likely than adults to correctly reject a target-absent lineup. Even adolescents (M = 12-13 years) did not reach an adult rate of correct rejection. Compared to simultaneous lineup presentation, sequential lineups increased the child-adult gap for correct rejections. Providing child witnesses with identification practice or training did not increase their correct rejection rates. Suggestions for children's inability to correctly reject target-absent lineups are discussed. Future directions for identification research are presented.

Identification of Lactobacillus from the Saliva of Adult Patients with Caries Using Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry

PubMed Central

Ma, Qingwei; Song, Yeqing; Zhang, Qian; Wang, Xiaoyan; Chen, Feng

2014-01-01

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been presented as a superior method for the detection of microorganisms in body fluid samples (e.g., blood, saliva, pus, etc.) However, the performance of MALDI-TOF MS in routine identification of caries-related Lactobacillus isolates from saliva of adult patients with caries has not been determined. In the present study, we introduced a new MALDI-TOF MS system for identification of lactobacilli. Saliva samples were collected from 120 subjects with caries. Bacteria were isolated and cultured, and each isolate was identified by both 16S rRNA sequencing and MALDI-TOF MS. The identification results obtained by MALDI-TOF MS were concordant at the genus level with those of conventional 16S rRNA-based sequencing for 88.6% of lactobacilli (62/70) and 95.5% of non-lactobacilli (21/22). Up to 96 results could be obtained in parallel on a single MALDI target, suggesting that this is a reliable high-throughput approach for routine identification of lactobacilli. However, additional reference strains are necessary to increase the sensitivity and specificity of species-level identification. PMID:25166027

Using a binaural biomimetic array to identify bottom objects ensonified by echolocating dolphins

USGS Publications Warehouse

Heiweg, D.A.; Moore, P.W.; Martin, S.W.; Dankiewicz, L.A.

2006-01-01

The development of a unique dolphin biomimetic sonar produced data that were used to study signal processing methods for object identification. Echoes from four metallic objects proud on the bottom, and a substrate-only condition, were generated by bottlenose dolphins trained to ensonify the targets in very shallow water. Using the two-element ('binaural') receive array, object echo spectra were collected and submitted for identification to four neural network architectures. Identification accuracy was evaluated over two receive array configurations, and five signal processing schemes. The four neural networks included backpropagation, learning vector quantization, genetic learning and probabilistic network architectures. The processing schemes included four methods that capitalized on the binaural data, plus a monaural benchmark process. All the schemes resulted in above-chance identification accuracy when applied to learning vector quantization and backpropagation. Beam-forming or concatenation of spectra from both receive elements outperformed the monaural benchmark, with higher sensitivity and lower bias. Ultimately, best object identification performance was achieved by the learning vector quantization network supplied with beam-formed data. The advantages of multi-element signal processing for object identification are clearly demonstrated in this development of a first-ever dolphin biomimetic sonar. ?? 2006 IOP Publishing Ltd.

Virtual DRI dataset development

NASA Astrophysics Data System (ADS)

Hixson, Jonathan G.; Teaney, Brian P.; May, Christopher; Maurer, Tana; Nelson, Michael B.; Pham, Justin R.

2017-05-01

The U.S. Army RDECOM CERDEC NVESD MSD's target acquisition models have been used for many years by the military analysis community for sensor design, trade studies, and field performance prediction. This paper analyzes the results of perception tests performed to compare the results of a field DRI (Detection, Recognition, and Identification Test) performed in 2009 to current Soldier performance viewing the same imagery in a laboratory environment and simulated imagery of the same data set. The purpose of the experiment is to build a robust data set for use in the virtual prototyping of infrared sensors. This data set will provide a strong foundation relating, model predictions, field DRI results and simulated imagery.

A RICH detector for hadron identification at Jlab

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

Mammoliti, Francesco; Cisbani, Evaristo; Cusanno, Francesco

2011-08-01

The “standard” Hall A apparatus at Jefferson Lab (TOF and aerogel threshold Cherenkov detectors) does not provide complete identification for proton, kaon and pion. To this aim, a proximity focusing C6F14/CsI RICH (Ring Image Cherenkov) detector has been designed, built, tested and operated to separate kaons from pions with a pion contamination of a few percent up to 2.4 GeV/c. Two quite different experimental investigations have benefitted of the RICH identification: on one side, the high-resolution hypernuclear spectroscopy series of experiments on carbon, beryllium and oxygen, devoted to the study of the lambda-nucleon potential. On the other side, the measurementsmore » of the single spin asymmetries of pion and kaon on a transversely polarized 3He target are of utmost interest in understanding QCD dynamics in the nucleon. We present the technical features of such a RICH detector and comment on the presently achieved performance in hadron identification.« less

A re-examination of the effects of biased lineup instructions in eyewitness identification.

PubMed

Clark, Steven E

2005-10-01

A meta-analytic review of research comparing biased and unbiased instructions in eyewitness identification experiments showed an asymmetry; specifically, that biased instructions led to a large and consistent decrease in accuracy in target-absent lineups, but produced inconsistent results for target-present lineups, with an average effect size near zero (Steblay, 1997). The results for target-present lineups are surprising, and are inconsistent with statistical decision theories (i.e., Green & Swets, 1966). A re-examination of the relevant studies and the meta-analysis of those studies shows clear evidence that correct identification rates do increase with biased lineup instructions, and that biased witnesses make correct identifications at a rate considerably above chance. Implications for theory, as well as police procedure and policy, are discussed.

A re-examination of the effects of biased lineup instructions in eyewitness identification.

PubMed

Clark, Steven E

2005-08-01

A meta-analytic review of research comparing biased and unbiased instructions in eyewitness identification experiments showed an asymmetry, specifically that biased instructions led to a large and consistent decrease in accuracy in target-absent lineups, but produced inconsistent results for target-present lineups, with an average effect size near zero (N. M. Steblay, 1997). The results for target-present lineups are surprising, and are inconsistent with statistical decision theories (i.e., D. M. Green & J. A. Swets, 1966). A re-examination of the relevant studies and the meta-analysis of those studies shows clear evidence that correct identification rates do increase with biased lineup instructions, and that biased witnesses make correct identifications at a rate considerably above chance. Implications for theory, as well as police procedure and policy, are discussed.

ManPortable and UGV LIVAR: advances in sensor suite integration bring improvements to target observation and identification for the electronic battlefield

NASA Astrophysics Data System (ADS)

Lynam, Jeff R.

2001-09-01

A more highly integrated, electro-optical sensor suite using Laser Illuminated Viewing and Ranging (LIVAR) techniques is being developed under the Army Advanced Concept Technology- II (ACT-II) program for enhanced manportable target surveillance and identification. The ManPortable LIVAR system currently in development employs a wide-array of sensor technologies that provides the foot-bound soldier and UGV significant advantages and capabilities in lightweight, fieldable, target location, ranging and imaging systems. The unit incorporates a wide field-of-view, 5DEG x 3DEG, uncooled LWIR passive sensor for primary target location. Laser range finding and active illumination is done with a triggered, flash-lamp pumped, eyesafe micro-laser operating in the 1.5 micron region, and is used in conjunction with a range-gated, electron-bombarded CCD digital camera to then image the target objective in a more- narrow, 0.3$DEG, field-of-view. Target range determination is acquired using the integrated LRF and a target position is calculated using data from other onboard devices providing GPS coordinates, tilt, bank and corrected magnetic azimuth. Range gate timing and coordinated receiver optics focus control allow for target imaging operations to be optimized. The onboard control electronics provide power efficient, system operations for extended field use periods from the internal, rechargeable battery packs. Image data storage, transmission, and processing performance capabilities are also being incorporated to provide the best all-around support, for the electronic battlefield, in this type of system. The paper will describe flash laser illumination technology, EBCCD camera technology with flash laser detection system, and image resolution improvement through frame averaging.

Visually-guided attention enhances target identification in a complex auditory scene.

PubMed

Best, Virginia; Ozmeral, Erol J; Shinn-Cunningham, Barbara G

2007-06-01

In auditory scenes containing many similar sound sources, sorting of acoustic information into streams becomes difficult, which can lead to disruptions in the identification of behaviorally relevant targets. This study investigated the benefit of providing simple visual cues for when and/or where a target would occur in a complex acoustic mixture. Importantly, the visual cues provided no information about the target content. In separate experiments, human subjects either identified learned birdsongs in the presence of a chorus of unlearned songs or recalled strings of spoken digits in the presence of speech maskers. A visual cue indicating which loudspeaker (from an array of five) would contain the target improved accuracy for both kinds of stimuli. A cue indicating which time segment (out of a possible five) would contain the target also improved accuracy, but much more for birdsong than for speech. These results suggest that in real world situations, information about where a target of interest is located can enhance its identification, while information about when to listen can also be helpful when targets are unfamiliar or extremely similar to their competitors.

Visually-guided Attention Enhances Target Identification in a Complex Auditory Scene

PubMed Central

Ozmeral, Erol J.; Shinn-Cunningham, Barbara G.

2007-01-01

In auditory scenes containing many similar sound sources, sorting of acoustic information into streams becomes difficult, which can lead to disruptions in the identification of behaviorally relevant targets. This study investigated the benefit of providing simple visual cues for when and/or where a target would occur in a complex acoustic mixture. Importantly, the visual cues provided no information about the target content. In separate experiments, human subjects either identified learned birdsongs in the presence of a chorus of unlearned songs or recalled strings of spoken digits in the presence of speech maskers. A visual cue indicating which loudspeaker (from an array of five) would contain the target improved accuracy for both kinds of stimuli. A cue indicating which time segment (out of a possible five) would contain the target also improved accuracy, but much more for birdsong than for speech. These results suggest that in real world situations, information about where a target of interest is located can enhance its identification, while information about when to listen can also be helpful when targets are unfamiliar or extremely similar to their competitors. PMID:17453308

Classification accuracy of claims-based methods for identifying providers failing to meet performance targets.

PubMed

Hubbard, Rebecca A; Benjamin-Johnson, Rhondee; Onega, Tracy; Smith-Bindman, Rebecca; Zhu, Weiwei; Fenton, Joshua J

2015-01-15

Quality assessment is critical for healthcare reform, but data sources are lacking for measurement of many important healthcare outcomes. With over 49 million people covered by Medicare as of 2010, Medicare claims data offer a potentially valuable source that could be used in targeted health care quality improvement efforts. However, little is known about the operating characteristics of provider profiling methods using claims-based outcome measures that may estimate provider performance with error. Motivated by the example of screening mammography performance, we compared approaches to identifying providers failing to meet guideline targets using Medicare claims data. We used data from the Breast Cancer Surveillance Consortium and linked Medicare claims to compare claims-based and clinical estimates of cancer detection rate. We then demonstrated the performance of claim-based estimates across a broad range of operating characteristics using simulation studies. We found that identification of poor performing providers was extremely sensitive to algorithm specificity, with no approach identifying more than 65% of poor performing providers when claims-based measures had specificity of 0.995 or less. We conclude that claims have the potential to contribute important information on healthcare outcomes to quality improvement efforts. However, to achieve this potential, development of highly accurate claims-based outcome measures should remain a priority. Copyright © 2014 John Wiley & Sons, Ltd.

Identification of Novel Molecular Targets for Endometrial Cancer Using a Drill-Down LC-MS/MS Approach with iTRAQ

PubMed Central

Voisin, Sébastien N.; Krakovska, Olga; Matta, Ajay; DeSouza, Leroi V.; Romaschin, Alexander D.; Colgan, Terence J.; Siu, K. W. Michael

2011-01-01

Background The number of patients with endometrial carcinoma (EmCa) with advanced stage or high histological grade is increasing and prognosis has not improved for over the last decade. There is an urgent need for the discovery of novel molecular targets for diagnosis, prognosis and treatment of EmCa, which will have the potential to improve the clinical strategy and outcome of this disease. Methodology and Results We used a “drill-down” proteomics approach to facilitate the identification of novel molecular targets for diagnosis, prognosis and/or therapeutic intervention for EmCa. Based on peptide ions identified and their retention times in the first LC-MS/MS analysis, an exclusion list was generated for subsequent iterations. A total of 1529 proteins have been identified below the Proteinpilot® 5% error threshold from the seven sets of iTRAQ experiments performed. On average, the second iteration added 78% new peptides to those identified after the first run, while the third iteration added 36% additional peptides. Of the 1529 proteins identified, only 40 satisfied our criteria for significant differential expression in EmCa in comparison to normal proliferative tissues. These proteins included metabolic enzymes (pyruvate kinase M2 and lactate dehydrogenase A); calcium binding proteins (S100A6, calcyphosine and calumenin), and proteins involved in regulating inflammation, proliferation and invasion (annexin A1, interleukin enhancer-binding factor 3, alpha-1-antitrypsin, macrophage capping protein and cathepsin B). Network analyses revealed regulation of these molecular targets by c-myc, Her2/neu and TNF alpha, suggesting intervention with these pathways may be a promising strategy for the development of novel molecular targeted therapies for EmCa. Conclusions Our analyses revealed the significance of drill-down proteomics approach in combination with iTRAQ to overcome some of the limitations of current proteomics strategies. This study led to the identification of a number of novel molecular targets having therapeutic potential for targeted molecular therapies for endometrial carcinoma. PMID:21305022

An evaluation of talker localization based on direction of arrival estimation and statistical sound source identification

NASA Astrophysics Data System (ADS)

Nishiura, Takanobu; Nakamura, Satoshi

2002-11-01

It is very important to capture distant-talking speech for a hands-free speech interface with high quality. A microphone array is an ideal candidate for this purpose. However, this approach requires localizing the target talker. Conventional talker localization algorithms in multiple sound source environments not only have difficulty localizing the multiple sound sources accurately, but also have difficulty localizing the target talker among known multiple sound source positions. To cope with these problems, we propose a new talker localization algorithm consisting of two algorithms. One is DOA (direction of arrival) estimation algorithm for multiple sound source localization based on CSP (cross-power spectrum phase) coefficient addition method. The other is statistical sound source identification algorithm based on GMM (Gaussian mixture model) for localizing the target talker position among localized multiple sound sources. In this paper, we particularly focus on the talker localization performance based on the combination of these two algorithms with a microphone array. We conducted evaluation experiments in real noisy reverberant environments. As a result, we confirmed that multiple sound signals can be identified accurately between ''speech'' or ''non-speech'' by the proposed algorithm. [Work supported by ATR, and MEXT of Japan.

Molecular Hybridization of Potent and Selective γ-Hydroxybutyric Acid (GHB) Ligands: Design, Synthesis, Binding Studies, and Molecular Modeling of Novel 3-Hydroxycyclopent-1-enecarboxylic Acid (HOCPCA) and trans-γ-Hydroxycrotonic Acid (T-HCA) Analogs.

PubMed

Krall, Jacob; Jensen, Claus Hatt; Bavo, Francesco; Falk-Petersen, Christina Birkedahl; Haugaard, Anne Stæhr; Vogensen, Stine Byskov; Tian, Yongsong; Nittegaard-Nielsen, Mia; Sigurdardóttir, Sara Björk; Kehler, Jan; Kongstad, Kenneth Thermann; Gloriam, David E; Clausen, Rasmus Prætorius; Harpsøe, Kasper; Wellendorph, Petrine; Frølund, Bente

2017-11-09

γ-Hydroxybutyric acid (GHB) is a neuroactive substance with specific high-affinity binding sites. To facilitate target identification and ligand optimization, we herein report a comprehensive structure-affinity relationship study for novel ligands targeting these binding sites. A molecular hybridization strategy was used based on the conformationally restricted 3-hydroxycyclopent-1-enecarboxylic acid (HOCPCA) and the linear GHB analog trans-4-hydroxycrotonic acid (T-HCA). In general, all structural modifications performed on HOCPCA led to reduced affinity. In contrast, introduction of diaromatic substituents into the 4-position of T-HCA led to high-affinity analogs (medium nanomolar K i ) for the GHB high-affinity binding sites as the most high-affinity analogs reported to date. The SAR data formed the basis for a three-dimensional pharmacophore model for GHB ligands, which identified molecular features important for high-affinity binding, with high predictive validity. These findings will be valuable in the further processes of both target characterization and ligand identification for the high-affinity GHB binding sites.

Novel targets of sulforaphane in primary cardiomyocytes identified by proteomic analysis.

PubMed

Angeloni, Cristina; Turroni, Silvia; Bianchi, Laura; Fabbri, Daniele; Motori, Elisa; Malaguti, Marco; Leoncini, Emanuela; Maraldi, Tullia; Bini, Luca; Brigidi, Patrizia; Hrelia, Silvana

2013-01-01

Cardiovascular diseases represent the main cause of mortality in the industrialized world and the identification of effective preventive strategies is of fundamental importance. Sulforaphane, an isothiocyanate from cruciferous vegetables, has been shown to up-regulate phase II enzymes in cardiomyocytes and counteract oxidative stress-induced apoptosis. Aim of the present study was the identification and characterization of novel sulforaphane targets in cardiomyocytes applying a proteomic approach. Two-dimensional gel electrophoresis and mass spectrometry were used to generate protein profiles of primary neonatal rat cardiomyocytes treated and untreated with 5 µM sulforaphane for 1-48 h. According to image analysis, 64 protein spots were found as differentially expressed and their functional correlations were investigated using the MetaCore program. We mainly focused on 3 proteins: macrophage migration inhibitory factor (MIF), CLP36 or Elfin, and glyoxalase 1, due to their possible involvement in cardioprotection. Validation of the time-dependent differential expression of these proteins was performed by western blotting. In particular, to gain insight into the cardioprotective role of the modulation of glyoxalase 1 by sulforaphane, further experiments were performed using methylglyoxal to mimic glycative stress. Sulforaphane was able to counteract methylglyoxal-induced apoptosis, ROS production, and glycative stress, likely through glyoxalase 1 up-regulation. In this study, we reported for the first time new molecular targets of sulforaphane, such as MIF, CLP36 and glyoxalase 1. In particular, we gave new insights into the anti-glycative role of sulforaphane in cardiomyocytes, confirming its pleiotropic behavior in counteracting cardiovascular diseases.

Individual differences in selective attention predict speech identification at a cocktail party

PubMed Central

Oberfeld, Daniel; Klöckner-Nowotny, Felicitas

2016-01-01

Listeners with normal hearing show considerable individual differences in speech understanding when competing speakers are present, as in a crowded restaurant. Here, we show that one source of this variance are individual differences in the ability to focus selective attention on a target stimulus in the presence of distractors. In 50 young normal-hearing listeners, the performance in tasks measuring auditory and visual selective attention was associated with sentence identification in the presence of spatially separated competing speakers. Together, the measures of selective attention explained a similar proportion of variance as the binaural sensitivity for the acoustic temporal fine structure. Working memory span, age, and audiometric thresholds showed no significant association with speech understanding. These results suggest that a reduced ability to focus attention on a target is one reason why some listeners with normal hearing sensitivity have difficulty communicating in situations with background noise. DOI: http://dx.doi.org/10.7554/eLife.16747.001 PMID:27580272

The Pitfalls of Companion Diagnostics: Evaluation of Discordant EGFR Mutation Results from a Clinical Laboratory and a Central Laboratory.

PubMed

Turner, Scott A; Peterson, Jason D; Pettus, Jason R; de Abreu, Francine B; Amos, Christopher I; Dragnev, Konstantin H; Tsongalis, Gregory J

2016-05-01

Accurate identification of somatic mutations in formalin-fixed, paraffin-embedded tumor tissue is required for enrollment into clinical trials for many novel targeted therapeutics, including trials requiring EGFR mutation status in non-small-cell lung carcinomas. Central clinical trial laboratories contracted to perform this analysis typically rely on US Food and Drug Administration-approved targeted assays to identify these mutations. We present two cases in which central laboratories inaccurately reported EGFR mutation status because of improper identification and isolation of tumor material and failure to accurately report assay limitations, resulting in enrollment denial. Such cases highlight the need for increased awareness by clinical trials of the limitation of these US Food and Drug Administration-approved assays and the necessity for a mechanism to reevaluate discordant results by alternative laboratory-developed procedures, including clinical next-generation sequencing. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Fluorescence lifetime-based contrast enhancement of indocyanine green-labeled tumors

NASA Astrophysics Data System (ADS)

Kumar, Anand T. N.; Carp, Stefan A.; Yang, Jing; Ross, Alana; Medarova, Zdravka; Ran, Chongzhao

2017-04-01

Although the development of tumor-targeted fluorescent probes is a major area of investigation, it will be several years before these probes are realized for clinical use. Here, we report an approach that employs indocyanine-green (ICG), a clinically approved, nontargeted dye, in conjunction with fluorescence lifetime (FLT) detection to provide high accuracy for tumor-tissue identification in mouse models of subcutaneous human breast and brain tmors. The improved performance relies on the distinct FLTs of ICG within tumors versus tissue autofluorescence and is further aided by the well-known enhanced permeability and retention of ICG in tumors and the clearance of ICG from normal tissue several hours after intravenous injection. We demonstrate that FLT detection can provide more than 98% sensitivity and specificity, and a 10-fold reduction in error rates compared to intensity-based detection. Our studies suggest the significant potential of FLT-contrast for accurate tumor-tissue identification using ICG and other targeted probes under development, both for intraoperative imaging and for ex-vivo margin assessment of surgical specimens.

Ultra-fast DNA-based multiplex convection PCR method for meat species identification with possible on-site applications.

PubMed

Song, Kyung-Young; Hwang, Hyun Jin; Kim, Jeong Hee

2017-08-15

The aim of this study was to develop an ultra-fast molecular detection method for meat identification using convection Palm polymerase chain reaction (PCR). The mitochondrial cytochrome b (Cyt b) gene was used as a target gene. Amplicon size was designed to be different for beef, lamb, and pork. When these primer sets were used, each species-specific set specifically detected the target meat species in singleplex and multiplex modes in a 24min PCR run. The detection limit was 1pg of DNA for each meat species. The convection PCR method could detect as low as 1% of meat adulteration. The stability of the assay was confirmed using thermal processed meats. We also showed that direct PCR can be successfully performed with mixed meats and food samples. These results suggest that the developed assay may be useful in the authentication of meats and meat products in laboratory and rapid on-site applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Examination of soldier target recognition with direct view optics

NASA Astrophysics Data System (ADS)

Long, Frederick H.; Larkin, Gabriella; Bisordi, Danielle; Dorsey, Shauna; Marianucci, Damien; Goss, Lashawnta; Bastawros, Michael; Misiuda, Paul; Rodgers, Glenn; Mazz, John P.

2017-10-01

Target recognition and identification is a problem of great military and scientific importance. To examine the correlation between target recognition and optical magnification, ten U.S. Army soldiers were tasked with identifying letters on targets at 800 and 1300 meters away. Letters were used since they are a standard method for measuring visual acuity. The letters were approximately 90 cm high, which is the size of a well-known rifle. Four direct view optics with angular magnifications of 1.5x, 4x, 6x, and 9x were used. The goal of this approach was to measure actual probabilities for correct target identification. Previous scientific literature suggests that target recognition can be modeled as a linear response problem in angular frequency space using the established values for the contrast sensitivity function for a healthy human eye and the experimentally measured modulation transfer function of the optic. At the 9x magnification, the soldiers could identify the letters with almost no errors (i.e., 97% probability of correct identification). At lower magnification, errors in letter identification were more frequent. The identification errors were not random but occurred most frequently with a few pairs of letters (e.g., O and Q), which is consistent with the literature for letter recognition. In addition, in the small subject sample of ten soldiers, there was considerable variation in the observer recognition capability at 1.5x and a range of 800 meters. This can be directly attributed to the variation in the observer visual acuity.

Grayscale Optical Correlator Workbench

NASA Technical Reports Server (NTRS)

Hanan, Jay; Zhou, Hanying; Chao, Tien-Hsin

2006-01-01

Grayscale Optical Correlator Workbench (GOCWB) is a computer program for use in automatic target recognition (ATR). GOCWB performs ATR with an accurate simulation of a hardware grayscale optical correlator (GOC). This simulation is performed to test filters that are created in GOCWB. Thus, GOCWB can be used as a stand-alone ATR software tool or in combination with GOC hardware for building (target training), testing, and optimization of filters. The software is divided into three main parts, denoted filter, testing, and training. The training part is used for assembling training images as input to a filter. The filter part is used for combining training images into a filter and optimizing that filter. The testing part is used for testing new filters and for general simulation of GOC output. The current version of GOCWB relies on the mathematical software tools from MATLAB binaries for performing matrix operations and fast Fourier transforms. Optimization of filters is based on an algorithm, known as OT-MACH, in which variables specified by the user are parameterized and the best filter is selected on the basis of an average result for correct identification of targets in multiple test images.

Molecular identification of python species: development and validation of a novel assay for forensic investigations.

PubMed

Ciavaglia, Sherryn A; Tobe, Shanan S; Donnellan, Stephen C; Henry, Julianne M; Linacre, Adrian M T

2015-05-01

Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Hyperspectral imaging using novel LWIR OPO for hazardous material detection and identification

NASA Astrophysics Data System (ADS)

Ruxton, Keith; Robertson, Gordon; Miller, Bill; Malcolm, Graeme P. A.; Maker, Gareth T.

2014-05-01

Current stand-off hyperspectral imaging detection solutions that operate in the mid-wave infrared (MWIR), nominally 2.5 - 5 μm spectral region, are limited by the number of absorption bands that can be addressed. This issue is most apparent when evaluating a scene with multiple absorbers with overlapping spectral features making accurate material identification challenging. This limitation can be overcome by moving to the long wave IR (LWIR) region, which is rich in characteristic absorption features, which can provide ample molecular information in order to perform presumptive identification relative to a spectral library. This work utilises an instrument platform to perform negative contrast imaging using a novel LWIR optical parametric oscillator (OPO) as the source. The OPO offers continuous tuning in the region 5.5 - 9.5 μm, which includes a number of molecular vibrations associated with the target material compositions. Scanning the scene of interest whilst sweeping the wavelength of the OPO emission will highlight the presence of a suspect material and by analysing the resulting absorption spectrum, presumptive identification is possible. This work presents a selection of initial results using the LWIR hyperspectral imaging platform on a range of white powder materials to highlight the benefit operating in the LWIR region compared to the MWIR.

Lineup Administrator Influences on Eyewitness Identification Decisions

ERIC Educational Resources Information Center

Clark, Steven E.; Marshall, Tanya E.; Rosenthal, Robert

2009-01-01

The present research examines how a lineup administrator may influence eyewitness identification decisions through different forms of influence, after providing the witness with standard, unbiased instructions. Participant-witnesses viewed a staged crime and were later shown a target-present or target-absent lineup. The lineup administrators…

Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments.

PubMed

Levander, Fredrik; James, Peter

2005-01-01

The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the analysis process. Two sets of MALDI samples, consisting of 142 and 421 gel spots, respectively, were analyzed in a highly automated manner. In the first set, the protein identification rate increased from 61% for MALDI-TOF only to 85% for MALDI-TOF combined with AP-MALDI-IT. In the second data set the increase in protein identification rate was from 44% to 58%. AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification.

Midwave infrared and visible sensor performance modeling: small craft identification discrimination criteria for maritime security

NASA Astrophysics Data System (ADS)

Krapels, Keith; Driggers, Ronald G.; Deaver, Dawne; Moker, Steven K.; Palmer, John

2007-10-01

The new emphasis on Anti-Terrorism and Force Protection (AT/FP), for both shore and sea platform protection, has resulted in a need for infrared imager design and evaluation tools that demonstrate field performance against U.S. Navy AT/FP requirements. In the design of infrared imaging systems for target acquisition, a discrimination criterion is required for successful sensor realization. It characterizes the difficulty of the task being performed by the observer and varies for different target sets. This criterion is used in both assessment of existing infrared sensor and in the design of new conceptual sensors. We collected 12 small craft signatures (military and civilian) in the visible band during the day and the long-wave and midwave infrared spectra in both the day and the night environments. These signatures were processed to determine the targets' characteristic dimension and contrast. They were also processed to band limit the signature's spatial information content (simulating longer range), and a perception experiment was performed to determine the task difficulty (N50 and V50). The results are presented and can be used for Navy and Coast Guard imaging infrared sensor design and evaluation.

TOD to TTP calibration

NASA Astrophysics Data System (ADS)

Bijl, Piet; Reynolds, Joseph P.; Vos, Wouter K.; Hogervorst, Maarten A.; Fanning, Jonathan D.

2011-05-01

The TTP (Targeting Task Performance) metric, developed at NVESD, is the current standard US Army model to predict EO/IR Target Acquisition performance. This model however does not have a corresponding lab or field test to empirically assess the performance of a camera system. The TOD (Triangle Orientation Discrimination) method, developed at TNO in The Netherlands, provides such a measurement. In this study, we make a direct comparison between TOD performance for a range of sensors and the extensive historical US observer performance database built to develop and calibrate the TTP metric. The US perception data were collected doing an identification task by military personnel on a standard 12 target, 12 aspect tactical vehicle image set that was processed through simulated sensors for which the most fundamental sensor parameters such as blur, sampling, spatial and temporal noise were varied. In the present study, we measured TOD sensor performance using exactly the same sensors processing a set of TOD triangle test patterns. The study shows that good overall agreement is obtained when the ratio between target characteristic size and TOD test pattern size at threshold equals 6.3. Note that this number is purely based on empirical data without any intermediate modeling. The calibration of the TOD to the TTP is highly beneficial to the sensor modeling and testing community for a variety of reasons. These include: i) a connection between requirement specification and acceptance testing, and ii) a very efficient method to quickly validate or extend the TTP range prediction model to new systems and tasks.

The neural substrates of action identification.

PubMed

Marsh, Abigail A; Kozak, Megan N; Wegner, Daniel M; Reid, Marguerite E; Yu, Henry H; Blair, R J R

2010-12-01

Mentalization is the process by which an observer views a target as possessing higher cognitive faculties such as goals, intentions and desires. Mentalization can be assessed using action identification paradigms, in which observers choose mentalistic (goals-focused) or mechanistic (action-focused) descriptions of targets' actions. Neural structures that play key roles in inferring goals and intentions from others' observed or imagined actions include temporo-parietal junction, ventral premotor cortex and extrastriate body area. We hypothesized that these regions play a role in action identification as well. Data collected using functional magnetic resonance imaging (fMRI) confirmed our predictions that activity in ventral premotor cortex and middle temporal gyrus near the extrastriate body area varies both as a function of the valence of the target and the extent to which actions are identified as goal-directed. In addition, the inferior parietal lobule is preferentially engaged when participants identify the actions of mentalized targets. Functional connectivity analyses suggest support from other regions, including the medial prefrontal cortex and amygdala, during mentalization. We found correlations between action identification and Autism Quotient scores, suggesting that understanding the neural correlates of action identification may enhance our understanding of the underpinnings of essential social cognitive processes.

Regularities in eyewitness identification.

PubMed

Clark, Steven E; Howell, Ryan T; Davey, Sherrie L

2008-06-01

What do eyewitness identification experiments typically show? We address this question through a meta-analysis of 94 comparisons between target-present and target-absent lineups. The analyses showed that: (a) correct identifications and correct-nonidentifications were uncorrelated, (b) suspect identifications were more diagnostic with respect to the suspect's guilt or innocence than any other response, (c) nonidentifications were diagnostic of the suspect's innocence, (d) the diagnosticity of foil identifications depended on lineup composition, and (e) don't know responses were nondiagnostic with respect to guilt or innocence. Results of diagnosticity analyses for simultaneous and sequential lineups varied for full-sample versus direct-comparison analyses. Diagnosticity patterns also varied as a function of lineup composition. Theoretical, forensic, and legal implications are discussed.

Identification of Direct Protein Targets of Small Molecules

PubMed Central

2010-01-01

Small-molecule target identification is a vital and daunting task for the chemical biology community as well as for researchers interested in applying the power of chemical genetics to impact biology and medicine. To overcome this “target ID” bottleneck, new technologies are being developed that analyze protein–drug interactions, such as drug affinity responsive target stability (DARTS), which aims to discover the direct binding targets (and off targets) of small molecules on a proteome scale without requiring chemical modification of the compound. Here, we review the DARTS method, discuss why it works, and provide new perspectives for future development in this area. PMID:21077692

Deployment of spatial attention to words in central and peripheral vision.

PubMed

Ducrot, Stéphanie; Grainger, Jonathan

2007-05-01

Four perceptual identification experiments examined the influence of spatial cues on the recognition of words presented in central vision (with fixation on either the first or last letter of the target word) and in peripheral vision (displaced left or right of a central fixation point). Stimulus location had a strong effect on word identification accuracy in both central and peripheral vision, showing a strong right visual field superiority that did not depend on eccentricity. Valid spatial cues improved word identification for peripherally presented targets but were largely ineffective for centrally presented targets. Effects of spatial cuing interacted with visual field effects in Experiment 1, with valid cues reducing the right visual field superiority for peripherally located targets, but this interaction was shown to depend on the type of neutral cue. These results provide further support for the role of attentional factors in visual field asymmetries obtained with targets in peripheral vision but not with centrally presented targets.

Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard

EPA Science Inventory

Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, r...

Advanced MR Imaging of the Human Nucleus Accumbens--Additional Guiding Tool for Deep Brain Stimulation.

PubMed

Lucas-Neto, Lia; Reimão, Sofia; Oliveira, Edson; Rainha-Campos, Alexandre; Sousa, João; Nunes, Rita G; Gonçalves-Ferreira, António; Campos, Jorge G

2015-07-01

The human nucleus accumbens (Acc) has become a target for deep brain stimulation (DBS) in some neuropsychiatric disorders. Nonetheless, even with the most recent advances in neuroimaging it remains difficult to accurately delineate the Acc and closely related subcortical structures, by conventional MRI sequences. It is our purpose to perform a MRI study of the human Acc and to determine whether there are reliable anatomical landmarks that enable the precise location and identification of the nucleus and its core/shell division. For the Acc identification and delineation, based on anatomical landmarks, T1WI, T1IR and STIR 3T-MR images were acquired in 10 healthy volunteers. Additionally, 32-direction DTI was obtained for Acc segmentation. Seed masks for the Acc were generated with FreeSurfer and probabilistic tractography was performed using FSL. The probability of connectivity between the seed voxels and distinct brain areas was determined and subjected to k-means clustering analysis, defining 2 different regions. With conventional T1WI, the Acc borders are better defined through its surrounding anatomical structures. The DTI color-coded vector maps and IR sequences add further detail in the Acc identification and delineation. Additionally, using probabilistic tractography it is possible to segment the Acc into a core and shell division and establish its structural connectivity with different brain areas. Advanced MRI techniques allow in vivo delineation and segmentation of the human Acc and represent an additional guiding tool in the precise and safe target definition for DBS. © 2015 International Neuromodulation Society.

Stem cells: a model for screening, discovery and development of drugs.

PubMed

Kitambi, Satish Srinivas; Chandrasekar, Gayathri

2011-01-01

The identification of normal and cancerous stem cells and the recent advances made in isolation and culture of stem cells have rapidly gained attention in the field of drug discovery and regenerative medicine. The prospect of performing screens aimed at proliferation, directed differentiation, and toxicity and efficacy studies using stem cells offers a reliable platform for the drug discovery process. Advances made in the generation of induced pluripotent stem cells from normal or diseased tissue serves as a platform to perform drug screens aimed at developing cell-based therapies against conditions like Parkinson's disease and diabetes. This review discusses the application of stem cells and cancer stem cells in drug screening and their role in complementing, reducing, and replacing animal testing. In addition to this, target identification and major advances in the field of personalized medicine using induced pluripotent cells are also discussed.

Mapping protein-protein interactions using yeast two-hybrid assays.

PubMed

Mehla, Jitender; Caufield, J Harry; Uetz, Peter

2015-05-01

Yeast two-hybrid (Y2H) screens are an efficient system for mapping protein-protein interactions and whole interactomes. The screens can be performed using random libraries or collections of defined open reading frames (ORFs) called ORFeomes. This protocol describes both library and array-based Y2H screening, with an emphasis on array-based assays. Array-based Y2H is commonly used to test a number of "prey" proteins for interactions with a single "bait" (target) protein or pool of proteins. The advantage of this approach is the direct identification of interacting protein pairs without further downstream experiments: The identity of the preys is known and does not require further confirmation. In contrast, constructing and screening a random prey library requires identification of individual prey clones and systematic retesting. Retesting is typically performed in an array format. © 2015 Cold Spring Harbor Laboratory Press.

Screening and identification of radical scavengers from Neo-Taraxacum siphonanthum by online rapid screening method and nuclear magnetic resonance experiments.

PubMed

Shi, Shu Yun; Zhang, Yu Ping; Zhou, Hong Hao; Huang, Ke Long; Jiang, Xin Yu

2010-01-01

An online rapid screening method, the high-performance liquid chromatography (HPLC)-diode array detector (DAD)-radical scavenging detection (RSD)-electrospray ionization (ESI)-mass spectroscopy (MS)/MS system, was developed for the screening and identification of radical scavengers from Neo-Taraxacum siphonanthum, a new species found in China in 1989. For further characterization, the target compounds were isolated by silica column chromatography, preparative high-performance liquid chromatography (HPLC), HSCCC, and Sephadex LH-20 column chromatography and elucidated on the basis of ultraviolet (UV), ESI-MS/MS, and nuclear magnetic resonance (NMR) spectroscopy, as well as the chemical analysis. Eighteen antioxidative polyphenols (5 caffeic acid derivatives and 13 flavonoid derivatives) were characterized from Neo-T. siphonanthum. The distribution of all compounds was discussed in a chemosystematic context, which suggested that the genera Neo-Taraxacum and Taraxacum might relate chemosystematically.

Multiple Level Crowding: Crowding at the Object Parts Level and at the Object Configural level.

PubMed

Kimchi, Ruth; Pirkner, Yossef

2015-01-01

In crowding, identification of a peripheral target in the presence of nearby flankers is worse than when the target appears alone. Prevailing theories hold that crowding occurs because of integration or "pooling" of low-level features at a single, relatively early stage of visual processing. Recent studies suggest that crowding can occur also between high-level object representations. The most relevant findings come from studies with faces and may be specific to faces. We examined whether crowding can occur at the object configural level in addition to part-level crowding, using nonface objects. Target (a disconnected square or diamond made of four elements) identification was measured at varying eccentricities. The flankers were similar either to the target parts or to the target configuration. The results showed crowding in both cases: Flankers interfered with target identification such that identification accuracy decreased with an increase in eccentricity, and no interference was observed at the fovea. Crowding by object parts, however, was weaker and had smaller spatial extent than crowding by object configurations; we related this finding to the relationship between crowding and perceptual organization. These results provide strong evidence that crowding occurs not only between object parts but also between configural representations of objects. © The Author(s) 2015.

Hyperspectral data collection for the assessment of target detection algorithms: the Viareggio 2013 trial

NASA Astrophysics Data System (ADS)

Rossi, Alessandro; Acito, Nicola; Diani, Marco; Corsini, Giovanni; De Ceglie, Sergio Ugo; Riccobono, Aldo; Chiarantini, Leandro

2014-10-01

Airborne hyperspectral imagery is valuable for military and civilian applications, such as target identification, detection of anomalies and changes within multiple acquisitions. In target detection (TD) applications, the performance assessment of different algorithms is an important and critical issue. In this context, the small number of public available hyperspectral data motivated us to perform an extensive measurement campaign including various operating scenarios. The campaign was organized by CISAM in cooperation with University of Pisa, Selex ES and CSSN-ITE, and it was conducted in Viareggio, Italy in May, 2013. The Selex ES airborne hyperspectral sensor SIM.GA was mounted on board of an airplane to collect images over different sites in the morning and afternoon of two subsequent days. This paper describes the hyperspectral data collection of the trial. Four different sites were set up, representing a complex urban scenario, two parking lots and a rural area. Targets with dimensions comparable to the sensor ground resolution were deployed in the sites to reproduce different operating situations. An extensive ground truth documentation completes the data collection. Experiments to test anomalous change detection techniques were set up changing the position of the deployed targets. Search and rescue scenarios were simulated to evaluate the performance of anomaly detection algorithms. Moreover, the reflectance signatures of the targets were measured on the ground to perform spectral matching in varying atmospheric and illumination conditions. The paper presents some preliminary results that show the effectiveness of hyperspectral data exploitation for the object detection tasks of interest in this work.

Automatic building identification under bomb damage conditions

NASA Astrophysics Data System (ADS)

Woodley, Robert; Noll, Warren; Barker, Joseph; Wunsch, Donald C., II

2009-05-01

Given the vast amount of image intelligence utilized in support of planning and executing military operations, a passive automated image processing capability for target identification is urgently required. Furthermore, transmitting large image streams from remote locations would quickly use available band width (BW) precipitating the need for processing to occur at the sensor location. This paper addresses the problem of automatic target recognition for battle damage assessment (BDA). We utilize an Adaptive Resonance Theory approach to cluster templates of target buildings. The results show that the network successfully classifies targets from non-targets in a virtual test bed environment.

Processor core for real time background identification of HD video based on OpenCV Gaussian mixture model algorithm

NASA Astrophysics Data System (ADS)

Genovese, Mariangela; Napoli, Ettore

2013-05-01

The identification of moving objects is a fundamental step in computer vision processing chains. The development of low cost and lightweight smart cameras steadily increases the request of efficient and high performance circuits able to process high definition video in real time. The paper proposes two processor cores aimed to perform the real time background identification on High Definition (HD, 1920 1080 pixel) video streams. The implemented algorithm is the OpenCV version of the Gaussian Mixture Model (GMM), an high performance probabilistic algorithm for the segmentation of the background that is however computationally intensive and impossible to implement on general purpose CPU with the constraint of real time processing. In the proposed paper, the equations of the OpenCV GMM algorithm are optimized in such a way that a lightweight and low power implementation of the algorithm is obtained. The reported performances are also the result of the use of state of the art truncated binary multipliers and ROM compression techniques for the implementation of the non-linear functions. The first circuit has commercial FPGA devices as a target and provides speed and logic resource occupation that overcome previously proposed implementations. The second circuit is oriented to an ASIC (UMC-90nm) standard cell implementation. Both implementations are able to process more than 60 frames per second in 1080p format, a frame rate compatible with HD television.

Multicenter accuracy and interobserver agreement of spot sign identification in acute intracerebral hemorrhage.

PubMed

Huynh, Thien J; Flaherty, Matthew L; Gladstone, David J; Broderick, Joseph P; Demchuk, Andrew M; Dowlatshahi, Dar; Meretoja, Atte; Davis, Stephen M; Mitchell, Peter J; Tomlinson, George A; Chenkin, Jordan; Chia, Tze L; Symons, Sean P; Aviv, Richard I

2014-01-01

Rapid, accurate, and reliable identification of the computed tomography angiography spot sign is required to identify patients with intracerebral hemorrhage for trials of acute hemostatic therapy. We sought to assess the accuracy and interobserver agreement for spot sign identification. A total of 131 neurology, emergency medicine, and neuroradiology staff and fellows underwent imaging certification for spot sign identification before enrolling patients in 3 trials targeting spot-positive intracerebral hemorrhage for hemostatic intervention (STOP-IT, SPOTLIGHT, STOP-AUST). Ten intracerebral hemorrhage cases (spot-positive/negative ratio, 1:1) were presented for evaluation of spot sign presence, number, and mimics. True spot positivity was determined by consensus of 2 experienced neuroradiologists. Diagnostic performance, agreement, and differences by training level were analyzed. Mean accuracy, sensitivity, and specificity for spot sign identification were 87%, 78%, and 96%, respectively. Overall sensitivity was lower than specificity (P<0.001) because of true spot signs incorrectly perceived as spot mimics. Interobserver agreement for spot sign presence was moderate (k=0.60). When true spots were correctly identified, 81% correctly identified the presence of single or multiple spots. Median time needed to evaluate the presence of a spot sign was 1.9 minutes (interquartile range, 1.2-3.1 minutes). Diagnostic performance, interobserver agreement, and time needed for spot sign evaluation were similar among staff physicians and fellows. Accuracy for spot identification is high with opportunity for improvement in spot interpretation sensitivity and interobserver agreement particularly through greater reliance on computed tomography angiography source data and awareness of limitations of multiplanar images. Further prospective study is needed.

[Contribution of Leishmania identification using polymerase chain reaction--restriction fragment length polymerase for epidemiological studies of cutaneous leishmaniasis in Tunisia].

PubMed

Bousslimi, N; Ben Abda, I; Ben Mously, R; Siala, E; Harrat, Z; Zallagua, N; Bouratbine, A; Aoun, K

2014-02-01

Three forms of cutaneous leishmaniasis (CL) are endemic in Tunisia. The identification of the causative species is useful to complete epidemiological data and to manage the cases. The aim of this study is to assess PCR-RFLP technique in the identification of Leishmania species responsible of CL in Tunisia and to compare the results of this technique to those of isoenzyme analysis. Sixty-one CL lesions were sampled. Dermal samples were tested by culture on NNN medium and analyzed by PCR-RFLP assay targeting the ITS1 region of ribosomal DNA. Species identification was performed by both iso-enzymatic typing for positive cultures and analysis of restriction profiles after enzymatic digestion by HaeIII of the obtained amplicons. Thirty-eight (62%) samples were positive by culture. The iso-enzymatic typing of 32 isolates identified 3 L. infantum, 23 L. major MON-25 and 6 L. tropica MON-8. Sixty samples were positive by PCR. The PCR-RFLP digestion profiles of the 56 PCR products identified 12 L. infantum, 38 L. major and 6 L. tropica. The results of both techniques were concordant in the 32 strains identified by both techniques. Species identification correlated with the geographical distribution of CL forms endemic in Tunisia. Results of PCR-RFLP revealed highly concordant with those of isoenzyme electrophoresis. Thanks to its simplicity, rapidity and ability to be performed directly on biological samples, this technique appears as an interesting alternative for the identification of Leishmania strains responsible of CL in Tunisia. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing

PubMed Central

Karimi, Ramin; Hajdu, Andras

2016-01-01

Comprehensive effort for low-cost sequencing in the past few years has led to the growth of complete genome databases. In parallel with this effort, a strong need, fast and cost-effective methods and applications have been developed to accelerate sequence analysis. Identification is the very first step of this task. Due to the difficulties, high costs, and computational challenges of alignment-based approaches, an alternative universal identification method is highly required. Like an alignment-free approach, DNA signatures have provided new opportunities for the rapid identification of species. In this paper, we present an effective pipeline HTSFinder (high-throughput signature finder) with a corresponding k-mer generator GkmerG (genome k-mers generator). Using this pipeline, we determine the frequency of k-mers from the available complete genome databases for the detection of extensive DNA signatures in a reasonably short time. Our application can detect both unique and common signatures in the arbitrarily selected target and nontarget databases. Hadoop and MapReduce as parallel and distributed computing tools with commodity hardware are used in this pipeline. This approach brings the power of high-performance computing into the ordinary desktop personal computers for discovering DNA signatures in large databases such as bacterial genome. A considerable number of detected unique and common DNA signatures of the target database bring the opportunities to improve the identification process not only for polymerase chain reaction and microarray assays but also for more complex scenarios such as metagenomics and next-generation sequencing analysis. PMID:26884678

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing.

PubMed

Karimi, Ramin; Hajdu, Andras

2016-01-01

Comprehensive effort for low-cost sequencing in the past few years has led to the growth of complete genome databases. In parallel with this effort, a strong need, fast and cost-effective methods and applications have been developed to accelerate sequence analysis. Identification is the very first step of this task. Due to the difficulties, high costs, and computational challenges of alignment-based approaches, an alternative universal identification method is highly required. Like an alignment-free approach, DNA signatures have provided new opportunities for the rapid identification of species. In this paper, we present an effective pipeline HTSFinder (high-throughput signature finder) with a corresponding k-mer generator GkmerG (genome k-mers generator). Using this pipeline, we determine the frequency of k-mers from the available complete genome databases for the detection of extensive DNA signatures in a reasonably short time. Our application can detect both unique and common signatures in the arbitrarily selected target and nontarget databases. Hadoop and MapReduce as parallel and distributed computing tools with commodity hardware are used in this pipeline. This approach brings the power of high-performance computing into the ordinary desktop personal computers for discovering DNA signatures in large databases such as bacterial genome. A considerable number of detected unique and common DNA signatures of the target database bring the opportunities to improve the identification process not only for polymerase chain reaction and microarray assays but also for more complex scenarios such as metagenomics and next-generation sequencing analysis.

Study on Urban Heat Island Intensity Level Identification Based on an Improved Restricted Boltzmann Machine.

PubMed

Zhang, Yang; Jiang, Ping; Zhang, Hongyan; Cheng, Peng

2018-01-23

Thermal infrared remote sensing has become one of the main technology methods used for urban heat island research. When applying urban land surface temperature inversion of the thermal infrared band, problems with intensity level division arise because the method is subjective. However, this method is one of the few that performs heat island intensity level identification. This paper will build an intensity level identifier for an urban heat island, by using weak supervision and thought-based learning in an improved, restricted Boltzmann machine (RBM) model. The identifier automatically initializes the annotation and optimizes the model parameters sequentially until the target identifier is completed. The algorithm needs very little information about the weak labeling of the target training sample and generates an urban heat island intensity spatial distribution map. This study can provide reliable decision-making support for urban ecological planning and effective protection of urban ecological security. The experimental results showed the following: (1) The heat island effect in Wuhan is existent and intense. Heat island areas are widely distributed. The largest heat island area is in Wuhan, followed by the sub-green island. The total area encompassed by heat island and strong island levels accounts for 54.16% of the land in Wuhan. (2) Partially based on improved RBM identification, this method meets the research demands of determining the spatial distribution characteristics of the internal heat island effect; its identification accuracy is superior to that of comparable methods.

Study on Urban Heat Island Intensity Level Identification Based on an Improved Restricted Boltzmann Machine

PubMed Central

Jiang, Ping; Zhang, Hongyan; Cheng, Peng

2018-01-01

Thermal infrared remote sensing has become one of the main technology methods used for urban heat island research. When applying urban land surface temperature inversion of the thermal infrared band, problems with intensity level division arise because the method is subjective. However, this method is one of the few that performs heat island intensity level identification. This paper will build an intensity level identifier for an urban heat island, by using weak supervision and thought-based learning in an improved, restricted Boltzmann machine (RBM) model. The identifier automatically initializes the annotation and optimizes the model parameters sequentially until the target identifier is completed. The algorithm needs very little information about the weak labeling of the target training sample and generates an urban heat island intensity spatial distribution map. This study can provide reliable decision-making support for urban ecological planning and effective protection of urban ecological security. The experimental results showed the following: (1) The heat island effect in Wuhan is existent and intense. Heat island areas are widely distributed. The largest heat island area is in Wuhan, followed by the sub-green island. The total area encompassed by heat island and strong island levels accounts for 54.16% of the land in Wuhan. (2) Partially based on improved RBM identification, this method meets the research demands of determining the spatial distribution characteristics of the internal heat island effect; its identification accuracy is superior to that of comparable methods. PMID:29360786

Integrated quantification and identification of aldehydes and ketones in biological samples.

PubMed

Siegel, David; Meinema, Anne C; Permentier, Hjalmar; Hopfgartner, Gérard; Bischoff, Rainer

2014-05-20

The identification of unknown compounds remains to be a bottleneck of mass spectrometry (MS)-based metabolomics screening experiments. Here, we present a novel approach which facilitates the identification and quantification of analytes containing aldehyde and ketone groups in biological samples by adding chemical information to MS data. Our strategy is based on rapid autosampler-in-needle-derivatization with p-toluenesulfonylhydrazine (TSH). The resulting TSH-hydrazones are separated by ultrahigh-performance liquid chromatography (UHPLC) and detected by electrospray ionization-quadrupole-time-of-flight (ESI-QqTOF) mass spectrometry using a SWATH (Sequential Window Acquisition of all Theoretical Fragment-Ion Spectra) data-independent high-resolution mass spectrometry (HR-MS) approach. Derivatization makes small, poorly ionizable or retained analytes amenable to reversed phase chromatography and electrospray ionization in both polarities. Negatively charged TSH-hydrazone ions furthermore show a simple and predictable fragmentation pattern upon collision induced dissociation, which enables the chemo-selective screening for unknown aldehydes and ketones via a signature fragment ion (m/z 155.0172). By means of SWATH, targeted and nontargeted application scenarios of the suggested derivatization route are enabled in the frame of a single UHPLC-ESI-QqTOF-HR-MS workflow. The method's ability to simultaneously quantify and identify molecules containing aldehyde and ketone groups is demonstrated using 61 target analytes from various compound classes and a (13)C labeled yeast matrix. The identification of unknowns in biological samples is detailed using the example of indole-3-acetaldehyde.

Identification of Buried Objects in GPR Using Amplitude Modulated Signals Extracted from Multiresolution Monogenic Signal Analysis

PubMed Central

Qiao, Lihong; Qin, Yao; Ren, Xiaozhen; Wang, Qifu

2015-01-01

It is necessary to detect the target reflections in ground penetrating radar (GPR) images, so that surface metal targets can be identified successfully. In order to accurately locate buried metal objects, a novel method called the Multiresolution Monogenic Signal Analysis (MMSA) system is applied in ground penetrating radar (GPR) images. This process includes four steps. First the image is decomposed by the MMSA to extract the amplitude component of the B-scan image. The amplitude component enhances the target reflection and suppresses the direct wave and reflective wave to a large extent. Then we use the region of interest extraction method to locate the genuine target reflections from spurious reflections by calculating the normalized variance of the amplitude component. To find the apexes of the targets, a Hough transform is used in the restricted area. Finally, we estimate the horizontal and vertical position of the target. In terms of buried object detection, the proposed system exhibits promising performance, as shown in the experimental results. PMID:26690146

Improvement of Automated Identification of the Heart Wall in Echocardiography by Suppressing Clutter Component

NASA Astrophysics Data System (ADS)

Takahashi, Hiroki; Hasegawa, Hideyuki; Kanai, Hiroshi

2013-07-01

For the facilitation of analysis and elimination of the operator dependence in estimating the myocardial function in echocardiography, we have previously developed a method for automated identification of the heart wall. However, there are misclassified regions because the magnitude-squared coherence (MSC) function of echo signals, which is one of the features in the previous method, is sensitively affected by the clutter components such as multiple reflection and off-axis echo from external tissue or the nearby myocardium. The objective of the present study is to improve the performance of automated identification of the heart wall. For this purpose, we proposed a method to suppress the effect of the clutter components on the MSC of echo signals by applying an adaptive moving target indicator (MTI) filter to echo signals. In vivo experimental results showed that the misclassified regions were significantly reduced using our proposed method in the longitudinal axis view of the heart.

Clinical outcomes in pediatric hemodialysis patients in the USA: lessons from CMS' ESRD CPM Project.

PubMed

Neu, Alicia M; Frankenfield, Diane L

2009-07-01

Although prospective randomized trials have provided important information and allowed the development of evidence-based guidelines in adult hemodialysis (HD) patients, with approximately 800 prevalent pediatric HD patients in the United States, such studies are difficult to perform in this population. Observational data obtained through the Center for Medicare & Medicaid Services' (CMS') End Stage Renal Disease (ESRD) Clinical Performance Measures (CPM) Project have allowed description of the clinical care provided to pediatric HD patients as well as identification of risk factors for failure to reach adult targets for clinical parameters such as hemoglobin, single-pool Kt/V (spKt/V) and serum albumin. In addition, studies linking data from the ESRD CPM Project and the United States Renal Data System have allowed evaluation of associations between achievement of those targets and the outcomes of hospitalization and death. The results of those studies, while unable to prove cause and effect, suggest that the adult ESRD CPM targets may assist in identifying pediatric HD patients at risk for poor outcomes.

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.

PubMed

Röst, Hannes L; Liu, Yansheng; D'Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi

2016-09-01

Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics data sets.

Colour-cueing in visual search.

PubMed

Laarni, J

2001-02-01

Several studies have shown that people can selectively attend to stimulus colour, e.g., in visual search, and that preknowledge of a target colour can improve response speed/accuracy. The purpose was to use a form-identification task to determine whether valid colour precues can produce benefits and invalid cues costs. The subject had to identify the orientation of a "T"-shaped element in a ring of randomly-oriented "L"s when either two or four of the elements were differently coloured. Contrary to Moore and Egeth's (1998) recent findings, colour-based attention did affect performance under data-limited conditions: Colour cues produced benefits when processing load was high; when the load was reduced, they incurred only costs. Surprisingly, a valid colour cue succeeded in improving performance in the high-load condition even when its validity was reduced to the chance level. Overall, the results suggest that knowledge of a target colour does not facilitate the processing of the target, but makes it possible to prioritize it.

Identification of Erwinia species isolated from apples and pears by differential PCR.

PubMed

Gehring, I; Geider, K

2012-04-01

Many pathogenic and epiphytic bacteria isolated from apples and pears belong to the genus Erwinia; these include the species E. amylovora, E. pyrifoliae, E. billingiae, E. persicina, E. rhapontici and E. tasmaniensis. Identification and classification of freshly isolated bacterial species often requires tedious taxonomic procedures. To facilitate routine identification of Erwinia species, we have developed a PCR method based on species-specific oligonucleotides (SSOs) from the sequences of the housekeeping genes recA and gpd. Using species-specific primers that we report here, differentiation was done with conventional PCR (cPCR) and quantitative PCR (qPCR) applying two consecutive primer annealing temperatures. The specificity of the primers depends on terminal Single Nucleotide Polymorphisms (SNPs) that are characteristic for the target species. These PCR assays enabled us to distinguish eight Erwinia species, as well as to identify new Erwinia isolates from plant surfaces. When performed with mixed bacterial cultures, they only detected a single target species. This method is a novel approach to classify strains within the genus Erwinia by PCR and it can be used to confirm other diagnostic data, especially when specific PCR detection methods are not already available. The method may be applied to classify species within other bacterial genera. Copyright © 2012 Elsevier B.V. All rights reserved.

Another look at category effects on colour perception and their left hemispheric lateralisation: no evidence from a colour identification task.

PubMed

Suegami, Takashi; Aminihajibashi, Samira; Laeng, Bruno

2014-05-01

The present study aimed to replicate category effects on colour perception and their lateralisation to the left cerebral hemisphere (LH). Previous evidence for lateralisation of colour category effects has been obtained with tasks where a differently coloured target was searched within a display and participants reported the lateral location of the target. However, a left/right spatial judgment may yield LH-laterality effects per se. Thus, we employed an identification task that does not require a spatial judgment and used the same colour set that previously revealed LH-lateralised category effects. The identification task was better performed with between-category colours than with within-category task both in terms of accuracy and latency, but such category effects were bilateral or RH-lateralised, and no evidence was found for LH-laterality effects. The accuracy scores, moreover, indicated that the category effects derived from low sensitivities for within-blue colours and did not reflect the effects of categorical structures on colour perception. Furthermore, the classic "category effects" were observed in participants' response biases, instead of sensitivities. The present results argue against both the LH-lateralised category effects on colour perception and the existence of colour category effects per se.

Development of a DNA Microarray-Based Assay for the Detection of Sugar Beet Root Rot Pathogens.

PubMed

Liebe, Sebastian; Christ, Daniela S; Ehricht, Ralf; Varrelmann, Mark

2016-01-01

Sugar beet root rot diseases that occur during the cropping season or in storage are accompanied by high yield losses and a severe reduction of processing quality. The vast diversity of microorganism species involved in rot development requires molecular tools allowing simultaneous identification of many different targets. Therefore, a new microarray technology (ArrayTube) was applied in this study to improve diagnosis of sugar beet root rot diseases. Based on three marker genes (internal transcribed spacer, translation elongation factor 1 alpha, and 16S ribosomal DNA), 42 well-performing probes enabled the identification of prevalent field pathogens (e.g., Aphanomyces cochlioides), storage pathogens (e.g., Botrytis cinerea), and ubiquitous spoilage fungi (e.g., Penicillium expansum). All probes were proven for specificity with pure cultures from 73 microorganism species as well as for in planta detection of their target species using inoculated sugar beet tissue. Microarray-based identification of root rot pathogens in diseased field beets was successfully confirmed by classical detection methods. The high discriminatory potential was proven by Fusarium species differentiation based on a single nucleotide polymorphism. The results demonstrate that the ArrayTube constitute an innovative tool allowing a rapid and reliable detection of plant pathogens particularly when multiple microorganism species are present.

Fusion of imaging and nonimaging data for surveillance aircraft

NASA Astrophysics Data System (ADS)

Shahbazian, Elisa; Gagnon, Langis; Duquet, Jean Remi; Macieszczak, Maciej; Valin, Pierre

1997-06-01

This paper describes a phased incremental integration approach for application of image analysis and data fusion technologies to provide automated intelligent target tracking and identification for airborne surveillance on board an Aurora Maritime Patrol Aircraft. The sensor suite of the Aurora consists of a radar, an identification friend or foe (IFF) system, an electronic support measures (ESM) system, a spotlight synthetic aperture radar (SSAR), a forward looking infra-red (FLIR) sensor and a link-11 tactical datalink system. Lockheed Martin Canada (LMCan) is developing a testbed, which will be used to analyze and evaluate approaches for combining the data provided by the existing sensors, which were initially not designed to feed a fusion system. Three concurrent research proof-of-concept activities provide techniques, algorithms and methodology into three sequential phases of integration of this testbed. These activities are: (1) analysis of the fusion architecture (track/contact/hybrid) most appropriate for the type of data available, (2) extraction and fusion of simple features from the imaging data into the fusion system performing automatic target identification, and (3) development of a unique software architecture which will permit integration and independent evolution, enhancement and optimization of various decision aid capabilities, such as multi-sensor data fusion (MSDF), situation and threat assessment (STA) and resource management (RM).

20180318 - Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard (ACS Spring)

EPA Science Inventory

Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, r...

Identification of NPM and DDX5 as Therapeutic Targets in TSC

DTIC Science & Technology

2017-12-01

Individuals with TSC develop benign tumors in multiple organs, including the retina, skin, lung, kidney and brain. The identification of valid targets in TSC...individuals. Individuals with TSC develop benign tumors in multiple organs, including the retina, skin, lung, kidney and brain. However, these lesions can

The Influence of Attention and Target Identification on Saccadic Eye Movements Depends on Prior Target Location

PubMed Central

Hardwick, David R.; Cutmore, Timothy R. H.; Hine, Trevor J.

2014-01-01

Saccadic latency is reduced by a temporal gap between fixation point and target, by identification of a target feature, and by movement in a new direction (inhibition of saccadic return, ISR). A simple additive model was compared with a shared resources model that predicts a three-way interaction. Twenty naïve participants made horizontal saccades to targets left and right of fixation in a randomised block design. There was a significant three-way interaction among the factors on saccade latency. This was revealed in a two-way interaction between feature identification and the gap versus no gap factor which was only apparent when the saccade was in the same direction as the previous saccade. No interaction was apparent when the saccade was in the opposite direction. This result supports an attentional inhibitory effect that is present during ISR to a previous location which is only partly released by the facilitative effect of feature identification and gap. Together, anticipatory error data and saccade latency interactions suggest a source of ISR at a higher level of attention, possibly localised in the dorsolateral prefrontal cortex and involving tonic activation. PMID:24719754

Virtual reality, ultrasound-guided liver biopsy simulator: development and performance discrimination

PubMed Central

Johnson, S J; Hunt, C M; Woolnough, H M; Crawshaw, M; Kilkenny, C; Gould, D A; England, A; Sinha, A; Villard, P F

2012-01-01

Objectives The aim of this article was to identify and prospectively investigate simulated ultrasound-guided targeted liver biopsy performance metrics as differentiators between levels of expertise in interventional radiology. Methods Task analysis produced detailed procedural step documentation allowing identification of critical procedure steps and performance metrics for use in a virtual reality ultrasound-guided targeted liver biopsy procedure. Consultant (n=14; male=11, female=3) and trainee (n=26; male=19, female=7) scores on the performance metrics were compared. Ethical approval was granted by the Liverpool Research Ethics Committee (UK). Independent t-tests and analysis of variance (ANOVA) investigated differences between groups. Results Independent t-tests revealed significant differences between trainees and consultants on three performance metrics: targeting, p=0.018, t=−2.487 (−2.040 to −0.207); probe usage time, p = 0.040, t=2.132 (11.064 to 427.983); mean needle length in beam, p=0.029, t=−2.272 (−0.028 to −0.002). ANOVA reported significant differences across years of experience (0–1, 1–2, 3+ years) on seven performance metrics: no-go area touched, p=0.012; targeting, p=0.025; length of session, p=0.024; probe usage time, p=0.025; total needle distance moved, p=0.038; number of skin contacts, p<0.001; total time in no-go area, p=0.008. More experienced participants consistently received better performance scores on all 19 performance metrics. Conclusion It is possible to measure and monitor performance using simulation, with performance metrics providing feedback on skill level and differentiating levels of expertise. However, a transfer of training study is required. PMID:21304005

Lateralization of spatial rather than temporal attention underlies the left hemifield advantage in rapid serial visual presentation.

PubMed

Asanowicz, Dariusz; Kruse, Lena; Śmigasiewicz, Kamila; Verleger, Rolf

2017-11-01

In bilateral rapid serial visual presentation (RSVP), the second of two targets, T1 and T2, is better identified in the left visual field (LVF) than in the right visual field (RVF). This LVF advantage may reflect hemispheric asymmetry in temporal attention or/and in spatial orienting of attention. Participants performed two tasks: the "standard" bilateral RSVP task (Exp.1) and its unilateral variant (Exp.1 & 2). In the bilateral task, spatial location was uncertain, thus target identification involved stimulus-driven spatial orienting. In the unilateral task, the targets were presented block-wise in the LVF or RVF only, such that no spatial orienting was needed for target identification. Temporal attention was manipulated in both tasks by varying the T1-T2 lag. The results showed that the LVF advantage disappeared when involvement of stimulus-driven spatial orienting was eliminated, whereas the manipulation of temporal attention had no effect on the asymmetry. In conclusion, the results do not support the hypothesis of hemispheric asymmetry in temporal attention, and provide further evidence that the LVF advantage reflects right hemisphere predominance in stimulus-driven orienting of spatial attention. These conclusions fit evidence that temporal attention is implemented by bilateral parietal areas and spatial attention by the right-lateralized ventral frontoparietal network. Copyright © 2017 Elsevier Inc. All rights reserved.

Developments for Personalized Medicine of Lung Cancer Subtypes: Mass Spectrometry-Based Clinical Proteogenomic Analysis of Oncogenic Mutations.

PubMed

Nishimura, Toshihide; Nakamura, Haruhiko

2016-01-01

Molecular therapies targeting lung cancers with mutated epidermal growth factor receptor (EGFR) by EGFR-tyrosin kinase inhibitors (EGFR-TKIs), gefitinib and erlotinib, changed the treatment system of lung cancer. It was revealed that drug efficacy differs by race (e.g., Caucasians vs. Asians) due to oncogenic driver mutations specific to each race, exemplified by gefitinib / erlotinib. The molecular target drugs for lung cancer with anaplastic lymphoma kinase (ALK) gene translocation (the fusion gene, EML4-ALK) was approved, and those targeting lung cancers addicted ROS1, RET, and HER2 have been under development. Both identification and quantification of gatekeeper mutations need to be performed using lung cancer tissue specimens obtained from patients to improve the treatment for lung cancer patients: (1) identification and quantitation data of targeted mutated proteins, including investigation of mutation heterogeneity within a tissue; (2) exploratory mass spectrometry (MS)-based clinical proteogenomic analysis of mutated proteins; and also importantly (3) analysis of dynamic protein-protein interaction (PPI) networks of proteins significantly related to a subgroup of patients with lung cancer not only with good efficacy but also with acquired resistance. MS-based proteogenomics is a promising approach to directly capture mutated and fusion proteins expressed in a clinical sample. Technological developments are further expected, which will provide a powerful solution for the stratification of patients and drug discovery (Precision Medicine).

Defining Human Failure Events for Petroleum Risk Analysis

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

Ronald L. Boring; Knut Øien

2014-06-01

In this paper, an identification and description of barriers and human failure events (HFEs) for human reliability analysis (HRA) is performed. The barriers, called target systems, are identified from risk significant accident scenarios represented as defined situations of hazard and accident (DSHAs). This report serves as the foundation for further work to develop petroleum HFEs compatible with the SPAR-H method and intended for reuse in future HRAs.

Integrated Fusion, Performance Prediction, and Sensor Management for Automatic Target Exploitation

DTIC Science & Technology

2007-05-30

with large region of attraction about the true minimum. The physical optics models provide features for high confidence identification of stationary...the detection test are used to estimate 3D object scattering; multiple images can be noncoherently combined to reconstruct a more complete object...Proc. SPIE Algorithms for Synthetic Aper- ture Radar Imagery XIII, The International Society for Optical Engineering, April 2006. [40] K. Varshney, M. C

Transcriptional network inference from functional similarity and expression data: a global supervised approach.

PubMed

Ambroise, Jérôme; Robert, Annie; Macq, Benoit; Gala, Jean-Luc

2012-01-06

An important challenge in system biology is the inference of biological networks from postgenomic data. Among these biological networks, a gene transcriptional regulatory network focuses on interactions existing between transcription factors (TFs) and and their corresponding target genes. A large number of reverse engineering algorithms were proposed to infer such networks from gene expression profiles, but most current methods have relatively low predictive performances. In this paper, we introduce the novel TNIFSED method (Transcriptional Network Inference from Functional Similarity and Expression Data), that infers a transcriptional network from the integration of correlations and partial correlations of gene expression profiles and gene functional similarities through a supervised classifier. In the current work, TNIFSED was applied to predict the transcriptional network in Escherichia coli and in Saccharomyces cerevisiae, using datasets of 445 and 170 affymetrix arrays, respectively. Using the area under the curve of the receiver operating characteristics and the F-measure as indicators, we showed the predictive performance of TNIFSED to be better than unsupervised state-of-the-art methods. TNIFSED performed slightly worse than the supervised SIRENE algorithm for the target genes identification of the TF having a wide range of yet identified target genes but better for TF having only few identified target genes. Our results indicate that TNIFSED is complementary to the SIRENE algorithm, and particularly suitable to discover target genes of "orphan" TFs.

Automatic de-identification of textual documents in the electronic health record: a review of recent research

PubMed Central

2010-01-01

Background In the United States, the Health Insurance Portability and Accountability Act (HIPAA) protects the confidentiality of patient data and requires the informed consent of the patient and approval of the Internal Review Board to use data for research purposes, but these requirements can be waived if data is de-identified. For clinical data to be considered de-identified, the HIPAA "Safe Harbor" technique requires 18 data elements (called PHI: Protected Health Information) to be removed. The de-identification of narrative text documents is often realized manually, and requires significant resources. Well aware of these issues, several authors have investigated automated de-identification of narrative text documents from the electronic health record, and a review of recent research in this domain is presented here. Methods This review focuses on recently published research (after 1995), and includes relevant publications from bibliographic queries in PubMed, conference proceedings, the ACM Digital Library, and interesting publications referenced in already included papers. Results The literature search returned more than 200 publications. The majority focused only on structured data de-identification instead of narrative text, on image de-identification, or described manual de-identification, and were therefore excluded. Finally, 18 publications describing automated text de-identification were selected for detailed analysis of the architecture and methods used, the types of PHI detected and removed, the external resources used, and the types of clinical documents targeted. All text de-identification systems aimed to identify and remove person names, and many included other types of PHI. Most systems used only one or two specific clinical document types, and were mostly based on two different groups of methodologies: pattern matching and machine learning. Many systems combined both approaches for different types of PHI, but the majority relied only on pattern matching, rules, and dictionaries. Conclusions In general, methods based on dictionaries performed better with PHI that is rarely mentioned in clinical text, but are more difficult to generalize. Methods based on machine learning tend to perform better, especially with PHI that is not mentioned in the dictionaries used. Finally, the issues of anonymization, sufficient performance, and "over-scrubbing" are discussed in this publication. PMID:20678228

Automatic de-identification of textual documents in the electronic health record: a review of recent research.

PubMed

Meystre, Stephane M; Friedlin, F Jeffrey; South, Brett R; Shen, Shuying; Samore, Matthew H

2010-08-02

In the United States, the Health Insurance Portability and Accountability Act (HIPAA) protects the confidentiality of patient data and requires the informed consent of the patient and approval of the Internal Review Board to use data for research purposes, but these requirements can be waived if data is de-identified. For clinical data to be considered de-identified, the HIPAA "Safe Harbor" technique requires 18 data elements (called PHI: Protected Health Information) to be removed. The de-identification of narrative text documents is often realized manually, and requires significant resources. Well aware of these issues, several authors have investigated automated de-identification of narrative text documents from the electronic health record, and a review of recent research in this domain is presented here. This review focuses on recently published research (after 1995), and includes relevant publications from bibliographic queries in PubMed, conference proceedings, the ACM Digital Library, and interesting publications referenced in already included papers. The literature search returned more than 200 publications. The majority focused only on structured data de-identification instead of narrative text, on image de-identification, or described manual de-identification, and were therefore excluded. Finally, 18 publications describing automated text de-identification were selected for detailed analysis of the architecture and methods used, the types of PHI detected and removed, the external resources used, and the types of clinical documents targeted. All text de-identification systems aimed to identify and remove person names, and many included other types of PHI. Most systems used only one or two specific clinical document types, and were mostly based on two different groups of methodologies: pattern matching and machine learning. Many systems combined both approaches for different types of PHI, but the majority relied only on pattern matching, rules, and dictionaries. In general, methods based on dictionaries performed better with PHI that is rarely mentioned in clinical text, but are more difficult to generalize. Methods based on machine learning tend to perform better, especially with PHI that is not mentioned in the dictionaries used. Finally, the issues of anonymization, sufficient performance, and "over-scrubbing" are discussed in this publication.

Benchmark data sets for structure-based computational target prediction.

PubMed

Schomburg, Karen T; Rarey, Matthias

2014-08-25

Structure-based computational target prediction methods identify potential targets for a bioactive compound. Methods based on protein-ligand docking so far face many challenges, where the greatest probably is the ranking of true targets in a large data set of protein structures. Currently, no standard data sets for evaluation exist, rendering comparison and demonstration of improvements of methods cumbersome. Therefore, we propose two data sets and evaluation strategies for a meaningful evaluation of new target prediction methods, i.e., a small data set consisting of three target classes for detailed proof-of-concept and selectivity studies and a large data set consisting of 7992 protein structures and 72 drug-like ligands allowing statistical evaluation with performance metrics on a drug-like chemical space. Both data sets are built from openly available resources, and any information needed to perform the described experiments is reported. We describe the composition of the data sets, the setup of screening experiments, and the evaluation strategy. Performance metrics capable to measure the early recognition of enrichments like AUC, BEDROC, and NSLR are proposed. We apply a sequence-based target prediction method to the large data set to analyze its content of nontrivial evaluation cases. The proposed data sets are used for method evaluation of our new inverse screening method iRAISE. The small data set reveals the method's capability and limitations to selectively distinguish between rather similar protein structures. The large data set simulates real target identification scenarios. iRAISE achieves in 55% excellent or good enrichment a median AUC of 0.67 and RMSDs below 2.0 Å for 74% and was able to predict the first true target in 59 out of 72 cases in the top 2% of the protein data set of about 8000 structures.

Noise reduction improves memory for target language speech in competing native but not foreign language speech.

PubMed

Ng, Elaine Hoi Ning; Rudner, Mary; Lunner, Thomas; Rönnberg, Jerker

2015-01-01

A hearing aid noise reduction (NR) algorithm reduces the adverse effect of competing speech on memory for target speech for individuals with hearing impairment with high working memory capacity. In the present study, we investigated whether the positive effect of NR could be extended to individuals with low working memory capacity, as well as how NR influences recall performance for target native speech when the masker language is non-native. A sentence-final word identification and recall (SWIR) test was administered to 26 experienced hearing aid users. In this test, target spoken native language (Swedish) sentence lists were presented in competing native (Swedish) or foreign (Cantonese) speech with or without binary masking NR algorithm. After each sentence list, free recall of sentence final words was prompted. Working memory capacity was measured using a reading span (RS) test. Recall performance was associated with RS. However, the benefit obtained from NR was not associated with RS. Recall performance was more disrupted by native than foreign speech babble and NR improved recall performance in native but not foreign competing speech. Noise reduction improved memory for speech heard in competing speech for hearing aid users. Memory for native speech was more disrupted by native babble than foreign babble, but the disruptive effect of native speech babble was reduced to that of foreign babble when there was NR.

Identification of novel targets for HIV-1: Molecular dynamics simulation and binding energy calculations

NASA Astrophysics Data System (ADS)

Pandey, Vishnudatt; Tiwari, Gargi; Mall, Vijaya Shri; Tiwari, Rakesh Kumar; Ojha, R. P.

2018-05-01

HIV-1 envelope glycoprotein-mediated fusion is managed by the concerted coalescence of the HIV-1 gp41 N- and C- helical regions, which is a product in the formation of 6-helix bundles. These two regions are considered prime targets for peptides and antibodies that inhibit HIV-1 entry. There are so many rational method aimed to attach a rationally designed artificial tail to the C-terminus of HIV-1 fusion inhibitors to increase their antiviral potency. Here M. D. simulation was performed to go insight for study of C-terminal tail of Ile-Asp-Leu (IDL).

Rapid Chemometric Filtering of Spectral Data

NASA Technical Reports Server (NTRS)

Beaman, Gregory; Pelletier, Michael; Seshadri, Suresh

2004-01-01

A method of rapid, programmable filtering of spectral transmittance, reflectance, or fluorescence data to measure the concentrations of chemical species has been proposed. By programmable is meant that a variety of spectral analyses can readily be performed and modified in software, firmware, and/or electronic hardware, without need to change optical filters or other optical hardware of the associated spectrometers. The method is intended to enable real-time identification of single or multiple target chemical species in applications that involve high-throughput screening of multiple samples. Examples of such applications include (but are not limited to) combinatorial chemistry, flow cytometry, bead assays, testing drugs, remote sensing, and identification of targets. The basic concept of the proposed method is to perform real-time crosscorrelations of a measured spectrum with one or more analytical function(s) of wavelength that could be, for example, the known spectra of target species. Assuming that measured spectral intensities are proportional to concentrations of target species plus background spectral intensities, then after subtraction of background levels, it should be possible to determine target species concentrations from cross-correlation values. Of course, the problem of determining the concentrations is more complex when spectra of different species overlap, but the problem can be solved by use of multiple analytical functions in combination with computational techniques that have been developed previously for analyses of this type. The method is applicable to the design and operation of a spectrometer in which spectrally dispersed light is measured by means of an active-pixel sensor (APS) array. The row or column dimension of such an array is generally chosen to be aligned along the spectral-dispersion dimension, so that each pixel intercepts light in a narrow spectral band centered on a wavelength that is a known function of the pixel position. The proposed method admits of two hardware implementations for computing cross-correlations in real time.

Radiological assessment of target materials for accelerator transmutation of waste (ATW) applications

NASA Astrophysics Data System (ADS)

Vickers, Linda Diane

This dissertation issues the first published document of the radiation absorbed dose rate (rad-h-1) to tissue from radioactive spallation products in Ta, W, Pb, Bi, and LBE target materials used in Accelerator Transmutation of Waste (ATW) applications. No previous works have provided an estimate of the absorbed dose rate (rad-h-1) from activated targets for ATW applications. The results of this dissertation are useful for planning the radiological safety assessment to personnel, and for the design, construction, maintenance, and disposition of target materials of high-energy particle accelerators for ATW applications (Charlton, 1996). In addition, this dissertation provides the characterization of target materials of high-energy particle accelerators for the parameters of: (1) spallation neutron yield (neutrons/proton), (2) spallation products yield (nuclides/proton), (3) energy-dependent spallation neutron fluence distribution, (4) spallation neutron flux, (5) identification of radioactive spallation products for consideration in safety of personnel to high radiation dose rates, and (6) identification of the optimum geometrical dimensions for the target applicable to the maximum radial spallation neutron leakage from the target. Pb and Bi target materials yielded the lowest absorbed dose rates (rad-h -1) for a 10-year irradiation/50-year decay scheme, and would be the preferred target materials for consideration of the radiological safety of personnel during ATW operations. A beneficial characteristic of these target materials is that they do not produce radioactive transuranic isotopes, which have very long half-lives and require special handling and disposition requirements. Furthermore, the targets are not considered High-Level Waste (HLW) such as reactor spent fuel for disposal purposes. It is a basic ATW system requirement that the spallation target after it has been expended should be disposable as Class C low-level radioactive waste. Therefore, the disposal of Pb and Bi targets would be optimally beneficial to the economy and environment. Future studies should relate the target performance to other system parameters, specifically solid and liquid blanket systems that contain the radioactive waste to be transmuted. The methodology of this dissertation may be applied to any target material of a high-energy particle accelerator.

Summary of tracking and identification methods

NASA Astrophysics Data System (ADS)

Blasch, Erik; Yang, Chun; Kadar, Ivan

2014-06-01

Over the last two decades, many solutions have arisen to combine target tracking estimation with classification methods. Target tracking includes developments from linear to non-linear and Gaussian to non-Gaussian processing. Pattern recognition includes detection, classification, recognition, and identification methods. Integrating tracking and pattern recognition has resulted in numerous approaches and this paper seeks to organize the various approaches. We discuss the terminology so as to have a common framework for various standards such as the NATO STANAG 4162 - Identification Data Combining Process. In a use case, we provide a comparative example highlighting that location information (as an example) with additional mission objectives from geographical, human, social, cultural, and behavioral modeling is needed to determine identification as classification alone does not allow determining identification or intent.

A peptide-retrieval strategy enables significant improvement of quantitative performance without compromising confidence of identification.

PubMed

Tu, Chengjian; Shen, Shichen; Sheng, Quanhu; Shyr, Yu; Qu, Jun

2017-01-30

Reliable quantification of low-abundance proteins in complex proteomes is challenging largely owing to the limited number of spectra/peptides identified. In this study we developed a straightforward method to improve the quantitative accuracy and precision of proteins by strategically retrieving the less confident peptides that were previously filtered out using the standard target-decoy search strategy. The filtered-out MS/MS spectra matched to confidently-identified proteins were recovered, and the peptide-spectrum-match FDR were re-calculated and controlled at a confident level of FDR≤1%, while protein FDR maintained at ~1%. We evaluated the performance of this strategy in both spectral count- and ion current-based methods. >60% increase of total quantified spectra/peptides was respectively achieved for analyzing a spike-in sample set and a public dataset from CPTAC. Incorporating the peptide retrieval strategy significantly improved the quantitative accuracy and precision, especially for low-abundance proteins (e.g. one-hit proteins). Moreover, the capacity of confidently discovering significantly-altered proteins was also enhanced substantially, as demonstrated with two spike-in datasets. In summary, improved quantitative performance was achieved by this peptide recovery strategy without compromising confidence of protein identification, which can be readily implemented in a broad range of quantitative proteomics techniques including label-free or labeling approaches. We hypothesize that more quantifiable spectra and peptides in a protein, even including less confident peptides, could help reduce variations and improve protein quantification. Hence the peptide retrieval strategy was developed and evaluated in two spike-in sample sets with different LC-MS/MS variations using both MS1- and MS2-based quantitative approach. The list of confidently identified proteins using the standard target-decoy search strategy was fixed and more spectra/peptides with less confidence matched to confident proteins were retrieved. However, the total peptide-spectrum-match false discovery rate (PSM FDR) after retrieval analysis was still controlled at a confident level of FDR≤1%. As expected, the penalty for occasionally incorporating incorrect peptide identifications is negligible by comparison with the improvements in quantitative performance. More quantifiable peptides, lower missing value rate, better quantitative accuracy and precision were significantly achieved for the same protein identifications by this simple strategy. This strategy is theoretically applicable for any quantitative approaches in proteomics and thereby provides more quantitative information, especially on low-abundance proteins. Published by Elsevier B.V.

Discerning cultural identification from a thinly sliced behavioral sample.

PubMed

Hamamura, Takeshi; Li, Liman Man Wai

2012-12-01

This research examined whether individual differences in cultural identification can be discerned at zero acquaintance. This issue was examined in Hong Kong, where the idiosyncrasy of cultural identification is a salient social-psychological issue. The participants were able to perceive accurately the targets' identification with Western culture from a video clip and from a still image. Findings also indicated that a stereotype of Western cultural identity (i.e., extraversion and particular hairstyle) facilitated these perceptions. Specifically, (a) the participants with a stronger stereotype were more accurate in perceiving Western cultural identification, (b) the targets who were experimentally manipulated to appear extraverted were rated as more strongly identifying with Western culture, and (c) the participants relatively unfamiliar with these stereotypes did not correctly perceive Western cultural identification. Implications of these findings on research on multiculturalism are also discussed.

Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance.

PubMed

Chaput, Ludovic; Martinez-Sanz, Juan; Saettel, Nicolas; Mouawad, Liliane

2016-01-01

In a structure-based virtual screening, the choice of the docking program is essential for the success of a hit identification. Benchmarks are meant to help in guiding this choice, especially when undertaken on a large variety of protein targets. Here, the performance of four popular virtual screening programs, Gold, Glide, Surflex and FlexX, is compared using the Directory of Useful Decoys-Enhanced database (DUD-E), which includes 102 targets with an average of 224 ligands per target and 50 decoys per ligand, generated to avoid biases in the benchmarking. Then, a relationship between these program performances and the properties of the targets or the small molecules was investigated. The comparison was based on two metrics, with three different parameters each. The BEDROC scores with α = 80.5, indicated that, on the overall database, Glide succeeded (score > 0.5) for 30 targets, Gold for 27, FlexX for 14 and Surflex for 11. The performance did not depend on the hydrophobicity nor the openness of the protein cavities, neither on the families to which the proteins belong. However, despite the care in the construction of the DUD-E database, the small differences that remain between the actives and the decoys likely explain the successes of Gold, Surflex and FlexX. Moreover, the similarity between the actives of a target and its crystal structure ligand seems to be at the basis of the good performance of Glide. When all targets with significant biases are removed from the benchmarking, a subset of 47 targets remains, for which Glide succeeded for only 5 targets, Gold for 4 and FlexX and Surflex for 2. The performance dramatic drop of all four programs when the biases are removed shows that we should beware of virtual screening benchmarks, because good performances may be due to wrong reasons. Therefore, benchmarking would hardly provide guidelines for virtual screening experiments, despite the tendency that is maintained, i.e., Glide and Gold display better performance than FlexX and Surflex. We recommend to always use several programs and combine their results. Graphical AbstractSummary of the results obtained by virtual screening with the four programs, Glide, Gold, Surflex and FlexX, on the 102 targets of the DUD-E database. The percentage of targets with successful results, i.e., with BDEROC(α = 80.5) > 0.5, when the entire database is considered are in Blue, and when targets with biased chemical libraries are removed are in Red.

Multi-centre evaluation of mass spectrometric identification of anaerobic bacteria using the VITEK® MS system.

PubMed

Garner, O; Mochon, A; Branda, J; Burnham, C-A; Bythrow, M; Ferraro, M; Ginocchio, C; Jennemann, R; Manji, R; Procop, G W; Richter, S; Rychert, J; Sercia, L; Westblade, L; Lewinski, M

2014-04-01

Accurate and timely identification of anaerobic bacteria is critical to successful treatment. Classic phenotypic methods for identification require long turnaround times and can exhibit poor species level identification. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an identification method that can provide rapid identification of anaerobes. We present a multi-centre study assessing the clinical performance of the VITEK(®) MS in the identification of anaerobic bacteria. Five different test sites analysed a collection of 651 unique anaerobic isolates comprising 11 different genera. Multiple species were included for several of the genera. Briefly, anaerobic isolates were applied directly to a well of a target plate. Matrix solution (α-cyano-4-hydroxycinnamic acid) was added and allowed to dry. Mass spectra results were generated with the VITEK(®) MS, and the comparative spectral analysis and organism identification were determined using the VITEK(®) MS database 2.0. Results were confirmed by 16S rRNA gene sequencing. Of the 651 isolates analysed, 91.2% (594/651) exhibited the correct species identification. An additional eight isolates were correctly identified to genus level, raising the rate of identification to 92.5%. Genus-level identification consisted of Actinomyces, Bacteroides and Prevotella species. Fusobacterium nucleatum, Actinomyces neuii and Bacteroides uniformis were notable for an increased percentage of no-identification results compared with the other anaerobes tested. VITEK(®) MS identification of clinically relevant anaerobes is highly accurate and represents a dramatic improvement over other phenotypic methods in accuracy and turnaround time. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Arrays of probes for positional sequencing by hybridization

DOEpatents

Cantor, Charles R [Boston, MA; Prezetakiewiczr, Marek [East Boston, MA; Smith, Cassandra L [Boston, MA; Sano, Takeshi [Waltham, MA

2008-01-15

This invention is directed to methods and reagents useful for sequencing nucleic acid targets utilizing sequencing by hybridization technology comprising probes, arrays of probes and methods whereby sequence information is obtained rapidly and efficiently in discrete packages. That information can be used for the detection, identification, purification and complete or partial sequencing of a particular target nucleic acid. When coupled with a ligation step, these methods can be performed under a single set of hybridization conditions. The invention also relates to the replication of probe arrays and methods for making and replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'- and/or 3'-overhangs.

Concealed identification symbols and nondestructive determination of the identification symbols

DOEpatents

Nance, Thomas A.; Gibbs, Kenneth M.

2014-09-16

The concealing of one or more identification symbols into a target object and the subsequent determination or reading of such symbols through non-destructive testing is described. The symbols can be concealed in a manner so that they are not visible to the human eye and/or cannot be readily revealed to the human eye without damage or destruction of the target object. The identification symbols can be determined after concealment by e.g., the compilation of multiple X-ray images. As such, the present invention can also provide e.g., a deterrent to theft and the recovery of lost or stolen objects.

An integrated control scheme for space robot after capturing non-cooperative target

NASA Astrophysics Data System (ADS)

Wang, Mingming; Luo, Jianjun; Yuan, Jianping; Walter, Ulrich

2018-06-01

How to identify the mass properties and eliminate the unknown angular momentum of space robotic system after capturing a non-cooperative target is of great challenge. This paper focuses on designing an integrated control framework which includes detumbling strategy, coordination control and parameter identification. Firstly, inverted and forward chain approaches are synthesized for space robot to obtain dynamic equation in operational space. Secondly, a detumbling strategy is introduced using elementary functions with normalized time, while the imposed end-effector constraints are considered. Next, a coordination control scheme for stabilizing both base and end-effector based on impedance control is implemented with the target's parameter uncertainty. With the measurements of the forces and torques exerted on the target, its mass properties are estimated during the detumbling process accordingly. Simulation results are presented using a 7 degree-of-freedom kinematically redundant space manipulator, which verifies the performance and effectiveness of the proposed method.

Structure identification for Non-Targeted Analytical Chemistry using the US EPA’s CompTox Chemistry Dashboard (ACS 2017 Fall meeting 3 of 3)

EPA Science Inventory

Identification of unknowns in non-targeted analyses (NTA) requires the integration of complementary data types to generate a confident consensus structure. Researchers use a variety of data and tools (e.g., chemical reference databases, spectral matching, fragment prediction too...

Methods, compounds and systems for detecting a microorganism in a sample

DOEpatents

Colston, Jr, Bill W.; Fitch, J. Patrick; Gardner, Shea N.; Williams, Peter L.; Wagner, Mark C.

2016-09-06

Methods to identify a set of probe polynucleotides suitable for detecting a set of targets and in particular methods for identification of primers suitable for detection of target microorganisms related polynucleotides, set of polynucleotides and compositions, and related methods and systems for detection and/or identification of microorganisms in a sample.

UniDrug-target: a computational tool to identify unique drug targets in pathogenic bacteria.

PubMed

Chanumolu, Sree Krishna; Rout, Chittaranjan; Chauhan, Rajinder S

2012-01-01

Targeting conserved proteins of bacteria through antibacterial medications has resulted in both the development of resistant strains and changes to human health by destroying beneficial microbes which eventually become breeding grounds for the evolution of resistances. Despite the availability of more than 800 genomes sequences, 430 pathways, 4743 enzymes, 9257 metabolic reactions and protein (three-dimensional) 3D structures in bacteria, no pathogen-specific computational drug target identification tool has been developed. A web server, UniDrug-Target, which combines bacterial biological information and computational methods to stringently identify pathogen-specific proteins as drug targets, has been designed. Besides predicting pathogen-specific proteins essentiality, chokepoint property, etc., three new algorithms were developed and implemented by using protein sequences, domains, structures, and metabolic reactions for construction of partial metabolic networks (PMNs), determination of conservation in critical residues, and variation analysis of residues forming similar cavities in proteins sequences. First, PMNs are constructed to determine the extent of disturbances in metabolite production by targeting a protein as drug target. Conservation of pathogen-specific protein's critical residues involved in cavity formation and biological function determined at domain-level with low-matching sequences. Last, variation analysis of residues forming similar cavities in proteins sequences from pathogenic versus non-pathogenic bacteria and humans is performed. The server is capable of predicting drug targets for any sequenced pathogenic bacteria having fasta sequences and annotated information. The utility of UniDrug-Target server was demonstrated for Mycobacterium tuberculosis (H37Rv). The UniDrug-Target identified 265 mycobacteria pathogen-specific proteins, including 17 essential proteins which can be potential drug targets. UniDrug-Target is expected to accelerate pathogen-specific drug targets identification which will increase their success and durability as drugs developed against them have less chance to develop resistances and adverse impact on environment. The server is freely available at http://117.211.115.67/UDT/main.html. The standalone application (source codes) is available at http://www.bioinformatics.org/ftp/pub/bioinfojuit/UDT.rar.

Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens

PubMed Central

Lo, Yu-Chen; Senese, Silvia; Li, Chien-Ming; Hu, Qiyang; Huang, Yong; Damoiseaux, Robert; Torres, Jorge Z.

2015-01-01

Target identification is one of the most critical steps following cell-based phenotypic chemical screens aimed at identifying compounds with potential uses in cell biology and for developing novel disease therapies. Current in silico target identification methods, including chemical similarity database searches, are limited to single or sequential ligand analysis that have limited capabilities for accurate deconvolution of a large number of compounds with diverse chemical structures. Here, we present CSNAP (Chemical Similarity Network Analysis Pulldown), a new computational target identification method that utilizes chemical similarity networks for large-scale chemotype (consensus chemical pattern) recognition and drug target profiling. Our benchmark study showed that CSNAP can achieve an overall higher accuracy (>80%) of target prediction with respect to representative chemotypes in large (>200) compound sets, in comparison to the SEA approach (60–70%). Additionally, CSNAP is capable of integrating with biological knowledge-based databases (Uniprot, GO) and high-throughput biology platforms (proteomic, genetic, etc) for system-wise drug target validation. To demonstrate the utility of the CSNAP approach, we combined CSNAP's target prediction with experimental ligand evaluation to identify the major mitotic targets of hit compounds from a cell-based chemical screen and we highlight novel compounds targeting microtubules, an important cancer therapeutic target. The CSNAP method is freely available and can be accessed from the CSNAP web server (http://services.mbi.ucla.edu/CSNAP/). PMID:25826798

The effects of divided attention on implicit and explicit memory performance.

PubMed

Schmitter-Edgecombe, M

1996-03-01

This study explored the nature of the relationship between attention available at learning and subsequent implicit and explicit memory performance. One hundred neurologically normal subjects rated their liking of target words on a five-point scale. Half of the subjects completed the word-rating task in a full attention condition and the other half performed the task in a divided attention condition. Following administration of the word-rating task, all subjects completed five memory tests, three implicit (category association, tachistoscopic identification, and perceptual clarification) and two explicit (semantic-cued recall and graphemic-cued recall), each bearing on a different subset of the list of previously presented target words. The results revealed that subjects in the divided attention condition performed significantly more poorly than subjects in the full attention condition on the explicit memory measures. In contrast, there were no significant group differences in performance on the implicit memory measures. These findings suggest that the attention to an episode that is necessary to produce later explicit memory may differ from that necessary to produce unconscious influences. The relationship between implicit memory, neurologic injury and automatic processes is discussed.

Applications of tuned mass dampers to improve performance of large space mirrors

NASA Astrophysics Data System (ADS)

Yingling, Adam J.; Agrawal, Brij N.

2014-01-01

In order for future imaging spacecraft to meet higher resolution imaging capability, it will be necessary to build large space telescopes with primary mirror diameters that range from 10 m to 20 m and do so with nanometer surface accuracy. Due to launch vehicle mass and volume constraints, these mirrors have to be deployable and lightweight, such as segmented mirrors using active optics to correct mirror surfaces with closed loop control. As a part of this work, system identification tests revealed that dynamic disturbances inherent in a laboratory environment are significant enough to degrade the optical performance of the telescope. Research was performed at the Naval Postgraduate School to identify the vibration modes most affecting the optical performance and evaluate different techniques to increase damping of those modes. Based on this work, tuned mass dampers (TMDs) were selected because of their simplicity in implementation and effectiveness in targeting specific modes. The selected damping mechanism was an eddy current damper where the damping and frequency of the damper could be easily changed. System identification of segments was performed to derive TMD specifications. Several configurations of the damper were evaluated, including the number and placement of TMDs, damping constant, and targeted structural modes. The final configuration consisted of two dampers located at the edge of each segment and resulted in 80% reduction in vibrations. The WFE for the system without dampers was 1.5 waves, with one TMD the WFE was 0.9 waves, and with two TMDs the WFE was 0.25 waves. This paper provides details of some of the work done in this area and includes theoretical predictions for optimum damping which were experimentally verified on a large aperture segmented system.

Bombing Target Identification from Limited Transect Data

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

Roberts, Barry L.; Hathaway, John E.; Pulsipher, Brent A.

2006-08-07

A series of sensor data combined with geostatistical techniques were used to determine likely target areas for a historic military aerial bombing range. Primary data consisted of magnetic anomaly information from limited magnetometer transects across the site. Secondary data included airborne LIDAR, orthophotography, and other general site characterization information. Identification of likely target areas relied primarily upon kriging estimates of magnetic anomaly densities across the site. Secondary information, such as impact crater locations, was used to refine the boundary delineations.

Factors affecting computer mouse use for young children: implications for AAC.

PubMed

Costigan, F Aileen; Light, Janice C; Newell, Karl M

2012-06-01

More than 12% of preschoolers receiving special education services have complex communication needs, including increasing numbers of children who do not have significant motor impairments (e.g., children with autism spectrum disorders, Down syndrome, etc.). In order to meet their diverse communication needs (e.g., face-to-face, written, Internet, telecommunication), these children may use mainstream technologies accessed via the mouse, yet little is known about factors that affect the mouse performance of young children. This study used a mixed factorial design to investigate the effects of age, target size, and angle of approach on accuracy and time required for accurate target selection with a mouse for 20 3-year-old and 20 4-year-old children. The 4-year-olds were generally more accurate and faster than the 3-year-olds. Target size and angle mediated differences in performance within age groups. The 3-year-olds were more accurate and faster in selecting the medium and large targets relative to the small target, were faster in selecting the large relative to the medium target, and were faster in selecting targets along the vertical relative to the diagonal angle. The 4-year-olds were faster in selecting the medium and large targets relative to the small target. Implications for improving access to AAC include the preliminary suggestion of age-related threshold target sizes that support sufficient accuracy, the possibility of efficiency benefits when target size is increased up to an age-related threshold, and identification of the potential utility of the vertical angle as a context for training navigational input device use.

Hierarchical relaxation methods for multispectral pixel classification as applied to target identification

NASA Astrophysics Data System (ADS)

Cohen, E. A., Jr.

1985-02-01

This report provides insights into the approaches toward image modeling as applied to target detection. The approach is that of examining the energy in prescribed wave-bands which emanate from a target and correlating the emissions. Typically, one might be looking at two or three infrared bands, possibly together with several visual bands. The target is segmented, using both first and second order modeling, into a set of interesting components and these components are correlated so as to enhance the classification process. A Markov-type model is used to provide an a priori assessment of the spatial relationships among critical parts of the target, and a stochastic model using the output of an initial probabilistic labeling is invoked. The tradeoff between this stochastic model and the Markov model is then optimized to yield a best labeling for identification purposes. In an identification of friend or foe (IFF) context, this methodology could be of interest, for it provides the ingredients for such a higher level of understanding.

Network-Based Approaches in Drug Discovery and Early Development

PubMed Central

Harrold, JM; Ramanathan, M; Mager, DE

2015-01-01

Identification of novel targets is a critical first step in the drug discovery and development process. Most diseases such as cancer, metabolic disorders, and neurological disorders are complex, and their pathogenesis involves multiple genetic and environmental factors. Finding a viable drug target–drug combination with high potential for yielding clinical success within the efficacy–toxicity spectrum is extremely challenging. Many examples are now available in which network-based approaches show potential for the identification of novel targets and for the repositioning of established targets. The objective of this article is to highlight network approaches for identifying novel targets with greater chances of gaining approved drugs with maximal efficacy and minimal side effects. Further enhancement of these approaches may emerge from effectively integrating computational systems biology with pharmacodynamic systems analysis. Coupling genomics, proteomics, and metabolomics databases with systems pharmacology modeling may aid in the development of disease-specific networks that can be further used to build confidence in target identification. PMID:24025802

Target identification of small molecules based on chemical biology approaches.

PubMed

Futamura, Yushi; Muroi, Makoto; Osada, Hiroyuki

2013-05-01

Recently, a phenotypic approach-screens that assess the effects of compounds on cells, tissues, or whole organisms-has been reconsidered and reintroduced as a complementary strategy of a target-based approach for drug discovery. Although the finding of novel bioactive compounds from large chemical libraries has become routine, the identification of their molecular targets is still a time-consuming and difficult process, making this step rate-limiting in drug development. In the last decade, we and other researchers have amassed a large amount of phenotypic data through progress in omics research and advances in instrumentation. Accordingly, the profiling methodologies using these datasets expertly have emerged to identify and validate specific molecular targets of drug candidates, attaining some progress in current drug discovery (e.g., eribulin). In the case of a compound that shows an unprecedented phenotype likely by inhibiting a first-in-class target, however, such phenotypic profiling is invalid. Under the circumstances, a photo-crosslinking affinity approach should be beneficial. In this review, we describe and summarize recent progress in both affinity-based (direct) and phenotypic profiling (indirect) approaches for chemical biology target identification.

Accurate and exact CNV identification from targeted high-throughput sequence data.

PubMed

Nord, Alex S; Lee, Ming; King, Mary-Claire; Walsh, Tom

2011-04-12

Massively parallel sequencing of barcoded DNA samples significantly increases screening efficiency for clinically important genes. Short read aligners are well suited to single nucleotide and indel detection. However, methods for CNV detection from targeted enrichment are lacking. We present a method combining coverage with map information for the identification of deletions and duplications in targeted sequence data. Sequencing data is first scanned for gains and losses using a comparison of normalized coverage data between samples. CNV calls are confirmed by testing for a signature of sequences that span the CNV breakpoint. With our method, CNVs can be identified regardless of whether breakpoints are within regions targeted for sequencing. For CNVs where at least one breakpoint is within targeted sequence, exact CNV breakpoints can be identified. In a test data set of 96 subjects sequenced across ~1 Mb genomic sequence using multiplexing technology, our method detected mutations as small as 31 bp, predicted quantitative copy count, and had a low false-positive rate. Application of this method allows for identification of gains and losses in targeted sequence data, providing comprehensive mutation screening when combined with a short read aligner.

Characterization of an elastic target in a shallow water waveguide by decomposition of the time-reversal operator.

PubMed

Philippe, Franck D; Prada, Claire; de Rosny, Julien; Clorennec, Dominique; Minonzio, Jean-Gabriel; Fink, Mathias

2008-08-01

This paper reports the results of an investigation into extracting of the backscattered frequency signature of a target in a waveguide. Retrieving the target signature is difficult because it is blurred by waveguide reflections and modal interference. It is shown that the decomposition of the time-reversal operator method provides a solution to this problem. Using a modal theory, this paper shows that the first singular value associated with a target is proportional to the backscattering form function. It is linked to the waveguide geometry through a factor that weakly depends on frequency as long as the target is far from the boundaries. Using the same approach, the second singular value is shown to be proportional to the second derivative of the angular form function which is a relevant parameter for target identification. Within this framework the coupling between two targets is considered. Small scale experimental studies are performed in the 3.5 MHz frequency range for 3 mm spheres in a 28 mm deep and 570 mm long waveguide and confirm the theoretical results.

The Statistical Analysis Techniques to Support the NGNP Fuel Performance Experiments

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

Bihn T. Pham; Jeffrey J. Einerson

2010-06-01

This paper describes the development and application of statistical analysis techniques to support the AGR experimental program on NGNP fuel performance. The experiments conducted in the Idaho National Laboratory’s Advanced Test Reactor employ fuel compacts placed in a graphite cylinder shrouded by a steel capsule. The tests are instrumented with thermocouples embedded in graphite blocks and the target quantity (fuel/graphite temperature) is regulated by the He-Ne gas mixture that fills the gap volume. Three techniques for statistical analysis, namely control charting, correlation analysis, and regression analysis, are implemented in the SAS-based NGNP Data Management and Analysis System (NDMAS) for automatedmore » processing and qualification of the AGR measured data. The NDMAS also stores daily neutronic (power) and thermal (heat transfer) code simulation results along with the measurement data, allowing for their combined use and comparative scrutiny. The ultimate objective of this work includes (a) a multi-faceted system for data monitoring and data accuracy testing, (b) identification of possible modes of diagnostics deterioration and changes in experimental conditions, (c) qualification of data for use in code validation, and (d) identification and use of data trends to support effective control of test conditions with respect to the test target. Analysis results and examples given in the paper show the three statistical analysis techniques providing a complementary capability to warn of thermocouple failures. It also suggests that the regression analysis models relating calculated fuel temperatures and thermocouple readings can enable online regulation of experimental parameters (i.e. gas mixture content), to effectively maintain the target quantity (fuel temperature) within a given range.« less

Identification of Sarcosine as a Target Molecule for the Canine Olfactory Detection of Prostate Carcinoma.

PubMed

Pacik, Dalibor; Plevova, Mariana; Urbanova, Lucie; Lackova, Zuzana; Strmiska, Vladislav; Necas, Alois; Heger, Zbynek; Adam, Vojtech

2018-03-21

The hypothesis that dogs can detect malignant tumours through the identification of specific molecules is nearly 30 years old. To date, several reports have described the successful detection of distinct types of cancer. However, is still a lack of data regarding the specific molecules that can be recognized by a dog's olfactory apparatus. Hence, we performed a study with artificially prepared, well-characterized urinary specimens that were enriched with sarcosine, a widely reported urinary biomarker for prostate cancer (PCa). For the purposes of the study, a German shepherd dog was utilized for analyses of 60 positive and 120 negative samples. Our study provides the first evidence that a sniffer dog specially trained for the olfactory detection of PCa can recognize sarcosine in artificial urine with a performance [sensitivity of 90%, specificity of 95%, and precision of 90% for the highest amount of sarcosine (10 µmol/L)] that is comparable to the identification of PCa-diagnosed subjects (sensitivity of 93.5% and specificity of 91.6%). This study casts light on the unrevealed phenomenon of PCa olfactory detection and opens the door for further studies with canine olfactory detection and cancer diagnostics.

Applying the multi-threat framework of stereotype threat in the context of digital gaming

PubMed Central

Pennington, Charlotte R.; McCann, Joseph J.

2018-01-01

Females often report experiencing stigmatisation pertaining to their competency in digital gaming communities. Employing the principles of the multi-threat framework of stereotype threat, the current research examined the impact of gender-related stereotypes on females’ gaming performance and related self-perceptions. In Experiment 1, 90 females were assigned to one of three conditions in which they were primed that their performance would be either diagnostic of their personal (self-as-target) or gender group’s ability (group-as-target) or would be non-diagnostic of gaming ability (control). In Experiment 2, 90 females were primed that their performance would be judged by a group of other females (in-group source) or males (out-group source), or would be non-diagnostic of ability (control). Participants then completed a casual gaming task, as well as measures of competence beliefs, self-efficacy and self-esteem. Findings from Experiment 1 indicate that neither a self-as-target nor a group-as-target stereotype affected significantly gaming performance, or game-related self-efficacy, self-esteem and competency beliefs. Findings from Experiment 2 reveal further that females’ gaming performance and associated self-perceptions were not impacted significantly by an in-group or out-group source of stereotype threat. The discussion turns to potential explanations for these findings, proposing that females may not perceive negative gender-gaming stereotypes to be an accurate representation of their personal or social group’s gaming ability. We also discuss the implications of the experimental design and difficulty, as well as the potential for domain identification to moderate performance outcomes under stereotype threat. PMID:29444126

Applying the multi-threat framework of stereotype threat in the context of digital gaming.

PubMed

Pennington, Charlotte R; Kaye, Linda K; McCann, Joseph J

2018-01-01

Females often report experiencing stigmatisation pertaining to their competency in digital gaming communities. Employing the principles of the multi-threat framework of stereotype threat, the current research examined the impact of gender-related stereotypes on females' gaming performance and related self-perceptions. In Experiment 1, 90 females were assigned to one of three conditions in which they were primed that their performance would be either diagnostic of their personal (self-as-target) or gender group's ability (group-as-target) or would be non-diagnostic of gaming ability (control). In Experiment 2, 90 females were primed that their performance would be judged by a group of other females (in-group source) or males (out-group source), or would be non-diagnostic of ability (control). Participants then completed a casual gaming task, as well as measures of competence beliefs, self-efficacy and self-esteem. Findings from Experiment 1 indicate that neither a self-as-target nor a group-as-target stereotype affected significantly gaming performance, or game-related self-efficacy, self-esteem and competency beliefs. Findings from Experiment 2 reveal further that females' gaming performance and associated self-perceptions were not impacted significantly by an in-group or out-group source of stereotype threat. The discussion turns to potential explanations for these findings, proposing that females may not perceive negative gender-gaming stereotypes to be an accurate representation of their personal or social group's gaming ability. We also discuss the implications of the experimental design and difficulty, as well as the potential for domain identification to moderate performance outcomes under stereotype threat.

Recommendations for Improving Identification and Quantification in Non-Targeted, GC-MS-Based Metabolomic Profiling of Human Plasma

PubMed Central

Wang, Hanghang; Muehlbauer, Michael J.; O’Neal, Sara K.; Newgard, Christopher B.; Hauser, Elizabeth R.; Shah, Svati H.

2017-01-01

The field of metabolomics as applied to human disease and health is rapidly expanding. In recent efforts of metabolomics research, greater emphasis has been placed on quality control and method validation. In this study, we report an experience with quality control and a practical application of method validation. Specifically, we sought to identify and modify steps in gas chromatography-mass spectrometry (GC-MS)-based, non-targeted metabolomic profiling of human plasma that could influence metabolite identification and quantification. Our experimental design included two studies: (1) a limiting-dilution study, which investigated the effects of dilution on analyte identification and quantification; and (2) a concentration-specific study, which compared the optimal plasma extract volume established in the first study with the volume used in the current institutional protocol. We confirmed that contaminants, concentration, repeatability and intermediate precision are major factors influencing metabolite identification and quantification. In addition, we established methods for improved metabolite identification and quantification, which were summarized to provide recommendations for experimental design of GC-MS-based non-targeted profiling of human plasma. PMID:28841195

Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis

PubMed Central

Hanson, Erin K.; Ballantyne, Jack

2014-01-01

Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen).  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive, screening of biological evidence. PMID:24715968

Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis.

PubMed

Hanson, Erin K; Ballantyne, Jack

2013-01-01

Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen).  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive, screening of biological evidence.

2-Aryl-5-carboxytetrazole as a New Photoaffinity Label for Drug Target Identification.

PubMed

Herner, András; Marjanovic, Jasmina; Lewandowski, Tracey M; Marin, Violeta; Patterson, Melanie; Miesbauer, Laura; Ready, Damien; Williams, Jon; Vasudevan, Anil; Lin, Qing

2016-11-09

Photoaffinity labels are powerful tools for dissecting ligand-protein interactions, and they have a broad utility in medicinal chemistry and drug discovery. Traditional photoaffinity labels work through nonspecific C-H/X-H bond insertion reactions with the protein of interest by the highly reactive photogenerated intermediate. Herein, we report a new photoaffinity label, 2-aryl-5-carboxytetrazole (ACT), that interacts with the target protein via a unique mechanism in which the photogenerated carboxynitrile imine reacts with a proximal nucleophile near the target active site. In two distinct case studies, we demonstrate that the attachment of ACT to a ligand does not significantly alter the binding affinity and specificity of the parent drug. Compared with diazirine and benzophenone, two commonly used photoaffinity labels, in two case studies ACT showed higher photo-cross-linking yields toward their protein targets in vitro based on mass spectrometry analysis. In the in situ target identification studies, ACT successfully captured the desired targets with an efficiency comparable to the diazirine. We expect that further development of this class of photoaffinity labels will lead to a broad range of applications across target identification, and validation and elucidation of the binding site in drug discovery.

2-Aryl-5-carboxytetrazole as a New Photoaffinity Label for Drug Target Identification

PubMed Central

2016-01-01

Photoaffinity labels are powerful tools for dissecting ligand–protein interactions, and they have a broad utility in medicinal chemistry and drug discovery. Traditional photoaffinity labels work through nonspecific C–H/X–H bond insertion reactions with the protein of interest by the highly reactive photogenerated intermediate. Herein, we report a new photoaffinity label, 2-aryl-5-carboxytetrazole (ACT), that interacts with the target protein via a unique mechanism in which the photogenerated carboxynitrile imine reacts with a proximal nucleophile near the target active site. In two distinct case studies, we demonstrate that the attachment of ACT to a ligand does not significantly alter the binding affinity and specificity of the parent drug. Compared with diazirine and benzophenone, two commonly used photoaffinity labels, in two case studies ACT showed higher photo-cross-linking yields toward their protein targets in vitro based on mass spectrometry analysis. In the in situ target identification studies, ACT successfully captured the desired targets with an efficiency comparable to the diazirine. We expect that further development of this class of photoaffinity labels will lead to a broad range of applications across target identification, and validation and elucidation of the binding site in drug discovery. PMID:27740749

Experimental Progress Toward Detection and Identification of Electromagnetically Complex Structures

DTIC Science & Technology

2008-12-01

M. Jaenisch and J. W. Handley Amtec Corporation Huntsville, Alabama 35816-3429 T.A. Baginski and A.S. Hodel Auburn University Auburn, Alabama...ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Amtec ...transmitter power is relatively low; consequently, our target is entirely above ground for now. Measurements are conducted at the Amtec Outdoor Test

Customizable PCR-microplate array for differential identification of multiple pathogens.

PubMed

Woubit, Abdela; Yehualaeshet, Teshome; Roberts, Sherrelle; Graham, Martha; Kim, Moonil; Samuel, Temesgen

2013-11-01

Customizable PCR-microplate arrays were developed for the rapid identification of Salmonella Typhimurium, Salmonella Saintpaul, Salmonella Typhi, Shigella dysenteriae, Escherichia coli O157:H7, Francisella tularensis subsp. tularensis, Francisella tularensis subsp. novicida, Vibrio cholerae, Vibrio parahaemolyticus, Yersinia pestis, and Yersinia pseudotuberculosis. Previously, we identified highly specific primers targeting each of these pathogens. Here, we report the development of customizable PCR-microplate arrays for simultaneous identification of the pathogens using the primers identified. A mixed aliquot of genomic DNA from 38 strains was used to validate three PCR-microplate array formats. Identical PCR conditions were used to run all the samples on the three formats. Specific amplifications were obtained on all three custom plates. In preliminary tests performed to evaluate the sensitivity of these assays in samples inoculated in the laboratory with Salmonella Typhimurium, amplifications were obtained from 1 g of beef hot dog inoculated at as low as 9 CFU/ml or from milk inoculated at as low as 78 CFU/ml. Such microplate arrays could be valuable tools for initial identification or secondary confirmation of contamination by these pathogens.

Direct-to-consumer genetic testing for predicting sports performance and talent identification: Consensus statement

PubMed Central

Webborn, Nick; Williams, Alun; McNamee, Mike; Bouchard, Claude; Pitsiladis, Yannis; Ahmetov, Ildus; Ashley, Euan; Byrne, Nuala; Camporesi, Silvia; Collins, Malcolm; Dijkstra, Paul; Eynon, Nir; Fuku, Noriyuki; Garton, Fleur C; Hoppe, Nils; Holm, Søren; Kaye, Jane; Klissouras, Vassilis; Lucia, Alejandro; Maase, Kamiel; Moran, Colin; North, Kathryn N; Pigozzi, Fabio; Wang, Guan

2015-01-01

The general consensus among sport and exercise genetics researchers is that genetic tests have no role to play in talent identification or the individualised prescription of training to maximise performance. Despite the lack of evidence, recent years have witnessed the rise of an emerging market of direct-to-consumer marketing (DTC) tests that claim to be able to identify children's athletic talents. Targeted consumers include mainly coaches and parents. There is concern among the scientific community that the current level of knowledge is being misrepresented for commercial purposes. There remains a lack of universally accepted guidelines and legislation for DTC testing in relation to all forms of genetic testing and not just for talent identification. There is concern over the lack of clarity of information over which specific genes or variants are being tested and the almost universal lack of appropriate genetic counselling for the interpretation of the genetic data to consumers. Furthermore independent studies have identified issues relating to quality control by DTC laboratories with different results being reported from samples from the same individual. Consequently, in the current state of knowledge, no child or young athlete should be exposed to DTC genetic testing to define or alter training or for talent identification aimed at selecting gifted children or adolescents. Large scale collaborative projects, may help to develop a stronger scientific foundation on these issues in the future. PMID:26582191

Molecular diagnosis of rhino-orbito-cerebral mucormycosis from fresh tissue samples.

PubMed

Zaman, Kamran; Rudramurthy, Shivaprakash Mandya; Das, Ashim; Panda, Naresh; Honnavar, Prasanna; Kaur, Harsimran; Chakrabarti, Arunaloke

2017-08-01

We aimed to evaluate a PCR-based technique for the diagnosis of mucormycosis and the identification of fungi from fresh tissue specimens in patients with rhino-orbito-cerebral-mucormycosis (ROCM). Fifty cases of ROCM were included in the study. Conventional identification was performed using microscopy and culture. Molecular diagnosis was performed by amplifying the ribosomal DNA using pan-fungal ITS primers and semi-nested Mucorales-specific primers of the 18S region. The amplified products were sequenced to identify the agents. The utility of PCR-RFLP of the 18S region of rDNA was evaluated to identify the Mucorales. The ROCM cases were diagnosed by the demonstration of aseptate ribbon-like hyphae in biopsy specimens collected from the patients. Isolation was possible in 24 (48 %) samples. The ITS2 PCR confirmed mucormycosis in 27 cases (54 %; CI 59.4-68.2). By comparison, Mucorales-specific PCR was able to amplify DNA and the sequence enabled the identification of Mucorales speciesin all the patients. PCR-RFLP of the 18S region of rDNA could only identify the agent to genus level. The molecular technique was able to identify Mucorales species in 26 (42 %) cases that were negative by culture. Mucorales-specific semi-nested PCR targeting the 18S region is a better technique than ITS2 PCR for diagnosis. PCR-RFLP of the 18S region helps in identification to genus level.

Children's identification of faces from lineups: the effects of lineup presentation and instructions on accuracy.

PubMed

Beresford, Jayne; Blades, Mark

2006-09-01

The authors investigated whether the type of lineup and instructions given to children 6-7 or 9-10 years of age affected their identification accuracy. Children witnessed a man stealing property and were later asked to identify him in either photo or video lineups. Some lineups contained the target and some did not. Two lineup procedures were used (standard or elimination), and 2 types of instruction were used (standard or cautioning about false identification). Standard lineups with cautioning instructions decreased target-absent errors with no associated reduction in correct identifications, but elimination lineups did not. Lineup media had an interaction effect whereby correct identifications were reduced in video but not photo elimination lineups. The results are discussed in a forensic context. (c) 2006 APA, all rights reserved

Detection of target-probe oligonucleotide hybridization using synthetic nanopore resistive pulse sensing.

PubMed

Booth, Marsilea Adela; Vogel, Robert; Curran, James M; Harbison, SallyAnn; Travas-Sejdic, Jadranka

2013-07-15

Despite the plethora of DNA sensor platforms available, a portable, sensitive, selective and economic sensor able to rival current fluorescence-based techniques would find use in many applications. In this research, probe oligonucleotide-grafted particles are used to detect target DNA in solution through a resistive pulse nanopore detection technique. Using carbodiimide chemistry, functionalized probe DNA strands are attached to carboxylated dextran-based magnetic particles. Subsequent incubation with complementary target DNA yields a change in surface properties as the two DNA strands hybridize. Particle-by-particle analysis with resistive pulse sensing is performed to detect these changes. A variable pressure method allows identification of changes in the surface charge of particles. As proof-of-principle, we demonstrate that target hybridization is selectively detected at micromolar concentrations (nanomoles of target) using resistive pulse sensing, confirmed by fluorescence and phase analysis light scattering as complementary techniques. The advantages, feasibility and limitations of using resistive pulse sensing for sample analysis are discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

LC-MS screening techniques for wastewater analysis and analytical data handling strategies: Sartans and their transformation products as an example.

PubMed

Letzel, Thomas; Bayer, Anne; Schulz, Wolfgang; Heermann, Alexandra; Lucke, Thomas; Greco, Giorgia; Grosse, Sylvia; Schüssler, Walter; Sengl, Manfred; Letzel, Marion

2015-10-01

A large number of anthropogenic trace contaminants such as pharmaceuticals, their human metabolites and further transformation products (TPs) enter wastewater treatment plants on a daily basis. A mixture of known, expected, and unknown molecules are discharged into the receiving aquatic environment because only partial elimination occurs for many of these chemicals during physical, biological and chemical treatment processes. In this study, an array of LC-MS methods from three collaborating laboratories was applied to detect and identify anthropogenic trace contaminants and their TPs in different waters. Starting with theoretical predictions of TPs, an efficient workflow using the combination of target, suspected-target and non-target strategies for the identification of these TPs in the environment was developed. These techniques and strategies were applied to study anti-hypertensive drugs from the sartan group (i.e., candesartan, eprosartan, irbesartan, olmesartan, and valsartan). Degradation experiments were performed in lab-scale wastewater treatment plants, and a screening workflow including an inter-laboratory approach was used for the identification of transformation products in the effluent samples. Subsequently, newly identified compounds were successfully analyzed in effluents of real wastewater treatment plants and river waters. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identification of control targets in Boolean molecular network models via computational algebra.

PubMed

Murrugarra, David; Veliz-Cuba, Alan; Aguilar, Boris; Laubenbacher, Reinhard

2016-09-23

Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The potential control targets can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. This paper presents a method for the identification of potential intervention targets in Boolean molecular network models using algebraic techniques. The approach exploits an algebraic representation of Boolean networks to encode the control candidates in the network wiring diagram as the solutions of a system of polynomials equations, and then uses computational algebra techniques to find such controllers. The control methods in this paper are validated through the identification of combinatorial interventions in the signaling pathways of previously reported control targets in two well studied systems, a p53-mdm2 network and a blood T cell lymphocyte granular leukemia survival signaling network. Supplementary data is available online and our code in Macaulay2 and Matlab are available via http://www.ms.uky.edu/~dmu228/ControlAlg . This paper presents a novel method for the identification of intervention targets in Boolean network models. The results in this paper show that the proposed methods are useful and efficient for moderately large networks.

A distributed computational search strategy for the identification of diagnostics targets: application to finding aptamer targets for methicillin-resistant staphylococci.

PubMed

Flanagan, Keith; Cockell, Simon; Harwood, Colin; Hallinan, Jennifer; Nakjang, Sirintra; Lawry, Beth; Wipat, Anil

2014-06-30

The rapid and cost-effective identification of bacterial species is crucial, especially for clinical diagnosis and treatment. Peptide aptamers have been shown to be valuable for use as a component of novel, direct detection methods. These small peptides have a number of advantages over antibodies, including greater specificity and longer shelf life. These properties facilitate their use as the detector components of biosensor devices. However, the identification of suitable aptamer targets for particular groups of organisms is challenging. We present a semi-automated processing pipeline for the identification of candidate aptamer targets from whole bacterial genome sequences. The pipeline can be configured to search for protein sequence fragments that uniquely identify a set of strains of interest. The system is also capable of identifying additional organisms that may be of interest due to their possession of protein fragments in common with the initial set. Through the use of Cloud computing technology and distributed databases, our system is capable of scaling with the rapidly growing genome repositories, and consequently of keeping the resulting data sets up-to-date. The system described is also more generically applicable to the discovery of specific targets for other diagnostic approaches such as DNA probes, PCR primers and antibodies.

A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci.

PubMed

Flanagan, Keith; Cockell, Simon; Harwood, Colin; Hallinan, Jennifer; Nakjang, Sirintra; Lawry, Beth; Wipat, Anil

2014-06-01

The rapid and cost-effective identification of bacterial species is crucial, especially for clinical diagnosis and treatment. Peptide aptamers have been shown to be valuable for use as a component of novel, direct detection methods. These small peptides have a number of advantages over antibodies, including greater specificity and longer shelf life. These properties facilitate their use as the detector components of biosensor devices. However, the identification of suitable aptamer targets for particular groups of organisms is challenging. We present a semi-automated processing pipeline for the identification of candidate aptamer targets from whole bacterial genome sequences. The pipeline can be configured to search for protein sequence fragments that uniquely identify a set of strains of interest. The system is also capable of identifying additional organisms that may be of interest due to their possession of protein fragments in common with the initial set. Through the use of Cloud computing technology and distributed databases, our system is capable of scaling with the rapidly growing genome repositories, and consequently of keeping the resulting data sets up-to-date. The system described is also more generically applicable to the discovery of specific targets for other diagnostic approaches such as DNA probes, PCR primers and antibodies.

Learning-based adaptive prescribed performance control of postcapture space robot-target combination without inertia identifications

NASA Astrophysics Data System (ADS)

Wei, Caisheng; Luo, Jianjun; Dai, Honghua; Bian, Zilin; Yuan, Jianping

2018-05-01

In this paper, a novel learning-based adaptive attitude takeover control method is investigated for the postcapture space robot-target combination with guaranteed prescribed performance in the presence of unknown inertial properties and external disturbance. First, a new static prescribed performance controller is developed to guarantee that all the involved attitude tracking errors are uniformly ultimately bounded by quantitatively characterizing the transient and steady-state performance of the combination. Then, a learning-based supplementary adaptive strategy based on adaptive dynamic programming is introduced to improve the tracking performance of static controller in terms of robustness and adaptiveness only utilizing the input/output data of the combination. Compared with the existing works, the prominent advantage is that the unknown inertial properties are not required to identify in the development of learning-based adaptive control law, which dramatically decreases the complexity and difficulty of the relevant controller design. Moreover, the transient and steady-state performance is guaranteed a priori by designer-specialized performance functions without resorting to repeated regulations of the controller parameters. Finally, the three groups of illustrative examples are employed to verify the effectiveness of the proposed control method.

Improving the identification accuracy of senior witnesses: do prelineup questions and sequential testing help?

PubMed

Memon, Amina; Gabbert, Fiona

2003-04-01

Eyewitness research has identified sequential lineup testing as a way of reducing false lineup choices while maintaining accurate identifications. The authors examined the usefulness of this procedure for reducing false choices in older adults. Young and senior witnesses viewed a crime video and were later presented with target present orabsent lineups in a simultaneous or sequential format. In addition, some participants received prelineup questions about their memory for a perpetrator's face and about their confidence in their ability to identify the culprit or to correctly reject the lineup. The sequential lineup reduced false choosing rates among young and older adults in target-absent conditions. In target-present conditions, sequential testing significantly reduced the correct identification rate in both age groups.

Research on quantitative relationship between NIIRS and the probabilities of discrimination

NASA Astrophysics Data System (ADS)

Bai, Honggang

2011-08-01

There are a large number of electro-optical (EO) and infrared (IR) sensors used on military platforms including ground vehicle, low altitude air vehicle, high altitude air vehicle, and satellite systems. Ground vehicle and low-altitude air vehicle (rotary and fixed-wing aircraft) sensors typically use the probabilities of discrimination (detection, recognition, and identification) as design requirements and system performance indicators. High-altitude air vehicles and satellite sensors have traditionally used the National Imagery Interpretation Rating Scale (NIIRS) performance measures for guidance in design and measures of system performance. Recently, there has a large effort to make strategic sensor information available to tactical forces or make the information of targets acquisition can be used by strategic systems. In this paper, the two techniques about the probabilities of discrimination and NIIRS for sensor design are presented separately. For the typical infrared remote sensor design parameters, the function of the probability of recognition and NIIRS scale as the distance R is given to Standard NATO Target and M1Abrams two different size targets based on the algorithm of predicting the field performance and NIIRS. For Standard NATO Target, M1Abrams, F-15, and B-52 four different size targets, the conversion from NIIRS to the probabilities of discrimination are derived and calculated, and the similarities and differences between NIIRS and the probabilities of discrimination are analyzed based on the result of calculation. Comparisons with preliminary calculation results show that the conversion between NIIRS and the probabilities of discrimination is probable although more validation experiments are needed.

Sensor fusion approaches for EMI and GPR-based subsurface threat identification

NASA Astrophysics Data System (ADS)

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

2011-06-01

Despite advances in both electromagnetic induction (EMI) and ground penetrating radar (GPR) sensing and related signal processing, neither sensor alone provides a perfect tool for detecting the myriad of possible buried objects that threaten the lives of Soldiers and civilians. However, while neither GPR nor EMI sensing alone can provide optimal detection across all target types, the two approaches are highly complementary. As a result, many landmine systems seek to make use of both sensing modalities simultaneously and fuse the results from both sensors to improve detection performance for targets with widely varying metal content and GPR responses. Despite this, little work has focused on large-scale comparisons of different approaches to sensor fusion and machine learning for combining data from these highly orthogonal phenomenologies. In this work we explore a wide array of pattern recognition techniques for algorithm development and sensor fusion. Results with the ARA Nemesis landmine detection system suggest that nonlinear and non-parametric classification algorithms provide significant performance benefits for single-sensor algorithm development, and that fusion of multiple algorithms can be performed satisfactorily using basic parametric approaches, such as logistic discriminant classification, for the targets under consideration in our data sets.

Small craft identification discrimination criteria N 50 and V 50 for visible and infrared sensors in maritime security

NASA Astrophysics Data System (ADS)

Krapels, Keith; Deaver, Dawne; Driggers, Ronald

2006-09-01

The new emphasis on Anti-Terrorism and Force Protection (AT/FP), for both shore and sea platform protection, has resulted in a need for infrared imager design and evaluation tools which demonstrate field performance against U.S. Navy AT/FP requirements. In the design of infrared imaging systems for target acquisition, a discrimination criterion is required for successful sensor realization. It characterizes the difficulty of the task being performed by the observer and varies for different target sets. This criterion is used in both assessment of existing infrared sensor and in the design of new conceptual sensors. In this experiment, we collected 12 small craft signatures (military and civilian) in the visible band during the day and the LWIR and MWIR spectra in both the day and the night environments. These signatures were processed to determine the targets' characteristic dimension and contrast. They were also processed to bandlimit the signature's spatial information content (simulating longer range) and a perception experiment was performed to determine the task difficulty (N 50 and V 50). The results are presented in this paper and can be used for Navy and Coast Guard imaging infrared sensor design and evaluation.

Identification of the Downstream Promoter Targets of Smad Tumor Suppressors in Human Breast Cancer Cells

DTIC Science & Technology

2004-10-01

signaling mediator Smad2, Smad3 and Smad4 which form oligomeric complexes and migrate into nucleus to function as transcription factors to modulate... Smad3 and Smad4. 2. Identification of the downstream promoter targets of Smad3 or Smad4 in breast cancer cells. 3. Identify Smad4 regulated downstream...Development of a novel chromatin immunoprecipitation assay (CHIPS) using a TAP-TAG system to isolate in vivo binding targets of Smad3 and Smad4

High-throughput identification of off-targets for the mechanistic study of severe adverse drug reactions induced by analgesics

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

Pan, Jian-Bo; Ji, Nan; Pan, Wen

2014-01-01

Drugs may induce adverse drug reactions (ADRs) when they unexpectedly bind to proteins other than their therapeutic targets. Identification of these undesired protein binding partners, called off-targets, can facilitate toxicity assessment in the early stages of drug development. In this study, a computational framework was introduced for the exploration of idiosyncratic mechanisms underlying analgesic-induced severe adverse drug reactions (SADRs). The putative analgesic-target interactions were predicted by performing reverse docking of analgesics or their active metabolites against human/mammal protein structures in a high-throughput manner. Subsequently, bioinformatics analyses were undertaken to identify ADR-associated proteins (ADRAPs) and pathways. Using the pathways and ADRAPsmore » that this analysis identified, the mechanisms of SADRs such as cardiac disorders were explored. For instance, 53 putative ADRAPs and 24 pathways were linked with cardiac disorders, of which 10 ADRAPs were confirmed by previous experiments. Moreover, it was inferred that pathways such as base excision repair, glycolysis/glyconeogenesis, ErbB signaling, calcium signaling, and phosphatidyl inositol signaling likely play pivotal roles in drug-induced cardiac disorders. In conclusion, our framework offers an opportunity to globally understand SADRs at the molecular level, which has been difficult to realize through experiments. It also provides some valuable clues for drug repurposing. - Highlights: • A novel computational framework was developed for mechanistic study of SADRs. • Off-targets of drugs were identified in large scale and in a high-throughput manner. • SADRs like cardiac disorders were systematically explored in molecular networks. • A number of ADR-associated proteins were identified.« less

FLASH LIDAR Based Relative Navigation

NASA Technical Reports Server (NTRS)

Brazzel, Jack; Clark, Fred; Milenkovic, Zoran

2014-01-01

Relative navigation remains the most challenging part of spacecraft rendezvous and docking. In recent years, flash LIDARs, have been increasingly selected as the go-to sensors for proximity operations and docking. Flash LIDARS are generally lighter and require less power that scanning Lidars. Flash LIDARs do not have moving parts, and they are capable of tracking multiple targets as well as generating a 3D map of a given target. However, there are some significant drawbacks of Flash Lidars that must be resolved if their use is to be of long-term significance. Overcoming the challenges of Flash LIDARs for navigation-namely, low technology readiness level, lack of historical performance data, target identification, existence of false positives, and performance of vision processing algorithms as intermediaries between the raw sensor data and the Kalman filter-requires a world-class testing facility, such as the Lockheed Martin Space Operations Simulation Center (SOSC). Ground-based testing is a critical step for maturing the next-generation flash LIDAR-based spacecraft relative navigation. This paper will focus on the tests of an integrated relative navigation system conducted at the SOSC in January 2014. The intent of the tests was to characterize and then improve the performance of relative navigation, while addressing many of the flash LIDAR challenges mentioned above. A section on navigation performance and future recommendation completes the discussion.

A strategy for comprehensive identification of sequential constituents using ultra-high-performance liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometer, application study on chlorogenic acids in Flos Lonicerae Japonicae.

PubMed

Zhang, Jia-yu; Wang, Zi-jian; Li, Yun; Liu, Ying; Cai, Wei; Li, Chen; Lu, Jian-qiu; Qiao, Yan-jiang

2016-01-15

The analytical methodologies for evaluation of multi-component system in traditional Chinese medicines (TCMs) have been inadequate or unacceptable. As a result, the unclarity of multi-component hinders the sufficient interpretation of their bioactivities. In this paper, an ultra-high-performance liquid chromatography coupled with linear ion trap-Orbitrap (UPLC-LTQ-Orbitrap)-based strategy focused on the comprehensive identification of TCM sequential constituents was developed. The strategy was characterized by molecular design, multiple ion monitoring (MIM), targeted database hits and mass spectral trees similarity filter (MTSF), and even more isomerism discrimination. It was successfully applied in the HRMS data-acquisition and processing of chlorogenic acids (CGAs) in Flos Lonicerae Japonicae (FLJ), and a total of 115 chromatographic peaks attributed to 18 categories were characterized, allowing a comprehensive revelation of CGAs in FLJ for the first time. This demonstrated that MIM based on molecular design could improve the efficiency to trigger MS/MS fragmentation reactions. Targeted database hits and MTSF searching greatly facilitated the processing of extremely large information data. Besides, the introduction of diagnostic product ions (DPIs) discrimination, ClogP analysis, and molecular simulation, raised the efficiency and accuracy to characterize sequential constituents especially position and geometric isomers. In conclusion, the results expanded our understanding on CGAs in FLJ, and the strategy could be exemplary for future research on the comprehensive identification of sequential constituents in TCMs. Meanwhile, it may propose a novel idea for analyzing sequential constituents, and is promising for quality control and evaluation of TCMs. Copyright © 2015 Elsevier B.V. All rights reserved.

The druggable genome and support for target identification and validation in drug development.

PubMed

Finan, Chris; Gaulton, Anna; Kruger, Felix A; Lumbers, R Thomas; Shah, Tina; Engmann, Jorgen; Galver, Luana; Kelley, Ryan; Karlsson, Anneli; Santos, Rita; Overington, John P; Hingorani, Aroon D; Casas, Juan P

2017-03-29

Target identification (determining the correct drug targets for a disease) and target validation (demonstrating an effect of target perturbation on disease biomarkers and disease end points) are important steps in drug development. Clinically relevant associations of variants in genes encoding drug targets model the effect of modifying the same targets pharmacologically. To delineate drug development (including repurposing) opportunities arising from this paradigm, we connected complex disease- and biomarker-associated loci from genome-wide association studies to an updated set of genes encoding druggable human proteins, to agents with bioactivity against these targets, and, where there were licensed drugs, to clinical indications. We used this set of genes to inform the design of a new genotyping array, which will enable association studies of druggable genes for drug target selection and validation in human disease. Copyright © 2017, American Association for the Advancement of Science.

Novel drug target identification for the treatment of dementia using multi-relational association mining.

PubMed

Nguyen, Thanh-Phuong; Priami, Corrado; Caberlotto, Laura

2015-07-08

Dementia is a neurodegenerative condition of the brain in which there is a progressive and permanent loss of cognitive and mental performance. Despite the fact that the number of people with dementia worldwide is steadily increasing and regardless of the advances in the molecular characterization of the disease, current medical treatments for dementia are purely symptomatic and hardly effective. We present a novel multi-relational association mining method that integrates the huge amount of scientific data accumulated in recent years to predict potential novel targets for innovative therapeutic treatment of dementia. Owing to the ability of processing large volumes of heterogeneous data, our method achieves a high performance and predicts numerous drug targets including several serine threonine kinase and a G-protein coupled receptor. The predicted drug targets are mainly functionally related to metabolism, cell surface receptor signaling pathways, immune response, apoptosis, and long-term memory. Among the highly represented kinase family and among the G-protein coupled receptors, DLG4 (PSD-95), and the bradikynin receptor 2 are highlighted also for their proposed role in memory and cognition, as described in previous studies. These novel putative targets hold promises for the development of novel therapeutic approaches for the treatment of dementia.

Novel drug target identification for the treatment of dementia using multi-relational association mining

PubMed Central

Nguyen, Thanh-Phuong; Priami, Corrado; Caberlotto, Laura

2015-01-01

Dementia is a neurodegenerative condition of the brain in which there is a progressive and permanent loss of cognitive and mental performance. Despite the fact that the number of people with dementia worldwide is steadily increasing and regardless of the advances in the molecular characterization of the disease, current medical treatments for dementia are purely symptomatic and hardly effective. We present a novel multi-relational association mining method that integrates the huge amount of scientific data accumulated in recent years to predict potential novel targets for innovative therapeutic treatment of dementia. Owing to the ability of processing large volumes of heterogeneous data, our method achieves a high performance and predicts numerous drug targets including several serine threonine kinase and a G-protein coupled receptor. The predicted drug targets are mainly functionally related to metabolism, cell surface receptor signaling pathways, immune response, apoptosis, and long-term memory. Among the highly represented kinase family and among the G-protein coupled receptors, DLG4 (PSD-95), and the bradikynin receptor 2 are highlighted also for their proposed role in memory and cognition, as described in previous studies. These novel putative targets hold promises for the development of novel therapeutic approaches for the treatment of dementia. PMID:26154857

Keeping It in Three Dimensions: Measuring the Development of Mental Rotation in Children with the Rotated Colour Cube Test (RCCT).

PubMed

Lütke, Nikolay; Lange-Küttner, Christiane

2015-08-03

This study introduces the new Rotated Colour Cube Test (RCCT) as a measure of object identification and mental rotation using single 3D colour cube images in a matching-to-sample procedure. One hundred 7- to 11-year-old children were tested with aligned or rotated cube models, distracters and targets. While different orientations of distracters made the RCCT more difficult, different colours of distracters had the opposite effect and made the RCCT easier because colour facilitated clearer discrimination between target and distracters. Ten-year-olds performed significantly better than 7- to 8-year-olds. The RCCT significantly correlated with children's performance on the Raven's Coloured Progressive Matrices Test (RCPM) presumably due to the shared multiple-choice format, but the RCCT was easier, as it did not require sequencing. Children from families with a high socio-economic status performed best on both tests, with boys outperforming girls on the more difficult RCCT test sections.

Neural networks: Alternatives to conventional techniques for automatic docking

NASA Technical Reports Server (NTRS)

Vinz, Bradley L.

1994-01-01

Automatic docking of orbiting spacecraft is a crucial operation involving the identification of vehicle orientation as well as complex approach dynamics. The chaser spacecraft must be able to recognize the target spacecraft within a scene and achieve accurate closing maneuvers. In a video-based system, a target scene must be captured and transformed into a pattern of pixels. Successful recognition lies in the interpretation of this pattern. Due to their powerful pattern recognition capabilities, artificial neural networks offer a potential role in interpretation and automatic docking processes. Neural networks can reduce the computational time required by existing image processing and control software. In addition, neural networks are capable of recognizing and adapting to changes in their dynamic environment, enabling enhanced performance, redundancy, and fault tolerance. Most neural networks are robust to failure, capable of continued operation with a slight degradation in performance after minor failures. This paper discusses the particular automatic docking tasks neural networks can perform as viable alternatives to conventional techniques.

Development of a Photo-Cross-Linkable Diaminoquinazoline Inhibitor for Target Identification in Plasmodium falciparum.

PubMed

Lubin, Alexandra S; Rueda-Zubiaurre, Ainoa; Matthews, Holly; Baumann, Hella; Fisher, Fabio R; Morales-Sanfrutos, Julia; Hadavizadeh, Kate S; Nardella, Flore; Tate, Edward W; Baum, Jake; Scherf, Artur; Fuchter, Matthew J

2018-04-13

Diaminoquinazolines represent a privileged scaffold for antimalarial discovery, including use as putative Plasmodium histone lysine methyltransferase inhibitors. Despite this, robust evidence for their molecular targets is lacking. Here we report the design and development of a small-molecule photo-cross-linkable probe to investigate the targets of our diaminoquinazoline series. We demonstrate the effectiveness of our designed probe for photoaffinity labeling of Plasmodium lysates and identify similarities between the target profiles of the probe and the representative diaminoquinazoline BIX-01294. Initial pull-down proteomics experiments identified 104 proteins from different classes, many of which are essential, highlighting the suitability of the developed probe as a valuable tool for target identification in Plasmodium falciparum.

PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach

PubMed Central

Liu, Xiaofeng; Ouyang, Sisheng; Yu, Biao; Liu, Yabo; Huang, Kai; Gong, Jiayu; Zheng, Siyuan; Li, Zhihua; Li, Honglin; Jiang, Hualiang

2010-01-01

In silico drug target identification, which includes many distinct algorithms for finding disease genes and proteins, is the first step in the drug discovery pipeline. When the 3D structures of the targets are available, the problem of target identification is usually converted to finding the best interaction mode between the potential target candidates and small molecule probes. Pharmacophore, which is the spatial arrangement of features essential for a molecule to interact with a specific target receptor, is an alternative method for achieving this goal apart from molecular docking method. PharmMapper server is a freely accessed web server designed to identify potential target candidates for the given small molecules (drugs, natural products or other newly discovered compounds with unidentified binding targets) using pharmacophore mapping approach. PharmMapper hosts a large, in-house repertoire of pharmacophore database (namely PharmTargetDB) annotated from all the targets information in TargetBank, BindingDB, DrugBank and potential drug target database, including over 7000 receptor-based pharmacophore models (covering over 1500 drug targets information). PharmMapper automatically finds the best mapping poses of the query molecule against all the pharmacophore models in PharmTargetDB and lists the top N best-fitted hits with appropriate target annotations, as well as respective molecule’s aligned poses are presented. Benefited from the highly efficient and robust triangle hashing mapping method, PharmMapper bears high throughput ability and only costs 1 h averagely to screen the whole PharmTargetDB. The protocol was successful in finding the proper targets among the top 300 pharmacophore candidates in the retrospective benchmarking test of tamoxifen. PharmMapper is available at http://59.78.96.61/pharmmapper. PMID:20430828

Serial position effects in the identification of letters, digits, and symbols.

PubMed

Tydgat, Ilse; Grainger, Jonathan

2009-04-01

In 6 experiments, the authors investigated the form of serial position functions for identification of letters, digits, and symbols presented in strings. The results replicated findings obtained with the target search paradigm, showing an interaction between the effects of serial position and type of stimulus, with symbols generating a distinct serial position function compared with letters and digits. When the task was 2-alternative forced choice, this interaction was driven almost exclusively by performance at the first position in the string, with letters and digits showing much higher levels of accuracy than symbols at this position. A final-position advantage was reinstated in Experiment 6 by placing the two alternative responses below the target string. The end-position (first and last positions) advantage for letters and digits compared with symbol stimuli was further confirmed with the bar-probe technique (postcued partial report) in Experiments 5 and 6. Overall, the results further support the existence of a specialized mechanism designed to optimize processing of strings of letters and digits by modifying the size and shape of retinotopic character detectors' receptive fields. (c) 2009 APA, all rights reserved.

Comprehensive analytical strategy for biomonitoring of pesticides in urine by liquid chromatography–orbitrap high resolution masss pectrometry.

PubMed

Roca, M; Leon, N; Pastor, A; Yusà, V

2014-12-29

In this study we propose an analytical strategy that combines a target approach for the quantitative analysis of contemporary pesticide metabolites with a comprehensive post-target screening for the identification of biomarkers of exposure to environmental contaminants in urine using liquid chromatography coupled to high-resolution mass spectrometry (LC–HRMS). The quantitative method for the target analysis of 29 urinary metabolites of organophosphate (OP) insecticides, synthetic pyrethroids, herbicides and fungicides was validated after a previous statistical optimization of the main factors governing the ion source ionization and a fragmentation study using the high energy collision dissociation (HCD) cell. The full scan accurate mass data were acquired with a resolving power of 50,000 FWHM (scan speed, 2 Hz), in both ESI+ and ESI− modes, and with and without HCD-fragmentation. The method – LOQ was lower than 3.2 μg L−1 for the majority of the analytes. For post-target screening a customized theoretical database was built, for the identification of 60 metabolites including pesticides, PAHs, phenols, and other metabolites of environmental pollutants. For identification purposes, accurate exact mass with less than 5 ppm, and diagnostic ions including isotopes and/or fragments were used. The analytical strategy was applied to 20 urine sample collected from children living in Valencia Region. Eleven target metabolites were detected with concentrations ranging from 1.18 to 131 μg L−1. Likewise, several compounds were tentatively identified in the post-target analysis belonging to the families of phthalates, phenols and parabenes. The proposed strategy is suitable for the determination of target pesticide biomarkers in urine in the framework of biomonitoring studies, and appropriate for the identification of other non-target metabolites.

What good is SWIR? Passive day comparison of VIS, NIR, and SWIR

NASA Astrophysics Data System (ADS)

Driggers, Ronald G.; Hodgkin, Van; Vollmerhausen, Richard

2013-06-01

This paper is the first of three papers associated with the military benefits of SWIR imaging. This paper describes the benefits associated with passive daytime operations with comparisons of SWIR, NIR, and VIS bands and sensors. This paper includes quantitative findings from previously published papers, analysis of open source data, summaries of various expert analyses, and calculations of notional system performance. We did not accept anecdotal findings as acceptable benefits. Topics include haze and fog penetration, atmospheric transmission, cloud and smoke penetration, target and background contrasts, spectral discrimination, turbulence degradation, and long range target identification. The second and third papers will address passive night imaging and active night imaging.

Integrated IR sensors

NASA Astrophysics Data System (ADS)

Tom, Michael; Trujillo, Edward

1994-06-01

Integrated infrared (IR) sensors which exploit modular avionics concepts can provide features such as operational flexibility, enhanced stealthiness, and ease of maintenance to meet the demands of tactical, airborne sensor systems. On-board, tactical airborne sensor systems perform target acquisition, tracking, identification, threat warning, missile launch detection, and ground mapping in support of situation awareness, self-defense, navigation, target attack, weapon support, and reconnaissance activities. The use of sensor suites for future tactical aircraft such as US Air Force's multirole fighter require a blend of sensor inputs and outputs that may vary over time. It is expected that special-role units of these tactical aircraft will be formed to conduct tasks and missions such as anti-shipping, reconnaissance, or suppression of enemy air defenses.

An Automated Method for Navigation Assessment for Earth Survey Sensors Using Island Targets

NASA Technical Reports Server (NTRS)

Patt, F. S.; Woodward, R. H.; Gregg, W. W.

1997-01-01

An automated method has been developed for performing navigation assessment on satellite-based Earth sensor data. The method utilizes islands as targets which can be readily located in the sensor data and identified with reference locations. The essential elements are an algorithm for classifying the sensor data according to source, a reference catalogue of island locations, and a robust pattern-matching algorithm for island identification. The algorithms were developed and tested for the Sea-viewing Wide Field-of-view Sensor (SeaWiFS), an ocean colour sensor. This method will allow navigation error statistics to be automatically generated for large numbers of points, supporting analysis over large spatial and temporal ranges.

Automated navigation assessment for earth survey sensors using island targets

NASA Technical Reports Server (NTRS)

Patt, Frederick S.; Woodward, Robert H.; Gregg, Watson W.

1997-01-01

An automated method has been developed for performing navigation assessment on satellite-based Earth sensor data. The method utilizes islands as targets which can be readily located in the sensor data and identified with reference locations. The essential elements are an algorithm for classifying the sensor data according to source, a reference catalog of island locations, and a robust pattern-matching algorithm for island identification. The algorithms were developed and tested for the Sea-viewing Wide Field-of-view Sensor (SeaWiFS), an ocean color sensor. This method will allow navigation error statistics to be automatically generated for large numbers of points, supporting analysis over large spatial and temporal ranges.

Target acquisition modeling over the exact optical path: extending the EOSTAR TDA with the TOD sensor performance model

NASA Astrophysics Data System (ADS)

Dijk, J.; Bijl, P.; Oppeneer, M.; ten Hove, R. J. M.; van Iersel, M.

2017-10-01

The Electro-Optical Signal Transmission and Ranging (EOSTAR) model is an image-based Tactical Decision Aid (TDA) for thermal imaging systems (MWIR/LWIR) developed for a sea environment with an extensive atmosphere model. The Triangle Orientation Discrimination (TOD) Target Acquisition model calculates the sensor and signal processing effects on a set of input triangle test pattern images, judges their orientation using humans or a Human Visual System (HVS) model and derives the system image quality and operational field performance from the correctness of the responses. Combination of the TOD model and EOSTAR, basically provides the possibility to model Target Acquisition (TA) performance over the exact path from scene to observer. In this method ship representative TOD test patterns are placed at the position of the real target, subsequently the combined effects of the environment (atmosphere, background, etc.), sensor and signal processing on the image are calculated using EOSTAR and finally the results are judged by humans. The thresholds are converted into Detection-Recognition-Identification (DRI) ranges of the real target. In experiments is shown that combination of the TOD model and the EOSTAR model is indeed possible. The resulting images look natural and provide insight in the possibilities of combining the two models. The TOD observation task can be done well by humans, and the measured TOD is consistent with analytical TOD predictions for the same camera that was modeled in the ECOMOS project.

Target specific compound identification using a support vector machine.

PubMed

Plewczynski, Dariusz; von Grotthuss, Marcin; Spieser, Stephane A H; Rychlewski, Leszek; Wyrwicz, Lucjan S; Ginalski, Krzysztof; Koch, Uwe

2007-03-01

In many cases at the beginning of an HTS-campaign, some information about active molecules is already available. Often known active compounds (such as substrate analogues, natural products, inhibitors of a related protein or ligands published by a pharmaceutical company) are identified in low-throughput validation studies of the biochemical target. In this study we evaluate the effectiveness of a support vector machine applied for those compounds and used to classify a collection with unknown activity. This approach was aimed at reducing the number of compounds to be tested against the given target. Our method predicts the biological activity of chemical compounds based on only the atom pairs (AP) two dimensional topological descriptors. The supervised support vector machine (SVM) method herein is trained on compounds from the MDL drug data report (MDDR) known to be active for specific protein target. For detailed analysis, five different biological targets were selected including cyclooxygenase-2, dihydrofolate reductase, thrombin, HIV-reverse transcriptase and antagonists of the estrogen receptor. The accuracy of compound identification was estimated using the recall and precision values. The sensitivities for all protein targets exceeded 80% and the classification performance reached 100% for selected targets. In another application of the method, we addressed the absence of an initial set of active compounds for a selected protein target at the beginning of an HTS-campaign. In such a case, virtual high-throughput screening (vHTS) is usually applied by using a flexible docking procedure. However, the vHTS experiment typically contains a large percentage of false positives that should be verified by costly and time-consuming experimental follow-up assays. The subsequent use of our machine learning method was found to improve the speed (since the docking procedure was not required for all compounds from the database) and also the accuracy of the HTS hit lists (the enrichment factor).

The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets

PubMed Central

Hassan, Syed S.; Jamal, Syed B.; Radusky, Leandro G.; Tiwari, Sandeep; Ullah, Asad; Ali, Javed; Behramand; de Carvalho, Paulo V. S. D.; Shams, Rida; Khan, Sabir; Figueiredo, Henrique C. P.; Barh, Debmalya; Ghosh, Preetam; Silva, Artur; Baumbach, Jan; Röttger, Richard; Turjanski, Adrián G.; Azevedo, Vasco A. C.

2018-01-01

Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the “pocketome druggability.” To this end, we first computed the “modelome” (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (∼9%) structure models. The amino acid sequences of these modeled structures were compared with the remaining 12 genomes and consequently, 438 conserved protein sequences were obtained. The RCSB-PDB database was consulted to check the template structures for these conserved proteins and as a result, 401 adequate 3D models were obtained. We subsequently predicted the protein pockets for the obtained set of models and kept only the conserved pockets that had highly druggable (HD) values (137 across all strains). Later, an off-target host homology analyses was performed considering the human proteome using NCBI database. Furthermore, the gene essentiality analysis was carried out that gave a final set of 10-conserved targets possessing highly druggable protein pockets. To check the target identification robustness of the pipeline used in this work, we crosschecked the final target list with another in-house target identification approach for C. diphtheriae thereby obtaining three common targets, these were; hisE-phosphoribosyl-ATP pyrophosphatase, glpX-fructose 1,6-bisphosphatase II, and rpsH-30S ribosomal protein S8. Our predicted results suggest that the in silico approach used could potentially aid in experimental polypharmacological target determination in C. diphtheriae and other pathogens, thereby, might complement the existing and new drug-discovery pipelines. PMID:29487617

Application of multi-target phytotherapeutic concept in malaria drug discovery: a systems biology approach in biomarker identification.

PubMed

Tarkang, Protus Arrey; Appiah-Opong, Regina; Ofori, Michael F; Ayong, Lawrence S; Nyarko, Alexander K

2016-01-01

There is an urgent need for new anti-malaria drugs with broad therapeutic potential and novel mode of action, for effective treatment and to overcome emerging drug resistance. Plant-derived anti-malarials remain a significant source of bioactive molecules in this regard. The multicomponent formulation forms the basis of phytotherapy. Mechanistic reasons for the poly-pharmacological effects of plants constitute increased bioavailability, interference with cellular transport processes, activation of pro-drugs/deactivation of active compounds to inactive metabolites and action of synergistic partners at different points of the same signaling cascade. These effects are known as the multi-target concept. However, due to the intrinsic complexity of natural products-based drug discovery, there is need to rethink the approaches toward understanding their therapeutic effect. This review discusses the multi-target phytotherapeutic concept and its application in biomarker identification using the modified reverse pharmacology - systems biology approach. Considerations include the generation of a product library, high throughput screening (HTS) techniques for efficacy and interaction assessment, High Performance Liquid Chromatography (HPLC)-based anti-malarial profiling and animal pharmacology. This approach is an integrated interdisciplinary implementation of tailored technology platforms coupled to miniaturized biological assays, to track and characterize the multi-target bioactive components of botanicals as well as identify potential biomarkers. While preserving biodiversity, this will serve as a primary step towards the development of standardized phytomedicines, as well as facilitate lead discovery for chemical prioritization and downstream clinical development.

Comprehensive benchmarking of SNV callers for highly admixed tumor data

PubMed Central

Bohnert, Regina; Vivas, Sonia

2017-01-01

Precision medicine attempts to individualize cancer therapy by matching tumor-specific genetic changes with effective targeted therapies. A crucial first step in this process is the reliable identification of cancer-relevant variants, which is considerably complicated by the impurity and heterogeneity of clinical tumor samples. We compared the impact of admixture of non-cancerous cells and low somatic allele frequencies on the sensitivity and precision of 19 state-of-the-art SNV callers. We studied both whole exome and targeted gene panel data and up to 13 distinct parameter configurations for each tool. We found vast differences among callers. Based on our comprehensive analyses we recommend joint tumor-normal calling with MuTect, EBCall or Strelka for whole exome somatic variant calling, and HaplotypeCaller or FreeBayes for whole exome germline calling. For targeted gene panel data on a single tumor sample, LoFreqStar performed best. We further found that tumor impurity and admixture had a negative impact on precision, and in particular, sensitivity in whole exome experiments. At admixture levels of 60% to 90% sometimes seen in pathological biopsies, sensitivity dropped significantly, even when variants were originally present in the tumor at 100% allele frequency. Sensitivity to low-frequency SNVs improved with targeted panel data, but whole exome data allowed more efficient identification of germline variants. Effective somatic variant calling requires high-quality pathological samples with minimal admixture, a consciously selected sequencing strategy, and the appropriate variant calling tool with settings optimized for the chosen type of data. PMID:29020110

Independent priming of location and color in identification of briefly presented letters.

PubMed

Ásgeirsson, Árni Gunnar; Kristjánsson, Árni; Bundesen, Claus

2014-01-01

Attention shifts are facilitated if the items to be attended remain the same across trials. Some researchers argue that this priming effect is perceptual, whereas others propose that priming is postperceptual, involving facilitated response selection. The experimental findings have not been consistent regarding the roles of variables such as task difficulty, response repetition, expectancies, and decision-making. Position priming, when repetition of a target position facilitates responses on a subsequent trial, is another source of disagreement among researchers. Experimental results have likewise been inconsistent as to whether position priming is dependent on the repetition of target features or has an independent effect on attention shifts. We attempted to isolate the perceptual components of priming by presenting brief (10-180 ms) search arrays to eight healthy observers. The task was to identify a color-singleton letter among distractors. All stimulus presentation contingencies were randomized, and responses were unspeeded, to avoid effects of observer expectation and postperceptual effects. Repeating target color and/or position strongly improved performance. The effects of color and position repetition were independent of one another and were stable across participants. The results argue for a strong perceptual component in priming, which biases selection toward recent target features and positions, showing that perceptual mechanisms are sufficient to produce priming in visual search and that such effects can be elicited with limited sensory evidence. The results are the first to demonstrate independent priming of color and position in the identification of briefly presented, postmasked stimuli.

Third-generation intelligent IR focal plane arrays

NASA Astrophysics Data System (ADS)

Caulfield, H. John; Jack, Michael D.; Pettijohn, Kevin L.; Schlesselmann, John D.; Norworth, Joe

1998-03-01

SBRC is at the forefront of industry in developing IR focal plane arrays including multi-spectral technology and '3rd generation' functions that mimic the human eye. 3rd generation devices conduct advanced processing on or near the FPA that serve to reduce bandwidth while performing needed functions such as automatic target recognition, uniformity correction and dynamic range enhancement. These devices represent a solution for processing the exorbitantly high bandwidth coming off large area FPAs without sacrificing systems sensitivity. SBRC's two-color approach leverages the company's HgCdTe technology to provide simultaneous multiband coverage, from short through long wave IR, with near theoretical performance. IR systems that are sensitive to different spectral bands achieve enhanced capabilities for target identification and advanced discrimination. This paper will provide a summary of the issues, the technology and the benefits of SBRC's third generation smart and two-color FPAs.

Towards Autonomous Modular UAV Missions: The Detection, Geo-Location and Landing Paradigm

PubMed Central

Kyristsis, Sarantis; Antonopoulos, Angelos; Chanialakis, Theofilos; Stefanakis, Emmanouel; Linardos, Christos; Tripolitsiotis, Achilles; Partsinevelos, Panagiotis

2016-01-01

Nowadays, various unmanned aerial vehicle (UAV) applications become increasingly demanding since they require real-time, autonomous and intelligent functions. Towards this end, in the present study, a fully autonomous UAV scenario is implemented, including the tasks of area scanning, target recognition, geo-location, monitoring, following and finally landing on a high speed moving platform. The underlying methodology includes AprilTag target identification through Graphics Processing Unit (GPU) parallelized processing, image processing and several optimized locations and approach algorithms employing gimbal movement, Global Navigation Satellite System (GNSS) readings and UAV navigation. For the experimentation, a commercial and a custom made quad-copter prototype were used, portraying a high and a low-computational embedded platform alternative. Among the successful targeting and follow procedures, it is shown that the landing approach can be successfully performed even under high platform speeds. PMID:27827883

Towards Autonomous Modular UAV Missions: The Detection, Geo-Location and Landing Paradigm.

PubMed

Kyristsis, Sarantis; Antonopoulos, Angelos; Chanialakis, Theofilos; Stefanakis, Emmanouel; Linardos, Christos; Tripolitsiotis, Achilles; Partsinevelos, Panagiotis

2016-11-03

Nowadays, various unmanned aerial vehicle (UAV) applications become increasingly demanding since they require real-time, autonomous and intelligent functions. Towards this end, in the present study, a fully autonomous UAV scenario is implemented, including the tasks of area scanning, target recognition, geo-location, monitoring, following and finally landing on a high speed moving platform. The underlying methodology includes AprilTag target identification through Graphics Processing Unit (GPU) parallelized processing, image processing and several optimized locations and approach algorithms employing gimbal movement, Global Navigation Satellite System (GNSS) readings and UAV navigation. For the experimentation, a commercial and a custom made quad-copter prototype were used, portraying a high and a low-computational embedded platform alternative. Among the successful targeting and follow procedures, it is shown that the landing approach can be successfully performed even under high platform speeds.

Study of environmental sound source identification based on hidden Markov model for robust speech recognition

NASA Astrophysics Data System (ADS)

Nishiura, Takanobu; Nakamura, Satoshi

2003-10-01

Humans communicate with each other through speech by focusing on the target speech among environmental sounds in real acoustic environments. We can easily identify the target sound from other environmental sounds. For hands-free speech recognition, the identification of the target speech from environmental sounds is imperative. This mechanism may also be important for a self-moving robot to sense the acoustic environments and communicate with humans. Therefore, this paper first proposes hidden Markov model (HMM)-based environmental sound source identification. Environmental sounds are modeled by three states of HMMs and evaluated using 92 kinds of environmental sounds. The identification accuracy was 95.4%. This paper also proposes a new HMM composition method that composes speech HMMs and an HMM of categorized environmental sounds for robust environmental sound-added speech recognition. As a result of the evaluation experiments, we confirmed that the proposed HMM composition outperforms the conventional HMM composition with speech HMMs and a noise (environmental sound) HMM trained using noise periods prior to the target speech in a captured signal. [Work supported by Ministry of Public Management, Home Affairs, Posts and Telecommunications of Japan.

Camouflage, detection and identification of moving targets

PubMed Central

Hall, Joanna R.; Cuthill, Innes C.; Baddeley, Roland; Shohet, Adam J.; Scott-Samuel, Nicholas E.

2013-01-01

Nearly all research on camouflage has investigated its effectiveness for concealing stationary objects. However, animals have to move, and patterns that only work when the subject is static will heavily constrain behaviour. We investigated the effects of different camouflages on the three stages of predation—detection, identification and capture—in a computer-based task with humans. An initial experiment tested seven camouflage strategies on static stimuli. In line with previous literature, background-matching and disruptive patterns were found to be most successful. Experiment 2 showed that if stimuli move, an isolated moving object on a stationary background cannot avoid detection or capture regardless of the type of camouflage. Experiment 3 used an identification task and showed that while camouflage is unable to slow detection or capture, camouflaged targets are harder to identify than uncamouflaged targets when similar background objects are present. The specific details of the camouflage patterns have little impact on this effect. If one has to move, camouflage cannot impede detection; but if one is surrounded by similar targets (e.g. other animals in a herd, or moving background distractors), then camouflage can slow identification. Despite previous assumptions, motion does not entirely ‘break’ camouflage. PMID:23486439

Camouflage, detection and identification of moving targets.

PubMed

Hall, Joanna R; Cuthill, Innes C; Baddeley, Roland; Shohet, Adam J; Scott-Samuel, Nicholas E

2013-05-07

Nearly all research on camouflage has investigated its effectiveness for concealing stationary objects. However, animals have to move, and patterns that only work when the subject is static will heavily constrain behaviour. We investigated the effects of different camouflages on the three stages of predation-detection, identification and capture-in a computer-based task with humans. An initial experiment tested seven camouflage strategies on static stimuli. In line with previous literature, background-matching and disruptive patterns were found to be most successful. Experiment 2 showed that if stimuli move, an isolated moving object on a stationary background cannot avoid detection or capture regardless of the type of camouflage. Experiment 3 used an identification task and showed that while camouflage is unable to slow detection or capture, camouflaged targets are harder to identify than uncamouflaged targets when similar background objects are present. The specific details of the camouflage patterns have little impact on this effect. If one has to move, camouflage cannot impede detection; but if one is surrounded by similar targets (e.g. other animals in a herd, or moving background distractors), then camouflage can slow identification. Despite previous assumptions, motion does not entirely 'break' camouflage.

Tools for in silico target fishing.

PubMed

Cereto-Massagué, Adrià; Ojeda, María José; Valls, Cristina; Mulero, Miquel; Pujadas, Gerard; Garcia-Vallve, Santiago

2015-01-01

Computational target fishing methods are designed to identify the most probable target of a query molecule. This process may allow the prediction of the bioactivity of a compound, the identification of the mode of action of known drugs, the detection of drug polypharmacology, drug repositioning or the prediction of the adverse effects of a compound. The large amount of information regarding the bioactivity of thousands of small molecules now allows the development of these types of methods. In recent years, we have witnessed the emergence of many methods for in silico target fishing. Most of these methods are based on the similarity principle, i.e., that similar molecules might bind to the same targets and have similar bioactivities. However, the difficult validation of target fishing methods hinders comparisons of the performance of each method. In this review, we describe the different methods developed for target prediction, the bioactivity databases most frequently used by these methods, and the publicly available programs and servers that enable non-specialist users to obtain these types of predictions. It is expected that target prediction will have a large impact on drug development and on the functional food industry. Copyright © 2014 Elsevier Inc. All rights reserved.

Determinants of ambulance response time: A study in Sabah, Malaysia

NASA Astrophysics Data System (ADS)

Chin, Su Na; Cheah, Phee Kheng; Arifin, Muhamad Yaakub; Wong, Boh Leng; Omar, Zaturrawiah; Yassin, Fouziah Md; Gabda, Darmesah

2017-04-01

Ambulance response time (ART) is one of the standard key performance indicators (KPI) in measuring the emergency medical services (EMS) delivery performances. When the mean time of ART of EMS system reaches the KPI target, it shows that the EMS system performs well. This paper considers the determinants of ART, using data sampled from 967 ambulance runs in a government hospital in Sabah. Multiple regression analysis with backward elimination was proposed for the identification of significant factors. Amongst the underlying factors, travel distance, age of patients, type of treatment and peak hours were identified to be significantly affecting ART. Identifying factors that influence ART helps the development of strategic improvement planning for reducing the ART.

Drug Target Mining and Analysis of the Chinese Tree Shrew for Pharmacological Testing

PubMed Central

Liu, Jie; Lee, Wen-hui; Zhang, Yun

2014-01-01

The discovery of new drugs requires the development of improved animal models for drug testing. The Chinese tree shrew is considered to be a realistic candidate model. To assess the potential of the Chinese tree shrew for pharmacological testing, we performed drug target prediction and analysis on genomic and transcriptomic scales. Using our pipeline, 3,482 proteins were predicted to be drug targets. Of these predicted targets, 446 and 1,049 proteins with the highest rank and total scores, respectively, included homologs of targets for cancer chemotherapy, depression, age-related decline and cardiovascular disease. Based on comparative analyses, more than half of drug target proteins identified from the tree shrew genome were shown to be higher similarity to human targets than in the mouse. Target validation also demonstrated that the constitutive expression of the proteinase-activated receptors of tree shrew platelets is similar to that of human platelets but differs from that of mouse platelets. We developed an effective pipeline and search strategy for drug target prediction and the evaluation of model-based target identification for drug testing. This work provides useful information for future studies of the Chinese tree shrew as a source of novel targets for drug discovery research. PMID:25105297

The Identification of War-Fighting Symbology With the Use of a Small Display

DTIC Science & Technology

2006-05-01

decreases in performance. Eight active-duty Soldiers determined if target symbols were present on or absent from map images containing distractor symbols...5 Figure 2. Examples of the no-map and map environments (not drawn to scale).............................8 Figure 3. Images presented in...a no-map or map background. Symbol size (i.e., stimulus intensity) was measured in “points”. “In typography , a point is about 1/72 of an inch

Performance Comparison of Feature Extraction Algorithms for Target Detection and Classification

DTIC Science & Technology

2013-01-01

Detection and Classification⋆ Soheil Bahrampour1 Asok Ray2 Soumalya Sarkar2 Thyagaraju Damarla3 Nasser M. Nasrabadi3 Keywords: Feature Extraction...USA email:soheil@psu.edu 2A. Ray and S. Sarkar are with the Department of Mechanical Engineering, Pennsylvania State University, University Park, PA...no. 1, pp. 22–29, 2001. [5] G. Mallapragada, A. Ray , and X. Jin, “Symbolic dynamic filtering and language measure for behavior identification of mobile

Meat Species Identification using Loop-mediated Isothermal Amplification Assay Targeting Species-specific Mitochondrial DNA.

PubMed

Cho, Ae-Ri; Dong, Hee-Jin; Cho, Seongbeom

2014-01-01

Meat source fraud and adulteration scandals have led to consumer demands for accurate meat identification methods. Nucleotide amplification assays have been proposed as an alternative method to protein-based assays for meat identification. In this study, we designed Loop-mediated isothermal amplification (LAMP) assays targeting species-specific mitochondrial DNA to identify and discriminate eight meat species; cattle, pig, horse, goat, sheep, chicken, duck, and turkey. The LAMP primer sets were designed and the target genes were discriminated according to their unique annealing temperature generated by annealing curve analysis. Their unique annealing temperatures were found to be 85.56±0.07℃ for cattle, 84.96±0.08℃ for pig, and 85.99±0.05℃ for horse in the BSE-LAMP set (Bos taurus, Sus scrofa domesticus and Equus caballus); 84.91±0.11℃ for goat and 83.90±0.11℃ for sheep in the CO-LAMP set (Capra hircus and Ovis aries); and 86.31±0.23℃ for chicken, 88.66±0.12℃ for duck, and 84.49±0.08℃ for turkey in the GAM-LAMP set (Gallus gallus, Anas platyrhynchos and Meleagris gallopavo). No cross-reactivity was observed in each set. The limits of detection (LODs) of the LAMP assays in raw and cooked meat were determined from 10 pg/μL to 100 fg/μL levels, and LODs in raw and cooked meat admixtures were determined from 0.01% to 0.0001% levels. The assays were performed within 30 min and showed greater sensitivity than that of the PCR assays. These novel LAMP assays provide a simple, rapid, accurate, and sensitive technology for discrimination of eight meat species.

In-depth 2-DE reference map of Aspergillus fumigatus and its proteomic profiling on exposure to itraconazole.

PubMed

Gautam, Poonam; Mushahary, Dolly; Hassan, Wazid; Upadhyay, Santosh Kumar; Madan, Taruna; Sirdeshmukh, Ravi; Sundaram, Curam Sreenivasacharlu; Sarma, Puranam Usha

2016-07-01

Aspergillus fumigatus (A. fumigatus) is a medically important opportunistic fungus that may lead to invasive aspergillosis in humans with weak immune system. Proteomic profiling of this fungus on exposure to itraconazole (ITC), an azole antifungal drug, may lead to identification of its molecular targets and better understanding on the development of drug resistance against ITC in A. fumigatus. Here, proteome analysis was performed using 2-DE followed by mass spectrometric analysis which resulted in identification of a total of 259 unique proteins. Further, proteome profiling of A. fumigatus was carried out on exposure to ITC, 0.154 μg/ml, the minimum inhibitory concentration (MIC50). Image analysis showed altered levels of 175 proteins (66 upregulated and 109 downregulated) of A. fumigatus treated with ITC as compared to the untreated control. Peptide mass fingerprinting led to the identification of 54 proteins (12 up-regulated and 42 down-regulated). The differentially expressed proteins include proteins related to cell stress, carbohydrate metabolism and amino acid metabolism. We also observed four proteins, including nucleotide phosphate kinase (NDK), that are reported to interact with calcineurin, a protein involved in regulation of cell morphology and fungal virulence. Comparison of differentially expressed proteins on exposure to ITC with artemisinin (ART), an antimalarial drug with antifungal activity(1), revealed a total of 26 proteins to be common among them suggesting that common proteins and pathways are targeted by these two antifungal agents. The proteins targeted by ITC may serve as important leads for development of new antifungal drugs. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Salivary bacterial fingerprints of established oral disease revealed by the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technique

PubMed Central

Belstrøm, Daniel; Paster, Bruce J.; Fiehn, Nils-Erik; Bardow, Allan; Holmstrup, Palle

2016-01-01

Background and objective The composition of the salivary microbiota, as determined using various molecular methods, has been reported to differentiate oral health from diseases. Thus, the purpose of this study was to utilize the newly developed molecular technique HOMINGS (Human Oral Microbe Identification using Next Generation Sequencing) for comparison of the salivary microbiota in patients with periodontitis, patients with dental caries, and orally healthy individuals. The hypothesis was that this method could add on to the existing knowledge on salivary bacterial profiles in oral health and disease. Design Stimulated saliva samples (n=30) were collected from 10 patients with untreated periodontitis, 10 patients with untreated dental caries, and 10 orally healthy individuals. Salivary microbiota was analyzed using HOMINGS and statistical analysis was performed using Kruskal–Wallis test with Benjamini–Hochberg's correction. Results From a total of 30 saliva samples, a mean number of probe targets of 205 (range 120–353) were identified, and a statistically significant higher mean number of targets was registered in samples from patients with periodontitis (mean 220, range 143–306) and dental caries (mean 221, range 165–353) as compared to orally healthy individuals (mean 174, range 120–260) (p=0.04 and p=0.04). Nine probe targets were identified with a different relative abundance between groups (p<0.05). Conclusions Cross-sectional comparison of salivary bacterial profiles by means of HOMINGS analysis showed that different salivary bacterial profiles were associated with oral health and disease. Future large-scale prospective studies are needed to evaluate if saliva-based screening for disease-associated oral bacterial profiles may be used for identification of patients at risk of acquiring periodontitis and dental caries. PMID:26782357

A quick responding quartz crystal microbalance sensor array based on molecular imprinted polyacrylic acids coating for selective identification of aldehydes in body odor.

PubMed

Jha, Sunil K; Hayashi, Kenshi

2015-03-01

In present work, a novel quartz crystal microbalance (QCM) sensor array has been developed for prompt identification of primary aldehydes in human body odor. Molecularly imprinted polymers (MIP) are prepared using the polyacrylic acid (PAA) polymer matrix and three organic acids (propenoic acid, hexanoic acid and octanoic acid) as template molecules, and utilized as QCM surface coating layer. The performance of MIP films is characterized by 4-element QCM sensor array (three coated with MIP layers and one with pure PAA for reference) dynamic and static responses to target aldehydes: hexanal, heptanal, and nonanal in single, binary, and tertiary mixtures at distinct concentrations. The target aldehydes were selected subsequent to characterization of body odor samples with solid phase-micro extraction gas chromatography mass spectrometer (SPME-GC-MS). The hexanoic acid and octanoic acid imprinted PAA exhibit fast response, and better sensitivity, selectivity and reproducibility than the propenoic acid, and non-imprinted PAA in array. The response time and recovery time for hexanoic acid imprinted PAA are obtained as 5 s and 12 s respectively to typical concentrations of binary and tertiary mixtures of aldehydes using the static response. Dynamic sensor array response matrix has been processed with principal component analysis (PCA) for visual, and support vector machine (SVM) classifier for quantitative identification of target odors. Aldehyde odors were identified successfully in principal component (PC) space. SVM classifier results maximum recognition rate 79% for three classes of binary odors and 83% including single, binary, and tertiary odor classes in 3-fold cross validation. Copyright © 2014 Elsevier B.V. All rights reserved.

The search for drug-targetable diagnostic, prognostic and predictive biomarkers in chronic graft-versus-host disease.

PubMed

Ren, Hong-Gang; Adom, Djamilatou; Paczesny, Sophie

2018-05-01

Chronic graft-versus-host disease (cGVHD) continues to be the leading cause of late morbidity and mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT), which is an increasingly applied curative method for both benign and malignant hematologic disorders. Biomarker identification is crucial for the development of noninvasive and cost-effective cGVHD diagnostic, prognostic, and predictive test for use in clinic. Furthermore, biomarkers may help to gain a better insight on ongoing pathophysiological processes. The recent widespread application of omics technologies including genomics, transcriptomics, proteomics and cytomics provided opportunities to discover novel biomarkers. Areas covered: This review focuses on biomarkers identified through omics that play a critical role in target identification for drug development, and that were verified in at least two independent cohorts. It also summarizes the current status on omics tools used to identify these useful cGVHD targets. We briefly list the biomarkers identified and verified so far. We further address challenges associated to their exploitation and application in the management of cGVHD patients. Finally, insights on biomarkers that are drug targetable and represent potential therapeutic targets are discussed. Expert commentary: We focus on biomarkers that play an essential role in target identification.

Large-scale identification of target proteins of a glycosyltransferase isozyme by Lectin-IGOT-LC/MS, an LC/MS-based glycoproteomic approach

PubMed Central

Sugahara, Daisuke; Kaji, Hiroyuki; Sugihara, Kazushi; Asano, Masahide; Narimatsu, Hisashi

2012-01-01

Model organisms containing deletion or mutation in a glycosyltransferase-gene exhibit various physiological abnormalities, suggesting that specific glycan motifs on certain proteins play important roles in vivo. Identification of the target proteins of glycosyltransferase isozymes is the key to understand the roles of glycans. Here, we demonstrated the proteome-scale identification of the target proteins specific for a glycosyltransferase isozyme, β1,4-galactosyltransferase-I (β4GalT-I). Although β4GalT-I is the most characterized glycosyltransferase, its distinctive contribution to β1,4-galactosylation has been hardly described so far. We identified a large number of candidates for the target proteins specific to β4GalT-I by comparative analysis of β4GalT-I-deleted and wild-type mice using the LC/MS-based technique with the isotope-coded glycosylation site-specific tagging (IGOT) of lectin-captured N-glycopeptides. Our approach to identify the target proteins in a proteome-scale offers common features and trends in the target proteins, which facilitate understanding of the mechanism that controls assembly of a particular glycan motif on specific proteins. PMID:23002422

50 CFR 622.60 - Adjustment of management measures.

Code of Federal Regulations, 2013 CFR

2013-10-01

... markings and identification, allowable biological catch (ABC) and ABC control rules, rebuilding plans, sale... harvested shrimp (maintaining shrimp in whole condition, use as bait), target effort and fishing mortality... identification, vessel markings and identification, ABC and ABC control rules, rebuilding plans, sale and...

50 CFR 622.60 - Adjustment of management measures.

Code of Federal Regulations, 2014 CFR

2014-10-01

... markings and identification, allowable biological catch (ABC) and ABC control rules, rebuilding plans, sale... harvested shrimp (maintaining shrimp in whole condition, use as bait), target effort and fishing mortality... identification, vessel markings and identification, ABC and ABC control rules, rebuilding plans, sale and...

Improved prediction of drug-target interactions using regularized least squares integrating with kernel fusion technique.

PubMed

Hao, Ming; Wang, Yanli; Bryant, Stephen H

2016-02-25

Identification of drug-target interactions (DTI) is a central task in drug discovery processes. In this work, a simple but effective regularized least squares integrating with nonlinear kernel fusion (RLS-KF) algorithm is proposed to perform DTI predictions. Using benchmark DTI datasets, our proposed algorithm achieves the state-of-the-art results with area under precision-recall curve (AUPR) of 0.915, 0.925, 0.853 and 0.909 for enzymes, ion channels (IC), G protein-coupled receptors (GPCR) and nuclear receptors (NR) based on 10 fold cross-validation. The performance can further be improved by using a recalculated kernel matrix, especially for the small set of nuclear receptors with AUPR of 0.945. Importantly, most of the top ranked interaction predictions can be validated by experimental data reported in the literature, bioassay results in the PubChem BioAssay database, as well as other previous studies. Our analysis suggests that the proposed RLS-KF is helpful for studying DTI, drug repositioning as well as polypharmacology, and may help to accelerate drug discovery by identifying novel drug targets. Published by Elsevier B.V.

[Exploring New Drug Targets through the Identification of Target Molecules of Bioactive Natural Products].

PubMed

Arai, Masayoshi

2016-01-01

With the development of cell biology and microbiology, it has become easy to culture many types of animal cells and microbes, and they are frequently used for phenotypic screening to explore medicinal seeds. On the other hand, it is recognized that cells and pathogenic microbes present in pathologic sites and infected regions of the human body display unique properties different from those under general culture conditions. We isolated several bioactive compounds from marine medicinal resources using constructed bioassay-guided separation focusing on the unique changes in the characteristics of cells and pathogenic microbes (Mycobacterium spp.) in the human body under disease conditions. In addition, we also carried out identification studies of target molecules of the bioactive compounds by methods utilizing the gene expression profile, transformants of cells or microbes, synthetic probe molecules of the isolated compounds, etc., since bioactive compounds isolated from the phenotypic screening system often target new molecules. This review presents our phenotypic screening systems, isolation of bioactive compounds from marine medicinal resources, and target identification of bioactive compounds.

Activity-based proteome profiling of potential cellular targets of Orlistat--an FDA-approved drug with anti-tumor activities.

PubMed

Yang, Peng-Yu; Liu, Kai; Ngai, Mun Hong; Lear, Martin J; Wenk, Markus R; Yao, Shao Q

2010-01-20

Orlistat, or tetrahydrolipstatin (THL), is an FDA-approved antiobesity drug with potential antitumor activities. Cellular off-targets and potential side effects of Orlistat in cancer therapies, however, have not been extensively explored thus far. In this study, we report the total of synthesis of THL-like protein-reactive probes, in which extremely conservative modifications (i.e., an alkyne handle) were introduced in the parental THL structure to maintain the native biological properties of Orlistat, while providing the necessary functionality for target identification via the bio-orthogonal click chemistry. With these natural productlike, cell-permeable probes, we were able to demonstrate, for the first time, this chemical proteomic approach is suitable for the identification of previously unknown cellular targets of Orlistat. In addition to the expected fatty acid synthase (FAS), we identified a total of eight new targets, some of which were further validated by experiments including Western blotting, recombinant protein expression, and site-directed mutagenesis. Our findings have important implications in the consideration of Orlistat as a potential anticancer drug at its early stages of development for cancer therapy. Our strategy should be broadly useful for off-target identification against quite a number of existing drugs and/or candidates, which are also covalent modifiers of their biological targets.

Serum-based six-miRNA signature as a potential marker for EC diagnosis: Comparison with TCGA miRNAseq dataset and identification of miRNA-mRNA target pairs by integrated analysis of TCGA miRNAseq and RNAseq datasets.

PubMed

Sharma, Priyanka; Saraya, Anoop; Sharma, Rinu

2018-01-30

To evaluate the diagnostic potential of a six microRNAs (miRNAs) panel consisting of miR-21, miR-144, miR-107, miR-342, miR-93 and miR-152 for esophageal cancer (EC) detection. The expression of miRNAs was analyzed in EC sera samples using quantitative real-time PCR. Risk score analysis was performed and linear regression models were then fitted to generate the six-miRNA panel. In addition, we made an effort to identify significantly dysregulated miRNAs and mRNAs in EC using the Cancer Genome Atlas (TCGA) miRNAseq and RNAseq datasets, respectively. Further, we identified significantly correlated miRNA-mRNA target pairs by integrating TCGA EC miRNAseq dataset with RNAseq dataset. The panel of circulating miRNAs showed enhanced sensitivity (87.5%) and specificity (90.48%) in terms of discriminating EC patients from normal subjects (area under the curve [AUC] = 0.968). Pathway enrichment analysis for potential targets of six miRNAs revealed 48 significant (P < 0.05) pathways, viz. pathways in cancer, mRNA surveillance, MAPK, Wnt, mTOR signaling, and so on. The expression data for mRNAs and miRNAs, downloaded from TCGA database, lead to identification of 2309 differentially expressed genes and 189 miRNAs. Gene ontology and pathway enrichment analysis showed that cell-cycle processes were most significantly enriched for differentially expressed mRNA. Integrated analysis of TCGA miRNAseq and RNAseq datasets resulted in identification of 53 063 significantly and negatively correlated miRNA-mRNA pairs. In summary, a novel and highly sensitive signature of serum miRNAs was identified for EC detection. Moreover, this is the first report identifying miRNA-mRNA target pairs from EC TCGA dataset, thus providing a comprehensive resource for understanding the interactions existing between miRNA and their target mRNAs in EC. © 2018 John Wiley & Sons Australia, Ltd.

Rapid and Accurate Molecular Identification of the Emerging Multidrug-Resistant Pathogen Candida auris

PubMed Central

Zhao, Yanan; Lockhart, Shawn R.; Berrio, Indira

2017-01-01

ABSTRACT Candida auris is an emerging multidrug-resistant fungal pathogen causing nosocomial and invasive infections associated with high mortality. C. auris is commonly misidentified as several different yeast species by commercially available phenotypic identification platforms. Thus, there is an urgent need for a reliable diagnostic method. In this paper, we present fast, robust, easy-to-perform and interpret PCR and real-time PCR assays to identify C. auris and related species: Candida duobushaemulonii, Candida haemulonii, and Candida lusitaniae. Targeting rDNA region nucleotide sequences, primers specific for C. auris only or C. auris and related species were designed. A panel of 140 clinical fungal isolates was used in both PCR and real-time PCR assays followed by electrophoresis or melting temperature analysis, respectively. The identification results from the assays were 100% concordant with DNA sequencing results. These molecular assays overcome the deficiencies of existing phenotypic tests to identify C. auris and related species. PMID:28539346

A comparison of signal detection theory to the objective threshold/strategic model of unconscious perception.

PubMed

Haase, Steven J; Fisk, Gary D

2011-08-01

A key problem in unconscious perception research is ruling out the possibility that weak conscious awareness of stimuli might explain the results. In the present study, signal detection theory was compared with the objective threshold/strategic model as explanations of results for detection and identification sensitivity in a commonly used unconscious perception task. In the task, 64 undergraduate participants detected and identified one of four briefly displayed, visually masked letters. Identification was significantly above baseline (i.e., proportion correct > .25) at the highest detection confidence rating. This result is most consistent with signal detection theory's continuum of sensory states and serves as a possible index of conscious perception. However, there was limited support for the other model in the form of a predicted "looker's inhibition" effect, which produced identification performance that was significantly below baseline. One additional result, an interaction between the target stimulus and type of mask, raised concerns for the generality of unconscious perception effects.

Rapid and Accurate Molecular Identification of the Emerging Multidrug-Resistant Pathogen Candida auris.

PubMed

Kordalewska, Milena; Zhao, Yanan; Lockhart, Shawn R; Chowdhary, Anuradha; Berrio, Indira; Perlin, David S

2017-08-01

Candida auris is an emerging multidrug-resistant fungal pathogen causing nosocomial and invasive infections associated with high mortality. C. auris is commonly misidentified as several different yeast species by commercially available phenotypic identification platforms. Thus, there is an urgent need for a reliable diagnostic method. In this paper, we present fast, robust, easy-to-perform and interpret PCR and real-time PCR assays to identify C. auris and related species: Candida duobushaemulonii , Candida haemulonii , and Candida lusitaniae Targeting rDNA region nucleotide sequences, primers specific for C. auris only or C. auris and related species were designed. A panel of 140 clinical fungal isolates was used in both PCR and real-time PCR assays followed by electrophoresis or melting temperature analysis, respectively. The identification results from the assays were 100% concordant with DNA sequencing results. These molecular assays overcome the deficiencies of existing phenotypic tests to identify C. auris and related species. Copyright © 2017 Kordalewska et al.

Verbal overshadowing of face memory does occur in children too!

PubMed Central

Dehon, Hedwige; Vanootighem, Valentine; Brédart, Serge

2013-01-01

Verbal descriptions of unfamiliar faces have been found to impair later identification of these faces in adults, a phenomenon known as the “verbal overshadowing effect” (VOE). Although determining whether children are good at describing unfamiliar individuals and whether these descriptions impair their recognition performance is critical to gaining a better understanding children's eyewitness ability, only a couple of studies have examined this dual issue in children and these found no evidence of VOE. However, as there are some methodological criticisms of these studies, we decided to conduct two further experiments in 7–8, 10–11, and 13–14-year-old children and in adults using a more optimal method for the VOE to be observed. Evidence of the VOE on face identification was found in both children and adults. Moreover, neither the accuracy of descriptions, nor delay nor target presence in the lineup was found to be associated with identification accuracy. The theoretical and developmental implications of these findings are discussed. PMID:24399985

PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide.

PubMed

Jiang, Ying; Gao, Ge; Fang, Gang; Gustafson, Eric L; Laverty, Maureen; Yin, Yanbin; Zhang, Yong; Luo, Jingchu; Greene, Jonathan R; Bayne, Marvin L; Hedrick, Joseph A; Murgolo, Nicholas J

2003-05-01

PepPat, a hybrid method that combines pattern matching with similarity scoring, is described. We also report PepPat's application in the identification of a novel tachykinin-like peptide. PepPat takes as input a query peptide and a user-specified regular expression pattern within the peptide. It first performs a database pattern match and then ranks candidates on the basis of their similarity to the query peptide. PepPat calculates similarity over the pattern spanning region, enhancing PepPat's sensitivity for short query peptides. PepPat can also search for a user-specified number of occurrences of a repeated pattern within the target sequence. We illustrate PepPat's application in short peptide ligand mining. As a validation example, we report the identification of a novel tachykinin-like peptide, C14TKL-1, and show it is an NK1 (neuokinin receptor 1) agonist whose message is widely expressed in human periphery. PepPat is offered online at: http://peppat.cbi.pku.edu.cn.

Rapid in situ identification of bioactive compounds in plants by in vivo nanospray high-resolution mass spectrometry.

PubMed

Chang, Qing; Peng, Yue'e; Dan, Conghui; Shuai, Qin; Hu, Shenghong

2015-03-25

A method for the rapid in situ identification of bioactive compounds in fresh plants has been developed using in vivo nanospray coupled to high-resolution mass spectrometry (HR-MS). Using a homemade in vivo nanospray ion source, the plant liquid was drawn out from a target region and ionized in situ. The ionized bioactive compounds were then identified using Q-Orbitrap HR-MS. The accurate mass measurements of these bioactive compounds were performed by full-scan or selected ion monitoring (SIM), and tandem mass spectrometry (MS/MS) was used in the structural elucidation. Without sample pretreatment, 12 bioactive compounds in 7 different plant species were identified, namely, isoalliin in onion; butylphthalide in celery; N-methylpelletierine, pelletierine, and pseudopelletierine in pomegranate; chlorogenic acid in crabapple; solamargine, solasonine, and solasodine in nightshade; aloin and aloe-emodin in aloe; and menthone in mint. This work demonstrates that in vivo nanospray HR-MS is a good method for rapid in situ identification of bioactive compounds in plants.

Aptamers as tools for target prioritization and lead identification.

PubMed

Burgstaller, Petra; Girod, Anne; Blind, Michael

2002-12-15

The increasing number of potential drug target candidates has driven the development of novel technologies designed to identify functionally important targets and enhance the subsequent lead discovery process. Highly specific synthetic nucleic acid ligands--also known as aptamers--offer a new exciting route in the drug discovery process by linking target validation directly with HTS. Recently, aptamers have proven to be valuable tools for modulating the function of endogenous cellular proteins in their natural environment. A set of technologies has been developed to use these sophisticated ligands for the validation of potential drug targets in disease models. Moreover, aptamers that are specific antagonists of protein function can act as substitute interaction partners in HTS assays to facilitate the identification of small-molecule lead compounds.

Species and hybrid identification of sturgeon caviar: a new molecular approach to detect illegal trade.

PubMed

Boscari, E; Barmintseva, A; Pujolar, J M; Doukakis, P; Mugue, N; Congiu, L

2014-05-01

Overexploitation of wild populations due to the high economic value of caviar has driven sturgeons to near extinction. The high prices commanded by caviar on world markets have made it a magnet for illegal and fraudulent caviar trade, often involving low-value farmed caviar being sold as top-quality caviar. We present a new molecular approach for the identification of pure sturgeon species and hybrids that are among the most commercialized species in Europe and North America. Our test is based on the discovery of species-specific single nucleotide polymorphisms (SNPs) in the ribosomal protein S7, supplemented with the Vimentin gene and the mitochondrial D-loop. Test validations performed in 702 specimens of target and nontarget sturgeon species demonstrated a 100% identification success for Acipenser naccarii, A. fulvescens, A. stellatus, A. sinensis and A. transmontanus. In addition to species identification, our approach allows the identification of Bester and AL hybrids, two of the most economically important hybrids in the world, with 80% and 100% success, respectively. Moreover, the approach has the potential to identify many other existing sturgeon hybrids. The development of a standardized sturgeon identification tool will directly benefit trade law enforcement, providing the tools to monitor and regulate the legal trade of caviar and protect sturgeon stocks from illicit producers and traders, hence contributing to safeguarding this group of heavily threatened species. © 2013 John Wiley & Sons Ltd.

Characterization of anti-leukemia components from Indigo naturalis using comprehensive two-dimensional K562/cell membrane chromatography and in silico target identification.

PubMed

Wu, Xunxun; Chen, Xiaofei; Dan, Jia; Cao, Yan; Gao, Shouhong; Guo, Zhiying; Zerbe, Philipp; Chai, Yifeng; Diao, Yong; Zhang, Lei

2016-05-06

Traditional Chinese Medicine (TCM) has been developed for thousands of years and has formed an integrated theoretical system based on a large amount of clinical practice. However, essential ingredients in TCM herbs have not been fully identified, and their precise mechanisms and targets are not elucidated. In this study, a new strategy combining comprehensive two-dimensional K562/cell membrane chromatographic system and in silico target identification was established to characterize active components from Indigo naturalis, a famous TCM herb that has been widely used for the treatment of leukemia in China, and their targets. Three active components, indirubin, tryptanthrin and isorhamnetin, were successfully characterized and their anti-leukemia effects were validated by cell viability and cell apoptosis assays. Isorhamnetin, with undefined cancer related targets, was selected for in silico target identification. Proto-oncogene tyrosine-protein kinase (Src) was identified as its membrane target and the dissociation constant (Kd) between Src and isorhamnetin was 3.81 μM. Furthermore, anti-leukemia effects of isorhamnetin were mediated by Src through inducing G2/M cell cycle arrest. The results demonstrated that the integrated strategy could efficiently characterize active components in TCM and their targets, which may bring a new light for a better understanding of the complex mechanism of herbal medicines.

Characterization of anti-leukemia components from Indigo naturalis using comprehensive two-dimensional K562/cell membrane chromatography and in silico target identification

PubMed Central

Wu, Xunxun; Chen, Xiaofei; Dan, Jia; Cao, Yan; Gao, Shouhong; Guo, Zhiying; Zerbe, Philipp; Chai, Yifeng; Diao, Yong; Zhang, Lei

2016-01-01

Traditional Chinese Medicine (TCM) has been developed for thousands of years and has formed an integrated theoretical system based on a large amount of clinical practice. However, essential ingredients in TCM herbs have not been fully identified, and their precise mechanisms and targets are not elucidated. In this study, a new strategy combining comprehensive two-dimensional K562/cell membrane chromatographic system and in silico target identification was established to characterize active components from Indigo naturalis, a famous TCM herb that has been widely used for the treatment of leukemia in China, and their targets. Three active components, indirubin, tryptanthrin and isorhamnetin, were successfully characterized and their anti-leukemia effects were validated by cell viability and cell apoptosis assays. Isorhamnetin, with undefined cancer related targets, was selected for in silico target identification. Proto-oncogene tyrosine-protein kinase (Src) was identified as its membrane target and the dissociation constant (Kd) between Src and isorhamnetin was 3.81 μM. Furthermore, anti-leukemia effects of isorhamnetin were mediated by Src through inducing G2/M cell cycle arrest. The results demonstrated that the integrated strategy could efficiently characterize active components in TCM and their targets, which may bring a new light for a better understanding of the complex mechanism of herbal medicines. PMID:27150638

A fully sealed plastic chip for multiplex PCR and its application in bacteria identification.

PubMed

Xu, Youchun; Yan, He; Zhang, Yan; Jiang, Kewei; Lu, Ying; Ren, Yonghong; Wang, Hui; Wang, Shan; Xing, Wanli

2015-07-07

Multiplex PCR is an effective tool for simultaneous multiple target detection but is limited by the intrinsic interference and competition among primer pairs when it is performed in one reaction tube. Dividing a multiplex PCR into many single PCRs is a simple strategy to overcome this issue. Here, we constructed a plastic, easy-to-use, fully sealed multiplex PCR chip based on reversible centrifugation for the simultaneous detection of 63 target DNA sequences. The structure of the chip is quite simple, which contains sine-shaped infusing channels and a number of reaction chambers connecting to one side of these channels. Primer pairs for multiplex PCR were sequentially preloaded in the different reaction chambers, and the chip was enclosed with PCR-compatible adhesive tape. For usage, the PCR master mix containing a DNA template is pipetted into the infusing channels and centrifuged into the reaction chambers, leaving the infusing channels filled with air to avoid cross-contamination of the different chambers. Then, the chip is sealed and placed on a flat thermal cycler for PCR. Finally, amplification products can be detected in situ using a fluorescence scanner or recovered by reverse centrifugation for further analyses. Therefore, our chip possesses two functions: 1) it can be used for multi-target detection based on end-point in situ fluorescence detection; and 2) it can work as a sample preparation unit for analyses that need multiplex PCR such as hybridization and target sequencing. The performance of this chip was carefully examined and further illustrated in the identification of 8 pathogenic bacterial genomic DNA samples and 13 drug-resistance genes. Due to simplicity of its structure and operation, accuracy and generality, high-throughput capacity, and versatile functions (i.e., for in situ detection and sample preparation), our multiplex PCR chip has great potential in clinical diagnostics and nucleic acid-based point-of-care testing.

Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing.

PubMed

O'Flaherty, Brigid M; Li, Yan; Tao, Ying; Paden, Clinton R; Queen, Krista; Zhang, Jing; Dinwiddie, Darrell L; Gross, Stephen M; Schroth, Gary P; Tong, Suxiang

2018-06-01

Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the genomes, allowing for identification of known viruses and full genome sequencing, while the second set targets regions conserved among viral families or genera, providing the ability to detect both known and potentially novel members of those virus groups. Efficiency of enrichment was assessed by NGS testing reference virus and clinical samples with known infection. We show significant improvement in viral identification using enriched NGS compared to unenriched NGS. Without enrichment, we observed an average of 0.3% targeted viral reads per sample. However, after enrichment, 50%-99% of the reads per sample were the targeted viral reads for both the reference isolates and clinical specimens using both probe sets. Importantly, dramatic improvements on genome coverage were also observed following virus-specific probe enrichment. The methods described here provide improved sensitivity for virus identification by NGS, allowing for a more comprehensive analysis of disease etiology. © 2018 O'Flaherty et al.; Published by Cold Spring Harbor Laboratory Press.

Providing Agility in C2 Environments Through Networked Information Processing: A Model of Expertise

DTIC Science & Technology

2014-06-01

personal benefits promoting self-esteem, pride, self-efficacy, personal identification with colleagues and organizations, obtaining a better...studies based on staged-event methods with “target-present” and “target-absent” lineups . The results show that when choosers make positive... identification , the correlation between confidence and accuracy was consistently high. Besides correct choosers have a higher mean confidence level than

Effect of motion on speech recognition.

PubMed

Davis, Timothy J; Grantham, D Wesley; Gifford, René H

2016-07-01

The benefit of spatial separation for talkers in a multi-talker environment is well documented. However, few studies have examined the effect of talker motion on speech recognition. In the current study, we evaluated the effects of (1) motion of the target or distracters, (2) a priori information about the target and distracter spatial configurations, and (3) target and distracter location. In total, seventeen young adults with normal hearing were tested in a large anechoic chamber in two experiments. In Experiment 1, seven stimulus conditions were tested using the Coordinate Response Measure (Bolia et al., 2000) speech corpus, in which subjects were required to report the key words in a target sentence presented simultaneously with two distracter sentences. As in previous studies, there was a significant improvement in key word identification for conditions in which the target and distracters were spatially separated as compared to the co-located conditions. In addition, 1) motion of either talker or distracter resulted in improved performance compared to stationary presentation (talker motion yielded significantly better performance than distracter motion) 2) a priori information regarding stimulus configuration was not beneficial, and 3) performance was significantly better with key words at 0° azimuth as compared to -60° (on the listener's left). Experiment 2 included two additional conditions designed to assess whether the benefit of motion observed in Experiment 1 was due to the motion itself or to the fact that the motion conditions introduced small spatial separations in the target and distracter key words. Results showed that small spatial separations (on the order of 5-8°) resulted in improved performance (relative to co-located key words) whether the sentences were moving or stationary. These results suggest that in the presence of distracting messages, motion of either target or distracters and/or small spatial separation of the key words may be beneficial for sound source segregation and thus for improved speech recognition. Copyright © 2016 Elsevier B.V. All rights reserved.

Screening and HPLC-Based Activity Profiling for New Antiprotozoal Leads from European Plants.

PubMed

Zimmermann, Stefanie; Thomi, Semira; Kaiser, Marcel; Hamburger, Matthias; Adams, Michael

2012-01-01

Based on a survey of remedies used in Renaissance Europe to treat malaria, we prepared and screened a library of 254 extracts from 61 plants for antiplasmodial activity in vitro. HPLC-based activity profiling was performed for targeted identification of active constituents in extracts. One of the most remarkable results was the identification of onopordopicrin, a germacranolide sesquiterpene lactone isolated from Arctium nemorosum as a potent inhibitor of P. falciparum with an IC(50) of 6.9 μM. It was tested similarly against Trypanosoma brucei rhodesiense, the parasite which causes African sleeping sickness. With an IC(50) of 0.37 μM, onopordopicrin was one of the most potent natural products reported so far. Cytotoxicity was determined against rat myoblast L6 cells (IC(50): 3.06).

[Development and application of reference materials containing mixed degradation products of amoxicillin and ampicillin].

PubMed

Li, Wei; Zhang, Wei-Qing; Li, Xiang; Hu, Chang-Qin

2014-09-01

Reference materials containing mixed degradation products of amoxicillin and ampicillin were developed after optimization of preparation processes. The target impurities were obtained by controlled stress testing, and each major component was identified with HPLC-MS and compared with single traceable reference standard each. The developed reference materials were applied to system suitability test for verifying HPLC system performed in accordance with set forth in China Pharmacopeia and identification of major impurities in samples based on retention and spectra information, which have advantages over the methods put forth in foreign pharmacopoeias. The development and application of the reference materials offer an effective way for rapid identification of impurities in chromatograms, and provide references for analyzing source of impurities and evaluation of drug quality.

Screening and HPLC-Based Activity Profiling for New Antiprotozoal Leads from European Plants

PubMed Central

Zimmermann, Stefanie; Thomi, Semira; Kaiser, Marcel; Hamburger, Matthias; Adams, Michael

2012-01-01

Based on a survey of remedies used in Renaissance Europe to treat malaria, we prepared and screened a library of 254 extracts from 61 plants for antiplasmodial activity in vitro. HPLC-based activity profiling was performed for targeted identification of active constituents in extracts. One of the most remarkable results was the identification of onopordopicrin, a germacranolide sesquiterpene lactone isolated from Arctium nemorosum as a potent inhibitor of P. falciparum with an IC50 of 6.9 μM. It was tested similarly against Trypanosoma brucei rhodesiense, the parasite which causes African sleeping sickness. With an IC50 of 0.37 μM, onopordopicrin was one of the most potent natural products reported so far. Cytotoxicity was determined against rat myoblast L6 cells (IC50: 3.06). PMID:22396915

In situ damage monitoring in vibration mechanics: diagnostics and predictive maintenance

NASA Astrophysics Data System (ADS)

Basseville, M.; Benveniste, A.; Gach-Devauchelle, B.; Goursat, M.; Bonnecase, D.; Dorey, P.; Prevosto, M.; Olagnon, M.

1993-09-01

A system identification approach is presented for damage monitoring in vibration mechanics. Identification, detection, and diagnostics are performed using accelerometer measurements from the system at work so that the excitation is not controlled, usually not observed and may involve turbulent phenomena. Targeted applications include power engineering (rotating machines, core and pipes of nuclear power plants), civil engineering (large buildings subject to hurricanes or earthquakes, bridges, dams, offshore structures), aeronautics (wings and other structures subject to strength), automobile, rail transportation etc. The method is illustrated by a laboratory example, and the results of 3 years industrial usage. This paper is a progress report on a 10 year project involving three people almost permanently. We describe here the whole approach but omit the technical details which are available in previous papers.

A centrifugal direct recombinase polymerase amplification (direct-RPA) microdevice for multiplex and real-time identification of food poisoning bacteria.

PubMed

Choi, Goro; Jung, Jae Hwan; Park, Byung Hyun; Oh, Seung Jun; Seo, Ji Hyun; Choi, Jong Seob; Kim, Do Hyun; Seo, Tae Seok

2016-06-21

In this study, we developed a centrifugal direct recombinase polymerase amplification (direct-RPA) microdevice for multiplex and real-time identification of food poisoning bacteria contaminated milk samples. The microdevice was designed to contain identical triplicate functional units and each unit has four reaction chambers, thereby making it possible to perform twelve direct-RPA reactions simultaneously. The integrated microdevice consisted of two layers: RPA reagents were injected in the top layer, while spiked milk samples with food poisoning bacteria were loaded into sample reservoirs in the bottom layer. For multiplex bacterial detection, the target gene-specific primers and probes were dried in each reaction chamber. The introduced samples and reagents could be equally aliquoted and dispensed into each reaction chamber by centrifugal force, and then the multiplex direct-RPA reaction was executed. The target genes of bacteria spiked in milk could be amplified at 39 °C without a DNA extraction step by using the direct-RPA cocktails, which were a combination of a direct PCR buffer and RPA enzymes. As the target gene amplification proceeded, the increased fluorescence signals coming from the reaction chambers were recorded in real-time at an interval of 2 min. The entire process, including the sample distribution, the direct-RPA reaction, and the real-time analysis, was accomplished with a custom-made portable genetic analyzer and a miniaturized optical detector. Monoplex, duplex, and triplex food poisoning bacteria (Salmonella enterica, Escherichia coli O157:H7, and Vibrio parahaemolyticus) detection was successfully performed with a detection sensitivity of 4 cells per 3.2 μL of milk samples within 30 min. By implementing the direct-PRA on the miniaturized centrifugal microsystem, the on-site food poisoning bacteria analysis would be feasible with high speed, sensitivity, and multiplicity.

Removal of endocrine disruptors and non-steroidal anti-inflammatory drugs through wastewater chlorination: the effect of pH, total suspended solids and humic acids and identification of degradation by-products.

PubMed

Noutsopoulos, Constantinos; Koumaki, Elena; Mamais, Daniel; Nika, Maria-Christina; Bletsou, Anna A; Thomaidis, Nikolaos S

2015-01-01

Endocrine disrupting chemicals (EDCs) and non-steroidal anti-inflammatory drugs (NSAIDs) are two groups of emerging pollutants the significance of which rests on their persistent detection in the aquatic environment and their possible adverse effects. Wastewater treatment plants are one of the major ways for transporting such chemicals in the aquatic environment. Chlorination is usually the last stage of treatment before wastewater being disposed to the aquatic environment. This work focuses on the evaluation of the effect of chlorine dose and specific wastewater characteristics (pH, total suspended solids and humic acids) on the removal of target EDCs and NSAIDs through chlorination. Another objective of this study is the identification of chlorination by-products of specific EDCs and NSAIDs and their dependence on contact time. Based on the results it is concluded that the effect of chlorine dose and humic acids concentration on the degradation of target compounds during chlorination is minimal. On the contrary, pH is a critical parameter which highly affects process performance. Moreover, it is concluded that not only the free available chlorine species, but also the properties of EDCs and NSAIDs under different pH conditions can affect chlorination process performance. The effect of TSS on the degradation of the target compounds during chlorination is more profound for chemicals with high Kow values and therefore higher affinity to partition to the particulate phase (i.e. nonylphenols, triclosan). Several degradation by-products were identified through chlorination of nonylphenol, bisphenol A and diclofenac. The dependence of these by-products on chlorination contact time is also demonstrated. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identification of potential mechanisms of toxicity after di-(2-ethylhexyl)-phthalate (DEHP) adult exposure in the liver using a systems biology approach

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

Eveillard, Alexandre; Lasserre, Frederic; Tayrac, Marie de

2009-05-01

Phthalates are industrial additives widely used as plasticizers. In addition to deleterious effects on male genital development, population studies have documented correlations between phthalates exposure and impacts on reproductive tract development and on the metabolic syndrome in male adults. In this work we investigated potential mechanisms underlying the impact of DEHP on adult mouse liver in vivo. A parallel analysis of hepatic transcript and metabolic profiles from adult mice exposed to varying DEHP doses was performed. Hepatic genes modulated by DEHP are predominantly PPAR{alpha} targets. However, the induction of prototypic cytochrome P450 genes strongly supports the activation of additional NRmore » pathways, including Constitutive Androstane Receptor (CAR). Integration of transcriptomic and metabonomic profiles revealed a correlation between the impacts of DEHP on genes and metabolites related to heme synthesis and to the Rev-erb{alpha} pathway that senses endogenous heme level. We further confirmed the combined impact of DEHP on the hepatic expression of Alas1, a critical enzyme in heme synthesis and on the expression of Rev-erb{alpha} target genes involved in the cellular clock and in energy metabolism. This work shows that DEHP interferes with hepatic CAR and Rev-erb{alpha} pathways which are both involved in the control of metabolism. The identification of these new hepatic pathways targeted by DEHP could contribute to metabolic and endocrine disruption associated with phthalate exposure. Gene expression profiles performed on microdissected testis territories displayed a differential responsiveness to DEHP. Altogether, this suggests that impacts of DEHP on adult organs, including testis, could be documented and deserve further investigations.« less

Early Identification of Student Performance and Effort Using an Online Homework System: A Pilot Study

NASA Astrophysics Data System (ADS)

Perdian, David C.

2013-10-01

Two distinct student groups, in terms of academic performance, were identified early in the semester as either being under-performing students or over-performing students using an online homework system. The students who are identified as under-performing received, on average, lower grades than their fellow students but spent more time completing the homework assignments. These students are great candidates for targeted advertisement of student resources such as tutoring services. The students who are identified in the over-performing student population received higher grades than their fellow students, but spent less time completing the homework assignments. These students are great candidates for honors programs, independent research projects, and peer-tutoring programs. Incorporating these evaluation criteria to online homework systems will allow instructors to quickly identify students in these academic student populations.

Digital imaging and remote sensing image generator (DIRSIG) as applied to NVESD sensor performance modeling

NASA Astrophysics Data System (ADS)

Kolb, Kimberly E.; Choi, Hee-sue S.; Kaur, Balvinder; Olson, Jeffrey T.; Hill, Clayton F.; Hutchinson, James A.

2016-05-01

The US Army's Communications Electronics Research, Development and Engineering Center (CERDEC) Night Vision and Electronic Sensors Directorate (referred to as NVESD) is developing a virtual detection, recognition, and identification (DRI) testing methodology using simulated imagery as a means of augmenting the field testing component of sensor performance evaluation, which is expensive, resource intensive, time consuming, and limited to the available target(s) and existing atmospheric visibility and environmental conditions at the time of testing. Existing simulation capabilities such as the Digital Imaging Remote Sensing Image Generator (DIRSIG) and NVESD's Integrated Performance Model Image Generator (NVIPM-IG) can be combined with existing detection algorithms to reduce cost/time, minimize testing risk, and allow virtual/simulated testing using full spectral and thermal object signatures, as well as those collected in the field. NVESD has developed an end-to-end capability to demonstrate the feasibility of this approach. Simple detection algorithms have been used on the degraded images generated by NVIPM-IG to determine the relative performance of the algorithms on both DIRSIG-simulated and collected images. Evaluating the degree to which the algorithm performance agrees between simulated versus field collected imagery is the first step in validating the simulated imagery procedure.

TargetM6A: Identifying N6-Methyladenosine Sites From RNA Sequences via Position-Specific Nucleotide Propensities and a Support Vector Machine.

PubMed

Li, Guang-Qing; Liu, Zi; Shen, Hong-Bin; Yu, Dong-Jun

2016-10-01

As one of the most ubiquitous post-transcriptional modifications of RNA, N 6 -methyladenosine ( [Formula: see text]) plays an essential role in many vital biological processes. The identification of [Formula: see text] sites in RNAs is significantly important for both basic biomedical research and practical drug development. In this study, we designed a computational-based method, called TargetM6A, to rapidly and accurately target [Formula: see text] sites solely from the primary RNA sequences. Two new features, i.e., position-specific nucleotide/dinucleotide propensities (PSNP/PSDP), are introduced and combined with the traditional nucleotide composition (NC) feature to formulate RNA sequences. The extracted features are further optimized to obtain a much more compact and discriminative feature subset by applying an incremental feature selection (IFS) procedure. Based on the optimized feature subset, we trained TargetM6A on the training dataset with a support vector machine (SVM) as the prediction engine. We compared the proposed TargetM6A method with existing methods for predicting [Formula: see text] sites by performing stringent jackknife tests and independent validation tests on benchmark datasets. The experimental results show that the proposed TargetM6A method outperformed the existing methods for predicting [Formula: see text] sites and remarkably improved the prediction performances, with MCC = 0.526 and AUC = 0.818. We also provided a user-friendly web server for TargetM6A, which is publicly accessible for academic use at http://csbio.njust.edu.cn/bioinf/TargetM6A.

Development of VIPER: a simulator for assessing vision performance of warfighters

NASA Astrophysics Data System (ADS)

Familoni, Jide; Thompson, Roger; Moyer, Steve; Mueller, Gregory; Williams, Tim; Nguyen, Hung-Quang; Espinola, Richard L.; Sia, Rose K.; Ryan, Denise S.; Rivers, Bruce A.

2016-05-01

Background: When evaluating vision, it is important to assess not just the ability to read letters on a vision chart, but also how well one sees in real life scenarios. As part of the Warfighter Refractive Eye Surgery Program (WRESP), visual outcomes are assessed before and after refractive surgery. A Warfighter's ability to read signs and detect and identify objects is crucial, not only when deployed in a military setting, but also in their civilian lives. Objective: VIPER, a VIsion PERformance simulator was envisioned as actual video-based simulated driving to test warfighters' functional vision under realistic conditions. Designed to use interactive video image controlled environments at daytime, dusk, night, and with thermal imaging vision, it simulates the experience of viewing and identifying road signs and other objects while driving. We hypothesize that VIPER will facilitate efficient and quantifiable assessment of changes in vision and measurement of functional military performance. Study Design: Video images were recorded on an isolated 1.1 mile stretch of road with separate target sets of six simulated road signs and six objects of military interest, separately. The video footage were integrated with customdesigned C++ based software that presented the simulated drive to an observer on a computer monitor at 10, 20 or 30 miles/hour. VIPER permits the observer to indicate when a target is seen and when it is identified. Distances at which the observer recognizes and identifies targets are automatically logged. Errors in recognition and identification are also recorded. This first report describes VIPER's development and a preliminary study to establish a baseline for its performance. In the study, nine soldiers viewed simulations at 10 miles/hour and 30 miles/hour, run in randomized order for each participant seated at 36 inches from the monitor. Relevance: Ultimately, patients are interested in how their vision will affect their ability to perform daily activities. In the military context, in addition to reading road signs, this includes vision with night sensors and identification of objects of military interest. Once completed and validated, VIPER will be used to evaluate functional performance before and after refractive surgery. Results: This initial study was to prove the principle, and its results at the time of this publication were very preliminary. Nine Soldiers viewed visible-day and IR-day VIPER simulations with civilian and military targets, separately, at 10 and 30 miles/hour. Analyses were performed separately for visible and IR, and also aggregated. Only the civilian targets are discussed in this report. At 10 miles/hour, the population detected civilian road signs at an aggregated average of 90.11 +/- 64.20 m, and identified them at 26.93 +/- 22.27m. At 30 miles/hour, the corresponding distances were 103.03 +/- 58.81 and 26.26 +/- 8.55, respectively. Conclusion: This preliminary report proves the principle and suggests that VIPER could be a useful clinical tool in longitudinal assessment of functional vision in warfighters.

A database de-identification framework to enable direct queries on medical data for secondary use.

PubMed

Erdal, B S; Liu, J; Ding, J; Chen, J; Marsh, C B; Kamal, J; Clymer, B D

2012-01-01

To qualify the use of patient clinical records as non-human-subject for research purpose, electronic medical record data must be de-identified so there is minimum risk to protected health information exposure. This study demonstrated a robust framework for structured data de-identification that can be applied to any relational data source that needs to be de-identified. Using a real world clinical data warehouse, a pilot implementation of limited subject areas were used to demonstrate and evaluate this new de-identification process. Query results and performances are compared between source and target system to validate data accuracy and usability. The combination of hashing, pseudonyms, and session dependent randomizer provides a rigorous de-identification framework to guard against 1) source identifier exposure; 2) internal data analyst manually linking to source identifiers; and 3) identifier cross-link among different researchers or multiple query sessions by the same researcher. In addition, a query rejection option is provided to refuse queries resulting in less than preset numbers of subjects and total records to prevent users from accidental subject identification due to low volume of data. This framework does not prevent subject re-identification based on prior knowledge and sequence of events. Also, it does not deal with medical free text de-identification, although text de-identification using natural language processing can be included due its modular design. We demonstrated a framework resulting in HIPAA Compliant databases that can be directly queried by researchers. This technique can be augmented to facilitate inter-institutional research data sharing through existing middleware such as caGrid.

RISC RNA sequencing for context-specific identification of in vivo microRNA targets.

PubMed

Matkovich, Scot J; Van Booven, Derek J; Eschenbacher, William H; Dorn, Gerald W

2011-01-07

MicroRNAs (miRs) are expanding our understanding of cardiac disease and have the potential to transform cardiovascular therapeutics. One miR can target hundreds of individual mRNAs, but existing methodologies are not sufficient to accurately and comprehensively identify these mRNA targets in vivo. To develop methods permitting identification of in vivo miR targets in an unbiased manner, using massively parallel sequencing of mouse cardiac transcriptomes in combination with sequencing of mRNA associated with mouse cardiac RNA-induced silencing complexes (RISCs). We optimized techniques for expression profiling small amounts of RNA without introducing amplification bias and applied this to anti-Argonaute 2 immunoprecipitated RISCs (RISC-Seq) from mouse hearts. By comparing RNA-sequencing results of cardiac RISC and transcriptome from the same individual hearts, we defined 1645 mRNAs consistently targeted to mouse cardiac RISCs. We used this approach in hearts overexpressing miRs from Myh6 promoter-driven precursors (programmed RISC-Seq) to identify 209 in vivo targets of miR-133a and 81 in vivo targets of miR-499. Consistent with the fact that miR-133a and miR-499 have widely differing "seed" sequences and belong to different miR families, only 6 targets were common to miR-133a- and miR-499-programmed hearts. RISC-sequencing is a highly sensitive method for general RISC profiling and individual miR target identification in biological context and is applicable to any tissue and any disease state.

Nuclear Security: Target Analysis

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

Singh, Surinder Paul; Gibbs, Philip W.; Bultz, Garl A.

2014-03-01

This objectives of this session were to understand the basic steps of target identification; describe the SNRI targets in detail; characterize specific targets with more detail; prioritize targets based on guidance documents; understand the graded safeguards concept; identify roll up and understand why it is a concern; and recognize the category for different materials.

Building high-quality assay libraries for targeted analysis of SWATH MS data.

PubMed

Schubert, Olga T; Gillet, Ludovic C; Collins, Ben C; Navarro, Pedro; Rosenberger, George; Wolski, Witold E; Lam, Henry; Amodei, Dario; Mallick, Parag; MacLean, Brendan; Aebersold, Ruedi

2015-03-01

Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale, by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) typically relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of crucial importance for the performance of the methods. Here we present a detailed protocol that has been successfully used to build high-quality, extensive reference libraries supporting targeted proteomics by SWATH MS. We describe each step of the process, including data acquisition by discovery proteomics, assertion of peptide-spectrum matches (PSMs), generation of consensus spectra and compilation of MS coordinates that uniquely define each targeted peptide. Crucial steps such as false discovery rate (FDR) control, retention time normalization and handling of post-translationally modified peptides are detailed. Finally, we show how to use the library to extract SWATH data with the open-source software Skyline. The protocol takes 2-3 d to complete, depending on the extent of the library and the computational resources available.

Identification of striated muscle activator of Rho signaling (STARS) as a novel calmodulin target by a newly developed genome-wide screen.

PubMed

Furuya, Yusui; Denda, Miwako; Sakane, Kyohei; Ogusu, Tomoko; Takahashi, Sumio; Magari, Masaki; Kanayama, Naoki; Morishita, Ryo; Tokumitsu, Hiroshi

2016-07-01

To search for novel target(s) of the Ca(2+)-signaling transducer, calmodulin (CaM), we performed a newly developed genome-wide CaM interaction screening of 19,676 GST-fused proteins expressed in human. We identified striated muscle activator of Rho signaling (STARS) as a novel CaM target and characterized its CaM binding ability and found that the Ca(2+)/CaM complex interacted stoichiometrically with the N-terminal region (Ala13-Gln35) of STARS in vitro as well as in living cells. Mutagenesis studies identified Ile20 and Trp33 as the essential hydrophobic residues in CaM anchoring. Furthermore, the CaM binding deficient mutant (Ile20Ala, Trp33Ala) of STARS further enhanced its stimulatory effect on SRF-dependent transcriptional activation. These results suggest a connection between Ca(2+)-signaling via excitation-contraction coupling and the regulation of STARS-mediated gene expression in muscles. Copyright © 2016 Elsevier Ltd. All rights reserved.

On-target digestion of collected bacteria for MALDI mass spectrometry.

PubMed

Dugas, Alton J; Murray, Kermit K

2008-10-03

An on-target protein digestion system was developed for the identification of microorganisms in collected bioaerosols using off-line matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Bacteria analysis techniques based on MALDI-MS were adapted for use with an orthogonal MALDI quadrupole-time-of-flight mass spectrometer. Bioaerosols were generated using a pneumatic nebulizer and infused into a chamber for sampling. An Andersen N6 single-stage impactor was used to collect the bioaerosols on a MALDI target. On-target digestion was carried out inside temporary mini-wells placed over the impacted samples. The wells served as miniature reactors for proteolysis. Collected test aerosol particles containing the protein cytochrome c and E. coli bacteria were proteolyzed in situ using trypsin or cyanogen bromide. A total of 19 unique proteins were identified for E. coli. Using the TOF-MS spectra of the digested samples, peptide mass mapping was performed using the MASCOT search engine and an iterative search technique.

Applying a Targeted Label-free Approach using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition

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

Yang, Feng; Jaitly, Navdeep; Jayachandran, Hemalatha

2007-10-12

To identify phosphoproteins regulated by the phosphoprotein phosphatase (PPP) family of S/T phosphatases, we performed a large-scale characterization of changes in protein phosphorylation on extracts from HeLa cells treated with or without calyculin A, a potent PPP enzyme inhibitor. A label-free comparative Phosphoproteomics approach using immobilized metal ion affinity chromatography and targeted tandem mass spectrometry was employed to discover and identify signatures based upon distinctive changes in abundance. Overall, 232 proteins were identified as either direct or indirect targets for PPP enzyme regulation. Most of the present identifications represent novel PPP enzyme targets at the level of both phosphorylation sitemore » and protein. These include phosphorylation sites within signaling proteins such as p120 Catenin, A Kinase Anchoring Protein 8, JunB, and Type II Phosphatidyl Inositol 4 Kinase. These data can be used to define underlying signaling pathways and events regulated by the PPP family of S/T phosphatases.« less

Identification of a Drug Targeting an Intrinsically Disordered Protein Involved in Pancreatic Adenocarcinoma

NASA Astrophysics Data System (ADS)

Neira, José L.; Bintz, Jennifer; Arruebo, María; Rizzuti, Bruno; Bonacci, Thomas; Vega, Sonia; Lanas, Angel; Velázquez-Campoy, Adrián; Iovanna, Juan L.; Abián, Olga

2017-01-01

Intrinsically disordered proteins (IDPs) are prevalent in eukaryotes, performing signaling and regulatory functions. Often associated with human diseases, they constitute drug-development targets. NUPR1 is a multifunctional IDP, over-expressed and involved in pancreatic ductal adenocarcinoma (PDAC) development. By screening 1120 FDA-approved compounds, fifteen candidates were selected, and their interactions with NUPR1 were characterized by experimental and simulation techniques. The protein remained disordered upon binding to all fifteen candidates. These compounds were tested in PDAC-derived cell-based assays, and all induced cell-growth arrest and senescence, reduced cell migration, and decreased chemoresistance, mimicking NUPR1-deficiency. The most effective compound completely arrested tumor development in vivo on xenografted PDAC-derived cells in mice. Besides reporting the discovery of a compound targeting an intact IDP and specifically active against PDAC, our study proves the possibility to target the ‘fuzzy’ interface of a protein that remains disordered upon binding to its natural biological partners or to selected drugs.

A Robust Symmetry-Based Approach to Exploit Terra-SAR-X Dual-Pol Data for Targets at Sea Observation

NASA Astrophysics Data System (ADS)

Velotto, D.; Nunziata, F.; Migliaccio, M.; Lehner, S.

2013-08-01

In this study a simple physical property, known as reflection symmetry, is exploited to differentiate the objects in marine scenes, i.e. sea surface and metallic targets. First the reflection property is verified and demonstrated against actual SAR images, by measuring the magnitude of the correlation between cross- polarized channels (i.e. HH/HV or VH/VV). Then, a sensitivity study is performed to show the potential of the proposed method in observing man-made metallic target at sea. The robustness of the proposed technique is demonstrated using coherent dual-polarimetric X- band SAR data acquired by the satellite TerraSAR-X in both cross-polarization combinations, with different incidence angle and weather conditions. Co-located ground truth information provided by Automatic Identification System (AIS) reports and harbor charts are used to locate ships, navigation aids and buoys. The proposed method outperforms standard single polarization SAR targets at sea observation independently of the radar geometry and oceanic phenomena.

Mood-specific effects in the allocation of attention across time.

PubMed

Rokke, Paul D; Lystad, Chad M

2015-01-01

Participants completed single and dual rapid serial visual presentation (RSVP) tasks. Across five experiments, either the mood of the participant or valence of the target was manipulated to create pairings in which the critical target was either mood congruent or mood noncongruent. When the second target (T2) in an RSVP stream was congruent with the participant's mood, performance was enhanced. This was true for happy and sad moods and in single- and dual-task conditions. In contrast, the effects of congruence varied when the focus was on the first target (T1). When in a sad mood and having attended to a sad T1, detection of a neutral T2 was impaired, resulting in a stronger attentional blink (AB). There was no effect of stimulus-mood congruence for T1 when in a happy mood. It was concluded that mood-congruence is important for stimulus detection, but that sadness uniquely influences post-identification processing when attention is first focused on mood-congruent information.

Evaluation of Waveform Structure Features on Time Domain Target Recognition under Cross Polarization

NASA Astrophysics Data System (ADS)

Selver, M. A.; Seçmen, M.; Zoral, E. Y.

2016-08-01

Classification of aircraft targets from scattered electromagnetic waves is a challenging application, which suffers from aspect angle dependency. In order to eliminate the adverse effects of aspect angle, various strategies were developed including the techniques that rely on extraction of several features and design of suitable classification systems to process them. Recently, a hierarchical method, which uses features that take advantage of waveform structure of the scattered signals, is introduced and shown to have effective results. However, this approach has been applied to the special cases that consider only a single planar component of electric field that cause no-cross polarization at the observation point. In this study, two small scale aircraft models, Boeing-747 and DC-10, are selected as the targets and various polarizations are used to analyse the cross-polarization effects on system performance of the aforementioned method. The results reveal the advantages and the shortcomings of using waveform structures in time-domain target identification.

Identification of a Drug Targeting an Intrinsically Disordered Protein Involved in Pancreatic Adenocarcinoma

PubMed Central

Neira, José L.; Bintz, Jennifer; Arruebo, María; Rizzuti, Bruno; Bonacci, Thomas; Vega, Sonia; Lanas, Angel; Velázquez-Campoy, Adrián; Iovanna, Juan L.; Abián, Olga

2017-01-01

Intrinsically disordered proteins (IDPs) are prevalent in eukaryotes, performing signaling and regulatory functions. Often associated with human diseases, they constitute drug-development targets. NUPR1 is a multifunctional IDP, over-expressed and involved in pancreatic ductal adenocarcinoma (PDAC) development. By screening 1120 FDA-approved compounds, fifteen candidates were selected, and their interactions with NUPR1 were characterized by experimental and simulation techniques. The protein remained disordered upon binding to all fifteen candidates. These compounds were tested in PDAC-derived cell-based assays, and all induced cell-growth arrest and senescence, reduced cell migration, and decreased chemoresistance, mimicking NUPR1-deficiency. The most effective compound completely arrested tumor development in vivo on xenografted PDAC-derived cells in mice. Besides reporting the discovery of a compound targeting an intact IDP and specifically active against PDAC, our study proves the possibility to target the ‘fuzzy’ interface of a protein that remains disordered upon binding to its natural biological partners or to selected drugs. PMID:28054562

Descriptions and identifications of strangers by youth and adult eyewitnesses.

PubMed

Pozzulo, Joanna D; Warren, Kelly L

2003-04-01

Two studies varying target gender and mode of target exposure were conducted to compare the quantity, nature, and accuracy of free recall person descriptions provided by youths and adults. In addition, the relation among age, identification accuracy, and number of descriptors reported was considered. Youths (10-14 years) reported fewer descriptors than adults. Exterior facial descriptors (e.g., hair items) were predominant and accurately reported by youths and adults. Accuracy was consistently problematic for youths when reporting body descriptors (e.g., height, weight) and interior facial features. Youths reported a similar number of descriptors when making accurate versus inaccurate identification decisions. This pattern also was consistent for adults. With target-absent lineups, the difference in the number of descriptors reported between adults and youths was greater when making a false positive versus correct rejection.

Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan).

PubMed

Singh, Vikas K; Khan, Aamir W; Saxena, Rachit K; Sinha, Pallavi; Kale, Sandip M; Parupalli, Swathi; Kumar, Vinay; Chitikineni, Annapurna; Vechalapu, Suryanarayana; Sameer Kumar, Chanda Venkata; Sharma, Mamta; Ghanta, Anuradha; Yamini, Kalinati Narasimhan; Muniswamy, Sonnappa; Varshney, Rajeev K

2017-07-01

Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time-consuming. In recent years, a number of single nucleotide polymorphism (SNP)-based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion-deletion (Indel) were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel-seq approach, which is a combination of whole-genome resequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in extreme bulks. Deployment of Indel-seq approach for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea has identified 16 Indels affecting 26 putative candidate genes. Of these 26 affected putative candidate genes, 24 genes showed effect in the upstream/downstream of the genic region and two genes showed effect in the genes. Validation of these 16 candidate Indels in other FW- and SMD-resistant and FW- and SMD-susceptible genotypes revealed a significant association of five Indels (three for FW and two for SMD resistance). Comparative analysis of Indel-seq with other genetic mapping approaches highlighted the importance of the approach in identification of significant genomic regions associated with target traits. Therefore, the Indel-seq approach can be used for quick and precise identification of candidate genomic regions for any target traits in any crop species. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Identifying novel radiotracers for PET imaging of the brain: application of LC-MS/MS to tracer identification.

PubMed

Barth, Vanessa; Need, Anne

2014-12-17

Nuclear medicine imaging biomarker applications are limited by the radiotracers available. Radiotracers enable the measurement of target engagement, or occupancy in relation to plasma exposure. These tracers can also be used as pharmacodynamic biomarkers to demonstrate functional consequences of binding a target. More recently, radiotracers have also been used for patient tailoring in Alzheimer's disease seen with amyloid imaging. Radiotracers for the central nervous system (CNS) are challenging to identify, as they require a unique intersection of multiple properties. Recent advances in tangential technologies, along with the use of iterative learning for the purposes of deriving in silico models, have opened up additional opportunities to identify radiotracers. Mass spectral technologies and in silico modeling have made it possible to measure and predict in vivo characteristics of molecules to indicate potential tracer performance. By analyzing these data alongside other measures, it is possible to delineate guidelines to increase the likelihood of selecting compounds that can perform as radiotracers or serve as the best starting point to develop a radiotracer following additional structural modification. The application of mass spectrometry based technologies is an efficient way to evaluate compounds as tracers in vivo, but more importantly enables the testing of potential tracers that have either no label site or complex labeling chemistry which may deter assessment by traditional means; therefore, use of this technology allows for more rapid iterative learning. The ability to differentially distribute toward target rich tissues versus tissue with no/less target present is a unique defining feature of a tracer. By testing nonlabeled compounds in vivo and analyzing tissue levels by LC-MS/MS, rapid assessment of a compound's ability to differentially distribute in a manner consistent with target expression biology guides the focus of chemistry resources for both designing and labeling tracer candidates. LC-MS/MS has only recently been used for de novo tracer identification; however, this connection of mass spectral technology to imaging has initiated engagement from a wider community that brings diverse backgrounds into the tracer discovery arena.

Retrieval does not always enhance suggestibility: testing can improve witness identification performance.

PubMed

LaPaglia, Jessica A; Chan, Jason C K

2012-12-01

Verbally recalling the appearance of a perpetrator and the details of an event can sometimes hinder later eyewitness memory performance. In two experiments, we investigated the effects of verbally recalling a face on people's ability to resist subsequent misinformation about that face. Participants watched a video of a theft and then completed either a recall test or a distractor activity. After a delay, some participants heard a piece of misinformation. Memory was assessed with a recall test in Experiment 1 and with a target-present lineup in Experiment 2. In both experiments, initial testing reduced eyewitness suggestibility for the face.

Identification of Technology Terms in Patents (Open Access, Published Version)

DTIC Science & Technology

2014-05-31

large set of human anno - tated examples of the target class(es) along with their tex- tual contexts to serve as training examples for generating a machine...perform the equiva- lent function in German and Chinese. 2.2. Manual annotation of terms Supervised learning requires a gold set of manually anno ...Npr, prev Jpr, prev J ). These were intended to capture, for ex- ample, the verb (and any prepositions/articles) for which the term is the object. prev

Identification and Therapeutic Targeting of Paracrine Senescence Factors in the Prostate Tumor Microenvironment

DTIC Science & Technology

2011-10-01

PROJECT NUMBER James P. Dean, M.D., Ph.D. 5e. TASK NUMBER E-Mail: amoreno@fhcrc.org 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S...secretion of STC1 were defined, but multiple studies seeking to define the function of STC1 in the prostate were uniformly negative. A clinical trial...men in the United States - could be prevented with more effective treatments. Overcoming tumor cell resistance to the effects of androgen

BHC80 ss Critical in Suppression of Snail-LSD1 Interaction and Breast Cancer Metastasis

DTIC Science & Technology

2012-01-01

as well as Snail/LSD1 binding to the target gene promoter. The identification and functional characterization of PAPR1 will potentially help us...demonstrated that LSD1 enhances the protein stability of Snail and cooperates with Snail to induce EMT, the function of BHC80, as well as potential...identified a new protein component of the Snail/LSD1 complex, and have performed initial experiments to characterize the function of this protein, which

Night Vision Camera

NASA Technical Reports Server (NTRS)

1996-01-01

PixelVision, Inc. developed the Night Video NV652 Back-illuminated CCD Camera, based on the expertise of a former Jet Propulsion Laboratory employee and a former employee of Scientific Imaging Technologies, Inc. The camera operates without an image intensifier, using back-illuminated and thinned CCD technology to achieve extremely low light level imaging performance. The advantages of PixelVision's system over conventional cameras include greater resolution and better target identification under low light conditions, lower cost and a longer lifetime. It is used commercially for research and aviation.

DeepMirTar: a deep-learning approach for predicting human miRNA targets.

PubMed

Wen, Ming; Cong, Peisheng; Zhang, Zhimin; Lu, Hongmei; Li, Tonghua

2018-06-01

MicroRNAs (miRNAs) are small noncoding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression by targeting messenger RNAs (mRNAs). Because the underlying mechanisms associated with miRNA binding to mRNA are not fully understood, a major challenge of miRNA studies involves the identification of miRNA-target sites on mRNA. In silico prediction of miRNA-target sites can expedite costly and time-consuming experimental work by providing the most promising miRNA-target-site candidates. In this study, we reported the design and implementation of DeepMirTar, a deep-learning-based approach for accurately predicting human miRNA targets at the site level. The predicted miRNA-target sites are those having canonical or non-canonical seed, and features, including high-level expert-designed, low-level expert-designed, and raw-data-level, were used to represent the miRNA-target site. Comparison with other state-of-the-art machine-learning methods and existing miRNA-target-prediction tools indicated that DeepMirTar improved overall predictive performance. DeepMirTar is freely available at https://github.com/Bjoux2/DeepMirTar_SdA. lith@tongji.edu.cn, hongmeilu@csu.edu.cn. Supplementary data are available at Bioinformatics online.

Novel Small Molecule Entry Inhibitors of Ebola Virus

PubMed Central

Basu, Arnab; Mills, Debra M.; Mitchell, Daniel; Ndungo, Esther; Williams, John D.; Herbert, Andrew S.; Dye, John M.; Moir, Donald T.; Chandran, Kartik; Patterson, Jean L.; Rong, Lijun; Bowlin, Terry L.

2015-01-01

Background. The current Ebola virus (EBOV) outbreak has highlighted the troubling absence of available antivirals or vaccines to treat infected patients and stop the spread of EBOV. The EBOV glycoprotein (GP) plays critical roles in the early stage of virus infection, including receptor binding and membrane fusion, making it a potential target for the development of anti-EBOV drugs. We report the identification of 2 novel EBOV inhibitors targeting viral entry. Methods. To identify small molecule inhibitors of EBOV entry, we carried out a cell-based high-throughput screening using human immunodeficiency virus–based pseudotyped viruses expressing EBOV-GP. Two compounds were identified, and mechanism-of-action studies were performed using immunoflourescence, AlphaLISA, and enzymatic assays for cathepsin B inhibition. Results. We report the identification of 2 novel entry inhibitors. These inhibitors (1) inhibit EBOV infection (50% inhibitory concentration, approximately 0.28 and approximately 10 µmol/L) at a late stage of entry, (2) induce Niemann-Pick C phenotype, and (3) inhibit GP–Niemann-Pick C1 (NPC1) protein interaction. Conclusions. We have identified 2 novel EBOV inhibitors, MBX2254 and MBX2270, that can serve as starting points for the development of an anti-EBOV therapeutic agent. Our findings also highlight the importance of NPC1-GP interaction in EBOV entry and the attractiveness of NPC1 as an antifiloviral therapeutic target. PMID:26206510

Identification of PTP1B and α-Glucosidase Inhibitory Serrulatanes from Eremophila spp. by Combined use of Dual High-Resolution PTP1B and α-Glucosidase Inhibition Profiling and HPLC-HRMS-SPE-NMR.

PubMed

Wubshet, Sileshi G; Tahtah, Yousof; Heskes, Allison M; Kongstad, Kenneth T; Pateraki, Irini; Hamberger, Björn; Møller, Birger L; Staerk, Dan

2016-04-22

According to the International Diabetes Federation, type 2 diabetes (T2D) has reached epidemic proportions, affecting more than 382 million people worldwide. Inhibition of protein tyrosine phosphatase-1B (PTP1B) and α-glucosidase is a recognized therapeutic approach for management of T2D and its associated complications. The lack of clinical drugs targeting PTP1B and side effects of the existing α-glucosidase drugs, emphasize the need for new drug leads for these T2D targets. In the present work, dual high-resolution PTP1B and α-glucosidase inhibition profiles of Eremophila gibbosa, E. glabra, and E. aff. drummondii "Kalgoorlie" were used for pinpointing α-glucosidase and/or PTP1B inhibitory constituents directly from the crude extracts. A subsequent targeted high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction-nuclear magnetic resonance spectroscopy (HPLC-HRMS-SPE-NMR) analysis and preparative-scale HPLC isolation led to identification of 21 metabolites from the three species, of which 16 were serrulatane-type diterpenoids (12 new) associated with either α-glucosidase and/or PTP1B inhibition. This is the first report of serrulatane-type diterpenoids as potential α-glucosidase and/or PTP1B inhibitors.

PDNAsite: Identification of DNA-binding Site from Protein Sequence by Incorporating Spatial and Sequence Context

PubMed Central

Zhou, Jiyun; Xu, Ruifeng; He, Yulan; Lu, Qin; Wang, Hongpeng; Kong, Bing

2016-01-01

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community. PMID:27282833

A pre-classification strategy based on UPLC-Triple-TOF/MS for metabolic screening and identification of Radix glehniae in rats.

PubMed

Wang, Shuang; Qi, Pengcheng; Zhou, Na; Zhao, Minmin; Ding, Weijing; Li, Song; Liu, Minyan; Wang, Qiao; Jin, Shumin

2016-10-01

Traditional Chinese Medicines (TCMs) have gained increasing popularity in modern society. However, the profiles of TCMs in vivo are still unclear owing to their complexity and low level in vivo. In this study, UPLC-Triple-TOF techniques were employed for data acquiring, and a novel pre-classification strategy was developed to rapidly and systematically screen and identify the absorbed constituents and metabolites of TCMs in vivo using Radix glehniae as the research object. In this strategy, pre-classification for absorbed constituents was first performed according to the similarity of their structures. Then representative constituents were elected from every class and analyzed separately to screen non-target absorbed constituents and metabolites in biosamples. This pre-classification strategy is basing on target (known) constituents to screen non-target (unknown) constituents from the massive data acquired by mass spectrometry. Finally, the screened candidate compounds were interpreted and identified based on a predicted metabolic pathway, well - studied fragmentation rules, a predicted metabolic pathway, polarity and retention time of the compounds, and some related literature. With this method, a total of 111 absorbed constituents and metabolites of Radix glehniae in rats' urine, plasma, and bile samples were screened and identified or tentatively characterized successfully. This strategy provides an idea for the screening and identification of the metabolites of other TCMs.

An Efficient Approach to Evaluate Reporter Ion Behavior from MALDI-MS/MS Data for Quantification Studies using Isobaric Tags

PubMed Central

Cologna, Stephanie M.; Crutchfield, Christopher A.; Searle, Brian C.; Blank, Paul S.; Toth, Cynthia L.; Ely, Alexa M.; Picache, Jaqueline A.; Backlund, Peter S.; Wassif, Christopher A.; Porter, Forbes D.; Yergey, Alfred L.

2017-01-01

Protein quantification, identification and abundance determination are important aspects of proteome characterization and are crucial in understanding biological mechanisms and human diseases. Different strategies are available to quantify proteins using mass spectrometric detection, and most are performed at the peptide level and include both targeted and un-targeted methodologies. Discovery-based or un-targeted approaches oftentimes use covalent tagging strategies (i.e., iTRAQ®, TMT™) where reporter ion signals collected in the tandem MS experiment are used for quantification. Herein we investigate the behavior of the iTRAQ 8-plex chemistry using MALDI-TOF/TOF instrumentation. The experimental design and data analysis approach described is simple and straightforward, which allows researchers to optimize data collection and proper analysis within a laboratory. iTRAQ reporter ion signals were normalized within each spectrum to remove peptide biases. An advantage of this approach is that missing reporter ion values can be accepted for purposes of protein identification and quantification with the need for ANOVA analysis. We investigate the distribution of reporter ion peak areas in an equimolar system and a mock biological system and provide recommendations for establishing fold-change cutoff values at the peptide level for iTRAQ datasets. These data provide a unique dataset available to the community for informatics training and analysis. PMID:26288259