Direct identification and recognition of yeast species from clinical material by using albicans ID and CHROMagar Candida plates.

PubMed

Baumgartner, C; Freydiere, A M; Gille, Y

1996-02-01

Two chromogenic media, Albicans ID and CHROMagar Candida agar plates, were compared with a reference medium, Sabouraud-chloramphenicol agar, and standard methods for the identification of yeast species. This study involved 951 clinical specimens. The detection rates for the two chromogenic media for polymicrobial specimens were 20% higher than that for the Sabouraud-chloramphenicol agar plates. The rates of identification of Candida albicans for Albicans ID and CHROMagar Candida agar plates were, respectively, 37.0 and 6.0% after 24 h of incubation and 93.6 and 92.2% after 72 h of incubation, with specificities of 99.8 and 100%. Furthermore, CHROMagar Candida plates identified 13 of 14 Candida tropicalis and 9 of 12 Candida krusei strains after 48 h of incubation.

SimExTargId: A comprehensive package for real-time LC-MS data acquisition and analysis.

PubMed

Edmands, William M B; Hayes, Josie; Rappaport, Stephen M

2018-05-22

Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis. Users are notified of detrimental instrument drift or errors by email. Also included are two shiny applications, targetId for real-time MS2 target identification, and peakMonitor to monitor targeted metabolites. SimExTargId is publicly available under GNU LGPL v3.0 license at https://github.com/JosieLHayes/simExTargId, which includes a vignette with example data. SimExTargId should be installed on a dedicated data-processing workstation or server that is networked to the LC-MS platform to facilitate MS1 profiling of metabolomic data. josie.hayes@berkeley.edu. Supplementary data are available at Bioinformatics online.

Proposed Confidence Scale and ID Score in the Identification of Known-Unknown Compounds Using High Resolution MS Data

NASA Astrophysics Data System (ADS)

Rochat, Bertrand

2017-04-01

High-resolution (HR) MS instruments recording HR-full scan allow analysts to go further beyond pre-acquisition choices. Untargeted acquisition can reveal unexpected compounds or concentrations and can be performed for preliminary diagnosis attempt. Then, revealed compounds will have to be identified for interpretations. Whereas the need of reference standards is mandatory to confirm identification, the diverse information collected from HRMS allows identifying unknown compounds with relatively high degree of confidence without reference standards injected in the same analytical sequence. However, there is a necessity to evaluate the degree of confidence in putative identifications, possibly before further targeted analyses. This is why a confidence scale and a score in the identification of (non-peptidic) known-unknown, defined as compounds with entries in database, is proposed for (LC-) HRMS data. The scale is based on two representative documents edited by the European Commission (2007/657/EC) and the Metabolomics Standard Initiative (MSI), in an attempt to build a bridge between the communities of metabolomics and screening labs. With this confidence scale, an identification (ID) score is determined as [a number, a letter, and a number] (e.g., 2D3), from the following three criteria: I, a General Identification Category (1, confirmed, 2, putatively identified, 3, annotated compounds/classes, and 4, unknown); II, a Chromatography Class based on the relative retention time (from the narrowest tolerance, A, to no chromatographic references, D); and III, an Identification Point Level (1, very high, 2, high, and 3, normal level) based on the number of identification points collected. Three putative identification examples of known-unknown will be presented.

MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species.

PubMed

Kim, Young Jin; Kim, Si Hyun; Park, Hyun-Jung; Park, Hae-Geun; Park, Dongchul; Song, Sae Am; Lee, Hee Joo; Yong, Dongeun; Choi, Jun Yong; Kook, Joong-Ki; Kim, Hye Ran; Shin, Jeong Hwan

2016-08-01

All 50 Clostridium difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF. For 18 non-difficile Clostridium strains, the identification results were correct in 0, 2, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively. MALDI-TOF could be used as the primary tool for identification of Clostridium species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Best practices for the implementation of the REAL ID Act.

DOT National Transportation Integrated Search

2015-10-01

The REAL ID Act specifies the minimum standards that must be used to produce and issue drivers license and : identification cards that are REAL ID compliant. Beginning in 2020, if a person does not possess a form of : identification that meets REA...

SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers

PubMed Central

Hass, Matthew R.; Liow, Hien-haw; Chen, Xiaoting; Sharma, Ankur; Inoue, Yukiko U.; Inoue, Takayoshi; Reeb, Ashley; Martens, Andrew; Fulbright, Mary; Raju, Saravanan; Stevens, Michael; Boyle, Scott; Park, Joo-Seop; Weirauch, Matthew T.; Brent, Michael; Kopan, Raphael

2015-01-01

SUMMARY We developed Split DamID (SpDamID), a protein complementation version of DamID, to mark genomic DNA bound in vivo by interacting or juxtapositioned transcription factors. Inactive halves of DAM (DNA Adenine Methyltransferase) were fused to protein pairs to be queried Interaction or proximity enabled DAM reconstitution and methylation of adenine in GATC. Inducible SpDamID was used to analyze Notch-mediated transcriptional activation. We demonstrate that Notch complexes label RBP sites broadly across the genome, and show that a subset of these complexes that recruit MAML and p300 undergo changes in chromatin accessibility in response to Notch signaling. SpDamID differentiates between monomeric and dimeric binding thereby allowing for identification of half-site motifs used by Notch dimers. Motif enrichment of Notch enhancers coupled with SpDamID reveals co-targeting of regulatory sequences by Notch and Runx1. SpDamID represents a sensitive and powerful tool that enables dynamic analysis of combinatorial protein-DNA transactions at a genome-wide level. PMID:26257285

A new module in neural differentiation control: two microRNAs upregulated by retinoic acid, miR-9 and -103, target the differentiation inhibitor ID2.

PubMed

Annibali, Daniela; Gioia, Ubaldo; Savino, Mauro; Laneve, Pietro; Caffarelli, Elisa; Nasi, Sergio

2012-01-01

The transcription factor ID2 is an important repressor of neural differentiation strongly implicated in nervous system cancers. MicroRNAs (miRNAs) are increasingly involved in differentiation control and cancer development. Here we show that two miRNAs upregulated on differentiation of neuroblastoma cells--miR-9 and miR-103--restrain ID2 expression by directly targeting the coding sequence and 3' untranslated region of the ID2 encoding messenger RNA, respectively. Notably, the two miRNAs show an inverse correlation with ID2 during neuroblastoma cell differentiation induced by retinoic acid. Overexpression of miR-9 and miR-103 in neuroblastoma cells reduces proliferation and promotes differentiation, as it was shown to occur upon ID2 inhibition. Conversely, an ID2 mutant that cannot be targeted by either miRNA prevents retinoic acid-induced differentiation more efficient than wild-type ID2. These findings reveal a new regulatory module involving two microRNAs upregulated during neural differentiation that directly target expression of the key differentiation inhibitor ID2, suggesting that its alteration may be involved in neural cancer development.

A New Module in Neural Differentiation Control: Two MicroRNAs Upregulated by Retinoic Acid, miR-9 and -103, Target the Differentiation Inhibitor ID2

PubMed Central

Savino, Mauro; Laneve, Pietro; Caffarelli, Elisa; Nasi, Sergio

2012-01-01

The transcription factor ID2 is an important repressor of neural differentiation strongly implicated in nervous system cancers. MicroRNAs (miRNAs) are increasingly involved in differentiation control and cancer development. Here we show that two miRNAs upregulated on differentiation of neuroblastoma cells – miR-9 and miR-103 – restrain ID2 expression by directly targeting the coding sequence and 3′ untranslated region of the ID2 encoding messenger RNA, respectively. Notably, the two miRNAs show an inverse correlation with ID2 during neuroblastoma cell differentiation induced by retinoic acid. Overexpression of miR-9 and miR-103 in neuroblastoma cells reduces proliferation and promotes differentiation, as it was shown to occur upon ID2 inhibition. Conversely, an ID2 mutant that cannot be targeted by either miRNA prevents retinoic acid-induced differentiation more efficient than wild-type ID2. These findings reveal a new regulatory module involving two microRNAs upregulated during neural differentiation that directly target expression of the key differentiation inhibitor ID2, suggesting that its alteration may be involved in neural cancer development. PMID:22848373

Towards Open-World Person Re-Identification by One-Shot Group-Based Verification.

PubMed

Zheng, Wei-Shi; Gong, Shaogang; Xiang, Tao

2016-03-01

Solving the problem of matching people across non-overlapping multi-camera views, known as person re-identification (re-id), has received increasing interests in computer vision. In a real-world application scenario, a watch-list (gallery set) of a handful of known target people are provided with very few (in many cases only a single) image(s) (shots) per target. Existing re-id methods are largely unsuitable to address this open-world re-id challenge because they are designed for (1) a closed-world scenario where the gallery and probe sets are assumed to contain exactly the same people, (2) person-wise identification whereby the model attempts to verify exhaustively against each individual in the gallery set, and (3) learning a matching model using multi-shots. In this paper, a novel transfer local relative distance comparison (t-LRDC) model is formulated to address the open-world person re-identification problem by one-shot group-based verification. The model is designed to mine and transfer useful information from a labelled open-world non-target dataset. Extensive experiments demonstrate that the proposed approach outperforms both non-transfer learning and existing transfer learning based re-id methods.

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

Advancements in the safe identification of explosives using a Raman handheld instrument (ACE-ID)

NASA Astrophysics Data System (ADS)

Arnó, Josep; Frunzi, Michael; Kittredge, Marina; Sparano, Brian

2014-05-01

Raman spectroscopy is the technology of choice to identify bulk solid and liquid phase unknown samples without the need to contact the substance. Materials can be identified through transparent and semi-translucent containers such as plastic and glass. ConOps in emergency response and military field applications require the redesign of conventional laboratory units for: field portability; shock, thermal and chemical attack resistance; easy and intuitive use in restrictive gear; reduced size, weight, and power. This article introduces a new handheld instrument (ACE-IDTM) designed to take Raman technology to the next level in terms of size, safety, speed, and analytical performance. ACE-ID is ruggedized for use in severe climates and terrains. It is lightweight and can be operated with just one hand. An intuitive software interface guides users through the entire identification process, making it easy-to-use by personnel of different skill levels including military explosive ordinance disposal technicians, civilian bomb squads and hazmat teams. Through the use of embedded advanced algorithms, the instrument is capable of providing fluorescence correction and analysis of binary mixtures. Instrument calibration is performed automatically upon startup without requiring user intervention. ACE-ID incorporates an optical rastering system that diffuses the laser energy over the sample. This important innovation significantly reduces the heat induced in dark samples and the probability of ignition of susceptible explosive materials. In this article, the explosives identification performance of the instrument will be provided in addition to a quantitative evaluation of the safety improvements derived from the reduced ignition probabilities.

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.

A Contextual Model for Identity Management (IdM) Interfaces

ERIC Educational Resources Information Center

Fuller, Nathaniel J.

2014-01-01

The usability of Identity Management (IdM) systems is highly dependent upon design that simplifies the processes of identification, authentication, and authorization. Recent findings reveal two critical problems that degrade IdM usability: (1) unfeasible techniques for managing various digital identifiers, and (2) ambiguous security interfaces.…

Fast Open-World Person Re-Identification.

PubMed

Zhu, Xiatian; Wu, Botong; Huang, Dongcheng; Zheng, Wei-Shi

2018-05-01

Existing person re-identification (re-id) methods typically assume that: 1) any probe person is guaranteed to appear in the gallery target population during deployment (i.e., closed-world) and 2) the probe set contains only a limited number of people (i.e., small search scale). Both assumptions are artificial and breached in real-world applications, since the probe population in target people search can be extremely vast in practice due to the ambiguity of probe search space boundary. Therefore, it is unrealistic that any probe person is assumed as one target people, and a large-scale search in person images is inherently demanded. In this paper, we introduce a new person re-id search setting, called large scale open-world (LSOW) re-id, characterized by huge size probe images and open person population in search thus more close to practical deployments. Under LSOW, the under-studied problem of person re-id efficiency is essential in addition to that of commonly studied re-id accuracy. We, therefore, develop a novel fast person re-id method, called Cross-view Identity Correlation and vErification (X-ICE) hashing, for joint learning of cross-view identity representation binarisation and discrimination in a unified manner. Extensive comparative experiments on three large-scale benchmarks have been conducted to validate the superiority and advantages of the proposed X-ICE method over a wide range of the state-of-the-art hashing models, person re-id methods, and their combinations.

76 FR 43196 - Implementation of the Truth in Caller ID Act

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-20

...In this Report and Order (Order), the Commission adopts rules to implement the Truth in Caller ID Act of 2009 (Truth in Caller ID Act, or Act). The Truth in Caller ID Act, and the Commission's implementing rules, prohibit any person or entity from knowingly altering or manipulating caller identification information with the intent to defraud, cause harm, or wrongfully obtain anything of value.

Combining CBT and Behavior-Analytic Approaches to Target Severe Emotion Dysregulation in Verbal Youth with ASD and ID

ERIC Educational Resources Information Center

Parent, Veronique; Birtwell, Kirstin B.; Lambright, Nathan; DuBard, Melanie

2016-01-01

This article presents an individual intervention combining cognitive-behavioral and behavior-analytic approaches to target severe emotion dysregulation in verbal youth with autism spectrum disorder (ASD) concurrent with intellectual disability (ID). The article focuses on two specific individuals who received the treatment within a therapeutic…

Full-Spectrum-Analysis Isotope ID

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

Mitchell, Dean J.; Harding, Lee; Thoreson, Gregory G.

2017-06-28

FSAIsotopeID analyzes gamma ray spectra to identify radioactive isotopes (radionuclides). The algorithm fits the entire spectrum with combinations of pre-computed templates for a comprehensive set of radionuclides with varying thicknesses and compositions of shielding materials. The isotope identification algorithm is suitable for the analysis of spectra collected by gamma-ray sensors ranging from medium-resolution detectors, such a NaI, to high-resolution detectors, such as HPGe. In addition to analyzing static measurements, the isotope identification algorithm is applied for the radiation search applications. The search subroutine maintains a running background spectrum that is passed to the isotope identification algorithm, and it also selectsmore » temporal integration periods that optimize the responsiveness and sensitivity. Gain stabilization is supported for both types of applications.« less

Clinical accuracy of a PLEX-ID flu device for simultaneous detection and identification of influenza viruses A and B.

PubMed

Tang, Yi-Wei; Lowery, Kristin S; Valsamakis, Alexandra; Schaefer, Virginia C; Chappell, James D; White-Abell, Jill; Quinn, Criziel D; Li, Haijing; Washington, Cicely A; Cromwell, Jenna; Giamanco, Chantel M; Forman, Michael; Holden, Jeffery; Rothman, Richard E; Parker, Michelle L; Ortenberg, Elaine V; Zhang, Lei; Lin, Yea-Lin; Gaydos, Charlotte A

2013-01-01

influenza A virus detection and H1N1-p subtyping. The PLEX-ID Flu assay demonstrated a high level of accuracy for the simultaneous detection and identification of influenza A and B viruses in patient specimens, providing a new laboratory tool for the rapid diagnosis and management of influenza A and B virus infections.

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

Influence of the Distribution of Tag IDs on RFID Memoryless Anti-Collision Protocols

PubMed Central

Cmiljanic, Nikola; Landaluce, Hugo; Perallos, Asier; Arjona, Laura

2017-01-01

In recent years, Radio Frequency Identification (RFID) has become very popular. The main feature of this technology is that RFID tags do not require close handling and no line of sight is required between the reader and the tags. RFID is a technology that uses radio frequencies in order to identify tags, which do not need to be positioned accurately relative to the reader. Tags share the communication channel, increasing the likelihood of causing a problem, viz., a message collision. Tree based protocols can resolve these collisions, but require a uniform tag ID distribution. This means they are very dependent of the distribution of the IDs of the tags. Tag IDs are written in the tag and contain a predefined bit string of data. A study of the influence of the tag ID distribution on the protocols’ behaviour is proposed here. A new protocol, called the Flexible Query window Tree (FQwT) is presented to estimate the tag ID distribution, taking into consideration the type of distribution. The aim is to create a flexible anti-collision protocol in order to identify a set of tags that constitute an ID distribution. As a result, the reader classifies tags into groups determined by using a distribution estimator. Simulations show that the FQwT protocol contributes to significant reductions in identification time and energy consumption regardless of the type of ID distribution. PMID:28817070

Influence of the Distribution of Tag IDs on RFID Memoryless Anti-Collision Protocols.

PubMed

Cmiljanic, Nikola; Landaluce, Hugo; Perallos, Asier; Arjona, Laura

2017-08-17

In recent years, Radio Frequency Identification (RFID) has become very popular. The main feature of this technology is that RFID tags do not require close handling and no line of sight is required between the reader and the tags. RFID is a technology that uses radio frequencies in order to identify tags, which do not need to be positioned accurately relative to the reader. Tags share the communication channel, increasing the likelihood of causing a problem, viz., a message collision. Tree based protocols can resolve these collisions, but require a uniform tag ID distribution. This means they are very dependent of the distribution of the IDs of the tags. Tag IDs are written in the tag and contain a predefined bit string of data. A study of the influence of the tag ID distribution on the protocols' behaviour is proposed here. A new protocol, called the Flexible Query window Tree (FQwT) is presented to estimate the tag ID distribution, taking into consideration the type of distribution. The aim is to create a flexible anti-collision protocol in order to identify a set of tags that constitute an ID distribution. As a result, the reader classifies tags into groups determined by using a distribution estimator. Simulations show that the FQwT protocol contributes to significant reductions in identification time and energy consumption regardless of the type of ID distribution.

National Plant Diagnostic Network, Taxonomic training videos: Introduction to AphID

USDA-ARS?s Scientific Manuscript database

Training is a critical part of aphid (Hemiptera: Aphididae) identification. This video provides visual instruction on the use of the expert system, AphID, for aphid examination and identification. The video demonstrates the use of different training modules that allow the user to gain familiarity wi...

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.

Broad-Range Direct Detection and Identification of Fungi by Use of the PLEX-ID PCR-Electrospray Ionization Mass Spectrometry (ESI-MS) System

PubMed Central

Simner, Patricia J.; Uhl, James R.; Hall, Leslie; Weber, Michelle M.; Walchak, Robert C.; Buckwalter, Seanne

2013-01-01

The PLEX-ID system is a novel technology that couples PCR amplification and electrospray ionization-mass spectrometry to identify pathogens directly in clinical specimens. The analytical performance of the PLEX-ID Broad Fungal assay was compared with that of traditional culture identification by using 91 characterized fungal culture isolates (64 manufacturer-claimed and 27 nonclaimed organisms) and directly by using 395 respiratory specimens. Discordant results were resolved by D2 large-subunit ribosomal DNA fungal sequencing. Environmental studies were performed to monitor for potential contamination. The PLEX-ID Broad Fungal assay correctly identified 95.6% (87/91) and 81.3% (74/91) of the culture isolates to the genus and species levels, respectively. Of the manufacturer-claimed organisms, 100% (64/64) and 92.2% (59/64) were correctly identified to the genus and species levels, respectively. Direct analysis of respiratory specimens resulted in 67.6% (267/395) and 66.6% (263/395) agreement with culture results to the genus and species levels, respectively, with 16.2% (64/395) of the results discordant with culture and 16.2% (64/395) not detected by the system. The majority (>95%) of the isolates not detected directly by the PLEX-ID system ultimately grew in low quantities in culture (≤20 colonies). In 20.3% (35/172) of the respiratory specimens where no growth was observed in culture, the PLEX-ID system identified a fungus, suggesting a potential increase in sensitivity over culture in some instances. The PLEX-ID system provides a rapid method for the detection of a broad array of fungi directly in respiratory specimens and has the potential of impacting turnaround times and patient care by reducing the need to wait for the growth of an organism in culture. PMID:23515540

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

Rapid identification of moulds and arthroconidial yeasts from positive blood cultures by MALDI-TOF mass spectrometry.

PubMed

de Almeida, João N; Sztajnbok, Jaques; da Silva, Afonso Rafael; Vieira, Vinicius Adriano; Galastri, Anne Layze; Bissoli, Leandro; Litvinov, Nadia; Del Negro, Gilda Maria Barbaro; Motta, Adriana Lopes; Rossi, Flávia; Benard, Gil

2016-11-01

Moulds and arthroconidial yeasts are potential life-threatening agents of fungemia in immunocompromised patients. Fast and accurate identification (ID) of these pathogens hastens initiation of targeted antifungal therapy, thereby improving the patients' prognosis. We describe a new strategy that enabled the identification of moulds and arthroconidial yeasts directly from positive blood cultures by MALDI-TOF mass spectrometry (MS). Positive blood cultures (BCs) with Gram staining showing hyphae and/or arthroconidia were prospectively selected and submitted to an in-house protein extraction protocol. Mass spectra were obtained by Vitek MS™ system, and identifications were carried out with in the research use only (RUO) mode with an extended database (SARAMIS™ [v.4.12] plus in-house database). Fusarium solani, Fusarium verticillioides, Exophiala dermatitidis, Saprochaete clavata, and Trichosporon asahii had correct species ID by MALDI-TOF MS analysis of positive BCs. All cases were related to critically ill patients with high mortality fungemia and direct ID from positive BCs was helpful for rapid administration of targeted antifungal therapy. © 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.

Effect of Refrigeration on Inoculated Micro-ID Strips

PubMed Central

Burdash, Nicholas M.; West, Marcia E.

1981-01-01

Since reading results after 4 h with the Micro-ID system is not always convenient, a study of 500 isolates indicated that identification at the species level is essentially unchanged when inoculated strips are refrigerated overnight and then incubated or incubated and then refrigerated overnight before reading. PMID:7026604

Fake ID ownership and heavy drinking in underage college students: prospective findings.

PubMed

Martinez, Julia A; Rutledge, Patricia C; Sher, Kenneth J

2007-06-01

The authors examined the ownership of false identification (fake ID) for the purpose of obtaining alcohol and the relation of fake ID ownership to heavy drinking in a longitudinal sample of college students under 21 years of age. A sample of 3,720 undergraduates was assessed the summer prior to college entrance and during the 4 semesters comprising freshman and sophomore years. Regression analyses were used to estimate bidirectional relations between consumption and fake ID ownership. Sex, Greek membership, and prior drinking were controlled. Results showed that fake ID ownership increased over time (12.5% pre-college to 32.2% fourth semester) and that Greek members were more likely than others to own fake IDs. Fake ID ownership predicted concurrent and next-semester heavy drinking with increasing strength over time. Also, the acquisition (onset) of fake ID ownership at each time point was predicted by previous-semester consumption. When traditional, robust risk factors of consumption are controlled, fake ID ownership meaningfully relates to heavy drinking in college. It thus presents a significant public health problem, addressable through training for alcohol servers and retailers, punitive measures toward fake ID owners, and other possible interventions.

Use of Sequenom Sample ID Plus® SNP Genotyping in Identification of FFPE Tumor Samples

PubMed Central

Miller, Jessica K.; Buchner, Nicholas; Timms, Lee; Tam, Shirley; Luo, Xuemei; Brown, Andrew M. K.; Pasternack, Danielle; Bristow, Robert G.; Fraser, Michael; Boutros, Paul C.; McPherson, John D.

2014-01-01

Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76–139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS). The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework. PMID:24551080

Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.

PubMed

Miller, Jessica K; Buchner, Nicholas; Timms, Lee; Tam, Shirley; Luo, Xuemei; Brown, Andrew M K; Pasternack, Danielle; Bristow, Robert G; Fraser, Michael; Boutros, Paul C; McPherson, John D

2014-01-01

Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS). The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.

ID card number detection algorithm based on convolutional neural network

NASA Astrophysics Data System (ADS)

Zhu, Jian; Ma, Hanjie; Feng, Jie; Dai, Leiyan

2018-04-01

In this paper, a new detection algorithm based on Convolutional Neural Network is presented in order to realize the fast and convenient ID information extraction in multiple scenarios. The algorithm uses the mobile device equipped with Android operating system to locate and extract the ID number; Use the special color distribution of the ID card, select the appropriate channel component; Use the image threshold segmentation, noise processing and morphological processing to take the binary processing for image; At the same time, the image rotation and projection method are used for horizontal correction when image was tilting; Finally, the single character is extracted by the projection method, and recognized by using Convolutional Neural Network. Through test shows that, A single ID number image from the extraction to the identification time is about 80ms, the accuracy rate is about 99%, It can be applied to the actual production and living environment.

[Expression of Id1 and Id3 in endometrial carcinoma and their roles in regulating biological behaviors of endometrial carcinoma cells in vitro].

PubMed

Sun, Lili; Li, Xuenong; Liu, Guobing

2013-06-01

To investigate the expression of inhibitor of DNA differentiation/DNA binding 1 (Id1) and Id3 in endometrial carcinoma and explore their roles in regulating the proliferation, invasion, migration and adhesion of endometrial carcinoma cells in vitro. Id1 and Id3 expression in 4 fresh endometrial cancer tissue specimens and matched adjacent tissues were detected using Western blotting. Two endometrial cancer cell lines, HEC-1-B and RL-952, were both divided into 4 groups, namely the untreated group, blank virus group, promoter group and Id1/Id3 double-knockdown group, and their expressions of MMP2, CXCR4 and P21 were detected by qRT-PCR and Western blotting. The proliferation, invasion, migration and adhesion of the cells were evaluated with MTT, Transwell, wound-healing, and adhesion assays. Endometrial carcinoma tissues showed significantly higher Id1 and Id3 expression than the adjacent tissues (P<0.05). In the two endometrial carcinoma cell lines, Id1/Id3 double-knockdown significantly decreased MMP2 and CXCR4 expression and increased P21 expression at both mRNA and protein levels (P<0.05), and resulted in suppressed cell proliferation, invasion, migration and adhesion. Id1 and Id3 expressions are up-regulated in endometrial carcinoma to promote the proliferation, invasion, migration and adhesion of the tumor cells by increasing MMP2 and CXCR4 expression and reducing P21 expression. Therapies targeting Id1/Id3 can be a novel strategy for treatment of endometrial carcinoma.

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.

MESSI: metabolic engineering target selection and best strain identification tool.

PubMed

Kang, Kang; Li, Jun; Lim, Boon Leong; Panagiotou, Gianni

2015-01-01

Metabolic engineering and synthetic biology are synergistically related fields for manipulating target pathways and designing microorganisms that can act as chemical factories. Saccharomyces cerevisiae's ideal bioprocessing traits make yeast a very attractive chemical factory for production of fuels, pharmaceuticals, nutraceuticals as well as a wide range of chemicals. However, future attempts of engineering S. cerevisiae's metabolism using synthetic biology need to move towards more integrative models that incorporate the high connectivity of metabolic pathways and regulatory processes and the interactions in genetic elements across those pathways and processes. To contribute in this direction, we have developed Metabolic Engineering target Selection and best Strain Identification tool (MESSI), a web server for predicting efficient chassis and regulatory components for yeast bio-based production. The server provides an integrative platform for users to analyse ready-to-use public high-throughput metabolomic data, which are transformed to metabolic pathway activities for identifying the most efficient S. cerevisiae strain for the production of a compound of interest. As input MESSI accepts metabolite KEGG IDs or pathway names. MESSI outputs a ranked list of S. cerevisiae strains based on aggregation algorithms. Furthermore, through a genome-wide association study of the metabolic pathway activities with the strains' natural variation, MESSI prioritizes genes and small variants as potential regulatory points and promising metabolic engineering targets. Users can choose various parameters in the whole process such as (i) weight and expectation of each metabolic pathway activity in the final ranking of the strains, (ii) Weighted AddScore Fuse or Weighted Borda Fuse aggregation algorithm, (iii) type of variants to be included, (iv) variant sets in different biological levels.Database URL: http://sbb.hku.hk/MESSI/. © The Author(s) 2015. Published by Oxford University

Three dimensional identification card and applications

NASA Astrophysics Data System (ADS)

Zhou, Changhe; Wang, Shaoqing; Li, Chao; Li, Hao; Liu, Zhao

2016-10-01

Three dimensional Identification Card, with its three-dimensional personal image displayed and stored for personal identification, is supposed be the advanced version of the present two-dimensional identification card in the future [1]. Three dimensional Identification Card means that there are three-dimensional optical techniques are used, the personal image on ID card is displayed to be three-dimensional, so we can see three dimensional personal face. The ID card also stores the three-dimensional face information in its inside electronics chip, which might be recorded by using two-channel cameras, and it can be displayed in computer as three-dimensional images for personal identification. Three-dimensional ID card might be one interesting direction to update the present two-dimensional card in the future. Three-dimension ID card might be widely used in airport custom, entrance of hotel, school, university, as passport for on-line banking, registration of on-line game, etc...

Categorization and identification of simultaneous targets.

PubMed

Theeuwes, J

1991-02-01

Early and late selection theories of visual attention disagree about whether identification occurs before or after selection. Studies showing the category effect, i.e., the time to detect a letter is hardly affected by the number of digits present in the display, are taken as evidence for late selection theories since these studies suggest parallel identification of all items in the display. As an extension of previous studies, in the present study two categorically different targets were presented simultaneously among a variable number of nontargets. Subjects were shown brief displays of two target letters among either 2, 4 or 6 nontarget digits. Subjects responded 'same' when the two letters were identical and 'different' otherwise. Since the 'same-different' response reflects the combined outcome of the simultaneous targets, late-selection theory predicts that the time to match the target letters is independent of the number of nontarget digits. Alternatively, early-selection theory predicts a linear increase of reaction time with display size since the presence of more than one target disrupts parallel preattentive processing, leading to a serial search through all items in the display. The results provide evidence for the early-selection view since reaction time increased linearly with the number of categorically different nontargets. A control experiment revealed that none of the alternative explanations could account for the display size effect.

Target tracking and surveillance by fusing stereo and RFID information

NASA Astrophysics Data System (ADS)

Raza, Rana H.; Stockman, George C.

2012-06-01

Ensuring security in high risk areas such as an airport is an important but complex problem. Effectively tracking personnel, containers, and machines is a crucial task. Moreover, security and safety require understanding the interaction of persons and objects. Computer vision (CV) has been a classic tool; however, variable lighting, imaging, and random occlusions present difficulties for real-time surveillance, resulting in erroneous object detection and trajectories. Determining object ID via CV at any instance of time in a crowded area is computationally prohibitive, yet the trajectories of personnel and objects should be known in real time. Radio Frequency Identification (RFID) can be used to reliably identify target objects and can even locate targets at coarse spatial resolution, while CV provides fuzzy features for target ID at finer resolution. Our research demonstrates benefits obtained when most objects are "cooperative" by being RFID tagged. Fusion provides a method to simplify the correspondence problem in 3D space. A surveillance system can query for unique object ID as well as tag ID information, such as target height, texture, shape and color, which can greatly enhance scene analysis. We extend geometry-based tracking so that intermittent information on ID and location can be used in determining a set of trajectories of N targets over T time steps. We show that partial-targetinformation obtained through RFID can reduce computation time (by 99.9% in some cases) and also increase the likelihood of producing correct trajectories. We conclude that real-time decision-making should be possible if the surveillance system can integrate information effectively between the sensor level and activity understanding level.

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.

Phytophthora-ID.org: A sequence-based Phytophthora identification tool

Treesearch

N.J. Grünwald; F.N. Martin; M.M. Larsen; C.M. Sullivan; C.M. Press; M.D. Coffey; E.M. Hansen; J.L. Parke

2010-01-01

Contemporary species identification relies strongly on sequence-based identification, yet resources for identification of many fungal and oomycete pathogens are rare. We developed two web-based, searchable databases for rapid identification of Phytophthora spp. based on sequencing of the internal transcribed spacer (ITS) or the cytochrome oxidase...

IFPTarget: A Customized Virtual Target Identification Method Based on Protein-Ligand Interaction Fingerprinting Analyses.

PubMed

Li, Guo-Bo; Yu, Zhu-Jun; Liu, Sha; Huang, Lu-Yi; Yang, Ling-Ling; Lohans, Christopher T; Yang, Sheng-Yong

2017-07-24

Small-molecule target identification is an important and challenging task for chemical biology and drug discovery. Structure-based virtual target identification has been widely used, which infers and prioritizes potential protein targets for the molecule of interest (MOI) principally via a scoring function. However, current "universal" scoring functions may not always accurately identify targets to which the MOI binds from the retrieved target database, in part due to a lack of consideration of the important binding features for an individual target. Here, we present IFPTarget, a customized virtual target identification method, which uses an interaction fingerprinting (IFP) method for target-specific interaction analyses and a comprehensive index (Cvalue) for target ranking. Evaluation results indicate that the IFP method enables substantially improved binding pose prediction, and Cvalue has an excellent performance in target ranking for the test set. When applied to screen against our established target library that contains 11,863 protein structures covering 2842 unique targets, IFPTarget could retrieve known targets within the top-ranked list and identified new potential targets for chemically diverse drugs. IFPTarget prediction led to the identification of the metallo-β-lactamase VIM-2 as a target for quercetin as validated by enzymatic inhibition assays. This study provides a new in silico target identification tool and will aid future efforts to develop new target-customized methods for target identification.

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.

The Role of Id2 Protein in Neuroblatoma in Children.

PubMed

Wieczorek, Aleksandra; Balwierz, Walentyna

2015-09-01

Id (DNA binding and/or differentiation) proteins occur physiologically during ontogenesis and negatively regulate the activity of other helix-loop-helix (HLH) proteins. Id2 protein causes block of cells differentiation in the S phase of the cell cycle and regulates the activity of Rb protein. The role of Id2 protein in physiological cell cycle progression and in neuroblastoma (NBL) pathogenesis was proposed by Lasorella. The aim of the study was evaluation of Id2 expression and its prognostic significance in NBL cells coming from primary tumors and evaluation of its prognostic significance, and correlation of Id2 expression with known prognostic factors. Sixty patients with primary NBL treated from 1991 to 2005 were included in the analysis. We found 50 patients with high and 10 patients with low intensity of Id2 expression. The median percentage of NBL cells with Id2 expression was 88 %. We found no correlation between the number of NBL cells or the intensity of Id2 expression and OS and DFS. In patients with stage 4 NBL, almost all patients had high expression of Id2 and it was significantly more common than in other disease stages (p = 0,03). We found no correlation between Id2 expression and other known prognostic factor in NBL patients. We assume that Id2 is not prognostic factor. However, due to its abundant expression in most of NBL cells and its role in cell cycle, it may be potential therapeutic target. Exact knowledge of expression time may be helpful in explaining mechanisms of oncogenesis.

Employing machine learning for reliable miRNA target identification in plants.

PubMed

Jha, Ashwani; Shankar, Ravi

2011-12-29

miRNAs are ~21 nucleotide long small noncoding RNA molecules, formed endogenously in most of the eukaryotes, which mainly control their target genes post transcriptionally by interacting and silencing them. While a lot of tools has been developed for animal miRNA target system, plant miRNA target identification system has witnessed limited development. Most of them have been centered around exact complementarity match. Very few of them considered other factors like multiple target sites and role of flanking regions. In the present work, a Support Vector Regression (SVR) approach has been implemented for plant miRNA target identification, utilizing position specific dinucleotide density variation information around the target sites, to yield highly reliable result. It has been named as p-TAREF (plant-Target Refiner). Performance comparison for p-TAREF was done with other prediction tools for plants with utmost rigor and where p-TAREF was found better performing in several aspects. Further, p-TAREF was run over the experimentally validated miRNA targets from species like Arabidopsis, Medicago, Rice and Tomato, and detected them accurately, suggesting gross usability of p-TAREF for plant species. Using p-TAREF, target identification was done for the complete Rice transcriptome, supported by expression and degradome based data. miR156 was found as an important component of the Rice regulatory system, where control of genes associated with growth and transcription looked predominant. The entire methodology has been implemented in a multi-threaded parallel architecture in Java, to enable fast processing for web-server version as well as standalone version. This also makes it to run even on a simple desktop computer in concurrent mode. It also provides a facility to gather experimental support for predictions made, through on the spot expression data analysis, in its web-server version. A machine learning multivariate feature tool has been implemented in parallel and

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 mi

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

Limitations of contrast enhancement for infrared target identification

NASA Astrophysics Data System (ADS)

Du Bosq, Todd W.; Fanning, Jonathan D.

2009-05-01

Contrast enhancement and dynamic range compression are currently being used to improve the performance of infrared imagers by increasing the contrast between the target and the scene content. Automatic contrast enhancement techniques do not always achieve this improvement. In some cases, the contrast can increase to a level of target saturation. This paper assesses the range-performance effects of contrast enhancement for target identification as a function of image saturation. Human perception experiments were performed to determine field performance using contrast enhancement on the U.S. Army RDECOM CERDEC NVESD standard military eight target set using an un-cooled LWIR camera. The experiments compare the identification performance of observers viewing contrast enhancement processed images at various levels of saturation. Contrast enhancement is modeled in the U.S. Army thermal target acquisition model (NVThermIP) by changing the scene contrast temperature. The model predicts improved performance based on any improved target contrast, regardless of specific feature saturation or enhancement. The measured results follow the predicted performance based on the target task difficulty metric used in NVThermIP for the non-saturated cases. The saturated images reduce the information contained in the target and performance suffers. The model treats the contrast of the target as uniform over spatial frequency. As the contrast is enhanced, the model assumes that the contrast is enhanced uniformly over the spatial frequencies. After saturation, the spatial cues that differentiate one tank from another are located in a limited band of spatial frequencies. A frequency dependent treatment of target contrast is needed to predict performance of over-processed images.

Guinea Pig ID-Like Families of SINEs

PubMed Central

Kass, David H.; Schaetz, Brian A.; Beitler, Lindsey; Bonney, Kevin M.; Jamison, Nicole; Wiesner, Cathy

2009-01-01

Previous studies have indicated a paucity of SINEs within the genomes of the guinea pig and nutria, representatives of the Hystricognathi suborder of rodents. More recent work has shown that the guinea pig genome contains a large number of B1 elements, expanding to various levels among different rodents. In this work we utilized A–B PCR and screened GenBank with sequences from isolated clones to identify potentially uncharacterized SINEs within the guinea pig genome, and identified numerous sequences with a high degree of similarity (>92%) specific to the guinea pig. The presence of A-tails and flanking direct repeats associated with these sequences supported the identification of a full-length SINE, with a consensus sequence notably distinct from other rodent SINEs. Although most similar to the ID SINE, it clearly was not derived from the known ID master gene (BC1), hence we refer to this element as guinea pig ID-like (GPIDL). Using the consensus to screen the guinea pig genomic database (Assembly CavPor2) with Ensembl BlastView, we estimated at least 100,000 copies, which contrasts markedly to just over 100 copies of ID elements. Additionally we provided evidence of recent integrations of GPIDL as two of seven analyzed conserved GPIDL-containing loci demonstrated presence/absence variants in Cavia porcellus and C. aperea. Using intra-IDL PCR and sequence analyses we also provide evidence that GPIDL is derived from a hystricognath-specific SINE family. These results demonstrate that this SINE family continues to contribute to the dynamics of genomes of hystricognath rodents. PMID:19232383

Guinea pig ID-like families of SINEs.

PubMed

Kass, David H; Schaetz, Brian A; Beitler, Lindsey; Bonney, Kevin M; Jamison, Nicole; Wiesner, Cathy

2009-05-01

Previous studies have indicated a paucity of SINEs within the genomes of the guinea pig and nutria, representatives of the Hystricognathi suborder of rodents. More recent work has shown that the guinea pig genome contains a large number of B1 elements, expanding to various levels among different rodents. In this work we utilized A-B PCR and screened GenBank with sequences from isolated clones to identify potentially uncharacterized SINEs within the guinea pig genome, and identified numerous sequences with a high degree of similarity (>92%) specific to the guinea pig. The presence of A-tails and flanking direct repeats associated with these sequences supported the identification of a full-length SINE, with a consensus sequence notably distinct from other rodent SINEs. Although most similar to the ID SINE, it clearly was not derived from the known ID master gene (BC1), hence we refer to this element as guinea pig ID-like (GPIDL). Using the consensus to screen the guinea pig genomic database (Assembly CavPor2) with Ensembl BlastView, we estimated at least 100,000 copies, which contrasts markedly to just over 100 copies of ID elements. Additionally we provided evidence of recent integrations of GPIDL as two of seven analyzed conserved GPIDL-containing loci demonstrated presence/absence variants in Cavia porcellus and C. aperea. Using intra-IDL PCR and sequence analyses we also provide evidence that GPIDL is derived from a hystricognath-specific SINE family. These results demonstrate that this SINE family continues to contribute to the dynamics of genomes of hystricognath rodents.

Employing machine learning for reliable miRNA target identification in plants

PubMed Central

2011-01-01

Background miRNAs are ~21 nucleotide long small noncoding RNA molecules, formed endogenously in most of the eukaryotes, which mainly control their target genes post transcriptionally by interacting and silencing them. While a lot of tools has been developed for animal miRNA target system, plant miRNA target identification system has witnessed limited development. Most of them have been centered around exact complementarity match. Very few of them considered other factors like multiple target sites and role of flanking regions. Result In the present work, a Support Vector Regression (SVR) approach has been implemented for plant miRNA target identification, utilizing position specific dinucleotide density variation information around the target sites, to yield highly reliable result. It has been named as p-TAREF (plant-Target Refiner). Performance comparison for p-TAREF was done with other prediction tools for plants with utmost rigor and where p-TAREF was found better performing in several aspects. Further, p-TAREF was run over the experimentally validated miRNA targets from species like Arabidopsis, Medicago, Rice and Tomato, and detected them accurately, suggesting gross usability of p-TAREF for plant species. Using p-TAREF, target identification was done for the complete Rice transcriptome, supported by expression and degradome based data. miR156 was found as an important component of the Rice regulatory system, where control of genes associated with growth and transcription looked predominant. The entire methodology has been implemented in a multi-threaded parallel architecture in Java, to enable fast processing for web-server version as well as standalone version. This also makes it to run even on a simple desktop computer in concurrent mode. It also provides a facility to gather experimental support for predictions made, through on the spot expression data analysis, in its web-server version. Conclusion A machine learning multivariate feature tool has been

Use of false ID cards and other deceptive methods to purchase alcoholic beverages during high school.

PubMed

Schwartz, R H; Farrow, J A; Banks, B; Giesel, A E

1998-01-01

Altered motor vehicle drivers's licenses or other falsified or counterfeit photo identification cards are widely and illegally used by teenagers to obtain beer and other alcohol beverages. We obtained information on the methods currently used by teenagers to purchase beer and wine by asking nine hundred teenagers, between 16-19 years old to complete a brief, confidential questionnaire. High school students most often obtained alcoholic beverages by requesting someone of legal age to purchase it for them. College students used borrowed, altered, or counterfeit identification (ID) more often than high school students. Photo IDs purchased through mail order from a magazine advertisement were used infrequently and when use was attempted, they were sometimes (25%) unsuccessful. Fifteen percent of high school students, 14% of college freshmen, and 24% of teenage drug abusers were able to purchase beer by the case with borrowed, altered, or fake ID. Suggestions to reduce sales of alcohol-containing beverages to minors include universal "carding" of prospective purchasers, use of two view or hologram photos on a drivers' license, requiring three different ID cards at the point of purchase, and penalties to stores that fail to make a good effort to identify underage customers.

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

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.

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.

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

Id1, Id2 and Id3 are induced in rat melanotrophs of the pituitary gland by dopamine suppression under continuous stress.

PubMed

Konishi, H; Ogawa, T; Nakagomi, S; Inoue, K; Tohyama, M; Kiyama, H

2010-09-15

In rats under continuous stress (CS) there is decreased hypothalamic dopaminergic innervation to the intermediate lobe (IL) of the pituitary gland, which causes hyperactivation and subsequent degeneration of melanotrophs in the IL. In this study, we investigated the molecular basis for the changes that occur in melanotrophs during CS. Using microarray analysis, we identified several genes differentially expressed in the IL under CS conditions. Among the genes up-regulated under CS conditions, we focused on the inhibitor of DNA binding/differentiation (Id) family of dominant negative basic helix-loop-helix (bHLH) transcription factors. RT-PCR, Western blotting and in situ hybridization confirmed the significant inductions of Id1, Id2 and Id3 in the IL of CS rats. Administration of the dopamine D2 receptor agonist bromocriptine prevented the inductions of Id1-3 in the IL of CS rats, whereas application of the dopamine D2 antagonist sulpiride induced significant expressions of Id1-3 in the IL of normal rats. Moreover, an in vitro study using primary cultured melanotrophs demonstrated a direct effect on Id1-3 inductions by dopamine suppression. These results suggest that the decreased dopamine levels in the IL during CS induce Id1-3 expressions in melanotrophs. Because Id family members inhibit various bHLH transcription factors, it is conceivable that the induced Id1-3 would cooperatively modulate gene expressions in melanotrophs under CS conditions to induce hormone secretion. (c) 2010 IBRO. Published by Elsevier Ltd. All rights reserved.

A Virtual Screening Approach for the Identification of High Affinity Small Molecules Targeting BCR-ABL1 Inhibitors for the Treatment of Chronic Myeloid Leukemia.

PubMed

Sharda, Saphy; Sarmandal, Palash; Cherukommu, Shirisha; Dindhoria, Kiran; Yadav, Manisha; Bandaru, Srinivas; Sharma, Anudeep; Sakhi, Aditi; Vyas, Tanmay; Hussain, Tajamul; Nayarisseri, Anuraj; Singh, Sanjeev Kumar

2017-01-01

CML originates due to reciprocal translocation in Philadelphia chromosome leading to the formation of fusion product BCR-ABL which constitutively activates tyrosine kinase signaling pathways eventually leading to abnormal proliferation of granulocytic cells. As a therapeutic strategy, BCR-ABL inhibitors have been clinically approved which terminates its phosphorylation activity and retards cancer progression. However, a number of patients develop resistance to inhibitors which demand for the discovery of new inhibitors. Given the drawbacks of present inhibitors, by high throughput virtual screening approaches, present study pursues to identify high affinity compounds targeting BCR-ABL1 anticipated to have safer pharmacological profiles. Five established BCR-ABL inhibitors formed the query compounds for identification of structurally similar compounds by Tanimoto coefficient based linear fingerprint search with a threshold of 95% against PubChemdatabase. Assisted by MolDock algorithm all compounds were docked against BCR-ABL protein in order to retrieve high affinity compounds. The parents and similars were further tested for their ADMET propertiesand bioactivity. Rebastinib formed higher affinity inhibitor than rest of the four established compound investigated in the study. Interestingly, Rebastinib similar compound with Pubchem ID: 67254402 was also shown to have highest affinity than other similars including the similars of respective five parents. In terms of ADMET properties Pubchem ID: 67254402 had appreciable ADMET profile and bioactivity. However, Rebastinib still stood as the best inhibitor in terms of binding affinity and ADMET properties than Pubchem ID: 67254402. Nevertheless, owing to the similar pharmacological properties with Rebastinib, Pubchem ID: 67254402 can be expected to form potential BCR-ABL inhibitor. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

ID'ing innate and innate-like lymphoid cells.

PubMed

Verykokakis, Mihalis; Zook, Erin C; Kee, Barbara L

2014-09-01

The immune system can be divided into innate and adaptive components that differ in their rate and mode of cellular activation, with innate immune cells being the first responders to invading pathogens. Recent advances in the identification and characterization of innate lymphoid cells have revealed reiterative developmental programs that result in cells with effector fates that parallel those of adaptive lymphoid cells and are tailored to effectively eliminate a broad spectrum of pathogenic challenges. However, activation of these cells can also be associated with pathologies such as autoimmune disease. One major distinction between innate and adaptive immune system cells is the constitutive expression of ID proteins in the former and inducible expression in the latter. ID proteins function as antagonists of the E protein transcription factors that play critical roles in lymphoid specification as well as B- and T-lymphocyte development. In this review, we examine the transcriptional mechanisms controlling the development of innate lymphocytes, including natural killer cells and the recently identified innate lymphoid cells (ILC1, ILC2, and ILC3), and innate-like lymphocytes, including natural killer T cells, with an emphasis on the known requirements for the ID proteins. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

TRIP-ID: A tool for a smart and interactive identification of Magic Formula tyre model parameters from experimental data acquired on track or test rig

NASA Astrophysics Data System (ADS)

Farroni, Flavio; Lamberti, Raffaele; Mancinelli, Nicolò; Timpone, Francesco

2018-03-01

Tyres play a key role in ground vehicles' dynamics because they are responsible for traction, braking and cornering. A proper tyre-road interaction model is essential for a useful and reliable vehicle dynamics model. In the last two decades Pacejka's Magic Formula (MF) has become a standard in simulation field. This paper presents a Tool, called TRIP-ID (Tyre Road Interaction Parameters IDentification), developed to characterize and to identify with a high grade of accuracy and reliability MF micro-parameters from experimental data deriving from telemetry or from test rig. The tool guides interactively the user through the identification process on the basis of strong diagnostic considerations about the experimental data made evident by the tool itself. A motorsport application of the tool is shown as a case study.

Design of a Covert RFID Tag Network for Target Discovery and Target Information Routing

PubMed Central

Pan, Qihe; Narayanan, Ram M.

2011-01-01

Radio frequency identification (RFID) tags are small electronic devices working in the radio frequency range. They use wireless radio communications to automatically identify objects or people without the need for line-of-sight or contact, and are widely used in inventory tracking, object location, environmental monitoring. This paper presents a design of a covert RFID tag network for target discovery and target information routing. In the design, a static or very slowly moving target in the field of RFID tags transmits a distinct pseudo-noise signal, and the RFID tags in the network collect the target information and route it to the command center. A map of each RFID tag’s location is saved at command center, which can determine where a RFID tag is located based on each RFID tag’s ID. We propose the target information collection method with target association and clustering, and we also propose the information routing algorithm within the RFID tag network. The design and operation of the proposed algorithms are illustrated through examples. Simulation results demonstrate the effectiveness of the design. PMID:22163693

Design of a covert RFID tag network for target discovery and target information routing.

PubMed

Pan, Qihe; Narayanan, Ram M

2011-01-01

Radio frequency identification (RFID) tags are small electronic devices working in the radio frequency range. They use wireless radio communications to automatically identify objects or people without the need for line-of-sight or contact, and are widely used in inventory tracking, object location, environmental monitoring. This paper presents a design of a covert RFID tag network for target discovery and target information routing. In the design, a static or very slowly moving target in the field of RFID tags transmits a distinct pseudo-noise signal, and the RFID tags in the network collect the target information and route it to the command center. A map of each RFID tag's location is saved at command center, which can determine where a RFID tag is located based on each RFID tag's ID. We propose the target information collection method with target association and clustering, and we also propose the information routing algorithm within the RFID tag network. The design and operation of the proposed algorithms are illustrated through examples. Simulation results demonstrate the effectiveness of the design.

Id-1 and Id-2 genes and products as markers of epithelial cancer

DOEpatents

Desprez, Pierre-Yves [El Cerrito, CA; Campisi, Judith [Berkeley, CA

2008-09-30

A method for detection and prognosis of breast cancer and other types of cancer. The method comprises detecting expression, if any, for both an Id-1 and an Id-2 genes, or the ratio thereof, of gene products in samples of breast tissue obtained from a patient. When expressed, Id-1 gene is a prognostic indicator that breast cancer cells are invasive and metastatic, whereas Id-2 gene is a prognostic indicator that breast cancer cells are localized and noninvasive in the breast tissue.

Id-1 and Id-2 genes and products as markers of epithelial cancer

DOEpatents

Desprez, Pierre-Yves [El Cerrito, CA; Campisi, Judith [Berkeley, CA

2011-10-04

A method for detection and prognosis of breast cancer and other types of cancer. The method comprises detecting expression, if any, for both an Id-1 and an Id-2 genes, or the ratio thereof, of gene products in samples of breast tissue obtained from a patient. When expressed, Id-1 gene is a prognostic indicator that breast cancer cells are invasive and metastatic, whereas Id-2 gene is a prognostic indicator that breast cancer cells are localized and noninvasive in the breast tissue.

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.

[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.

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

IMBLMS phase B4, additional tasks 5.0. Microbial identification system

NASA Technical Reports Server (NTRS)

1971-01-01

A laboratory study was undertaken to provide simplified procedures leading to the presumptive identification (I/D) of defined microorganisms on-board an orbiting spacecraft. Identifications were to be initiated by nonprofessional bacteriologists, (crew members) on a contingency basis only. Key objectives/constraints for this investigation were as follows:(1) I/D procedures based on limited, defined diagnostic tests, (2) testing oriented about ten selected microorganisms, (3) provide for definitive I/D key and procedures per selected organism, (4) define possible occurrences of false positives for the resulting I/D key by search of the appropriate literature, and (5) evaluation of the I/D key and procedure through a limited field trial on randomly selected subjects using the I/D key.

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.

Role of ID Proteins in BMP4 Inhibition of Profibrotic Effects of TGF-β2 in Human TM Cells.

PubMed

Mody, Avani A; Wordinger, Robert J; Clark, Abbot F

2017-02-01

Increased expression of TGF-β2 in primary open-angle glaucoma (POAG) aqueous humor (AH) and trabecular meshwork (TM) causes deposition of extracellular matrix (ECM) in the TM and elevated IOP. Bone morphogenetic proteins (BMPs) regulate TGF-β2-induced ECM production. The underlying mechanism for BMP4 inhibition of TGF-β2-induced fibrosis remains undetermined. Bone morphogenic protein 4 induces inhibitor of DNA binding proteins (ID1, ID3), which suppress transcription factor activities to regulate gene expression. Our study will determine whether ID1and ID3 proteins are downstream targets of BMP4, which attenuates TGF-β2 induction of ECM proteins in TM cells. Primary human TM cells were treated with BMP4, and ID1 and ID3 mRNA, and protein expression was determined by quantitative PCR (Q-PCR) and Western immunoblotting. Intracellular ID1 and ID3 protein localization was studied by immunocytochemistry. Transformed human TM cells (GTM3 cells) were transfected with ID1 or ID3 expression vectors to determine their potential inhibitory effects on TGF-β2-induced fibronectin and plasminogen activator inhibitor-I (PAI-1) protein expression. Basal expression of ID1-3 was detected in primary human TM cells. Bone morphogenic protein 4 significantly induced early expression of ID1 and ID3 mRNA (P < 0.05) and protein in primary TM cells, and a BMP receptor inhibitor blocked this induction. Overexpression of ID1 and ID3 significantly inhibited TGF-β2-induced expression of fibronectin and PAI-1 in TM cells (P < 0.01). Bone morphogenic protein 4 induced ID1 and ID3 expression suppresses TGF-β2 profibrotic activity in human TM cells. In the future, targeting specific regulators may control the TGF-β2 profibrotic effects on the TM, leading to disease modifying IOP lowering therapies.

Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing.

PubMed

Marshall, Owen J; Southall, Tony D; Cheetham, Seth W; Brand, Andrea H

2016-09-01

This protocol is an extension to: Nat. Protoc. 2, 1467-1478 (2007); doi:10.1038/nprot.2007.148; published online 7 June 2007The ability to profile transcription and chromatin binding in a cell-type-specific manner is a powerful aid to understanding cell-fate specification and cellular function in multicellular organisms. We recently developed targeted DamID (TaDa) to enable genome-wide, cell-type-specific profiling of DNA- and chromatin-binding proteins in vivo without cell isolation. As a protocol extension, this article describes substantial modifications to an existing protocol, and it offers additional applications. TaDa builds upon DamID, a technique for detecting genome-wide DNA-binding profiles of proteins, by coupling it with the GAL4 system in Drosophila to enable both temporal and spatial resolution. TaDa ensures that Dam-fusion proteins are expressed at very low levels, thus avoiding toxicity and potential artifacts from overexpression. The modifications to the core DamID technique presented here also increase the speed of sample processing and throughput, and adapt the method to next-generation sequencing technology. TaDa is robust, reproducible and highly sensitive. Compared with other methods for cell-type-specific profiling, the technique requires no cell-sorting, cross-linking or antisera, and binding profiles can be generated from as few as 10,000 total induced cells. By profiling the genome-wide binding of RNA polymerase II (Pol II), TaDa can also identify transcribed genes in a cell-type-specific manner. Here we describe a detailed protocol for carrying out TaDa experiments and preparing the material for next-generation sequencing. Although we developed TaDa in Drosophila, it should be easily adapted to other organisms with an inducible expression system. Once transgenic animals are obtained, the entire experimental procedure-from collecting tissue samples to generating sequencing libraries-can be accomplished within 5 d.

RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences.

PubMed

Brule, C E; Dean, K M; Grayhack, E J

2016-01-01

The identification and analysis of sequences that regulate gene expression is critical because regulated gene expression underlies biology. RNA-ID is an efficient and sensitive method to discover and investigate regulatory sequences in the yeast Saccharomyces cerevisiae, using fluorescence-based assays to detect green fluorescent protein (GFP) relative to a red fluorescent protein (RFP) control in individual cells. Putative regulatory sequences can be inserted either in-frame or upstream of a superfolder GFP fusion protein whose expression, like that of RFP, is driven by the bidirectional GAL1,10 promoter. In this chapter, we describe the methodology to identify and study cis-regulatory sequences in the RNA-ID system, explaining features and variations of the RNA-ID reporter, as well as some applications of this system. We describe in detail the methods to analyze a single regulatory sequence, from construction of a single GFP variant to assay of variants by flow cytometry, as well as modifications required to screen libraries of different strains simultaneously. We also describe subsequent analyses of regulatory sequences. © 2016 Elsevier Inc. All rights reserved.

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.

Author Identification Systems

ERIC Educational Resources Information Center

Wagner, A. Ben

2009-01-01

Many efforts are currently underway to disambiguate author names and assign unique identification numbers so that publications by a given scholar can be reliably grouped together. This paper reviews a number of operational and in-development services. Some systems like ResearcherId.Com depend on self-registration and self-identification of a…

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.

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

Laser range profiling for small target recognition

NASA Astrophysics Data System (ADS)

Steinvall, Ove; Tulldahl, Michael

2017-03-01

Long range identification (ID) or ID at closer range of small targets has its limitations in imaging due to the demand for very high-transverse sensor resolution. This is, therefore, a motivation to look for one-dimensional laser techniques for target ID. These include laser vibrometry and laser range profiling. Laser vibrometry can give good results, but is not always robust as it is sensitive to certain vibrating parts on the target being in the field of view. Laser range profiling is attractive because the maximum range can be substantial, especially for a small laser beam width. A range profiler can also be used in a scanning mode to detect targets within a certain sector. The same laser can also be used for active imaging when the target comes closer and is angularly resolved. Our laser range profiler is based on a laser with a pulse width of 6 ns (full width half maximum). This paper will show both experimental and simulated results for laser range profiling of small boats out to a 6 to 7-km range and a unmanned arrial vehicle (UAV) mockup at close range (1.3 km). The naval experiments took place in the Baltic Sea using many other active and passive electro-optical sensors in addition to the profiling system. The UAV experiments showed the need for a high-range resolution, thus we used a photon counting system in addition to the more conventional profiler used in the naval experiments. This paper shows the influence of target pose and range resolution on the capability of classification. The typical resolution (in our case 0.7 m) obtainable with a conventional range finder type of sensor can be used for large target classification with a depth structure over 5 to 10 m or more, but for smaller targets such as a UAV a high resolution (in our case 7.5 mm) is needed to reveal depth structures and surface shapes. This paper also shows the need for 3-D target information to build libraries for comparison of measured and simulated range profiles. At closer ranges

ID2 collaborates with ID3 to suppress iNKT and innate-like tumors1

PubMed Central

Li, Jia; Roy, Sumedha; Kim, Young-Mi; Li, Shibo; Zhang, Baojun; Love, Cassandra; Reddy, Anupama; Rajagopalan, Deepthi; Dave, Sandeep; Diehl, Anna Mae; Zhuang, Yuan

2017-01-01

Inhibitor of DNA binding (ID) proteins, including ID1-4, are transcriptional regulators involved in promoting cell proliferation and survival in various cell types. Although upregulation of Id proteins has been associated with a broad spectrum of tumors, recent studies have identified that ID3 plays a tumor suppressor role in the development of Burkitt’s lymphoma in humans and Hepatosplenic T cell lymphomas in mice. Here, we report rapid lymphoma development in Id2/Id3 double knockout (L-DKO) mice caused by unchecked expansion of either invariant Natural Killer T (iNKT) cells, or a unique subset of innate-like, CD1d-independent T cells. These populations started expansion in neonatal mice and, upon malignant transformation, caused fatality at age between 3–11 months. The malignant cells also gave rise to lymphomas upon transfer to Rag-deficient and wild-type hosts, reaffirming their inherent tumorigenic potential. Microarray analysis revealed a significantly modified program in these neonatal iNKT cells that ultimately led to their malignant transformation. The lymphoma cells demonstrated chromosome instability, along with upregulation of several different signaling pathways, including the cytokine-cytokine receptor interaction pathway, which can promote their expansion and migration. Dysregulation of genes with reported driver mutations and the NF-kB pathway were found to be shared between L-DKO lymphomas and human NKT tumors. Our work identifies a distinct premalignant state and multiple tumoriogenic pathways caused by loss function of ID2 and ID3. Thus, conditional deletion of Id2 and Id3 in developing T cells establishes a unique animal model for iNKT and relevant innate-like lymphomas. PMID:28258199

Targeted stock identification using multilocus genotype 'familyprinting'

USGS Publications Warehouse

Letcher, B.H.; King, T.L.

1999-01-01

We present an approach to stock identification of small, targeted populations that uses multilocus microsatellite genotypes of individual mating adults to uniquely identify first- and second-generation offspring in a mixture. We call the approach 'familyprinting'; unlike DNA fingerprinting where tissue samples of individuals are matched, offspring from various families are assigned to pairs of parents or sets of four grandparents with known genotypes. The basic unit of identification is the family, but families can be nested within a variety of stock units ranging from naturally reproducing groups of fish in a small tributary or pond from which mating adults can be sampled to large or small collections of families produced in hatcheries and stocked in specific locations. We show that, with as few as seven alleles per locus using four loci without error, first-generation offspring can be uniquely assigned to the correct family. For second-generation applications in a hatchery more alleles per locus (10) and loci (10) are required for correct assignment of all offspring to the correct set of grandparents. Using microsatellite DNA variation from an Atlantic salmon (Salmo solar) restoration river (Connecticut River, USA), we also show that this population contains sufficient genetic diversity in sea-run returns for 100% correct first, generation assignment and 97% correct second-generation assignment using 14 loci. We are currently using first- and second-generation familyprinting in this population with the ultimate goal of identifying stocking tributary. In addition to within-river familyprinting, there also appears to be sufficient genetic diversity within and between Atlantic salmon populations for identification of 'familyprinted' fish in a mixture of multiple populations. We also suggest that second-generation familyprinting with multiple populations may also provide a tool for examining stock structure. Familyprinting with microsatellite DNA markers is a viable

TGFβ-Id1 Signaling Opposes Twist1 and Promotes Metastatic Colonization Via a Mesenchymal-to-Epithelial Transition

PubMed Central

Stankic, Marko; Pavlovic, Svetlana; Chin, Yvette; Brogi, Edi; Padua, David; Norton, Larry; Massague, Joan; Benezra, Robert

2014-01-01

SUMMARY ID genes are required for breast cancer colonization of the lungs, but the mechanism remains poorly understood. Here, we show that Id1 expression induces a stem-like phenotype in breast cancer cells, while retaining epithelial properties, contrary to the notion that cancer stem-like properties are inextricably linked to the mesenchymal state. During metastatic colonization, Id1 induces a mesenchymal-to-epithelial transition (MET), specifically in cells whose mesenchymal state is dependent on the Id1 target protein Twist1 but not at the primary site, where this state is controlled by the zinc-finger protein Snail1. Knockdown of Id expression in metastasizing cells prevents MET and dramatically reduces lung colonization. Furthermore, Id1 is induced by TGFβ only in cells that have first undergone EMT, demonstrating that EMT is a pre-requisite for subsequent Id1-induced MET during lung colonization. Collectively, these studies underscore the importance of Id-mediated phenotypic switching during distinct stages of breast cancer metastasis. PMID:24332369

Targeted Feature Detection for Data-Dependent Shotgun Proteomics.

PubMed

Weisser, Hendrik; Choudhary, Jyoti S

2017-08-04

Label-free quantification of shotgun LC-MS/MS data is the prevailing approach in quantitative proteomics but remains computationally nontrivial. The central data analysis step is the detection of peptide-specific signal patterns, called features. Peptide quantification is facilitated by associating signal intensities in features with peptide sequences derived from MS2 spectra; however, missing values due to imperfect feature detection are a common problem. A feature detection approach that directly targets identified peptides (minimizing missing values) but also offers robustness against false-positive features (by assigning meaningful confidence scores) would thus be highly desirable. We developed a new feature detection algorithm within the OpenMS software framework, leveraging ideas and algorithms from the OpenSWATH toolset for DIA/SRM data analysis. Our software, FeatureFinderIdentification ("FFId"), implements a targeted approach to feature detection based on information from identified peptides. This information is encoded in an MS1 assay library, based on which ion chromatogram extraction and detection of feature candidates are carried out. Significantly, when analyzing data from experiments comprising multiple samples, our approach distinguishes between "internal" and "external" (inferred) peptide identifications (IDs) for each sample. On the basis of internal IDs, two sets of positive (true) and negative (decoy) feature candidates are defined. A support vector machine (SVM) classifier is then trained to discriminate between the sets and is subsequently applied to the "uncertain" feature candidates from external IDs, facilitating selection and confidence scoring of the best feature candidate for each peptide. This approach also enables our algorithm to estimate the false discovery rate (FDR) of the feature selection step. We validated FFId based on a public benchmark data set, comprising a yeast cell lysate spiked with protein standards that provide a known

MicroRNAs and intellectual disability (ID) in Down syndrome, X-linked ID, and Fragile X syndrome

PubMed Central

Siew, Wei-Hong; Tan, Kai-Leng; Babaei, Maryam Abbaspour; Cheah, Pike-See; Ling, King-Hwa

2013-01-01

Intellectual disability (ID) is one of the many features manifested in various genetic syndromes leading to deficits in cognitive function among affected individuals. ID is a feature affected by polygenes and multiple environmental factors. It leads to a broad spectrum of affected clinical and behavioral characteristics among patients. Until now, the causative mechanism of ID is unknown and the progression of the condition is poorly understood. Advancement in technology and research had identified various genetic abnormalities and defects as the potential cause of ID. However, the link between these abnormalities with ID is remained inconclusive and the roles of many newly discovered genetic components such as non-coding RNAs have not been thoroughly investigated. In this review, we aim to consolidate and assimilate the latest development and findings on a class of small non-coding RNAs known as microRNAs (miRNAs) involvement in ID development and progression with special focus on Down syndrome (DS) and X-linked ID (XLID) [including Fragile X syndrome (FXS)]. PMID:23596395

Microbial identification and automated antibiotic susceptibility testing directly from positive blood cultures using MALDI-TOF MS and VITEK 2.

PubMed

Wattal, C; Oberoi, J K

2016-01-01

The study addresses the utility of Matrix Assisted Laser Desorption/Ionisation Time-Of-Flight mass spectrometry (MALDI-TOF MS) using VITEK MS and the VITEK 2 antimicrobial susceptibility testing (AST) system for direct identification (ID) and timely AST from positive blood culture bottles using a lysis-filtration method (LFM). Between July and December 2014, a total of 140 non-duplicate mono-microbial blood cultures were processed. An aliquot of positive blood culture broth was incubated with lysis buffer before the bacteria were filtered and washed. Micro-organisms recovered from the filter were first identified using VITEK MS and its suspension was used for direct AST by VITEK 2 once the ID was known. Direct ID and AST results were compared with classical methods using solid growth. Out of the 140 bottles tested, VITEK MS resulted in 70.7 % correct identification to the genus and/ or species level. For the 103 bottles where identification was possible, there was agreement in 97 samples (94.17 %) with classical culture. Compared to the routine method, the direct AST resulted in category agreement in 860 (96.5 %) of 891 bacteria-antimicrobial agent combinations tested. The results of direct ID and AST were available 16.1 hours before those of the standard approach on average. The combined use of VITEK MS and VITEK 2 directly on samples from positive blood culture bottles using a LFM technique can result in rapid and reliable ID and AST results in blood stream infections to result in early institution of targeted treatment. The combination of LFM and AST using VITEK 2 was found to expedite AST more reliably.

Coupling Molecular Modeling to the Traditional "IR-ID" Exercise in the Introductory Organic Chemistry Laboratory

ERIC Educational Resources Information Center

Stokes-Huby, Heather; Vitale, Dale E.

2007-01-01

This exercise integrates the infrared unknown identification ("IR-ID") experiment common to most organic laboratory syllabi with computer molecular modeling. In this modification students are still required to identify unknown compounds from their IR spectra, but must additionally match some of the absorptions with computed frequencies they…

Rapid identification of mutations in the IDS gene of Hunter patients: Analysis of mRNA by the protein truncation test

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

Hogervorst, F.B.L.; Tuijn, A.C. van der; Ommen, G.J.B. van

Hunter syndrome is an X-linked recessive disorder constituting phenotypes ranging from mild to severe. The gene affected in Hunter syndrome is iduronate-2-sulfatase (IDS). The identification of mutations leading to a defective enzyme could be of benefit for the diagnosis and prognosis of patients. At this moment a variety of mutations have been found, including large deletions and base substitutions. We have previously described a method, designated the protein truncation test (PTT), for the detection of mutations leading to premature translation termination. The method combines reverse transcription and PCR (RT-PCR) with in vitro transcript/translation of the products generated. To facilitate amore » PTT analysis, the forward primer is modified by addition of a T7 promoter sequence and an in-frame protein translation initiation sequence. In our department the method has been successfully applied for DMD and FAP. Here we report on the PTT analysis of 8 Hunter patients, all of them without major gene alterations as determined by Southern analysis. Total RNA was isolated from cultured skin fibroblasts or peripheral blood lymphocytes. PTT analysis revealed 4 novel mutations in the IDS gene: two missense mutations and two frameshift mutations (splice donor site alteration in intron 6 and a 13 bp deletion in exon 9). Furthermore, PTT proved to be a simple method to identify carriers. Currently, we use the generated RT-PCR products of the remaining patients for automated sequence analysis. PTT may be of great value in screening disorders in which affected genes give rise to truncated protein products.« less

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.

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.

RNAi screen for rapid therapeutic target identification in leukemia patients

PubMed Central

Tyner, Jeffrey W.; Deininger, Michael W.; Loriaux, Marc M.; Chang, Bill H.; Gotlib, Jason R.; Willis, Stephanie G.; Erickson, Heidi; Kovacsovics, Tibor; O'Hare, Thomas; Heinrich, Michael C.; Druker, Brian J.

2009-01-01

Targeted therapy has vastly improved outcomes in certain types of cancer. Extension of this paradigm across a broad spectrum of malignancies will require an efficient method to determine the molecular vulnerabilities of cancerous cells. Improvements in sequencing technology will soon enable high-throughput sequencing of entire genomes of cancer patients; however, determining the relevance of identified sequence variants will require complementary functional analyses. Here, we report an RNAi-assisted protein target identification (RAPID) technology that individually assesses targeting of each member of the tyrosine kinase gene family. We demonstrate that RAPID screening of primary leukemia cells from 30 patients identifies targets that are critical to survival of the malignant cells from 10 of these individuals. We identify known, activating mutations in JAK2 and K-RAS, as well as patient-specific sensitivity to down-regulation of FLT1, CSF1R, PDGFR, ROR1, EPHA4/5, JAK1/3, LMTK3, LYN, FYN, PTK2B, and N-RAS. We also describe a previously undescribed, somatic, activating mutation in the thrombopoietin receptor that is sensitive to down-stream pharmacologic inhibition. Hence, the RAPID technique can quickly identify molecular vulnerabilities in malignant cells. Combination of this technique with whole-genome sequencing will represent an ideal tool for oncogenic target identification such that specific therapies can be matched with individual patients. PMID:19433805

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.

The Performance of Eyewitnesses with Intellectual Disabilities on Photographic Identification Line-Ups

ERIC Educational Resources Information Center

Wilcock, Rachel; Henry, Lucy

2013-01-01

Despite the large number of people with intellectual disabilities (ID) and the fact they are more likely to be victims and witnesses of crime, only two published studies have investigated their performance on identification line-up parades. In the present study we examined the identification performance of adults with and without ID on both a…

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.

Identification of targets for rational pharmacological therapy in childhood craniopharyngioma.

PubMed

Gump, Jacob M; Donson, Andrew M; Birks, Diane K; Amani, Vladimir M; Rao, Karun K; Griesinger, Andrea M; Kleinschmidt-DeMasters, B K; Johnston, James M; Anderson, Richard C E; Rosenfeld, Amy; Handler, Michael; Gore, Lia; Foreman, Nicholas; Hankinson, Todd C

2015-05-21

Pediatric adamantinomatous craniopharyngioma (ACP) is a histologically benign but clinically aggressive brain tumor that arises from the sellar/suprasellar region. Despite a high survival rate with current surgical and radiation therapy (75-95 % at 10 years), ACP is associated with debilitating visual, endocrine, neurocognitive and psychological morbidity, resulting in excheptionally poor quality of life for survivors. Identification of an effective pharmacological therapy could drastically decrease morbidity and improve long term outcomes for children with ACP. Using mRNA microarray gene expression analysis of 15 ACP patient samples, we have found several pharmaceutical targets that are significantly and consistently overexpressed in our panel of ACP relative to other pediatric brain tumors, pituitary tumors, normal pituitary and normal brain tissue. Among the most highly expressed are several targets of the kinase inhibitor dasatinib - LCK, EPHA2 and SRC; EGFR pathway targets - AREG, EGFR and ERBB3; and other potentially actionable cancer targets - SHH, MMP9 and MMP12. We confirm by western blot that a subset of these targets is highly expressed in ACP primary tumor samples. We report here the first published transcriptome for ACP and the identification of targets for rational therapy. Experimental drugs targeting each of these gene products are currently being tested clinically and pre-clinically for the treatment of other tumor types. This study provides a rationale for further pre-clinical and clinical studies of novel pharmacological treatments for ACP. Development of mouse and cell culture models for ACP will further enable the translation of these targets from the lab to the clinic, potentially ushering in a new era in the treatment of ACP.

Id-1 promotes osteosarcoma cell growth and inhibits cell apoptosis via PI3K/AKT signaling pathway

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

Hao, Liang; Liao, Qi; Tang, Qiang

2016-02-12

Accumulating evidence reveals that Id-1 is upregulated and functions as a potential tumor promoter in several human cancer types. However, the role of Id-1 in osteosarcoma (OS) is unknown. In present study, we found that Id-1 expression was elevated in OS tissues than adjacent normal bone tissues. More importantly, we demonstrated that overexpression of Id-1 is significantly correlated with tumor progression and poor survival in OS patients. Furthermore, increased expression of Id-1 was observed in OS cell lines and ectopic expression of Id-1 significantly enhanced in vitro cell proliferation and promoted in vivo tumor growth, whereas knockdown of Id-1 suppressed OS cellsmore » growth. Moreover, our experimental data revealed that Id-1 promotes cell proliferation by facilitating cell cycle progression and inhibits cell apoptosis. Mechanistically, the effects of Id-1 in OS cells is at least partly through activation of PI3K/Akt signaling pathway. Therefore, we identified a tumorigenic role of Id-1 in OS and suggested a potential therapeutic target for OS patients. - Highlights: • Id-1 expression is positively correlated in OS patients with poor prognosis. • Overexpression of Id-1 promotes OS cell growth in vitro and in vivo. • Id-1induces cell cycle progression and inhibits cell apoptosis. • PI3K/Akt signaling pathway contributed to the oncogenic effects of Id-1 in OS cells.« less

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.

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.

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.

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.

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.

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.

Towards fraud-proof ID documents using multiple data hiding technologies and biometrics

NASA Astrophysics Data System (ADS)

Picard, Justin; Vielhauer, Claus; Thorwirth, Niels

2004-06-01

Identity documents, such as ID cards, passports, and driver's licenses, contain textual information, a portrait of the legitimate holder, and eventually some other biometric characteristics such as a fingerprint or handwritten signature. As prices for digital imaging technologies fall, making them more widely available, we have seen an exponential increase in the ease and the number of counterfeiters that can effectively forge documents. Today, with only limited knowledge of technology and a small amount of money, a counterfeiter can effortlessly replace a photo or modify identity information on a legitimate document to the extent that it is very diffcult to differentiate from the original. This paper proposes a virtually fraud-proof ID document based on a combination of three different data hiding technologies: digital watermarking, 2-D bar codes, and Copy Detection Pattern, plus additional biometric protection. As will be shown, that combination of data hiding technologies protects the document against any forgery, in principle without any requirement for other security features. To prevent a genuine document to be used by an illegitimate user,biometric information is also covertly stored in the ID document, to be used for identification at the detector.

20 ans après: a second mutation in MAOA identified by targeted high-throughput sequencing in a family with altered behavior and cognition

PubMed Central

Piton, Amélie; Poquet, Hélène; Redin, Claire; Masurel, Alice; Lauer, Julia; Muller, Jean; Thevenon, Julien; Herenger, Yvan; Chancenotte, Sophie; Bonnet, Marlène; Pinoit, Jean-Michel; Huet, Frédéric; Thauvin-Robinet, Christel; Jaeger, Anne-Sophie; Le Gras, Stéphanie; Jost, Bernard; Gérard, Bénédicte; Peoc'h, Katell; Launay, Jean-Marie; Faivre, Laurence; Mandel, Jean-Louis

2014-01-01

Intellectual disability (ID) is characterized by an extraordinary genetic heterogeneity, with >250 genes that have been implicated in monogenic forms of ID. Because this complexity precluded systematic testing for mutations and because clinical features are often non-specific, for some of these genes only few cases or families have been unambiguously documented. It is the case of the X-linked gene encoding monoamine oxidase A (MAOA), for which only one nonsense mutation has been identified in Brunner syndrome, characterized in a single family by mild non-dysmorphic ID and impulsive, violent and aggressive behaviors. We have performed targeted high-throughput sequencing of 220 genes, including MAOA, in patients with undiagnosed ID. We identified a c.797_798delinsTT (p.C266F) missense mutation in MAOA in a boy with autism spectrum disorder, attention deficit and autoaggressive behavior. Two maternal uncles carry the mutation and have severe ID, with a history of maltreatment in early childhood. This novel missense mutation decreases MAOA enzymatic activity, leading to abnormal levels of urinary monoamines. The identification of this new point mutation confirms, for the first time since 1993, the monogenic implication of the MAOA gene in ID of various degrees, autism and behavioral disturbances. The variable expressivity of the mutation observed in male patients of this family may involve gene–environment interactions, and the identification of a perturbation in monoamine metabolism should be taken into account when prescribing psychoactive drugs in such patients. PMID:24169519

20 ans après: a second mutation in MAOA identified by targeted high-throughput sequencing in a family with altered behavior and cognition.

PubMed

Piton, Amélie; Poquet, Hélène; Redin, Claire; Masurel, Alice; Lauer, Julia; Muller, Jean; Thevenon, Julien; Herenger, Yvan; Chancenotte, Sophie; Bonnet, Marlène; Pinoit, Jean-Michel; Huet, Frédéric; Thauvin-Robinet, Christel; Jaeger, Anne-Sophie; Le Gras, Stéphanie; Jost, Bernard; Gérard, Bénédicte; Peoc'h, Katell; Launay, Jean-Marie; Faivre, Laurence; Mandel, Jean-Louis

2014-06-01

Intellectual disability (ID) is characterized by an extraordinary genetic heterogeneity, with >250 genes that have been implicated in monogenic forms of ID. Because this complexity precluded systematic testing for mutations and because clinical features are often non-specific, for some of these genes only few cases or families have been unambiguously documented. It is the case of the X-linked gene encoding monoamine oxidase A (MAOA), for which only one nonsense mutation has been identified in Brunner syndrome, characterized in a single family by mild non-dysmorphic ID and impulsive, violent and aggressive behaviors. We have performed targeted high-throughput sequencing of 220 genes, including MAOA, in patients with undiagnosed ID. We identified a c.797_798delinsTT (p.C266F) missense mutation in MAOA in a boy with autism spectrum disorder, attention deficit and autoaggressive behavior. Two maternal uncles carry the mutation and have severe ID, with a history of maltreatment in early childhood. This novel missense mutation decreases MAOA enzymatic activity, leading to abnormal levels of urinary monoamines. The identification of this new point mutation confirms, for the first time since 1993, the monogenic implication of the MAOA gene in ID of various degrees, autism and behavioral disturbances. The variable expressivity of the mutation observed in male patients of this family may involve gene-environment interactions, and the identification of a perturbation in monoamine metabolism should be taken into account when prescribing psychoactive drugs in such patients.

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.

Advanced algorithms for the identification of mixtures using condensed-phase FT-IR spectroscopy

NASA Astrophysics Data System (ADS)

Arnó, Josep; Andersson, Greger; Levy, Dustin; Tomczyk, Carol; Zou, Peng; Zuidema, Eric

2011-06-01

FT-IR spectroscopy is the technology of choice to identify solid and liquid phase unknown samples. Advances in instrument portability have made possible the use of FT-IR spectroscopy in emergency response and military field applications. The samples collected in those harsh environments are rarely pure and typically contain multiple chemical species in water, sand, or inorganic matrices. In such critical applications, it is also desired that in addition to broad chemical identification, the user is warned immediately if the sample contains a threat or target class material (i.e. biological, narcotic, explosive). The next generation HazMatID 360 combines the ruggedized design and functionality of the current HazMatID with advanced mixture analysis algorithms. The advanced FT-IR instrument allows effective chemical assessment of samples that may contain one or more interfering materials like water or dirt. The algorithm was the result of years of cumulative experience based on thousands of real-life spectra sent to our ReachBack spectral analysis service by customers in the field. The HazMatID 360 combines mixture analysis with threat detection and chemical hazard classification capabilities to provide, in record time, crucial information to the user. This paper will provide an overview of the software and algorithm enhancements, in addition to examples of improved performance in mixture identification.

Identification of STAT target genes in adipocytes

PubMed Central

Zhao, Peng; Stephens, Jacqueline M.

2013-01-01

Adipocytes play important roles in lipid storage, energy homeostasis and whole body insulin sensitivity. Studies in the last two decades have identified the hormones and cytokines that activate specific STATs in adipocytes in vitro and in vivo. Five of the seven STAT family members are expressed in adipocyte (STATs 1, 3, 5A, 5B and 6). Many transcription factors, including STATs, have been shown to play an important role in adipose tissue development and function. This review will summarize the importance of adipocytes, indicate the cytokines and hormones that utilize the JAK-STAT signaling pathway in fat cells and focus on the identification of STAT target genes in mature adipocytes. To date, specific target genes have been identified for STATs, 1, 5A and 5B, but not for STATs 3 and 6. PMID:24058802

DriveID: safety innovation through individuation.

PubMed

Sawyer, Ben; Teo, Grace; Mouloua, Mustapha

2012-01-01

The driving task is highly complex and places considerable perceptual, physical and cognitive demands on the driver. As driving is fundamentally an information processing activity, distracted or impaired drivers have diminished safety margins compared with non- distracted drivers (Hancock and Parasuraman, 1992; TRB 1998 a & b). This competition for sensory and decision making capacities can lead to failures that cost lives. Some groups, teens and elderly drivers for example, have patterns of systematically poor perceptual, physical and cognitive performance while driving. Although there are technologies developed to aid these different drivers, these systems are often misused and underutilized. The DriveID project aims to design and develop a passive, automated face identification system capable of robustly identifying the driver of the vehicle, retrieve a stored profile, and intelligently prescribing specific accident prevention systems and driving environment customizations.

Reducing patient identification errors related to glucose point-of-care testing.

PubMed

Alreja, Gaurav; Setia, Namrata; Nichols, James; Pantanowitz, Liron

2011-01-01

Patient identification (ID) errors in point-of-care testing (POCT) can cause test results to be transferred to the wrong patient's chart or prevent results from being transmitted and reported. Despite the implementation of patient barcoding and ongoing operator training at our institution, patient ID errors still occur with glucose POCT. The aim of this study was to develop a solution to reduce identification errors with POCT. Glucose POCT was performed by approximately 2,400 clinical operators throughout our health system. Patients are identified by scanning in wristband barcodes or by manual data entry using portable glucose meters. Meters are docked to upload data to a database server which then transmits data to any medical record matching the financial number of the test result. With a new model, meters connect to an interface manager where the patient ID (a nine-digit account number) is checked against patient registration data from admission, discharge, and transfer (ADT) feeds and only matched results are transferred to the patient's electronic medical record. With the new process, the patient ID is checked prior to testing, and testing is prevented until ID errors are resolved. When averaged over a period of a month, ID errors were reduced to 3 errors/month (0.015%) in comparison with 61.5 errors/month (0.319%) before implementing the new meters. Patient ID errors may occur with glucose POCT despite patient barcoding. The verification of patient identification should ideally take place at the bedside before testing occurs so that the errors can be addressed in real time. The introduction of an ADT feed directly to glucose meters reduced patient ID errors in POCT.

Targeted Feature Detection for Data-Dependent Shotgun Proteomics

PubMed Central

2017-01-01

Label-free quantification of shotgun LC–MS/MS data is the prevailing approach in quantitative proteomics but remains computationally nontrivial. The central data analysis step is the detection of peptide-specific signal patterns, called features. Peptide quantification is facilitated by associating signal intensities in features with peptide sequences derived from MS2 spectra; however, missing values due to imperfect feature detection are a common problem. A feature detection approach that directly targets identified peptides (minimizing missing values) but also offers robustness against false-positive features (by assigning meaningful confidence scores) would thus be highly desirable. We developed a new feature detection algorithm within the OpenMS software framework, leveraging ideas and algorithms from the OpenSWATH toolset for DIA/SRM data analysis. Our software, FeatureFinderIdentification (“FFId”), implements a targeted approach to feature detection based on information from identified peptides. This information is encoded in an MS1 assay library, based on which ion chromatogram extraction and detection of feature candidates are carried out. Significantly, when analyzing data from experiments comprising multiple samples, our approach distinguishes between “internal” and “external” (inferred) peptide identifications (IDs) for each sample. On the basis of internal IDs, two sets of positive (true) and negative (decoy) feature candidates are defined. A support vector machine (SVM) classifier is then trained to discriminate between the sets and is subsequently applied to the “uncertain” feature candidates from external IDs, facilitating selection and confidence scoring of the best feature candidate for each peptide. This approach also enables our algorithm to estimate the false discovery rate (FDR) of the feature selection step. We validated FFId based on a public benchmark data set, comprising a yeast cell lysate spiked with protein standards

Evaluation of red blood cell and platelet antigen genotyping platforms (ID CORE XT/ID HPA XT) in routine clinical practice.

PubMed

Finning, Kirstin; Bhandari, Radhika; Sellers, Fiona; Revelli, Nicoletta; Villa, Maria Antonietta; Muñiz-Díaz, Eduardo; Nogués, Núria

2016-03-01

High-throughput genotyping platforms enable simultaneous analysis of multiple polymorphisms for blood group typing. BLOODchip® ID is a genotyping platform based on Luminex® xMAP technology for simultaneous determination of 37 red blood cell (RBC) antigens (ID CORE XT) and 18 human platelet antigens (HPA) (ID HPA XT) using the BIDS XT software. In this international multicentre study, the performance of ID CORE XT and ID HPA XT, using the centres' current genotyping methods as the reference for comparison, and the usability and practicality of these systems, were evaluated under working laboratory conditions. DNA was extracted from whole blood in EDTA with Qiagen methodologies. Ninety-six previously phenotyped/genotyped samples were processed per assay: 87 testing samples plus five positive controls and four negative controls. Results were available for 519 samples: 258 with ID CORE XT and 261 with ID HPA XT. There were three "no calls" that were either caused by human error or resolved after repeating the test. Agreement between the tests and reference methods was 99.94% for ID CORE XT (9,540/9,546 antigens determined) and 100% for ID HPA XT (all 4,698 alleles determined). There were six discrepancies in antigen results in five RBC samples, four of which (in VS, N, S and Do(a)) could not be investigated due to lack of sufficient sample to perform additional tests and two of which (in S and C) were resolved in favour of ID CORE XT (100% accuracy). The total hands-on time was 28-41 minutes for a batch of 16 samples. Compared with the reference platforms, ID CORE XT and ID HPA XT were considered simpler to use and had shorter processing times. ID CORE XT and ID HPA XT genotyping platforms for RBC and platelet systems were accurate and user-friendly in working laboratory settings.

A non-parametric peak calling algorithm for DamID-Seq.

PubMed

Li, Renhua; Hempel, Leonie U; Jiang, Tingbo

2015-01-01

Protein-DNA interactions play a significant role in gene regulation and expression. In order to identify transcription factor binding sites (TFBS) of double sex (DSX)-an important transcription factor in sex determination, we applied the DNA adenine methylation identification (DamID) technology to the fat body tissue of Drosophila, followed by deep sequencing (DamID-Seq). One feature of DamID-Seq data is that induced adenine methylation signals are not assured to be symmetrically distributed at TFBS, which renders the existing peak calling algorithms for ChIP-Seq, including SPP and MACS, inappropriate for DamID-Seq data. This challenged us to develop a new algorithm for peak calling. A challenge in peaking calling based on sequence data is estimating the averaged behavior of background signals. We applied a bootstrap resampling method to short sequence reads in the control (Dam only). After data quality check and mapping reads to a reference genome, the peaking calling procedure compromises the following steps: 1) reads resampling; 2) reads scaling (normalization) and computing signal-to-noise fold changes; 3) filtering; 4) Calling peaks based on a statistically significant threshold. This is a non-parametric method for peak calling (NPPC). We also used irreproducible discovery rate (IDR) analysis, as well as ChIP-Seq data to compare the peaks called by the NPPC. We identified approximately 6,000 peaks for DSX, which point to 1,225 genes related to the fat body tissue difference between female and male Drosophila. Statistical evidence from IDR analysis indicated that these peaks are reproducible across biological replicates. In addition, these peaks are comparable to those identified by use of ChIP-Seq on S2 cells, in terms of peak number, location, and peaks width.

Effect of visual target blurring on accommodation under distance viewing

NASA Astrophysics Data System (ADS)

Iwata, Yo; Handa, Tomoya; Ishikawa, Hitoshi

2018-04-01

Abstract ID="ASec1"> Purpose To examine the effect of visual target blurring on accommodation. ID="ASec2"> Methods We evaluated the objective refraction values when the visual target (asterisk; 8°) was changed from the state without Gaussian blur (15 s) to the state with Gaussian blur adapted [0(without blur) → 10, 0 → 50, 0 → 100: 15 s each]. ID="ASec3"> Results In Gaussian blur 10, when blurring of the target occurred, refraction value did not change significantly. In Gaussian blur 50 and 100, when blurring of the target occurred, the refraction value became significantly myopic. ID="ASec4"> Conclusion Blurring of the distant visual target results in intervention of accommodation.

Evaluation of the pathotec Rapid I-D system for identification of Enterobacteriaceae.

PubMed Central

Smith, P B; Rhoden, D L; Tomfohrde, K M

1975-01-01

The PathoTec Rapid I-D System for identifying Enterobacteriaceae was evaluated with 471 cultures. In 4,910 individual test comparisons, 95.5% of the results agreed, with results of only two test strips, those for esculin hydrolysis and urease production, agreeing with conventional tests in less than 94% of the trials. The PathoTec system exhibited 94.3% accuracy in identifying these cultures in a double-blind study with conventional media and procedures as the alternate system. Two newly developed test strips, for 0-nitrophenyl-beta-D-galactopyranoside and ornithine decarboxylase, were found to be highly reliable. PMID:1041590

Reducing patient identification errors related to glucose point-of-care testing

PubMed Central

Alreja, Gaurav; Setia, Namrata; Nichols, James; Pantanowitz, Liron

2011-01-01

Background: Patient identification (ID) errors in point-of-care testing (POCT) can cause test results to be transferred to the wrong patient's chart or prevent results from being transmitted and reported. Despite the implementation of patient barcoding and ongoing operator training at our institution, patient ID errors still occur with glucose POCT. The aim of this study was to develop a solution to reduce identification errors with POCT. Materials and Methods: Glucose POCT was performed by approximately 2,400 clinical operators throughout our health system. Patients are identified by scanning in wristband barcodes or by manual data entry using portable glucose meters. Meters are docked to upload data to a database server which then transmits data to any medical record matching the financial number of the test result. With a new model, meters connect to an interface manager where the patient ID (a nine-digit account number) is checked against patient registration data from admission, discharge, and transfer (ADT) feeds and only matched results are transferred to the patient's electronic medical record. With the new process, the patient ID is checked prior to testing, and testing is prevented until ID errors are resolved. Results: When averaged over a period of a month, ID errors were reduced to 3 errors/month (0.015%) in comparison with 61.5 errors/month (0.319%) before implementing the new meters. Conclusion: Patient ID errors may occur with glucose POCT despite patient barcoding. The verification of patient identification should ideally take place at the bedside before testing occurs so that the errors can be addressed in real time. The introduction of an ADT feed directly to glucose meters reduced patient ID errors in POCT. PMID:21633490

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

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

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.

Comparative evaluation of the drug interaction screening programs MediQ and ID PHARMA CHECK in neurological inpatients.

PubMed

Zorina, Olesya I; Haueis, Patrick; Semmler, Alexander; Marti, Isabelle; Gonzenbach, Roman R; Guzek, Markus; Kullak-Ublick, Gerd A; Weller, Michael; Russmann, Stefan

2012-08-01

The comparative evaluation of clinical decision support software (CDSS) programs regarding their sensitivity and positive predictive value for the identification of clinically relevant drug interactions. In this research, we used a cross-sectional study that identified potential drug interactions using the CDSS MediQ and the ID PHARMA CHECK in 484 neurological inpatients. Interactions were reclassified according to the Zurich Interaction System, a multidimensional classification that incorporates the Operational Classification of Drug Interactions. In 484 patients with 2812 prescriptions, MediQ and ID PHARMA CHECK generated a total of 1759 and 1082 alerts, respectively. MediQ identified 658 unique potentially interacting combinations, 8 classified as "high danger," 164 as "average danger," and 486 as "low danger." ID PHARMA CHECK detected 336 combinations assigned to one or several of 12 risk and management categories. Altogether, both CDSS issued alerts relating to 808 unique potentially interacting combinations. According to the Zurich Interaction System, 6 of these were contraindicated, 25 were provisionally contraindicated, 190 carried a conditional risk, and 587 had a minimal risk of adverse events. The positive predictive value for alerts having at least a conditional risk was 0.24 for MediQ and 0.48 for ID PHARMA CHECK. CDSS showed major differences in the identification and grading of interactions, and many interactions were only identified by one of the two CDSS. For both programs, only a small proportion of all identified interactions appeared clinically relevant, and the selected display of alerts that imply management changes is a key issue in the further development and local setup of such programs. Copyright © 2012 John Wiley & Sons, Ltd.

Can technology help to reduce underage drinking? Evidence from the false ID laws with scanner provision.

PubMed

Yörük, Barış K

2014-07-01

Underage drinkers often use false identification to purchase alcohol or gain access into bars. In recent years, several states have introduced laws that provide incentives to retailers and bar owners who use electronic scanners to ensure that the customer is 21 years or older and uses a valid identification to purchase alcohol. This paper is the first to investigate the effects of these laws using confidential data from the National Longitudinal Survey of Youth, 1997 Cohort (NLSY97). Using a difference-in-differences methodology, I find that the false ID laws with scanner provision significantly reduce underage drinking, including up to a 0.22 drink decrease in the average number of drinks consumed by underage youth per day. This effect is observed particularly in the short-run and more pronounced for non-college students and those who are relatively younger. These results are also robust under alternative model specifications. The findings of this paper highlight the importance of false ID laws in reducing alcohol consumption among underage youth. Copyright © 2014 Elsevier B.V. All rights reserved.

Can technology help to reduce underage drinking? Evidence from the false ID laws with scanner provision*

PubMed Central

Yörük, Barış K.

2014-01-01

Underage drinkers often use false identification to purchase alcohol or gain access into bars. In recent years, several states have introduced laws that provide incentives to retailers and bar owners who use electronic scanners to ensure that the customer is 21 years or older and uses a valid identification to purchase alcohol. This paper is the first to investigate the effects of these laws using confidential data from the National Longitudinal Survey of Youth, 1997 Cohort (NLSY97). Using a difference-in-differences methodology, I find that the false ID laws with scanner provision significantly reduce underage drinking, including up to a 0.22 drink decrease in the average number of drinks consumed by underage youth per day. This effect is observed particularly in the short-run and more pronounced for non-college students and those who are relatively younger. These results are also robust under alternative model specifications. The findings of this paper highlight the importance of false ID laws in reducing alcohol consumption among underage youth. PMID:24732386

Inactivation of ID4 promotes a CRPC phenotype with constitutive AR activation through FKBP52.

PubMed

Joshi, Jugal Bharat; Patel, Divya; Morton, Derrick J; Sharma, Pankaj; Zou, Jin; Hewa Bostanthirige, Dhanushka; Gorantla, Yamini; Nagappan, Peri; Komaragiri, Shravan Kumar; Sivils, Jeffrey C; Xie, Huan; Palaniappan, Ravi; Wang, Guangdi; Cox, Marc B; Chaudhary, Jaideep

2017-04-01

Castration-resistant prostate cancer (CRPC) is the emergence of prostate cancer cells that have adapted to the androgen-depleted environment of the prostate. In recent years, targeting multiple chaperones and co-chaperones (e.g., Hsp27, FKBP52) that promote androgen receptor (AR) signaling and/or novel AR regulatory mechanisms have emerged as promising alternative treatments for CRPC. We have shown that inactivation of inhibitor of differentiation 4 (ID4), a dominant-negative helix loop helix protein, promotes de novo steroidogenesis and CRPC with a gene expression signature that resembles constitutive AR activity in castrated mice. In this study, we investigated the underlying mechanism through which loss of ID4 potentiates AR signaling. Proteomic analysis between prostate cancer cell line LNCaP (L+ns) and LNCaP lacking ID4 (L(-)ID4) revealed elevated levels of Hsp27 and FKBP52, suggesting a role for these AR-associated co-chaperones in promoting constitutively active AR signaling in L(-)ID4 cells. Interestingly, protein interaction studies demonstrated a direct interaction between ID4 and the 52-kDa FK506-binding protein (FKBP52) in vitro, but not with AR. An increase in FKBP52-dependent AR transcriptional activity was observed in L(-)ID4 cells. Moreover, pharmacological inhibition of FKBP52-AR signaling, by treatment with MJC13, attenuated the tumor growth, weight, and volume in L(-)ID4 xenografts. Together, our results demonstrate that ID4 selectively regulates AR activity through direct interaction with FKBP52, and its loss, promotes CRPC through FKBP52-mediated AR signaling. © 2016 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.

Five years of health promoting work with bottle shops on the Central Coast of NSW Australia. How can we best ensure outlets check ID?

PubMed

Bauer, Lyndon; Smith, Jeff; Kajons, Nicole; Tutt, Doug

2018-04-24

Australian surveys indicate that a large proportion of packaged liquor outlets do not check identification for young people before selling alcohol to them. There are a substantial number of presentations to Emergency Departments from young people aged 15 to 17 years. This subgroup is second only to those aged 18 to 24 years. In the 15- to 17-year-old age group, supply from direct purchase or underage friends, who have purchased alcohol, represents substantial sources of alcohol that is more likely to be consumed without parental supervision. Teenagers 18-19 years of age approached a randomly selected sample of bottle shops, on the NSW Central Coast Region, to attempt to purchase alcohol without producing identification (ID). Legally we are unable to test with teens under the age of 18. If outlets do not check ID for customers 18 or 19 years of age, we propose they might not check identification for 15- to 17-year-olds. A raft of local interventions was employed over four-survey periods to attempt to reduce selling rates. The lowest alcohol sales without ID occurred in 2015 when NSW Liquor and Gaming successfully prosecuted a Central Coast outlet for an underage sale. The rate of alcohol sales without checking ID each year was as follows: 2012-43.8%, 2014-37.55%, 2015-21.5% and 2016-45%. Alcohol sales to young customers without checking ID are common, widespread and seemingly resistant to non-punitive interventions. The NSW Liquor Act could be modified to allow compliance testing and much more practical enforcement. While Central Coast bottle shops have a better record than other Australian areas showing some improvements with our non-punitive industry education interventions, the results need to improve substantially to stifle primary supply. © 2018 Australian Health Promotion Association.

Atlas-based identification of targets for functional radiosurgery

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

Stancanello, Joseph; Romanelli, Pantaleo; Modugno, Nicola

2006-06-15

Functional disorders of the brain, such as Parkinson's disease, dystonia, epilepsy, and neuropathic pain, may exhibit poor response to medical therapy. In such cases, surgical intervention may become necessary. Modern surgical approaches to such disorders include radio-frequency lesioning and deep brain stimulation (DBS). The subthalamic nucleus (STN) is one of the most useful stereotactic targets available: STN DBS is known to induce substantial improvement in patients with end-stage Parkinson's disease. Other targets include the Globus Pallidus pars interna (GPi) for dystonia and Parkinson's disease, and the centromedian nucleus of the thalamus (CMN) for neuropathic pain. Radiosurgery is an attractive noninvasivemore » alternative to treat some functional brain disorders. The main technical limitation to radiosurgery is that the target can be selected only on the basis of magnetic resonance anatomy without electrophysiological confirmation. The aim of this work is to provide a method for the correct atlas-based identification of the target to be used in functional neurosurgery treatment planning. The coordinates of STN, CMN, and GPi were identified in the Talairach and Tournoux atlas and transformed to the corresponding regions of the Montreal Neurological Institute (MNI) electronic atlas. Binary masks describing the target nuclei were created. The MNI electronic atlas was deformed onto the patient magnetic resonance imaging-T1 scan by applying an affine transformation followed by a local nonrigid registration. The first transformation was based on normalized cross correlation and the second on optimization of a two-part objective function consisting of similarity criteria and weighted regularization. The obtained deformation field was then applied to the target masks. The minimum distance between the surface of an implanted electrode and the surface of the deformed mask was calculated. The validation of the method consisted of comparing the electrode

Optical ID Tags for Secure Verification of Multispectral Visible and NIR Signatures

NASA Astrophysics Data System (ADS)

Pérez-Cabré, Elisabet; Millán, María S.; Javidi, Bahram

2008-04-01

We propose to combine information from visible (VIS) and near infrared (NIR) spectral bands to increase robustness on security systems and deter from unauthorized use of optical tags that permit the identification of a given person or object. The signature that identifies the element under surveillance will be only obtained by the appropriate combination of the visible content and the NIR data. The fully-phase encryption technique is applied to avoid an easy recognition of the resultant signature at the naked eye and an easy reproduction using conventional devices for imaging or scanning. The obtained complex-amplitude encrypted distribution is encoded on an identity (ID) tag. Spatial multiplexing of the encrypted signature allows us to build a distortion-invariant ID tag, so that remote authentication can be achieved even if the tag is captured under rotation or at different distances. We explore the possibility of using partial information of the encrypted distribution. Simulation results are provided and discussed.

Leveraging 3D chemical similarity, target and phenotypic data in the identification of drug-protein and drug-adverse effect associations.

PubMed

Vilar, Santiago; Hripcsak, George

2016-01-01

Drug-target identification is crucial to discover novel applications for existing drugs and provide more insights about mechanisms of biological actions, such as adverse drug effects (ADEs). Computational methods along with the integration of current big data sources provide a useful framework for drug-target and drug-adverse effect discovery. In this article, we propose a method based on the integration of 3D chemical similarity, target and adverse effect data to generate a drug-target-adverse effect predictor along with a simple leveraging system to improve identification of drug-targets and drug-adverse effects. In the first step, we generated a system for multiple drug-target identification based on the application of 3D drug similarity into a large target dataset extracted from the ChEMBL. Next, we developed a target-adverse effect predictor combining targets from ChEMBL with phenotypic information provided by SIDER data source. Both modules were linked to generate a final predictor that establishes hypothesis about new drug-target-adverse effect candidates. Additionally, we showed that leveraging drug-target candidates with phenotypic data is very useful to improve the identification of drug-targets. The integration of phenotypic data into drug-target candidates yielded up to twofold precision improvement. In the opposite direction, leveraging drug-phenotype candidates with target data also yielded a significant enhancement in the performance. The modeling described in the current study is simple and efficient and has applications at large scale in drug repurposing and drug safety through the identification of mechanism of action of biological effects.

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.

The Antibody Response of Pregnant Cameroonian Women to VAR2CSA ID1-ID2a, a Small Recombinant Protein Containing the CSA-Binding Site

PubMed Central

Babakhanyan, Anna; Leke, Rose G. F.; Salanti, Ali; Bobbili, Naveen; Gwanmesia, Philomina; Leke, Robert J. I.; Quakyi, Isabella A.; Chen, John J.; Taylor, Diane Wallace

2014-01-01

In pregnant women, Plasmodium falciparum-infected erythrocytes expressing the VAR2CSA antigen bind to chondroitin sulfate A in the placenta causing placental malaria. The binding site of VAR2CSA is present in the ID1-ID2a region. This study sought to determine if pregnant Cameroonian women naturally acquire antibodies to ID1-ID2a and if antibodies to ID1-ID2a correlate with absence of placental malaria at delivery. Antibody levels to full-length VAR2CSA and ID1-ID2a were measured in plasma samples from 745 pregnant Cameroonian women, 144 Cameroonian men, and 66 US subjects. IgM levels and IgG avidity to ID1-ID2a were also determined. As expected, antibodies to ID1-ID2a were absent in US controls. Although pregnant Cameroonian women developed increasing levels of antibodies to full-length VAR2CSA during pregnancy, no increase in either IgM or IgG to ID1-ID2a was observed. Surprisingly, no differences in antibody levels to ID1-ID2a were detected between Cameroonian men and pregnant women. For example, in rural settings only 8–9% of males had antibodies to full-length VAR2CSA, but 90–96% had antibodies to ID1-ID2a. In addition, no significant difference in the avidity of IgG to ID1-ID2a was found between pregnant women and Cameroonian men, and no correlation between antibody levels at delivery and absence of placental malaria was found. Thus, the response to ID1-ID2a was not pregnancy specific, but predominantly against cross-reactivity epitopes, which may have been induced by other PfEMP1 antigens, malarial antigens, or microbes. Currently, ID1-ID2a is a leading vaccine candidate, since it binds to the CSA with the same affinity as the full-length molecule and elicits binding-inhibitory antibodies in animals. Further studies are needed to determine if the presence of naturally acquired cross-reactive antibodies in women living in malaria endemic countries will alter the response to ID1-ID2a following vaccination with ID1-ID2a. PMID:24505415

Decreasing patient identification band errors by standardizing processes.

PubMed

Walley, Susan Chu; Berger, Stephanie; Harris, Yolanda; Gallizzi, Gina; Hayes, Leslie

2013-04-01

Patient identification (ID) bands are an essential component in patient ID. Quality improvement methodology has been applied as a model to reduce ID band errors although previous studies have not addressed standardization of ID bands. Our specific aim was to decrease ID band errors by 50% in a 12-month period. The Six Sigma DMAIC (define, measure, analyze, improve, and control) quality improvement model was the framework for this study. ID bands at a tertiary care pediatric hospital were audited from January 2011 to January 2012 with continued audits to June 2012 to confirm the new process was in control. After analysis, the major improvement strategy implemented was standardization of styles of ID bands and labels. Additional interventions included educational initiatives regarding the new ID band processes and disseminating institutional and nursing unit data. A total of 4556 ID bands were audited with a preimprovement ID band error average rate of 9.2%. Significant variation in the ID band process was observed, including styles of ID bands. Interventions were focused on standardization of the ID band and labels. The ID band error rate improved to 5.2% in 9 months (95% confidence interval: 2.5-5.5; P < .001) and was maintained for 8 months. Standardization of ID bands and labels in conjunction with other interventions resulted in a statistical decrease in ID band error rates. This decrease in ID band error rates was maintained over the subsequent 8 months.

Evaluation of ID-PaGIA syphilis antibody test.

PubMed

Naaber, Paul; Makoid, Ene; Aus, Anneli; Loivukene, Krista; Poder, Airi

2009-01-01

Laboratory diagnosis of syphilis is usually accomplished by serology. There are currently a large number of different commercial treponemal tests available that vary in format, sensitivity and specificity. To evaluate the ID-PaGIA Syphilis Antibody Test as an alternative to other specific treponemal tests for primary screening or confirmation of diagnosis. Serum samples from healthy adults (n = 100) were used for detection of specificity of ID-PaGIA. To evaluate sensitivity of ID-PaGIA serum samples (n = 101) from patients with confirmed or suspected syphilis were tested for syphilis antibodies with FTA-Abs IgM, ID-PaGIA, ELISA IgM and TPHA tests. No false-positive results were found with ID-PaGIA. Sensitivity of various treponemal tests was the following: FTA-Abs IgM: 95.5%, ID-PaGIA and ELISA IgM: 94%, and TPHA 75%. The positive and negative predictive values of ID-PaGIA were 100 and 89.5%, respectively. Compared with other treponemal tests ID-PaGIA has excellent sensitivity and specificity.

Genome-Wide Cell Type-Specific Mapping of In Vivo Chromatin Protein Binding Using an FLP-Inducible DamID System in Drosophila.

PubMed

Pindyurin, Alexey V

2017-01-01

A thorough study of the genome-wide binding patterns of chromatin proteins is essential for understanding the regulatory mechanisms of genomic processes in eukaryotic nuclei, including DNA replication, transcription, and repair. The DNA adenine methyltransferase identification (DamID) method is a powerful tool to identify genomic binding sites of chromatin proteins. This method does not require fixation of cells and the use of specific antibodies, and has been used to generate genome-wide binding maps of more than a hundred different proteins in Drosophila tissue culture cells. Recent versions of inducible DamID allow performing cell type-specific profiling of chromatin proteins even in small samples of Drosophila tissues that contain heterogeneous cell types. Importantly, with these methods sorting of cells of interest or their nuclei is not necessary as genomic DNA isolated from the whole tissue can be used as an input. Here, I describe in detail an FLP-inducible DamID method, namely generation of suitable transgenic flies, activation of the Dam transgenes by the FLP recombinase, isolation of DNA from small amounts of dissected tissues, and subsequent identification of the DNA binding sites of the chromatin proteins.

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

Generating unique IDs from patient identification data using security models.

PubMed

Mohammed, Emad A; Slack, Jonathan C; Naugler, Christopher T

2016-01-01

The use of electronic health records (EHRs) has continued to increase within healthcare systems in the developed and developing nations. EHRs allow for increased patient safety, grant patients easier access to their medical records, and offer a wealth of data to researchers. However, various bioethical, financial, logistical, and information security considerations must be addressed while transitioning to an EHR system. The need to encrypt private patient information for data sharing is one of the foremost challenges faced by health information technology. We describe the usage of the message digest-5 (MD5) and secure hashing algorithm (SHA) as methods for encrypting electronic medical data. In particular, we present an application of the MD5 and SHA-1 algorithms in encrypting a composite message from private patient information. The results show that the composite message can be used to create a unique one-way encrypted ID per patient record that can be used for data sharing. The described software tool can be used to share patient EMRs between practitioners without revealing patients identifiable data.

Generating unique IDs from patient identification data using security models

PubMed Central

Mohammed, Emad A.; Slack, Jonathan C.; Naugler, Christopher T.

2016-01-01

Background: The use of electronic health records (EHRs) has continued to increase within healthcare systems in the developed and developing nations. EHRs allow for increased patient safety, grant patients easier access to their medical records, and offer a wealth of data to researchers. However, various bioethical, financial, logistical, and information security considerations must be addressed while transitioning to an EHR system. The need to encrypt private patient information for data sharing is one of the foremost challenges faced by health information technology. Method: We describe the usage of the message digest-5 (MD5) and secure hashing algorithm (SHA) as methods for encrypting electronic medical data. In particular, we present an application of the MD5 and SHA-1 algorithms in encrypting a composite message from private patient information. Results: The results show that the composite message can be used to create a unique one-way encrypted ID per patient record that can be used for data sharing. Conclusion: The described software tool can be used to share patient EMRs between practitioners without revealing patients identifiable data. PMID:28163977

Identification of neuronal target genes for CCAAT/Enhancer Binding Proteins

PubMed Central

Kfoury, N.; Kapatos, G.

2009-01-01

CCAAT/Enhancer Binding Proteins (C/EBPs) play pivotal roles in development and plasticity of the nervous system. Identification of the physiological targets of C/EBPs (C/EBP target genes) should therefore provide insight into the underlying biology of these processes. We used unbiased genome-wide mapping to identify 115 C/EBPβ target genes in PC12 cells that include transcription factors, neurotransmitter receptors, ion channels, protein kinases and synaptic vesicle proteins. C/EBPβ binding sites were located primarily within introns, suggesting novel regulatory functions, and were associated with binding sites for other developmentally important transcription factors. Experiments using dominant negatives showed C/EBPβ to repress transcription of a subset of target genes. Target genes in rat brain were subsequently found to preferentially bind C/EBPα, β and δ. Analysis of the hippocampal transcriptome of C/EBPβ knockout mice revealed dysregulation of a high percentage of transcripts identified as C/EBP target genes. These results support the hypothesis that C/EBPs play non-redundant roles in the brain. PMID:19103292

Systematic and Open Identification of Researchers and Authors: Focus on Open Researcher and Contributor ID

PubMed Central

Akazhanov, Nurbek A.; Voronov, Alexander A.; Kitas, George D.

2014-01-01

Unique identifiers of researchers and authors can help all stakeholders of scientific communications improve their workflows. There have been several attempts to establish professional networks of scholars and list their scholarly achievements on digital platforms. Some of these platforms such as Google Scholar, Web of Knowledge and PubMed are searched to pick relevant peer reviewers, assess authors' publication history or choose suitable candidates for research and academic projects. However, each of these hubs has its specific applications, limiting the universal use for permanent tagging of researcher profiles. The Open Researcher and Contributor ID (ORCID) initiative, launched in 2012, is aimed at registering scholarly contributors and averting the persistent ambiguity of recorded author names. The ORCID registry is growing fast and integrating with other ID-generating platforms, thereby increasing the functionality of the integrated systems. ORCID identifiers are increasingly used for selecting peer reviewers and acknowledging various scholarly contributions (e.g., published articles, reviewer comments, conference presentations). The initiative offers unique opportunities for transparent disclosures of author contributions and competing interests and improving ethical standards of research, editing, and publishing. PMID:25408574

Systematic and open identification of researchers and authors: focus on open researcher and contributor ID.

PubMed

Gasparyan, Armen Yuri; Akazhanov, Nurbek A; Voronov, Alexander A; Kitas, George D

2014-11-01

Unique identifiers of researchers and authors can help all stakeholders of scientific communications improve their workflows. There have been several attempts to establish professional networks of scholars and list their scholarly achievements on digital platforms. Some of these platforms such as Google Scholar, Web of Knowledge and PubMed are searched to pick relevant peer reviewers, assess authors' publication history or choose suitable candidates for research and academic projects. However, each of these hubs has its specific applications, limiting the universal use for permanent tagging of researcher profiles. The Open Researcher and Contributor ID (ORCID) initiative, launched in 2012, is aimed at registering scholarly contributors and averting the persistent ambiguity of recorded author names. The ORCID registry is growing fast and integrating with other ID-generating platforms, thereby increasing the functionality of the integrated systems. ORCID identifiers are increasingly used for selecting peer reviewers and acknowledging various scholarly contributions (e.g., published articles, reviewer comments, conference presentations). The initiative offers unique opportunities for transparent disclosures of author contributions and competing interests and improving ethical standards of research, editing, and publishing.

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

Targeted nanodiamonds for identification of subcellular protein assemblies in mammalian cells

PubMed Central

Lake, Michael P.; Bouchard, Louis-S.

2017-01-01

Transmission electron microscopy (TEM) can be used to successfully determine the structures of proteins. However, such studies are typically done ex situ after extraction of the protein from the cellular environment. Here we describe an application for nanodiamonds as targeted intensity contrast labels in biological TEM, using the nuclear pore complex (NPC) as a model macroassembly. We demonstrate that delivery of antibody-conjugated nanodiamonds to live mammalian cells using maltotriose-conjugated polypropylenimine dendrimers results in efficient localization of nanodiamonds to the intended cellular target. We further identify signatures of nanodiamonds under TEM that allow for unambiguous identification of individual nanodiamonds from a resin-embedded, OsO4-stained environment. This is the first demonstration of nanodiamonds as labels for nanoscale TEM-based identification of subcellular protein assemblies. These results, combined with the unique fluorescence properties and biocompatibility of nanodiamonds, represent an important step toward the use of nanodiamonds as markers for correlated optical/electron bioimaging. PMID:28636640

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

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.

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.

Identification and validation nucleolin as a target of curcumol in nasopharyngeal carcinoma cells.

PubMed

Wang, Juan; Wu, Jiacai; Li, Xumei; Liu, Haowei; Qin, Jianli; Bai, Zhun; Chi, Bixia; Chen, Xu

2018-06-30

Identification of the specific protein target(s) of a drug is a critical step in unraveling its mechanisms of action (MOA) in many natural products. Curcumol, isolated from well known Chinese medicinal plant Curcuma zedoary, has been shown to possess multiple biological activities. It can inhibit nasopharyngeal carcinoma (NPC) proliferation and induce apoptosis, but its target protein(s) in NPC cells remains unclear. In this study, we employed a mass spectrometry-based chemical proteomics approach reveal the possible protein targets of curcumol in NPC cells. Cellular thermal shift assay (CETSA), molecular docking and cell-based assay was used to validate the binding interactions. Chemical proteomics capturing uncovered that NCL is a target of curcumol in NPC cells, Molecular docking showed that curcumol bound to NCL with an -7.8 kcal/mol binding free energy. Cell function analysis found that curcumol's treatment leads to a degradation of NCL in NPC cells, and it showed slight effects on NP69 cells. In conclusion, our results providing evidences that NCL is a target protein of curcumol. We revealed that the anti-cancer effects of curcumol in NPC cells are mediated, at least in part, by NCL inhibition. Many natural products showed high bioactivity, while their mechanisms of action (MOA) are very poor or completely missed. Understanding the MOA of natural drugs can thoroughly exploit their therapeutic potential and minimize their adverse side effects. Identification of the specific protein target(s) of a drug is a critical step in unraveling its MOA. Compound-centric chemical proteomics is a classic chemical proteomics approach which integrates chemical synthesis with cell biology and mass spectrometry (MS) to identify protein targets of natural products determine the drug mechanism of action, describe its toxicity, and figure out the possible cause of off-target. It is an affinity-based chemical proteomics method to identify small molecule-protein interactions

Long range thermal weapon sights for the German future infantryman program IdZ

NASA Astrophysics Data System (ADS)

Breiter, Rainer; Ihle, Tobias; Mauk, Karl-Heinz; Münzberg, Mario; Rode, Werner

2007-04-01

In December 2004 AIM started the series production of the HuntIR long range thermal weapon sight. The sight is fielded in the Germany Future Infantryman (IdZ) basic system and since that time in continuous service in various out of area missions with German participation. For very long identification ranges >1500m cooled technology still outperforms uncooled sights, even with respect to smaller size and lower weight because the typical F/1 design of uncooled systems overcompensates cooler weight for focal length >175mm. The HuntIR sight is therefore based on a cooled MWIR detection module for long range battlefield surveillance and target engagement. The device specifically is a perfect match to state of the art small arms like 0.50 cal sniper rifles or crew served weapons like the 40mm high velocity grenade machine gun (GMG) which provide engagement ranges >1500m and need an adequate sight performance beyond that. A recent modification of HuntIR was done to provide a wider field of view for improved situation awareness in urban operations and specifically to allow the engagement of the 40mm GMG in ranges between 250-1200m. The qualification tests of the sight by the German infantry were successfully completed mid 2006. To match the demand of the follow-up program IdZ-ES additional components have to be integrated. Most important are a laser range finder (LRF), 3 axis digital magnetic compass (DMC) and a wireless data link. LRF and DMC together with a highly sophisticated fire control computer provide improved first round hit probability, the DMC additionally improves the fire control in any case of steep trajectories or for pronounced ballistic trajectories to avoid any need to precisely level the GMG. This new sight is done under the brand name RangIR. An important additional feature is the interface for air burst ammunition (ABM). The optical distance is measured by the LRF, the fire control computer accurately evaluates the trajectory under the given angle

R&D100: IC ID

ScienceCinema

Hamlet, Jason; Pierson, Lyndon; Bauer, Todd

2018-06-25

Supply chain security to detect, deter, and prevent the counterfeiting of networked and stand-alone integrated circuits (ICs) is critical to cyber security. Sandia National Laboratory researchers have developed IC ID to leverage Physically Unclonable Functions (PUFs) and strong cryptographic authentication to create a unique fingerprint for each integrated circuit. IC ID assures the authenticity of ICs to prevent tampering or malicious substitution.

nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays

PubMed Central

Du, Pan; Kibbe, Warren A; Lin, Simon M

2007-01-01

Background Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe. Results We have devised a unique, non-degenerate encoding scheme that can be used as a universal representation to identify an oligonucleotide across manufacturers. We have named the encoded representation 'nuID', for nucleotide universal identifier. Inspired by the fact that the raw sequence of the oligonucleotide is the true definition of identity for a probe, the encoding algorithm uniquely and non-degenerately transforms the sequence itself into a compact identifier (a lossless compression). In addition, we added a redundancy check (checksum) to validate the integrity of the identifier. These two steps, encoding plus checksum, result in an nuID, which is a unique, non-degenerate, permanent, robust and efficient representation of the probe sequence. For commercial applications that require the sequence identity to be confidential, we have an encryption schema for nuID. We demonstrate the utility of nuIDs for the annotation of Illumina microarrays, and we believe it has universal applicability as a source-independent naming convention for oligomers. Reviewers This article was reviewed by Itai Yanai, Rong Chen (nominated by Mark Gerstein), and Gregory Schuler (nominated by David Lipman). PMID:17540033

Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems for the identification of clinical filamentous fungi.

PubMed

Huang, Yanfei; Zhang, Mingxin; Zhu, Min; Wang, Mei; Sun, Yufeng; Gu, Haitong; Cao, Jingjing; Li, Xue; Zhang, Shaoya; Wang, Jinglin; Lu, Xinxin

2017-07-01

Infections caused by filamentous fungi have become a health concern, and require rapid and accurate identification in order for effective treatment of the pathogens. To compare the performance of two MALDI-TOF MS systems (Bruker Microflex LT and Xiamen Microtyper) in the identification of filamentous fungal species. A total of 374 clinical filamentous fungal isolates sequentially collected in the Clinical Laboratory at the Beijing Tongren Hospital between January 2014 and December 2015 were identified by traditional phenotypic methods, Bruker Microflex LT and Xiamen Microtyper MALDI-TOF MS, respectively. The discrepancy between these methods was resolved by sequencing for definitive identification. Bruker Microflex LT and Xiamen Microtyper had similar correct species ID (98.9 vs. 99.2%), genus ID (99.7 vs. 100%), mis-ID (0.3 vs. 0%) and no ID (0 vs. 0). The rate of correct species identification by both MALDI-TOF MS (98.9 and 99.2%, respectively) was much higher compared with phenotypic approach (91.9%). Both MALDI-TOF MS systems provide accurate identification of clinical filamentous fungi compared with conventional phenotypic method, and have the potential to replace identification for routine identification of these fungi in clinical mycology laboratories. Both systems have similar performance in the identification of clinical filamentous fungi.

Nurses' Behaviors and Visual Scanning Patterns May Reduce Patient Identification Errors

ERIC Educational Resources Information Center

Marquard, Jenna L.; Henneman, Philip L.; He, Ze; Jo, Junghee; Fisher, Donald L.; Henneman, Elizabeth A.

2011-01-01

Patient identification (ID) errors occurring during the medication administration process can be fatal. The aim of this study is to determine whether differences in nurses' behaviors and visual scanning patterns during the medication administration process influence their capacities to identify patient ID errors. Nurse participants (n = 20)…

Lightweight ECC based RFID authentication integrated with an ID verifier transfer protocol.

PubMed

He, Debiao; Kumar, Neeraj; Chilamkurti, Naveen; Lee, Jong-Hyouk

2014-10-01

The radio frequency identification (RFID) technology has been widely adopted and being deployed as a dominant identification technology in a health care domain such as medical information authentication, patient tracking, blood transfusion medicine, etc. With more and more stringent security and privacy requirements to RFID based authentication schemes, elliptic curve cryptography (ECC) based RFID authentication schemes have been proposed to meet the requirements. However, many recently published ECC based RFID authentication schemes have serious security weaknesses. In this paper, we propose a new ECC based RFID authentication integrated with an ID verifier transfer protocol that overcomes the weaknesses of the existing schemes. A comprehensive security analysis has been conducted to show strong security properties that are provided from the proposed authentication scheme. Moreover, the performance of the proposed authentication scheme is analyzed in terms of computational cost, communicational cost, and storage requirement.

Comparison of Three Commercial Systems for Identification of Yeasts Commonly Isolated in the Clinical Microbiology Laboratory

PubMed Central

Wadlin, Jill K.; Hanko, Gayle; Stewart, Rebecca; Pape, John; Nachamkin, Irving

1999-01-01

We evaluated three commercial systems (RapID Yeast Plus System; Innovative Diagnostic Systems, Norcross, Ga.; API 20C Aux; bioMerieux-Vitek, Hazelwood, Mo.; and Vitek Yeast Biochemical Card, bioMerieux-Vitek) against an auxinographic and microscopic morphologic reference method for the ability to identify yeasts commonly isolated in our clinical microbiology laboratory. Two-hundred one yeast isolates were compared in the study. The RapID Yeast Plus System was significantly better than either API 20C Aux (193 versus 167 correct identifications; P < 0.0001) or the Vitek Yeast Biochemical Card (193 versus 173 correct identifications; P = 0.003) for obtaining correct identifications to the species level without additional testing. There was no significant difference between results obtained with API 20C Aux and the Vitek Yeast Biochemical Card system (P = 0.39). The API 20C Aux system did not correctly identify any of the Candida krusei isolates (n = 23) without supplemental testing and accounted for the major differences between the API 20C Aux and RapID Yeast Plus systems. Overall, the RapID Yeast Plus System was easy to use and is a good system for the routine identification of clinically relevant yeasts. PMID:10325356

IDS contribution to ITRF2008

NASA Astrophysics Data System (ADS)

Valette, Jean-Jacques; Lemoine, Frank G.; Ferrage, Pascale; Yaya, Philippe; Altamimi, Zuheir; Willis, Pascal; Soudarin, Laurent

2010-12-01

For the first time, the International DORIS Service (IDS) has produced a technique level combination based on the contributions of seven analysis centers (ACs), including the European Space Operations Center (ESOC), Geodetic Observatory Pecny (GOP), Geoscience Australia (GAU), the NASA Goddard Space Flight Center (GSFC), the Institut Géographique National (IGN), the Institute of Astronomy, Russian Academy of Sciences (INASAN, named as INA), and CNES/CLS (named as LCA). The ACs used five different software packages to process the DORIS data from 1992 to 2008, including NAPEOS (ESA), Bernese (GOP), GEODYN (GAU, GSC), GIPSY/OASIS (INA), and GINS (LCA). The data from seven DORIS satellites, TOPEX/Poseidon, SPOT-2, SPOT-3, SPOT-4, SPOT-5, Envisat and Jason-1 were processed and all the analysis centers produced weekly SINEX files in either variance-covariance or normal equation format. The processing by the analysis centers used the latest GRACE-derived gravity models, forward modelling of atmospheric gravity, updates to the radiation pressure modelling to improve the DORIS geocenter solutions, denser parameterization of empirically determined drag coefficients to improve station and EOP solutions, especially near the solar maximum in 2001-2002, updated troposphere mapping functions, and an ITRF2005-derived station set for orbit determination, DPOD2005. The CATREF software was used to process the weekly AC solutions, and produce three iterations of an IDS global weekly combination. Between the development of the initial solution IDS-1, and the final solution, IDS-3, the ACs improved their analysis strategies and submitted updated solutions to eliminate troposphere-derived biases in the solution scale, to reduce drag-related degradations in station positioning, and to refine the estimation strategy to improve the combination geocenter solution. An analysis of the frequency content of the individual AC geocenter and scale solutions was used as the basis to define the

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

ID-based encryption scheme with revocation

NASA Astrophysics Data System (ADS)

Othman, Hafizul Azrie; Ismail, Eddie Shahril

2017-04-01

In 2015, Meshram proposed an efficient ID-based cryptographic encryption based on the difficulty of solving discrete logarithm and integer-factoring problems. The scheme was pairing free and claimed to be secure against adaptive chosen plaintext attacks (CPA). Later, Tan et al. proved that the scheme was insecure by presenting a method to recover the secret master key and to obtain prime factorization of modulo n. In this paper, we propose a new pairing-free ID-based encryption scheme with revocation based on Meshram's ID-based encryption scheme, which is also secure against Tan et al.'s attacks.

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.

Perspectives: Are Voter Photo Identification Laws a Good Idea?

ERIC Educational Resources Information Center

Middleton, Tiffany

2012-01-01

As the 2012 presidential election approaches, controversy grows over recent statewide legislative initiatives that impose stricter identification requirements on voters. These new voter identification laws--especially those that require voters to produce a government-issued photo ID--are the subject of intense debates. During 2011, seven states…

Advances in the Study of Aptamer-Protein Target Identification Using the Chromatographic Approach.

PubMed

Drabik, Anna; Ner-Kluza, Joanna; Mielczarek, Przemyslaw; Civit, Laia; Mayer, Günter; Silberring, Jerzy

2018-06-01

Ever since the development of the process known as the systematic evolution of ligands by exponential enrichment (SELEX), aptamers have been widely used in a variety of studies, including the exploration of new diagnostic tools and the discovery of new treatment methods. Aptamers' ability to bind to proteins with high affinity and specificity, often compared to that of antibodies, enables the search for potential cancer biomarkers and helps us understand the mechanisms of carcinogenesis. The blind spot of those investigations is usually the difficulty in the selective extraction of targets attached to the aptamer. There are many studies describing the cell SELEX for the prime choice of aptamers toward living cancer cells or even whole tumors in the animal models. However, a dilemma arises when a large number of proteins are being identified as potential targets, which is often the case. In this article, we present a new analytical approach designed to selectively target proteins bound to aptamers. During studies, we have focused on the unambiguous identification of the molecular targets of aptamers characterized by high specificity to the prostate cancer cells. We have compared four assay approaches using electrophoretic and chromatographic methods for "fishing out" aptamer protein targets followed by mass spectrometry identification. We have established a new methodology, based on the fluorescent-tagged oligonucleotides commonly used for flow-cytometry experiments or as optic aptasensors, that allowed the detection of specific aptamer-protein interactions by mass spectrometry. The use of atto488-labeled aptamers for the tracking of the formation of specific aptamer-target complexes provides the possibility of studying putative protein counterparts without needing to apply enrichment techniques. Significantly, changes in the hydrophobic properties of atto488-labeled aptamer-protein complexes facilitate their separation by reverse-phase chromatography combined with

Contemporary microbiology and identification of Corynebacteria spp. causing infections in human.

PubMed

Zasada, A A; Mosiej, E

2018-06-01

The Corynebacterium is a genus of bacteria of growing clinical importance. Progress in medicine results in growing population of immunocompromised patients and growing number of infections caused by opportunistic pathogens. A new infections caused by new Corynebacterium species and species previously regarded as commensal micro-organisms have been described. Parallel with changes in Corynebacteria infections, the microbiological laboratory diagnostic possibilities are changing. But identification of this group of bacteria to the species level remains difficult. In the paper, we present various manual, semi-automated and automated assays used in clinical laboratories for Corynebacterium identification, such as API Coryne, RapID CB Plus, BBL Crystal Gram Positive ID System, MICRONAUT-RPO, VITEK 2, BD Phoenix System, Sherlock Microbial ID System, MicroSeq Microbial Identification System, Biolog Microbial Identification Systems, MALDI-TOF MS systems, polymerase chain reaction (PCR)-based and sequencing-based assays. The presented assays are based on various properties, like biochemical tests, specific DNA sequences, composition of cellular fatty acids, protein profiles and have specific limitations. The number of opportunistic infections caused by Corynebacteria is increasing due to increase in number of immunocompromised patients. New Corynebacterium species and new human infections, caused by this group of bacteria, has been described recently. However, identification of Corynebacteria is still a challenge despite application of sophisticated laboratory methods. In the study we present possibilities and limitations of various commercial systems for identification of Corynebacteria. © 2018 The Society for Applied Microbiology.

Identification of lactoferricin B intracellular targets using an Escherichia coli proteome chip.

PubMed

Tu, Yu-Hsuan; Ho, Yu-Hsuan; Chuang, Ying-Chih; Chen, Po-Chung; Chen, Chien-Sheng

2011-01-01

Lactoferricin B (LfcinB) is a well-known antimicrobial peptide. Several studies have indicated that it can inhibit bacteria by affecting intracellular activities, but the intracellular targets of this antimicrobial peptide have not been identified. Therefore, we used E. coli proteome chips to identify the intracellular target proteins of LfcinB in a high-throughput manner. We probed LfcinB with E. coli proteome chips and further conducted normalization and Gene Ontology (GO) analyses. The results of the GO analyses showed that the identified proteins were associated with metabolic processes. Moreover, we validated the interactions between LfcinB and chip assay-identified proteins with fluorescence polarization (FP) assays. Sixteen proteins were identified, and an E. coli interaction database (EcID) analysis revealed that the majority of the proteins that interact with these 16 proteins affected the tricarboxylic acid (TCA) cycle. Knockout assays were conducted to further validate the FP assay results. These results showed that phosphoenolpyruvate carboxylase was a target of LfcinB, indicating that one of its mechanisms of action may be associated with pyruvate metabolism. Thus, we used pyruvate assays to conduct an in vivo validation of the relationship between LfcinB and pyruvate level in E. coli. These results showed that E. coli exposed to LfcinB had abnormal pyruvate amounts, indicating that LfcinB caused an accumulation of pyruvate. In conclusion, this study successfully revealed the intracellular targets of LfcinB using an E. coli proteome chip approach.

Identification of Lactoferricin B Intracellular Targets Using an Escherichia coli Proteome Chip

PubMed Central

Chen, Po-Chung; Chen, Chien-Sheng

2011-01-01

Lactoferricin B (LfcinB) is a well-known antimicrobial peptide. Several studies have indicated that it can inhibit bacteria by affecting intracellular activities, but the intracellular targets of this antimicrobial peptide have not been identified. Therefore, we used E. coli proteome chips to identify the intracellular target proteins of LfcinB in a high-throughput manner. We probed LfcinB with E. coli proteome chips and further conducted normalization and Gene Ontology (GO) analyses. The results of the GO analyses showed that the identified proteins were associated with metabolic processes. Moreover, we validated the interactions between LfcinB and chip assay-identified proteins with fluorescence polarization (FP) assays. Sixteen proteins were identified, and an E. coli interaction database (EcID) analysis revealed that the majority of the proteins that interact with these 16 proteins affected the tricarboxylic acid (TCA) cycle. Knockout assays were conducted to further validate the FP assay results. These results showed that phosphoenolpyruvate carboxylase was a target of LfcinB, indicating that one of its mechanisms of action may be associated with pyruvate metabolism. Thus, we used pyruvate assays to conduct an in vivo validation of the relationship between LfcinB and pyruvate level in E. coli. These results showed that E. coli exposed to LfcinB had abnormal pyruvate amounts, indicating that LfcinB caused an accumulation of pyruvate. In conclusion, this study successfully revealed the intracellular targets of LfcinB using an E. coli proteome chip approach. PMID:22164243

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.

Multimodal biometrics for identity documents (MBioID).

PubMed

Dessimoz, Damien; Richiardi, Jonas; Champod, Christophe; Drygajlo, Andrzej

2007-04-11

The MBioID initiative has been set up to address the following germane question: What and how biometric technologies could be deployed in identity documents in the foreseeable future? This research effort proposes to look at current and future practices and systems of establishing and using biometric identity documents (IDs) and evaluate their effectiveness in large-scale developments. The first objective of the MBioID project is to present a review document establishing the current state-of-the-art related to the use of multimodal biometrics in an IDs application. This research report gives the main definitions, properties and the framework of use related to biometrics, an overview of the main standards developed in the biometric industry and standardisation organisations to ensure interoperability, as well as some of the legal framework and the issues associated to biometrics such as privacy and personal data protection. The state-of-the-art in terms of technological development is also summarised for a range of single biometric modalities (2D and 3D face, fingerprint, iris, on-line signature and speech), chosen according to ICAO recommendations and availabilities, and for various multimodal approaches. This paper gives a summary of the main elements of that report. The second objective of the MBioID project is to propose relevant acquisition and evaluation protocols for a large-scale deployment of biometric IDs. Combined with the protocols, a multimodal database will be acquired in a realistic way, in order to be as close as possible to a real biometric IDs deployment. In this paper, the issues and solutions related to the acquisition setup are briefly presented.

Tag ID Subdivision Scheme for Efficient Authentication and Security-Enhancement of RFID System in USN

NASA Astrophysics Data System (ADS)

Lee, Kijeong; Park, Byungjoo; Park, Gil-Cheol

Radio frequency identification (RFID) is a generic term that is used to describe a system that transmits the identity (in the form of a unique serial number) of an object or person wirelessly, using radio waves. However, there are security threats in the RFID system related to its technical components. For example, illegal RFID tag readers can read tag ID and recognize most RFID Readers, a security threat that needs in-depth attention. Previous studies show some ideas on how to minimize these security threats like studying the security protocols between tag, reader and Back-end DB. In this research, the team proposes an RFID Tag ID Subdivision Scheme to authenticate the permitted tag only in USN (Ubiquitous Sensor Network). Using the proposed scheme, the Back-end DB authenticates selected tags only to minimize security threats like eavesdropping and decreasing traffic in Back-end DB.

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

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.

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.

Human Identification by Cross-Correlation and Pattern Matching of Personalized Heartbeat: Influence of ECG Leads and Reference Database Size.

PubMed

Jekova, Irena; Krasteva, Vessela; Schmid, Ramun

2018-01-27

Human identification (ID) is a biometric task, comparing single input sample to many stored templates to identify an individual in a reference database. This paper aims to present the perspectives of personalized heartbeat pattern for reliable ECG-based identification. The investigations are using a database with 460 pairs of 12-lead resting electrocardiograms (ECG) with 10-s durations recorded at time-instants T1 and T2 > T1 + 1 year. Intra-subject long-term ECG stability and inter-subject variability of personalized PQRST (500 ms) and QRS (100 ms) patterns is quantified via cross-correlation, amplitude ratio and pattern matching between T1 and T2 using 7 features × 12-leads. Single and multi-lead ID models are trained on the first 230 ECG pairs. Their validation on 10, 20, ... 230 reference subjects (RS) from the remaining 230 ECG pairs shows: (i) two best single-lead ID models using lead II for a small population RS = (10-140) with identification accuracy AccID = (89.4-67.2)% and aVF for a large population RS = (140-230) with AccID = (67.2-63.9)%; (ii) better performance of the 6-lead limb vs. the 6-lead chest ID model-(91.4-76.1)% vs. (90.9-70)% for RS = (10-230); (iii) best performance of the 12-lead ID model-(98.4-87.4)% for RS = (10-230). The tolerable reference database size, keeping AccID > 80%, is RS = 30 in the single-lead ID scenario (II); RS = 50 (6 chest leads); RS = 100 (6 limb leads), RS > 230-maximal population in this study (12-lead ECG).

Systematic Identification of Combinatorial Drivers and Targets in Cancer Cell Lines

PubMed Central

Tabchy, Adel; Eltonsy, Nevine; Housman, David E.; Mills, Gordon B.

2013-01-01

There is an urgent need to elicit and validate highly efficacious targets for combinatorial intervention from large scale ongoing molecular characterization efforts of tumors. We established an in silico bioinformatic platform in concert with a high throughput screening platform evaluating 37 novel targeted agents in 669 extensively characterized cancer cell lines reflecting the genomic and tissue-type diversity of human cancers, to systematically identify combinatorial biomarkers of response and co-actionable targets in cancer. Genomic biomarkers discovered in a 141 cell line training set were validated in an independent 359 cell line test set. We identified co-occurring and mutually exclusive genomic events that represent potential drivers and combinatorial targets in cancer. We demonstrate multiple cooperating genomic events that predict sensitivity to drug intervention independent of tumor lineage. The coupling of scalable in silico and biologic high throughput cancer cell line platforms for the identification of co-events in cancer delivers rational combinatorial targets for synthetic lethal approaches with a high potential to pre-empt the emergence of resistance. PMID:23577104

Systematic identification of combinatorial drivers and targets in cancer cell lines.

PubMed

Tabchy, Adel; Eltonsy, Nevine; Housman, David E; Mills, Gordon B

2013-01-01

There is an urgent need to elicit and validate highly efficacious targets for combinatorial intervention from large scale ongoing molecular characterization efforts of tumors. We established an in silico bioinformatic platform in concert with a high throughput screening platform evaluating 37 novel targeted agents in 669 extensively characterized cancer cell lines reflecting the genomic and tissue-type diversity of human cancers, to systematically identify combinatorial biomarkers of response and co-actionable targets in cancer. Genomic biomarkers discovered in a 141 cell line training set were validated in an independent 359 cell line test set. We identified co-occurring and mutually exclusive genomic events that represent potential drivers and combinatorial targets in cancer. We demonstrate multiple cooperating genomic events that predict sensitivity to drug intervention independent of tumor lineage. The coupling of scalable in silico and biologic high throughput cancer cell line platforms for the identification of co-events in cancer delivers rational combinatorial targets for synthetic lethal approaches with a high potential to pre-empt the emergence of resistance.

Best Practices in Intellectual Disability Identification

ERIC Educational Resources Information Center

Fiorello, Catherine A.; Jenkins, Tiffany K.

2018-01-01

This article is an overview of identification of intellectual disabilities (ID), with a focus on meeting legal and ethical requirements when assessing children from culturally and linguistically diverse backgrounds and those living in poverty. Specific procedures and recommended instruments will be reviewed.

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

Biometrics, identification and surveillance.

PubMed

Lyon, David

2008-11-01

Governing by identity describes the emerging regime of a globalizing, mobile world. Governance depends on identification but identification increasingly depends on biometrics. This 'solution' to difficulties of verification is described and some technical weaknesses are discussed. The role of biometrics in classification systems is also considered and is shown to contain possible prejudice in relation to racialized criteria of identity. Lastly, the culture of biometric identification is shown to be limited to abstract data, artificially separated from the lived experience of the body including the orientation to others. It is proposed that creators of national ID systems in particular address these crucial deficiencies in their attempt to provide new modes of verification.

Brain-targeted stem cell gene therapy corrects mucopolysaccharidosis type II via multiple mechanisms.

PubMed

Gleitz, Hélène Fe; Liao, Ai Yin; Cook, James R; Rowlston, Samuel F; Forte, Gabriella Ma; D'Souza, Zelpha; O'Leary, Claire; Holley, Rebecca J; Bigger, Brian W

2018-06-08

The pediatric lysosomal storage disorder mucopolysaccharidosis type II is caused by mutations in IDS, resulting in accumulation of heparan and dermatan sulfate, causing severe neurodegeneration, skeletal disease, and cardiorespiratory disease. Most patients manifest with cognitive symptoms, which cannot be treated with enzyme replacement therapy, as native IDS does not cross the blood-brain barrier. We tested a brain-targeted hematopoietic stem cell gene therapy approach using lentiviral IDS fused to ApoEII (IDS.ApoEII) compared to a lentivirus expressing normal IDS or a normal bone marrow transplant. In mucopolysaccharidosis II mice, all treatments corrected peripheral disease, but only IDS.ApoEII mediated complete normalization of brain pathology and behavior, providing significantly enhanced correction compared to IDS. A normal bone marrow transplant achieved no brain correction. Whilst corrected macrophages traffic to the brain, secreting IDS/IDS.ApoEII enzyme for cross-correction, IDS.ApoEII was additionally more active in plasma and was taken up and transcytosed across brain endothelia significantly better than IDS via both heparan sulfate/ApoE-dependent receptors and mannose-6-phosphate receptors. Brain-targeted hematopoietic stem cell gene therapy provides a promising therapy for MPS II patients. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

Particular Biochemical Profiles for Enterohemorrhagic Escherichia coli O157:H7 Isolates on the ID 32E System

PubMed Central

Leclercq, Alexandre; Lambert, Bernard; Pierard, Denis; Mahillon, Jacques

2001-01-01

The ability of the ID 32E system to identify and discriminate 74 Escherichia coli O157 isolates among 106 E. coli non-O157 isolates was evaluated. The results showed atypical biochemical reactions but accurate identification at the species level and no unique biochemical profile numbers for E. coli O157, although these numbers were distinct from those of other serotypes. PMID:11230449

Combined Cycle Engine Large-Scale Inlet for Mode Transition Experiments: System Identification Rack Hardware Design

NASA Technical Reports Server (NTRS)

Thomas, Randy; Stueber, Thomas J.

2013-01-01

The System Identification (SysID) Rack is a real-time hardware-in-the-loop data acquisition (DAQ) and control instrument rack that was designed and built to support inlet testing in the NASA Glenn Research Center 10- by 10-Foot Supersonic Wind Tunnel. This instrument rack is used to support experiments on the Combined-Cycle Engine Large-Scale Inlet for Mode Transition Experiment (CCE? LIMX). The CCE?LIMX is a testbed for an integrated dual flow-path inlet configuration with the two flow paths in an over-and-under arrangement such that the high-speed flow path is located below the lowspeed flow path. The CCE?LIMX includes multiple actuators that are designed to redirect airflow from one flow path to the other; this action is referred to as "inlet mode transition." Multiple phases of experiments have been planned to support research that investigates inlet mode transition: inlet characterization (Phase-1) and system identification (Phase-2). The SysID Rack hardware design met the following requirements to support Phase-1 and Phase-2 experiments: safely and effectively move multiple actuators individually or synchronously; sample and save effector control and position sensor feedback signals; automate control of actuator positioning based on a mode transition schedule; sample and save pressure sensor signals; and perform DAQ and control processes operating at 2.5 KHz. This document describes the hardware components used to build the SysID Rack including their function, specifications, and system interface. Furthermore, provided in this document are a SysID Rack effectors signal list (signal flow); system identification experiment setup; illustrations indicating a typical SysID Rack experiment; and a SysID Rack performance overview for Phase-1 and Phase-2 experiments. The SysID Rack described in this document was a useful tool to meet the project objectives.

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

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

Identification of human microRNA targets from isolated argonaute protein complexes.

PubMed

Beitzinger, Michaela; Peters, Lasse; Zhu, Jia Yun; Kremmer, Elisabeth; Meister, Gunter

2007-06-01

MicroRNAs (miRNAs) constitute a class of small non-coding RNAs that regulate gene expression on the level of translation and/or mRNA stability. Mammalian miRNAs associate with members of the Argonaute (Ago) protein family and bind to partially complementary sequences in the 3' untranslated region (UTR) of specific target mRNAs. Computer algorithms based on factors such as free binding energy or sequence conservation have been used to predict miRNA target mRNAs. Based on such predictions, up to one third of all mammalian mRNAs seem to be under miRNA regulation. However, due to the low degree of complementarity between the miRNA and its target, such computer programs are often imprecise and therefore not very reliable. Here we report the first biochemical identification approach of miRNA targets from human cells. Using highly specific monoclonal antibodies against members of the Ago protein family, we co-immunoprecipitate Ago-bound mRNAs and identify them by cloning. Interestingly, most of the identified targets are also predicted by different computer programs. Moreover, we randomly analyzed six different target candidates and were able to experimentally validate five as miRNA targets. Our data clearly indicate that miRNA targets can be experimentally identified from Ago complexes and therefore provide a new tool to directly analyze miRNA function.

Reduction in pediatric identification band errors: a quality collaborative.

PubMed

Phillips, Shannon Connor; Saysana, Michele; Worley, Sarah; Hain, Paul D

2012-06-01

Accurate and consistent placement of a patient identification (ID) band is used in health care to reduce errors associated with patient misidentification. Multiple safety organizations have devoted time and energy to improving patient ID, but no multicenter improvement collaboratives have shown scalability of previously successful interventions. We hoped to reduce by half the pediatric patient ID band error rate, defined as absent, illegible, or inaccurate ID band, across a quality improvement learning collaborative of hospitals in 1 year. On the basis of a previously successful single-site intervention, we conducted a self-selected 6-site collaborative to reduce ID band errors in heterogeneous pediatric hospital settings. The collaborative had 3 phases: preparatory work and employee survey of current practice and barriers, data collection (ID band failure rate), and intervention driven by data and collaborative learning to accelerate change. The collaborative audited 11377 patients for ID band errors between September 2009 and September 2010. The ID band failure rate decreased from 17% to 4.1% (77% relative reduction). Interventions including education of frontline staff regarding correct ID bands as a safety strategy; a change to softer ID bands, including "luggage tag" type ID bands for some patients; and partnering with families and patients through education were applied at all institutions. Over 13 months, a collaborative of pediatric institutions significantly reduced the ID band failure rate. This quality improvement learning collaborative demonstrates that safety improvements tested in a single institution can be disseminated to improve quality of care across large populations of children.

ID-Viewer: a visual analytics architecture for infectious diseases surveillance and response management in Pakistan.

PubMed

Ali, M A; Ahsan, Z; Amin, M; Latif, S; Ayyaz, A; Ayyaz, M N

2016-05-01

Globally, disease surveillance systems are playing a significant role in outbreak detection and response management of Infectious Diseases (IDs). However, in developing countries like Pakistan, epidemic outbreaks are difficult to detect due to scarcity of public health data and absence of automated surveillance systems. Our research is intended to formulate an integrated service-oriented visual analytics architecture for ID surveillance, identify key constituents and set up a baseline for easy reproducibility of such systems in the future. This research focuses on development of ID-Viewer, which is a visual analytics decision support system for ID surveillance. It is a blend of intelligent approaches to make use of real-time streaming data from Emergency Departments (EDs) for early outbreak detection, health care resource allocation and epidemic response management. We have developed a robust service-oriented visual analytics architecture for ID surveillance, which provides automated mechanisms for ID data acquisition, outbreak detection and epidemic response management. Classification of chief-complaints is accomplished using dynamic classification module, which employs neural networks and fuzzy-logic to categorize syndromes. Standard routines by Center for Disease Control (CDC), i.e. c1-c3 (c1-mild, c2-medium and c3-ultra), and spatial scan statistics are employed for detection of temporal and spatio-temporal disease outbreaks respectively. Prediction of imminent disease threats is accomplished using support vector regression for early warnings and response planning. Geographical visual analytics displays are developed that allow interactive visualization of syndromic clusters, monitoring disease spread patterns, and identification of spatio-temporal risk zones. We analysed performance of surveillance framework using ID data for year 2011-2015. Dynamic syndromic classifier is able to classify chief-complaints to appropriate syndromes with high classification

Identification of distant drug off-targets by direct superposition of binding pocket surfaces.

PubMed

Schumann, Marcel; Armen, Roger S

2013-01-01

Correctly predicting off-targets for a given molecular structure, which would have the ability to bind a large range of ligands, is both particularly difficult and important if they share no significant sequence or fold similarity with the respective molecular target ("distant off-targets"). A novel approach for identification of off-targets by direct superposition of protein binding pocket surfaces is presented and applied to a set of well-studied and highly relevant drug targets, including representative kinases and nuclear hormone receptors. The entire Protein Data Bank is searched for similar binding pockets and convincing distant off-target candidates were identified that share no significant sequence or fold similarity with the respective target structure. These putative target off-target pairs are further supported by the existence of compounds that bind strongly to both with high topological similarity, and in some cases, literature examples of individual compounds that bind to both. Also, our results clearly show that it is possible for binding pockets to exhibit a striking surface similarity, while the respective off-target shares neither significant sequence nor significant fold similarity with the respective molecular target ("distant off-target").

TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples.

PubMed

Bandyopadhyay, Sanghamitra; Mitra, Ramkrishna

2009-10-15

Prediction of microRNA (miRNA) target mRNAs using machine learning approaches is an important area of research. However, most of the methods suffer from either high false positive or false negative rates. One reason for this is the marked deficiency of negative examples or miRNA non-target pairs. Systematic identification of non-target mRNAs is still not addressed properly, and therefore, current machine learning approaches are compelled to rely on artificially generated negative examples for training. In this article, we have identified approximately 300 tissue-specific negative examples using a novel approach that involves expression profiling of both miRNAs and mRNAs, miRNA-mRNA structural interactions and seed-site conservation. The newly generated negative examples are validated with pSILAC dataset, which elucidate the fact that the identified non-targets are indeed non-targets.These high-throughput tissue-specific negative examples and a set of experimentally verified positive examples are then used to build a system called TargetMiner, a support vector machine (SVM)-based classifier. In addition to assessing the prediction accuracy on cross-validation experiments, TargetMiner has been validated with a completely independent experimental test dataset. Our method outperforms 10 existing target prediction algorithms and provides a good balance between sensitivity and specificity that is not reflected in the existing methods. We achieve a significantly higher sensitivity and specificity of 69% and 67.8% based on a pool of 90 feature set and 76.5% and 66.1% using a set of 30 selected feature set on the completely independent test dataset. In order to establish the effectiveness of the systematically generated negative examples, the SVM is trained using a different set of negative data generated using the method in Yousef et al. A significantly higher false positive rate (70.6%) is observed when tested on the independent set, while all other factors are kept the

Unique identification code for medical fundus images using blood vessel pattern for tele-ophthalmology applications.

PubMed

Singh, Anushikha; Dutta, Malay Kishore; Sharma, Dilip Kumar

2016-10-01

Identification of fundus images during transmission and storage in database for tele-ophthalmology applications is an important issue in modern era. The proposed work presents a novel accurate method for generation of unique identification code for identification of fundus images for tele-ophthalmology applications and storage in databases. Unlike existing methods of steganography and watermarking, this method does not tamper the medical image as nothing is embedded in this approach and there is no loss of medical information. Strategic combination of unique blood vessel pattern and patient ID is considered for generation of unique identification code for the digital fundus images. Segmented blood vessel pattern near the optic disc is strategically combined with patient ID for generation of a unique identification code for the image. The proposed method of medical image identification is tested on the publically available DRIVE and MESSIDOR database of fundus image and results are encouraging. Experimental results indicate the uniqueness of identification code and lossless recovery of patient identity from unique identification code for integrity verification of fundus images. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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

Computational Identification of MicroRNAs and Their Targets from Finger Millet (Eleusine coracana).

PubMed

Usha, S; Jyothi, M N; Suchithra, B; Dixit, Rekha; Rai, D V; Nagesh Babu, R

2017-03-01

MicroRNAs are endogenous small RNAs regulating intrinsic normal growth and development of plant. Discovering miRNAs, their targets and further inferring their functions had become routine process to comprehend the normal biological processes of miRNAs and their roles in plant development. In this study, we used homology-based analysis with available expressed sequence tag of finger millet (Eleusine coracana) to predict conserved miRNAs. Three potent miRNAs targeting 88 genes were identified. The newly identified miRNAs were found to be homologous with miR166 and miR1310. The targets recognized were transcription factors and enzymes, and GO analysis showed these miRNAs played varied roles in gene regulation. The identification of miRNAs and their targets is anticipated to hasten the pace of key epigenetic regulators in plant development.

Identification of Distant Drug Off-Targets by Direct Superposition of Binding Pocket Surfaces

PubMed Central

Schumann, Marcel; Armen, Roger S.

2013-01-01

Correctly predicting off-targets for a given molecular structure, which would have the ability to bind a large range of ligands, is both particularly difficult and important if they share no significant sequence or fold similarity with the respective molecular target (“distant off-targets”). A novel approach for identification of off-targets by direct superposition of protein binding pocket surfaces is presented and applied to a set of well-studied and highly relevant drug targets, including representative kinases and nuclear hormone receptors. The entire Protein Data Bank is searched for similar binding pockets and convincing distant off-target candidates were identified that share no significant sequence or fold similarity with the respective target structure. These putative target off-target pairs are further supported by the existence of compounds that bind strongly to both with high topological similarity, and in some cases, literature examples of individual compounds that bind to both. Also, our results clearly show that it is possible for binding pockets to exhibit a striking surface similarity, while the respective off-target shares neither significant sequence nor significant fold similarity with the respective molecular target (“distant off-target”). PMID:24391782

Biodistribution and Pharmacokinetics of EGFR-Targeted Thiolated Gelatin Nanoparticles Following Systemic Administration in Pancreatic Tumor-Bearing Mice

PubMed Central

Xu, Jing; Gattacceca, Florence; Amiji, Mansoor

2013-01-01

The objective of this study was to evaluate qualitative and quantitative biodistribution of epidermal growth factor receptor (EGFR)-targeted thiolated type B gelatin nanoparticles in vivo in a subcutaneous human pancreatic adenocarcinoma (Panc-1) bearing female SCID Beige mice. EGFR-targeted nanoparticles showed preferential and sustained accumulation in the tumor mass, especially at early time points. Higher blood concentrations and higher tumor accumulations were observed with PEG-modified and EGFR-targeted nanoparticles during the study (AUClast: 17.38 and 19.56 %ID/mL*h in blood, 187 and 322 %ID/g*h in tumor for PEG-modified and EGFR-targeted nanoparticles, respectively), as compared to control, unmodified particles (AUClast: 10.71 %ID/mL*h in blood and 138 %ID/g*h in tumor). EGFR-targeted nanoparticles displayed almost twice tumor targeting efficiency than either PEG-modified or the unmodified nanoparticles, highlighting the efficacy of the active targeting strategy. In conclusion, this study shows that EGFR-targeted and PEG-modified nanoparticles were suitable vehicles for specific systemic delivery in subcutaneous Panc-1 tumor xenograft models. PMID:23544877

Biodistribution and pharmacokinetics of EGFR-targeted thiolated gelatin nanoparticles following systemic administration in pancreatic tumor-bearing mice.

PubMed

Xu, Jing; Gattacceca, Florence; Amiji, Mansoor

2013-05-06

The objective of this study was to evaluate qualitative and quantitative biodistribution of epidermal growth factor receptor (EGFR)-targeted thiolated type B gelatin nanoparticles in vivo in subcutaneous human pancreatic adenocarcinoma (Panc-1) bearing female SCID Beige mice. EGFR-targeted nanoparticles showed preferential and sustained accumulation in the tumor mass, especially at early time points. Higher blood concentrations and higher tumor accumulations were observed with PEG-modified and EGFR-targeted nanoparticles during the study (AUClast: 17.38 and 19.56%ID/mL·h in blood, 187 and 322%ID/g·h in tumor for PEG-modified and EGFR-targeted nanoparticles, respectively), as compared to control, unmodified particles (AUClast: 10.71%ID/mL·h in blood and 138%ID/g·h in tumor). EGFR-targeted nanoparticles displayed almost twice tumor targeting efficiency than either PEG-modified or the unmodified nanoparticles, highlighting the efficacy of the active targeting strategy. In conclusion, this study shows that EGFR-targeted and PEG-modified nanoparticles were suitable vehicles for specific systemic delivery in subcutaneous Panc-1 tumor xenograft models.

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.

Enhanced ID Pit Sizing Using Multivariate Regression Algorithm

NASA Astrophysics Data System (ADS)

Krzywosz, Kenji

2007-03-01

EPRI is funding a program to enhance and improve the reliability of inside diameter (ID) pit sizing for balance-of plant heat exchangers, such as condensers and component cooling water heat exchangers. More traditional approaches to ID pit sizing involve the use of frequency-specific amplitude or phase angles. The enhanced multivariate regression algorithm for ID pit depth sizing incorporates three simultaneous input parameters of frequency, amplitude, and phase angle. A set of calibration data sets consisting of machined pits of various rounded and elongated shapes and depths was acquired in the frequency range of 100 kHz to 1 MHz for stainless steel tubing having nominal wall thickness of 0.028 inch. To add noise to the acquired data set, each test sample was rotated and test data acquired at 3, 6, 9, and 12 o'clock positions. The ID pit depths were estimated using a second order and fourth order regression functions by relying on normalized amplitude and phase angle information from multiple frequencies. Due to unique damage morphology associated with the microbiologically-influenced ID pits, it was necessary to modify the elongated calibration standard-based algorithms by relying on the algorithm developed solely from the destructive sectioning results. This paper presents the use of transformed multivariate regression algorithm to estimate ID pit depths and compare the results with the traditional univariate phase angle analysis. Both estimates were then compared with the destructive sectioning results.

PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database.

PubMed

Wang, Xia; Shen, Yihang; Wang, Shiwei; Li, Shiliang; Zhang, Weilin; Liu, Xiaofeng; Lai, Luhua; Pei, Jianfeng; Li, Honglin

2017-07-03

The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. The original version of PharmMapper includes more than 7000 target pharmacophores derived from complex crystal structures with corresponding protein target annotations. In this article, we present a new version of the PharmMapper web server, of which the backend pharmacophore database is six times larger than the earlier one, with a total of 23 236 proteins covering 16 159 druggable pharmacophore models and 51 431 ligandable pharmacophore models. The expanded target data cover 450 indications and 4800 molecular functions compared to 110 indications and 349 molecular functions in our last update. In addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores. It also features an improved user interface. The proposed web server is freely available at http://lilab.ecust.edu.cn/pharmmapper/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

A new efficient method of generating photoaffinity beads for drug target identification.

PubMed

Nishiya, Yoichi; Hamada, Tomoko; Abe, Masayuki; Takashima, Michio; Tsutsumi, Kyoko; Okawa, Katsuya

2017-02-15

Affinity purification is one of the most prevalent methods for the target identification of small molecules. Preparation of an appropriate chemical for immobilization, however, is a tedious and time-consuming process. A decade ago, a photoreaction method for generating affinity beads was reported, where compounds are mixed with agarose beads carrying a photoreactive group (aryldiazirine) and then irradiated with ultraviolet light under dry conditions to form covalent attachment. Although the method has proven useful for identifying drug targets, the beads suffer from inefficient ligand incorporation and tend to shrink and aggregate, which can cause nonspecific binding and low reproducibility. We therefore decided to craft affinity beads free from these shortcomings without compromising the ease of preparation. We herein report a modified method; first, a compound of interest is mixed with a crosslinker having an activated ester and a photoreactive moiety on each end. This mixture is then dried in a glass tube and irradiated with ultraviolet light. Finally, the conjugates are dissolved and reacted with agarose beads with a primary amine. This protocol enabled us to immobilize compounds more efficiently (approximately 500-fold per bead compared to the original method) and generated beads without physical deterioration. We herein demonstrated that the new FK506-immobilized beads specifically isolated more FKBP12 than the original beads, thereby proving our method to be applicable to target identification experiments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Applications of CRISPR genome editing technology in drug target identification and validation.

PubMed

Lu, Quinn; Livi, George P; Modha, Sundip; Yusa, Kosuke; Macarrón, Ricardo; Dow, David J

2017-06-01

The analysis of pharmaceutical industry data indicates that the major reason for drug candidates failing in late stage clinical development is lack of efficacy, with a high proportion of these due to erroneous hypotheses about target to disease linkage. More than ever, there is a requirement to better understand potential new drug targets and their role in disease biology in order to reduce attrition in drug development. Genome editing technology enables precise modification of individual protein coding genes, as well as noncoding regulatory sequences, enabling the elucidation of functional effects in human disease relevant cellular systems. Areas covered: This article outlines applications of CRISPR genome editing technology in target identification and target validation studies. Expert opinion: Applications of CRISPR technology in target validation studies are in evidence and gaining momentum. Whilst technical challenges remain, we are on the cusp of CRISPR being applied in complex cell systems such as iPS derived differentiated cells and stem cell derived organoids. In the meantime, our experience to date suggests that precise genome editing of putative targets in primary cell systems is possible, offering more human disease relevant systems than conventional cell lines.

The inhibitor of differentiation-1 (Id1) enables lung cancer liver colonization through activation of an EMT program in tumor cells and establishment of the pre-metastatic niche.

PubMed

Castañón, Eduardo; Soltermann, Alex; López, Inés; Román, Marta; Ecay, Margarita; Collantes, María; Redrado, Miriam; Baraibar, Iosune; López-Picazo, José María; Rolfo, Christian; Vidal-Vanaclocha, Fernando; Raez, Luis; Weder, Walter; Calvo, Alfonso; Gil-Bazo, Ignacio

2017-08-28

Id1 promotes carcinogenesis and metastasis, and predicts prognosis of non-small cell lung cancer (NSCLC)-adenocarcionoma patients. We hypothesized that Id1 may play a critical role in lung cancer colonization of the liver by affecting both tumor cells and the microenvironment. Depleted levels of Id1 in LLC (Lewis lung carcinoma cells, LLC shId1) significantly reduced cell proliferation and migration in vitro. Genetic loss of Id1 in the host tissue (Id1 -/- mice) impaired liver colonization and increased survival of Id1 -/- animals. Histologically, the presence of Id1 in tumor cells of liver metastasis was responsible for liver colonization. Microarray analysis comparing liver tumor nodules from Id1 +/+ mice and Id1 -/- mice injected with LLC control cells revealed that Id1 loss reduces the levels of EMT-related proteins, such as vimentin. In tissue microarrays containing 532 NSCLC patients' samples, we found that Id1 significantly correlated with vimentin and other EMT-related proteins. Id1 loss decreased the levels of vimentin, integrinβ1, TGFβ1 and snail, both in vitro and in vivo. Therefore, Id1 enables both LLC and the host microenvironment for an effective liver colonization, and may represent a novel therapeutic target to avoid NSCLC liver metastasis. Copyright © 2017 Elsevier B.V. All rights reserved.

Security analysis for biometric data in ID documents

NASA Astrophysics Data System (ADS)

Schimke, Sascha; Kiltz, Stefan; Vielhauer, Claus; Kalker, Ton

2005-03-01

In this paper we analyze chances and challenges with respect to the security of using biometrics in ID documents. We identify goals for ID documents, set by national and international authorities, and discuss the degree of security, which is obtainable with the inclusion of biometric into documents like passports. Starting from classical techniques for manual authentication of ID card holders, we expand our view towards automatic methods based on biometrics. We do so by reviewing different human biometric attributes by modality, as well as by discussing possible techniques for storing and handling the particular biometric data on the document. Further, we explore possible vulnerabilities of potential biometric passport systems. Based on the findings of that discussion we will expand upon two exemplary approaches for including digital biometric data in the context of ID documents and present potential risks attack scenarios along with technical aspects such as capacity and robustness.

Preventing the threat of credit-card fraud: Factors influencing cashiers' identification-checking behavior.

PubMed

Downing, Christopher; Howard, E Henry; Goodwin, Christina; Geller, E Scott

2016-01-01

Two studies examined factors influencing cashiers' identification (ID)-checking behavior in order to inform the development of interventions to prevent credit-card fraud. In both studies, research assistants made credit purchases in various stores and noted the cashiers' ID-checking behavior. In the first study, the store type, whether the cashier swiped the credit/debit card, the amount of the purchase, and whether the credit/debit card was signed significantly influenced ID-checking behavior. In the second study, an A-B-A design was used to evaluate the impact of a "Check my ID" prompt placed on the credit/debit card. The prompt increased cashiers' ID-checking behavior from 5.9% at Baseline to 10.3% during the Intervention. When the prompt was removed, the cashiers' ID-checking behavior decreased to 7.2%. Implications for further intervention research to prevent credit-card fraud are discussed.

NHEXAS PHASE I MARYLAND STUDY--STANDARD OPERATING PROCEDURE FOR IDENTIFICATION NUMBERS FOR SAMPLES AND FORMS (G03)

EPA Science Inventory

The purpose of this SOP is to indicate the proper method for assigning unique Identification Numbers for all samples taken and forms used in the collection of NHEXAS Pilot Studies. All data tracking procedures were built upon these ID numbers. Inspection of these ID numbers pro...

Neuronal Target Identification Requires AHA-1-Mediated Fine-Tuning of Wnt Signaling in C. elegans

PubMed Central

Zhang, Jingyan; Li, Xia; Jevince, Angela R.; Guan, Liying; Wang, Jiaming; Hall, David H.; Huang, Xun; Ding, Mei

2013-01-01

Electrical synaptic transmission through gap junctions is a vital mode of intercellular communication in the nervous system. The mechanism by which reciprocal target cells find each other during the formation of gap junctions, however, is poorly understood. Here we show that gap junctions are formed between BDU interneurons and PLM mechanoreceptors in C. elegans and the connectivity of BDU with PLM is influenced by Wnt signaling. We further identified two PAS-bHLH family transcription factors, AHA-1 and AHR-1, which function cell-autonomously within BDU and PLM to facilitate the target identification process. aha-1 and ahr-1 act genetically upstream of cam-1. CAM-1, a membrane-bound receptor tyrosine kinase, is present on both BDU and PLM cells and likely serves as a Wnt antagonist. By binding to a cis-regulatory element in the cam-1 promoter, AHA-1 enhances cam-1 transcription. Our study reveals a Wnt-dependent fine-tuning mechanism that is crucial for mutual target cell identification during the formation of gap junction connections. PMID:23825972

Comparison of Perinatal Risk Factors Associated with Autism Spectrum Disorder (ASD), Intellectual Disability (ID), and Co-Occurring ASD and ID

ERIC Educational Resources Information Center

Schieve, Laura A.; Clayton, Heather B.; Durkin, Maureen S.; Wingate, Martha S.; Drews-Botsch, Carolyn

2015-01-01

While studies report associations between perinatal outcomes and both autism spectrum disorder (ASD) and intellectual disability (ID), there has been little study of ASD with versus without co-occurring ID. We compared perinatal risk factors among 7547 children in the 2006-2010 Autism and Developmental Disability Monitoring Network classified as…

Biolog(TM) ID as compared to 16S ribosomal RNA ID for environmental isolates from the deep subsurface

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

McKinsey, P.C.

2000-05-05

The U.S. Dept of Energy (DOE) Subsurface Microbial Culture Collection (SMCC) contains nearly 10,000 strains of microorganisms isolated from terrestrial subsurface environments. Many of the aerobic, gram-negative, chemoheterotrophs isolated from the DOE Savannah River Site (SRS) have previously been identified by phylogenetic analysis of 16S ribosomal RNA (rRNA) gene nucleotide sequences. These SMCC isolates are currently being examined using Biolog GN Microplates and the Biolog Microstation System in order to gain knowledge of their metabolic capabilities and to compare Biolog IDs with 16S IDs. To accommodate the particular needs of these subsurface isolates, which are often incapable of growing undermore » high-nutrient conditions, Biolog's recommendations for inoculating isolates into Biolog GN Microplates have been altered. The isolates are grown on low nutrient media, sodium thioglycolate (3mM) is added to the culture media to inhibit capsule formation, and a low density of bacteria is inoculated into the microplate. Using these altered inoculation criteria, 60 percent of these SMCC isolates have a Biolog genus ID that matches the 16S rRNA ID. These results indicate that the Biolog System can be a good means of identifying unusual environmental isolates, even when recommended inoculation procedures are altered to accommodate particular isolate needs.« less

Pharmacogenetics and target identification in diabetes.

PubMed

Pearson, Ewan R

2018-02-24

In diabetes, pharmacogenetics can be used both to identify patient subgroups who will have most benefit and/or least harm from a particularly treatment, and to gain insights into the molecular mechanisms of drug action and disease aetiology. There is increasing evidence that genetic variation alters response to diabetes treatments-both in terms of glycaemic response and side effects. This can be seen with dramatic impact on clinical care, in patients with genetic forms of diabetes such as Maturity Onset Diabetes of the Young caused by HNF1A mutations, and Neonatal diabetes due to activating mutations in ABCC8 or KCNJ11. Beyond monogenic diabetes, pharmacogenetic variants have yet to impact on clinical practice, yet the effect sizes (e.g. for metformin intolerance and OCT1 variants; or for metformin action and SLC2A2 variants) are potentially of clinical utility, especially if the genotype is already known at the point of prescribing. Over the next few years, increasing cohort sizes and linkage at scale to electronic medical records will provide considerable potential for stratification and novel target identification in diabetes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Novel ID-based anti-collision approach for RFID

NASA Astrophysics Data System (ADS)

Zhang, De-Gan; Li, Wen-Bin

2016-09-01

Novel correlation ID-based (CID) anti-collision approach for RFID under the banner of the Internet of Things (IOT) has been presented in this paper. The key insights are as follows: according to the deterministic algorithms which are based on the binary search tree, we propose a method to increase the association between tags so that tags can initiatively send their own ID under certain trigger conditions, at the same time, we present a multi-tree search method for querying. When the number of tags is small, by replacing the actual ID with the temporary ID, it can greatly reduce the number of times that the reader reads and writes to tag's ID. Active tags send data to the reader by the way of modulation binary pulses. When applying this method to the uncertain ALOHA algorithms, the reader can determine the locations of the empty slots according to the position of the binary pulse, so it can avoid the decrease in efficiency which is caused by reading empty slots when reading slots. Theory and experiment show that this method can greatly improve the recognition efficiency of the system when applied to either the search tree or the ALOHA anti-collision algorithms.

Gene silencing in Tribolium castaneum as a tool for the targeted identification of candidate RNAi targets in crop pests.

PubMed

Knorr, Eileen; Fishilevich, Elane; Tenbusch, Linda; Frey, Meghan L F; Rangasamy, Murugesan; Billion, Andre; Worden, Sarah E; Gandra, Premchand; Arora, Kanika; Lo, Wendy; Schulenberg, Greg; Valverde-Garcia, Pablo; Vilcinskas, Andreas; Narva, Kenneth E

2018-02-01

RNAi shows potential as an agricultural technology for insect control, yet, a relatively low number of robust lethal RNAi targets have been demonstrated to control insects of agricultural interest. In the current study, a selection of lethal RNAi target genes from the iBeetle (Tribolium castaneum) screen were used to demonstrate efficacy of orthologous targets in the economically important coleopteran pests Diabrotica virgifera virgifera and Meligethes aeneus. Transcript orthologs of 50 selected genes were analyzed in D. v. virgifera diet-based RNAi bioassays; 21 of these RNAi targets showed mortality and 36 showed growth inhibition. Low dose injection- and diet-based dsRNA assays in T. castaneum and D. v. virgifera, respectively, enabled the identification of the four highly potent RNAi target genes: Rop, dre4, ncm, and RpII140. Maize was genetically engineered to express dsRNA directed against these prioritized candidate target genes. T 0 plants expressing Rop, dre4, or RpII140 RNA hairpins showed protection from D. v. virgifera larval feeding damage. dsRNA targeting Rop, dre4, ncm, and RpII140 in M. aeneus also caused high levels of mortality both by injection and feeding. In summary, high throughput systems for model organisms can be successfully used to identify potent RNA targets for difficult-to-work with agricultural insect pests.

Report of the Federation of European Laboratory Animal Science Associations Working Group on animal identification.

PubMed

Dahlborn, K; Bugnon, P; Nevalainen, T; Raspa, M; Verbost, P; Spangenberg, E

2013-01-01

The primary aim of this report is to assist scientists in selecting more reliable/suitable identification (ID) methods for their studies. This is especially true for genetically altered (GA) animals where individual identification is strictly necessary to link samples, research design and genotype. The aim of this Federation of European Laboratory Animal Science Associations working group was to provide an update of the methods used to identify rodents in different situations and to assess their implications for animal welfare. ID procedures are an indispensable prerequisite for conducting good science but the degree of invasiveness differs between the different methods; therefore, one needs to make a good ethical evaluation of the method chosen. Based on the scientific literature the advantages and disadvantages of various methods have been presented comprehensively and this report is intended as a practical guide for researchers. New upcoming methods have been included next to the traditional techniques. Ideally, an ID method should provide reliable identification, be technically easy to apply and not inflict adverse effects on animals while taking into account the type of research. There is no gold standard method because each situation is unique; however, more studies are needed to better evaluate ID systems and the desirable introduction of new and modern approaches will need to be assessed by detailed scientific evaluation.

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

Chronic arsenic intoxication diagnostic score (CAsIDS).

PubMed

Dani, Sergio Ulhoa; Walter, Gerhard Franz

2018-01-01

Arsenic and its compounds are well-established, potent, environmentally widespread and persistent toxicants with metabolic, genotoxic, mutagenic, teratogenic, epigenetic and carcinogenic effects. Arsenic occurs naturally in the Earth's crust, but anthropogenic arsenic emissions have surmounted the emissions from important natural sources such as volcanism. Inorganic arsenicals exhibit acute and chronic toxicities in virtually all cell types and tissues, and hence arsenic intoxication affects multiple systems. Whereas acute arsenic intoxication is rare and relatively easy to diagnose, chronic arsenic intoxication (CAsI) is common but goes often misdiagnosed. Based on a review of the literature as well as our own clinical experience, we propose a chronic arsenic intoxication diagnostic score (CAsIDS). A distinctive feature of CAsIDS is the use of bone arsenic load as an essential criterion for the individual risk assessment of chronic arsenic intoxication, combined with a systemic clinical assessment. We present clinical examples where CAsIDS is applied for the diagnosis of CAsI, review the main topics of the toxicity of arsenic in different cell and organ systems and discuss the therapy and prevention of disease caused or aggravated by chronic arsenic intoxication. CAsIDS can help physicians establish the diagnosis of CAsI and associated conditions. Copyright © 2017 John Wiley & Sons, Ltd.

Development of a Robust star identification technique for use in attitude determination of the ACE spacecraft

NASA Technical Reports Server (NTRS)

Woodard, Mark; Rohrbaugh, Dave

1995-01-01

The Advanced Composition Explorer (ACE) spacecraft is designed to fly in a spin-stabilized attitude. The spacecraft will carry two attitude sensors - a digital fine Sun sensor and a charge coupled device (CCD) star tracker - to allow ground-based determination of the spacecraft attitude and spin rate. Part of the processing that must be performed on the CCD star tracker data is the star identification. Star data received from the spacecraft must be matched with star information in the SKYMAP catalog to determine exactly which stars the sensor is tracking. This information, along with the Sun vector measured by the Sun sensor, is used to determine the spacecraft attitude. Several existing star identification (star ID) systems were examined to determine whether they could be modified for use on the ACE mission. Star ID systems which exist for three-axis stabilized spacecraft tend to be complex in nature and many require fairly good knowledge of the spacecraft attitude, making their use for ACE excessive. Star ID systems used for spinners carrying traditional slit star sensors would have to be modified to model the CCD star tracker. The ACE star ID algorithm must also be robust, in that it will be able to correctly identify stars even though the attitude is not known to a high degree of accuracy, and must be very efficient to allow real-time star identification. The paper presents the star ID algorithm that was developed for ACE. Results from prototype testing are also presented to demonstrate the efficiency, accuracy, and robustness of the algorithm.

Laser range profiling for small target recognition

NASA Astrophysics Data System (ADS)

Steinvall, Ove; Tulldahl, Michael

2016-05-01

The detection and classification of small surface and airborne targets at long ranges is a growing need for naval security. Long range ID or ID at closer range of small targets has its limitations in imaging due to the demand on very high transverse sensor resolution. It is therefore motivated to look for 1D laser techniques for target ID. These include vibrometry, and laser range profiling. Vibrometry can give good results but is also sensitive to certain vibrating parts on the target being in the field of view. Laser range profiling is attractive because the maximum range can be substantial, especially for a small laser beam width. A range profiler can also be used in a scanning mode to detect targets within a certain sector. The same laser can also be used for active imaging when the target comes closer and is angular resolved. The present paper will show both experimental and simulated results for laser range profiling of small boats out to 6-7 km range and a UAV mockup at close range (1.3 km). We obtained good results with the profiling system both for target detection and recognition. Comparison of experimental and simulated range waveforms based on CAD models of the target support the idea of having a profiling system as a first recognition sensor and thus narrowing the search space for the automatic target recognition based on imaging at close ranges. The naval experiments took place in the Baltic Sea with many other active and passive EO sensors beside the profiling system. Discussion of data fusion between laser profiling and imaging systems will be given. The UAV experiments were made from the rooftop laboratory at FOI.

The ID23-2 structural biology microfocus beamline at the ESRF

PubMed Central

Flot, David; Mairs, Trevor; Giraud, Thierry; Guijarro, Matias; Lesourd, Marc; Rey, Vicente; van Brussel, Denis; Morawe, Christian; Borel, Christine; Hignette, Olivier; Chavanne, Joel; Nurizzo, Didier; McSweeney, Sean; Mitchell, Edward

2010-01-01

The first phase of the ESRF beamline ID23 to be constructed was ID23-1, a tunable MAD-capable beamline which opened to users in early 2004. The second phase of the beamline to be constructed is ID23-2, a monochromatic microfocus beamline dedicated to macromolecular crystallography experiments. Beamline ID23-2 makes use of well characterized optical elements: a single-bounce silicon (111) monochromator and two mirrors in Kirkpatrick–Baez geometry to focus the X-ray beam. A major design goal of the ID23-2 beamline is to provide a reliable, easy-to-use and routine microfocus beam. ID23-2 started operation in November 2005, as the first beamline dedicated to microfocus macromolecular crystallography. The beamline has taken the standard automated ESRF macromolecular crystallography environment (both hardware and software), allowing users of ID23-2 to be rapidly familiar with the microfocus environment. This paper describes the beamline design, the special considerations taken into account given the microfocus beam, and summarizes the results of the first years of the beamline operation. PMID:20029119

Vehicle Re-Identification by Deep Hidden Multi-View Inference.

PubMed

Zhou, Yi; Liu, Li; Shao, Ling

2018-07-01

Vehicle re-identification (re-ID) is an area that has received far less attention in the computer vision community than the prevalent person re-ID. Possible reasons for this slow progress are the lack of appropriate research data and the special 3D structure of a vehicle. Previous works have generally focused on some specific views (e.g., front); but, these methods are less effective in realistic scenarios, where vehicles usually appear in arbitrary views to cameras. In this paper, we focus on the uncertainty of vehicle viewpoint in re-ID, proposing two end-to-end deep architectures: the Spatially Concatenated ConvNet and convolutional neural network (CNN)-LSTM bi-directional loop. Our models exploit the great advantages of the CNN and long short-term memory (LSTM) to learn transformations across different viewpoints of vehicles. Thus, a multi-view vehicle representation containing all viewpoints' information can be inferred from the only one input view, and then used for learning to measure distance. To verify our models, we also introduce a Toy Car RE-ID data set with images from multiple viewpoints of 200 vehicles. We evaluate our proposed methods on the Toy Car RE-ID data set and the public Multi-View Car, VehicleID, and VeRi data sets. Experimental results illustrate that our models achieve consistent improvements over the state-of-the-art vehicle re-ID approaches.

A robust star identification algorithm with star shortlisting

NASA Astrophysics Data System (ADS)

Mehta, Deval Samirbhai; Chen, Shoushun; Low, Kay Soon

2018-05-01

A star tracker provides the most accurate attitude solution in terms of arc seconds compared to the other existing attitude sensors. When no prior attitude information is available, it operates in "Lost-In-Space (LIS)" mode. Star pattern recognition, also known as star identification algorithm, forms the most crucial part of a star tracker in the LIS mode. Recognition reliability and speed are the two most important parameters of a star pattern recognition technique. In this paper, a novel star identification algorithm with star ID shortlisting is proposed. Firstly, the star IDs are shortlisted based on worst-case patch mismatch, and later stars are identified in the image by an initial match confirmed with a running sequential angular match technique. The proposed idea is tested on 16,200 simulated star images having magnitude uncertainty, noise stars, positional deviation, and varying size of the field of view. The proposed idea is also benchmarked with the state-of-the-art star pattern recognition techniques. Finally, the real-time performance of the proposed technique is tested on the 3104 real star images captured by a star tracker SST-20S currently mounted on a satellite. The proposed technique can achieve an identification accuracy of 98% and takes only 8.2 ms for identification on real images. Simulation and real-time results depict that the proposed technique is highly robust and achieves a high speed of identification suitable for actual space applications.

Algorithm of reducing the false positives in IDS based on correlation Analysis

NASA Astrophysics Data System (ADS)

Liu, Jianyi; Li, Sida; Zhang, Ru

2018-03-01

This paper proposes an algorithm of reducing the false positives in IDS based on correlation Analysis. Firstly, the algorithm analyzes the distinguishing characteristics of false positives and real alarms, and preliminary screen the false positives; then use the method of attribute similarity clustering to the alarms and further reduces the amount of alarms; finally, according to the characteristics of multi-step attack, associated it by the causal relationship. The paper also proposed a reverse causation algorithm based on the attack association method proposed by the predecessors, turning alarm information into a complete attack path. Experiments show that the algorithm simplifies the number of alarms, improve the efficiency of alarm processing, and contribute to attack purposes identification and alarm accuracy improvement.

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

Network Understanding of Herb Medicine via Rapid Identification of Ingredient-Target Interactions

NASA Astrophysics Data System (ADS)

Zhang, Hai-Ping; Pan, Jian-Bo; Zhang, Chi; Ji, Nan; Wang, Hao; Ji, Zhi-Liang

2014-01-01

Today, herb medicines have become the major source for discovery of novel agents in countermining diseases. However, many of them are largely under-explored in pharmacology due to the limitation of current experimental approaches. Therefore, we proposed a computational framework in this study for network understanding of herb pharmacology via rapid identification of putative ingredient-target interactions in human structural proteome level. A marketing anti-cancer herb medicine in China, Yadanzi (Brucea javanica), was chosen for mechanistic study. Total 7,119 ingredient-target interactions were identified for thirteen Yadanzi active ingredients. Among them, about 29.5% were estimated to have better binding affinity than their corresponding marketing drug-target interactions. Further Bioinformatics analyses suggest that simultaneous manipulation of multiple proteins in the MAPK signaling pathway and the phosphorylation process of anti-apoptosis may largely answer for Yadanzi against non-small cell lung cancers. In summary, our strategy provides an efficient however economic solution for systematic understanding of herbs' power.

Network understanding of herb medicine via rapid identification of ingredient-target interactions.

PubMed

Zhang, Hai-Ping; Pan, Jian-Bo; Zhang, Chi; Ji, Nan; Wang, Hao; Ji, Zhi-Liang

2014-01-16

Today, herb medicines have become the major source for discovery of novel agents in countermining diseases. However, many of them are largely under-explored in pharmacology due to the limitation of current experimental approaches. Therefore, we proposed a computational framework in this study for network understanding of herb pharmacology via rapid identification of putative ingredient-target interactions in human structural proteome level. A marketing anti-cancer herb medicine in China, Yadanzi (Brucea javanica), was chosen for mechanistic study. Total 7,119 ingredient-target interactions were identified for thirteen Yadanzi active ingredients. Among them, about 29.5% were estimated to have better binding affinity than their corresponding marketing drug-target interactions. Further Bioinformatics analyses suggest that simultaneous manipulation of multiple proteins in the MAPK signaling pathway and the phosphorylation process of anti-apoptosis may largely answer for Yadanzi against non-small cell lung cancers. In summary, our strategy provides an efficient however economic solution for systematic understanding of herbs' power.

Recombinant DNA technology for melanoma immunotherapy: anti-Id DNA vaccines targeting high molecular weight melanoma-associated antigen.

PubMed

Barucca, A; Capitani, M; Cesca, M; Tomassoni, D; Kazmi, U; Concetti, F; Vincenzetti, L; Concetti, A; Venanzi, F M

2014-11-01

Anti-idiotypic MK2-23 monoclonal antibody (anti-Id MK2-23 mAb), which mimics the high molecular weight melanoma-associated antigen (HMW-MAA), has been used to implement active immunotherapy against melanoma. However, due to safety and standardization issues, this approach never entered extensive clinical trials. In the present study, we investigated the usage of DNA vaccines as an alternative to MK2-23 mAb immunization. MK2-23 DNA plasmids coding for single chain (scFv) MK2-23 antibody were constructed via the insertion of variable heavy (V H) and light (V L) chains of MK2-23 into the pVAC-1mcs plasmids. Two alternative MK2-23 plasmids format V H/V L, and V L/V H were assembled. We demonstrate that both polypeptides expressed by scFv plasmids in vitro retained the ability to mimic HMW-MAA antigen, and to elicit specific anti-HMW-MAA humoral and cellular immunoresponses in immunized mice. Notably, MK2-23 scFv DNA vaccines impaired the onset and growth of transplantable B16 melanoma cells not engineered to express HMW-MAA. This pilot study suggests that optimized MK2-23 scFv DNA vaccines could potentially provide a safer and cost-effective alternative to anti-Id antibody immunization, for melanoma immunotherapy.

Identification of pathogenic gene variants in small families with intellectually disabled siblings by exome sequencing.

PubMed

Schuurs-Hoeijmakers, Janneke H M; Vulto-van Silfhout, Anneke T; Vissers, Lisenka E L M; van de Vondervoort, Ilse I G M; van Bon, Bregje W M; de Ligt, Joep; Gilissen, Christian; Hehir-Kwa, Jayne Y; Neveling, Kornelia; del Rosario, Marisol; Hira, Gausiya; Reitano, Santina; Vitello, Aurelio; Failla, Pinella; Greco, Donatella; Fichera, Marco; Galesi, Ornella; Kleefstra, Tjitske; Greally, Marie T; Ockeloen, Charlotte W; Willemsen, Marjolein H; Bongers, Ernie M H F; Janssen, Irene M; Pfundt, Rolph; Veltman, Joris A; Romano, Corrado; Willemsen, Michèl A; van Bokhoven, Hans; Brunner, Han G; de Vries, Bert B A; de Brouwer, Arjan P M

2013-12-01

Intellectual disability (ID) is a common neurodevelopmental disorder affecting 1-3% of the general population. Mutations in more than 10% of all human genes are considered to be involved in this disorder, although the majority of these genes are still unknown. We investigated 19 small non-consanguineous families with two to five affected siblings in order to identify pathogenic gene variants in known, novel and potential ID candidate genes. Non-consanguineous families have been largely ignored in gene identification studies as small family size precludes prior mapping of the genetic defect. Using exome sequencing, we identified pathogenic mutations in three genes, DDHD2, SLC6A8, and SLC9A6, of which the latter two have previously been implicated in X-linked ID phenotypes. In addition, we identified potentially pathogenic mutations in BCORL1 on the X-chromosome and in MCM3AP, PTPRT, SYNE1, and ZNF528 on autosomes. We show that potentially pathogenic gene variants can be identified in small, non-consanguineous families with as few as two affected siblings, thus emphasising their value in the identification of syndromic and non-syndromic ID genes.

The influence of camouflage, obstruction, familiarity and spatial ability on target identification from an unmanned ground vehicle.

PubMed

Fincannon, Thomas; Keebler, Joseph R; Jentsch, Florian; Curtis, Michael

2013-01-01

The purpose of this study was to examine the effects of environmental and cognitive factors on the identification of targets from an unmanned ground vehicle (UGV). This was accomplished by manipulating obstruction, camouflage and familiarity of objects in the environment, while also measuring spatial ability. The effects of these variables on target identification were studied by measuring performance of participants that observed pre-recorded video from a 1:35 scaled military operations in urban terrain facility. Analyses indicated that a combination of camouflage and obstruction caused the most detrimental effects on performance, and that there were differences in the recognition of familiar and unfamiliar targets. Further analysis indicated that these detrimental effects could only be overcome with a combination of target familiarity and spatial ability. The findings highlight the degree to which environmental factors hinder performance and the need for a multidimensional approach for improving performance under these conditions. Areas in need of future research are also discussed. Cognitive theory is applied to the problem of perception from UGVs. Results from an experimental study indicate that a combination of camouflage and obstruction caused the most detrimental effects on performance, with differences in the recognition of both familiar and unfamiliar targets. Familiarity and spatial ability interacted to predict the performance.

RGSS-ID: an approach to new radiologic reporting system.

PubMed

Ikeda, M; Sakuma, S; Maruyama, K

1990-01-01

RGSS-ID is a developmental computer system that applies artificial intelligence (AI) methods to a reporting system. The representation scheme called Generalized Finding Representation (GFR) is proposed to bridge the gap between natural language expressions in the radiology report and AI methods. The entry process of RGSS-ID is made mainly by selecting items; our system allows a radiologist to compose a sentence which can be completely parsed by the computer. Further RGSS-ID encodes findings into the expression corresponding to GFR, and stores this expression into the knowledge data base. The final printed report is made in the natural language.

Enabling OpenID Authentication for VO-integrated Portals

NASA Astrophysics Data System (ADS)

Plante, R.; Yekkirala, V.; Baker, W.

2012-09-01

To support interoperating services that share proprietary data and other user-specific information, the VAO Project provides login services for browser-based portals built on the open standard, OpenID. To help portal developers take advantage of this service, we have developed a downloadable toolkit for integrating OpenID single sign-on support into any portal. This toolkit provides APIs in a few languages commonly used on the server-side as well as a command-line version for use in any language. In addition to describing how to use this toolkit, we also discuss the general VAO framework for single sign-on. While a portal may, if it wishes, support any OpenID provider, the VAO service provides a few extra features to support VO interoperability. This includes a portal's ability to retrieve (with the user's permission) an X.509 certificate representing the authenticated user so that the portal can access other restricted services on the user's behalf. Other standard features of OpenID allow portals to request other information about the user; this feature will be used in the future for sharing information about a user's group membership to enable sharing within a group of collaborating scientists.

77 FR 55813 - Transition of DOE-ID Public Reading Room

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-11

... to the INL Research Library at 1776 Science Center Drive, Idaho Falls, ID 83401, beginning September... Library, 1776 Science Center Drive, Idaho Falls, ID 83401. FOR FURTHER INFORMATION CONTACT: Clayton...

Validation of a rapid DNA process with the RapidHIT® ID system using GlobalFiler® Express chemistry, a platform optimized for decentralized testing environments.

PubMed

Salceda, Susana; Barican, Arnaldo; Buscaino, Jacklyn; Goldman, Bruce; Klevenberg, Jim; Kuhn, Melissa; Lehto, Dennis; Lin, Frank; Nguyen, Phong; Park, Charles; Pearson, Francesca; Pittaro, Rick; Salodkar, Sayali; Schueren, Robert; Smith, Corey; Troup, Charles; Tsou, Dean; Vangbo, Mattias; Wunderle, Justus; King, David

2017-05-01

The RapidHIT ® ID is a fully automated sample-to-answer system for short tandem repeat (STR)-based human identification. The RapidHIT ID has been optimized for use in decentralized environments and processes presumed single source DNA samples, generating Combined DNA Index System (CODIS)-compatible DNA profiles in less than 90min. The system is easy to use, requiring less than one minute of hands-on time. Profiles are reviewed using centralized linking software, RapidLINK™ (IntegenX, Pleasanton, CA), a software tool designed to collate DNA profiles from single or multiple RapidHIT ID systems at different geographic locations. The RapidHIT ID has been designed to employ GlobalFiler ® Express and AmpFLSTR ® NGMSElect™, Thermo Fisher Scientific (Waltham, MA) STR chemistries. The Developmental Validation studies were performed using GlobalFiler ® Express with single source reference samples according to Scientific Working Group for DNA Analysis Methods guidelines. These results show that multiple RapidHIT ID systems networked with RapidLINK software form a highly reliable system for wide-scale deployment in locations such as police booking stations and border crossings enabling real-time testing of arrestees, potential human trafficking victims, and other instances where rapid turnaround is essential. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

How to save distressed IDS-physician marriages: a case study.

PubMed

Collins, H; Johnson, B A

1998-04-01

A hospital-driven IDS that encounters serious problems resulting from ownership of a physician practice should address those problems by focusing on three core areas: vision and leadership, effectiveness of operations, and physician compensation arrangements. If changes in these areas do not lead to improvements, the IDS may need to consider organizational restructuring. In one case study, a hospital-driven IDS faced the problem of owning a poorly performing MSO with a captive physician group. The IDS's governing board determined that the organization lacked effective communication with the physicians and that realization of the organization's vision would require greater physician involvement in organizational decision making. The organization is expected to undergo some corporate reorganization in which physicians will acquire an equity interest in the enterprise.

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.

Picture This: How to Establish an Effective School ID Card Program

ERIC Educational Resources Information Center

Finkelstein, David

2013-01-01

Most school districts do not have an ID card policy that everyone knows and follows, yet. many school districts are implementing ID card programs to address concerns about safety, efficiency, and convenience. A well-thought-out ID card program leads to greater security and smoother operations throughout the school and should thus be a priority.…

Application modeling ipv6 (internet protocol version 6) on e-id card for identification number for effectiveness and efficiency of registration process identification of population

NASA Astrophysics Data System (ADS)

Pardede, A. M. H.; Maulita, Y.; Buaton, R.

2018-03-01

When someone wants to be registered in an institution such as Birth Certificate, School, Higher Education, e-ID card, Tax, BPJS, Bank, Driving License, Passport and others then have to register and do registration one by one and have registration number or account respectively agency. It may be said that everyone is bothered with the registration process, from the moment of birth must be registered to be registered as a resident, to enter the school must also registration, it is considered ineffective and efficient because one must continue to register one by one and there is repetition of ownership registration number which vary each agency. Seeing these problems need to find a solution or attempt how to keep the affairs of registration is not repetitive and quite once and the number applies to all agencies. The presence of the latest technology that IPv6 brings opportunities for the efficiency and effectiveness of the registration system. The method used in this research is the exploration and modeling of system development with NDLC (Network Development Life Cycle) to produce a model to build IPv6 implementation on e-ID card. The results of the study will show that the public has one registration number.

Using Survey IDs to Enhance Survey Research and Administration

ERIC Educational Resources Information Center

Edgeley, Catrin M.

2017-01-01

Survey IDs are short strings of unique characters assigned to each recipient in a sample population. Extension research can benefit from the improved organization of survey implementation and data collection, better researcher-respondent communication, and reduced survey material costs supported through the use of survey IDs. This article outlines…

Conformal image-guided microbeam radiation therapy at the ESRF biomedical beamline ID17

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

Donzelli, Mattia, E-mail: donzelli@esrf.fr; Bräuer-Krisch, Elke; Nemoz, Christian

Purpose: Upcoming veterinary trials in microbeam radiation therapy (MRT) demand for more advanced irradiation techniques than in preclinical research with small animals. The treatment of deep-seated tumors in cats and dogs with MRT requires sophisticated irradiation geometries from multiple ports, which impose further efforts to spare the normal tissue surrounding the target. Methods: This work presents the development and benchmarking of a precise patient alignment protocol for MRT at the biomedical beamline ID17 of the European Synchrotron Radiation Facility (ESRF). The positioning of the patient prior to irradiation is verified by taking x-ray projection images from different angles. Results: Usingmore » four external fiducial markers of 1.7  mm diameter and computed tomography-based treatment planning, a target alignment error of less than 2  mm can be achieved with an angular deviation of less than 2{sup ∘}. Minor improvements on the protocol and the use of smaller markers indicate that even a precision better than 1  mm is technically feasible. Detailed investigations concerning the imaging dose lead to the conclusion that doses for skull radiographs lie in the same range as dose reference levels for human head radiographs. A currently used online dose monitor for MRT has been proven to give reliable results for the imaging beam. Conclusions: The ESRF biomedical beamline ID17 is technically ready to apply conformal image-guided MRT from multiple ports to large animals during future veterinary trials.« less

Ablation of the transcriptional regulator Id1 enhances energy expenditure, increases insulin sensitivity, and protects against age and diet induced insulin resistance, and hepatosteatosis

PubMed Central

Satyanarayana, Ande; Klarmann, Kimberly D.; Gavrilova, Oksana; Keller, Jonathan R.

2012-01-01

Obesity is a major health concern that contributes to the development of diabetes, hyperlipidemia, coronary artery disease, and cancer. Id proteins are helix-loop-helix transcription factors that regulate the proliferation and differentiation of cells from multiple tissues, including adipocytes. We screened mouse tissues for the expression of Id1 and found that Id1 protein is highly expressed in brown adipose tissue (BAT) and white adipose tissue (WAT), suggesting a role for Id1 in adipogenesis and cell metabolism. Id1−/− mice are viable but show a significant reduction in fat mass (P<0.005) over the life of the animal that was not due to decreased number of adipocytes. Analysis of Id1−/− mice revealed higher energy expenditure, increased lipolysis, and fatty acid oxidation, resulting in reduced triglyceride accumulation in WAT compared to Id1+/+ mice. Serum levels of triglycerides (193.9±32.2 vs. 86.5±33.8, P<0.0005), cholesterol (189.4±33.8 vs. 110.6±8.23, P<0.0005) and leptin (1263±835 vs. 222±260, P<0.005) were significantly lower in aged Id1−/− mice compared to Id1+/+ mice. Id1-deficient mice have higher resting (P<0.005) and total (P<0.05) O2 consumption and lower respiratory exchange ratio (P<0.005), confirming that Id1−/− mice use a higher proportion of lipid as an energy source for the increased energy expenditure. The expression of PGC1α and UCP1 were 2- to 3-fold up-regulated in Id1−/− BAT, suggesting that loss of Id1 increases thermogenesis. As a consequence of higher energy expenditure and reduced fat mass, Id1−/− mice displayed enhanced insulin sensitivity. Id1 deficiency protected mice against age- and high-fat-diet-induced adiposity, insulin resistance, and hepatosteatosis. Our findings suggest that Id1 plays a critical role in the regulation of energy homeostasis and could be a potential target in the treatment of insulin resistance and fatty liver disease.—Satyanarayana, A., Klarmann, K. D., Gavrilova, l O., Keller

ISS/IDS Detector Study

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

Cervera-Villanueva, A.

2008-02-21

This article summarises the results obtained by the detector working group of the 'International Scooping Study' (ISS) of a future neutrino oscillations facility. Special emphasis is put on far detectors, for which some of the main issues are identified. A detector R and D strategy in the context of the 'International Design Study' (IDS) for a neutrino factory is also presented.

Target Abundance-Based Fitness Screening (TAFiS) Facilitates Rapid Identification of Target-Specific and Physiologically Active Chemical Probes

PubMed Central

Butts, Arielle; DeJarnette, Christian; Peters, Tracy L.; Parker, Josie E.; Kerns, Morgan E.; Eberle, Karen E.; Kelly, Steve L.

2017-01-01

-generation target-based whole-cell screening approach that incorporates the principles of both chemical genetics and competitive fitness, which enables the identification of target-specific and physiologically active compounds from a single screen. We have chosen to validate this approach using the important human fungal pathogen Candida albicans with the intention of pursuing novel antifungal targets. However, this approach is broadly applicable and is expected to dramatically reduce the time and resources required to progress from screening hit to lead compound. PMID:28989971

Evaluation of the Microbial Identification System for identification of clinically isolated yeasts.

PubMed Central

Crist, A E; Johnson, L M; Burke, P J

1996-01-01

The Microbial Identification System (MIS; Microbial ID, Inc., Newark, Del.) was evaluated for the identification of 550 clinically isolated yeasts. The organisms evaluated were fresh clinical isolates identified by methods routinely used in our laboratory (API 20C and conventional methods) and included Candida albicans (n = 294), C. glabrata (n = 145), C. tropicalis (n = 58), C. parapsilosis (n = 33), and other yeasts (n = 20). In preparation for fatty acid analysis, yeasts were inoculated onto Sabouraud dextrose agar and incubated at 28 degrees C for 24 h. Yeasts were harvested, saponified, derivatized, and extracted, and fatty acid analysis was performed according to the manufacturer's instructions. Fatty acid profiles were analyzed, and computer identifications were made with the Yeast Clinical Library (database version 3.8). Of the 550 isolates tested, 374 (68.0%) were correctly identified to the species level, with 87 (15.8%) being incorrectly identified and 89 (16.2%) giving no identification. Repeat testing of isolates giving no identification resulted in an additional 18 isolates being correctly identified. This gave the MIS an overall identification rate of 71.3%. The most frequently misidentified yeast was C. glabrata, which was identified as Saccharomyces cerevisiae 32.4% of the time. On the basis of these results, the MIS, with its current database, does not appear suitable for the routine identification of clinically important yeasts. PMID:8880489

Efficient Identification of Murine M2 Macrophage Peptide Targeting Ligands by Phage Display and Next-Generation Sequencing.

PubMed

Liu, Gary W; Livesay, Brynn R; Kacherovsky, Nataly A; Cieslewicz, Maryelise; Lutz, Emi; Waalkes, Adam; Jensen, Michael C; Salipante, Stephen J; Pun, Suzie H

2015-08-19

Peptide ligands are used to increase the specificity of drug carriers to their target cells and to facilitate intracellular delivery. One method to identify such peptide ligands, phage display, enables high-throughput screening of peptide libraries for ligands binding to therapeutic targets of interest. However, conventional methods for identifying target binders in a library by Sanger sequencing are low-throughput, labor-intensive, and provide a limited perspective (<0.01%) of the complete sequence space. Moreover, the small sample space can be dominated by nonspecific, preferentially amplifying "parasitic sequences" and plastic-binding sequences, which may lead to the identification of false positives or exclude the identification of target-binding sequences. To overcome these challenges, we employed next-generation Illumina sequencing to couple high-throughput screening and high-throughput sequencing, enabling more comprehensive access to the phage display library sequence space. In this work, we define the hallmarks of binding sequences in next-generation sequencing data, and develop a method that identifies several target-binding phage clones for murine, alternatively activated M2 macrophages with a high (100%) success rate: sequences and binding motifs were reproducibly present across biological replicates; binding motifs were identified across multiple unique sequences; and an unselected, amplified library accurately filtered out parasitic sequences. In addition, we validate the Multiple Em for Motif Elicitation tool as an efficient and principled means of discovering binding sequences.

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...

ID4 promotes AR expression and blocks tumorigenicity of PC3 prostate cancer cells

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

Komaragiri, Shravan Kumar; Bostanthirige, Dhanushka H.; Morton, Derrick J.

Deregulation of tumor suppressor genes is associated with tumorigenesis and the development of cancer. In prostate cancer, ID4 is epigenetically silenced and acts as a tumor suppressor. In normal prostate epithelial cells, ID4 collaborates with androgen receptor (AR) and p53 to exert its tumor suppressor activity. Previous studies have shown that ID4 promotes tumor suppressive function of AR whereas loss of ID4 results in tumor promoter activity of AR. Previous study from our lab showed that ectopic ID4 expression in DU145 attenuates proliferation and promotes AR expression suggesting that ID4 dependent AR activity is tumor suppressive. In this study, wemore » examined the effect of ectopic expression of ID4 on highly malignant prostate cancer cell, PC3. Here we show that stable overexpression of ID4 in PC3 cells leads to increased apoptosis and decreased cell proliferation and migration. In addition, in vivo studies showed a decrease in tumor size and volume of ID4 overexpressing PC3 cells, in nude mice. At the molecular level, these changes were associated with increased androgen receptor (AR), p21, and AR dependent FKBP51 expression. At the mechanistic level, ID4 may regulate the expression or function of AR through specific but yet unknown AR co-regulators that may determine the final outcome of AR function. - Highlights: • ID4 expression induces AR expression in PC3 cells, which generally lack AR. • ID4 expression increased apoptosis and decreased cell proliferation and invasion. • Overexpression of ID4 reduces tumor growth of subcutaneous xenografts in vivo. • ID4 induces p21 and FKBP51 expression- co-factors of AR tumor suppressor activity.« less

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

PubMed Central

Damienikan, Aliaksandr U.

2016-01-01

The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

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.

Defining the safe current limit for opening ID photon shutter

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

Seletskiy, S.

The NSLS-II storage ring is protected from possible damage from insertion devices (IDs) synchrotron radiation by a dedicated active interlock system (AIS). It monitors electron beam position and angle and triggers beam drop if beam orbit exceeds the boundaries of pre-calculated active interlock envelope (AIE). The beamlines (BL) and beamline frontends (FE) are designed under assumption that the electron beam is interlocked within the AIE. For historic reasons the AIS engages the ID active interlock (AI-ID) at any non-zero beam current whenever the ID photon shutter (IDPS) is getting opened. Such arrangement creates major inconveniences for BLs commissioning. Apparently theremore » is some IDPS safe current limit (SCL) under which the IDPS can be opened without interlocking the e-beam. The goal of this paper is to find such limit.« less

The Self-Identity Protein IdsD Is Communicated between Cells in Swarming Proteus mirabilis Colonies.

PubMed

Saak, Christina C; Gibbs, Karine A

2016-12-15

Proteus mirabilis is a social bacterium that is capable of self (kin) versus nonself recognition. Swarming colonies of this bacterium expand outward on surfaces to centimeter-scale distances due to the collective motility of individual cells. Colonies of genetically distinct populations remain separate, while those of identical populations merge. Ids proteins are essential for this recognition behavior. Two of these proteins, IdsD and IdsE, encode identity information for each strain. These two proteins bind in vitro in an allele-restrictive manner. IdsD-IdsE binding is correlated with the merging of populations, whereas a lack of binding is correlated with the separation of populations. Key questions remained about the in vivo interactions of IdsD and IdsE, specifically, whether IdsD and IdsE bind within single cells or whether IdsD-IdsE interactions occur across neighboring cells and, if so, which of the two proteins is exchanged. Here we demonstrate that IdsD must originate from another cell to communicate identity and that this nonresident IdsD interacts with IdsE resident in the recipient cell. Furthermore, we show that unbound IdsD in recipient cells does not cause cell death and instead appears to contribute to a restriction in the expansion radius of the swarming colony. We conclude that P. mirabilis communicates IdsD between neighboring cells for nonlethal kin recognition, which suggests that the Ids proteins constitute a type of cell-cell communication. We demonstrate that self (kin) versus nonself recognition in P. mirabilis entails the cell-cell communication of an identity-encoding protein that is exported from one cell and received by another. We further show that this intercellular exchange affects swarm colony expansion in a nonlethal manner, which adds social communication to the list of potential swarm-related regulatory factors. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The Self-Identity Protein IdsD Is Communicated between Cells in Swarming Proteus mirabilis Colonies

PubMed Central

Saak, Christina C.

2016-01-01

ABSTRACT Proteus mirabilis is a social bacterium that is capable of self (kin) versus nonself recognition. Swarming colonies of this bacterium expand outward on surfaces to centimeter-scale distances due to the collective motility of individual cells. Colonies of genetically distinct populations remain separate, while those of identical populations merge. Ids proteins are essential for this recognition behavior. Two of these proteins, IdsD and IdsE, encode identity information for each strain. These two proteins bind in vitro in an allele-restrictive manner. IdsD-IdsE binding is correlated with the merging of populations, whereas a lack of binding is correlated with the separation of populations. Key questions remained about the in vivo interactions of IdsD and IdsE, specifically, whether IdsD and IdsE bind within single cells or whether IdsD-IdsE interactions occur across neighboring cells and, if so, which of the two proteins is exchanged. Here we demonstrate that IdsD must originate from another cell to communicate identity and that this nonresident IdsD interacts with IdsE resident in the recipient cell. Furthermore, we show that unbound IdsD in recipient cells does not cause cell death and instead appears to contribute to a restriction in the expansion radius of the swarming colony. We conclude that P. mirabilis communicates IdsD between neighboring cells for nonlethal kin recognition, which suggests that the Ids proteins constitute a type of cell-cell communication. IMPORTANCE We demonstrate that self (kin) versus nonself recognition in P. mirabilis entails the cell-cell communication of an identity-encoding protein that is exported from one cell and received by another. We further show that this intercellular exchange affects swarm colony expansion in a nonlethal manner, which adds social communication to the list of potential swarm-related regulatory factors. PMID:27672195

Experimental design and data analysis of Ago-RIP-Seq experiments for the identification of microRNA targets.

PubMed

Tichy, Diana; Pickl, Julia Maria Anna; Benner, Axel; Sültmann, Holger

2017-03-31

The identification of microRNA (miRNA) target genes is crucial for understanding miRNA function. Many methods for the genome-wide miRNA target identification have been developed in recent years; however, they have several limitations including the dependence on low-confident prediction programs and artificial miRNA manipulations. Ago-RNA immunoprecipitation combined with high-throughput sequencing (Ago-RIP-Seq) is a promising alternative. However, appropriate statistical data analysis algorithms taking into account the experimental design and the inherent noise of such experiments are largely lacking.Here, we investigate the experimental design for Ago-RIP-Seq and examine biostatistical methods to identify de novo miRNA target genes. Statistical approaches considered are either based on a negative binomial model fit to the read count data or applied to transformed data using a normal distribution-based generalized linear model. We compare them by a real data simulation study using plasmode data sets and evaluate the suitability of the approaches to detect true miRNA targets by sensitivity and false discovery rates. Our results suggest that simple approaches like linear regression models on (appropriately) transformed read count data are preferable. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Benefit Analyses of Technologies for Automatic Identification to Be Implemented in the Healthcare Sector

NASA Astrophysics Data System (ADS)

Krey, Mike; Schlatter, Ueli

The tasks and objectives of automatic identification (Auto-ID) are to provide information on goods and products. It has already been established for years in the areas of logistics and trading and can no longer be ignored by the German healthcare sector. Some German hospitals have already discovered the capabilities of Auto-ID. Improvements in quality, safety and reductions in risk, cost and time are aspects and areas where improvements are achievable. Privacy protection, legal restraints, and the personal rights of patients and staff members are just a few aspects which make the heath care sector a sensible field for the implementation of Auto-ID. Auto-ID in this context contains the different technologies, methods and products for the registration, provision and storage of relevant data. With the help of a quantifiable and science-based evaluation, an answer is sought as to which Auto-ID has the highest capability to be implemented in healthcare business.

[Concurrent validity of the HAWIK-IV and the Intelligence and Development Scales (IDS)].

PubMed

Hagmann-von Arx, Priska; Grob, Alexander; Petermann, Franz; Daseking, Monika

2012-01-01

The present study examined the concurrent validity of the Hamburg Wechsler Intelligenztest für Kinder - IV (HAWIK-IV; Petermann & Petermann, 2010) and the Intelligence and Development Scales (IDS; Grob, Meyer & Hagmann-von Arx, 2009). HAWIK-IV and IDS were administered in counterbalanced order to N = 172 children aged 6 to 11 years. The study presents the descriptive statistics, correlations, and an exploratory factor analysis of the data. There is a high correlation between HAWIK-IV Full Scale IQ and IDS intelligence score (r = .83). HAWIK-IV indices showed moderate to high correlations with the cognitive scales of the IDS (Cognition, Language, Mathematics). Low to absent correlations were found between HAWIK-IV indices and the noncognitive scales of the IDS (Social-Emotional Competence, Psychomotor, Achievement Motivation). The factor structure can be interpreted meaningfully and allows integration of the IDS cognitive, language, and mathematical subtests into the four HAWIK-IV indices. The results show that HAWIK-IV and IDS test results can be related to each other.

Regulation of Id2 expression in EL4 T lymphoma cells overexpressing growth hormone.

PubMed

Weigent, Douglas A

2009-01-01

In previous studies, we have shown that overexpression of growth hormone (GH) in cells of the immune system upregulates proteins involved in cell growth and protects from apoptosis. Here, we report that overexpression of GH in EL4 T lymphoma cells (GHo) also significantly increased levels of the inhibitor of differentiation-2 (Id2). The increase in Id2 was suggested in both Id2 promoter luciferase assays and by Western analysis for Id2 protein. To identify the regulatory elements that mediate transcriptional activation by GH in the Id2 promoter, promoter deletion analysis was performed. Deletion analysis revealed that transactivation involved a 301-132bp region upstream to the Id2 transcriptional start site. The pattern in the human GHo Jurkat T lymphoma cell line paralleled that found in the mouse GHo EL4 T lymphoma cell line. Significantly less Id2 was detected in the nucleus of GHo EL4 T lymphoma cells compared to vector alone controls. Although serum increased the levels of Id2 in control vector alone cells, no difference was found in the total levels of Id2 in GHo EL4 T lymphoma cells treated with or without serum. The increase in Id2 expression in GHo EL4 T lymphoma cells measured by Id2 promoter luciferase expression and Western blot analysis was blocked by the overexpression of a dominant-negative mutant of STAT5. The results suggest that in EL4 T lymphoma cells overexpressing GH, there is an upregulation of Id2 protein that appears to involve STAT protein activity.

Midkine-A functions upstream of Id2a to regulate cell cycle kinetics in the developing vertebrate retina

PubMed Central

2012-01-01

Background Midkine is a small heparin binding growth factor expressed in numerous tissues during development. The unique midkine gene in mammals has two paralogs in zebrafish: midkine-a (mdka) and midkine-b (mdkb). In the zebrafish retina, during both larval development and adult photoreceptor regeneration, mdka is expressed in retinal stem and progenitor cells and functions as a molecular component of the retina’s stem cell niche. In this study, loss-of-function and conditional overexpression were used to investigate the function of Mdka in the retina of the embryonic zebrafish. Results The results show that during early retinal development Mdka functions to regulate cell cycle kinetics. Following targeted knockdown of Mdka synthesis, retinal progenitors cycle more slowly, and this results in microphthalmia, a diminished rate of cell cycle exit and a temporal delay of cell cycle exit and neuronal differentiation. In contrast, Mdka overexpression results in acceleration of the cell cycle and retinal overgrowth. Mdka gain-of-function, however, does not temporally advance cell cycle exit. Experiments to identify a potential Mdka signaling pathway show that Mdka functions upstream of the HLH regulatory protein, Id2a. Gene expression analysis shows Mdka regulates id2a expression, and co-injection of Mdka morpholinos and id2a mRNA rescues the Mdka loss-of-function phenotype. Conclusions These data show that in zebrafish, Mdka resides in a shared Id2a pathway to regulate cell cycle kinetics in retinal progenitors. This is the first study to demonstrate the function of Midkine during retinal development and adds Midkine to the list of growth factors that transcriptionally regulate Id proteins. PMID:23111152

Midkine-A functions upstream of Id2a to regulate cell cycle kinetics in the developing vertebrate retina.

PubMed

Luo, Jing; Uribe, Rosa A; Hayton, Sarah; Calinescu, Anda-Alexandra; Gross, Jeffrey M; Hitchcock, Peter F

2012-10-30

Midkine is a small heparin binding growth factor expressed in numerous tissues during development. The unique midkine gene in mammals has two paralogs in zebrafish: midkine-a (mdka) and midkine-b (mdkb). In the zebrafish retina, during both larval development and adult photoreceptor regeneration, mdka is expressed in retinal stem and progenitor cells and functions as a molecular component of the retina's stem cell niche. In this study, loss-of-function and conditional overexpression were used to investigate the function of Mdka in the retina of the embryonic zebrafish. The results show that during early retinal development Mdka functions to regulate cell cycle kinetics. Following targeted knockdown of Mdka synthesis, retinal progenitors cycle more slowly, and this results in microphthalmia, a diminished rate of cell cycle exit and a temporal delay of cell cycle exit and neuronal differentiation. In contrast, Mdka overexpression results in acceleration of the cell cycle and retinal overgrowth. Mdka gain-of-function, however, does not temporally advance cell cycle exit. Experiments to identify a potential Mdka signaling pathway show that Mdka functions upstream of the HLH regulatory protein, Id2a. Gene expression analysis shows Mdka regulates id2a expression, and co-injection of Mdka morpholinos and id2a mRNA rescues the Mdka loss-of-function phenotype. These data show that in zebrafish, Mdka resides in a shared Id2a pathway to regulate cell cycle kinetics in retinal progenitors. This is the first study to demonstrate the function of Midkine during retinal development and adds Midkine to the list of growth factors that transcriptionally regulate Id proteins.

Iron Deficiency (ID) at Both Birth and 9 Months Predicts Right Frontal EEG Asymmetry in Infancy

PubMed Central

Armony-Sivan, Rinat; Zhu, Bingquan; Clark, Katy M.; Richards, Blair; Ji, Chai; Kaciroti, Niko; Shao, Jie

2016-01-01

This study considered effects of timing and duration of iron deficiency (ID) on frontal EEG asymmetry in infancy. In healthy term Chinese infants, EEG was recorded at 9 months in three experimental conditions: baseline, peek-a-boo, and stranger approach. Eighty infants provided data for all conditions. Prenatal ID was defined as low cord ferritin or high ZPP/H. Postnatal ID was defined as ≥ two abnormal iron measures at 9 months. Study groups were pre- and postnatal ID, prenatal ID only, postnatal ID only, and not ID. GLM repeated measure analysis showed a main effect for iron group. The pre- and postnatal ID group had negative asymmetry scores, reflecting right frontal EEG asymmetry (mean ±SE: −.18 ±.07) versus prenatal ID only (.00 ±.04), postnatal ID only (.03 ±.04), and not ID (.02 ±.04). Thus, ID at both birth and 9 months was associated with right frontal EEG asymmetry, a neural correlate of behavioral withdrawal and negative emotions. PMID:26668100

Psychometrics and latent structure of the IDS and QIDS with young adult students.

PubMed

González, David Andrés; Boals, Adriel; Jenkins, Sharon Rae; Schuler, Eric R; Taylor, Daniel

2013-07-01

Students and young adults have high rates of suicide and depression, thus are a population of interest. To date, there is no normative psychometric information on the IDS and QIDS in these populations. Furthermore, there is equivocal evidence on the factor structure and subscales of the IDS. Two samples of young adult students (ns=475 and 1681) were given multiple measures to test the psychometrics and dimensionality of the IDS and QIDS. The IDS, its subscales, and QIDS had acceptable internal consistencies (αs=.79-90) and favorable convergent and divergent validity correlations. A three-factor structure and two Rasch-derived subscales best fit the IDS. The samples were collected from one university, which may influence generalizability. The IDS and QIDS are desirable measures of depressive symptoms when studying young adult students. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of ingredients on sensory profile of idli.

PubMed

Durgadevi, Manoharan; Shetty, Prathapkumar H

2014-09-01

Idli is a traditional fermented food and is consumed in India and Srilanka. The objective of the present study is to select the ingredients for optimum desirable product characteristics and to identify the optimum ratios of ingredients and fermentation time with respect to sensory attributes using Response Surface Methodology (RSM). The sensory attributes included were color, appearance, texture, taste and overall quality. Preliminary trials were conducted using five variants of rice and common black gram dhal before framing a model using Central Composite Rotatable Design (CCRD). From the study it was found that a desirable score of 0.7439 was obtained for sensory attributes of idli made with the ratio of 3: 1.475 for IR20 idli rice and ADT3 variety black gram (with husk removed after soaking) fermented for 10.2 h. Principal Component Analysis (PCA) helped to discriminate the samples and attributes within the data matrix, depending upon their inter relationships.

78 FR 65555 - Establishment of Class E Airspace; Salmon, ID

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-01

...-0531; Airspace Docket No. 13-ANM-20] Establishment of Class E Airspace; Salmon, ID AGENCY: Federal... at the Salmon VHF Omni-Directional Radio Range/Distance Measuring Equipment (VOR/DME) navigation aid, Salmon, ID, to facilitate vectoring of Instrument Flight Rules (IFR) aircraft under control of Salt Lake...

Drug target identification using network analysis: Taking active components in Sini decoction as an example

NASA Astrophysics Data System (ADS)

Chen, Si; Jiang, Hailong; Cao, Yan; Wang, Yun; Hu, Ziheng; Zhu, Zhenyu; Chai, Yifeng

2016-04-01

Identifying the molecular targets for the beneficial effects of active small-molecule compounds simultaneously is an important and currently unmet challenge. In this study, we firstly proposed network analysis by integrating data from network pharmacology and metabolomics to identify targets of active components in sini decoction (SND) simultaneously against heart failure. To begin with, 48 potential active components in SND against heart failure were predicted by serum pharmacochemistry, text mining and similarity match. Then, we employed network pharmacology including text mining and molecular docking to identify the potential targets of these components. The key enriched processes, pathways and related diseases of these target proteins were analyzed by STRING database. At last, network analysis was conducted to identify most possible targets of components in SND. Among the 25 targets predicted by network analysis, tumor necrosis factor α (TNF-α) was firstly experimentally validated in molecular and cellular level. Results indicated that hypaconitine, mesaconitine, higenamine and quercetin in SND can directly bind to TNF-α, reduce the TNF-α-mediated cytotoxicity on L929 cells and exert anti-myocardial cell apoptosis effects. We envisage that network analysis will also be useful in target identification of a bioactive compound.

Drug target identification using network analysis: Taking active components in Sini decoction as an example

PubMed Central

Chen, Si; Jiang, Hailong; Cao, Yan; Wang, Yun; Hu, Ziheng; Zhu, Zhenyu; Chai, Yifeng

2016-01-01

Identifying the molecular targets for the beneficial effects of active small-molecule compounds simultaneously is an important and currently unmet challenge. In this study, we firstly proposed network analysis by integrating data from network pharmacology and metabolomics to identify targets of active components in sini decoction (SND) simultaneously against heart failure. To begin with, 48 potential active components in SND against heart failure were predicted by serum pharmacochemistry, text mining and similarity match. Then, we employed network pharmacology including text mining and molecular docking to identify the potential targets of these components. The key enriched processes, pathways and related diseases of these target proteins were analyzed by STRING database. At last, network analysis was conducted to identify most possible targets of components in SND. Among the 25 targets predicted by network analysis, tumor necrosis factor α (TNF-α) was firstly experimentally validated in molecular and cellular level. Results indicated that hypaconitine, mesaconitine, higenamine and quercetin in SND can directly bind to TNF-α, reduce the TNF-α-mediated cytotoxicity on L929 cells and exert anti-myocardial cell apoptosis effects. We envisage that network analysis will also be useful in target identification of a bioactive compound. PMID:27095146

[Evaluation of mass spectrometry for the identification of clinically interesting yeasts].

PubMed

Galán, Fátima; García-Agudo, Lidia; Guerrero, Inmaculada; Marín, Pilar; García-Tapia, Ana; García-Martos, Pedro; Rodríguez-Iglesias, Manuel

2015-01-01

Identification of yeasts is based on morphological, biochemical and nutritional characteristics, and using molecular methods. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, a new method for the identification of microorganisms, has demonstrated to be very useful. The aim of this study is to evaluate this new method in the identification of yeasts. A total of 600 strains of yeasts isolated from clinical specimens belonging to 9 genera and 43 species were tested. Identification was made by sequencing of the ITS regions of ribosomal DNA, assimilation of carbon compounds (ID 32C), and mass spectrometry on a Microflex spectrometer (Bruker Daltonics GmbH, Germany). A total of 569 strains (94.8%) were identified to species level by ID 32C, and 580 (96.7%) by MALDI-TOF. Concordance between both methods was observed for 553 strains (92.2%), with 100% in clinically relevant species: C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, and almost 100% in C. krusei. MALDI-TOF identified species requiring molecular methods: Candida dubliniensis, C. nivariensis, C. metapsilosis and C. orthopsilosis. Some irregularities were observed in the identification of arthroconidia yeast and basidiomycetes. MALDI-TOF is a rapid, effective and economic method, which enables the identification of most clinically important yeasts and the differentiation of closely related species. It would be desirable to include more species in its database to expand its performance. Copyright © 2014 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Evaluation of a PSMA-targeted BNF nanoparticle construct

NASA Astrophysics Data System (ADS)

Behnam Azad, Babak; Banerjee, Sangeeta R.; Pullambhatla, Mrudula; Lacerda, Silvia; Foss, Catherine A.; Wang, Yuchuan; Ivkov, Robert; Pomper, Martin G.

2015-02-01

Early detection enables improved prognosis for prostate cancer (PCa). A promising target for imaging and therapy of PCa is the prostate-specific membrane antigen (PSMA), which exhibits both expression within the epithelium of PCa cells, and becomes internalized upon ligand binding. Here we report the synthesis of a PSMA-targeted bionized nanoferrite (BNF) nanoparticle and its biological evaluation in an experimental model of PCa. The BNF nanoparticle formulation exhibits properties conducive to targeted imaging such as stealth, prolonged circulation time and enhanced clearance from non-target sites. Optical imaging of the targeted BNF in vivo indicates preferential accumulation in PSMA+ tumors 4 h post-injection, suggesting target specificity. On the other hand, non-targeted nanoparticles exhibit lower uptake with similar accumulation in both PSMA+ and PSMA- tumors indicating tumor access without preferential accumulation. Imaging with single photon emission computed tomography (SPECT) and biodistribution studies of a modified construct indicate highest tumor accumulation at 48 h post-injection [4.3 +/- 0.4 percentage injected dose per gram of tissue (%ID g-1)], with tumor/blood and tumor/muscle ratios of 7.5 +/- 2.4 and 11.6 +/- 1.2 %ID g-1, respectively. Ex vivo fluorescence microscopy, Prussian blue staining, immunohistochemistry and biodistribution studies confirm enhanced nanoparticle uptake in PSMA+ tumors compared to those not expressing PSMA. The BNF nano-formulation described is promising for PSMA-targeted imaging applications in vivo.Early detection enables improved prognosis for prostate cancer (PCa). A promising target for imaging and therapy of PCa is the prostate-specific membrane antigen (PSMA), which exhibits both expression within the epithelium of PCa cells, and becomes internalized upon ligand binding. Here we report the synthesis of a PSMA-targeted bionized nanoferrite (BNF) nanoparticle and its biological evaluation in an experimental model of

How effective are risk assessments/measures for predicting future aggressive behaviour in adults with intellectual disabilities (ID): A systematic review and meta-analysis.

PubMed

Lofthouse, Rachael; Golding, Laura; Totsika, Vasiliki; Hastings, Richard; Lindsay, William

2017-12-01

Risk assessments assist professionals in the identification and management of risk of aggression. The present study aimed to systematically review evidence on the efficacy of assessments for managing the risk of physical aggression in adults with intellectual disabilities (ID). A literature search was conducted using the databases PsycINFO, EMBASE, MEDLINE, Web of Science, and Google Scholar. Electronic and hand searches identified 14 studies that met the inclusion criteria. Standardised mean difference effect sizes Area Under Curve (AUC) were calculated for studies. Random effects subgroup analysis was used to compare different types of risk measures (Actuarial, Structured Professional Judgment and dynamic), and prospective vs. catch-up longitudinal study designs. Overall, evidence of predictive validity was found for risk measures with ID populations: (AUC)=0.724, 95% CI [0.681, 0.768]. There was no variation in the performance of different types of risk measures, or different study design. Risk assessment measures predict the likelihood of aggression in ID population and are comparable to those in mainstream populations. Further meta-analysis is necessary when risk measures are more established in this population. Copyright © 2017 Elsevier Ltd. All rights reserved.

An essential role for the Id1/PI3K/Akt/NFkB/survivin signalling pathway in promoting the proliferation of endothelial progenitor cells in vitro.

PubMed

Li, Wei; Wang, Hang; Kuang, Chun-Yan; Zhu, Jin-Kun; Yu, Yang; Qin, Zhe-Xue; Liu, Jie; Huang, Lan

2012-04-01

The enhancement of re-endothelialisation is a critical therapeutic option for repairing injured blood vessels. Endothelial progenitor cells (EPCs) are the major source of cells that participate in endothelium repair and contribute to re-endothelialisation by reducing neointima formation after vascular injury. The over-expression of the inhibitor of differentiation or DNA binding 1 (Id1) significantly improved EPC proliferation. This study aimed to investigate the effects of Id1 on the phosphatidylinositol-3-kinase (PI3K)/Akt/nuclear factor kappa B (NFκB)/survivin signalling pathway and its significance in promoting EPC proliferation in vitro. Spleen-derived EPCs were cultured as previously described. Id1 was presented at low levels in EPCs, and was rapidly up-regulated by stimulation with vascular endothelial growth factor. We demonstrated that transient transfection of Id1 into EPCs activated the PI3K/Akt/NFκB/survivin signalling pathway and promoted EPC proliferation. The proliferation of EPCs was extensively inhibited by silencing of endogenous Id1, and knockdown of Id1 expression led to suppression of PI3K/Akt/NFκB/survivin signalling pathway in EPCs. In addition, blockade by the PI3K-specific inhibitor LY294002, Akt inhibitor, the NFκB inhibitor BAY 11-7082, the survivin inhibitor Curcumin, or the survivin inhibitor YM155 reduced the effects of Id1 transfection. These results suggest that the Id1/PI3K/Akt/NFκB/survivin signalling pathway plays a critical role in EPC proliferation. The Id1/PI3K/Akt/NFκB/survivin signalling pathway may represent a novel therapeutic target in the prevention of restenosis after vascular injury.

Hazard identification and risk assessment for biologics targeting the immune system.

PubMed

Weir, Andrea B

2008-01-01

Biologic pharmaceuticals include a variety of products, such as monoclonal antibodies, fusion proteins and cytokines. Products in those classes include immunomodulatory biologics, which are intended to enhance or diminish the activity of the immune system. Immunomodulatory biologics have been approved by the U.S. FDA for a variety of indications, including cancer and inflammatory conditions. Prior to gaining approval for marketing, sponsoring companies for all types of products must demonstrate a product's safety in toxicology studies conducted in animals and show safety and efficacy in clinical trials conducted in patients. The overall goal of toxicology studies, which applies to immunomodulatory and other product types, is to identify the hazards that products pose to humans. Because biologics are generally highly selective for specific targets (receptors/epitopes), conducting toxicology studies in animal models with the target is essential. Such animals are referred to as pharmacologically relevant. Endpoints routinely included in toxicology studies, such as hematology, organ weight and histopathology, can be used to assess the effect of a product on the structure of the immune system. Additionally, specialized endpoints, such as immunophenotyping and immune function tests, can be used to define effects of immunomodulatory products on the immune system. Following hazard identification, risks posed to patients are assessed and managed. Risks can be managed through clinical trial design and risk communication, a practice that applies to immunomodulatory and other product types. Examples of risk management in clinical trial design include establishing a safe starting dose, defining the appropriate patient population and establishing appropriate patient monitoring. Risk communication starts during clinical trials and continues after product approval. A combination of hazard identification, risk assessment and risk management allows for drug development to proceed

idRHa+ProMod - Rail Hardening Control System

NASA Astrophysics Data System (ADS)

Ferro, L.

2016-03-01

idRHa+ProMod is the process control system developed by Primetals Technologies to foresee the thermo-mechanical evolution and micro-structural composition of rail steels subjected to slack quenching into idRHa+ Rail Hardening equipments in a simulation environment. This tool can be used both off-line or in-line, giving the user the chance to test and study the best cooling strategies or letting the automatic control system free to adjust the proper cooling recipe. Optimization criteria have been tailored in order to determine the best cooling conditions according to the metallurgical requirements imposed by the main rail standards and also taking into account the elastoplastic bending phenomena occurring during all stages of the head hardening process. The computational core of idRHa+ProMod is a thermal finite element procedure coupled with special algorithms developed to work out the main thermo-physical properties of steel, to predict the non-isothermal austenite decomposition into all the relevant phases and subsequently to evaluate the amount of latent heat of transformation released, the compound thermal expansion coefficient and the amount of plastic deformation in the material. Air mist and air blades boundary conditions have been carefully investigated by means of pilot plant tests aimed to study the jet impingement on rail surfaces and the cooling efficiency at all working conditions. Heat transfer coefficients have been further checked and adjusted directly on field during commissioning. idRHa+ is a trademark of Primetals Technologies Italy Srl

ID4 promotes AR expression and blocks tumorigenicity of PC3 prostate cancer cells.

PubMed

Komaragiri, Shravan Kumar; Bostanthirige, Dhanushka H; Morton, Derrick J; Patel, Divya; Joshi, Jugal; Upadhyay, Sunil; Chaudhary, Jaideep

2016-09-09

Deregulation of tumor suppressor genes is associated with tumorigenesis and the development of cancer. In prostate cancer, ID4 is epigenetically silenced and acts as a tumor suppressor. In normal prostate epithelial cells, ID4 collaborates with androgen receptor (AR) and p53 to exert its tumor suppressor activity. Previous studies have shown that ID4 promotes tumor suppressive function of AR whereas loss of ID4 results in tumor promoter activity of AR. Previous study from our lab showed that ectopic ID4 expression in DU145 attenuates proliferation and promotes AR expression suggesting that ID4 dependent AR activity is tumor suppressive. In this study, we examined the effect of ectopic expression of ID4 on highly malignant prostate cancer cell, PC3. Here we show that stable overexpression of ID4 in PC3 cells leads to increased apoptosis and decreased cell proliferation and migration. In addition, in vivo studies showed a decrease in tumor size and volume of ID4 overexpressing PC3 cells, in nude mice. At the molecular level, these changes were associated with increased androgen receptor (AR), p21, and AR dependent FKBP51 expression. At the mechanistic level, ID4 may regulate the expression or function of AR through specific but yet unknown AR co-regulators that may determine the final outcome of AR function. Copyright © 2016 Elsevier Inc. All rights reserved.

Implementing electronic identification for performance recording in sheep: II. Cost-benefit analysis in meat and dairy farms.

PubMed

Ait-Saidi, A; Caja, G; Salama, A A K; Milán, M J

2014-12-01

Costs and secondary benefits of implementing electronic identification (e-ID) for performance recording (i.e., lambing, body weight, inventory, and milk yield) in dairy and meat ewes were assessed by using the results from a previous study in which manual (M), semiautomatic (SA), and automatic (AU) data collection systems were compared. Ewes were identified with visual ear tags and electronic rumen boluses. The M system used visual identification, on-paper data recording, and manual data uploading to a computer. The SA system used e-ID with a handheld reader in which performances were typed and automatic uploaded to a computer. The use of a personal digital assistant (PDA) for recording and automatic data uploading, which transformed M in a SA system, was also considered. The AU system was only used for BW recording and consisted of e-ID, automatic data recording in an electronic scale, and uploading to a computer. The cost-benefit study was applied to 2 reference sheep farms of 700 meat ewes, under extensive or intensive production systems, and of 400 dairy ewes, practicing once- or twice-a-day machine milkings. Sensitivity analyses under voluntary and mandatory e-ID scenarios were also included. Benefits of using e-ID for SA or AU performance recording mainly depended on sheep farm purpose, number of test days per year, handheld reader and PDA prices, and flock size. Implementing e-ID for SA and AU performance recording saved approximately 50% of the time required by the M system, and increased the reliability of the data collected. Use of e-ID increased the cost of performance recording in a voluntary e-ID scenario, paying only partially the investment made (15 to 70%). For the mandatory e-ID scenario, in which the cost of e-ID devices was not included, savings paid 100% of the extra costs needed for using e-ID in all farm types and conditions. In both scenarios, the reader price was the most important extra cost (40 to 90%) for implementing e-ID in sheep farms

Biometrics and ID Cards — Enablers for Personal Security

NASA Astrophysics Data System (ADS)

Reisen, Andreas

The electronic ID card is a modernization and security project of the German Government. On the one hand, the multifunctional card is intended to boost security and the convenience of e-government and e-business applications. On the other hand, the new biometric ID card should allow citizens to use it as a travel document in the Schengen area and for specific destinations outside the European Union also in the future.

Pharmacologic Management of Duchenne Muscular Dystrophy: Target Identification and Preclinical Trials

PubMed Central

Kornegay, Joe N.; Spurney, Christopher F.; Nghiem, Peter P.; Brinkmeyer-Langford, Candice L.; Hoffman, Eric P.; Nagaraju, Kanneboyina

2014-01-01

Duchenne muscular dystrophy (DMD) is an X-linked human disorder in which absence of the protein dystrophin causes degeneration of skeletal and cardiac muscle. For the sake of treatment development, over and above definitive genetic and cell-based therapies, there is considerable interest in drugs that target downstream disease mechanisms. Drug candidates have typically been chosen based on the nature of pathologic lesions and presumed underlying mechanisms and then tested in animal models. Mammalian dystrophinopathies have been characterized in mice (mdx mouse) and dogs (golden retriever muscular dystrophy [GRMD]). Despite promising results in the mdx mouse, some therapies have not shown efficacy in DMD. Although the GRMD model offers a higher hurdle for translation, dogs have primarily been used to test genetic and cellular therapies where there is greater risk. Failed translation of animal studies to DMD raises questions about the propriety of methods and models used to identify drug targets and test efficacy of pharmacologic intervention. The mdx mouse and GRMD dog are genetically homologous to DMD but not necessarily analogous. Subcellular species differences are undoubtedly magnified at the whole-body level in clinical trials. This problem is compounded by disparate cultures in clinical trials and preclinical studies, pointing to a need for greater rigor and transparency in animal experiments. Molecular assays such as mRNA arrays and genome-wide association studies allow identification of genetic drug targets more closely tied to disease pathogenesis. Genes in which polymorphisms have been directly linked to DMD disease progression, as with osteopontin, are particularly attractive targets. PMID:24936034

Identification of novel plant peroxisomal targeting signals by a combination of machine learning methods and in vivo subcellular targeting analyses.

PubMed

Lingner, Thomas; Kataya, Amr R; Antonicelli, Gerardo E; Benichou, Aline; Nilssen, Kjersti; Chen, Xiong-Yan; Siemsen, Tanja; Morgenstern, Burkhard; Meinicke, Peter; Reumann, Sigrun

2011-04-01

In the postgenomic era, accurate prediction tools are essential for identification of the proteomes of cell organelles. Prediction methods have been developed for peroxisome-targeted proteins in animals and fungi but are missing specifically for plants. For development of a predictor for plant proteins carrying peroxisome targeting signals type 1 (PTS1), we assembled more than 2500 homologous plant sequences, mainly from EST databases. We applied a discriminative machine learning approach to derive two different prediction methods, both of which showed high prediction accuracy and recognized specific targeting-enhancing patterns in the regions upstream of the PTS1 tripeptides. Upon application of these methods to the Arabidopsis thaliana genome, 392 gene models were predicted to be peroxisome targeted. These predictions were extensively tested in vivo, resulting in a high experimental verification rate of Arabidopsis proteins previously not known to be peroxisomal. The prediction methods were able to correctly infer novel PTS1 tripeptides, which even included novel residues. Twenty-three newly predicted PTS1 tripeptides were experimentally confirmed, and a high variability of the plant PTS1 motif was discovered. These prediction methods will be instrumental in identifying low-abundance and stress-inducible peroxisomal proteins and defining the entire peroxisomal proteome of Arabidopsis and agronomically important crop plants.

Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species.

PubMed

Arbefeville, S; Harris, A; Ferrieri, P

2017-09-01

Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data. 85 common and uncommon clinically relevant fungi isolated from clinical specimens were sequenced for the D2 region of the large subunit (LSU) of ribosomal RNA (rRNA) gene with the MicroSEQ® Kit and the ITS regions with the in house developed assay. The generated sequenced data were analyzed with the online GenBank and MycoBank public databases. The D2 region of the LSU rRNA gene identified 89.4% or 92.9% of the 85 isolates to the genus level and the full ITS region (f-ITS) 96.5% or 100%, using GenBank or MycoBank, respectively, when compared to the consensus ID. When comparing species-level designations to the consensus ID, D2 region of the LSU rRNA gene aligned with 44.7% (38/85) or 52.9% (45/85) of these isolates in GenBank or MycoBank, respectively. By comparison, f-ITS possessed greater specificity, followed by ITS1, then ITS2 regions using GenBank or MycoBank. Using GenBank or MycoBank, D2 region of the LSU rRNA gene outperformed phenotypic based ID at the genus level. Comparing rates of ID between D2 region of the LSU rRNA gene and the ITS regions in GenBank or MycoBank at the species level against the consensus ID, f-ITS and ITS2 exceeded performance of the D2 region of the LSU rRNA gene, but ITS1 had similar performance to the D2 region of the LSU rRNA gene using MycoBank. Our results indicated that the MicroSEQ® D2 LSU r

Internal validation of the RapidHIT® ID system.

PubMed

Wiley, Rachel; Sage, Kelly; LaRue, Bobby; Budowle, Bruce

2017-11-01

Traditionally, forensic DNA analysis has required highly skilled forensic geneticists in a dedicated laboratory to generate short tandem repeat (STR) profiles. STR profiles are routinely used either to associate or exclude potential donors of forensic biological evidence. The typing of forensic reference samples has become more demanding, especially with the requirement in some jurisdictions to DNA profile arrestees. The Rapid DNA (RDNA) platform, the RapidHIT ® ID (IntegenX ® , Pleasanton, CA), is a fully automated system capable of processing reference samples in approximately 90min with minimal human intervention. Thus, the RapidHIT ID instrument can be deployed to non-laboratory environments (e.g., booking stations) and run by trained atypical personnel such as law enforcement. In order to implement the RapidHIT ID platform, validation studies are needed to define the performance and limitations of the system. Internal validation studies were undertaken with four early-production RapidHIT ID units. Reliable and concordant STR profiles were obtained from reference buccal swabs. Throughout the study, no contamination was observed. The overall first-pass success rate with an "expert-like system" was 72%, which is comparable to another current RDNA platform commercially available. The system's second-pass success rate (involving manual interpretation on first-pass inconclusive results) increased to 90%. Inhibitors (i.e., coffee, smoking tobacco, and chewing tobacco) did not appear to affect typing by the instrument system; however, substrate (i.e., swab type) did impact typing success. Additionally, one desirable feature not available with other Rapid systems is that in the event of a system failed run, a swab can be recovered and subsequently re-analyzed in a new sample cartridge. Therefore, rarely should additional sampling or swab consumption be necessary. The RapidHIT ID system is a robust and reliable tool capable of generating complete STR profiles within

miR-ID: A novel, circularization-based platform for detection of microRNAs

PubMed Central

Kumar, Pavan; Johnston, Brian H.; Kazakov, Sergei A.

2011-01-01

MicroRNAs (miRNAs) are important regulators of gene expression and have great potential as biomarkers, prognostic indicators, and therapeutic targets. Determining the expression patterns of these molecules is essential for elucidating their biogenesis, regulation, relation to disease, and response to therapy. Although PCR-based assays are commonly used for expression profiling of miRNAs, the small size, sequence heterogeneity, and (in some cases) end modifications of miRNAs constrain the performance of existing PCR methods. Here we introduce miR-ID, a novel method that avoids these constraints while providing superior sensitivity and sequence specificity at a lower cost. It also has the unique ability to differentiate unmodified small RNAs from those carrying 2′-OMe groups at their 3′-ends while detecting both forms. miR-ID is comprised of the following steps: (1) circularization of the miRNA by a ligase; (2) reverse transcription of the circularized miRNA (RTC), producing tandem repeats of a DNA sequence complementary to the miRNA; and (3) qPCR amplification of segments of this multimeric cDNA using 5′-overlapping primers and a nonspecific dye such as SYBR Green. No chemically modified probes (e.g., TaqMan) or primers (e.g., LNA) are required. The circular RNA and multimeric cDNA templates provide unmatched flexibility in the positioning of primers, which may include straddling the boundaries between these repetitive miRNA sequences. miR-ID is based on new findings that are themselves of general interest, including reverse transcription of small RNA circles and the use of 5′-overlapping primers for detection of repetitive sequences by qPCR. PMID:21169480

Low Physical Fitness Levels in Older Adults with ID: Results of the HA-ID Study

ERIC Educational Resources Information Center

Hilgenkamp, Thessa I. M.; van Wijck, Ruud; Evenhuis, Heleen M.

2012-01-01

Physical fitness is as important to aging adults with ID as in the general population, but to date, the physical fitness levels of this group are unknown. Comfortable walking speed, muscle strength (grip strength), muscle endurance (30 s Chair stand) and cardiorespiratory endurance (10 m incremental shuttle walking test) were tested in a sample of…

To ID or Not to ID? Changes in Classification Rates of Intellectual Disability Using "DSM-5"

ERIC Educational Resources Information Center

Papazoglou, Aimilia; Jacobson, Lisa A.; McCabe, Marie; Kaufmann, Walter; Zabel, T. Andrew

2014-01-01

The "Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition" ("DSM-5") diagnostic criteria for intellectual disability (ID) include a change to the definition of adaptive impairment. New criteria require impairment in one adaptive domain rather than two or more skill areas. The authors examined the diagnostic…

Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification.

PubMed

Schmedes, Sarah E; Woerner, August E; Novroski, Nicole M M; Wendt, Frank R; King, Jonathan L; Stephens, Kathryn M; Budowle, Bruce

2018-01-01

The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals. Those studies utilize either targeted 16S rRNA or shotgun metagenomic sequencing to characterize skin microbiomes; however, these approaches have limited species and strain resolution and susceptibility to stochastic effects, respectively. Clade-specific markers from the skin microbiome, using supervised learning, can predict individual identity using skin microbiomes from their respective donors with high accuracy. In this study the hidSkinPlex is presented, a novel targeted sequencing method using skin microbiome markers developed for human identification. The hidSkinPlex (comprised of 286 bacterial (and phage) family-, genus-, species-, and subspecies-level markers), initially was evaluated on three bacterial control samples represented in the panel (i.e., Propionibacterium acnes, Propionibacterium granulosum, and Rothia dentocariosa) to assess the performance of the multiplex. The hidSkinPlex was further evaluated for prediction purposes. The hidSkinPlex markers were used to attribute skin microbiomes collected from eight individuals from three body sites (i.e., foot (Fb), hand (Hp) and manubrium (Mb)) to their host donor. Supervised learning, specifically regularized multinomial logistic regression and 1-nearest-neighbor classification were used to classify skin microbiomes to their hosts with up to 92% (Fb), 96% (Mb

ETR BASEMENT, TRA642, INTERIOR. BASEMENT. CUBICLE INTERIOR (SEE PHOTOS ID33G101 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

ETR BASEMENT, TRA-642, INTERIOR. BASEMENT. CUBICLE INTERIOR (SEE PHOTOS ID-33-G-101 AND ID-33-G-102) WITH TANK AND SODIUM-RELATED APPARATUS. CAMERA STANDS BEFORE ROLL-UP DOOR SHOWN IN PHOTO ID-33-G-101. INL NEGATIVE NO. HD24-3-3. Mike Crane, Photographer, 11/2000 - Idaho National Engineering Laboratory, Test Reactor Area, Materials & Engineering Test Reactors, Scoville, Butte County, ID

Prognostic stratification improvement by integrating ID1/ID3/IGJ gene expression signature and immunophenotypic profile in adult patients with B-ALL.

PubMed

Cruz-Rodriguez, Nataly; Combita, Alba L; Enciso, Leonardo J; Raney, Lauren F; Pinzon, Paula L; Lozano, Olga C; Campos, Alba M; Peñaloza, Niyireth; Solano, Julio; Herrera, Maria V; Zabaleta, Jovanny; Quijano, Sandra

2017-02-28

Survival of adults with B-Acute Lymphoblastic Leukemia requires accurate risk stratification of patients in order to provide the appropriate therapy. Contemporary techniques, using clinical and cytogenetic variables are incomplete for prognosis prediction. To improve the classification of adult patients diagnosed with B-ALL into prognosis groups, two strategies were examined and combined: the expression of the ID1/ID3/IGJ gene signature by RT-PCR and the immunophenotypic profile of 19 markers proposed in the EuroFlow protocol by Flow Cytometry in bone marrow samples. Both techniques were correlated to stratify patients into prognostic groups. An inverse relationship between survival and expression of the three-genes signature was observed and an immunophenotypic profile associated with clinical outcome was identified. Markers CD10 and CD20 were correlated with simultaneous overexpression of ID1, ID3 and IGJ. Patients with simultaneous expression of the poor prognosis gene signature and overexpression of CD10 or CD20, had worse Event Free Survival and Overall Survival than patients who had either the poor prognosis gene expression signature or only CD20 or CD10 overexpressed. By utilizing the combined evaluation of these two immunophenotypic markers along with the poor prognosis gene expression signature, the risk stratification can be significantly strengthened. Further studies including a large number of patients are needed to confirm these findings.

Annual audits of IDS risk contract settlements improve payment accuracy.

PubMed

Pearce, J W

1999-12-01

Integrated delivery systems (IDSs) should conduct annual audits of payers' settlements under risk contracts to verify that the payer attributed the appropriate amounts of revenue and charged the appropriate claims expenses to the IDS. In particular, IDSs should verify that payers calculated revenues and expenses based on consistent member counts and that the determined commercial revenue was based on the actual premiums paid. IDSs also should determine whether payers have used appropriate demographic factors and countywide rates as a basis for determining Medicare revenue, charged the IDS for claims only for valid members, paid capitated providers the correct capitation amounts, and used appropriate historical data to estimate the amounts of incurred-but-not-reported claims attributed to the IDS.

In Situ Identification of Cyanobacteria with Horseradish Peroxidase-Labeled, rRNA-Targeted Oligonucleotide Probes

PubMed Central

Schönhuber, Wilhelm; Zarda, Boris; Eix, Stella; Rippka, Rosmarie; Herdman, Michael; Ludwig, Wolfgang; Amann, Rudolf

1999-01-01

Individual cyanobacterial cells are normally identified in environmental samples only on the basis of their pigmentation and morphology. However, these criteria are often insufficient for the differentiation of species. Here, a whole-cell hybridization technique is presented that uses horseradish peroxidase (HRP)-labeled, rRNA-targeted oligonucleotides for in situ identification of cyanobacteria. This indirect method, in which the probe-conferred enzyme has to be visualized in an additional step, was necessary since fluorescently monolabeled oligonucleotides were insufficient to overstain the autofluorescence of the target cells. Initially, a nonfluorescent detection assay was developed and successfully applied to cyanobacterial mats. Later, it was demonstrated that tyramide signal amplification (TSA) resulted in fluorescent signals far above the level of autofluorescence. Furthermore, TSA-based detection of HRP was more sensitive than that based on nonfluorescent substrates. Critical points of the assay, such as cell fixation and permeabilization, specificity, and sensitivity, were systematically investigated by using four oligonucleotides newly designed to target groups of cyanobacteria. PMID:10049892

Whole exome sequencing is necessary to clarify ID/DD cases with de novo copy number variants of uncertain significance: Two proof-of-concept examples.

PubMed

Giorgio, Elisa; Ciolfi, Andrea; Biamino, Elisa; Caputo, Viviana; Di Gregorio, Eleonora; Belligni, Elga Fabia; Calcia, Alessandro; Gaidolfi, Elena; Bruselles, Alessandro; Mancini, Cecilia; Cavalieri, Simona; Molinatto, Cristina; Cirillo Silengo, Margherita; Ferrero, Giovanni Battista; Tartaglia, Marco; Brusco, Alfredo

2016-07-01

Whole exome sequencing (WES) is a powerful tool to identify clinically undefined forms of intellectual disability/developmental delay (ID/DD), especially in consanguineous families. Here we report the genetic definition of two sporadic cases, with syndromic ID/DD for whom array-Comparative Genomic Hybridization (aCGH) identified a de novo copy number variant (CNV) of uncertain significance. The phenotypes included microcephaly with brachycephaly and a distinctive facies in one proband, and hypotonia in the legs and mild ataxia in the other. WES allowed identification of a functionally relevant homozygous variant affecting a known disease gene for rare syndromic ID/DD in each proband, that is, c.1423C>T (p.Arg377*) in the Trafficking Protein Particle Complex 9 (TRAPPC9), and c.154T>C (p.Cys52Arg) in the Very Low Density Lipoprotein Receptor (VLDLR). Four mutations affecting TRAPPC9 have been previously reported, and the present finding further depicts this syndromic form of ID, which includes microcephaly with brachycephaly, corpus callosum hypoplasia, facial dysmorphism, and overweight. VLDLR-associated cerebellar hypoplasia (VLDLR-CH) is characterized by non-progressive congenital ataxia and moderate-to-profound intellectual disability. The c.154T>C (p.Cys52Arg) mutation was associated with a very mild form of ataxia, mild intellectual disability, and cerebellar hypoplasia without cortical gyri simplification. In conclusion, we report two novel cases with rare causes of autosomal recessive ID, which document how interpreting de novo array-CGH variants represents a challenge in consanguineous families; as such, clinical WES should be considered in diagnostic testing. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Improving HybrID: How to best combine indirect and direct encoding in evolutionary algorithms

PubMed Central

Helms, Lucas; Clune, Jeff

2017-01-01

Many challenging engineering problems are regular, meaning solutions to one part of a problem can be reused to solve other parts. Evolutionary algorithms with indirect encoding perform better on regular problems because they reuse genomic information to create regular phenotypes. However, on problems that are mostly regular, but contain some irregularities, which describes most real-world problems, indirect encodings struggle to handle the irregularities, hurting performance. Direct encodings are better at producing irregular phenotypes, but cannot exploit regularity. An algorithm called HybrID combines the best of both: it first evolves with indirect encoding to exploit problem regularity, then switches to direct encoding to handle problem irregularity. While HybrID has been shown to outperform both indirect and direct encoding, its initial implementation required the manual specification of when to switch from indirect to direct encoding. In this paper, we test two new methods to improve HybrID by eliminating the need to manually specify this parameter. Auto-Switch-HybrID automatically switches from indirect to direct encoding when fitness stagnates. Offset-HybrID simultaneously evolves an indirect encoding with directly encoded offsets, eliminating the need to switch. We compare the original HybrID to these alternatives on three different problems with adjustable regularity. The results show that both Auto-Switch-HybrID and Offset-HybrID outperform the original HybrID on different types of problems, and thus offer more tools for researchers to solve challenging problems. The Offset-HybrID algorithm is particularly interesting because it suggests a path forward for automatically and simultaneously combining the best traits of indirect and direct encoding. PMID:28334002

Improving HybrID: How to best combine indirect and direct encoding in evolutionary algorithms.

PubMed

Helms, Lucas; Clune, Jeff

2017-01-01

Many challenging engineering problems are regular, meaning solutions to one part of a problem can be reused to solve other parts. Evolutionary algorithms with indirect encoding perform better on regular problems because they reuse genomic information to create regular phenotypes. However, on problems that are mostly regular, but contain some irregularities, which describes most real-world problems, indirect encodings struggle to handle the irregularities, hurting performance. Direct encodings are better at producing irregular phenotypes, but cannot exploit regularity. An algorithm called HybrID combines the best of both: it first evolves with indirect encoding to exploit problem regularity, then switches to direct encoding to handle problem irregularity. While HybrID has been shown to outperform both indirect and direct encoding, its initial implementation required the manual specification of when to switch from indirect to direct encoding. In this paper, we test two new methods to improve HybrID by eliminating the need to manually specify this parameter. Auto-Switch-HybrID automatically switches from indirect to direct encoding when fitness stagnates. Offset-HybrID simultaneously evolves an indirect encoding with directly encoded offsets, eliminating the need to switch. We compare the original HybrID to these alternatives on three different problems with adjustable regularity. The results show that both Auto-Switch-HybrID and Offset-HybrID outperform the original HybrID on different types of problems, and thus offer more tools for researchers to solve challenging problems. The Offset-HybrID algorithm is particularly interesting because it suggests a path forward for automatically and simultaneously combining the best traits of indirect and direct encoding.

78 FR 8596 - Hartford Financial Services Group, Inc., Commercial/Actuarial/ Information Delivery Services (IDS...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-06

... Delivery Services (IDS)/Corporate & Financial Reporting group, Hartford, Connecticut (The Hartford-IDS... technology applications for corporate, regulatory, and financial reporting. Pursuant to 29 CFR 90.18(c...., Commercial/Actuarial/Information Delivery Services (IDS)/ Corporate & Financial Reporting group, Hartford...

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

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.

Impaired Thermogenesis and a Molecular Signature for Brown Adipose Tissue in Id2 Null Mice

PubMed Central

Zhou, Peng; Robles-Murguia, Maricela; Mathew, Deepa; Duffield, Giles E.

2016-01-01

Inhibitor of DNA binding 2 (ID2) is a helix-loop-helix transcriptional repressor rhythmically expressed in many adult tissues. Our previous studies have demonstrated that Id2 null mice have sex-specific elevated glucose uptake in brown adipose tissue (BAT). Here we further explored the role of Id2 in the regulation of core body temperature over the circadian cycle and the impact of Id2 deficiency on genes involved in insulin signaling and adipogenesis in BAT. We discovered a reduced core body temperature in Id2−/− mice. Moreover, in Id2−/− BAT, 30 genes including Irs1, PPARs, and PGC-1s were identified as differentially expressed in a sex-specific pattern. These data provide valuable insights into the impact of Id2 deficiency on energy homeostasis of mice in a sex-specific manner. PMID:27144179

UXO detection and identification based on intrinsic target polarizabilities: A case history

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

Gasperikova, E.; Smith, J.T.; Morrison, H.F.

2008-07-15

Electromagnetic induction data parameterized in time dependent object intrinsic polarizabilities allow discrimination of unexploded ordnance (UXO) from false targets (scrap metal). Data from a cart-mounted system designed for discrimination of UXO with 20 mm to 155 mm diameters are used. Discrimination of UXO from irregular scrap metal is based on the principal dipole polarizabilities of a target. A near-intact UXO displays a single major polarizability coincident with the long axis of the object and two equal smaller transverse polarizabilities, whereas metal scraps have distinct polarizability signatures that rarely mimic those of elongated symmetric bodies. Based on a training data setmore » of known targets, object identification was made by estimating the probability that an object is a single UXO. Our test survey took place on a military base where both 4.2-inch mortar shells and scrap metal were present. The results show that we detected and discriminated correctly all 4.2-inch mortars, and in that process we added 7%, and 17%, respectively, of dry holes (digging scrap) to the total number of excavations in two different survey modes. We also demonstrated a mode of operation that might be more cost effective than the current practice.« less

DE-Cadherin regulates unconventional Myosin ID and Myosin IC in Drosophila left-right asymmetry establishment.

PubMed

Petzoldt, Astrid G; Coutelis, Jean-Baptiste; Géminard, Charles; Spéder, Pauline; Suzanne, Magali; Cerezo, Delphine; Noselli, Stéphane

2012-05-01

In bilateria, positioning and looping of visceral organs requires proper left-right (L/R) asymmetry establishment. Recent work in Drosophila has identified a novel situs inversus gene encoding the unconventional type ID myosin (MyoID). In myoID mutant flies, the L/R axis is inverted, causing reversed looping of organs, such as the gut, spermiduct and genitalia. We have previously shown that MyoID interacts physically with β-Catenin, suggesting a role of the adherens junction in Drosophila L/R asymmetry. Here, we show that DE-Cadherin co-immunoprecipitates with MyoID and is required for MyoID L/R activity. We further demonstrate that MyoIC, a closely related unconventional type I myosin, can antagonize MyoID L/R activity by preventing its binding to adherens junction components, both in vitro and in vivo. Interestingly, DE-Cadherin inhibits MyoIC, providing a protective mechanism to MyoID function. Conditional genetic experiments indicate that DE-Cadherin, MyoIC and MyoID show temporal synchronicity for their function in L/R asymmetry. These data suggest that following MyoID recruitment by β-Catenin at the adherens junction, DE-Cadherin has a twofold effect on Drosophila L/R asymmetry by promoting MyoID activity and repressing that of MyoIC. Interestingly, the product of the vertebrate situs inversus gene inversin also physically interacts with β-Catenin, suggesting that the adherens junction might serve as a conserved platform for determinants to establish L/R asymmetry both in vertebrates and invertebrates.

Vitamin D Pathway Status and the Identification of Target Genes in the Mouse Mammary Gland

DTIC Science & Technology

2013-01-01

12 Palmer HG et al. The vitamin D receptor is a Wnt effector that controls hair follicle differentiation and specifies tumor type in adult epidermis...AD_________________ Award Number: W81XWH-11-1-0152 TITLE: Vitamin D pathway status and the...December 2012 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-11-1-0152 Vitamin D pathway status and the identification of target genes in the

Electronic p-Chip-Based System for Identification of Glass Slides and Tissue Cassettes in Histopathology Laboratories.

PubMed

Mandecki, Wlodek; Qian, Jay; Gedzberg, Katie; Gruda, Maryanne; Rodriguez, Efrain Frank; Nesbitt, Leslie; Riben, Michael

2018-01-01

The tagging system is based on a small, electronic, wireless, laser-light-activated microtransponder named "p-Chip." The p-Chip is a silicon integrated circuit, the size of which is 600 μm × 600 μm × 100 μm. Each p-Chip contains a unique identification code stored within its electronic memory that can be retrieved with a custom reader. These features allow the p-Chip to be used as an unobtrusive and scarcely noticeable ID tag on glass slides and tissue cassettes. The system is comprised of p-Chip-tagged sample carriers, a dedicated benchtop p-Chip ID reader that can accommodate both objects, and an additional reader (the Wand), with an adapter for reading IDs of glass slides stored vertically in drawers. On slides, p-Chips are attached with adhesive to the center of the short edge, and on cassettes - embedded directly into the plastic. ID readout is performed by bringing the reader to the proximity of the chip. Standard histopathology laboratory protocols were used for testing. Very good ID reading efficiency was observed for both glass slides and cassettes. When processed slides are stored in vertical filing drawers, p-Chips remain readable without the need to remove them from the storage location, thereby improving the speed of searches in collections. On the cassettes, the ID continues to be readable through a thin layer of paraffin. Both slides and tissue cassettes can be read with the same reader, reducing the need for redundant equipment. The p-Chip is stable to all chemical challenges commonly used in the histopathology laboratory, tolerates temperature extremes, and remains durable in long-term storage. The technology is compatible with laboratory information management systems software systems. The p-Chip system is very well suited for identification of glass slides and cassettes in the histopathology laboratory.

Security and Privacy Improvements for the Belgian eID Technology

NASA Astrophysics Data System (ADS)

Verhaeghe, Pieter; Lapon, Jorn; de Decker, Bart; Naessens, Vincent; Verslype, Kristof

The Belgian Electronic Identity Card enables Belgian citizens to prove their identity digitally and to sign electronic documents. At the end of 2009, every Belgian citizen older than 12 years will have such an eID card. In the future, usage of the eID card may be mandatory. However, irresponsible use of the card may cause harm to individuals.

78 FR 25406 - Proposed Modification of Class E Airspace; Twin Falls, ID

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-01

...) Global Positioning System (GPS) and the Instrument Landing System (ILS) or Localizer (LOC) standard... the earth. * * * * * ANM ID E5 Twin Falls, ID [Modified] Twin Falls Joslin Field-Magic Valley Regional...

MALDI-TOF MS Versus VITEK®2: Comparison of Systems for the Identification of Microorganisms Responsible for Bacteremia.

PubMed

Febbraro, Filomena; Rodio, Donatella Maria; Puggioni, Gianluca; Antonelli, Guido; Pietropaolo, Valeria; Trancassini, Maria

2016-12-01

We evaluated the reliability and accuracy of the combined use of MALDI-TOF MS and classical ID VITEK 2 to identify monomicrobial infection in blood culture bottles. In total, 70 consecutive positive blood cultures were included in this study. Positive blood culture bottles were subjected to Gram staining and subcultured on solid media. Isolates grown from such culture media were used for classical ID using VITEK 2 system. In parallel, an aliquot was subjected to a lysing-centrifugation method and used for the identification with the MALDI-TOF system. Results evidenced the correct genus and species identification of 91.4 % of microorganisms responsible for bacteremia with an agreement to the species and the genus level. If compared with the standard method VITEK 2 , our simple and cost-effective sample preparation method would be very useful for rapid identification of microorganisms using blood culture bottles. In fact, the direct method showed rapid and reliable results, especially for the gram-negative group.

Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

PubMed Central

Li, Yiyan; Yang, Xing; Zhao, Weian

2018-01-01

Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies. PMID:28850804

Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing.

PubMed

Li, Yiyan; Yang, Xing; Zhao, Weian

2017-12-01

Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.

PubMed

Pyysalo, Sampo; Ohta, Tomoko; Rak, Rafal; Sullivan, Dan; Mao, Chunhong; Wang, Chunxia; Sobral, Bruno; Tsujii, Jun'ichi; Ananiadou, Sophia

2012-06-26

We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and Epigenetics and Post-translational Modifications (EPI), and the supporting task on Entity Relations (REL). The two main tasks represent extensions of the event extraction model introduced in the BioNLP Shared Task 2009 (ST'09) to two new areas of biomedical scientific literature, each motivated by the needs of specific biocuration tasks. The ID task concerns the molecular mechanisms of infection, virulence and resistance, focusing in particular on the functions of a class of signaling systems that are ubiquitous in bacteria. The EPI task is dedicated to the extraction of statements regarding chemical modifications of DNA and proteins, with particular emphasis on changes relating to the epigenetic control of gene expression. By contrast to these two application-oriented main tasks, the REL task seeks to support extraction in general by separating challenges relating to part-of relations into a subproblem that can be addressed by independent systems. Seven groups participated in each of the two main tasks and four groups in the supporting task. The participating systems indicated advances in the capability of event extraction methods and demonstrated generalization in many aspects: from abstracts to full texts, from previously considered subdomains to new ones, and from the ST'09 extraction targets to other entities and events. The highest performance achieved in the supporting task REL, 58% F-score, is broadly comparable with levels reported for other relation extraction tasks. For the ID task, the highest-performing system achieved 56% F-score, comparable to the state-of-the-art performance at the established ST'09 task. In the EPI task, the best result was 53% F-score for the full set of extraction targets and 69% F-score for a reduced set of core extraction targets, approaching a level of performance sufficient

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011

PubMed Central

2012-01-01

We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and Epigenetics and Post-translational Modifications (EPI), and the supporting task on Entity Relations (REL). The two main tasks represent extensions of the event extraction model introduced in the BioNLP Shared Task 2009 (ST'09) to two new areas of biomedical scientific literature, each motivated by the needs of specific biocuration tasks. The ID task concerns the molecular mechanisms of infection, virulence and resistance, focusing in particular on the functions of a class of signaling systems that are ubiquitous in bacteria. The EPI task is dedicated to the extraction of statements regarding chemical modifications of DNA and proteins, with particular emphasis on changes relating to the epigenetic control of gene expression. By contrast to these two application-oriented main tasks, the REL task seeks to support extraction in general by separating challenges relating to part-of relations into a subproblem that can be addressed by independent systems. Seven groups participated in each of the two main tasks and four groups in the supporting task. The participating systems indicated advances in the capability of event extraction methods and demonstrated generalization in many aspects: from abstracts to full texts, from previously considered subdomains to new ones, and from the ST'09 extraction targets to other entities and events. The highest performance achieved in the supporting task REL, 58% F-score, is broadly comparable with levels reported for other relation extraction tasks. For the ID task, the highest-performing system achieved 56% F-score, comparable to the state-of-the-art performance at the established ST'09 task. In the EPI task, the best result was 53% F-score for the full set of extraction targets and 69% F-score for a reduced set of core extraction targets, approaching a level of performance sufficient

STARR: shortwave-targeted agile Raman robot for the detection and identification of emplaced explosives

NASA Astrophysics Data System (ADS)

Gomer, Nathaniel R.; Gardner, Charles W.

2014-05-01

In order to combat the threat of emplaced explosives (land mines, etc.), ChemImage Sensor Systems (CISS) has developed a multi-sensor, robot mounted sensor capable of identification and confirmation of potential threats. The system, known as STARR (Shortwave-infrared Targeted Agile Raman Robot), utilizes shortwave infrared spectroscopy for the identification of potential threats, combined with a visible short-range standoff Raman hyperspectral imaging (HSI) system for material confirmation. The entire system is mounted onto a Talon UGV (Unmanned Ground Vehicle), giving the sensor an increased area search rate and reducing the risk of injury to the operator. The Raman HSI system utilizes a fiber array spectral translator (FAST) for the acquisition of high quality Raman chemical images, allowing for increased sensitivity and improved specificity. An overview of the design and operation of the system will be presented, along with initial detection results of the fusion sensor.

78 FR 45478 - Proposed Establishment of Class E Airspace; Salmon, ID

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-29

...-0531; Airspace Docket No. 13-ANM-20] Proposed Establishment of Class E Airspace; Salmon, ID AGENCY... action proposes to establish Class E airspace at the Salmon VHF Omni-Directional Radio Range/Distance Measuring Equipment (VOR/DME) navigation aid, Salmon, ID, to facilitate vectoring of Instrument Flight Rules...

A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification.

PubMed

Guo, Wei-Feng; Zhang, Shao-Wu; Shi, Qian-Qian; Zhang, Cheng-Ming; Zeng, Tao; Chen, Luonan

2018-01-19

The advances in target control of complex networks not only can offer new insights into the general control dynamics of complex systems, but also be useful for the practical application in systems biology, such as discovering new therapeutic targets for disease intervention. In many cases, e.g. drug target identification in biological networks, we usually require a target control on a subset of nodes (i.e., disease-associated genes) with minimum cost, and we further expect that more driver nodes consistent with a certain well-selected network nodes (i.e., prior-known drug-target genes). Therefore, motivated by this fact, we pose and address a new and practical problem called as target control problem with objectives-guided optimization (TCO): how could we control the interested variables (or targets) of a system with the optional driver nodes by minimizing the total quantity of drivers and meantime maximizing the quantity of constrained nodes among those drivers. Here, we design an efficient algorithm (TCOA) to find the optional driver nodes for controlling targets in complex networks. We apply our TCOA to several real-world networks, and the results support that our TCOA can identify more precise driver nodes than the existing control-fucus approaches. Furthermore, we have applied TCOA to two bimolecular expert-curate networks. Source code for our TCOA is freely available from http://sysbio.sibcb.ac.cn/cb/chenlab/software.htm or https://github.com/WilfongGuo/guoweifeng . In the previous theoretical research for the full control, there exists an observation and conclusion that the driver nodes tend to be low-degree nodes. However, for target control the biological networks, we find interestingly that the driver nodes tend to be high-degree nodes, which is more consistent with the biological experimental observations. Furthermore, our results supply the novel insights into how we can efficiently target control a complex system, and especially many evidences on the

Near-Field Chipless Radio-Frequency Identification (RFID) Sensing and Identification System with Switching Reading.

PubMed

Paredes, Ferran; Herrojo, Cristian; Mata-Contreras, Javier; Moras, Miquel; Núñez, Alba; Ramon, Eloi; Martín, Ferran

2018-04-09

A chipless radio-frequency identification (chipless-RFID) and sensing system, where tags are read by proximity (near-field) through a switch, is presented. The tags consist of a set of identical resonant elements (split-ring resonators or SRRs), printed or etched at predefined and equidistant positions, forming a linear chain, each SRR providing a bit of information. The logic state ('1' or '0') associated with each resonator depends on whether it is present or not in the predefined position. The reader is an array of power splitters used to feed a set of SRR-loaded transmission lines (in equal number to the number of resonant elements, or bits, of the tag). The feeding (interrogation) signal is a harmonic (single-tone) signal tuned to a frequency in the vicinity of the fundamental resonance of the SRRs. The set of SRR-loaded lines must be designed so that the corresponding SRRs are in perfect alignment with the SRRs of the tag, provided the tag is positioned on top of the reader. Thus, in a reading operation, as long as the tag is very close to the reader, the SRRs of the tag modify (decrease) the transmission coefficient of the corresponding reader line (through electromagnetic coupling between both SRRs), and the amplitude of the output signal is severely reduced. Therefore, the identification (ID) code of the tag is contained in the amplitudes of the output signals of the SRR-loaded lines, which can be inferred sequentially by means of a switching system. Unlike previous chipless-RFID systems based on near-field and sequential bit reading, the tags in the proposed system can be merely positioned on top of the reader, conveniently aligned, without the need to mechanically place them across the reader. Since tag reading is only possible if the tag is very close to the reader, this system can be also used as a proximity sensor with applications such as target identification. The proposed chipless-RFID and sensing approach is validated by reading a designed 4-bit

Near-Field Chipless Radio-Frequency Identification (RFID) Sensing and Identification System with Switching Reading

PubMed Central

Mata-Contreras, Javier; Moras, Miquel; Ramon, Eloi; Martín, Ferran

2018-01-01

A chipless radio-frequency identification (chipless-RFID) and sensing system, where tags are read by proximity (near-field) through a switch, is presented. The tags consist of a set of identical resonant elements (split-ring resonators or SRRs), printed or etched at predefined and equidistant positions, forming a linear chain, each SRR providing a bit of information. The logic state (‘1’ or ‘0’) associated with each resonator depends on whether it is present or not in the predefined position. The reader is an array of power splitters used to feed a set of SRR-loaded transmission lines (in equal number to the number of resonant elements, or bits, of the tag). The feeding (interrogation) signal is a harmonic (single-tone) signal tuned to a frequency in the vicinity of the fundamental resonance of the SRRs. The set of SRR-loaded lines must be designed so that the corresponding SRRs are in perfect alignment with the SRRs of the tag, provided the tag is positioned on top of the reader. Thus, in a reading operation, as long as the tag is very close to the reader, the SRRs of the tag modify (decrease) the transmission coefficient of the corresponding reader line (through electromagnetic coupling between both SRRs), and the amplitude of the output signal is severely reduced. Therefore, the identification (ID) code of the tag is contained in the amplitudes of the output signals of the SRR-loaded lines, which can be inferred sequentially by means of a switching system. Unlike previous chipless-RFID systems based on near-field and sequential bit reading, the tags in the proposed system can be merely positioned on top of the reader, conveniently aligned, without the need to mechanically place them across the reader. Since tag reading is only possible if the tag is very close to the reader, this system can be also used as a proximity sensor with applications such as target identification. The proposed chipless-RFID and sensing approach is validated by reading a designed

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

Intra-tumoral delivery of functional ID4 protein via PCL/maltodextrin nano-particle inhibits prostate cancer growth

PubMed Central

Morton, Derrick; Sharma, Pankaj; Gorantla, Yamini; Joshi, Jugal; Nagappan, Perri; Pallaniappan, Ravi; Chaudhary, Jaideep

2016-01-01

ID4, a helix loop helix transcriptional regulator has emerged as a tumor suppressor in prostate cancer. Epigenetic silencing of ID4 promotes prostate cancer whereas ectopic expression in prostate cancer cell lines blocks cancer phenotype. To directly investigate the anti-tumor property, full length human recombinant ID4 encapsulated in biodegradable Polycaprolactone/Maltodextrin (PCL-MD) nano-carrier was delivered to LNCaP cells in which the native ID4 was stably silenced (LNCaP(-)ID4). The cellular uptake of ID4 resulted in increased apoptosis, decreased proliferation and colony formation. Intratumoral delivery of PCL-MD ID4 into growing LNCaP(-)ID4 tumors in SCID mice significantly reduced the tumor volume compared to the tumors treated with chemotherapeutic Docetaxel. The study supports the feasibility of using nano-carrier encapsulated ID4 protein as a therapeutic. Mechanistically, ID4 may assimilate multiple regulatory pathways for example epigenetic re-programming, integration of multiple AR co-regulators or signaling pathways resulting in tumor suppressor activity of ID4. PMID:27487149

ACE insertion/deletion (I/D) polymorphism and diabetic nephropathy.

PubMed

Rahimi, Zohreh

2012-10-01

Angiotensin converting enzyme (ACE) gene encodes ACE, a key component of renin angiotensin system (RAS), plays an important role in blood pressure homeostasis by generating the vasoconstrictor peptide angiotensin II. Directory of Open Access Journals (DOAJ), Google Scholar, Pubmed (NLM), LISTA (EBSCO) and Web of Science have been searched. The presence of ACE insertion/deletion (I/D) polymorphism affects the plasma level of ACE. ACE DD genotype is associated with the highest systemic and renal ACE levels compared with the lowest ACE activity in carriers of II genotype. In this review focus has been performed on the study of ACE I/D polymorphism in various populations and its influence on the risk of onset and progression of diabetic nephropathy. Also, association between ACE I/D polymorphism and response to ACE inhibitor and angiotensin II receptor antagonists will be reviewed. Further, synergistic effect of this polymorphism and variants of some genes on the risk of development of diabetic nephropathy will be discussed.

Human target acquisition performance

NASA Astrophysics Data System (ADS)

Teaney, Brian P.; Du Bosq, Todd W.; Reynolds, Joseph P.; Thompson, Roger; Aghera, Sameer; Moyer, Steven K.; Flug, Eric; Espinola, Richard; Hixson, Jonathan

2012-06-01

The battlefield has shifted from armored vehicles to armed insurgents. Target acquisition (identification, recognition, and detection) range performance involving humans as targets is vital for modern warfare. The acquisition and neutralization of armed insurgents while at the same time minimizing fratricide and civilian casualties is a mounting concern. U.S. Army RDECOM CERDEC NVESD has conducted many experiments involving human targets for infrared and reflective band sensors. The target sets include human activities, hand-held objects, uniforms & armament, and other tactically relevant targets. This paper will define a set of standard task difficulty values for identification and recognition associated with human target acquisition performance.

Robust wafer identification recognition based on asterisk-shape filter and high-low score comparison method.

PubMed

Hsu, Wei-Chih; Yu, Tsan-Ying; Chen, Kuan-Liang

2009-12-10

Wafer identifications (wafer ID) can be used to identify wafers from each other so that wafer processing can be traced easily. Wafer ID recognition is one of the problems of optical character recognition. The process to recognize wafer IDs is similar to that used in recognizing car license-plate characters. However, due to some unique characteristics, such as the irregular space between two characters and the unsuccessive strokes of wafer ID, it will not get a good result to recognize wafer ID by directly utilizing the approaches used in car license-plate character recognition. Wafer ID scratches are engraved by a laser scribe almost along the following four fixed directions: horizontal, vertical, plus 45 degrees , and minus 45 degrees orientations. The closer to the center line of a wafer ID scratch, the higher the gray level will be. These and other characteristics increase the difficulty to recognize the wafer ID. In this paper a wafer ID recognition scheme based on an asterisk-shape filter and a high-low score comparison method is proposed to cope with the serious influence of uneven luminance and make recognition more efficiently. Our proposed approach consists of some processing stages. Especially in the final recognition stage, a template-matching method combined with stroke analysis is used as a recognizing scheme. This is because wafer IDs are composed of Semiconductor Equipment and Materials International (SEMI) standard Arabic numbers and English alphabets, and thus the template ID images are easy to obtain. Furthermore, compared with the approach that requires prior training, such as a support vector machine, which often needs a large amount of training image samples, no prior training is required for our approach. The testing results show that our proposed scheme can efficiently and correctly segment out and recognize the wafer ID with high performance.

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.

Idaho National Laboratory Supervisory Control and Data Acquisition Intrusion Detection System (SCADA IDS)

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

Jared Verba; Michael Milvich

2008-05-01

Current Intrusion Detection System (IDS) technology is not suited to be widely deployed inside a Supervisory, Control and Data Acquisition (SCADA) environment. Anomaly- and signature-based IDS technologies have developed methods to cover information technology-based networks activity and protocols effectively. However, these IDS technologies do not include the fine protocol granularity required to ensure network security inside an environment with weak protocols lacking authentication and encryption. By implementing a more specific and more intelligent packet inspection mechanism, tailored traffic flow analysis, and unique packet tampering detection, IDS technology developed specifically for SCADA environments can be deployed with confidence in detecting maliciousmore » activity.« less

ID-SERS Based Reference Method for Quantification of Large Biomolecules on a Single Chip

NASA Astrophysics Data System (ADS)

Yaghobian, Fatemeh; Stosch, Rainer; Henrion, André; Güttler, Bernd

2010-08-01

Accuracy and precision of quantitative SERS results have been significantly increased by applying a method based on the so-called isotope-dilution (ID) principle. In this ID-SERS approach, an isotopically labeled analogue of the target molecule (isotopologue) is spiked to the sample at a known concentration. Due to the slight difference in their molar masses, some Raman bands of the heavier isotopologue are red-shifted with respect to the same signals resulting from the unlabelled compound. As a result, spectra evaluation is reduced to the determination of intensity ratios rather than absolute intensities, and the unknown quantity of the analyte can be calculated from the known quantity of the standard. This procedure is of particular interest in the development of highly accurate reference procedures for metrology in chemistry. Because the sample is spiked prior to any further treatment, potential loss of material or matrix effects would equally affect both isotopologues, without influencing the final result. The method has been successfully applied for quantifying small diagnostic marker molecules like creatinine at their relevant serum concentration levels using silver colloids as SERS substrates. Now, the ID-SERS approach has been realized as a "one-chip" approach using "Bio-chips" made of intrinsically grown spherical silver nanoparticles with gaps less than 10 nm in between (Fig. 1). In addition, the scope of the method has been extended to larger biomolecules like peptides which will be shown using the example of the human growth-hormone (hGH) peptide T12 at physiologically relevant serum concentration levels (Fig. 2). Further developments towards the quantification of full proteins will also be reported.

Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.

PubMed

Wen, Qiang; Goldenson, Benjamin; Silver, Serena J; Schenone, Monica; Dancik, Vlado; Huang, Zan; Wang, Ling-Zhi; Lewis, Timothy A; An, W Frank; Li, Xiaoyu; Bray, Mark-Anthony; Thiollier, Clarisse; Diebold, Lauren; Gilles, Laure; Vokes, Martha S; Moore, Christopher B; Bliss-Moreau, Meghan; Verplank, Lynn; Tolliday, Nicola J; Mishra, Rama; Vemula, Sasidhar; Shi, Jianjian; Wei, Lei; Kapur, Reuben; Lopez, Cécile K; Gerby, Bastien; Ballerini, Paola; Pflumio, Francoise; Gilliland, D Gary; Goldberg, Liat; Birger, Yehudit; Izraeli, Shai; Gamis, Alan S; Smith, Franklin O; Woods, William G; Taub, Jeffrey; Scherer, Christina A; Bradner, James E; Goh, Boon-Cher; Mercher, Thomas; Carpenter, Anne E; Gould, Robert J; Clemons, Paul A; Carr, Steven A; Root, David E; Schreiber, Stuart L; Stern, Andrew M; Crispino, John D

2012-08-03

The mechanism by which cells decide to skip mitosis to become polyploid is largely undefined. Here we used a high-content image-based screen to identify small-molecule probes that induce polyploidization of megakaryocytic leukemia cells and serve as perturbagens to help understand this process. Our study implicates five networks of kinases that regulate the switch to polyploidy. Moreover, we find that dimethylfasudil (diMF, H-1152P) selectively increased polyploidization, mature cell-surface marker expression, and apoptosis of malignant megakaryocytes. An integrated target identification approach employing proteomic and shRNA screening revealed that a major target of diMF is Aurora kinase A (AURKA). We further find that MLN8237 (Alisertib), a selective inhibitor of AURKA, induced polyploidization and expression of mature megakaryocyte markers in acute megakaryocytic leukemia (AMKL) blasts and displayed potent anti-AMKL activity in vivo. Our findings provide a rationale to support clinical trials of MLN8237 and other inducers of polyploidization and differentiation in AMKL. Copyright © 2012 Elsevier Inc. All rights reserved.

Development and Evaluation of LEGUME ID: A ToolBook Multimedia Module.

ERIC Educational Resources Information Center

Hannaway, David B.; And Others

1992-01-01

Describes the development and advantages of LEGUME ID, a multimedia module for agricultural education. LEGUME ID is an example of how teachers, given the opportunity through accessible computer software programs, can create powerful teaching tools. Summarized is a student response to the use of this teacher-produced software program. (MCO)

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

Rethinking the REAL ID Act and National Identification Cards as a Counterterrorism Tool

DTIC Science & Technology

2009-12-01

federal government imposing national identification standards on states are also actively engaged in the debate. Michael Boldin , a 36-year-old Web...on the RIA.94 Boldin states, “Maine resisted, the government backed off, and soon all of these other states were doing the same thing.”95 Since...that acquires biometric data from an individual, extracts a feature set from the data, compares this feature set against the feature set stored in a

Evaluation of the sensitivity of the 'Wiley registry of tandem mass spectral data, MSforID' with MS/MS data of the 'NIST/NIH/EPA mass spectral library'.

PubMed

Oberacher, Herbert; Whitley, Graeme; Berger, Bernd

2013-04-01

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the 'Wiley Registry of Tandem Mass Spectral Data, MSforID' (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the 'NIST/NIH/EPA Mass Spectral Library' (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross-validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library. Copyright © 2013 John Wiley & Sons, Ltd.

Identification of Host-Targeted Small Molecules That Restrict Intracellular Mycobacterium tuberculosis Growth

PubMed Central

Silvis, Melanie R.; Luo, Samantha S.; Sogi, Kimberly; Vokes, Martha; Bray, Mark-Anthony; Carpenter, Anne E.; Moore, Christopher B.; Siddiqi, Noman; Rubin, Eric J.; Hung, Deborah T.

2014-01-01

Mycobacterium tuberculosis remains a significant threat to global health. Macrophages are the host cell for M. tuberculosis infection, and although bacteria are able to replicate intracellularly under certain conditions, it is also clear that macrophages are capable of killing M. tuberculosis if appropriately activated. The outcome of infection is determined at least in part by the host-pathogen interaction within the macrophage; however, we lack a complete understanding of which host pathways are critical for bacterial survival and replication. To add to our understanding of the molecular processes involved in intracellular infection, we performed a chemical screen using a high-content microscopic assay to identify small molecules that restrict mycobacterial growth in macrophages by targeting host functions and pathways. The identified host-targeted inhibitors restrict bacterial growth exclusively in the context of macrophage infection and predominantly fall into five categories: G-protein coupled receptor modulators, ion channel inhibitors, membrane transport proteins, anti-inflammatories, and kinase modulators. We found that fluoxetine, a selective serotonin reuptake inhibitor, enhances secretion of pro-inflammatory cytokine TNF-α and induces autophagy in infected macrophages, and gefitinib, an inhibitor of the Epidermal Growth Factor Receptor (EGFR), also activates autophagy and restricts growth. We demonstrate that during infection signaling through EGFR activates a p38 MAPK signaling pathway that prevents macrophages from effectively responding to infection. Inhibition of this pathway using gefitinib during in vivo infection reduces growth of M. tuberculosis in the lungs of infected mice. Our results support the concept that screening for inhibitors using intracellular models results in the identification of tool compounds for probing pathways during in vivo infection and may also result in the identification of new anti-tuberculosis agents that work by

RadNet Air Data From Boise, ID

EPA Pesticide Factsheets

This page presents radiation air monitoring and air filter analysis data for Boise, ID from EPA's RadNet system. RadNet is a nationwide network of monitoring stations that measure radiation in air, drinking water and precipitation.

ACE ID genotype and the muscle strength and size response to unilateral resistance training.

PubMed

Pescatello, Linda S; Kostek, Matthew A; Gordish-Dressman, Heather; Thompson, Paul D; Seip, Richard L; Price, Thomas B; Angelopoulos, Theodore J; Clarkson, Priscilla M; Gordon, Paul M; Moyna, Niall M; Visich, Paul S; Zoeller, Robert F; Devaney, Joseph M; Hoffman, Eric P

2006-06-01

To examine associations among the angiotensin I-converting enzyme (ACE) insertion (I)/deletion (D) polymorphism and the response to a 12-wk (2 d.wk) unilateral, upper-arm resistance training (RT) program in the trained (T, nondominant) and untrained (UT, dominant) arms. Subjects were 631 (mean+/-SEM, 24.2+/-0.2 yr) white (80%) men (42%) and women (58%). The ACE ID genotype was in Hardy-Weinberg equilibrium with frequencies of 23.1, 46.1, and 30.8% for ACE II, ID, and DD, respectively (chi=1.688, P=0.430). Maximum voluntary contraction (MVC) and one-repetition maximum (1RM) assessed peak elbow flexor muscle strength. Magnetic resonance imaging measured biceps muscle cross-sectional area (CSA). Multiple variable and repeated-measures ANCOVA tested whether muscle strength and size differed at baseline and pre- to post-RT among T and UT and ACE ID genotype. Baseline muscle strength and size were greater in UT than T (P<0.001) and did not differ among ACE ID genotype in either arm (P >or= 0.05). In T, MVC increases were greater for ACE II/ID (22%) than DD (17%) (P<0.05), whereas 1RM (51%) and CSA (19%) gains were not different among ACE ID genotype pre- to post-RT (P >or= 0.05). In UT, MVC increased among ACE II/ID (7%) (P<0.001) but was similar among ACE DD (2%) pre- to post-RT (P >or= 0.05). In UT, 1RM (11%) and CSA (2%) increases were greater for ACE DD/ID than ACE II (1RM, 7%; CSA, -0.1%) (P<0.05). ACE ID genotype explained approximately 1% of the MVC response to RT in T and approximately 2% of MVC, 2% of 1RM, and 4% of CSA response in UT (P<0.05). ACE ID genotype is associated with the contralateral effects of unilateral RT, perhaps more so than with the muscle strength and size adaptations that result from RT.

Addiction to the IGF2-ID1-IGF2 circuit for maintenance of the breast cancer stem-like cells

PubMed Central

Tominaga, K; Shimamura, T; Kimura, N; Murayama, T; Matsubara, D; Kanauchi, H; Niida, A; Shimizu, S; Nishioka, K; Tsuji, E-i; Yano, M; Sugano, S; Shimono, Y; Ishii, H; Saya, H; Mori, M; Akashi, K; Tada, K-i; Ogawa, T; Tojo, A; Miyano, S; Gotoh, N

2017-01-01

The transcription factor nuclear factor-κB (NF-κB) has important roles for tumorigenesis, but how it regulates cancer stem cells (CSCs) remains largely unclear. We identified insulin-like growth factor 2 (IGF2) is a key target of NF-κB activated by HER2/HER3 signaling to form tumor spheres in breast cancer cells. The IGF2 receptor, IGF1 R, was expressed at high levels in CSC-enriched populations in primary breast cancer cells. Moreover, IGF2-PI3K (IGF2-phosphatidyl inositol 3 kinase) signaling induced expression of a stemness transcription factor, inhibitor of DNA-binding 1 (ID1), and IGF2 itself. ID1 knockdown greatly reduced IGF2 expression, and tumor sphere formation. Finally, treatment with anti-IGF1/2 antibodies blocked tumorigenesis derived from the IGF1Rhigh CSC-enriched population in a patient-derived xenograft model. Thus, NF-κB may trigger IGF2-ID1-IGF2-positive feedback circuits that allow cancer stem-like cells to appear. Then, they may become addicted to the circuits. As the circuits are the Achilles' heels of CSCs, it will be critical to break them for eradication of CSCs. PMID:27546618

Microorganism Identification Based On MALDI-TOF-MS Fingerprints

NASA Astrophysics Data System (ADS)

Elssner, Thomas; Kostrzewa, Markus; Maier, Thomas; Kruppa, Gary

Advances in MALDI-TOF mass spectrometry have enabled the ­development of a rapid, accurate and specific method for the identification of bacteria directly from colonies picked from culture plates, which we have named the MALDI Biotyper. The picked colonies are placed on a target plate, a drop of matrix solution is added, and a pattern of protein molecular weights and intensities, "the protein fingerprint" of the bacteria, is produced by the MALDI-TOF mass spectrometer. The obtained protein mass fingerprint representing a molecular signature of the microorganism is then matched against a database containing a library of previously measured protein mass fingerprints, and scores for the match to every library entry are produced. An ID is obtained if a score is returned over a pre-set threshold. The sensitivity of the techniques is such that only approximately 104 bacterial cells are needed, meaning that an overnight culture is sufficient, and the results are obtained in minutes after culture. The improvement in time to result over biochemical methods, and the capability to perform a non-targeted identification of bacteria and spores, potentially makes this method suitable for use in the detect-to-treat timeframe in a bioterrorism event. In the case of white-powder samples, the infectious spore is present in sufficient quantity in the powder so that the MALDI Biotyper result can be obtained directly from the white powder, without the need for culture. While spores produce very different patterns from the vegetative colonies of the corresponding bacteria, this problem is overcome by simply including protein fingerprints of the spores in the library. Results on spores can be returned within minutes, making the method suitable for use in the "detect-to-protect" timeframe.

Efficient coding and detection of ultra-long IDs for visible light positioning systems.

PubMed

Zhang, Hualong; Yang, Chuanchuan

2018-05-14

Visible light positioning (VLP) is a promising technique to complement Global Navigation Satellite System (GNSS) such as Global positioning system (GPS) and BeiDou Navigation Satellite System (BDS) which features the advantage of low-cost and high accuracy. The situation becomes even more crucial for indoor environments, where satellite signals are weak or even unavailable. For large-scale application of VLP, there would be a considerable number of Light emitting diode (LED) IDs, which bring forward the demand of long LED ID detection. In particular, to provision indoor localization globally, a convenient way is to program a unique ID into each LED during manufacture. This poses a big challenge for image sensors, such as the CMOS camera in everybody's hands since the long ID covers the span of multiple frames. In this paper, we investigate the detection of ultra-long ID using rolling shutter cameras. By analyzing the pattern of data loss in each frame, we proposed a novel coding technique to improve the efficiency of LED ID detection. We studied the performance of Reed-Solomon (RS) code in this system and designed a new coding method which considered the trade-off between performance and decoding complexity. Coding technique decreases the number of frames needed in data processing, significantly reduces the detection time, and improves the accuracy of detection. Numerical and experimental results show that the detected LED ID can be much longer with the coding technique. Besides, our proposed coding method is proved to achieve a performance close to that of RS code while the decoding complexity is much lower.

An ID Network System to Prepare for Global Environmental/Health Concerns

NASA Astrophysics Data System (ADS)

Asano, Shoichiro; Yoneda, Susumu

Climate change and/or pandemics are global life threatening concerns. For verifying and utilizing monitored data for solving to the Climate Change concerns, a network system based on device ID would be proposed. In this paper, we review the recent standardization initiatives in ITU-T, and propose an ID network that can be used to verify the solutions.

Odors identification differences in deficit and nondeficit schizophrenia.

PubMed

Pełka-Wysiecka, Justyna; Wroński, Michał; Bieńkowski, Przemysław; Murawiec, Sławomir; Samochowiec, Agnieszka; Samochowiec, Jerzy

2016-04-01

There is evidence that deficit schizophrenia (DS) is associated with neuroanatomical changes in structures including those involved in olfaction. Olfactory dysfunction, which includes impaired odor identification, is found in patients with schizophrenia and their family members. 82 patients with DS and 72 patients with NDS (nondeficit schizophrenia), somatically healthy and without acute psychotic symptoms undertook a smell identification test using the 16-item Sniffin' Sticks ID test. Demographic and psychometric data were collected. No differences in the course of the illness, perinatal history and demographic data were found between the DS and NDS groups. No differences in the number of correctly identified odor samples were found. Some differences in the qualitative identification of samples between DS and NDS were found in the groups of female (fewer correct identifications of cinnamon and pineapple smells in DS) and male patients (fewer correct identifications of the smell of rose and more correct identifications of the smell of orange than in NDS). No overall differences between DS and NDS regarding odors identification have been found. The results seem to indicate some specific deficits in the identification of markers of rose, pineapple, orange and cinnamon. Copyright © 2015 Institute of Pharmacology, Polish Academy of Sciences. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

Identification and Characterization of Lactic Acid Bacteria in a Commercial Probiotic Culture

PubMed Central

MENCONI, Anita; KALLAPURA, Gopala; LATORRE, Juan D.; MORGAN, Marion J.; PUMFORD, Neil R.; HARGIS, Billy M.; TELLEZ, Guillermo

2014-01-01

The aim of the present study was to describe the identification and characterization (physiological properties) of two strains of lactic acid bacteria (LAB 18 and 48) present in a commercial probiotic culture, FloraMax®-B11. Isolates were characterized morphologically, and identified biochemically. In addition, the MIDI System ID, the Biolog ID System, and 16S rRNA sequence analyses for identification of LAB 18 and LAB 48 strains were used to compare the identification results. Tolerance and resistance to acidic pH, high osmotic concentration of NaCl, and bile salts were tested in broth medium. In vitro assessment of antimicrobial activity against enteropathogenic bacteria and susceptibility to antibiotics were also tested. The results obtained in this study showed tolerance of LAB 18 and LAB 48 to pH 3.0, 6.5% NaCl and a high bile salt concentration (0.6%). Both strains evaluated showed in vitro antibacterial activity against Salmonella enterica serovar Enteritidis, Escherichia coli (O157:H7), and Campylobacter jejuni. These are important characteristics of lactic acid bacteria that should be evaluated when selecting strains to be used as probiotics. Antimicrobial activity of these effective isolates may contribute to efficacy, possibly by direct antimicrobial activity in vivo. PMID:24936379

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...

Apolipoprotein e4 Is Associated with More Rapid Decline in Odor Identification than in Odor Threshold or Dementia Rating Scale Scores

ERIC Educational Resources Information Center

Calhoun-Haney, R.; Murphy, C.

2005-01-01

Individuals with the apolipoprotein E e4 genetic risk factor for Alzheimer's disease (AD) show deficits in olfactory function. The purpose of the present study was to examine longitudinally odor identification (odor ID), odor threshold, picture identification, and global cognitive status in allele positive (e4+) and negative (e4-) persons.…

Redesigning photo-ID to improve unfamiliar face matching performance.

PubMed

White, David; Burton, A Mike; Jenkins, Rob; Kemp, Richard I

2014-06-01

Viewers find it difficult to match photos of unfamiliar faces for identity. Despite this, the use of photographic ID is widespread. In this study we ask whether it is possible to improve face matching performance by replacing single photographs on ID documents with multiple photos or an average image of the bearer. In 3 experiments we compare photo-to-photo matching with photo-to-average matching (where the average is formed from multiple photos of the same person) and photo-to-array matching (where the array comprises separate photos of the same person). We consistently find an accuracy advantage for average images and photo arrays over single photos, and show that this improvement is driven by performance in match trials. In the final experiment, we find a benefit of 4-image arrays relative to average images for unfamiliar faces, but not for familiar faces. We propose that conventional photo-ID format can be improved, and discuss this finding in the context of face recognition more generally. PsycINFO Database Record (c) 2014 APA, 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

78 FR 51677 - Children's Online Privacy Protection Rule Proposed Parental Consent Method; AssertID, Inc...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-21

...-AB20 Children's Online Privacy Protection Rule Proposed Parental Consent Method; AssertID, Inc. Application for Approval of Parental Consent Method AGENCY: Federal Trade Commission (FTC or Commission... concerning the proposed parental consent method submitted by AssertID, Inc. (``AssertID'') under the...

Eddy current signal comparison for tube identification

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

Glass, S. W., E-mail: Bill.Glass@areva.com, E-mail: Ratko.Vojvodic@areva.com; Vojvodic, R., E-mail: Bill.Glass@areva.com, E-mail: Ratko.Vojvodic@areva.com

2015-03-31

Inspection of nuclear power plant steam generator tubes is required to justify continued safe plant operation. The steam generators consist of thousands of tubes with nominal diameters of 15 to 22mm, approximately 1mm wall thickness, and 20 to 30m in length. The tubes are inspected by passing an eddy current probe through the tubes from tube end to tube end. It is critical to know exactly which tube identification (row and column) is associated with each tube's data. This is controlled by a precision manipulator that provides the tube ID to the eddy current system. Historically there have been somemore » instances where the manipulator incorrectly reported the tube ID. This can have serious consequences including lack of inspection of a tube, or if a pluggable indication is detected, the tube is likely to be mis-plugged thereby risking a primary to secondary leak.« less

Core Proteomic Analysis of Unique Metabolic Pathways of Salmonella enterica for the Identification of Potential Drug Targets.

PubMed

Uddin, Reaz; Sufian, Muhammad

2016-01-01

Infections caused by Salmonella enterica, a Gram-negative facultative anaerobic bacteria belonging to the family of Enterobacteriaceae, are major threats to the health of humans and animals. The recent availability of complete genome data of pathogenic strains of the S. enterica gives new avenues for the identification of drug targets and drug candidates. We have used the genomic and metabolic pathway data to identify pathways and proteins essential to the pathogen and absent from the host. We took the whole proteome sequence data of 42 strains of S. enterica and Homo sapiens along with KEGG-annotated metabolic pathway data, clustered proteins sequences using CD-HIT, identified essential genes using DEG database and discarded S. enterica homologs of human proteins in unique metabolic pathways (UMPs) and characterized hypothetical proteins with SVM-prot and InterProScan. Through this core proteomic analysis we have identified enzymes essential to the pathogen. The identification of 73 enzymes common in 42 strains of S. enterica is the real strength of the current study. We proposed all 73 unexplored enzymes as potential drug targets against the infections caused by the S. enterica. The study is comprehensive around S. enterica and simultaneously considered every possible pathogenic strain of S. enterica. This comprehensiveness turned the current study significant since, to the best of our knowledge it is the first subtractive core proteomic analysis of the unique metabolic pathways applied to any pathogen for the identification of drug targets. We applied extensive computational methods to shortlist few potential drug targets considering the druggability criteria e.g. Non-homologous to the human host, essential to the pathogen and playing significant role in essential metabolic pathways of the pathogen (i.e. S. enterica). In the current study, the subtractive proteomics through a novel approach was applied i.e. by considering only proteins of the unique metabolic

77 FR 68065 - Amendment of Class D and Class E Airspace; Lewiston, ID

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-15

... Measuring Equipment (VOR/ DME), and the Lewiston-Nez Perce Instrument Landing System (ILS) Localizer... feet or more above the surface of the earth. * * * * * ANM ID E5 Lewiston, ID [Modified] Lewiston-Nez...

Development of a cryogenic DC-low noise amplifier for SQuID-based readout electronics

NASA Astrophysics Data System (ADS)

Macculi, C.; Torrioli, G.; Di Giorgio, A.; Spinoglio, L.; Piro, Luigi

2014-07-01

We present the preliminary results of the design and test activities for a DC cryogenic low noise amplifier for the SAFARI imaging spectrometer, planned to be onboard the SPICA mission, necessary not only to drive, as usual, the voltage signal produced by the SQuID but also to boost such signals over about 7 meter of path towards the warm feedback electronics. This development has been done in the framework of the mission preparation studies, within the European Consortium for the development of the SAFARI instrument. The actual configuration of the SAFARI focal plane assembly (FPA), indeed, foresees a long distance to the warm back end electronics. It is therefore mandatory to boost the faint electric signal coming from the SQuID device by keeping under control both power dissipation and noise: this is the main role of the designed Cryogenic Low Noise Amplifier (LNA). Working at 136K, it has a differential input gain-stage, and a differential balanced voltage buffer output stage, running at few mW target overall power. At present the design is based on the use of Heterojunction Si:Ge transistors, the required bandwidth is DC-4MHz and the required noise lower than 1 nV/rtHz.

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

Toward operation of series IDs at BL43LXU of SPring-8

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

Baron, A. Q. R.; Tanaka, T.; Soutome, K.

2016-07-27

This paper discusses two issues relating to using 3 small gap insertion devices in series at BL43LXU of SPring-8 to make a uniquely powerful source in the 15-26 keV region of the x-ray spectrum. The issues discussed are (1) damage to the covers of the downstream IDs by radiation from the upstream IDs and (2) proper steering of the electron beam to get the best photon beam properties. After tests in several configurations, including one where an ID was run without an impedance-reducing cover, the damage issue was solved by installing a distributed absorber in the most downstream ID. Themore » steering issues were mostly resolved by the introduction of appropriate corrector magnets and feedback. The paper is written from the viewpoint of an interested beamline scientist impressed with the cooperation of different groups to make a source for new science possible.« less

Overestimation of the 25(OH)D serum concentration with the automated IDS EIA kit.

PubMed

Cavalier, Etienne; Huberty, Véronique; Cormier, Catherine; Souberbielle, Jean-Claude

2011-02-01

We have recently observed an increasing number of patients presenting very high serum levels of 25-hydroxyvitamin D [25(OH)D] (> 150 ng/mL), which, in all cases, had been measured with the IDS EIA kit adapted on different "open" automated platforms. We performed a comparison between the IDS EIA kit adapted on two different "open"automated platforms and the DiaSorin RIA. We found a systematic bias (higher levels with the IDS EIA kit) for concentrations more than 50-60 ng/mL that was less obvious when the IDS EIA was used in its manual procedure. We thus suggest to use the IDS EIA kit in its manual procedure rather than to adapt it on an automated platform, and to interpret cautiously a 25(OH)D greater than 100 ng/mL with this kit. Copyright © 2011 American Society for Bone and Mineral Research.

Id expression in amphioxus and lamprey highlights the role of gene cooption during neural crest evolution

NASA Technical Reports Server (NTRS)

Meulemans, Daniel; McCauley, David; Bronner-Fraser, Marianne

2003-01-01

Neural crest cells are unique to vertebrates and generate many of the adult structures that differentiate them from their closest invertebrate relatives, the cephalochordates. Id genes are robust markers of neural crest cells at all stages of development. We compared Id gene expression in amphioxus and lamprey to ask if cephalochordates deploy Id genes at the neural plate border and dorsal neural tube in a manner similar to vertebrates. Furthermore, we examined whether Id expression in these cells is a basal vertebrate trait or a derived feature of gnathostomes. We found that while expression of Id genes in the mesoderm and endoderm is conserved between amphioxus and vertebrates, expression in the lateral neural plate border and dorsal neural tube is a vertebrate novelty. Furthermore, expression of lamprey Id implies that recruitment of Id genes to these cells occurred very early in the vertebrate lineage. Based on expression in amphioxus we postulate that Id cooption conferred sensory cell progenitor-like properties upon the lateral neurectoderm, and pharyngeal mesoderm-like properties upon cranial neural crest. Amphioxus Id expression is also consistent with homology between the anterior neurectoderm of amphioxus and the presumptive placodal ectoderm of vertebrates. These observations support the idea that neural crest evolution was driven in large part by cooption of multipurpose transcriptional regulators from other tissues and cell types.

Target identification by image analysis.

PubMed

Fetz, V; Prochnow, H; Brönstrup, M; Sasse, F

2016-05-04

Covering: 1997 to the end of 2015Each biologically active compound induces phenotypic changes in target cells that are characteristic for its mode of action. These phenotypic alterations can be directly observed under the microscope or made visible by labelling structural elements or selected proteins of the cells with dyes. A comparison of the cellular phenotype induced by a compound of interest with the phenotypes of reference compounds with known cellular targets allows predicting its mode of action. While this approach has been successfully applied to the characterization of natural products based on a visual inspection of images, recent studies used automated microscopy and analysis software to increase speed and to reduce subjective interpretation. In this review, we give a general outline of the workflow for manual and automated image analysis, and we highlight natural products whose bacterial and eucaryotic targets could be identified through such approaches.

The Implementation of C-ID, R2D2 Model on Learning Reading Comprehension

ERIC Educational Resources Information Center

Rayanto, Yudi Hari; Rusmawan, Putu Ngurah

2016-01-01

The purposes of this research are to find out, (1) whether C-ID, R2D2 model is effective to be implemented on learning Reading comprehension, (2) college students' activity during the implementation of C-ID, R2D2 model on learning Reading comprehension, and 3) college students' learning achievement during the implementation of C-ID, R2D2 model on…

Application of the Reference Method Isotope Dilution Gas Chromatography Mass Spectrometry (ID/GC/MS) to Establish Metrological Traceability for Calibration and Control of Blood Glucose Test Systems

PubMed Central

Andreis, Elisabeth; Küllmer, Kai

2014-01-01

Self-monitoring of blood glucose (BG) by means of handheld BG systems is a cornerstone in diabetes therapy. The aim of this article is to describe a procedure with proven traceability for calibration and evaluation of BG systems to guarantee reliable BG measurements. Isotope dilution gas chromatography mass spectrometry (ID/GC/MS) is a method that fulfills all requirements to be used in a higher-order reference measurement procedure. However, this method is not applicable for routine measurements because of the time-consuming sample preparation. A hexokinase method with perchloric acid (PCA) sample pretreatment is used in a measurement procedure for such purposes. This method is directly linked to the ID/GC/MS method by calibration with a glucose solution that has an ID/GC/MS-determined target value. BG systems are calibrated with whole blood samples. The glucose levels in such samples are analyzed by this ID/GC/MS-linked hexokinase method to establish traceability to higher-order reference material. For method comparison, the glucose concentrations in 577 whole blood samples were measured using the PCA-hexokinase method and the ID/GC/MS method; this resulted in a mean deviation of 0.1%. The mean deviation between BG levels measured in >500 valid whole blood samples with BG systems and the ID/GC/MS was 1.1%. BG systems allow a reliable glucose measurement if a true reference measurement procedure, with a noninterrupted traceability chain using ID/GC/MS linked hexokinase method for calibration of BG systems, is implemented. Systems should be calibrated by means of a traceable and defined measurement procedure to avoid bias. PMID:24876614

Drug target identification in protozoan parasites.

PubMed

Müller, Joachim; Hemphill, Andrew

2016-08-01

Despite the fact that diseases caused by protozoan parasites represent serious challenges for public health, animal production and welfare, only a limited panel of drugs has been marketed for clinical applications. Herein, the authors investigate two strategies, namely whole organism screening and target-based drug design. The present pharmacopoeia has resulted from whole organism screening, and the mode of action and targets of selected drugs are discussed. However, the more recent extensive genome sequencing efforts and the development of dry and wet lab genomics and proteomics that allow high-throughput screening of interactions between micromolecules and recombinant proteins has resulted in target-based drug design as the predominant focus in anti-parasitic drug development. Selected examples of target-based drug design studies are presented, and calcium-dependent protein kinases, important drug targets in apicomplexan parasites, are discussed in more detail. Despite the enormous efforts in target-based drug development, this approach has not yet generated market-ready antiprotozoal drugs. However, whole-organism screening approaches, comprising of both in vitro and in vivo investigations, should not be disregarded. The repurposing of already approved and marketed drugs could be a suitable strategy to avoid fastidious approval procedures, especially in the case of neglected or veterinary parasitoses.

Drug target identification in protozoan parasites

PubMed Central

Müller, Joachim; Hemphill, Andrew

2016-01-01

Introduction Despite the fact that diseases caused by protozoan parasites represent serious challenges for public health, animal production and welfare, only a limited panel of drugs has been marketed for clinical applications. Areas covered Herein, the authors investigate two strategies, namely whole organism screening and target-based drug design. The present pharmacopoeia has resulted from whole organism screening, and the mode of action and targets of selected drugs are discussed. However, the more recent extensive genome sequencing efforts and the development of dry and wet lab genomics and proteomics that allow high-throughput screening of interactions between micromolecules and recombinant proteins has resulted in target-based drug design as the predominant focus in anti-parasitic drug development. Selected examples of target-based drug design studies are presented, and calcium-dependent protein kinases, important drug targets in apicomplexan parasites, are discussed in more detail. Expert opinion Despite the enormous efforts in target-based drug development, this approach has not yet generated market-ready antiprotozoal drugs. However, whole-organism screening approaches, comprising of both in vitro and in vivo investigations, should not be disregarded. The repurposing of already approved and marketed drugs could be a suitable strategy to avoid fastidious approval procedures, especially in the case of neglected or veterinary parasitoses. PMID:27238605

Enhancing bioactive peptide release and identification using targeted enzymatic hydrolysis of milk proteins.

PubMed

Nongonierma, Alice B; FitzGerald, Richard J

2018-06-01

Milk proteins have been extensively studied for their ability to yield a range of bioactive peptides following enzymatic hydrolysis/digestion. However, many hurdles still exist regarding the widespread utilization of milk protein-derived bioactive peptides as health enhancing agents for humans. These mostly arise from the fact that most milk protein-derived bioactive peptides are not highly potent. In addition, they may be degraded during gastrointestinal digestion and/or have a low intestinal permeability. The targeted release of bioactive peptides during the enzymatic hydrolysis of milk proteins may allow the generation of particularly potent bioactive hydrolysates and peptides. Therefore, the development of milk protein hydrolysates capable of improving human health requires, in the first instance, optimized targeted release of specific bioactive peptides. The targeted hydrolysis of milk proteins has been aided by a range of in silico tools. These include peptide cutters and predictive modeling linking bioactivity to peptide structure [i.e., molecular docking, quantitative structure activity relationship (QSAR)], or hydrolysis parameters [design of experiments (DOE)]. Different targeted enzymatic release strategies employed during the generation of milk protein hydrolysates are reviewed herein and their limitations are outlined. In addition, specific examples are provided to demonstrate how in silico tools may help in the identification and discovery of potent milk protein-derived peptides. It is anticipated that the development of novel strategies employing a range of in silico tools may help in the generation of milk protein hydrolysates containing potent and bioavailable peptides, which in turn may be used to validate their health promoting effects in humans. Graphical abstract The targeted enzymatic hydrolysis of milk proteins may allow the generation of highly potent and bioavailable bioactive peptides.

Electronic p-Chip-Based System for Identification of Glass Slides and Tissue Cassettes in Histopathology Laboratories

PubMed Central

Mandecki, Wlodek; Qian, Jay; Gedzberg, Katie; Gruda, Maryanne; Rodriguez, Efrain “Frank”; Nesbitt, Leslie; Riben, Michael

2018-01-01

Background: The tagging system is based on a small, electronic, wireless, laser-light-activated microtransponder named “p-Chip.” The p-Chip is a silicon integrated circuit, the size of which is 600 μm × 600 μm × 100 μm. Each p-Chip contains a unique identification code stored within its electronic memory that can be retrieved with a custom reader. These features allow the p-Chip to be used as an unobtrusive and scarcely noticeable ID tag on glass slides and tissue cassettes. Methods: The system is comprised of p-Chip-tagged sample carriers, a dedicated benchtop p-Chip ID reader that can accommodate both objects, and an additional reader (the Wand), with an adapter for reading IDs of glass slides stored vertically in drawers. On slides, p-Chips are attached with adhesive to the center of the short edge, and on cassettes – embedded directly into the plastic. ID readout is performed by bringing the reader to the proximity of the chip. Standard histopathology laboratory protocols were used for testing. Results: Very good ID reading efficiency was observed for both glass slides and cassettes. When processed slides are stored in vertical filing drawers, p-Chips remain readable without the need to remove them from the storage location, thereby improving the speed of searches in collections. On the cassettes, the ID continues to be readable through a thin layer of paraffin. Both slides and tissue cassettes can be read with the same reader, reducing the need for redundant equipment. Conclusions: The p-Chip is stable to all chemical challenges commonly used in the histopathology laboratory, tolerates temperature extremes, and remains durable in long-term storage. The technology is compatible with laboratory information management systems software systems. The p-Chip system is very well suited for identification of glass slides and cassettes in the histopathology laboratory. PMID:29692946

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

NASA Astrophysics Data System (ADS)

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-04-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ~10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

PubMed Central

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-01-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ∼10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level. PMID:28382928

cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies.

PubMed

Chase, John H; Bolyen, Evan; Rideout, Jai Ram; Caporaso, J Gregory

2016-01-01

The number of samples in high-throughput comparative "omics" studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential that we transition to better-designed sample identifiers. Ideally, sample identifiers should be globally unique across projects, project teams, and institutions; short (to facilitate manual transcription); correctable with respect to common types of transcription errors; opaque, meaning that they do not contain information about the samples; and compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign universally unique identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials, such as swabs or microcentrifuge tubes, however, so cual-id additionally generates human-friendly 4- to 12-character identifiers that map to their UUIDs and are unique within a project. By convention, we use "cual-id" to refer to the software, "CualID" to refer to the short, human-friendly identifiers, and "UUID" to refer to the globally unique identifiers. CualIDs are used by humans when they manually write or enter identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. Finally, cual-id optionally generates printable label sticker sheets containing Code 128 bar codes and CualIDs for labeling of sample collection and processing materials. IMPORTANCE The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for

76 FR 31388 - Idaho Disaster #ID-00014

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-31

... SMALL BUSINESS ADMINISTRATION [Disaster Declaration 12603 and 12604] Idaho Disaster ID-00014... declaration of a major disaster for Public Assistance Only for the State of Idaho (FEMA-- 1987--DR), dated 05..., Clearwater, Idaho, Nez Perce, Shoshone, Nez Perce Tribe. The Interest Rates are: Percent For Physical Damage...

75 FR 45682 - Idaho Disaster #ID-00010

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-03

... SMALL BUSINESS ADMINISTRATION [Disaster Declaration 12250 and 12251] Idaho Disaster ID-00010... declaration of a major disaster for Public Assistance Only for the State of Idaho (FEMA-1927- DR), dated 07/27... adversely affected by the disaster: Primary Counties: Adams, Gem, Idaho, Lewis, Payette, Valley, Washington...

Ameliorative effect of IDS 30, a stinging nettle leaf extract, on chronic colitis.

PubMed

Konrad, Astrid; Mähler, Michael; Arni, Stephan; Flogerzi, Beatrice; Klingelhöfer, Sonja; Seibold, Frank

2005-01-01

Anti-TNF-alpha antibodies are very effective in the treatment of acute Crohn's disease, but are limited by the decline of their effectiveness after repeated applications. The stinging nettle leaf extract, IDS 30, is an adjuvant remedy in rheumatic diseases dependent on a cytokine suppressive effect. We investigated the effect of IDS 30 on disease activity of murine colitis in different models. C3H.IL-10-/- and BALB/c mice with colitis induced by dextran sodium sulphate (DSS) were treated with either IDS 30 or water. Mice were monitored for clinical signs of colitis. Inflammation was scored histologically, and faecal IL-1beta and mucosal cytokines were measured by ELISA. Mononuclear cell proliferation of spleen and Peyer's patches were quantified by 3H-thymidine. Mice with chronic DSS colitis or IL-10-/- mice treated with IDS 30 clinically and histologically revealed significantly (p < 0.05) fewer signs of colitis than untreated animals. Furthermore, faecal IL-1beta and mucosal TNF-alpha concentrations were significantly lower (p < 0.05) in treated mice. Mononuclear cell proliferation after stimulation with lipopolysaccharide was significantly (p < 0.001) reduced in mice treated with IDS 30. The long-term use of IDS 30 is effective in the prevention of chronic murine colitis. This effect seems to be due to a decrease in the Th1 response and may be a new therapeutic option for prolonging remission in inflammatory bowel disease.

Nurses' behaviors and visual scanning patterns may reduce patient identification errors.

PubMed

Marquard, Jenna L; Henneman, Philip L; He, Ze; Jo, Junghee; Fisher, Donald L; Henneman, Elizabeth A

2011-09-01

Patient identification (ID) errors occurring during the medication administration process can be fatal. The aim of this study is to determine whether differences in nurses' behaviors and visual scanning patterns during the medication administration process influence their capacities to identify patient ID errors. Nurse participants (n = 20) administered medications to 3 patients in a simulated clinical setting, with 1 patient having an embedded ID error. Error-identifying nurses tended to complete more process steps in a similar amount of time than non-error-identifying nurses and tended to scan information across artifacts (e.g., ID band, patient chart, medication label) rather than fixating on several pieces of information on a single artifact before fixating on another artifact. Non-error-indentifying nurses tended to increase their durations of off-topic conversations-a type of process interruption-over the course of the trials; the difference between groups was significant in the trial with the embedded ID error. Error-identifying nurses tended to have their most fixations in a row on the patient's chart, whereas non-error-identifying nurses did not tend to have a single artifact on which they consistently fixated. Finally, error-identifying nurses tended to have predictable eye fixation sequences across artifacts, whereas non-error-identifying nurses tended to have seemingly random eye fixation sequences. This finding has implications for nurse training and the design of tools and technologies that support nurses as they complete the medication administration process. (c) 2011 APA, all rights reserved.

Installation, commissioning and performance of IDs installed at ALBA

NASA Astrophysics Data System (ADS)

Campmany, J.; Marcos, J.; Massana, V.; Becheri, F.; Gigante, J. V.; Colldelram, C.; Ribó, Ll

2013-03-01

The new synchrotron light source ALBA is currently starting regular operation. Up to 6 beamlines are using light produced by Insertion Devices. There are up to four types of IDs: 2 Apple-II undulators (EU62 and EU71) operating at low energies, one conventional wiggler (MPW80) operating in the range of 2 - 20 keV, two in-vacuum undulators (IVU21) operating in the range 5 - 30 keV and a superconducting wiggler (SCW30) operating in the range of (up to) 40 keV. The main IDs characteristics, their influence on the beam dynamics and a first characterization of their light will be presented.

ERβ1 inhibits the migration and invasion of breast cancer cells through upregulation of E-cadherin in a Id1-dependent manner

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

Zhou, Yan; Ming, Jia; Xu, Yan

2015-02-06

Highlights: • Expression of ERβ1 was positively correlated with E-cadherin in breast cancer cell. • ERβ1 upregulates E-cadherin expression in breast cancer cell lines. • ERβ1 upregulates E-cadherin expression in a Id1-dependent manner. - Abstract: ERβ1 is a member of the nuclear receptor superfamily of ligand-regulated transcription factors. It plays an important role in regulating the progression of breast cancer. However, the mechanisms of ERβ1 in tumorigenesis, metastasis and prognosis are still not fully clear. In this study, we showed that the expression of ERβ1 was positively correlated with E-cadherin expression in breast cancer cell lines. In addition, we foundmore » that ERβ1 upregulates E-cadherin expression in breast cancer cell lines. Furthermore, we also found that ERβ1 inhibits the migration and invasion of breast cancer cells and upregulated E-cadherin expression in a Id1-dependent manner. Taken together, our study provides further understanding of the molecular mechanism of ERβ1 in tumor metastasis and suggests the feasibility of developing novel therapeutic approaches to target Id1 to inhibit breast cancer metastasis.« less

In silico identification and characterization of conserved miRNAs and their target genes in sweet potato (Ipomoea batatas L.) Expressed Sequence Tags (ESTs)

PubMed Central

Dehury, Budheswar; Panda, Debashis; Sahu, Jagajjit; Sahu, Mousumi; Sarma, Kishore; Barooah, Madhumita; Sen, Priyabrata; Modi, Mahendra Kumar

2013-01-01

The endogenous small non-coding micro RNAs (miRNAs), which are typically ~21–24 nt nucleotides, play a crucial role in regulating the intrinsic normal growth of cells and development of the plants as well as in maintaining the integrity of genomes. These small non-coding RNAs function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets, and further inferring miRNA functions is a routine process to understand normal biological processes of miRNAs and their roles in the development of plants. Comparative genomics based approach using expressed sequence tags (EST) and genome survey sequences (GSS) offer a cost-effective platform for identification and characterization of miRNAs and their target genes in plants. Despite the fact that sweet potato (Ipomoea batatas L.) is an important staple food source for poor small farmers throughout the world, the role of miRNA in various developmental processes remains largely unknown. In this paper, we report the computational identification of miRNAs and their target genes in sweet potato from their ESTs. Using comparative genomics-based approach, 8 potential miRNA candidates belonging to miR168, miR2911, and miR156 families were identified from 23 406 ESTs in sweet potato. A total of 42 target genes were predicted and their probable functions were illustrated. Most of the newly identified miRNAs target transcription factors as well as genes involved in plant growth and development, signal transduction, metabolism, defense, and stress response. The identification of miRNAs and their targets is expected to accelerate the pace of miRNA discovery, leading to an improved understanding of the role of miRNA in development and physiology of sweet potato, as well as stress response. PMID:24067297

40. CALCINER CELL SECTIONS. TOGETHER WITH HAER ID33C37 ILLUSTRATES COMPLEXITY ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

40. CALCINER CELL SECTIONS. TOGETHER WITH HAER ID-33-C-37 ILLUSTRATES COMPLEXITY OF PIPING. INEEL DRAWING NUMBER 200-0633-00-287-106446. FLUOR NUMBER 5775-CPP-P-51. - Idaho National Engineering Laboratory, Old Waste Calcining Facility, Scoville, Butte County, ID

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing.

PubMed

Park, Bongsoo; Park, Jongsun; Cheong, Kyeong-Chae; Choi, Jaeyoung; Jung, Kyongyong; Kim, Donghan; Lee, Yong-Hwan; Ward, Todd J; O'Donnell, Kerry; Geiser, David M; Kang, Seogchan

2011-01-01

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education.

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing

PubMed Central

Park, Bongsoo; Park, Jongsun; Cheong, Kyeong-Chae; Choi, Jaeyoung; Jung, Kyongyong; Kim, Donghan; Lee, Yong-Hwan; Ward, Todd J.; O'Donnell, Kerry; Geiser, David M.; Kang, Seogchan

2011-01-01

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education. PMID:21087991

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 agents effective against multiple toxins and viruses by host-oriented cell targeting.

PubMed

Zilbermintz, Leeor; Leonardi, William; Jeong, Sun-Young; Sjodt, Megan; McComb, Ryan; Ho, Chi-Lee C; Retterer, Cary; Gharaibeh, Dima; Zamani, Rouzbeh; Soloveva, Veronica; Bavari, Sina; Levitin, Anastasia; West, Joel; Bradley, Kenneth A; Clubb, Robert T; Cohen, Stanley N; Gupta, Vivek; Martchenko, Mikhail

2015-08-27

A longstanding and still-increasing threat to the effective treatment of infectious diseases is resistance to antimicrobial countermeasures. Potentially, the targeting of host proteins and pathways essential for the detrimental effects of pathogens offers an approach that may discover broad-spectrum anti-pathogen countermeasures and circumvent the effects of pathogen mutations leading to resistance. Here we report implementation of a strategy for discovering broad-spectrum host-oriented therapies against multiple pathogenic agents by multiplex screening of drugs for protection against the detrimental effects of multiple pathogens, identification of host cell pathways inhibited by the drug, and screening for effects of the agent on other pathogens exploiting the same pathway. We show that a clinically used antimalarial drug, Amodiaquine, discovered by this strategy, protects host cells against infection by multiple toxins and viruses by inhibiting host cathepsin B. Our results reveal the practicality of discovering broadly acting anti-pathogen countermeasures that target host proteins exploited by pathogens.

Association between ACE gene I/D polymorphism and clinical presentation and prognosis of sarcoidosis.

PubMed

Alía, P; Mañá, J; Capdevila, O; Alvarez, A; Navarro, M A

2005-01-01

Serum angiotensin converting enzyme (SACE) concentration is considered a marker of sarcoidosis activity. This concentration is influenced by an insertion/deletion (I/D) polymorphism of the ACE gene, such that SACE levels follow the pattern DD>ID>II. The aim of our work was to study the relationship between I/D polymorphism and susceptibility to sarcoidosis, as well as the relation between this polymorphism and the clinical presentation and evolution of the disease in 177 sarcoidosis patients. A group of 104 individuals without sarcoidosis was included as control. Genotyping was done by a polymerase chain reaction (PCR) method, and SACE concentration at diagnosis was determined by a kinetic method. No differences were observed in genotype or allele distributions between patients and controls, nor between patients considering the type of presentation (Löfgren versus non-Löfgren) and evolution of the disease (acute versus chronic). As reported for healthy populations, SACE concentrations followed the pattern DD>ID>II in sarcoidosis patients, but significant differences between genotypes existed only in the Löfgren group (p = 0.003) and in acute patients (p = 0.02). SACE concentrations at diagnosis were lower in acute patients (p = 0.05) and in Löfgren's syndrome (p = 0.04), but this seemed to occur only in ID individuals (p = 0.02 and p = 0.01, respectively). No relation was thus found between I/D polymorphism and susceptibility to sarcoidosis, but ACE I/D genotyping may improve the assessment of disease activity, both at diagnosis and during the follow-up of treated and untreated patients.

SubID, a non-median dichotomization tool for heterogeneous populations, reveals the pan-cancer significance of INPP4B and its regulation by EVI1 in AML.

PubMed

Dzneladze, Irakli; Woolley, John F; Rossell, Carla; Han, Youqi; Rashid, Ayesha; Jain, Michael; Reimand, Jüri; Minden, Mark D; Salmena, Leonardo

2018-01-01

Our previous studies demonstrated that INPP4B, a member of the PI3K/Akt signaling pathway, is overexpressed in a subset of AML patients and is associated with lower response to chemotherapy and shorter survival. INPP4B expression analysis in AML revealed a right skewed frequency distribution with 25% of patients expressing significantly higher levels than the majority. The 75% low/25% high cut-off revealed the prognostic power of INPP4B expression status in AML, which would not have been apparent with a standard median cut-off approach. Our identification of a clinically relevant non-median cut-off for INPP4B indicated a need for a generalizable non-median dichotomization approach to optimally study clinically relevant genes. To address this need, we developed Subgroup Identifier (SubID), a tool which examines the relationship between a continuous variable (e.g. gene expression), and a test parameter (e.g. CoxPH or Fisher's exact P values). In our study, Fisher's exact SubID was used to reveal EVI1 as a transcriptional regulator of INPP4B in AML; a finding which was validated in vitro. Next, we used CoxPH SubID to conduct a pan-cancer analysis of INPP4B's prognostic significance. Our analysis revealed that INPP4Blow is associated with shorter survival in kidney clear cell, liver hepatocellular, and bladder urothelial carcinomas. Conversely, INPP4Blow was shown to be associated with increased survival in pancreatic adenocarcinoma in three independent datasets. Overall, our study describes the development and application of a novel subgroup identification tool used to identify prognostically significant rare subgroups based upon gene expression, and for investigating the association between a gene with skewed frequency distribution and potentially important upstream and downstream genes that relate to the index gene.

SubID, a non-median dichotomization tool for heterogeneous populations, reveals the pan-cancer significance of INPP4B and its regulation by EVI1 in AML

PubMed Central

Han, Youqi; Rashid, Ayesha; Jain, Michael; Reimand, Jüri; Minden, Mark D.; Salmena, Leonardo

2018-01-01

Our previous studies demonstrated that INPP4B, a member of the PI3K/Akt signaling pathway, is overexpressed in a subset of AML patients and is associated with lower response to chemotherapy and shorter survival. INPP4B expression analysis in AML revealed a right skewed frequency distribution with 25% of patients expressing significantly higher levels than the majority. The 75% low/25% high cut-off revealed the prognostic power of INPP4B expression status in AML, which would not have been apparent with a standard median cut-off approach. Our identification of a clinically relevant non-median cut-off for INPP4B indicated a need for a generalizable non-median dichotomization approach to optimally study clinically relevant genes. To address this need, we developed Subgroup Identifier (SubID), a tool which examines the relationship between a continuous variable (e.g. gene expression), and a test parameter (e.g. CoxPH or Fisher’s exact P values). In our study, Fisher’s exact SubID was used to reveal EVI1 as a transcriptional regulator of INPP4B in AML; a finding which was validated in vitro. Next, we used CoxPH SubID to conduct a pan-cancer analysis of INPP4B’s prognostic significance. Our analysis revealed that INPP4Blow is associated with shorter survival in kidney clear cell, liver hepatocellular, and bladder urothelial carcinomas. Conversely, INPP4Blow was shown to be associated with increased survival in pancreatic adenocarcinoma in three independent datasets. Overall, our study describes the development and application of a novel subgroup identification tool used to identify prognostically significant rare subgroups based upon gene expression, and for investigating the association between a gene with skewed frequency distribution and potentially important upstream and downstream genes that relate to the index gene. PMID:29415082

Are the Conventional Commercial Yeast Identification Methods Still Helpful in the Era of New Clinical Microbiology Diagnostics? A Meta-Analysis of Their Accuracy

PubMed Central

Efremov, Ljupcho; Leoncini, Emanuele; Amore, Rosarita; Posteraro, Patrizia; Ricciardi, Walter

2015-01-01

Accurate identification of pathogenic species is important for early appropriate patient management, but growing diversity of infectious species/strains makes the identification of clinical yeasts increasingly difficult. Among conventional methods that are commercially available, the API ID32C, AuxaColor, and Vitek 2 systems are currently the most used systems in routine clinical microbiology. We performed a systematic review and meta-analysis to estimate and to compare the accuracy of the three systems, in order to assess whether they are still of value for the species-level identification of medically relevant yeasts. After adopting rigorous selection criteria, we included 26 published studies involving Candida and non-Candida yeasts that were tested with the API ID32C (674 isolates), AuxaColor (1,740 isolates), and Vitek 2 (2,853 isolates) systems. The random-effects pooled identification ratios at the species level were 0.89 (95% confidence interval [CI], 0.80 to 0.95) for the API ID32C system, 0.89 (95% CI, 0.83 to 0.93) for the AuxaColor system, and 0.93 (95% CI, 0.89 to 0.96) for the Vitek 2 system (P for heterogeneity, 0.255). Overall, the accuracy of studies using phenotypic analysis-based comparison methods was comparable to that of studies using molecular analysis-based comparison methods. Subanalysis of studies conducted on Candida yeasts showed that the Vitek 2 system was significantly more accurate (pooled ratio, 0.94 [95% CI, 0.85 to 0.99]) than the API ID32C system (pooled ratio, 0.84 [95% CI, 0.61 to 0.99]) and the AuxaColor system (pooled ratio, 0.76 [95% CI, 0.67 to 0.84]) with respect to uncommon species (P for heterogeneity, <0.05). Subanalysis of studies conducted on non-Candida yeasts (i.e., Cryptococcus, Rhodotorula, Saccharomyces, and Trichosporon) revealed pooled identification accuracies of ≥98% for the Vitek 2, API ID32C (excluding Cryptococcus), and AuxaColor (only Rhodotorula) systems, with significant low or null levels of

Are the Conventional Commercial Yeast Identification Methods Still Helpful in the Era of New Clinical Microbiology Diagnostics? A Meta-Analysis of Their Accuracy.

PubMed

Posteraro, Brunella; Efremov, Ljupcho; Leoncini, Emanuele; Amore, Rosarita; Posteraro, Patrizia; Ricciardi, Walter; Sanguinetti, Maurizio

2015-08-01

Accurate identification of pathogenic species is important for early appropriate patient management, but growing diversity of infectious species/strains makes the identification of clinical yeasts increasingly difficult. Among conventional methods that are commercially available, the API ID32C, AuxaColor, and Vitek 2 systems are currently the most used systems in routine clinical microbiology. We performed a systematic review and meta-analysis to estimate and to compare the accuracy of the three systems, in order to assess whether they are still of value for the species-level identification of medically relevant yeasts. After adopting rigorous selection criteria, we included 26 published studies involving Candida and non-Candida yeasts that were tested with the API ID32C (674 isolates), AuxaColor (1,740 isolates), and Vitek 2 (2,853 isolates) systems. The random-effects pooled identification ratios at the species level were 0.89 (95% confidence interval [CI], 0.80 to 0.95) for the API ID32C system, 0.89 (95% CI, 0.83 to 0.93) for the AuxaColor system, and 0.93 (95% CI, 0.89 to 0.96) for the Vitek 2 system (P for heterogeneity, 0.255). Overall, the accuracy of studies using phenotypic analysis-based comparison methods was comparable to that of studies using molecular analysis-based comparison methods. Subanalysis of studies conducted on Candida yeasts showed that the Vitek 2 system was significantly more accurate (pooled ratio, 0.94 [95% CI, 0.85 to 0.99]) than the API ID32C system (pooled ratio, 0.84 [95% CI, 0.61 to 0.99]) and the AuxaColor system (pooled ratio, 0.76 [95% CI, 0.67 to 0.84]) with respect to uncommon species (P for heterogeneity, <0.05). Subanalysis of studies conducted on non-Candida yeasts (i.e., Cryptococcus, Rhodotorula, Saccharomyces, and Trichosporon) revealed pooled identification accuracies of ≥98% for the Vitek 2, API ID32C (excluding Cryptococcus), and AuxaColor (only Rhodotorula) systems, with significant low or null levels of

39. CALCINER CELL PLANS. TOGETHER WITH HAER ID33C37 ILLUSTRATES COMPLEXITY ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

39. CALCINER CELL PLANS. TOGETHER WITH HAER ID-33-C-37 ILLUSTRATES COMPLEXITY OF PIPING. INEEL DRAWING NUMBER 200-0633-00-287-106445. FLUOR NUMBER 5775-CPP-633-P-50 - Idaho National Engineering Laboratory, Old Waste Calcining Facility, Scoville, Butte County, ID

Using Cell-ID 1.4 with R for Microscope-Based Cytometry

PubMed Central

Bush, Alan; Chernomoretz, Ariel; Yu, Richard; Gordon, Andrew

2012-01-01

This unit describes a method for quantifying various cellular features (e.g., volume, total and subcellular fluorescence localization) from sets of microscope images of individual cells. It includes procedures for tracking cells over time. One purposefully defocused transmission image (sometimes referred to as bright-field or BF) is acquired to segment the image and locate each cell. Fluorescent images (one for each of the color channels to be analyzed) are then acquired by conventional wide-field epifluorescence or confocal microscopy. This method uses the image processing capabilities of Cell-ID (Gordon et al., 2007, as updated here) and data analysis by the statistical programming framework R (R-Development-Team, 2008), which we have supplemented with a package of routines for analyzing Cell-ID output. Both Cell-ID and the analysis package are open-source. PMID:23026908

Identification of a pharmacological target for genioglossus reactivation throughout sleep.

PubMed

Grace, Kevin P; Hughes, Stuart W; Horner, Richard L

2014-01-01

Obstructive sleep apnea (OSA) is a significant public health problem caused by repeated episodes of upper airway closure that occur only during sleep. Attempts to treat OSA pharmacologically have been unsuccessful because there has not been identification of a target operating at cranial motor nuclei, blockade of which can reactivate pharyngeal muscle activity throughout sleep. Increasing potassium conductance is a common mechanism by which state-dependent neuromodulators reduce motoneuron excitability. Therefore, we aimed to determine if potassium channel blockade is an effective strategy to reactivate the pharyngeal musculature throughout sleep. In rats chronically instrumented for recording sleep-wake states and respiratory motor activities, we locally microperfused pharmacological agents into the hypoglossal motor pool to modulate potassium channels of three major classes: inwardly rectifying, two-pore domain, and voltage-gated. Microperfusion of the inwardly rectifying potassium channel blocker, barium, as well as the voltage-gated potassium channel blockers, tetraethylammonium and 4-aminopyridine, increased tonic and respiratory-related genioglossus activities throughout nonrapid eye movement (non-REM) and rapid eye movement (REM) sleep to 133-300% of levels present during baseline wakefulness. In contrast, microperfusion of methanandamide (TWIK-related acid-sensitive potassium [TASK] channel blocker/cannabinoid receptor agonist) activated genioglossus in wakefulness but not in sleep. These findings establish proof-of-principle that targeted blockade of certain potassium channels at the hypoglossal motor pool is an effective strategy for reversing upper airway hypotonia and causing sustained reactivation of genioglossus throughout nonrapid eye movement and rapid eye movement sleep. These findings identify an important new direction for translational approaches to the pharmacological treatment of obstructive sleep apnea.

Standoff chemical D and Id with extended LWIR hyperspectral imaging spectroradiometer

NASA Astrophysics Data System (ADS)

Prel, Florent; Moreau, Louis; Lavoie, Hugo; Bouffard, François; Thériault, Jean-Marc; Vallieres, Christian; Roy, Claude; Dubé, Denis

2013-05-01

Standoff detection and identification (D and Id) of unknown volatile chemicals such as chemical pollutants and consequences of industrial incidents has been increasingly desired for first responders and for environmental monitoring. On site gas detection sensors are commercially available and several of them can even detect more than one chemical species, however only few of them have the capabilities of detecting a wide variety of gases at long and safe distances. The ABB Hyperspectral Imaging Spectroradiometer (MR-i), configured for gas detection detects and identifies a wide variety of chemical species including toxic industrial chemicals (TICs) and surrogates several kilometers away from the sensor. This configuration is called iCATSI for improved Compact Atmospheric Sounding Interferometer. iCATSI is a standoff passive system. The modularity of the MR-i platform allows optimization of the detection configuration with a 256 x 256 Focal Plane Array imager or a line scanning imager both covering the long wave IR atmospheric window up to 14 μm. The uniqueness of its extended LWIR cut off enables to detect more chemicals as well as provide higher probability of detection than usual LWIR sensors.

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

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

Lessons Learned from Development of De-identification System for Biomedical Research in a Korean Tertiary Hospital.

PubMed

Shin, Soo-Yong; Lyu, Yongman; Shin, Yongdon; Choi, Hyo Joung; Park, Jihyun; Kim, Woo-Sung; Lee, Jae Ho

2013-06-01

The Korean government has enacted two laws, namely, the Personal Information Protection Act and the Bioethics and Safety Act to prevent the unauthorized use of medical information. To protect patients' privacy by complying with governmental regulations and improve the convenience of research, Asan Medical Center has been developing a de-identification system for biomedical research. We reviewed Korean regulations to define the scope of the de-identification methods and well-known previous biomedical research platforms to extract the functionalities of the systems. Based on these review results, we implemented necessary programs based on the Asan Medical Center Information System framework which was built using the Microsoft. NET Framework and C#. The developed de-identification system comprises three main components: a de-identification tool, a search tool, and a chart review tool. The de-identification tool can substitute a randomly assigned research ID for a hospital patient ID, remove the identifiers in the structured format, and mask them in the unstructured format, i.e., texts. This tool achieved 98.14% precision and 97.39% recall for 6,520 clinical notes. The search tool can find the number of patients which satisfies given search criteria. The chart review tool can provide de-identified patient's clinical data for review purposes. We found that a clinical data warehouse was essential for successful implementation of the de-identification system, and this system should be tightly linked to an electronic Institutional Review Board system for easy operation of honest brokers. Additionally, we found that a secure cloud environment could be adopted to protect patients' privacy more thoroughly.

Identification of highly effective target genes for RNAi-mediated control of emerald ash borer, Agrilus planipennis.

PubMed

Rodrigues, Thais B; Duan, Jian J; Palli, Subba R; Rieske, Lynne K

2018-03-22

Recent study has shown that RNA interference (RNAi) is efficient in emerald ash borer (EAB), Agrilus planipennis, and that ingestion of double-stranded RNA (dsRNA) targeting specific genes causes gene silencing and mortality in neonates. Here, we report on the identification of highly effective target genes for RNAi-mediated control of EAB. We screened 13 candidate genes in neonate larvae and selected the most effective target genes for further investigation, including their effect on EAB adults and on a non-target organism, Tribolium castaneum. The two most efficient target genes selected, hsp (heat shock 70-kDa protein cognate 3) and shi (shibire), caused up to 90% mortality of larvae and adults. In EAB eggs, larvae, and adults, the hsp is expressed at higher levels when compared to that of shi. Ingestion of dsHSP and dsSHI caused mortality in both neonate larvae and adults. Administration of a mixture of both dsRNAs worked better than either dsRNA by itself. In contrast, injection of EAB.dsHSP and EAB.dsSHI did not cause mortality in T. castaneum. Thus, the two genes identified cause high mortality in the EAB with no apparent phenotype effects in a non-target organism, the red flour beetle, and could be used in RNAi-mediated control of this invasive pest.

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.

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

Genetic modification of human B-cell development: B-cell development is inhibited by the dominant negative helix loop helix factor Id3.

PubMed

Jaleco, A C; Stegmann, A P; Heemskerk, M H; Couwenberg, F; Bakker, A Q; Weijer, K; Spits, H

1999-10-15

Transgenic and gene targeted mice have contributed greatly to our understanding of the mechanisms underlying B-cell development. We describe here a model system that allows us to apply molecular genetic techniques to the analysis of human B-cell development. We constructed a retroviral vector with a multiple cloning site connected to a gene encoding green fluorescent protein by an internal ribosomal entry site. Human CD34(+)CD38(-) fetal liver cells, cultured overnight in a combination of stem cell factor and interleukin-7 (IL-7), could be transduced with 30% efficiency. We ligated the gene encoding the dominant negative helix loop helix (HLH) factor Id3 that inhibits many enhancing basic HLH transcription factors into this vector. CD34(+)CD38(-) FL cells were transduced with Id3-IRES-GFP and cultured with the murine stromal cell line S17. In addition, we cultured the transduced cells in a reaggregate culture system with an SV-transformed human fibroblast cell line (SV19). It was observed that overexpression of Id3 inhibited development of B cells in both culture systems. B-cell development was arrested at a stage before expression of the IL-7Ralpha. The development of CD34(+)CD38(-) cells into CD14(+) myeloid cells in the S17 system was not inhibited by overexpression of Id3. Moreover, Id3(+) cells, although inhibited in their B-cell development, were still able to develop into natural killer (NK) cells when cultured in a combination of Flt-3L, IL-7, and IL-15. These findings confirm the essential role of bHLH factors in B-cell development and demonstrate the feasibility of retrovirus-mediated gene transfer as a tool to genetically modify human B-cell development.

Id1 suppresses anti-tumour immune responses and promotes tumour progression by impairing myeloid cell maturation.

PubMed

Papaspyridonos, Marianna; Matei, Irina; Huang, Yujie; do Rosario Andre, Maria; Brazier-Mitouart, Helene; Waite, Janelle C; Chan, April S; Kalter, Julie; Ramos, Ilyssa; Wu, Qi; Williams, Caitlin; Wolchok, Jedd D; Chapman, Paul B; Peinado, Hector; Anandasabapathy, Niroshana; Ocean, Allyson J; Kaplan, Rosandra N; Greenfield, Jeffrey P; Bromberg, Jacqueline; Skokos, Dimitris; Lyden, David

2015-04-29

A central mechanism of tumour progression and metastasis involves the generation of an immunosuppressive 'macroenvironment' mediated in part through tumour-secreted factors. Here we demonstrate that upregulation of the Inhibitor of Differentiation 1 (Id1), in response to tumour-derived factors, such as TGFβ, is responsible for the switch from dendritic cell (DC) differentiation to myeloid-derived suppressor cell expansion during tumour progression. Genetic inactivation of Id1 largely corrects the myeloid imbalance, whereas Id1 overexpression in the absence of tumour-derived factors re-creates it. Id1 overexpression leads to systemic immunosuppression by downregulation of key molecules involved in DC differentiation and suppression of CD8 T-cell proliferation, thus promoting primary tumour growth and metastatic progression. Furthermore, advanced melanoma patients have increased plasma TGFβ levels and express higher levels of ID1 in myeloid peripheral blood cells. This study reveals a critical role for Id1 in suppressing the anti-tumour immune response during tumour progression and metastasis.

Comparison between PGAA and ID-AMS analysis for determining chlorine content in whole rock basalt

NASA Astrophysics Data System (ADS)

di Nicola, L.; Schnabel, C.; Wilcken, K. M.; Gméling, K.

2009-04-01

Accurate determination of chlorine concentrations in terrestrial rocks is of importance for the interpretation of terrestrial in-situ cosmogenic 36Cl. Neutron capture by 35Cl, together with production from Ca and K, is one of the three major production pathways of 36Cl in rocks. Here, we present an inter-comparison of chlorine determinations by two procedures. The first approach is an independent Cl determination by prompt gamma (neutron) activation analysis (PGAA). The second method is isotope dilution based on isotopically-enriched stable chlorine carrier added during chemical sample preparation for accelerator mass spectrometry (ID-AMS). Twenty six (26) whole rock samples have been processed for PGAA and ID-AMS analyses. Elemental analysis by PGAA provides concentrations of major, minor and trace elements including the target elements for 36Cl production (K, Ca, Ti, and Fe), as well as of neutron absorbers and neutron moderators (H, B, Cl, Sm and Gd). The Cl concentrations determined during this study constitute the first inter-comparison for concentrations below 100 μCl/g. Our results show no significant difference in Cl concentrations between methods, and comparable uncertainties. This agreement guarantees that during the procedure we employ for whole rock sample no significant loss of stable chlorine from either the spike or the sample occurs before isotopic equilibration, prior to AgCl precipitation. Furthermore, we show that the elemental analysis by PGAA offers anadvance for the interpretation of 36Cl measurements. It allows simultaneous measurement of major and most trace element concentrations with a precision necessary for calculating the relative contributions to 36Cl production rates of the different mechanisms. Finally, the Cl concentration can be used to optimize the amount of isotopically-enriched spike for AMS-ID sample preparation for 36Cl.

RadNet Air Data From Idaho Falls, ID

EPA Pesticide Factsheets

This page presents radiation air monitoring and air filter analysis data for Idaho Falls, ID from EPA's RadNet system. RadNet is a nationwide network of monitoring stations that measure radiation in air, drinking water and precipitation.

Emotional System for Military Target Identification

DTIC Science & Technology

2009-10-01

algorithm [23], and used it to solve a facial recognition problem. In other works [24,25], we explored the potential of using emotional neural...other application areas, such as security ( facial recognition ) and medical (blood cell identification), can be also efficiently used in military...Application of an emotional neural network to facial recognition . Neural Computing and Applications, 18(4), 309-320. [25] Khashman, A. (2009). Blood cell

Rethinking Social Network Assessment for Students with Intellectual Disabilities (ID) in Postsecondary Education

ERIC Educational Resources Information Center

Eisenman, Laura T.; Farley-Ripple, Elizabeth; Culnane, Mary; Freedman, Brian

2013-01-01

Social networks of persons with intellectual disabilities (ID) have been characterized as smaller and less diverse than those of typical peers. Advocates have focused on strengthening those social networks by expanding circles of social support, protection, and friendship. As young adults with ID experience increasing levels of community…

Integrated Design System (IDS) Tools for the Spacecraft Aeroassist/Entry Vehicle Design Process

NASA Technical Reports Server (NTRS)

Olynick, David; Braun, Robert; Langhoff, Steven R. (Technical Monitor)

1997-01-01

The definition of the Integrated Design System technology focus area as presented in the NASA Information Technology center of excellence strategic plan is described. The need for IDS tools in the aeroassist/entry vehicle design process is illustrated. Initial and future plans for spacecraft IDS tool development are discussed.

Transcriptome-wide identification of Rauvolfia serpentina microRNAs and prediction of their potential targets.

PubMed

Prakash, Pravin; Rajakani, Raja; Gupta, Vikrant

2016-04-01

MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 19-24 nucleotides (nt) in length and considered as potent regulators of gene expression at transcriptional and post-transcriptional levels. Here we report the identification and characterization of 15 conserved miRNAs belonging to 13 families from Rauvolfia serpentina through in silico analysis of available nucleotide dataset. The identified mature R. serpentina miRNAs (rse-miRNAs) ranged between 20 and 22nt in length, and the average minimal folding free energy index (MFEI) value of rse-miRNA precursor sequences was found to be -0.815 kcal/mol. Using the identified rse-miRNAs as query, their potential targets were predicted in R. serpentina and other plant species. Gene Ontology (GO) annotation showed that predicted targets of rse-miRNAs include transcription factors as well as genes involved in diverse biological processes such as primary and secondary metabolism, stress response, disease resistance, growth, and development. Few rse-miRNAs were predicted to target genes of pharmaceutically important secondary metabolic pathways such as alkaloids and anthocyanin biosynthesis. Phylogenetic analysis showed the evolutionary relationship of rse-miRNAs and their precursor sequences to homologous pre-miRNA sequences from other plant species. The findings under present study besides giving first hand information about R. serpentina miRNAs and their targets, also contributes towards the better understanding of miRNA-mediated gene regulatory processes in plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identification of the major yeasts isolated from high moisture corn and corn silages in the United States using genetic and biochemical methods.

PubMed

Santos, M C; Golt, C; Joerger, R D; Mechor, G D; Mourão, Gerson B; Kung, L

2017-02-01

The objective of this study was to identify species of yeasts in samples of high moisture corn (HMC) and corn silage (CS) collected from farms throughout the United States. Samples were plated and colonies were isolated for identification using DNA analysis. Randomly selected colonies were also identified by fatty acid methyl esters (FAME) and by physiological substrate profiling (ID 32C). For CS, Candida ethanolica, Saccharomyces bulderi, Pichia anomala, Kazachstania unispora, and Saccharomyces cerevisiae were the predominant yeasts. Pichia anomala, Issatchenkia orientalis, S. cerevisiae, and Pichia fermentans were the prevalent species in HMC. The 3 identification methods were in agreement at the species level for 16.6% of the isolates and showed no agreement for 25.7%. Agreement in species identification between ID 32C and DNA analysis, FAME and ID 32C, and FAME and DNA analysis was 41.1, 14.4, and 2.2%, respectively. Pichia anomala and I. orientalis were able to grow on lactic acid, whereas S. cerevisiae metabolized sugars (galactose, sucrose, and glucose) but failed to use lactic acid. The yeast diversity in CS and HMC varied due to type of feed and location. Differences in species assignments were seen among methods, but identification using substrate profiling generally corresponded with that based on DNA analysis. These findings provide information about the species that may be expected in silages, and this knowledge may lead to interventions that control unwanted yeasts. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genomic identification of potential targets unique to Candida albicans for the discovery of antifungal agents.

PubMed

Tripathi, Himanshu; Luqman, Suaib; Meena, Abha; Khan, Feroz

2014-01-01

Despite of modern antifungal therapy, the mortality rates of invasive infection with human fungal pathogen Candida albicans are up to 40%. Studies suggest that drug resistance in the three most common species of human fungal pathogens viz., C. albicans, Aspergillus fumigatus (causing mortality rate up to 90%) and Cryptococcus neoformans (causing mortality rate up to 70%) is due to mutations in the target enzymes or high expression of drug transporter genes. Drug resistance in human fungal pathogens has led to an imperative need for the identification of new targets unique to fungal pathogens. In the present study, we have used a comparative genomics approach to find out potential target proteins unique to C. albicans, an opportunistic fungus responsible for severe infection in immune-compromised human. Interestingly, many target proteins of existing antifungal agents showed orthologs in human cells. To identify unique proteins, we have compared proteome of C. albicans [SC5314] i.e., 14,633 total proteins retrieved from the RefSeq database of NCBI, USA with proteome of human and non-pathogenic yeast Saccharomyces cerevisiae. Results showed that 4,568 proteins were identified unique to C. albicans as compared to those of human and later when these unique proteins were compared with S. cerevisiae proteome, finally 2,161 proteins were identified as unique proteins and after removing repeats total 1,618 unique proteins (42 functionally known, 1,566 hypothetical and 10 unknown) were selected as potential antifungal drug targets unique to C. albicans.

Motion-Based System Identification and Fault Detection and Isolation Technologies for Thruster Controlled Spacecraft

NASA Technical Reports Server (NTRS)

Wilson, Edward; Sutter, David W.; Berkovitz, Dustin; Betts, Bradley J.; Kong, Edmund; delMundo, Rommel; Lages, Christopher R.; Mah, Robert W.; Papasin, Richard

2003-01-01

By analyzing the motions of a thruster-controlled spacecraft, it is possible to provide on-line (1) thruster fault detection and isolation (FDI), and (2) vehicle mass- and thruster-property identification (ID). Technologies developed recently at NASA Ames have significantly improved the speed and accuracy of these ID and FDI capabilities, making them feasible for application to a broad class of spacecraft. Since these technologies use existing sensors, the improved system robustness and performance that comes with the thruster fault tolerance and system ID can be achieved through a software-only implementation. This contrasts with the added cost, mass, and hardware complexity commonly required by FDI. Originally developed in partnership with NASA - Johnson Space Center to provide thruster FDI capability for the X-38 during re-entry, these technologies are most recently being applied to the MIT SPHERES experimental spacecraft to fly on the International Space Station in 2004. The model-based FDI uses a maximum-likelihood calculation at its core, while the ID is based upon recursive least squares estimation. Flight test results from the SPHERES implementation, as flown aboard the NASA KC-1 35A 0-g simulator aircraft in November 2003 are presented.

Downregulation of Id1 by small interfering RNA in gastric cancer inhibits cell growth via the Akt pathway

PubMed Central

YANG, GUANG; ZHANG, YAN; XIONG, JIANJUN; WU, JING; YANG, CHANGFU; HUANG, HONGBING; ZHU, ZHENYU

2012-01-01

Inhibitor of differentiation or DNA binding (Id1) is a member of the helix-loop-helix transcription factor family that is overexpressed in various types of cancer, including gastric carcinoma. Previous studies showed that Id1 is a prognostic marker in patients with gastric cancer. However, the role of Id1 in the proliferation of human gastric cancer cells has yet to be clarified. In the present study, we downregulated the Id1 gene in SGC-7901 gastric cancer cells by RNA interference, and we also constructed a recombinant plasmid-expressing Id1 to investigate its effects on the proliferation of SGC-7901 cells. Results showed that the downregulation of Id1 inhibited proliferation of SGC-7901 cells, while the upregulation of Id1 had no effect on SGC-7901 cell proliferation. The potential mechanism was also investigated. The changes of certain proteins associated with cell proliferation, apoptosis and the cell cycle were detected by western blotting. Furthermore, we demonstrated a positive correlation between Id1 and phospho-Akt expression in SGC-7901 cells. PMID:22245935

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.

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.

Angiotensin-converting enzyme (ACE) I/D polymorphism is a risk factor of allergic rhinitis.

PubMed

Li, P; Cao, L; Han, X

2017-08-30

Some previous studies and meta-analysis investigated the association between ACE I/D polymorphism and allergic rhinitis risk. However, the results were conflicting. This meta-analysis, therefore, was performed to evaluate the association between ACE I/D polymorphism and allergic rhinitis risk. Online electronic databases (PubMed and EMBASE) were searched. The strength was evaluated by calculating the OR and 95% CI. Five studies were finally included in this meta-analysis. These studies included 681 cases and 629 controls. ACE I/D polymorphism was significantly associated with allergic rhinitis risk (OR = 1.17; 95% CI 1.07 - 1.29; P = 0.001). In the subgroup analysis of race, Asians showed the increased allergic rhinitis risk (OR = 1.15; 95% CI 1.02 - 1.30; P = 0.03). In a stratified analysis by age, adults with ACE I/D polymorphism showed the increased allergic rhinitis risk (OR = 1.16; 95% CI 1.04 - 1.29; P = 0.006). However, children did not have the significantly increased allergic rhinitis risk (OR = 1.24; 95% CI 0.99 - 1.56; P = 0.06). In conclusion, this meta-analysis indicated that ACE I/D polymorphism was significantly associated with allergic rhinitis risk.

Identification of plant glutaredoxin targets.

PubMed

Rouhier, Nicolas; Villarejo, Arsenio; Srivastava, Manoj; Gelhaye, Eric; Keech, Olivier; Droux, Michel; Finkemeier, Iris; Samuelsson, Göran; Dietz, Karl Josef; Jacquot, Jean-Pierre; Wingsle, Gunnar

2005-01-01

Glutaredoxins (Grxs) are small ubiquitous proteins of the thioredoxin (Trx) family, which catalyze dithiol-disulfide exchange reactions or reduce protein-mixed glutathione disulfides. In plants, several Trx-interacting proteins have been isolated from different compartments, whereas very few Grx-interacting proteins are known. We describe here the determination of Grx target proteins using a mutated poplar Grx, various tissular and subcellular plant extracts, and liquid chromatography coupled to tandem mass spectrometry detection. We have identified 94 putative targets, involved in many processes, including oxidative stress response [peroxiredoxins (Prxs), ascorbate peroxidase, catalase], nitrogen, sulfur, and carbon metabolisms (methionine synthase, alanine aminotransferase, phosphoglycerate kinase), translation (elongation factors E and Tu), or protein folding (heat shock protein 70). Some of these proteins were previously found to interact with Trx or to be glutathiolated in other organisms, but others could be more specific partners of Grx. To substantiate further these data, Grx was shown to support catalysis of the stroma beta-type carbonic anhydrase and Prx IIF of Arabidopsis thaliana, but not of poplar 2-Cys Prx. Overall, these data suggest that the interaction could occur randomly either with exposed cysteinyl disulfide bonds formed within or between target proteins or with mixed disulfides between a protein thiol and glutathione.

Detecting Autophagy and Autophagy Flux in Chronic Myeloid Leukemia Cells Using a Cyto-ID Fluorescence Spectrophotometric Assay.

PubMed

Guo, Sujuan; Pridham, Kevin J; Sheng, Zhi

2016-01-01

Autophagy is a catabolic process whereby cellular components are degraded to fuel cells for longer survival during stress. Hence, autophagy plays a vital role in determining cell fate and is central for homeostasis and pathogenesis of many human diseases including chronic myeloid leukemia (CML). It has been well established that autophagy is important for the leukemogenesis as well as drug resistance in CML. Thus, autophagy is an intriguing therapeutic target. However, current approaches that detect autophagy lack reliability and often fail to provide quantitative measurements. To overcome this hurdle and facilitate the development of autophagy-related therapies, we have recently developed an autophagy assay termed as the Cyto-ID fluorescence spectrophotometric assay. This method uses a cationic fluorescence dye, Cyto-ID, which specifically labels autophagic compartments and is detected by a spectrophotometer to permit a large-scale and quantitative analysis. As such, it allows rapid, reliable, and quantitative detection of autophagy and estimation of autophagy flux. In this chapter, we further provide technical details of this method and step-by-step protocols for measuring autophagy or autophagy flux in CML cell lines as well as primary hematopoietic cells.

[Comparison of different methods for the identification of Candida species isolated from clinical specimens].

PubMed

Cetinkaya, Zafer; Altindiş, Mustafa; Aktepe, Orhan Cem; Karabiçak, Nilgün

2003-10-01

The aim of this study was to compare the different methods for the identification of Candida strains isolated from clinical specimens. The methods of germ tube examination, chlamydospore examination formed on the rice Tween-80 (RT-80) agar and evaluation of colony morphologies on the two chromogenic agars (CHROMagar Candida, Albicans ID), were compared with a reference API 20C AUX (bioMerieux, France) automated system based on the carbohydrate assimilation, for the identification of a total 255 Candida isolates. Of them, 173 (67.8%) were identified as C. albicans, 37 (14.5%) were C. glabrata, 23 (9%) were C. krusei, 9 (3.5%) were C. tropicalis, 9 (3.5%) were C. kefyr, 2 (0.8%) were C. guillermondii and 2 (0.8%) were C. parapsilosis, by API 20C AUX system. In the view of these results, 146 (84.4%) of C. albicans strains were identified by germ tube examination, 161 (93.1%) of C. albicans strains and 208 (81.5%) of total strains were identified by chlamydospore examination. 169 (97.7%) of C. albicans strains and 231 (90.6%) of total strains were identified by CHROMagar Candida method, and 168 (97.1%) of C. albicans strains were identified by Albicans ID method, correctly. In the CHROMagar Candida medium, 169 C. albicans isolates have produced bright green colored colonies, whereas 33 (89.2%) isolates which produced dark pink/purple colored colonies were identified as C. glabrata, 7 (77.8%) isolates which produced metalical blue colored colonies were identified as C. tropicalis and 22 (95.6%) isolates which produced pale pink colored colonies were identified as C. krusei. In the Albicans ID medium, four of the 172 isolates which were evaluated as C. albicans initially by producing blue colored colonies, have been identified as C. tropicalis by API 20C AUX system. The sensitivities and specificities of germ tube examination, RT-80, CHROMagar Candida and Albicans ID methods were found as follows, respectively; 84.4% and 100%, 93.1% and 100%, 97.7% and 100%, 99.4% and 95

Negotiating roadblocks to IDS-physician equity joint ventures.

PubMed

Dubow, S F; Benoff, M

1998-09-01

Integrated delivery systems (IDSs) may find that forming an equity joint venture relationship with a physician group practice is the best way to integrate physicians into their networks. IDSs have a choice between two basic equity structures: affiliated group practice, in which a management services organization (MSO) handles all practice management infrastructure and the physician group is a physician-only organization; and integrated group practice, in which the physician group encompasses both the physician practice and the administrative infrastructure. The choice of equity structure and how it should be implemented hinge on several legal issues, including the existence of a corporate-practice-of-medicine statute in the IDS's state, compliance with the Federal antikickback statute and Stark laws, and various issues regarding the IDS's tax-exempt status. IDSs also should consider pragmatic issues, particularly those associated with aligning the economic incentives of the two partners.

Access Control for Mobile Assessment Systems Using ID.

PubMed

Nakayama, Masaharu; Ishii, Tadashi; Morino, Kazuma

2015-01-01

The assessment of shelters during disaster is critical to ensure the health of evacuees and prevent pandemic. In the Ishinomaki area, one of the areas most damaged by the Great East Japan Earthquake, the highly organized assessment helped to successfully manage a total of 328 shelters with a total of 46,480 evacuees. The input and analysis of vast amounts of data was tedious work for staff members. However, a web-based assessment system that utilized mobile devices was thought to decrease workload and standardize the evaluation form. The necessary access of information should be controlled in order to maintain individuals' privacy. We successfully developed an access control system using IDs. By utilizing a unique numerical ID, users can access the input form or assessment table. This avoids unnecessary queries to the server, resulting in a quick response and easy availability, even with poor internet connection.

Do we need a Unique Scientist ID for publications in biomedicine?

PubMed

Bohne-Lang, Andreas; Lang, Elke

2005-03-22

BACKGROUND: The PubMed database contains nearly 15 million references from more than 4,800 biomedical journals. In general, authors of scientific articles are addressed by their last name and forename initial. DISCUSSION: In general, names can be too common and not unique enough to be search criteria. Today, Ph.D. students, other researchers and women publish scientific work. A person may not only have one name but several names and publish under each name. A Unique Scientist ID could help to address people in peer-to-peer (P2P) networks. As a starting point, perhaps PubMed could generate and manage such a scientist ID. SUMMARY: A Unique Scientist ID would improve knowledge management in science. Unfortunately in some of the publications, and then within the online databases, only one letter abbreviates the author's forename. A common name with only one initial could retrieve pertinent citations, but include many false drops (retrieval matching searched criteria but indisputably irrelevant).

The Numbers Game: Phasing in Generated ID Numbers at the University of Oregon

ERIC Educational Resources Information Center

Eveland, Sue

2005-01-01

With all the recent headlines about security breaches and information loss at financial and educational institutions, the higher education community needs to address the issue of using social security numbers as ID numbers. The University of Oregon undertook a change process to assign generated ID numbers to all records in their information…

Cox-2-derived PGE2 induces Id1-dependent radiation resistance and self-renewal in experimental glioblastoma.

PubMed

Cook, Peter J; Thomas, Rozario; Kingsley, Philip J; Shimizu, Fumiko; Montrose, David C; Marnett, Lawrence J; Tabar, Viviane S; Dannenberg, Andrew J; Benezra, Robert

2016-10-01

In glioblastoma (GBM), Id1 serves as a functional marker for self-renewing cancer stem-like cells. We investigated the mechanism by which cyclooxygenase-2 (Cox-2)-derived prostaglandin E2 (PGE2) induces Id1 and increases GBM self-renewal and radiation resistance. Mouse and human GBM cells were stimulated with dimethyl-PGE2 (dmPGE2), a stabilized form of PGE2, to test for Id1 induction. To elucidate the signal transduction pathway governing the increase in Id1, a combination of short interfering RNA knockdown and small molecule inhibitors and activators of PGE2 signaling were used. Western blotting, quantitative real-time (qRT)-PCR, and chromatin immunoprecipitation assays were employed. Sphere formation and radiation resistance were measured in cultured primary cells. Immunohistochemical analyses were carried out to evaluate the Cox-2-Id1 axis in experimental GBM. In GBM cells, dmPGE2 stimulates the EP4 receptor leading to activation of ERK1/2 MAPK. This leads, in turn, to upregulation of the early growth response1 (Egr1) transcription factor and enhanced Id1 expression. Activation of this pathway increases self-renewal capacity and resistance to radiation-induced DNA damage, which are dependent on Id1. In GBM, Cox-2-derived PGE2 induces Id1 via EP4-dependent activation of MAPK signaling and the Egr1 transcription factor. PGE2-mediated induction of Id1 is required for optimal tumor cell self-renewal and radiation resistance. Collectively, these findings identify Id1 as a key mediator of PGE2-dependent modulation of radiation response and lend insight into the mechanisms underlying radiation resistance in GBM patients. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing

PubMed Central

Redin, Claire; Gérard, Bénédicte; Lauer, Julia; Herenger, Yvan; Muller, Jean; Quartier, Angélique; Masurel-Paulet, Alice; Willems, Marjolaine; Lesca, Gaétan; El-Chehadeh, Salima; Le Gras, Stéphanie; Vicaire, Serge; Philipps, Muriel; Dumas, Michaël; Geoffroy, Véronique; Feger, Claire; Haumesser, Nicolas; Alembik, Yves; Barth, Magalie; Bonneau, Dominique; Colin, Estelle; Dollfus, Hélène; Doray, Bérénice; Delrue, Marie-Ange; Drouin-Garraud, Valérie; Flori, Elisabeth; Fradin, Mélanie; Francannet, Christine; Goldenberg, Alice; Lumbroso, Serge; Mathieu-Dramard, Michèle; Martin-Coignard, Dominique; Lacombe, Didier; Morin, Gilles; Polge, Anne; Sukno, Sylvie; Thauvin-Robinet, Christel; Thevenon, Julien; Doco-Fenzy, Martine; Genevieve, David; Sarda, Pierre; Edery, Patrick; Isidor, Bertrand; Jost, Bernard; Olivier-Faivre, Laurence; Mandel, Jean-Louis; Piton, Amélie

2014-01-01

Background Intellectual disability (ID) is characterised by an extreme genetic heterogeneity. Several hundred genes have been associated to monogenic forms of ID, considerably complicating molecular diagnostics. Trio-exome sequencing was recently proposed as a diagnostic approach, yet remains costly for a general implementation. Methods We report the alternative strategy of targeted high-throughput sequencing of 217 genes in which mutations had been reported in patients with ID or autism as the major clinical concern. We analysed 106 patients with ID of unknown aetiology following array-CGH analysis and other genetic investigations. Ninety per cent of these patients were males, and 75% sporadic cases. Results We identified 26 causative mutations: 16 in X-linked genes (ATRX, CUL4B, DMD, FMR1, HCFC1, IL1RAPL1, IQSEC2, KDM5C, MAOA, MECP2, SLC9A6, SLC16A2, PHF8) and 10 de novo in autosomal-dominant genes (DYRK1A, GRIN1, MED13L, TCF4, RAI1, SHANK3, SLC2A1, SYNGAP1). We also detected four possibly causative mutations (eg, in NLGN3) requiring further investigations. We present detailed reasoning for assigning causality for each mutation, and associated patients’ clinical information. Some genes were hit more than once in our cohort, suggesting they correspond to more frequent ID-associated conditions (KDM5C, MECP2, DYRK1A, TCF4). We highlight some unexpected genotype to phenotype correlations, with causative mutations being identified in genes associated to defined syndromes in patients deviating from the classic phenotype (DMD, TCF4, MECP2). We also bring additional supportive (HCFC1, MED13L) or unsupportive (SHROOM4, SRPX2) evidences for the implication of previous candidate genes or mutations in cognitive disorders. Conclusions With a diagnostic yield of 25% targeted sequencing appears relevant as a first intention test for the diagnosis of ID, but importantly will also contribute to a better understanding regarding the specific contribution of the many genes

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.

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

Culture-Independent Identification of Periodontitis-Associated Porphyromonas and Tannerella Populations by Targeted Molecular Analysis

PubMed Central

de Lillo, A.; Booth, V.; Kyriacou, L.; Weightman, A. J.; Wade, W. G.

2004-01-01

Periodontitis is the commonest bacterial disease of humans and is the major cause of adult tooth loss. About half of the oral microflora is unculturable; and 16S rRNA PCR, cloning, and sequencing techniques have demonstrated the high level of species richness of the oral microflora. In the present study, a PCR primer set specific for the genera Porphyromonas and Tannerella was designed and used to analyze the bacterial populations in subgingival plaque samples from inflamed shallow and deep sites in subjects with periodontitis and shallow sites in age- and sex-matched controls. A total of 308 clones were sequenced and found to belong to one of six Porphyromonas or Tannerella species or phylotypes, one of which, Porphyromonas P3, was novel. Tannerella forsythensis was found in significantly higher proportions in patients than in controls. Porphyromonas catoniae and Tannerella phylotype BU063 appeared to be associated with shallow sites. Targeted culture-independent molecular ecology studies have a valuable role to play in the identification of bacterial targets for further investigations of the pathogenesis of bacterial infections. PMID:15583276

Identification of gram-negative bacilli using the Autobac IDX.

PubMed

Burdash, N M; Welborn, A L; Teti, G; Bannister, E R; Manos, J P

1985-01-01

The Autobac IDX is a new system for the rapid identification of clinically significant members of the Enterobacteriaceae and Aeromonas, Acinetobacter, Alcaligenes, Flavobacterium, Moraxella, and Pseudomonas species. The use of 18 differentially inhibitory compounds such as dyes and antibiotics along with a computerized algorithm based on a multivariate analysis provides the basis for the identification of 30 different groups of gram-negative bacilli. Required preliminary tests include observations on the presence or absence of swarming on a sheep blood agar plate and noting the following: growth, lactose fermentation, and bile precipitation from a MacConkey plate. Spot indole and spot oxidase tests must be performed as well. Identification by the Autobac IDX System takes 3-6 hr after completion of the preliminary tests. From a total of 403 isolates tested, the Autobac system agreed with the MicroID AND N/F systems on 382 identifications (94.8%). Four isolates, two Acinetobacter anitratus, one Serratia marcescens and one Moraxella osloensis could not be identified by IDX. Additional testing was required on 35 (8.7%) of the isolates.

Lessons Learned from Development of De-identification System for Biomedical Research in a Korean Tertiary Hospital

PubMed Central

Shin, Soo-Yong; Lyu, Yongman; Shin, Yongdon; Choi, Hyo Joung; Park, Jihyun; Kim, Woo-Sung

2013-01-01

Objectives The Korean government has enacted two laws, namely, the Personal Information Protection Act and the Bioethics and Safety Act to prevent the unauthorized use of medical information. To protect patients' privacy by complying with governmental regulations and improve the convenience of research, Asan Medical Center has been developing a de-identification system for biomedical research. Methods We reviewed Korean regulations to define the scope of the de-identification methods and well-known previous biomedical research platforms to extract the functionalities of the systems. Based on these review results, we implemented necessary programs based on the Asan Medical Center Information System framework which was built using the Microsoft. NET Framework and C#. Results The developed de-identification system comprises three main components: a de-identification tool, a search tool, and a chart review tool. The de-identification tool can substitute a randomly assigned research ID for a hospital patient ID, remove the identifiers in the structured format, and mask them in the unstructured format, i.e., texts. This tool achieved 98.14% precision and 97.39% recall for 6,520 clinical notes. The search tool can find the number of patients which satisfies given search criteria. The chart review tool can provide de-identified patient's clinical data for review purposes. Conclusions We found that a clinical data warehouse was essential for successful implementation of the de-identification system, and this system should be tightly linked to an electronic Institutional Review Board system for easy operation of honest brokers. Additionally, we found that a secure cloud environment could be adopted to protect patients' privacy more thoroughly. PMID:23882415

Identification of Novel Pax8 Targets in FRTL-5 Thyroid Cells by Gene Silencing and Expression Microarray Analysis

PubMed Central

Di Palma, Tina; Conti, Anna; de Cristofaro, Tiziana; Scala, Serena; Nitsch, Lucio; Zannini, Mariastella

2011-01-01

Background The differentiation program of thyroid follicular cells (TFCs), by far the most abundant cell population of the thyroid gland, relies on the interplay between sequence-specific transcription factors and transcriptional coregulators with the basal transcriptional machinery of the cell. However, the molecular mechanisms leading to the fully differentiated thyrocyte are still the object of intense study. The transcription factor Pax8, a member of the Paired-box gene family, has been demonstrated to be a critical regulator required for proper development and differentiation of thyroid follicular cells. Despite being Pax8 well-characterized with respect to its role in regulating genes involved in thyroid differentiation, genomics approaches aiming at the identification of additional Pax8 targets are lacking and the biological pathways controlled by this transcription factor are largely unknown. Methodology/Principal Findings To identify unique downstream targets of Pax8, we investigated the genome-wide effect of Pax8 silencing comparing the transcriptome of silenced versus normal differentiated FRTL-5 thyroid cells. In total, 2815 genes were found modulated 72 h after Pax8 RNAi, induced or repressed. Genes previously reported to be regulated by Pax8 in FRTL-5 cells were confirmed. In addition, novel targets genes involved in functional processes such as DNA replication, anion transport, kinase activity, apoptosis and cellular processes were newly identified. Transcriptome analysis highlighted that Pax8 is a key molecule for thyroid morphogenesis and differentiation. Conclusions/Significance This is the first large-scale study aimed at the identification of new genes regulated by Pax8, a master regulator of thyroid development and differentiation. The biological pathways and target genes controlled by Pax8 will have considerable importance to understand thyroid disease progression as well as to set up novel therapeutic strategies. PMID:21966443

Identification of a novel LMF1 nonsense mutation responsible for severe hypertriglyceridemia by targeted next-generation sequencing.

PubMed