Distributed Adaptive Binary Quantization for Fast Nearest Neighbor Search.

PubMed

Xianglong Liu; Zhujin Li; Cheng Deng; Dacheng Tao

2017-11-01

Hashing has been proved an attractive technique for fast nearest neighbor search over big data. Compared with the projection based hashing methods, prototype-based ones own stronger power to generate discriminative binary codes for the data with complex intrinsic structure. However, existing prototype-based methods, such as spherical hashing and K-means hashing, still suffer from the ineffective coding that utilizes the complete binary codes in a hypercube. To address this problem, we propose an adaptive binary quantization (ABQ) method that learns a discriminative hash function with prototypes associated with small unique binary codes. Our alternating optimization adaptively discovers the prototype set and the code set of a varying size in an efficient way, which together robustly approximate the data relations. Our method can be naturally generalized to the product space for long hash codes, and enjoys the fast training linear to the number of the training data. We further devise a distributed framework for the large-scale learning, which can significantly speed up the training of ABQ in the distributed environment that has been widely deployed in many areas nowadays. The extensive experiments on four large-scale (up to 80 million) data sets demonstrate that our method significantly outperforms state-of-the-art hashing methods, with up to 58.84% performance gains relatively.

Visual search asymmetries within color-coded and intensity-coded displays.

PubMed

Yamani, Yusuke; McCarley, Jason S

2010-06-01

Color and intensity coding provide perceptual cues to segregate categories of objects within a visual display, allowing operators to search more efficiently for needed information. Even within a perceptually distinct subset of display elements, however, it may often be useful to prioritize items representing urgent or task-critical information. The design of symbology to produce search asymmetries (Treisman & Souther, 1985) offers a potential technique for doing this, but it is not obvious from existing models of search that an asymmetry observed in the absence of extraneous visual stimuli will persist within a complex color- or intensity-coded display. To address this issue, in the current study we measured the strength of a visual search asymmetry within displays containing color- or intensity-coded extraneous items. The asymmetry persisted strongly in the presence of extraneous items that were drawn in a different color (Experiment 1) or a lower contrast (Experiment 2) than the search-relevant items, with the targets favored by the search asymmetry producing highly efficient search. The asymmetry was attenuated but not eliminated when extraneous items were drawn in a higher contrast than search-relevant items (Experiment 3). Results imply that the coding of symbology to exploit visual search asymmetries can facilitate visual search for high-priority items even within color- or intensity-coded displays. PsycINFO Database Record (c) 2010 APA, all rights reserved.

76 FR 11432 - Coding of Design Marks in Registrations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-02

... on the old paper search designations. The USPTO will continue to code all pending applications that... system, the Trademark Search Facility Classification Code Index (``TC Index''), stems from its... infrequent use of the TC Index codes in searches by the public; and its costliness to maintain, especially in...

ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite

PubMed Central

2010-01-01

Background Successful application of crosslinking combined with mass spectrometry for studying proteins and protein complexes requires specifically-designed crosslinking reagents, experimental techniques, and data analysis software. Using isotopically-coded ("heavy and light") versions of the crosslinker and cleavable crosslinking reagents is analytically advantageous for mass spectrometric applications and provides a "handle" that can be used to distinguish crosslinked peptides of different types, and to increase the confidence of the identification of the crosslinks. Results Here, we describe a program suite designed for the analysis of mass spectrometric data obtained with isotopically-coded cleavable crosslinkers. The suite contains three programs called: DX, DXDX, and DXMSMS. DX searches the mass spectra for the presence of ion signal doublets resulting from the light and heavy isotopic forms of the isotopically-coded crosslinking reagent used. DXDX searches for possible mass matches between cleaved and uncleaved isotopically-coded crosslinks based on the established chemistry of the cleavage reaction for a given crosslinking reagent. DXMSMS assigns the crosslinks to the known protein sequences, based on the isotopically-coded and un-coded MS/MS fragmentation data of uncleaved and cleaved peptide crosslinks. Conclusion The combination of these three programs, which are tailored to the analytical features of the specific isotopically-coded cleavable crosslinking reagents used, represents a powerful software tool for automated high-accuracy peptide crosslink identification. See: http://www.creativemolecules.com/CM_Software.htm PMID:20109223

Incidence and trends of central line associated pneumothorax using radiograph report text search versus administrative database codes.

PubMed

Reeson, Marc; Forster, Alan; van Walraven, Carl

2018-05-25

Central line associated pneumothorax (CLAP) could be a good quality of care indicator because they are objectively measured, clearly undesirable and possibly avoidable. We measured the incidence and trends of CLAP using radiograph report text search with manual review and compared them with measures using routinely collected health administrative data. For each hospitalisation to a tertiary care teaching hospital between 2002 and 2015, we searched all chest radiography reports for a central line with a sensitive computer algorithm. Screen positive reports were manually reviewed to confirm central lines. The index and subsequent chest radiography reports were screened for pneumothorax followed by manual confirmation. Diagnostic and procedural codes were used to identify CLAP in administrative data. In 685 044 hospitalisations, 10 819 underwent central line insertion (1.6%) with CLAP occurring 181 times (1.7%). CLAP risk did not change over time. Codes for CLAP were inaccurate (sensitivity 13.8%, positive predictive value 6.6%). However, overall code-based CLAP risk (1.8%) was almost identical to actual values possibly because patient strata with inflated CLAP risk were balanced by more common strata having underestimated CLAP risk. Code-based methods inflated central line incidence 2.2 times and erroneously concluded that CLAP risk decreased significantly over time. Using valid methods, CLAP incidence was similar to those in the literature but has not changed over time. Although administrative database codes for CLAP were very inaccurate, they generated CLAP risks very similar to actual values because of offsetting errors. In contrast to those from radiograph report text search with manual review, CLAP trends decreased significantly using administrative data. Hospital CLAP risk should not be measured using administrative data. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Pattern-based integer sample motion search strategies in the context of HEVC

NASA Astrophysics Data System (ADS)

Maier, Georg; Bross, Benjamin; Grois, Dan; Marpe, Detlev; Schwarz, Heiko; Veltkamp, Remco C.; Wiegand, Thomas

2015-09-01

The H.265/MPEG-H High Efficiency Video Coding (HEVC) standard provides a significant increase in coding efficiency compared to its predecessor, the H.264/MPEG-4 Advanced Video Coding (AVC) standard, which however comes at the cost of a high computational burden for a compliant encoder. Motion estimation (ME), which is a part of the inter-picture prediction process, typically consumes a high amount of computational resources, while significantly increasing the coding efficiency. In spite of the fact that both H.265/MPEG-H HEVC and H.264/MPEG-4 AVC standards allow processing motion information on a fractional sample level, the motion search algorithms based on the integer sample level remain to be an integral part of ME. In this paper, a flexible integer sample ME framework is proposed, thereby allowing to trade off significant reduction of ME computation time versus coding efficiency penalty in terms of bit rate overhead. As a result, through extensive experimentation, an integer sample ME algorithm that provides a good trade-off is derived, incorporating a combination and optimization of known predictive, pattern-based and early termination techniques. The proposed ME framework is implemented on a basis of the HEVC Test Model (HM) reference software, further being compared to the state-of-the-art fast search algorithm, which is a native part of HM. It is observed that for high resolution sequences, the integer sample ME process can be speed-up by factors varying from 3.2 to 7.6, resulting in the bit-rate overhead of 1.5% and 0.6% for Random Access (RA) and Low Delay P (LDP) configurations, respectively. In addition, the similar speed-up is observed for sequences with mainly Computer-Generated Imagery (CGI) content while trading off the bit rate overhead of up to 5.2%.

State of the States 2016: Arts Education State Policy Summary

ERIC Educational Resources Information Center

Aragon, Stephanie

2016-01-01

The "State of the States 2016" summarizes state policies for arts education identified in statute or administrative code for all 50 states and the District of Columbia. Information is based on a comprehensive search of state education statute and codes on each state's relevant websites. Complete results from this review are available in…

Electrode channel selection based on backtracking search optimization in motor imagery brain-computer interfaces.

PubMed

Dai, Shengfa; Wei, Qingguo

2017-01-01

Common spatial pattern algorithm is widely used to estimate spatial filters in motor imagery based brain-computer interfaces. However, use of a large number of channels will make common spatial pattern tend to over-fitting and the classification of electroencephalographic signals time-consuming. To overcome these problems, it is necessary to choose an optimal subset of the whole channels to save computational time and improve the classification accuracy. In this paper, a novel method named backtracking search optimization algorithm is proposed to automatically select the optimal channel set for common spatial pattern. Each individual in the population is a N-dimensional vector, with each component representing one channel. A population of binary codes generate randomly in the beginning, and then channels are selected according to the evolution of these codes. The number and positions of 1's in the code denote the number and positions of chosen channels. The objective function of backtracking search optimization algorithm is defined as the combination of classification error rate and relative number of channels. Experimental results suggest that higher classification accuracy can be achieved with much fewer channels compared to standard common spatial pattern with whole channels.

Sub-Selective Quantization for Learning Binary Codes in Large-Scale Image Search.

PubMed

Li, Yeqing; Liu, Wei; Huang, Junzhou

2018-06-01

Recently with the explosive growth of visual content on the Internet, large-scale image search has attracted intensive attention. It has been shown that mapping high-dimensional image descriptors to compact binary codes can lead to considerable efficiency gains in both storage and performing similarity computation of images. However, most existing methods still suffer from expensive training devoted to large-scale binary code learning. To address this issue, we propose a sub-selection based matrix manipulation algorithm, which can significantly reduce the computational cost of code learning. As case studies, we apply the sub-selection algorithm to several popular quantization techniques including cases using linear and nonlinear mappings. Crucially, we can justify the resulting sub-selective quantization by proving its theoretic properties. Extensive experiments are carried out on three image benchmarks with up to one million samples, corroborating the efficacy of the sub-selective quantization method in terms of image retrieval.

A GIS-based Quantitative Approach for the Search of Clandestine Graves, Italy.

PubMed

Somma, Roberta; Cascio, Maria; Silvestro, Massimiliano; Torre, Eliana

2018-05-01

Previous research on the RAG color-coded prioritization systems for the discovery of clandestine graves has not considered all the factors influencing the burial site choice within a GIS project. The goal of this technical note was to discuss a GIS-based quantitative approach for the search of clandestine graves. The method is based on cross-referenced RAG maps with cumulative suitability factors to host a burial, leading to the editing of different search scenarios for ground searches showing high-(Red), medium-(Amber), and low-(Green) priority areas. The application of this procedure allowed several outcomes to be determined: If the concealment occurs at night, then the "search scenario without the visibility" will be the most effective one; if the concealment occurs in daylight, then the "search scenario with the DSM-based visibility" will be most appropriate; the different search scenarios may be cross-referenced with offender's confessions and eyewitnesses' testimonies to verify the veracity of their statements. © 2017 American Academy of Forensic Sciences.

Underestimated prevalence of heart failure in hospital inpatients: a comparison of ICD codes and discharge letter information.

PubMed

Kaspar, Mathias; Fette, Georg; Güder, Gülmisal; Seidlmayer, Lea; Ertl, Maximilian; Dietrich, Georg; Greger, Helmut; Puppe, Frank; Störk, Stefan

2018-04-17

Heart failure is the predominant cause of hospitalization and amongst the leading causes of death in Germany. However, accurate estimates of prevalence and incidence are lacking. Reported figures originating from different information sources are compromised by factors like economic reasons or documentation quality. We implemented a clinical data warehouse that integrates various information sources (structured parameters, plain text, data extracted by natural language processing) and enables reliable approximations to the real number of heart failure patients. Performance of ICD-based diagnosis in detecting heart failure was compared across the years 2000-2015 with (a) advanced definitions based on algorithms that integrate various sources of the hospital information system, and (b) a physician-based reference standard. Applying these methods for detecting heart failure in inpatients revealed that relying on ICD codes resulted in a marked underestimation of the true prevalence of heart failure, ranging from 44% in the validation dataset to 55% (single year) and 31% (all years) in the overall analysis. Percentages changed over the years, indicating secular changes in coding practice and efficiency. Performance was markedly improved using search and permutation algorithms from the initial expert-specified query (F1 score of 81%) to the computer-optimized query (F1 score of 86%) or, alternatively, optimizing precision or sensitivity depending on the search objective. Estimating prevalence of heart failure using ICD codes as the sole data source yielded unreliable results. Diagnostic accuracy was markedly improved using dedicated search algorithms. Our approach may be transferred to other hospital information systems.

Evaluating the protein coding potential of exonized transposable element sequences

PubMed Central

Piriyapongsa, Jittima; Rutledge, Mark T; Patel, Sanil; Borodovsky, Mark; Jordan, I King

2007-01-01

Background Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS) and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons. Results We compared the ability of three classes of sequence similarity search methods to detect TE-derived sequences among data sets of experimentally characterized proteins: 1-a profile-based hidden Markov model (HMM) approach, 2-BLAST methods and 3-RepeatMasker. Profile based methods are more sensitive and more selective than the other methods evaluated. However, the application of profile-based search methods to the detection of TE-derived sequences among well-curated experimentally characterized protein data sets did not turn up many more cases than had been previously detected and nowhere near as many cases as recent genome-wide searches have. We observed that the different search methods used were complementary in the sense that they yielded largely non-overlapping sets of hits and differed in their ability to recover known cases of TE-derived CDS. The probabilistic analysis of TE-derived exon sequences indicates that these sequences have low protein coding potential on average. In particular, non-autonomous TEs that do not encode protein sequences, such as Alu elements, are frequently exonized but unlikely to encode protein sequences. Conclusion The exaptation of the numerous TE sequences found in exons as bona fide protein coding sequences may prove to be far less common than has been suggested by the analysis of complete genomes. We hypothesize that many exonized TE sequences actually function as post-transcriptional regulators of gene expression, rather than coding sequences, which may act through a variety of double stranded RNA related regulatory pathways. Indeed, their relatively high copy numbers and similarity to sequences dispersed throughout the genome suggests that exonized TE sequences could serve as master regulators with a wide scope of regulatory influence. Reviewers: This article was reviewed by Itai Yanai, Kateryna D. Makova, Melissa Wilson (nominated by Kateryna D. Makova) and Cedric Feschotte (nominated by John M. Logsdon Jr.). PMID:18036258

A loosely coupled framework for terminology controlled distributed EHR search for patient cohort identification in clinical research.

PubMed

Zhao, Lei; Lim Choi Keung, Sarah N; Taweel, Adel; Tyler, Edward; Ogunsina, Ire; Rossiter, James; Delaney, Brendan C; Peterson, Kevin A; Hobbs, F D Richard; Arvanitis, Theodoros N

2012-01-01

Heterogeneous data models and coding schemes for electronic health records present challenges for automated search across distributed data sources. This paper describes a loosely coupled software framework based on the terminology controlled approach to enable the interoperation between the search interface and heterogeneous data sources. Software components interoperate via common terminology service and abstract criteria model so as to promote component reuse and incremental system evolution.

Kangaroo – A pattern-matching program for biological sequences

PubMed Central

2002-01-01

Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats. PMID:12150718

Error control techniques for satellite and space communications

NASA Technical Reports Server (NTRS)

Costello, Daniel J., Jr.

1992-01-01

Worked performed during the reporting period is summarized. Construction of robustly good trellis codes for use with sequential decoding was developed. The robustly good trellis codes provide a much better trade off between free distance and distance profile. The unequal error protection capabilities of convolutional codes was studied. The problem of finding good large constraint length, low rate convolutional codes for deep space applications is investigated. A formula for computing the free distance of 1/n convolutional codes was discovered. Double memory (DM) codes, codes with two memory units per unit bit position, were studied; a search for optimal DM codes is being conducted. An algorithm for constructing convolutional codes from a given quasi-cyclic code was developed. Papers based on the above work are included in the appendix.

MedlinePlus Connect: Web Application

MedlinePlus

... will result in a query to the MedlinePlus search engine. If you specify a code and the name/ ... system or problem code, will use the MedlinePlus search engine (English only): https://connect.medlineplus.gov/application?mainSearchCriteria. ...

A hardware-oriented concurrent TZ search algorithm for High-Efficiency Video Coding

NASA Astrophysics Data System (ADS)

Doan, Nghia; Kim, Tae Sung; Rhee, Chae Eun; Lee, Hyuk-Jae

2017-12-01

High-Efficiency Video Coding (HEVC) is the latest video coding standard, in which the compression performance is double that of its predecessor, the H.264/AVC standard, while the video quality remains unchanged. In HEVC, the test zone (TZ) search algorithm is widely used for integer motion estimation because it effectively searches the good-quality motion vector with a relatively small amount of computation. However, the complex computation structure of the TZ search algorithm makes it difficult to implement it in the hardware. This paper proposes a new integer motion estimation algorithm which is designed for hardware execution by modifying the conventional TZ search to allow parallel motion estimations of all prediction unit (PU) partitions. The algorithm consists of the three phases of zonal, raster, and refinement searches. At the beginning of each phase, the algorithm obtains the search points required by the original TZ search for all PU partitions in a coding unit (CU). Then, all redundant search points are removed prior to the estimation of the motion costs, and the best search points are then selected for all PUs. Compared to the conventional TZ search algorithm, experimental results show that the proposed algorithm significantly decreases the Bjøntegaard Delta bitrate (BD-BR) by 0.84%, and it also reduces the computational complexity by 54.54%.

A Measure of Search Efficiency in a Real World Search Task (PREPRINT)

DTIC Science & Technology

2009-02-16

Search Task 5a. CONTRACT NUMBER N00173-08-1-G030 5b. GRANT NUMBER NRL BAA 08-09, 55-07-01 5c. PROGRAM ELEMENT NUMBER 0602782N 6. AUTHOR(S... Beck , Melissa R. Ph.D (LSU) Maura C. Lohrenz (NRL Code 7440.1) J. Gregory Trafton (NRL Code 5515) 5d. PROJECT NUMBER 08294 5e. TASK NUMBER... Beck 19b. TELEPHONE NUMBER (Include area code) (225)578-7214 Standard Form 298 (Rev. 8/98) Prescribed by ANSI Std. Z39.18 A measure of search

New interactive CESAR

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

Fox, P.B.; Yatabe, M.

1987-01-01

The Nuclear Criticality Safety Analytical Methods Resource Center announces the availability of a new interactive version of CESAR, a critical experiments storage and retrieval program available on the Nuclear Criticality Information System (NCIS) data base at Lawrence Livermore National Laboratory. The original version of CESAR did not include interactive search capabilities. The CESAR data base was developed to provide a convenient, readily accessible means of storing and retrieving code input data for the SCALE criticality safety analytical sequences and the codes comprising those sequences. The data base includes data for both cross-section preparation and criticality safety calculations.

Flexible patient information search and retrieval framework: pilot implementation

NASA Astrophysics Data System (ADS)

Erdal, Selnur; Catalyurek, Umit V.; Saltz, Joel; Kamal, Jyoti; Gurcan, Metin N.

2007-03-01

Medical centers collect and store significant amount of valuable data pertaining to patients' visit in the form of medical free-text. In addition, standardized diagnosis codes (International Classification of Diseases, Ninth Revision, Clinical Modification: ICD9-CM) related to those dictated reports are usually available. In this work, we have created a framework where image searches could be initiated through a combination of free-text reports as well as ICD9 codes. This framework enables more comprehensive search on existing large sets of patient data in a systematic way. The free text search is enriched by computer-aided inclusion of additional search terms enhanced by a thesaurus. This combination of enriched search allows users to access to a larger set of relevant results from a patient-centric PACS in a simpler way. Therefore, such framework is of particular use in tasks such as gathering images for desired patient populations, building disease models, and so on. As the motivating application of our framework, we implemented a search engine. This search engine processed two years of patient data from the OSU Medical Center's Information Warehouse and identified lung nodule location information using a combination of UMLS Meta-Thesaurus enhanced text report searches along with ICD9 code searches on patients that have been discharged. Five different queries with various ICD9 codes involving lung cancer were carried out on 172552 cases. Each search was completed under a minute on average per ICD9 code and the inclusion of UMLS thesaurus increased the number of relevant cases by 45% on average.

What is the prevalence of health-related searches on the World Wide Web? Qualitative and quantitative analysis of search engine queries on the Internet

PubMed Central

Eysenbach, G.; Kohler, Ch.

2003-01-01

While health information is often said to be the most sought after information on the web, empirical data on the actual frequency of health-related searches on the web are missing. In the present study we aimed to determine the prevalence of health-related searches on the web by analyzing search terms entered by people into popular search engines. We also made some preliminary attempts in qualitatively describing and classifying these searches. Occasional difficulties in determining what constitutes a “health-related” search led us to propose and validate a simple method to automatically classify a search string as “health-related”. This method is based on determining the proportion of pages on the web containing the search string and the word “health”, as a proportion of the total number of pages with the search string alone. Using human codings as gold standard we plotted a ROC curve and determined empirically that if this “co-occurance rate” is larger than 35%, the search string can be said to be health-related (sensitivity: 85.2%, specificity 80.4%). The results of our “human” codings of search queries determined that about 4.5% of all searches are “health-related”. We estimate that globally a minimum of 6.75 Million health-related searches are being conducted on the web every day, which is roughly the same number of searches that have been conducted on the NLM Medlars system in 1996 in a full year. PMID:14728167

Real-time speech encoding based on Code-Excited Linear Prediction (CELP)

NASA Technical Reports Server (NTRS)

Leblanc, Wilfrid P.; Mahmoud, S. A.

1988-01-01

This paper reports on the work proceeding with regard to the development of a real-time voice codec for the terrestrial and satellite mobile radio environments. The codec is based on a complexity reduced version of code-excited linear prediction (CELP). The codebook search complexity was reduced to only 0.5 million floating point operations per second (MFLOPS) while maintaining excellent speech quality. Novel methods to quantize the residual and the long and short term model filters are presented.

Constructions for finite-state codes

NASA Technical Reports Server (NTRS)

Pollara, F.; Mceliece, R. J.; Abdel-Ghaffar, K.

1987-01-01

A class of codes called finite-state (FS) codes is defined and investigated. These codes, which generalize both block and convolutional codes, are defined by their encoders, which are finite-state machines with parallel inputs and outputs. A family of upper bounds on the free distance of a given FS code is derived from known upper bounds on the minimum distance of block codes. A general construction for FS codes is then given, based on the idea of partitioning a given linear block into cosets of one of its subcodes, and it is shown that in many cases the FS codes constructed in this way have a d sub free which is as large as possible. These codes are found without the need for lengthy computer searches, and have potential applications for future deep-space coding systems. The issue of catastropic error propagation (CEP) for FS codes is also investigated.

Robust hashing with local models for approximate similarity search.

PubMed

Song, Jingkuan; Yang, Yi; Li, Xuelong; Huang, Zi; Yang, Yang

2014-07-01

Similarity search plays an important role in many applications involving high-dimensional data. Due to the known dimensionality curse, the performance of most existing indexing structures degrades quickly as the feature dimensionality increases. Hashing methods, such as locality sensitive hashing (LSH) and its variants, have been widely used to achieve fast approximate similarity search by trading search quality for efficiency. However, most existing hashing methods make use of randomized algorithms to generate hash codes without considering the specific structural information in the data. In this paper, we propose a novel hashing method, namely, robust hashing with local models (RHLM), which learns a set of robust hash functions to map the high-dimensional data points into binary hash codes by effectively utilizing local structural information. In RHLM, for each individual data point in the training dataset, a local hashing model is learned and used to predict the hash codes of its neighboring data points. The local models from all the data points are globally aligned so that an optimal hash code can be assigned to each data point. After obtaining the hash codes of all the training data points, we design a robust method by employing l2,1 -norm minimization on the loss function to learn effective hash functions, which are then used to map each database point into its hash code. Given a query data point, the search process first maps it into the query hash code by the hash functions and then explores the buckets, which have similar hash codes to the query hash code. Extensive experimental results conducted on real-life datasets show that the proposed RHLM outperforms the state-of-the-art methods in terms of search quality and efficiency.

An optimization program based on the method of feasible directions: Theory and users guide

NASA Technical Reports Server (NTRS)

Belegundu, Ashok D.; Berke, Laszlo; Patnaik, Surya N.

1994-01-01

The theory and user instructions for an optimization code based on the method of feasible directions are presented. The code was written for wide distribution and ease of attachment to other simulation software. Although the theory of the method of feasible direction was developed in the 1960's, many considerations are involved in its actual implementation as a computer code. Included in the code are a number of features to improve robustness in optimization. The search direction is obtained by solving a quadratic program using an interior method based on Karmarkar's algorithm. The theory is discussed focusing on the important and often overlooked role played by the various parameters guiding the iterations within the program. Also discussed is a robust approach for handling infeasible starting points. The code was validated by solving a variety of structural optimization test problems that have known solutions obtained by other optimization codes. It has been observed that this code is robust: it has solved a variety of problems from different starting points. However, the code is inefficient in that it takes considerable CPU time as compared with certain other available codes. Further work is required to improve its efficiency while retaining its robustness.

Application of grammar-based codes for lossless compression of digital mammograms

NASA Astrophysics Data System (ADS)

Li, Xiaoli; Krishnan, Srithar; Ma, Ngok-Wah

2006-01-01

A newly developed grammar-based lossless source coding theory and its implementation was proposed in 1999 and 2000, respectively, by Yang and Kieffer. The code first transforms the original data sequence into an irreducible context-free grammar, which is then compressed using arithmetic coding. In the study of grammar-based coding for mammography applications, we encountered two issues: processing time and limited number of single-character grammar G variables. For the first issue, we discover a feature that can simplify the matching subsequence search in the irreducible grammar transform process. Using this discovery, an extended grammar code technique is proposed and the processing time of the grammar code can be significantly reduced. For the second issue, we propose to use double-character symbols to increase the number of grammar variables. Under the condition that all the G variables have the same probability of being used, our analysis shows that the double- and single-character approaches have the same compression rates. By using the methods proposed, we show that the grammar code can outperform three other schemes: Lempel-Ziv-Welch (LZW), arithmetic, and Huffman on compression ratio, and has similar error tolerance capabilities as LZW coding under similar circumstances.

Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability.

PubMed

Santos, José; Monteagudo, Ángel

2017-03-27

The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutation adverse effect as the main selection factor in the evolution of the code. We have used simulated evolution in a computer to search for optimized codes, which helps to obtain information about the optimization level of the canonical code in its evolution. A genetic algorithm searches for efficient codes in a fitness landscape that corresponds with the adaptability of possible hypothetical genetic codes. The lower the effects of errors or mutations in the codon bases of a hypothetical code, the more efficient or optimal is that code. The inclusion of the fitness sharing technique in the evolutionary algorithm allows the extent to which the canonical genetic code is in an area corresponding to a deep local minimum to be easily determined, even in the high dimensional spaces considered. The analyses show that the canonical code is not in a deep local minimum and that the fitness landscape is not a multimodal fitness landscape with deep and separated peaks. Moreover, the canonical code is clearly far away from the areas of higher fitness in the landscape. Given the non-presence of deep local minima in the landscape, although the code could evolve and different forces could shape its structure, the fitness landscape nature considered in the error minimization theory does not explain why the canonical code ended its evolution in a location which is not an area of a localized deep minimum of the huge fitness landscape.

A systematic review of validated methods to capture acute bronchospasm using administrative or claims data.

PubMed

Sharifi, Mona; Krishanswami, Shanthi; McPheeters, Melissa L

2013-12-30

To identify and assess billing, procedural, or diagnosis code, or pharmacy claim-based algorithms used to identify acute bronchospasm in administrative and claims databases. We searched the MEDLINE database from 1991 to September 2012 using controlled vocabulary and key terms related to bronchospasm, wheeze and acute asthma. We also searched the reference lists of included studies. Two investigators independently assessed the full text of studies against pre-determined inclusion criteria. Two reviewers independently extracted data regarding participant and algorithm characteristics. Our searches identified 677 citations of which 38 met our inclusion criteria. In these 38 studies, the most commonly used ICD-9 code was 493.x. Only 3 studies reported any validation methods for the identification of bronchospasm, wheeze or acute asthma in administrative and claims databases; all were among pediatric populations and only 2 offered any validation statistics. Some of the outcome definitions utilized were heterogeneous and included other disease based diagnoses, such as bronchiolitis and pneumonia, which are typically of an infectious etiology. One study offered the validation of algorithms utilizing Emergency Department triage chief complaint codes to diagnose acute asthma exacerbations with ICD-9 786.07 (wheezing) revealing the highest sensitivity (56%), specificity (97%), PPV (93.5%) and NPV (76%). There is a paucity of studies reporting rigorous methods to validate algorithms for the identification of bronchospasm in administrative data. The scant validated data available are limited in their generalizability to broad-based populations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fast Exact Search in Hamming Space With Multi-Index Hashing.

PubMed

Norouzi, Mohammad; Punjani, Ali; Fleet, David J

2014-06-01

There is growing interest in representing image data and feature descriptors using compact binary codes for fast near neighbor search. Although binary codes are motivated by their use as direct indices (addresses) into a hash table, codes longer than 32 bits are not being used as such, as it was thought to be ineffective. We introduce a rigorous way to build multiple hash tables on binary code substrings that enables exact k-nearest neighbor search in Hamming space. The approach is storage efficient and straight-forward to implement. Theoretical analysis shows that the algorithm exhibits sub-linear run-time behavior for uniformly distributed codes. Empirical results show dramatic speedups over a linear scan baseline for datasets of up to one billion codes of 64, 128, or 256 bits.

PIPI: PTM-Invariant Peptide Identification Using Coding Method.

PubMed

Yu, Fengchao; Li, Ning; Yu, Weichuan

2016-12-02

In computational proteomics, the identification of peptides with an unlimited number of post-translational modification (PTM) types is a challenging task. The computational cost associated with database search increases exponentially with respect to the number of modified amino acids and linearly with respect to the number of potential PTM types at each amino acid. The problem becomes intractable very quickly if we want to enumerate all possible PTM patterns. To address this issue, one group of methods named restricted tools (including Mascot, Comet, and MS-GF+) only allow a small number of PTM types in database search process. Alternatively, the other group of methods named unrestricted tools (including MS-Alignment, ProteinProspector, and MODa) avoids enumerating PTM patterns with an alignment-based approach to localizing and characterizing modified amino acids. However, because of the large search space and PTM localization issue, the sensitivity of these unrestricted tools is low. This paper proposes a novel method named PIPI to achieve PTM-invariant peptide identification. PIPI belongs to the category of unrestricted tools. It first codes peptide sequences into Boolean vectors and codes experimental spectra into real-valued vectors. For each coded spectrum, it then searches the coded sequence database to find the top scored peptide sequences as candidates. After that, PIPI uses dynamic programming to localize and characterize modified amino acids in each candidate. We used simulation experiments and real data experiments to evaluate the performance in comparison with restricted tools (i.e., Mascot, Comet, and MS-GF+) and unrestricted tools (i.e., Mascot with error tolerant search, MS-Alignment, ProteinProspector, and MODa). Comparison with restricted tools shows that PIPI has a close sensitivity and running speed. Comparison with unrestricted tools shows that PIPI has the highest sensitivity except for Mascot with error tolerant search and ProteinProspector. These two tools simplify the task by only considering up to one modified amino acid in each peptide, which results in a higher sensitivity but has difficulty in dealing with multiple modified amino acids. The simulation experiments also show that PIPI has the lowest false discovery proportion, the highest PTM characterization accuracy, and the shortest running time among the unrestricted tools.

Clinician search behaviors may be influenced by search engine design.

PubMed

Lau, Annie Y S; Coiera, Enrico; Zrimec, Tatjana; Compton, Paul

2010-06-30

Searching the Web for documents using information retrieval systems plays an important part in clinicians' practice of evidence-based medicine. While much research focuses on the design of methods to retrieve documents, there has been little examination of the way different search engine capabilities influence clinician search behaviors. Previous studies have shown that use of task-based search engines allows for faster searches with no loss of decision accuracy compared with resource-based engines. We hypothesized that changes in search behaviors may explain these differences. In all, 75 clinicians (44 doctors and 31 clinical nurse consultants) were randomized to use either a resource-based or a task-based version of a clinical information retrieval system to answer questions about 8 clinical scenarios in a controlled setting in a university computer laboratory. Clinicians using the resource-based system could select 1 of 6 resources, such as PubMed; clinicians using the task-based system could select 1 of 6 clinical tasks, such as diagnosis. Clinicians in both systems could reformulate search queries. System logs unobtrusively capturing clinicians' interactions with the systems were coded and analyzed for clinicians' search actions and query reformulation strategies. The most frequent search action of clinicians using the resource-based system was to explore a new resource with the same query, that is, these clinicians exhibited a "breadth-first" search behaviour. Of 1398 search actions, clinicians using the resource-based system conducted 401 (28.7%, 95% confidence interval [CI] 26.37-31.11) in this way. In contrast, the majority of clinicians using the task-based system exhibited a "depth-first" search behavior in which they reformulated query keywords while keeping to the same task profiles. Of 585 search actions conducted by clinicians using the task-based system, 379 (64.8%, 95% CI 60.83-68.55) were conducted in this way. This study provides evidence that different search engine designs are associated with different user search behaviors.

Searching the Social Sciences Citation Index on BRS.

ERIC Educational Resources Information Center

Janke, Richard V.

1980-01-01

Concentrates on describing and illustrating by example the unique BRS features of the online Social Sciences Citation Index. Appendices provide a key to the BRS/SSCI citation elements, BRS standardized language codes, publication type codes, author's classification of BRS/SSCI subject category codes, search examples, and database specifications.…

CodeSlinger: a case study in domain-driven interactive tool design for biomedical coding scheme exploration and use.

PubMed

Flowers, Natalie L

2010-01-01

CodeSlinger is a desktop application that was developed to aid medical professionals in the intertranslation, exploration, and use of biomedical coding schemes. The application was designed to provide a highly intuitive, easy-to-use interface that simplifies a complex business problem: a set of time-consuming, laborious tasks that were regularly performed by a group of medical professionals involving manually searching coding books, searching the Internet, and checking documentation references. A workplace observation session with a target user revealed the details of the current process and a clear understanding of the business goals of the target user group. These goals drove the design of the application's interface, which centers on searches for medical conditions and displays the codes found in the application's database that represent those conditions. The interface also allows the exploration of complex conceptual relationships across multiple coding schemes.

Extracting information from the text of electronic medical records to improve case detection: a systematic review

PubMed Central

Carroll, John A; Smith, Helen E; Scott, Donia; Cassell, Jackie A

2016-01-01

Background Electronic medical records (EMRs) are revolutionizing health-related research. One key issue for study quality is the accurate identification of patients with the condition of interest. Information in EMRs can be entered as structured codes or unstructured free text. The majority of research studies have used only coded parts of EMRs for case-detection, which may bias findings, miss cases, and reduce study quality. This review examines whether incorporating information from text into case-detection algorithms can improve research quality. Methods A systematic search returned 9659 papers, 67 of which reported on the extraction of information from free text of EMRs with the stated purpose of detecting cases of a named clinical condition. Methods for extracting information from text and the technical accuracy of case-detection algorithms were reviewed. Results Studies mainly used US hospital-based EMRs, and extracted information from text for 41 conditions using keyword searches, rule-based algorithms, and machine learning methods. There was no clear difference in case-detection algorithm accuracy between rule-based and machine learning methods of extraction. Inclusion of information from text resulted in a significant improvement in algorithm sensitivity and area under the receiver operating characteristic in comparison to codes alone (median sensitivity 78% (codes + text) vs 62% (codes), P = .03; median area under the receiver operating characteristic 95% (codes + text) vs 88% (codes), P = .025). Conclusions Text in EMRs is accessible, especially with open source information extraction algorithms, and significantly improves case detection when combined with codes. More harmonization of reporting within EMR studies is needed, particularly standardized reporting of algorithm accuracy metrics like positive predictive value (precision) and sensitivity (recall). PMID:26911811

Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding.

PubMed

Palkowski, Marek; Bielecki, Wlodzimierz

2018-01-15

RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunately, RNA secondary structure approaches, such as Nussinov's recurrence, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. This allows us to apply powerful polyhedral compilation techniques based on the transitive closure of dependence graphs to generate parallel tiled code implementing Nussinov's RNA folding. Such techniques are within the iteration space slicing framework - the transitive dependences are applied to the statement instances of interest to produce valid tiles. The main problem at generating parallel tiled code is defining a proper tile size and tile dimension which impact parallelism degree and code locality. To choose the best tile size and tile dimension, we first construct parallel parametric tiled code (parameters are variables defining tile size). With this purpose, we first generate two nonparametric tiled codes with different fixed tile sizes but with the same code structure and then derive a general affine model, which describes all integer factors available in expressions of those codes. Using this model and known integer factors present in the mentioned expressions (they define the left-hand side of the model), we find unknown integers in this model for each integer factor available in the same fixed tiled code position and replace in this code expressions, including integer factors, with those including parameters. Then we use this parallel parametric tiled code to implement the well-known tile size selection (TSS) technique, which allows us to discover in a given search space the best tile size and tile dimension maximizing target code performance. For a given search space, the presented approach allows us to choose the best tile size and tile dimension in parallel tiled code implementing Nussinov's RNA folding. Experimental results, received on modern Intel multi-core processors, demonstrate that this code outperforms known closely related implementations when the length of RNA strands is bigger than 2500.

Mindfulness-Based Approaches in the Treatment of Disordered Gambling: A Systematic Review and Meta-Analysis

ERIC Educational Resources Information Center

Maynard, Brandy R.; Wilson, Alyssa N.; Labuzienski, Elizabeth; Whiting, Seth W.

2018-01-01

Background and Aims: To examine the effects of mindfulness-based interventions on gambling behavior and symptoms, urges, and financial outcomes. Method: Systematic review and meta-analytic procedures were employed to search, select, code, and analyze studies conducted between 1980 and 2014, assessing the effects of mindfulness-based interventions…

The inclusion of disability as a condition for termination of parental rights.

PubMed

Lightfoot, Elizabeth; Hill, Katharine; LaLiberte, Traci

2010-12-01

All 50 states and the District of Columbia have statutes outlining the grounds for terminating parental rights (TPR) in relation to child abuse and neglect. Although recent research has found that parents with disabilities are not more likely to maltreat their children than parents without disabilities (Glaun & Brown, 1999; Oyserman, Mowbray, Meares, & Firminger, 2000), studies have found very high rates of TPR of parents with disabilities (Accardo & Whitman, 1989). The objective of this study is to examine how states are including disability in their TPR statutes. This study used legal document analysis, consisting of a comprehensive Boolean search of the state codes of the 50 states and District of Columbia (DC) relating to TPR, using the most recent state code available on Lexis-Nexis in August 2005. TPR and related statutes were searched for contemporary and historical disability related terms and their common cognates, such as: "mental," "disability," "handicap," and "incapacity." Two researchers independently conducted the searches, and the searches were reconciled. A code list was then developed to measure for inclusion of disability, preciseness, scope, use of language, and references to accessibility or fairness. Statutes were then reanalyzed, and groupings developed. Thirty-seven states included disability-related grounds for termination of parental rights, while 14 states did not include disability language as grounds for termination. Many of these state codes used outdated terminology, imprecise definitions, and emphasized disability status rather than behavior. All of the 14 states that do not include disability in TPR grounds allowed for termination based on neglectful parental behavior that may be influenced by a disability. The use of disability language in TPR statutes can put an undue focus on the condition of having a disability, rather than parenting behavior. This paper recommends that states consider removing disability language from their statutes, as such language risks taking the emphasis away from the assessment based on parenting behavior. Copyright © 2010 Elsevier Ltd. All rights reserved.

Visual Search Asymmetries within Color-Coded and Intensity-Coded Displays

ERIC Educational Resources Information Center

Yamani, Yusuke; McCarley, Jason S.

2010-01-01

Color and intensity coding provide perceptual cues to segregate categories of objects within a visual display, allowing operators to search more efficiently for needed information. Even within a perceptually distinct subset of display elements, however, it may often be useful to prioritize items representing urgent or task-critical information.…

Hierarchical content-based image retrieval by dynamic indexing and guided search

NASA Astrophysics Data System (ADS)

You, Jane; Cheung, King H.; Liu, James; Guo, Linong

2003-12-01

This paper presents a new approach to content-based image retrieval by using dynamic indexing and guided search in a hierarchical structure, and extending data mining and data warehousing techniques. The proposed algorithms include: a wavelet-based scheme for multiple image feature extraction, the extension of a conventional data warehouse and an image database to an image data warehouse for dynamic image indexing, an image data schema for hierarchical image representation and dynamic image indexing, a statistically based feature selection scheme to achieve flexible similarity measures, and a feature component code to facilitate query processing and guide the search for the best matching. A series of case studies are reported, which include a wavelet-based image color hierarchy, classification of satellite images, tropical cyclone pattern recognition, and personal identification using multi-level palmprint and face features.

Fast neutron counting in a mobile, trailer-based search platform

NASA Astrophysics Data System (ADS)

Hayward, Jason P.; Sparger, John; Fabris, Lorenzo; Newby, Robert J.

2017-12-01

Trailer-based search platforms for detection of radiological and nuclear threats are often based upon coded aperture gamma-ray imaging, because this method can be rendered insensitive to local variations in gamma background while still localizing the source well. Since gamma source emissions are rather easily shielded, in this work we consider the addition of fast neutron counting to a mobile platform for detection of sources containing Pu. A proof-of-concept system capable of combined gamma and neutron coded-aperture imaging was built inside of a trailer and used to detect a 252Cf source while driving along a roadway. Neutron detector types employed included EJ-309 in a detector plane and EJ-299-33 in a front mask plane. While the 252Cf gamma emissions were not readily detectable while driving by at 16.9 m standoff, the neutron emissions can be detected while moving. Mobile detection performance for this system and a scaled-up system design are presented, along with implications for threat sensing.

Using clinician text notes in electronic medical record data to validate transgender-related diagnosis codes.

PubMed

Blosnich, John R; Cashy, John; Gordon, Adam J; Shipherd, Jillian C; Kauth, Michael R; Brown, George R; Fine, Michael J

2018-04-04

Transgender individuals are vulnerable to negative health risks and outcomes, but research remains limited because data sources, such as electronic medical records (EMRs), lack standardized collection of gender identity information. Most EMR do not include the gold standard of self-identified gender identity, but International Classification of Diseases (ICDs) includes diagnostic codes indicating transgender-related clinical services. However, it is unclear if these codes can indicate transgender status. The objective of this study was to determine the extent to which patients' clinician notes in EMR contained transgender-related terms that could corroborate ICD-coded transgender identity. Data are from the US Department of Veterans Affairs Corporate Data Warehouse. Transgender patients were defined by the presence of ICD9 and ICD10 codes associated with transgender-related clinical services, and a 3:1 comparison group of nontransgender patients was drawn. Patients' clinician text notes were extracted and searched for transgender-related words and phrases. Among 7560 patients defined as transgender based on ICD codes, the search algorithm identified 6753 (89.3%) with transgender-related terms. Among 22 072 patients defined as nontransgender without ICD codes, 246 (1.1%) had transgender-related terms; after review, 11 patients were identified as transgender, suggesting a 0.05% false negative rate. Using ICD-defined transgender status can facilitate health services research when self-identified gender identity data are not available in EMR.

On models of the genetic code generated by binary dichotomic algorithms.

PubMed

Gumbel, Markus; Fimmel, Elena; Danielli, Alberto; Strüngmann, Lutz

2015-02-01

In this paper we introduce the concept of a BDA-generated model of the genetic code which is based on binary dichotomic algorithms (BDAs). A BDA-generated model is based on binary dichotomic algorithms (BDAs). Such a BDA partitions the set of 64 codons into two disjoint classes of size 32 each and provides a generalization of known partitions like the Rumer dichotomy. We investigate what partitions can be generated when a set of different BDAs is applied sequentially to the set of codons. The search revealed that these models are able to generate code tables with very different numbers of classes ranging from 2 to 64. We have analyzed whether there are models that map the codons to their amino acids. A perfect matching is not possible. However, we present models that describe the standard genetic code with only few errors. There are also models that map all 64 codons uniquely to 64 classes showing that BDAs can be used to identify codons precisely. This could serve as a basis for further mathematical analysis using coding theory, for example. The hypothesis that BDAs might reflect a molecular mechanism taking place in the decoding center of the ribosome is discussed. The scan demonstrated that binary dichotomic partitions are able to model different aspects of the genetic code very well. The search was performed with our tool Beady-A. This software is freely available at http://mi.informatik.hs-mannheim.de/beady-a. It requires a JVM version 6 or higher. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Evaluation of a visual layering methodology for colour coding control room displays.

PubMed

Van Laar, Darren; Deshe, Ofer

2002-07-01

Eighteen people participated in an experiment in which they were asked to search for targets on control room like displays which had been produced using three different coding methods. The monochrome coding method displayed the information in black and white only, the maximally discriminable method contained colours chosen for their high perceptual discriminability, the visual layers method contained colours developed from psychological and cartographic principles which grouped information into a perceptual hierarchy. The visual layers method produced significantly faster search times than the other two coding methods which did not differ significantly from each other. Search time also differed significantly for presentation order and for the method x order interaction. There was no significant difference between the methods in the number of errors made. Participants clearly preferred the visual layers coding method. Proposals are made for the design of experiments to further test and develop the visual layers colour coding methodology.

Multipath search coding of stationary signals with applications to speech

NASA Astrophysics Data System (ADS)

Fehn, H. G.; Noll, P.

1982-04-01

This paper deals with the application of multipath search coding (MSC) concepts to the coding of stationary memoryless and correlated sources, and of speech signals, at a rate of one bit per sample. Use is made of three MSC classes: (1) codebook coding, or vector quantization, (2) tree coding, and (3) trellis coding. This paper explains the performances of these coders and compares them both with those of conventional coders and with rate-distortion bounds. The potentials of MSC coding strategies are demonstrated by illustrations. The paper reports also on results of MSC coding of speech, where both the strategy of adaptive quantization and of adaptive prediction were included in coder design.

Discrete Cosine Transform Image Coding With Sliding Block Codes

NASA Astrophysics Data System (ADS)

Divakaran, Ajay; Pearlman, William A.

1989-11-01

A transform trellis coding scheme for images is presented. A two dimensional discrete cosine transform is applied to the image followed by a search on a trellis structured code. This code is a sliding block code that utilizes a constrained size reproduction alphabet. The image is divided into blocks by the transform coding. The non-stationarity of the image is counteracted by grouping these blocks in clusters through a clustering algorithm, and then encoding the clusters separately. Mandela ordered sequences are formed from each cluster i.e identically indexed coefficients from each block are grouped together to form one dimensional sequences. A separate search ensues on each of these Mandela ordered sequences. Padding sequences are used to improve the trellis search fidelity. The padding sequences absorb the error caused by the building up of the trellis to full size. The simulations were carried out on a 256x256 image ('LENA'). The results are comparable to any existing scheme. The visual quality of the image is enhanced considerably by the padding and clustering.

The Open Spectral Database: an open platform for sharing and searching spectral data.

PubMed

Chalk, Stuart J

2016-01-01

A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data is compressed in the JCAMP-DX file. What is needed is a single resource that allows submission of JCAMP-DX files, export of the raw data in multiple formats, searching based on multiple chemical identifiers, and is open in terms of license and access. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is now available. Built using open source tools, using open code (hosted on GitHub), providing open data, and open to community input about design and functionality, the OSDB is available for anyone to submit spectral data, making it searchable and available to the scientific community. This paper details the concept and coding, internal architecture, export formats, Representational State Transfer (REST) Application Programming Interface and options for submission of data. The OSDB website went live in November 2015. Concurrently, the GitHub repository was made available at https://github.com/stuchalk/OSDB/, and is open for collaborators to join the project, submit issues, and contribute code. The combination of a scripting environment (PHPStorm), a PHP Framework (CakePHP), a relational database (MySQL) and a code repository (GitHub) provides all the capabilities to easily develop REST based websites for ingestion, curation and exposure of open chemical data to the community at all levels. It is hoped this software stack (or equivalent ones in other scripting languages) will be leveraged to make more chemical data available for both humans and computers.

Spherical hashing: binary code embedding with hyperspheres.

PubMed

Heo, Jae-Pil; Lee, Youngwoon; He, Junfeng; Chang, Shih-Fu; Yoon, Sung-Eui

2015-11-01

Many binary code embedding schemes have been actively studied recently, since they can provide efficient similarity search, and compact data representations suitable for handling large scale image databases. Existing binary code embedding techniques encode high-dimensional data by using hyperplane-based hashing functions. In this paper we propose a novel hypersphere-based hashing function, spherical hashing, to map more spatially coherent data points into a binary code compared to hyperplane-based hashing functions. We also propose a new binary code distance function, spherical Hamming distance, tailored for our hypersphere-based binary coding scheme, and design an efficient iterative optimization process to achieve both balanced partitioning for each hash function and independence between hashing functions. Furthermore, we generalize spherical hashing to support various similarity measures defined by kernel functions. Our extensive experiments show that our spherical hashing technique significantly outperforms state-of-the-art techniques based on hyperplanes across various benchmarks with sizes ranging from one to 75 million of GIST, BoW and VLAD descriptors. The performance gains are consistent and large, up to 100 percent improvements over the second best method among tested methods. These results confirm the unique merits of using hyperspheres to encode proximity regions in high-dimensional spaces. Finally, our method is intuitive and easy to implement.

Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined.

PubMed

Falkner, Jayson; Andrews, Philip

2005-05-15

Comparing tandem mass spectra (MSMS) against a known dataset of protein sequences is a common method for identifying unknown proteins; however, the processing of MSMS by current software often limits certain applications, including comprehensive coverage of post-translational modifications, non-specific searches and real-time searches to allow result-dependent instrument control. This problem deserves attention as new mass spectrometers provide the ability for higher throughput and as known protein datasets rapidly grow in size. New software algorithms need to be devised in order to address the performance issues of conventional MSMS protein dataset-based protein identification. This paper describes a novel algorithm based on converting a collection of monoisotopic, centroided spectra to a new data structure, named 'peptide finite state machine' (PFSM), which may be used to rapidly search a known dataset of protein sequences, regardless of the number of spectra searched or the number of potential modifications examined. The algorithm is verified using a set of commercially available tryptic digest protein standards analyzed using an ABI 4700 MALDI TOFTOF mass spectrometer, and a free, open source PFSM implementation. It is illustrated that a PFSM can accurately search large collections of spectra against large datasets of protein sequences (e.g. NCBI nr) using a regular desktop PC; however, this paper only details the method for identifying peptide and subsequently protein candidates from a dataset of known protein sequences. The concept of using a PFSM as a peptide pre-screening technique for MSMS-based search engines is validated by using PFSM with Mascot and XTandem. Complete source code, documentation and examples for the reference PFSM implementation are freely available at the Proteome Commons, http://www.proteomecommons.org and source code may be used both commercially and non-commercially as long as the original authors are credited for their work.

Faster sequence homology searches by clustering subsequences.

PubMed

Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

2015-04-15

Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis. We developed a fast homology search method based on database subsequence clustering, and implemented it as GHOSTZ. This method clusters similar subsequences from a database to perform an efficient seed search and ungapped extension by reducing alignment candidates based on triangle inequality. The database subsequence clustering technique achieved an ∼2-fold increase in speed without a large decrease in search sensitivity. When we measured with metagenomic data, GHOSTZ is ∼2.2-2.8 times faster than RAPSearch and is ∼185-261 times faster than BLASTX. The source code is freely available for download at http://www.bi.cs.titech.ac.jp/ghostz/ akiyama@cs.titech.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

CSTutor: A Sketch-Based Tool for Visualizing Data Structures

ERIC Educational Resources Information Center

Buchanan, Sarah; Laviola, Joseph J., Jr.

2014-01-01

We present CSTutor, a sketch-based interface designed to help students understand data structures, specifically Linked Lists, Binary Search Trees, AVL Trees, and Heaps. CSTutor creates an environment that seamlessly combines a user's sketched diagram and code. In each of these data structure modes, the user can naturally sketch a data structure on…

Pattern recognition of electronic bit-sequences using a semiconductor mode-locked laser and spatial light modulators

NASA Astrophysics Data System (ADS)

Bhooplapur, Sharad; Akbulut, Mehmetkan; Quinlan, Franklyn; Delfyett, Peter J.

2010-04-01

A novel scheme for recognition of electronic bit-sequences is demonstrated. Two electronic bit-sequences that are to be compared are each mapped to a unique code from a set of Walsh-Hadamard codes. The codes are then encoded in parallel on the spectral phase of the frequency comb lines from a frequency-stabilized mode-locked semiconductor laser. Phase encoding is achieved by using two independent spatial light modulators based on liquid crystal arrays. Encoded pulses are compared using interferometric pulse detection and differential balanced photodetection. Orthogonal codes eight bits long are compared, and matched codes are successfully distinguished from mismatched codes with very low error rates, of around 10-18. This technique has potential for high-speed, high accuracy recognition of bit-sequences, with applications in keyword searches and internet protocol packet routing.

Application of a VLSI vector quantization processor to real-time speech coding

NASA Technical Reports Server (NTRS)

Davidson, G.; Gersho, A.

1986-01-01

Attention is given to a working vector quantization processor for speech coding that is based on a first-generation VLSI chip which efficiently performs the pattern-matching operation needed for the codebook search process (CPS). Using this chip, the CPS architecture has been successfully incorporated into a compact, single-board Vector PCM implementation operating at 7-18 kbits/sec. A real time Adaptive Vector Predictive Coder system using the CPS has also been implemented.

Random search optimization based on genetic algorithm and discriminant function

NASA Technical Reports Server (NTRS)

Kiciman, M. O.; Akgul, M.; Erarslanoglu, G.

1990-01-01

The general problem of optimization with arbitrary merit and constraint functions, which could be convex, concave, monotonic, or non-monotonic, is treated using stochastic methods. To improve the efficiency of the random search methods, a genetic algorithm for the search phase and a discriminant function for the constraint-control phase were utilized. The validity of the technique is demonstrated by comparing the results to published test problem results. Numerical experimentation indicated that for cases where a quick near optimum solution is desired, a general, user-friendly optimization code can be developed without serious penalties in both total computer time and accuracy.

Quantum Error Correction Protects Quantum Search Algorithms Against Decoherence

PubMed Central

Botsinis, Panagiotis; Babar, Zunaira; Alanis, Dimitrios; Chandra, Daryus; Nguyen, Hung; Ng, Soon Xin; Hanzo, Lajos

2016-01-01

When quantum computing becomes a wide-spread commercial reality, Quantum Search Algorithms (QSA) and especially Grover’s QSA will inevitably be one of their main applications, constituting their cornerstone. Most of the literature assumes that the quantum circuits are free from decoherence. Practically, decoherence will remain unavoidable as is the Gaussian noise of classic circuits imposed by the Brownian motion of electrons, hence it may have to be mitigated. In this contribution, we investigate the effect of quantum noise on the performance of QSAs, in terms of their success probability as a function of the database size to be searched, when decoherence is modelled by depolarizing channels’ deleterious effects imposed on the quantum gates. Moreover, we employ quantum error correction codes for limiting the effects of quantum noise and for correcting quantum flips. More specifically, we demonstrate that, when we search for a single solution in a database having 4096 entries using Grover’s QSA at an aggressive depolarizing probability of 10−3, the success probability of the search is 0.22 when no quantum coding is used, which is improved to 0.96 when Steane’s quantum error correction code is employed. Finally, apart from Steane’s code, the employment of Quantum Bose-Chaudhuri-Hocquenghem (QBCH) codes is also considered. PMID:27924865

Novel Integration of Frame Rate Up Conversion and HEVC Coding Based on Rate-Distortion Optimization.

PubMed

Guo Lu; Xiaoyun Zhang; Li Chen; Zhiyong Gao

2018-02-01

Frame rate up conversion (FRUC) can improve the visual quality by interpolating new intermediate frames. However, high frame rate videos by FRUC are confronted with more bitrate consumption or annoying artifacts of interpolated frames. In this paper, a novel integration framework of FRUC and high efficiency video coding (HEVC) is proposed based on rate-distortion optimization, and the interpolated frames can be reconstructed at encoder side with low bitrate cost and high visual quality. First, joint motion estimation (JME) algorithm is proposed to obtain robust motion vectors, which are shared between FRUC and video coding. What's more, JME is embedded into the coding loop and employs the original motion search strategy in HEVC coding. Then, the frame interpolation is formulated as a rate-distortion optimization problem, where both the coding bitrate consumption and visual quality are taken into account. Due to the absence of original frames, the distortion model for interpolated frames is established according to the motion vector reliability and coding quantization error. Experimental results demonstrate that the proposed framework can achieve 21% ~ 42% reduction in BDBR, when compared with the traditional methods of FRUC cascaded with coding.

Construction of FuzzyFind Dictionary using Golay Coding Transformation for Searching Applications

NASA Astrophysics Data System (ADS)

Kowsari, Kamram

2015-03-01

searching through a large volume of data is very critical for companies, scientists, and searching engines applications due to time complexity and memory complexity. In this paper, a new technique of generating FuzzyFind Dictionary for text mining was introduced. We simply mapped the 23 bits of the English alphabet into a FuzzyFind Dictionary or more than 23 bits by using more FuzzyFind Dictionary, and reflecting the presence or absence of particular letters. This representation preserves closeness of word distortions in terms of closeness of the created binary vectors within Hamming distance of 2 deviations. This paper talks about the Golay Coding Transformation Hash Table and how it can be used on a FuzzyFind Dictionary as a new technology for using in searching through big data. This method is introduced by linear time complexity for generating the dictionary and constant time complexity to access the data and update by new data sets, also updating for new data sets is linear time depends on new data points. This technique is based on searching only for letters of English that each segment has 23 bits, and also we have more than 23-bit and also it could work with more segments as reference table.

In silico search for functionally similar proteins involved in meiosis and recombination in evolutionarily distant organisms.

PubMed

Bogdanov, Yuri F; Dadashev, Sergei Y; Grishaeva, Tatiana M

2003-01-01

Evolutionarily distant organisms have not only orthologs, but also nonhomologous proteins that build functionally similar subcellular structures. For instance, this is true with protein components of the synaptonemal complex (SC), a universal ultrastructure that ensures the successful pairing and recombination of homologous chromosomes during meiosis. We aimed at developing a method to search databases for genes that code for such nonhomologous but functionally analogous proteins. Advantage was taken of the ultrastructural parameters of SC and the conformation of SC proteins responsible for these. Proteins involved in SC central space are known to be similar in secondary structure. Using published data, we found a highly significant correlation between the width of the SC central space and the length of rod-shaped central domain of mammalian and yeast intermediate proteins forming transversal filaments in the SC central space. Basing on this, we suggested a method for searching genome databases of distant organisms for genes whose virtual proteins meet the above correlation requirement. Our recent finding of the Drosophila melanogaster CG17604 gene coding for synaptonemal complex transversal filament protein received experimental support from another lab. With the same strategy, we showed that the Arabidopsis thaliana and Caenorhabditis elegans genomes contain unique genes coding for such proteins.

A systematic review of validated methods for identifying patients with rheumatoid arthritis using administrative or claims data.

PubMed

Chung, Cecilia P; Rohan, Patricia; Krishnaswami, Shanthi; McPheeters, Melissa L

2013-12-30

To review the evidence supporting the validity of billing, procedural, or diagnosis code, or pharmacy claim-based algorithms used to identify patients with rheumatoid arthritis (RA) in administrative and claim databases. We searched the MEDLINE database from 1991 to September 2012 using controlled vocabulary and key terms related to RA and reference lists of included studies were searched. Two investigators independently assessed the full text of studies against pre-determined inclusion criteria and extracted the data. Data collected included participant and algorithm characteristics. Nine studies reported validation of computer algorithms based on International Classification of Diseases (ICD) codes with or without free-text, medication use, laboratory data and the need for a diagnosis by a rheumatologist. These studies yielded positive predictive values (PPV) ranging from 34 to 97% to identify patients with RA. Higher PPVs were obtained with the use of at least two ICD and/or procedure codes (ICD-9 code 714 and others), the requirement of a prescription of a medication used to treat RA, or requirement of participation of a rheumatologist in patient care. For example, the PPV increased from 66 to 97% when the use of disease-modifying antirheumatic drugs and the presence of a positive rheumatoid factor were required. There have been substantial efforts to propose and validate algorithms to identify patients with RA in automated databases. Algorithms that include more than one code and incorporate medications or laboratory data and/or required a diagnosis by a rheumatologist may increase the PPV. Copyright © 2013 Elsevier Ltd. All rights reserved.

Combining structured and unstructured data to identify a cohort of ICU patients who received dialysis

PubMed Central

Abhyankar, Swapna; Demner-Fushman, Dina; Callaghan, Fiona M; McDonald, Clement J

2014-01-01

Objective To develop a generalizable method for identifying patient cohorts from electronic health record (EHR) data—in this case, patients having dialysis—that uses simple information retrieval (IR) tools. Methods We used the coded data and clinical notes from the 24 506 adult patients in the Multiparameter Intelligent Monitoring in Intensive Care database to identify patients who had dialysis. We used SQL queries to search the procedure, diagnosis, and coded nursing observations tables based on ICD-9 and local codes. We used a domain-specific search engine to find clinical notes containing terms related to dialysis. We manually validated the available records for a 10% random sample of patients who potentially had dialysis and a random sample of 200 patients who were not identified as having dialysis based on any of the sources. Results We identified 1844 patients that potentially had dialysis: 1481 from the three coded sources and 1624 from the clinical notes. Precision for identifying dialysis patients based on available data was estimated to be 78.4% (95% CI 71.9% to 84.2%) and recall was 100% (95% CI 86% to 100%). Conclusions Combining structured EHR data with information from clinical notes using simple queries increases the utility of both types of data for cohort identification. Patients identified by more than one source are more likely to meet the inclusion criteria; however, including patients found in any of the sources increases recall. This method is attractive because it is available to researchers with access to EHR data and off-the-shelf IR tools. PMID:24384230

Team interaction during surgery: a systematic review of communication coding schemes.

PubMed

Tiferes, Judith; Bisantz, Ann M; Guru, Khurshid A

2015-05-15

Communication problems have been systematically linked to human errors in surgery and a deep understanding of the underlying processes is essential. Although a number of tools exist to assess nontechnical skills, methods to study communication and other team-related processes are far from being standardized, making comparisons challenging. We conducted a systematic review to analyze methods used to study events in the operating room (OR) and to develop a synthesized coding scheme for OR team communication. Six electronic databases were accessed to search for articles that collected individual events during surgery and included detailed coding schemes. Additional articles were added based on cross-referencing. That collection was then classified based on type of events collected, environment type (real or simulated), number of procedures, type of surgical task, team characteristics, method of data collection, and coding scheme characteristics. All dimensions within each coding scheme were grouped based on emergent content similarity. Categories drawn from articles, which focused on communication events, were further analyzed and synthesized into one common coding scheme. A total of 34 of 949 articles met the inclusion criteria. The methodological characteristics and coding dimensions of the articles were summarized. A priori coding was used in nine studies. The synthesized coding scheme for OR communication included six dimensions as follows: information flow, period, statement type, topic, communication breakdown, and effects of communication breakdown. The coding scheme provides a standardized coding method for OR communication, which can be used to develop a priori codes for future studies especially in comparative effectiveness research. Copyright © 2015 Elsevier Inc. All rights reserved.

Efficient Proximity Computation Techniques Using ZIP Code Data for Smart Cities †

PubMed Central

Murdani, Muhammad Harist; Hong, Bonghee

2018-01-01

In this paper, we are interested in computing ZIP code proximity from two perspectives, proximity between two ZIP codes (Ad-Hoc) and neighborhood proximity (Top-K). Such a computation can be used for ZIP code-based target marketing as one of the smart city applications. A naïve approach to this computation is the usage of the distance between ZIP codes. We redefine a distance metric combining the centroid distance with the intersecting road network between ZIP codes by using a weighted sum method. Furthermore, we prove that the results of our combined approach conform to the characteristics of distance measurement. We have proposed a general and heuristic approach for computing Ad-Hoc proximity, while for computing Top-K proximity, we have proposed a general approach only. Our experimental results indicate that our approaches are verifiable and effective in reducing the execution time and search space. PMID:29587366

Efficient Proximity Computation Techniques Using ZIP Code Data for Smart Cities †.

PubMed

Murdani, Muhammad Harist; Kwon, Joonho; Choi, Yoon-Ho; Hong, Bonghee

2018-03-24

In this paper, we are interested in computing ZIP code proximity from two perspectives, proximity between two ZIP codes ( Ad-Hoc ) and neighborhood proximity ( Top-K ). Such a computation can be used for ZIP code-based target marketing as one of the smart city applications. A naïve approach to this computation is the usage of the distance between ZIP codes. We redefine a distance metric combining the centroid distance with the intersecting road network between ZIP codes by using a weighted sum method. Furthermore, we prove that the results of our combined approach conform to the characteristics of distance measurement. We have proposed a general and heuristic approach for computing Ad-Hoc proximity, while for computing Top-K proximity, we have proposed a general approach only. Our experimental results indicate that our approaches are verifiable and effective in reducing the execution time and search space.

catsHTM: A Tool for Fast Accessing and Cross-matching Large Astronomical Catalogs

NASA Astrophysics Data System (ADS)

Soumagnac, Maayane T.; Ofek, Eran O.

2018-07-01

Fast access to large catalogs is required for some astronomical applications. Here we introduce the catsHTM tool, consisting of several large catalogs reformatted into HDF5-based file format, which can be downloaded and used locally. To allow fast access, the catalogs are partitioned into hierarchical triangular meshes and stored in HDF5 files. Several tools are provided to perform efficient cone searches at resolutions spanning from a few arc-seconds to degrees, within a few milliseconds time. The first released version includes the following catalogs (by alphabetical order): 2MASS, 2MASS extended sources, AKARI, APASS, Cosmos, DECaLS/DR5, FIRST, GAIA/DR1, GAIA/DR2, GALEX/DR6Plus7, HSC/v2, IPHAS/DR2, NED redshifts, NVSS, Pan-STARRS1/DR1, PTF photometric catalog, ROSAT faint source, SDSS sources, SDSS/DR14 spectroscopy, SkyMapper, Spitzer/SAGE, Spitzer/IRAC galactic center, UCAC4, UKIDSS/DR10, VST/ATLAS/DR3, VST/KiDS/DR3, WISE and XMM. We provide Python code that allows to perform cone searches, as well as MATLAB code for performing cone searches, catalog cross-matching, general searches, as well as load and create these catalogs.

A Different Web-Based Geocoding Service Using Fuzzy Techniques

NASA Astrophysics Data System (ADS)

Pahlavani, P.; Abbaspour, R. A.; Zare Zadiny, A.

2015-12-01

Geocoding - the process of finding position based on descriptive data such as address or postal code - is considered as one of the most commonly used spatial analyses. Many online map providers such as Google Maps, Bing Maps and Yahoo Maps present geocoding as one of their basic capabilities. Despite the diversity of geocoding services, users usually face some limitations when they use available online geocoding services. In existing geocoding services, proximity and nearness concept is not modelled appropriately as well as these services search address only by address matching based on descriptive data. In addition there are also some limitations in display searching results. Resolving these limitations can enhance efficiency of the existing geocoding services. This paper proposes the idea of integrating fuzzy technique with geocoding process to resolve these limitations. In order to implement the proposed method, a web-based system is designed. In proposed method, nearness to places is defined by fuzzy membership functions and multiple fuzzy distance maps are created. Then these fuzzy distance maps are integrated using fuzzy overlay technique for obtain the results. Proposed methods provides different capabilities for users such as ability to search multi-part addresses, searching places based on their location, non-point representation of results as well as displaying search results based on their priority.

A new cue to figure-ground coding: top-bottom polarity.

PubMed

Hulleman, Johan; Humphreys, Glyn W

2004-11-01

We present evidence for a new figure-ground cue: top-bottom polarity. In an explicit reporting task, participants were more likely to interpret stimuli with a wide base and a narrow top as a figure. A similar advantage for wide-based stimuli also occurred in a visual short-term memory task, where the stimuli had ambiguous figure-ground relations. Further support comes from a figural search task. Figural search is a discrimination task in which participants are set to search for a symmetric target in a display with ambiguous figure-ground organization. We show that figural search was easier when stimuli with a top-bottom polarity were placed in an orientation where they had a wide base and a narrow top, relative to when this orientation was inverted. This polarity effect was present when participants were set to use color to parse figure from ground, and it was magnified when the participants did not have any foreknowledge of the color of the symmetric target. Taken together the results suggest that top-bottom polarity influences figure-ground assignment, with wide base stimuli being preferred as a figure. In addition, the figural search task can serve as a useful procedure to examine figure-ground assignment.

A systematic review of validated methods to capture myopericarditis using administrative or claims data.

PubMed

Idowu, Rachel T; Carnahan, Ryan; Sathe, Nila A; McPheeters, Melissa L

2013-12-30

To identify algorithms that can capture incident cases of myocarditis and pericarditis in administrative and claims databases; these algorithms can eventually be used to identify cardiac inflammatory adverse events following vaccine administration. We searched MEDLINE from 1991 to September 2012 using controlled vocabulary and key terms related to myocarditis. We also searched the reference lists of included studies. Two investigators independently assessed the full text of studies against pre-determined inclusion criteria. Two reviewers independently extracted data regarding participant and algorithm characteristics as well as study conduct. Nine publications (including one study reported in two publications) met criteria for inclusion. Two studies performed medical record review in order to confirm that these coding algorithms actually captured patients with the disease of interest. One of these studies identified five potential cases, none of which were confirmed as acute myocarditis upon review. The other study, which employed a search algorithm based on diagnostic surveillance (using ICD-9 codes 420.90, 420.99, 422.90, 422.91 and 429.0) and sentinel reporting, identified 59 clinically confirmed cases of myopericarditis among 492,671 United States military service personnel who received smallpox vaccine between 2002 and 2003. Neither study provided algorithm validation statistics (positive predictive value, sensitivity, or specificity). A validated search algorithm is currently unavailable for identifying incident cases of pericarditis or myocarditis. Several authors have published unvalidated ICD-9-based search algorithms that appear to capture myocarditis events occurring in the context of other underlying cardiac or autoimmune conditions. Copyright © 2013. Published by Elsevier Ltd.

Deep Hashing for Scalable Image Search.

PubMed

Lu, Jiwen; Liong, Venice Erin; Zhou, Jie

2017-05-01

In this paper, we propose a new deep hashing (DH) approach to learn compact binary codes for scalable image search. Unlike most existing binary codes learning methods, which usually seek a single linear projection to map each sample into a binary feature vector, we develop a deep neural network to seek multiple hierarchical non-linear transformations to learn these binary codes, so that the non-linear relationship of samples can be well exploited. Our model is learned under three constraints at the top layer of the developed deep network: 1) the loss between the compact real-valued code and the learned binary vector is minimized, 2) the binary codes distribute evenly on each bit, and 3) different bits are as independent as possible. To further improve the discriminative power of the learned binary codes, we extend DH into supervised DH (SDH) and multi-label SDH by including a discriminative term into the objective function of DH, which simultaneously maximizes the inter-class variations and minimizes the intra-class variations of the learned binary codes with the single-label and multi-label settings, respectively. Extensive experimental results on eight widely used image search data sets show that our proposed methods achieve very competitive results with the state-of-the-arts.

The role of crossover operator in evolutionary-based approach to the problem of genetic code optimization.

PubMed

Błażej, Paweł; Wnȩtrzak, Małgorzata; Mackiewicz, Paweł

2016-12-01

One of theories explaining the present structure of canonical genetic code assumes that it was optimized to minimize harmful effects of amino acid replacements resulting from nucleotide substitutions and translational errors. A way to testify this concept is to find the optimal code under given criteria and compare it with the canonical genetic code. Unfortunately, the huge number of possible alternatives makes it impossible to find the optimal code using exhaustive methods in sensible time. Therefore, heuristic methods should be applied to search the space of possible solutions. Evolutionary algorithms (EA) seem to be ones of such promising approaches. This class of methods is founded both on mutation and crossover operators, which are responsible for creating and maintaining the diversity of candidate solutions. These operators possess dissimilar characteristics and consequently play different roles in the process of finding the best solutions under given criteria. Therefore, the effective searching for the potential solutions can be improved by applying both of them, especially when these operators are devised specifically for a given problem. To study this subject, we analyze the effectiveness of algorithms for various combinations of mutation and crossover probabilities under three models of the genetic code assuming different restrictions on its structure. To achieve that, we adapt the position based crossover operator for the most restricted model and develop a new type of crossover operator for the more general models. The applied fitness function describes costs of amino acid replacement regarding their polarity. Our results indicate that the usage of crossover operators can significantly improve the quality of the solutions. Moreover, the simulations with the crossover operator optimize the fitness function in the smaller number of generations than simulations without this operator. The optimal genetic codes without restrictions on their structure minimize the costs about 2.7 times better than the canonical genetic code. Interestingly, the optimal codes are dominated by amino acids characterized by polarity close to its average value for all amino acids. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Mutual information-based analysis of JPEG2000 contexts.

PubMed

Liu, Zhen; Karam, Lina J

2005-04-01

Context-based arithmetic coding has been widely adopted in image and video compression and is a key component of the new JPEG2000 image compression standard. In this paper, the contexts used in JPEG2000 are analyzed using the mutual information, which is closely related to the compression performance. We first show that, when combining the contexts, the mutual information between the contexts and the encoded data will decrease unless the conditional probability distributions of the combined contexts are the same. Given I, the initial number of contexts, and F, the final desired number of contexts, there are S(I, F) possible context classification schemes where S(I, F) is called the Stirling number of the second kind. The optimal classification scheme is the one that gives the maximum mutual information. Instead of using an exhaustive search, the optimal classification scheme can be obtained through a modified generalized Lloyd algorithm with the relative entropy as the distortion metric. For binary arithmetic coding, the search complexity can be reduced by using dynamic programming. Our experimental results show that the JPEG2000 contexts capture the correlations among the wavelet coefficients very well. At the same time, the number of contexts used as part of the standard can be reduced without loss in the coding performance.

Development of a CFD code for casting simulation

NASA Technical Reports Server (NTRS)

Murph, Jesse E.

1992-01-01

The task of developing a computational fluid dynamics (CFD) code to accurately model the mold filling phase of a casting operation was accomplished in a systematic manner. First the state-of-the-art was determined through a literature search, a code search, and participation with casting industry personnel involved in consortium startups. From this material and inputs from industry personnel, an evaluation of the currently available codes was made. It was determined that a few of the codes already contained sophisticated CFD algorithms and further validation of one of these codes could preclude the development of a new CFD code for this purpose. With industry concurrence, ProCAST was chosen for further evaluation. Two benchmark cases were used to evaluate the code's performance using a Silicon Graphics Personal Iris system. The results of these limited evaluations (because of machine and time constraints) are presented along with discussions of possible improvements and recommendations for further evaluation.

Beam-steering efficiency optimization method based on a rapid-search algorithm for liquid crystal optical phased array.

PubMed

Xiao, Feng; Kong, Lingjiang; Chen, Jian

2017-06-01

A rapid-search algorithm to improve the beam-steering efficiency for a liquid crystal optical phased array was proposed and experimentally demonstrated in this paper. This proposed algorithm, in which the value of steering efficiency is taken as the objective function and the controlling voltage codes are considered as the optimization variables, consisted of a detection stage and a construction stage. It optimized the steering efficiency in the detection stage and adjusted its search direction adaptively in the construction stage to avoid getting caught in a wrong search space. Simulations had been conducted to compare the proposed algorithm with the widely used pattern-search algorithm using criteria of convergence rate and optimized efficiency. Beam-steering optimization experiments had been performed to verify the validity of the proposed method.

Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra*

PubMed Central

Richards, Alicia L.; Vincent, Catherine E.; Guthals, Adrian; Rose, Christopher M.; Westphall, Michael S.; Bandeira, Nuno; Coon, Joshua J.

2013-01-01

We report the use of neutron-encoded (NeuCode) stable isotope labeling of amino acids in cell culture for the purpose of C-terminal product ion annotation. Two NeuCode labeling isotopologues of lysine, 13C615N2 and 2H8, which differ by 36 mDa, were metabolically embedded in a sample proteome, and the resultant labeled proteins were combined, digested, and analyzed via liquid chromatography and mass spectrometry. With MS/MS scan resolving powers of ∼50,000 or higher, product ions containing the C terminus (i.e. lysine) appear as a doublet spaced by exactly 36 mDa, whereas N-terminal fragments exist as a single m/z peak. Through theory and experiment, we demonstrate that over 90% of all y-type product ions have detectable doublets. We report on an algorithm that can extract these neutron signatures with high sensitivity and specificity. In other words, of 15,503 y-type product ion peaks, the y-type ion identification algorithm correctly identified 14,552 (93.2%) based on detection of the NeuCode doublet; 6.8% were misclassified (i.e. other ion types that were assigned as y-type products). Searching NeuCode labeled yeast with PepNovo+ resulted in a 34% increase in correct de novo identifications relative to searching through MS/MS only. We use this tool to simplify spectra prior to database searching, to sort unmatched tandem mass spectra for spectral richness, for correlation of co-fragmented ions to their parent precursor, and for de novo sequence identification. PMID:24043425

KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella.

PubMed

Jouraku, Akiya; Yamamoto, Kimiko; Kuwazaki, Seigo; Urio, Masahiro; Suetsugu, Yoshitaka; Narukawa, Junko; Miyamoto, Kazuhisa; Kurita, Kanako; Kanamori, Hiroyuki; Katayose, Yuichi; Matsumoto, Takashi; Noda, Hiroaki

2013-07-09

The diamondback moth (DBM), Plutella xylostella, is one of the most harmful insect pests for crucifer crops worldwide. DBM has rapidly evolved high resistance to most conventional insecticides such as pyrethroids, organophosphates, fipronil, spinosad, Bacillus thuringiensis, and diamides. Therefore, it is important to develop genomic and transcriptomic DBM resources for analysis of genes related to insecticide resistance, both to clarify the mechanism of resistance of DBM and to facilitate the development of insecticides with a novel mode of action for more effective and environmentally less harmful insecticide rotation. To contribute to this goal, we developed KONAGAbase, a genomic and transcriptomic database for DBM (KONAGA is the Japanese word for DBM). KONAGAbase provides (1) transcriptomic sequences of 37,340 ESTs/mRNAs and 147,370 RNA-seq contigs which were clustered and assembled into 84,570 unigenes (30,695 contigs, 50,548 pseudo singletons, and 3,327 singletons); and (2) genomic sequences of 88,530 WGS contigs with 246,244 degenerate contigs and 106,455 singletons from which 6,310 de novo identified repeat sequences and 34,890 predicted gene-coding sequences were extracted. The unigenes and predicted gene-coding sequences were clustered and 32,800 representative sequences were extracted as a comprehensive putative gene set. These sequences were annotated with BLAST descriptions, Gene Ontology (GO) terms, and Pfam descriptions, respectively. KONAGAbase contains rich graphical user interface (GUI)-based web interfaces for easy and efficient searching, browsing, and downloading sequences and annotation data. Five useful search interfaces consisting of BLAST search, keyword search, BLAST result-based search, GO tree-based search, and genome browser are provided. KONAGAbase is publicly available from our website (http://dbm.dna.affrc.go.jp/px/) through standard web browsers. KONAGAbase provides DBM comprehensive transcriptomic and draft genomic sequences with useful annotation information with easy-to-use web interfaces, which helps researchers to efficiently search for target sequences such as insect resistance-related genes. KONAGAbase will be continuously updated and additional genomic/transcriptomic resources and analysis tools will be provided for further efficient analysis of the mechanism of insecticide resistance and the development of effective insecticides with a novel mode of action for DBM.

Publicizing Your Web Resources for Maximum Exposure.

ERIC Educational Resources Information Center

Smith, Kerry J.

2001-01-01

Offers advice to librarians for marketing their Web sites on Internet search engines. Advises against relying solely on spiders and recommends adding metadata to the source code and delivering that information directly to the search engines. Gives an overview of metadata and typical coding for meta tags. Includes Web addresses for a number of…

Parallel-vector computation for linear structural analysis and non-linear unconstrained optimization problems

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Al-Nasra, M.; Zhang, Y.; Baddourah, M. A.; Agarwal, T. K.; Storaasli, O. O.; Carmona, E. A.

1991-01-01

Several parallel-vector computational improvements to the unconstrained optimization procedure are described which speed up the structural analysis-synthesis process. A fast parallel-vector Choleski-based equation solver, pvsolve, is incorporated into the well-known SAP-4 general-purpose finite-element code. The new code, denoted PV-SAP, is tested for static structural analysis. Initial results on a four processor CRAY 2 show that using pvsolve reduces the equation solution time by a factor of 14-16 over the original SAP-4 code. In addition, parallel-vector procedures for the Golden Block Search technique and the BFGS method are developed and tested for nonlinear unconstrained optimization. A parallel version of an iterative solver and the pvsolve direct solver are incorporated into the BFGS method. Preliminary results on nonlinear unconstrained optimization test problems, using pvsolve in the analysis, show excellent parallel-vector performance indicating that these parallel-vector algorithms can be used in a new generation of finite-element based structural design/analysis-synthesis codes.

A systematic review of validated methods for identifying anaphylaxis, including anaphylactic shock and angioneurotic edema, using administrative and claims data.

PubMed

Schneider, Gary; Kachroo, Sumesh; Jones, Natalie; Crean, Sheila; Rotella, Philip; Avetisyan, Ruzan; Reynolds, Matthew W

2012-01-01

The Food and Drug Administration's Mini-Sentinel pilot program initially aims to conduct active surveillance to refine safety signals that emerge for marketed medical products. A key facet of this surveillance is to develop and understand the validity of algorithms for identifying health outcomes of interest from administrative and claims data. This article summarizes the process and findings of the algorithm review of anaphylaxis. PubMed and Iowa Drug Information Service searches were conducted to identify citations applicable to the anaphylaxis health outcome of interest. Level 1 abstract reviews and Level 2 full-text reviews were conducted to find articles using administrative and claims data to identify anaphylaxis and including validation estimates of the coding algorithms. Our search revealed limited literature focusing on anaphylaxis that provided administrative and claims data-based algorithms and validation estimates. Only four studies identified via literature searches provided validated algorithms; however, two additional studies were identified by Mini-Sentinel collaborators and were incorporated. The International Classification of Diseases, Ninth Revision, codes varied, as did the positive predictive value, depending on the cohort characteristics and the specific codes used to identify anaphylaxis. Research needs to be conducted on designing validation studies to test anaphylaxis algorithms and estimating their predictive power, sensitivity, and specificity. Copyright © 2012 John Wiley & Sons, Ltd.

Accuracy and Completeness of Clinical Coding Using ICD-10 for Ambulatory Visits

PubMed Central

Horsky, Jan; Drucker, Elizabeth A.; Ramelson, Harley Z.

2017-01-01

This study describes a simulation of diagnostic coding using an EHR. Twenty-three ambulatory clinicians were asked to enter appropriate codes for six standardized scenarios with two different EHRs. Their interactions with the query interface were analyzed for patterns and variations in search strategies and the resulting sets of entered codes for accuracy and completeness. Just over a half of entered codes were appropriate for a given scenario and about a quarter were omitted. Crohn’s disease and diabetes scenarios had the highest rate of inappropriate coding and code variation. The omission rate was higher for secondary than for primary visit diagnoses. Codes for immunization, dialysis dependence and nicotine dependence were the most often omitted. We also found a high rate of variation in the search terms used to query the EHR for the same diagnoses. Changes to the training of clinicians and improved design of EHR query modules may lower the rate of inappropriate and omitted codes. PMID:29854158

A Very Efficient Transfer Function Bounding Technique on Bit Error Rate for Viterbi Decoded, Rate 1/N Convolutional Codes

NASA Technical Reports Server (NTRS)

Lee, P. J.

1984-01-01

For rate 1/N convolutional codes, a recursive algorithm for finding the transfer function bound on bit error rate (BER) at the output of a Viterbi decoder is described. This technique is very fast and requires very little storage since all the unnecessary operations are eliminated. Using this technique, we find and plot bounds on the BER performance of known codes of rate 1/2 with K 18, rate 1/3 with K 14. When more than one reported code with the same parameter is known, we select the code that minimizes the required signal to noise ratio for a desired bit error rate of 0.000001. This criterion of determining goodness of a code had previously been found to be more useful than the maximum free distance criterion and was used in the code search procedures of very short constraint length codes. This very efficient technique can also be used for searches of longer constraint length codes.

A Darwinian approach to control-structure design

NASA Technical Reports Server (NTRS)

Zimmerman, David C.

1993-01-01

Genetic algorithms (GA's), as introduced by Holland (1975), are one form of directed random search. The form of direction is based on Darwin's 'survival of the fittest' theories. GA's are radically different from the more traditional design optimization techniques. GA's work with a coding of the design variables, as opposed to working with the design variables directly. The search is conducted from a population of designs (i.e., from a large number of points in the design space), unlike the traditional algorithms which search from a single design point. The GA requires only objective function information, as opposed to gradient or other auxiliary information. Finally, the GA is based on probabilistic transition rules, as opposed to deterministic rules. These features allow the GA to attack problems with local-global minima, discontinuous design spaces and mixed variable problems, all in a single, consistent framework.

Optimising the use of electronic health records to estimate the incidence of rheumatoid arthritis in primary care: what information is hidden in free text?

PubMed Central

2013-01-01

Background Primary care databases are a major source of data for epidemiological and health services research. However, most studies are based on coded information, ignoring information stored in free text. Using the early presentation of rheumatoid arthritis (RA) as an exemplar, our objective was to estimate the extent of data hidden within free text, using a keyword search. Methods We examined the electronic health records (EHRs) of 6,387 patients from the UK, aged 30 years and older, with a first coded diagnosis of RA between 2005 and 2008. We listed indicators for RA which were present in coded format and ran keyword searches for similar information held in free text. The frequency of indicator code groups and keywords from one year before to 14 days after RA diagnosis were compared, and temporal relationships examined. Results One or more keyword for RA was found in the free text in 29% of patients prior to the RA diagnostic code. Keywords for inflammatory arthritis diagnoses were present for 14% of patients whereas only 11% had a diagnostic code. Codes for synovitis were found in 3% of patients, but keywords were identified in an additional 17%. In 13% of patients there was evidence of a positive rheumatoid factor test in text only, uncoded. No gender differences were found. Keywords generally occurred close in time to the coded diagnosis of rheumatoid arthritis. They were often found under codes indicating letters and communications. Conclusions Potential cases may be missed or wrongly dated when coded data alone are used to identify patients with RA, as diagnostic suspicions are frequently confined to text. The use of EHRs to create disease registers or assess quality of care will be misleading if free text information is not taken into account. Methods to facilitate the automated processing of text need to be developed and implemented. PMID:23964710

Engineering calculations for communications satellite systems planning

NASA Technical Reports Server (NTRS)

Martin, C. H.; Gonsalvez, D. J.; Levis, C. A.; Wang, C. W.

1983-01-01

Progress is reported on a computer code to improve the efficiency of spectrum and orbit utilization for the Broadcasting Satellite Service in the 12 GHz band for Region 2. It implements a constrained gradient search procedure using an exponential objective function based on aggregate signal to noise ratio and an extended line search in the gradient direction. The procedure is tested against a manually generated initial scenario and appears to work satisfactorily. In this test it was assumed that alternate channels use orthogonal polarizations at any one satellite location.

Hybrid real-code ant colony optimisation for constrained mechanical design

NASA Astrophysics Data System (ADS)

Pholdee, Nantiwat; Bureerat, Sujin

2016-01-01

This paper proposes a hybrid meta-heuristic based on integrating a local search simplex downhill (SDH) method into the search procedure of real-code ant colony optimisation (ACOR). This hybridisation leads to five hybrid algorithms where a Monte Carlo technique, a Latin hypercube sampling technique (LHS) and a translational propagation Latin hypercube design (TPLHD) algorithm are used to generate an initial population. Also, two numerical schemes for selecting an initial simplex are investigated. The original ACOR and its hybrid versions along with a variety of established meta-heuristics are implemented to solve 17 constrained test problems where a fuzzy set theory penalty function technique is used to handle design constraints. The comparative results show that the hybrid algorithms are the top performers. Using the TPLHD technique gives better results than the other sampling techniques. The hybrid optimisers are a powerful design tool for constrained mechanical design problems.

blastjs: a BLAST+ wrapper for Node.js.

PubMed

Page, Martin; MacLean, Dan; Schudoma, Christian

2016-02-27

To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite are the most widely employed bioinformatic method for these database searches. Recent trends in bioinformatics application development show an increasing number of JavaScript apps that are based on modern frameworks such as Node.js. Until now, there is no way of using database searches with the BLAST+ suite from a Node.js codebase. We developed blastjs, a Node.js library that wraps the search tools of the BLAST+ suite and thus allows to easily add significant functionality to any Node.js-based application. blastjs is a library that allows the incorporation of BLAST+ functionality into bioinformatics applications based on JavaScript and Node.js. The library was designed to be as user-friendly as possible and therefore requires only a minimal amount of code in the client application. The library is freely available under the MIT license at https://github.com/teammaclean/blastjs.

Safe pill-dispensing.

PubMed

Testa, Massimiliano; Pollard, John

2007-01-01

Each patient is supplied with a smart-card containing a Radio Frequency IDentification (RFID) chip storing a unique identification code. The patient places the Smart-card on a pill-dispenser unit containing an RFID reader. The RFID chip is read and the code sent to a Base-station via a wireless Bluetooth link. A database containing both patient details and treatment information is queried at the Base-station using the RFID as the search key. The patient's treatment data (i.e., drug names, quantities, time, etc.) are retrieved and sent back to the pill-dispenser unit via Bluetooth. Appropriate quantities of the required medications are automatically dispensed, unless the patient has already taken his/her daily dose. Safe, confidential communication and operation is ensured.

USGS launches online database: Lichens in National Parks

USGS Publications Warehouse

Bennett, Jim

2005-01-01

If you are interested in lichens and National Parks, now you can query a lichen database that combines these two elements. Using pull-down menus you can: search by park, specifying either species list or the references used for that area; search by species (a report will show the parks in which species are found); and search by reference codes, which are available from the first query. The reference code search allows you to obtain the complete citation for each lichen species listed in a National Park.The result pages from these queries can be printed directly from the web browser, or can be copied and pasted into a word processor.

Coding visual features extracted from video sequences.

PubMed

Baroffio, Luca; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

2014-05-01

Visual features are successfully exploited in several applications (e.g., visual search, object recognition and tracking, etc.) due to their ability to efficiently represent image content. Several visual analysis tasks require features to be transmitted over a bandwidth-limited network, thus calling for coding techniques to reduce the required bit budget, while attaining a target level of efficiency. In this paper, we propose, for the first time, a coding architecture designed for local features (e.g., SIFT, SURF) extracted from video sequences. To achieve high coding efficiency, we exploit both spatial and temporal redundancy by means of intraframe and interframe coding modes. In addition, we propose a coding mode decision based on rate-distortion optimization. The proposed coding scheme can be conveniently adopted to implement the analyze-then-compress (ATC) paradigm in the context of visual sensor networks. That is, sets of visual features are extracted from video frames, encoded at remote nodes, and finally transmitted to a central controller that performs visual analysis. This is in contrast to the traditional compress-then-analyze (CTA) paradigm, in which video sequences acquired at a node are compressed and then sent to a central unit for further processing. In this paper, we compare these coding paradigms using metrics that are routinely adopted to evaluate the suitability of visual features in the context of content-based retrieval, object recognition, and tracking. Experimental results demonstrate that, thanks to the significant coding gains achieved by the proposed coding scheme, ATC outperforms CTA with respect to all evaluation metrics.

Cis-encoded non-coding antisense RNAs in streptococci and other low GC Gram (+) bacterial pathogens

PubMed Central

Cho, Kyu Hong; Kim, Jeong-Ho

2015-01-01

Due to recent advances of bioinformatics and high throughput sequencing technology, discovery of regulatory non-coding RNAs in bacteria has been increased to a great extent. Based on this bandwagon, many studies searching for trans-acting small non-coding RNAs in streptococci have been performed intensively, especially in the important human pathogen, group A and B streptococci. However, studies for cis-encoded non-coding antisense RNAs in streptococci have been scarce. A recent study shows antisense RNAs are involved in virulence gene regulation in group B streptococcus, S. agalactiae. This suggests antisense RNAs could have important roles in the pathogenesis of streptococcal pathogens. In this review, we describe recent discoveries of chromosomal cis-encoded antisense RNAs in streptococcal pathogens and other low GC Gram (+) bacteria to provide a guide for future studies. PMID:25859258

Validity of International Classification of Diseases (ICD) coding for dengue infections in hospital discharge records in Malaysia.

PubMed

Woon, Yuan-Liang; Lee, Keng-Yee; Mohd Anuar, Siti Fatimah Zahra; Goh, Pik-Pin; Lim, Teck-Onn

2018-04-20

Hospitalization due to dengue illness is an important measure of dengue morbidity. However, limited studies are based on administrative database because the validity of the diagnosis codes is unknown. We validated the International Classification of Diseases, 10th revision (ICD) diagnosis coding for dengue infections in the Malaysian Ministry of Health's (MOH) hospital discharge database. This validation study involves retrospective review of available hospital discharge records and hand-search medical records for years 2010 and 2013. We randomly selected 3219 hospital discharge records coded with dengue and non-dengue infections as their discharge diagnoses from the national hospital discharge database. We then randomly sampled 216 and 144 records for patients with and without codes for dengue respectively, in keeping with their relative frequency in the MOH database, for chart review. The ICD codes for dengue were validated against lab-based diagnostic standard (NS1 or IgM). The ICD-10-CM codes for dengue had a sensitivity of 94%, modest specificity of 83%, positive predictive value of 87% and negative predictive value 92%. These results were stable between 2010 and 2013. However, its specificity decreased substantially when patients manifested with bleeding or low platelet count. The diagnostic performance of the ICD codes for dengue in the MOH's hospital discharge database is adequate for use in health services research on dengue.

System description: IVY

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

McCune, W.; Shumsky, O.

2000-02-04

IVY is a verified theorem prover for first-order logic with equality. It is coded in ACL2, and it makes calls to the theorem prover Otter to search for proofs and to the program MACE to search for countermodels. Verifications of Otter and MACE are not practical because they are coded in C. Instead, Otter and MACE give detailed proofs and models that are checked by verified ACL2 programs. In addition, the initial conversion to clause form is done by verified ACL2 code. The verification is done with respect to finite interpretations.

Weighted bi-prediction for light field image coding

NASA Astrophysics Data System (ADS)

Conti, Caroline; Nunes, Paulo; Ducla Soares, Luís.

2017-09-01

Light field imaging based on a single-tier camera equipped with a microlens array - also known as integral, holoscopic, and plenoptic imaging - has currently risen up as a practical and prospective approach for future visual applications and services. However, successfully deploying actual light field imaging applications and services will require developing adequate coding solutions to efficiently handle the massive amount of data involved in these systems. In this context, self-similarity compensated prediction is a non-local spatial prediction scheme based on block matching that has been shown to achieve high efficiency for light field image coding based on the High Efficiency Video Coding (HEVC) standard. As previously shown by the authors, this is possible by simply averaging two predictor blocks that are jointly estimated from a causal search window in the current frame itself, referred to as self-similarity bi-prediction. However, theoretical analyses for motion compensated bi-prediction have suggested that it is still possible to achieve further rate-distortion performance improvements by adaptively estimating the weighting coefficients of the two predictor blocks. Therefore, this paper presents a comprehensive study of the rate-distortion performance for HEVC-based light field image coding when using different sets of weighting coefficients for self-similarity bi-prediction. Experimental results demonstrate that it is possible to extend the previous theoretical conclusions to light field image coding and show that the proposed adaptive weighting coefficient selection leads to up to 5 % of bit savings compared to the previous self-similarity bi-prediction scheme.

Speech coding at low to medium bit rates

NASA Astrophysics Data System (ADS)

Leblanc, Wilfred Paul

1992-09-01

Improved search techniques coupled with improved codebook design methodologies are proposed to improve the performance of conventional code-excited linear predictive coders for speech. Improved methods for quantizing the short term filter are developed by employing a tree search algorithm and joint codebook design to multistage vector quantization. Joint codebook design procedures are developed to design locally optimal multistage codebooks. Weighting during centroid computation is introduced to improve the outlier performance of the multistage vector quantizer. Multistage vector quantization is shown to be both robust against input characteristics and in the presence of channel errors. Spectral distortions of about 1 dB are obtained at rates of 22-28 bits/frame. Structured codebook design procedures for excitation in code-excited linear predictive coders are compared to general codebook design procedures. Little is lost using significant structure in the excitation codebooks while greatly reducing the search complexity. Sparse multistage configurations are proposed for reducing computational complexity and memory size. Improved search procedures are applied to code-excited linear prediction which attempt joint optimization of the short term filter, the adaptive codebook, and the excitation. Improvements in signal to noise ratio of 1-2 dB are realized in practice.

Searching hospital discharge records for snow sport injury: no easy run?

PubMed

Smartt, Pamela F M; Chalmers, David J

2012-01-01

When using hospital discharge data to shape sports injury prevention policy, it is important to correctly identify cases. The objectives of this study were to examine the ease with which snow-skiing and snowboarding injury cases could be identified from national hospital discharge data and to assess the suitability of the information obtained for shaping policy. Hospital discharges for 2000-2004 were linked to compensated claims and searched sequentially using coded and narrative information. One thousand three hundred seventy-six eligible cases were identified, with 717 classified as snowboarding and 659 as snow-skiing. For the most part, cases could not be identified and distinguished using simple searches of coded data; keyword searches of narratives played a key role in case identification but not in describing the mechanism of injury. Identification and characterisation of snow sport injury from in-patient discharge records is problematic due to inadequacies in the coding systems and/or their implementation. Narrative reporting could be improved.

ICD-10 codes used to identify adverse drug events in administrative data: a systematic review.

PubMed

Hohl, Corinne M; Karpov, Andrei; Reddekopp, Lisa; Doyle-Waters, Mimi; Stausberg, Jürgen

2014-01-01

Adverse drug events, the unintended and harmful effects of medications, are important outcome measures in health services research. Yet no universally accepted set of International Classification of Diseases (ICD) revision 10 codes or coding algorithms exists to ensure their consistent identification in administrative data. Our objective was to synthesize a comprehensive set of ICD-10 codes used to identify adverse drug events. We developed a systematic search strategy and applied it to five electronic reference databases. We searched relevant medical journals, conference proceedings, electronic grey literature and bibliographies of relevant studies, and contacted content experts for unpublished studies. One author reviewed the titles and abstracts for inclusion and exclusion criteria. Two authors reviewed eligible full-text articles and abstracted data in duplicate. Data were synthesized in a qualitative manner. Of 4241 titles identified, 41 were included. We found a total of 827 ICD-10 codes that have been used in the medical literature to identify adverse drug events. The median number of codes used to search for adverse drug events was 190 (IQR 156-289) with a large degree of variability between studies in the numbers and types of codes used. Authors commonly used external injury (Y40.0-59.9) and disease manifestation codes. Only two papers reported on the sensitivity of their code set. Substantial variability exists in the methods used to identify adverse drug events in administrative data. Our work may serve as a point of reference for future research and consensus building in this area.

ICD-10 codes used to identify adverse drug events in administrative data: a systematic review

PubMed Central

Hohl, Corinne M; Karpov, Andrei; Reddekopp, Lisa; Stausberg, Jürgen

2014-01-01

Background Adverse drug events, the unintended and harmful effects of medications, are important outcome measures in health services research. Yet no universally accepted set of International Classification of Diseases (ICD) revision 10 codes or coding algorithms exists to ensure their consistent identification in administrative data. Our objective was to synthesize a comprehensive set of ICD-10 codes used to identify adverse drug events. Methods We developed a systematic search strategy and applied it to five electronic reference databases. We searched relevant medical journals, conference proceedings, electronic grey literature and bibliographies of relevant studies, and contacted content experts for unpublished studies. One author reviewed the titles and abstracts for inclusion and exclusion criteria. Two authors reviewed eligible full-text articles and abstracted data in duplicate. Data were synthesized in a qualitative manner. Results Of 4241 titles identified, 41 were included. We found a total of 827 ICD-10 codes that have been used in the medical literature to identify adverse drug events. The median number of codes used to search for adverse drug events was 190 (IQR 156–289) with a large degree of variability between studies in the numbers and types of codes used. Authors commonly used external injury (Y40.0–59.9) and disease manifestation codes. Only two papers reported on the sensitivity of their code set. Conclusions Substantial variability exists in the methods used to identify adverse drug events in administrative data. Our work may serve as a point of reference for future research and consensus building in this area. PMID:24222671

Uncertainty Assessment of Hypersonic Aerothermodynamics Prediction Capability

NASA Technical Reports Server (NTRS)

Bose, Deepak; Brown, James L.; Prabhu, Dinesh K.; Gnoffo, Peter; Johnston, Christopher O.; Hollis, Brian

2011-01-01

The present paper provides the background of a focused effort to assess uncertainties in predictions of heat flux and pressure in hypersonic flight (airbreathing or atmospheric entry) using state-of-the-art aerothermodynamics codes. The assessment is performed for four mission relevant problems: (1) shock turbulent boundary layer interaction on a compression corner, (2) shock turbulent boundary layer interaction due a impinging shock, (3) high-mass Mars entry and aerocapture, and (4) high speed return to Earth. A validation based uncertainty assessment approach with reliance on subject matter expertise is used. A code verification exercise with code-to-code comparisons and comparisons against well established correlations is also included in this effort. A thorough review of the literature in search of validation experiments is performed, which identified a scarcity of ground based validation experiments at hypersonic conditions. In particular, a shortage of useable experimental data at flight like enthalpies and Reynolds numbers is found. The uncertainty was quantified using metrics that measured discrepancy between model predictions and experimental data. The discrepancy data is statistically analyzed and investigated for physics based trends in order to define a meaningful quantified uncertainty. The detailed uncertainty assessment of each mission relevant problem is found in the four companion papers.

Scene-aware joint global and local homographic video coding

NASA Astrophysics Data System (ADS)

Peng, Xiulian; Xu, Jizheng; Sullivan, Gary J.

2016-09-01

Perspective motion is commonly represented in video content that is captured and compressed for various applications including cloud gaming, vehicle and aerial monitoring, etc. Existing approaches based on an eight-parameter homography motion model cannot deal with this efficiently, either due to low prediction accuracy or excessive bit rate overhead. In this paper, we consider the camera motion model and scene structure in such video content and propose a joint global and local homography motion coding approach for video with perspective motion. The camera motion is estimated by a computer vision approach, and camera intrinsic and extrinsic parameters are globally coded at the frame level. The scene is modeled as piece-wise planes, and three plane parameters are coded at the block level. Fast gradient-based approaches are employed to search for the plane parameters for each block region. In this way, improved prediction accuracy and low bit costs are achieved. Experimental results based on the HEVC test model show that up to 9.1% bit rate savings can be achieved (with equal PSNR quality) on test video content with perspective motion. Test sequences for the example applications showed a bit rate savings ranging from 3.7 to 9.1%.

Two Upper Bounds for the Weighted Path Length of Binary Trees. Report No. UIUCDCS-R-73-565.

ERIC Educational Resources Information Center

Pradels, Jean Louis

Rooted binary trees with weighted nodes are structures encountered in many areas, such as coding theory, searching and sorting, information storage and retrieval. The path length is a meaningful quantity which gives indications about the expected time of a search or the length of a code, for example. In this paper, two sharp bounds for the total…

Microsoft Licenses Berkeley Lab's Home Energy Saver Code for Its Energy

Science.gov Websites

-based tool for calculating energy use in residential buildings. About one million people visit the Home Management Software | Berkeley Lab Berkeley Lab A-Z Index Directory Submit Web People Navigation Berkeley Lab Search Submit Web People Close About the Lab Leadership/Organization Calendar News

Joint Machine Learning and Game Theory for Rate Control in High Efficiency Video Coding.

PubMed

Gao, Wei; Kwong, Sam; Jia, Yuheng

2017-08-25

In this paper, a joint machine learning and game theory modeling (MLGT) framework is proposed for inter frame coding tree unit (CTU) level bit allocation and rate control (RC) optimization in High Efficiency Video Coding (HEVC). First, a support vector machine (SVM) based multi-classification scheme is proposed to improve the prediction accuracy of CTU-level Rate-Distortion (R-D) model. The legacy "chicken-and-egg" dilemma in video coding is proposed to be overcome by the learning-based R-D model. Second, a mixed R-D model based cooperative bargaining game theory is proposed for bit allocation optimization, where the convexity of the mixed R-D model based utility function is proved, and Nash bargaining solution (NBS) is achieved by the proposed iterative solution search method. The minimum utility is adjusted by the reference coding distortion and frame-level Quantization parameter (QP) change. Lastly, intra frame QP and inter frame adaptive bit ratios are adjusted to make inter frames have more bit resources to maintain smooth quality and bit consumption in the bargaining game optimization. Experimental results demonstrate that the proposed MLGT based RC method can achieve much better R-D performances, quality smoothness, bit rate accuracy, buffer control results and subjective visual quality than the other state-of-the-art one-pass RC methods, and the achieved R-D performances are very close to the performance limits from the FixedQP method.

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

PubMed

Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

2005-01-01

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

OpenRBC: Redefining the Frontier of Red Blood Cell Simulations at Protein Resolution

NASA Astrophysics Data System (ADS)

Tang, Yu-Hang; Lu, Lu; Li, He; Grinberg, Leopold; Sachdeva, Vipin; Evangelinos, Constantinos; Karniadakis, George

We present a from-scratch development of OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment - simulating an entire mammal red blood cell lipid bilayer and cytoskeleton modeled by 4 million mesoscopic particles - on a single shared memory node. To achieve this, we invented an adaptive spatial searching algorithm to accelerate the computation of short-range pairwise interactions in an extremely sparse 3D space. The algorithm is based on a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated over the course of the simulation. The algorithm enables the construction of a lattice-free cell list, i.e. the key spatial searching data structure in our code, in O (N) time and space space with cells whose position and shape adapts automatically to the local density and curvature. The code implements NUMA/NUCA-aware OpenMP parallelization and achieves perfect scaling with up to hundreds of hardware threads. The code outperforms a legacy solver by more than 8 times in time-to-solution and more than 20 times in problem size, thus providing a new venue for probing the cytomechanics of red blood cells. This work was supported by the Department of Energy (DOE) Collaboratory on Mathematics for Mesoscopic Model- ing of Materials (CM4). YHT acknowledges partial financial support from an IBM Ph.D. Scholarship Award.

Where to search top-K biomedical ontologies?

PubMed

Oliveira, Daniela; Butt, Anila Sahar; Haller, Armin; Rebholz-Schuhmann, Dietrich; Sahay, Ratnesh

2018-03-20

Searching for precise terms and terminological definitions in the biomedical data space is problematic, as researchers find overlapping, closely related and even equivalent concepts in a single or multiple ontologies. Search engines that retrieve ontological resources often suggest an extensive list of search results for a given input term, which leads to the tedious task of selecting the best-fit ontological resource (class or property) for the input term and reduces user confidence in the retrieval engines. A systematic evaluation of these search engines is necessary to understand their strengths and weaknesses in different search requirements. We have implemented seven comparable Information Retrieval ranking algorithms to search through ontologies and compared them against four search engines for ontologies. Free-text queries have been performed, the outcomes have been judged by experts and the ranking algorithms and search engines have been evaluated against the expert-based ground truth (GT). In addition, we propose a probabilistic GT that is developed automatically to provide deeper insights and confidence to the expert-based GT as well as evaluating a broader range of search queries. The main outcome of this work is the identification of key search factors for biomedical ontologies together with search requirements and a set of recommendations that will help biomedical experts and ontology engineers to select the best-suited retrieval mechanism in their search scenarios. We expect that this evaluation will allow researchers and practitioners to apply the current search techniques more reliably and that it will help them to select the right solution for their daily work. The source code (of seven ranking algorithms), ground truths and experimental results are available at https://github.com/danielapoliveira/bioont-search-benchmark.

Hazards and Possibilities of Optical Breakdown Effects Below the Threshold for Shockwave and Bubble Formation

DTIC Science & Technology

2006-07-01

precision of the determination of Rmax, we established a refined method based on the model of bubble formation described above in section 3.6.1 and the...development can be modeled by hydrodynamic codes based on tabulated equation-of-state data . This has previously demonstrated on ps optical breakdown...per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and

Numerical classification of coding sequences

NASA Technical Reports Server (NTRS)

Collins, D. W.; Liu, C. C.; Jukes, T. H.

1992-01-01

DNA sequences coding for protein may be represented by counts of nucleotides or codons. A complete reading frame may be abbreviated by its base count, e.g. A76C158G121T74, or with the corresponding codon table, e.g. (AAA)0(AAC)1(AAG)9 ... (TTT)0. We propose that these numerical designations be used to augment current methods of sequence annotation. Because base counts and codon tables do not require revision as knowledge of function evolves, they are well-suited to act as cross-references, for example to identify redundant GenBank entries. These descriptors may be compared, in place of DNA sequences, to extract homologous genes from large databases. This approach permits rapid searching with good selectivity.

Android platform based smartphones for a logistical remote association repair framework.

PubMed

Lien, Shao-Fan; Wang, Chun-Chieh; Su, Juhng-Perng; Chen, Hong-Ming; Wu, Chein-Hsing

2014-06-25

The maintenance of large-scale systems is an important issue for logistics support planning. In this paper, we developed a Logistical Remote Association Repair Framework (LRARF) to aid repairmen in keeping the system available. LRARF includes four subsystems: smart mobile phones, a Database Management System (DBMS), a Maintenance Support Center (MSC) and wireless networks. The repairman uses smart mobile phones to capture QR-codes and the images of faulty circuit boards. The captured QR-codes and images are transmitted to the DBMS so the invalid modules can be recognized via the proposed algorithm. In this paper, the Linear Projective Transform (LPT) is employed for fast QR-code calibration. Moreover, the ANFIS-based data mining system is used for module identification and searching automatically for the maintenance manual corresponding to the invalid modules. The inputs of the ANFIS-based data mining system are the QR-codes and image features; the output is the module ID. DBMS also transmits the maintenance manual back to the maintenance staff. If modules are not recognizable, the repairmen and center engineers can obtain the relevant information about the invalid modules through live video. The experimental results validate the applicability of the Android-based platform in the recognition of invalid modules. In addition, the live video can also be recorded synchronously on the MSC for later use.

Pyramid image codes

NASA Technical Reports Server (NTRS)

Watson, Andrew B.

1990-01-01

All vision systems, both human and machine, transform the spatial image into a coded representation. Particular codes may be optimized for efficiency or to extract useful image features. Researchers explored image codes based on primary visual cortex in man and other primates. Understanding these codes will advance the art in image coding, autonomous vision, and computational human factors. In cortex, imagery is coded by features that vary in size, orientation, and position. Researchers have devised a mathematical model of this transformation, called the Hexagonal oriented Orthogonal quadrature Pyramid (HOP). In a pyramid code, features are segregated by size into layers, with fewer features in the layers devoted to large features. Pyramid schemes provide scale invariance, and are useful for coarse-to-fine searching and for progressive transmission of images. The HOP Pyramid is novel in three respects: (1) it uses a hexagonal pixel lattice, (2) it uses oriented features, and (3) it accurately models most of the prominent aspects of primary visual cortex. The transform uses seven basic features (kernels), which may be regarded as three oriented edges, three oriented bars, and one non-oriented blob. Application of these kernels to non-overlapping seven-pixel neighborhoods yields six oriented, high-pass pyramid layers, and one low-pass (blob) layer.

Does the Holland Code Predict Job Satisfaction and Productivity in Clothing Factory Workers?

ERIC Educational Resources Information Center

Heesacker, Martin; And Others

1988-01-01

Administered Self-Directed Search to sewing machine operators to determine Holland code, and assessed work productivity, job satisfaction, absenteeism, and insurance claims. Most workers were of the Social code. Social subjects were the most satisfied, Conventional and Realistic subjects next, and subjects of other codes less so. Productivity of…

Transiting exoplanet candidates from K2 Campaigns 5 and 6

NASA Astrophysics Data System (ADS)

Pope, Benjamin J. S.; Parviainen, Hannu; Aigrain, Suzanne

2016-10-01

We introduce a new transit search and vetting pipeline for observations from the K2 mission, and present the candidate transiting planets identified by this pipeline out of the targets in Campaigns 5 and 6. Our pipeline uses the Gaussian process-based K2SC code to correct for the K2 pointing systematics and simultaneously model stellar variability. The systematics-corrected, variability-detrended light curves are searched for transits with the box-least-squares method, and a period-dependent detection threshold is used to generate a preliminary candidate list. Two or three individuals vet each candidate manually to produce the final candidate list, using a set of automatically generated transit fits and assorted diagnostic tests to inform the vetting. We detect 145 single-planet system candidates and 5 multi-planet systems, independently recovering the previously published hot Jupiters EPIC 212110888b, WASP-55b (EPIC 212300977b) and Qatar-2b (EPIC 212756297b). We also report the outcome of reconnaissance spectroscopy carried out for all candidates with Kepler magnitude Kp ≤ 13, identifying 12 targets as likely false positives. We compare our results to those of other K2 transit search pipelines, noting that ours performs particularly well for variable and/or active stars, but that the results are very similar overall. All the light curves and code used in the transit search and vetting process are publicly available, as are the follow-up spectra.

OntoADR a semantic resource describing adverse drug reactions to support searching, coding, and information retrieval.

PubMed

Souvignet, Julien; Declerck, Gunnar; Asfari, Hadyl; Jaulent, Marie-Christine; Bousquet, Cédric

2016-10-01

Efficient searching and coding in databases that use terminological resources requires that they support efficient data retrieval. The Medical Dictionary for Regulatory Activities (MedDRA) is a reference terminology for several countries and organizations to code adverse drug reactions (ADRs) for pharmacovigilance. Ontologies that are available in the medical domain provide several advantages such as reasoning to improve data retrieval. The field of pharmacovigilance does not yet benefit from a fully operational ontology to formally represent the MedDRA terms. Our objective was to build a semantic resource based on formal description logic to improve MedDRA term retrieval and aid the generation of on-demand custom groupings by appropriately and efficiently selecting terms: OntoADR. The method consists of the following steps: (1) mapping between MedDRA terms and SNOMED-CT, (2) generation of semantic definitions using semi-automatic methods, (3) storage of the resource and (4) manual curation by pharmacovigilance experts. We built a semantic resource for ADRs enabling a new type of semantics-based term search. OntoADR adds new search capabilities relative to previous approaches, overcoming the usual limitations of computation using lightweight description logic, such as the intractability of unions or negation queries, bringing it closer to user needs. Our automated approach for defining MedDRA terms enabled the association of at least one defining relationship with 67% of preferred terms. The curation work performed on our sample showed an error level of 14% for this automated approach. We tested OntoADR in practice, which allowed us to build custom groupings for several medical topics of interest. The methods we describe in this article could be adapted and extended to other terminologies which do not benefit from a formal semantic representation, thus enabling better data retrieval performance. Our custom groupings of MedDRA terms were used while performing signal detection, which suggests that the graphical user interface we are currently implementing to process OntoADR could be usefully integrated into specialized pharmacovigilance software that rely on MedDRA. Copyright © 2016 Elsevier Inc. All rights reserved.

New knowledge-based genetic algorithm for excavator boom structural optimization

NASA Astrophysics Data System (ADS)

Hua, Haiyan; Lin, Shuwen

2014-03-01

Due to the insufficiency of utilizing knowledge to guide the complex optimal searching, existing genetic algorithms fail to effectively solve excavator boom structural optimization problem. To improve the optimization efficiency and quality, a new knowledge-based real-coded genetic algorithm is proposed. A dual evolution mechanism combining knowledge evolution with genetic algorithm is established to extract, handle and utilize the shallow and deep implicit constraint knowledge to guide the optimal searching of genetic algorithm circularly. Based on this dual evolution mechanism, knowledge evolution and population evolution can be connected by knowledge influence operators to improve the configurability of knowledge and genetic operators. Then, the new knowledge-based selection operator, crossover operator and mutation operator are proposed to integrate the optimal process knowledge and domain culture to guide the excavator boom structural optimization. Eight kinds of testing algorithms, which include different genetic operators, are taken as examples to solve the structural optimization of a medium-sized excavator boom. By comparing the results of optimization, it is shown that the algorithm including all the new knowledge-based genetic operators can more remarkably improve the evolutionary rate and searching ability than other testing algorithms, which demonstrates the effectiveness of knowledge for guiding optimal searching. The proposed knowledge-based genetic algorithm by combining multi-level knowledge evolution with numerical optimization provides a new effective method for solving the complex engineering optimization problem.

Behavior and neural basis of near-optimal visual search

PubMed Central

Ma, Wei Ji; Navalpakkam, Vidhya; Beck, Jeffrey M; van den Berg, Ronald; Pouget, Alexandre

2013-01-01

The ability to search efficiently for a target in a cluttered environment is one of the most remarkable functions of the nervous system. This task is difficult under natural circumstances, as the reliability of sensory information can vary greatly across space and time and is typically a priori unknown to the observer. In contrast, visual-search experiments commonly use stimuli of equal and known reliability. In a target detection task, we randomly assigned high or low reliability to each item on a trial-by-trial basis. An optimal observer would weight the observations by their trial-to-trial reliability and combine them using a specific nonlinear integration rule. We found that humans were near-optimal, regardless of whether distractors were homogeneous or heterogeneous and whether reliability was manipulated through contrast or shape. We present a neural-network implementation of near-optimal visual search based on probabilistic population coding. The network matched human performance. PMID:21552276

Trends in chemical ecology revealed with a personal computer program for searching data bases of scientific references and abstracts.

PubMed

Byers, J A

1992-09-01

A compiled program, JCE-REFS.EXE (coded in the QuickBASIC language), for use on IBM-compatible personal computers is described. The program converts a DOS text file of current B-I-T-S (BIOSIS Information Transfer System) or BIOSIS Previews references into a DOS file of citations, including abstracts, in a general style used by scientific journals. The latter file can be imported directly into a word processor or the program can convert the file into a random access data base of the references. The program can search the data base for up to 40 text strings with Boolean logic. Selected references in the data base can be exported as a DOS text file of citations. Using the search facility, articles in theJournal of Chemical Ecology from 1975 to 1991 were searched for certain key words in regard to semiochemicals, taxa, methods, chemical classes, and biological terms to determine trends in usage over the period. Positive trends were statistically significant in the use of the words: semiochemical, allomone, allelochemic, deterrent, repellent, plants, angiosperms, dicots, wind tunnel, olfactometer, electrophysiology, mass spectrometry, ketone, evolution, physiology, herbivore, defense, and receptor. Significant negative trends were found for: pheromone, vertebrates, mammals, Coleoptera, Scolytidae,Dendroctonus, lactone, isomer, and calling.

Real-time Automatic Search for Multi-wavelength Counterparts of DWF Transients

NASA Astrophysics Data System (ADS)

Murphy, Christopher; Cucchiara, Antonino; Andreoni, Igor; Cooke, Jeff; Hegarty, Sarah

2018-01-01

The Deeper Wider Faster (DWF) survey aims to find and classify the fastest transients in the Universe. DWF utilizes the Dark Energy Camera (DECam), collecting a continuous sequence of 20s images over a 3 square degree field of view.Once an interesting transient is detected during DWF observations, the DWF collaboration has access to several facilities for rapid follow-up in multiple wavelengths (from gamma to radio).An online web tool has been designed to help with real-time visual classification of possible astrophysical transients in data collected by the DWF observing program. The goal of this project is to create a python-based code to improve the classification process by querying several existing archive databases. Given the DWF transient location and search radius, the developed code will extract a list of possible counterparts and all available information (e.g. magnitude, radio fluxes, distance separation).Thanks to this tool, the human classifier can make a quicker decision in order to trigger the collaboration rapid-response resources.

A decoding procedure for the Reed-Solomon codes

NASA Technical Reports Server (NTRS)

Lim, R. S.

1978-01-01

A decoding procedure is described for the (n,k) t-error-correcting Reed-Solomon (RS) code, and an implementation of the (31,15) RS code for the I4-TENEX central system. This code can be used for error correction in large archival memory systems. The principal features of the decoder are a Galois field arithmetic unit implemented by microprogramming a microprocessor, and syndrome calculation by using the g(x) encoding shift register. Complete decoding of the (31,15) code is expected to take less than 500 microsecs. The syndrome calculation is performed by hardware using the encoding shift register and a modified Chien search. The error location polynomial is computed by using Lin's table, which is an interpretation of Berlekamp's iterative algorithm. The error location numbers are calculated by using the Chien search. Finally, the error values are computed by using Forney's method.

Find a Podiatrist

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Observational Coding Systems of Parent-Child Interactions During Painful Procedures: A Systematic Review.

PubMed

Bai, Jinbing; Swanson, Kristen M; Santacroce, Sheila J

2018-01-01

Parent interactions with their child can influence the child's pain and distress during painful procedures. Reliable and valid interaction analysis systems (IASs) are valuable tools for capturing these interactions. The extent to which IASs are used in observational research of parent-child interactions is unknown in pediatric populations. To identify and evaluate studies that focus on assessing psychometric properties of initial iterations/publications of observational coding systems of parent-child interactions during painful procedures. To identify and evaluate studies that focus on assessing psychometric properties of initial iterations/publications of observational coding systems of parent-child interactions during painful procedures. Computerized databases searched included PubMed, CINAHL, PsycINFO, Health and Psychosocial Instruments, and Scopus. Timeframes covered from inception of the database to January 2017. Studies were included if they reported use or psychometrics of parent-child IASs. First assessment was whether the parent-child IASs were theory-based; next, using the Society of Pediatric Psychology Assessment Task Force criteria IASs were assigned to one of three categories: well-established, approaching well-established, or promising. A total of 795 studies were identified through computerized searches. Eighteen studies were ultimately determined to be eligible for inclusion in the review and 17 parent-child IASs were identified from these 18 studies. Among the 17 coding systems, 14 were suitable for use in children age 3 years or more; two were theory-based; and 11 included verbal and nonverbal parent behaviors that promoted either child coping or child distress. Four IASs were assessed as well-established; seven approached well-established; and six were promising. Findings indicate a need for the development of theory-based parent-child IASs that consider both verbal and nonverbal parent behaviors during painful procedures. Findings also suggest a need for further testing of those parent-child IASs deemed "approaching well-established" or "promising". © 2017 World Institute of Pain.

The contribution to immediate serial recall of rehearsal, search speed, access to lexical memory, and phonological coding: an investigation at the construct level.

PubMed

Tehan, Gerald; Fogarty, Gerard; Ryan, Katherine

2004-07-01

Rehearsal speed has traditionally been seen to be the prime determinant of individual differences in memory span. Recent studies, in the main using young children as the participant population, have suggested other contributors to span performance. In the present research, we used structural equation modeling to explore, at the construct level, individual differences in immediate serial recall with respect to rehearsal, search, phonological coding, and speed of access to lexical memory. We replicated standard short-term phenomena; we showed that the variables that influence children's span performance influence adult performance in the same way; and we showed that speed of access to lexical memory and facility with phonological codes appear to be more potent sources of individual differences in immediate memory than is either rehearsal speed or search factors.

Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed.

PubMed

Eisinger, Daniel; Tsatsaronis, George; Bundschus, Markus; Wieneke, Ulrich; Schroeder, Michael

2013-04-15

Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms.Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources.

Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed

PubMed Central

2013-01-01

Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms. Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources. PMID:23734562

Parallel coding of conjunctions in visual search.

PubMed

Found, A

1998-10-01

Two experiments investigated whether the conjunctive nature of nontarget items influenced search for a conjunction target. Each experiment consisted of two conditions. In both conditions, the target item was a red bar tilted to the right, among white tilted bars and vertical red bars. As well as color and orientation, display items also differed in terms of size. Size was irrelevant to search in that the size of the target varied randomly from trial to trial. In one condition, the size of items correlated with the other attributes of display items (e.g., all red items were big and all white items were small). In the other condition, the size of items varied randomly (i.e., some red items were small and some were big, and some white items were big and some were small). Search was more efficient in the size-correlated condition, consistent with the parallel coding of conjunctions in visual search.

Evolutionary Construction of Block-Based Neural Networks in Consideration of Failure

NASA Astrophysics Data System (ADS)

Takamori, Masahito; Koakutsu, Seiichi; Hamagami, Tomoki; Hirata, Hironori

In this paper we propose a modified gene coding and an evolutionary construction in consideration of failure in evolutionary construction of Block-Based Neural Networks. In the modified gene coding, we arrange the genes of weights on a chromosome in consideration of the position relation of the genes of weight and structure. By the modified gene coding, the efficiency of search by crossover is increased. Thereby, it is thought that improvement of the convergence rate of construction and shortening of construction time can be performed. In the evolutionary construction in consideration of failure, the structure which is adapted for failure is built in the state where failure occured. Thereby, it is thought that BBNN can be reconstructed in a short time at the time of failure. To evaluate the proposed method, we apply it to pattern classification and autonomous mobile robot control problems. The computational experiments indicate that the proposed method can improve convergence rate of construction and shorten of construction and reconstruction time.

Neural networks for data compression and invariant image recognition

NASA Technical Reports Server (NTRS)

Gardner, Sheldon

1989-01-01

An approach to invariant image recognition (I2R), based upon a model of biological vision in the mammalian visual system (MVS), is described. The complete I2R model incorporates several biologically inspired features: exponential mapping of retinal images, Gabor spatial filtering, and a neural network associative memory. In the I2R model, exponentially mapped retinal images are filtered by a hierarchical set of Gabor spatial filters (GSF) which provide compression of the information contained within a pixel-based image. A neural network associative memory (AM) is used to process the GSF coded images. We describe a 1-D shape function method for coding of scale and rotationally invariant shape information. This method reduces image shape information to a periodic waveform suitable for coding as an input vector to a neural network AM. The shape function method is suitable for near term applications on conventional computing architectures equipped with VLSI FFT chips to provide a rapid image search capability.

Modernizing the ATLAS simulation infrastructure

NASA Astrophysics Data System (ADS)

Di Simone, A.; CollaborationAlbert-Ludwigs-Universitt Freiburg, ATLAS; Institut, Physikalisches; Br., 79104 Freiburg i.; Germany

2017-10-01

The ATLAS Simulation infrastructure has been used to produce upwards of 50 billion proton-proton collision events for analyses ranging from detailed Standard Model measurements to searches for exotic new phenomena. In the last several years, the infrastructure has been heavily revised to allow intuitive multithreading and significantly improved maintainability. Such a massive update of a legacy code base requires careful choices about what pieces of code to completely rewrite and what to wrap or revise. The initialization of the complex geometry was generalized to allow new tools and geometry description languages, popular in some detector groups. The addition of multithreading requires Geant4-MT and GaudiHive, two frameworks with fundamentally different approaches to multithreading, to work together. It also required enforcing thread safety throughout a large code base, which required the redesign of several aspects of the simulation, including truth, the record of particle interactions with the detector during the simulation. These advances were possible thanks to close interactions with the Geant4 developers.

Stakeholders perspectives on the key components of community-based interventions coordinating care in dementia: a qualitative systematic review.

PubMed

Backhouse, Amy; Richards, David A; McCabe, Rose; Watkins, Ross; Dickens, Chris

2017-11-22

Interventions aiming to coordinate services for the community-based dementia population vary in components, organisation and implementation. In this review we aimed to investigate the views of stakeholders on the key components of community-based interventions coordinating care in dementia. We searched four databases from inception to June 2015; Medline, The Cochrane Library, EMBASE and PsycINFO, this was aided by a search of four grey literature databases, and backward and forward citation tracking of included papers. Title and abstract screening was followed by a full text screen by two independent reviewers, and quality was assessed using the CASP appraisal tool. We then conducted thematic synthesis on extracted data. A total of seven papers from five independent studies were included in the review, and encompassed the views of over 100 participants from three countries. Through thematic synthesis we identified 32 initial codes that were grouped into 5 second-order themes: (1) case manager had four associated codes and described preferences for the case manager personal and professional attributes, including a sound knowledge in dementia and availability of local services; (2) communication had five associated codes and emphasized the importance stakeholders placed on multichannel communication with service users, as well as between multidisciplinary teams and across organisations; (3) intervention had 11 associated codes which focused primarily on the practicalities of implementation such as the contact type and frequency between case managers and service users, and the importance of case manager training and service evaluation; (4) resources had five associated codes which outlined stakeholder views on the required resources for coordinating interventions and potential overlap with existing resources, as well as arising issues when available resources do not meet those required for successful implementation; and (5) support had seven associated codes that reflect the importance that was placed on the support network around the case manager and the investment of professionals involved directly in care as well as the wider professional network. The synthesis of relevant qualitative studies has shown how various stakeholder groups considered dementia care coordination interventions to be acceptable, useful and appropriate for dementia care, and have clear preferences for components, implementation methods and settings of these interventions. By incorporating stakeholders' perspectives and preferences when planning and developing coordinating interventions we may increase the likelihood of successful implementation and patient benefits.

NOAA Weather Radio - SAME

Science.gov Websites

Station Search Coverage Maps Outages View Outages Report Outages Information General Information Receiver Information Reception Problems NWR Alarms Automated Voices FIPS Codes NWR - Special Needs SAME USING SAME SAME FIPS (Federal Information Processing Standards) code changes and / or SAME location code changes

Indexing, Browsing, and Searching of Digital Video.

ERIC Educational Resources Information Center

Smeaton, Alan F.

2004-01-01

Presents a literature review that covers the following topics related to indexing, browsing, and searching of digital video: video coding and standards; conventional approaches to accessing digital video; automatically structuring and indexing digital video; searching, browsing, and summarization; measurement and evaluation of the effectiveness of…

A Comparison of Source Code Plagiarism Detection Engines

NASA Astrophysics Data System (ADS)

Lancaster, Thomas; Culwin, Fintan

2004-06-01

Automated techniques for finding plagiarism in student source code submissions have been in use for over 20 years and there are many available engines and services. This paper reviews the literature on the major modern detection engines, providing a comparison of them based upon the metrics and techniques they deploy. Generally the most common and effective techniques are seen to involve tokenising student submissions then searching pairs of submissions for long common substrings, an example of what is defined to be a paired structural metric. Computing academics are recommended to use one of the two Web-based detection engines, MOSS and JPlag. It is shown that whilst detection is well established there are still places where further research would be useful, particularly where visual support of the investigation process is possible.

LSE-Sign: A lexical database for Spanish Sign Language.

PubMed

Gutierrez-Sigut, Eva; Costello, Brendan; Baus, Cristina; Carreiras, Manuel

2016-03-01

The LSE-Sign database is a free online tool for selecting Spanish Sign Language stimulus materials to be used in experiments. It contains 2,400 individual signs taken from a recent standardized LSE dictionary, and a further 2,700 related nonsigns. Each entry is coded for a wide range of grammatical, phonological, and articulatory information, including handshape, location, movement, and non-manual elements. The database is accessible via a graphically based search facility which is highly flexible both in terms of the search options available and the way the results are displayed. LSE-Sign is available at the following website: http://www.bcbl.eu/databases/lse/.

National Centers for Environmental Prediction

Science.gov Websites

Organization Search Enter text Search Navigation Bar End Cap Search EMC Go Branches Global Climate and Weather Modeling Mesoscale Modeling Marine Modeling and Analysis Teams Climate Data Assimilation Ensembles and Post Model Configuration Collaborators Documentation and Code FAQ Operational Change Log Parallel Experiment

Behavior Change Techniques in Apps for Medication Adherence: A Content Analysis.

PubMed

Morrissey, Eimear C; Corbett, Teresa K; Walsh, Jane C; Molloy, Gerard J

2016-05-01

There are a vast number of smartphone applications (apps) aimed at promoting medication adherence on the market; however, the theory and evidence base in terms of applying established health behavior change techniques underpinning these apps remains unclear. This study aimed to code these apps using the Behavior Change Technique Taxonomy (v1) for the presence or absence of established behavior change techniques. The sample of apps was identified through systematic searches in both the Google Play Store and Apple App Store in February 2015. All apps that fell into the search categories were downloaded for analysis. The downloaded apps were screened with exclusion criteria, and suitable apps were reviewed and coded for behavior change techniques in March 2015. Two researchers performed coding independently. In total, 166 medication adherence apps were identified and coded. The number of behavior change techniques contained in an app ranged from zero to seven (mean=2.77). A total of 12 of a possible 96 behavior change techniques were found to be present across apps. The most commonly included behavior change techniques were "action planning" and "prompt/cues," which were included in 96% of apps, followed by "self-monitoring" (37%) and "feedback on behavior" (36%). The current extent to which established behavior change techniques are used in medication adherence apps is limited. The development of medication adherence apps may not have benefited from advances in the theory and practice of health behavior change. Copyright © 2016 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes

NASA Technical Reports Server (NTRS)

Lin, Shu

1998-01-01

A code trellis is a graphical representation of a code, block or convolutional, in which every path represents a codeword (or a code sequence for a convolutional code). This representation makes it possible to implement Maximum Likelihood Decoding (MLD) of a code with reduced decoding complexity. The most well known trellis-based MLD algorithm is the Viterbi algorithm. The trellis representation was first introduced and used for convolutional codes [23]. This representation, together with the Viterbi decoding algorithm, has resulted in a wide range of applications of convolutional codes for error control in digital communications over the last two decades. There are two major reasons for this inactive period of research in this area. First, most coding theorists at that time believed that block codes did not have simple trellis structure like convolutional codes and maximum likelihood decoding of linear block codes using the Viterbi algorithm was practically impossible, except for very short block codes. Second, since almost all of the linear block codes are constructed algebraically or based on finite geometries, it was the belief of many coding theorists that algebraic decoding was the only way to decode these codes. These two reasons seriously hindered the development of efficient soft-decision decoding methods for linear block codes and their applications to error control in digital communications. This led to a general belief that block codes are inferior to convolutional codes and hence, that they were not useful. Chapter 2 gives a brief review of linear block codes. The goal is to provide the essential background material for the development of trellis structure and trellis-based decoding algorithms for linear block codes in the later chapters. Chapters 3 through 6 present the fundamental concepts, finite-state machine model, state space formulation, basic structural properties, state labeling, construction procedures, complexity, minimality, and sectionalization of trellises. Chapter 7 discusses trellis decomposition and subtrellises for low-weight codewords. Chapter 8 first presents well known methods for constructing long powerful codes from short component codes or component codes of smaller dimensions, and then provides methods for constructing their trellises which include Shannon and Cartesian product techniques. Chapter 9 deals with convolutional codes, puncturing, zero-tail termination and tail-biting.Chapters 10 through 13 present various trellis-based decoding algorithms, old and new. Chapter 10 first discusses the application of the well known Viterbi decoding algorithm to linear block codes, optimum sectionalization of a code trellis to minimize computation complexity, and design issues for IC (integrated circuit) implementation of a Viterbi decoder. Then it presents a new decoding algorithm for convolutional codes, named Differential Trellis Decoding (DTD) algorithm. Chapter 12 presents a suboptimum reliability-based iterative decoding algorithm with a low-weight trellis search for the most likely codeword. This decoding algorithm provides a good trade-off between error performance and decoding complexity. All the decoding algorithms presented in Chapters 10 through 12 are devised to minimize word error probability. Chapter 13 presents decoding algorithms that minimize bit error probability and provide the corresponding soft (reliability) information at the output of the decoder. Decoding algorithms presented are the MAP (maximum a posteriori probability) decoding algorithm and the Soft-Output Viterbi Algorithm (SOVA) algorithm. Finally, the minimization of bit error probability in trellis-based MLD is discussed.

Development of free-piston Stirling engine performance and optimization codes based on Martini simulation technique

NASA Technical Reports Server (NTRS)

Martini, William R.

1989-01-01

A FORTRAN computer code is described that could be used to design and optimize a free-displacer, free-piston Stirling engine similar to the RE-1000 engine made by Sunpower. The code contains options for specifying displacer and power piston motion or for allowing these motions to be calculated by a force balance. The engine load may be a dashpot, inertial compressor, hydraulic pump or linear alternator. Cycle analysis may be done by isothermal analysis or adiabatic analysis. Adiabatic analysis may be done using the Martini moving gas node analysis or the Rios second-order Runge-Kutta analysis. Flow loss and heat loss equations are included. Graphical display of engine motions and pressures and temperatures are included. Programming for optimizing up to 15 independent dimensions is included. Sample performance results are shown for both specified and unconstrained piston motions; these results are shown as generated by each of the two Martini analyses. Two sample optimization searches are shown using specified piston motion isothermal analysis. One is for three adjustable input and one is for four. Also, two optimization searches for calculated piston motion are presented for three and for four adjustable inputs. The effect of leakage is evaluated. Suggestions for further work are given.

Wavelet domain textual coding of Ottoman script images

NASA Astrophysics Data System (ADS)

Gerek, Oemer N.; Cetin, Enis A.; Tewfik, Ahmed H.

1996-02-01

Image coding using wavelet transform, DCT, and similar transform techniques is well established. On the other hand, these coding methods neither take into account the special characteristics of the images in a database nor are they suitable for fast database search. In this paper, the digital archiving of Ottoman printings is considered. Ottoman documents are printed in Arabic letters. Witten et al. describes a scheme based on finding the characters in binary document images and encoding the positions of the repeated characters This method efficiently compresses document images and is suitable for database research, but it cannot be applied to Ottoman or Arabic documents as the concept of character is different in Ottoman or Arabic. Typically, one has to deal with compound structures consisting of a group of letters. Therefore, the matching criterion will be according to those compound structures. Furthermore, the text images are gray tone or color images for Ottoman scripts for the reasons that are described in the paper. In our method the compound structure matching is carried out in wavelet domain which reduces the search space and increases the compression ratio. In addition to the wavelet transformation which corresponds to the linear subband decomposition, we also used nonlinear subband decomposition. The filters in the nonlinear subband decomposition have the property of preserving edges in the low resolution subband image.

Cloud based, Open Source Software Application for Mitigating Herbicide Drift

NASA Astrophysics Data System (ADS)

Saraswat, D.; Scott, B.

2014-12-01

The spread of herbicide resistant weeds has resulted in the need for clearly marked fields. In response to this need, the University of Arkansas Cooperative Extension Service launched a program named Flag the Technology in 2011. This program uses color-coded flags as a visual alert of the herbicide trait technology within a farm field. The flag based program also serves to help avoid herbicide misapplication and prevent herbicide drift damage between fields with differing crop technologies. This program has been endorsed by Southern Weed Science Society of America and is attracting interest from across the USA, Canada, and Australia. However, flags have risk of misplacement or disappearance due to mischief or severe windstorms/thunderstorms, respectively. This presentation will discuss the design and development of a cloud-based, free application utilizing open-source technologies, called Flag the Technology Cloud (FTTCloud), for allowing agricultural stakeholders to color code their farm fields for indicating herbicide resistant technologies. The developed software utilizes modern web development practices, widely used design technologies, and basic geographic information system (GIS) based interactive interfaces for representing, color-coding, searching, and visualizing fields. This program has also been made compatible for a wider usability on different size devices- smartphones, tablets, desktops and laptops.

Adaptive Correlation Space Adjusted Open-Loop Tracking Approach for Vehicle Positioning with Global Navigation Satellite System in Urban Areas

PubMed Central

Ruan, Hang; Li, Jian; Zhang, Lei; Long, Teng

2015-01-01

For vehicle positioning with Global Navigation Satellite System (GNSS) in urban areas, open-loop tracking shows better performance because of its high sensitivity and superior robustness against multipath. However, no previous study has focused on the effects of the code search grid size on the code phase measurement accuracy of open-loop tracking. Traditional open-loop tracking methods are performed by the batch correlators with fixed correlation space. The code search grid size, which is the correlation space, is a constant empirical value and the code phase measuring accuracy will be largely degraded due to the improper grid size, especially when the signal carrier-to-noise density ratio (C/N0) varies. In this study, the Adaptive Correlation Space Adjusted Open-Loop Tracking Approach (ACSA-OLTA) is proposed to improve the code phase measurement dependent pseudo range accuracy. In ACSA-OLTA, the correlation space is adjusted according to the signal C/N0. The novel Equivalent Weighted Pseudo Range Error (EWPRE) is raised to obtain the optimal code search grid sizes for different C/N0. The code phase measuring errors of different measurement calculation methods are analyzed for the first time. The measurement calculation strategy of ACSA-OLTA is derived from the analysis to further improve the accuracy but reduce the correlator consumption. Performance simulation and real tests confirm that the pseudo range and positioning accuracy of ASCA-OLTA are better than the traditional open-loop tracking methods in the usual scenarios of urban area. PMID:26343683

A Novel Design of Reconfigurable Wavelength-Time Optical Codes to Enhance Security in Optical CDMA Networks

NASA Astrophysics Data System (ADS)

Nasaruddin; Tsujioka, Tetsuo

An optical CDMA (OCDMA) system is a flexible technology for future broadband multiple access networks. A secure OCDMA network in broadband optical access technologies is also becoming an issue of great importance. In this paper, we propose novel reconfigurable wavelength-time (W-T) optical codes that lead to secure transmission in OCDMA networks. The proposed W-T optical codes are constructed by using quasigroups (QGs) for wavelength hopping and one-dimensional optical orthogonal codes (OOCs) for time spreading; we call them QGs/OOCs. Both QGs and OOCs are randomly generated by a computer search to ensure that an eavesdropper could not improve its interception performance by making use of the coding structure. Then, the proposed reconfigurable QGs/OOCs can provide more codewords, and many different code set patterns, which differ in both wavelength and time positions for given code parameters. Moreover, the bit error probability of the proposed codes is analyzed numerically. To realize the proposed codes, a secure system is proposed by employing reconfigurable encoders/decoders based on array waveguide gratings (AWGs), which allow the users to change their codeword patterns to protect against eavesdropping. Finally, the probability of breaking a certain codeword in the proposed system is evaluated analytically. The results show that the proposed codes and system can provide a large codeword pattern, and decrease the probability of breaking a certain codeword, to enhance OCDMA network security.

Android Platform Based Smartphones for a Logistical Remote Association Repair Framework

PubMed Central

Lien, Shao-Fan; Wang, Chun-Chieh; Su, Juhng-Perng; Chen, Hong-Ming; Wu, Chein-Hsing

2014-01-01

The maintenance of large-scale systems is an important issue for logistics support planning. In this paper, we developed a Logistical Remote Association Repair Framework (LRARF) to aid repairmen in keeping the system available. LRARF includes four subsystems: smart mobile phones, a Database Management System (DBMS), a Maintenance Support Center (MSC) and wireless networks. The repairman uses smart mobile phones to capture QR-codes and the images of faulty circuit boards. The captured QR-codes and images are transmitted to the DBMS so the invalid modules can be recognized via the proposed algorithm. In this paper, the Linear Projective Transform (LPT) is employed for fast QR-code calibration. Moreover, the ANFIS-based data mining system is used for module identification and searching automatically for the maintenance manual corresponding to the invalid modules. The inputs of the ANFIS-based data mining system are the QR-codes and image features; the output is the module ID. DBMS also transmits the maintenance manual back to the maintenance staff. If modules are not recognizable, the repairmen and center engineers can obtain the relevant information about the invalid modules through live video. The experimental results validate the applicability of the Android-based platform in the recognition of invalid modules. In addition, the live video can also be recorded synchronously on the MSC for later use. PMID:24967603

Searching the scientific literature: implications for quantitative and qualitative reviews.

PubMed

Wu, Yelena P; Aylward, Brandon S; Roberts, Michael C; Evans, Spencer C

2012-08-01

Literature reviews are an essential step in the research process and are included in all empirical and review articles. Electronic databases are commonly used to gather this literature. However, several factors can affect the extent to which relevant articles are retrieved, influencing future research and conclusions drawn. The current project examined articles obtained by comparable search strategies in two electronic archives using an exemplar search to illustrate factors that authors should consider when designing their own search strategies. Specifically, literature searches were conducted in PsycINFO and PubMed targeting review articles on two exemplar disorders (bipolar disorder and attention deficit/hyperactivity disorder) and issues of classification and/or differential diagnosis. Articles were coded for relevance and characteristics of article content. The two search engines yielded significantly different proportions of relevant articles overall and by disorder. Keywords differed across search engines for the relevant articles identified. Based on these results, it is recommended that when gathering literature for review papers, multiple search engines should be used, and search syntax and strategies be tailored to the unique capabilities of particular engines. For meta-analyses and systematic reviews, authors may consider reporting the extent to which different archives or sources yielded relevant articles for their particular review. Copyright © 2012 Elsevier Ltd. All rights reserved.

BSIFT: toward data-independent codebook for large scale image search.

PubMed

Zhou, Wengang; Li, Houqiang; Hong, Richang; Lu, Yijuan; Tian, Qi

2015-03-01

Bag-of-Words (BoWs) model based on Scale Invariant Feature Transform (SIFT) has been widely used in large-scale image retrieval applications. Feature quantization by vector quantization plays a crucial role in BoW model, which generates visual words from the high- dimensional SIFT features, so as to adapt to the inverted file structure for the scalable retrieval. Traditional feature quantization approaches suffer several issues, such as necessity of visual codebook training, limited reliability, and update inefficiency. To avoid the above problems, in this paper, a novel feature quantization scheme is proposed to efficiently quantize each SIFT descriptor to a descriptive and discriminative bit-vector, which is called binary SIFT (BSIFT). Our quantizer is independent of image collections. In addition, by taking the first 32 bits out from BSIFT as code word, the generated BSIFT naturally lends itself to adapt to the classic inverted file structure for image indexing. Moreover, the quantization error is reduced by feature filtering, code word expansion, and query sensitive mask shielding. Without any explicit codebook for quantization, our approach can be readily applied in image search in some resource-limited scenarios. We evaluate the proposed algorithm for large scale image search on two public image data sets. Experimental results demonstrate the index efficiency and retrieval accuracy of our approach.

Color coding of control room displays: the psychocartography of visual layering effects.

PubMed

Van Laar, Darren; Deshe, Ofer

2007-06-01

To evaluate which of three color coding methods (monochrome, maximally discriminable, and visual layering) used to code four types of control room display format (bars, tables, trend, mimic) was superior in two classes of task (search, compare). It has recently been shown that color coding of visual layers, as used in cartography, may be used to color code any type of information display, but this has yet to be fully evaluated. Twenty-four people took part in a 2 (task) x 3 (coding method) x 4 (format) wholly repeated measures design. The dependent variables assessed were target location reaction time, error rates, workload, and subjective feedback. Overall, the visual layers coding method produced significantly faster reaction times than did the maximally discriminable and the monochrome methods for both the search and compare tasks. No significant difference in errors was observed between conditions for either task type. Significantly less perceived workload was experienced with the visual layers coding method, which was also rated more highly than the other coding methods on a 14-item visual display quality questionnaire. The visual layers coding method is superior to other color coding methods for control room displays when the method supports the user's task. The visual layers color coding method has wide applicability to the design of all complex information displays utilizing color coding, from the most maplike (e.g., air traffic control) to the most abstract (e.g., abstracted ecological display).

Balancing Particle and Mesh Computation in a Particle-In-Cell Code

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

Worley, Patrick H; D'Azevedo, Eduardo; Hager, Robert

2016-01-01

The XGC1 plasma microturbulence particle-in-cell simulation code has both particle-based and mesh-based computational kernels that dominate performance. Both of these are subject to load imbalances that can degrade performance and that evolve during a simulation. Each separately can be addressed adequately, but optimizing just for one can introduce significant load imbalances in the other, degrading overall performance. A technique has been developed based on Golden Section Search that minimizes wallclock time given prior information on wallclock time, and on current particle distribution and mesh cost per cell, and also adapts to evolution in load imbalance in both particle and meshmore » work. In problems of interest this doubled the performance on full system runs on the XK7 at the Oak Ridge Leadership Computing Facility compared to load balancing only one of the kernels.« less

National Centers for Environmental Prediction

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Organization Search Enter text Search Navigation Bar End Cap Search EMC Go Branches Global Climate and Weather Modeling Mesoscale Modeling Marine Modeling and Analysis Teams Climate Data Assimilation Ensembles and Post Configuration Collaborators Documentation and Code FAQ Operational Change Log Parallel Experiment Change Log

National Centers for Environmental Prediction

Science.gov Websites

Organization Search Enter text Search Navigation Bar End Cap Search EMC Go Branches Global Climate and Weather Modeling Mesoscale Modeling Marine Modeling and Analysis Teams Climate Data Assimilation Ensembles and Post Collaborators Documentation and Code FAQ Operational Change Log Parallel Experiment Change Log Contacts

Low-Density Parity-Check (LDPC) Codes Constructed from Protographs

NASA Astrophysics Data System (ADS)

Thorpe, J.

2003-08-01

We introduce a new class of low-density parity-check (LDPC) codes constructed from a template called a protograph. The protograph serves as a blueprint for constructing LDPC codes of arbitrary size whose performance can be predicted by analyzing the protograph. We apply standard density evolution techniques to predict the performance of large protograph codes. Finally, we use a randomized search algorithm to find good protographs.

MyMolDB: a micromolecular database solution with open source and free components.

PubMed

Xia, Bing; Tai, Zheng-Fu; Gu, Yu-Cheng; Li, Bang-Jing; Ding, Li-Sheng; Zhou, Yan

2011-10-01

To manage chemical structures in small laboratories is one of the important daily tasks. Few solutions are available on the internet, and most of them are closed source applications. The open-source applications typically have limited capability and basic cheminformatics functionalities. In this article, we describe an open-source solution to manage chemicals in research groups based on open source and free components. It has a user-friendly interface with the functions of chemical handling and intensive searching. MyMolDB is a micromolecular database solution that supports exact, substructure, similarity, and combined searching. This solution is mainly implemented using scripting language Python with a web-based interface for compound management and searching. Almost all the searches are in essence done with pure SQL on the database by using the high performance of the database engine. Thus, impressive searching speed has been archived in large data sets for no external Central Processing Unit (CPU) consuming languages were involved in the key procedure of the searching. MyMolDB is an open-source software and can be modified and/or redistributed under GNU General Public License version 3 published by the Free Software Foundation (Free Software Foundation Inc. The GNU General Public License, Version 3, 2007. Available at: http://www.gnu.org/licenses/gpl.html). The software itself can be found at http://code.google.com/p/mymoldb/. Copyright © 2011 Wiley Periodicals, Inc.

Defining pediatric traumatic brain injury using International Classification of Diseases Version 10 Codes: a systematic review.

PubMed

Chan, Vincy; Thurairajah, Pravheen; Colantonio, Angela

2015-02-04

Although healthcare administrative data are commonly used for traumatic brain injury (TBI) research, there is currently no consensus or consistency on the International Classification of Diseases Version 10 (ICD-10) codes used to define TBI among children and youth internationally. This study systematically reviewed the literature to explore the range of ICD-10 codes that are used to define TBI in this population. The identification of the range of ICD-10 codes to define this population in administrative data is crucial, as it has implications for policy, resource allocation, planning of healthcare services, and prevention strategies. The databases MEDLINE, MEDLINE In-Process, Embase, PsychINFO, CINAHL, SPORTDiscus, and Cochrane Database of Systematic Reviews were systematically searched. Grey literature was searched using Grey Matters and Google. Reference lists of included articles were also searched for relevant studies. Two reviewers independently screened all titles and abstracts using pre-defined inclusion and exclusion criteria. A full text screen was conducted on articles that met the first screen inclusion criteria. All full text articles that met the pre-defined inclusion criteria were included for analysis in this systematic review. A total of 1,326 publications were identified through the predetermined search strategy and 32 articles/reports met all eligibility criteria for inclusion in this review. Five articles specifically examined children and youth aged 19 years or under with TBI. ICD-10 case definitions ranged from the broad injuries to the head codes (ICD-10 S00 to S09) to concussion only (S06.0). There was overwhelming consensus on the inclusion of ICD-10 code S06, intracranial injury, while codes S00 (superficial injury of the head), S03 (dislocation, sprain, and strain of joints and ligaments of head), and S05 (injury of eye and orbit) were only used by articles that examined head injury, none of which specifically examined children and youth. This review provides evidence for discussion on how best to use ICD codes for different goals. This is an important first step in reaching an appropriate definition and can inform future work on reaching consensus on the ICD-10 codes to define TBI for this vulnerable population.

Coding accuracy for Parkinson's disease hospital admissions: implications for healthcare planning in the UK.

PubMed

Muzerengi, S; Rick, C; Begaj, I; Ives, N; Evison, F; Woolley, R L; Clarke, C E

2017-05-01

Hospital Episode Statistics data are used for healthcare planning and hospital reimbursements. Reliability of these data is dependent on the accuracy of individual hospitals reporting Secondary Uses Service (SUS) which includes hospitalisation. The number and coding accuracy for Parkinson's disease hospital admissions at a tertiary centre in Birmingham was assessed. Retrospective, routine-data-based study. A retrospective electronic database search for all Parkinson's disease patients admitted to the tertiary hospital over a 4-year period (2009-2013) was performed on the SUS database using International Classification of Disease codes, and on the local inpatient electronic prescription database, Prescription and Information Communications System, using medication prescriptions. Capture-recapture methods were used to estimate the number of patients and admissions missed by both databases. From the two databases, between July 2009 and June 2013, 1068 patients with Parkinson's disease accounted for 1999 admissions. During these admissions, the Parkinson's disease was coded as a primary or secondary diagnosis. Ninety-one percent of these admissions were recorded on the SUS database. Capture-recapture methods estimated that the number of Parkinson's disease patients admitted during this period was 1127 patients (95% confidence interval: 1107-1146). A supplementary search of both SUS and Prescription and Information Communications System was undertaken using the hospital numbers of these 1068 patients. This identified another 479 admissions. SUS database under-estimated Parkinson's disease admissions by 27% during the study period. The accuracy of disease coding is critical for healthcare policy planning and must be improved. If the under-reporting of Parkinson's disease admissions on the SUS database is repeated nationally, expenditure on Parkinson's disease admissions in England is under-estimated by approximately £61 million per year. Copyright © 2016 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Evaluating Coding Accuracy in General Surgery Residents' Accreditation Council for Graduate Medical Education Procedural Case Logs.

PubMed

Balla, Fadi; Garwe, Tabitha; Motghare, Prasenjeet; Stamile, Tessa; Kim, Jennifer; Mahnken, Heidi; Lees, Jason

The Accreditation Council for Graduate Medical Education (ACGME) case log captures resident operative experience based on Current Procedural Terminology (CPT) codes and is used to track operative experience during residency. With increasing emphasis on resident operative experiences, coding is more important than ever. It has been shown in other surgical specialties at similar institutions that the residents' ACGME case log may not accurately reflect their operative experience. What barriers may influence this remains unclear. As the only objective measure of resident operative experience, an accurate case log is paramount in representing one's operative experience. This study aims to determine the accuracy of procedural coding by general surgical residents at a single institution. Data were collected from 2 consecutive graduating classes of surgical residents' ACGME case logs from 2008 to 2014. A total of 5799 entries from 7 residents were collected. The CPT codes entered by residents were compared to departmental billing records submitted by the attending surgeon for each procedure. Assigned CPT codes by institutional American Academy of Professional Coders certified abstract coders were considered the "gold standard." A total of 4356 (75.12%) of 5799 entries were identified in billing records. Excel 2010 and SAS 9.3 were used for analysis. In the event of multiple codes for the same patient, any match between resident codes and billing record codes was considered a "correct" entry. A 4-question survey was distributed to all current general surgical residents at our institution for feedback on coding habits, limitations to accurate coding, and opinions on ACGME case log representation of their operative experience. All 7 residents had a low percentage of correctly entered CPT codes. The overall accuracy proportion for all residents was 52.82% (range: 43.32%-60.07%). Only 1 resident showed significant improvement in accuracy during his/her training (p = 0.0043). The survey response rate was 100%. Survey results indicated that inability to find the precise code within the ACGME search interface and unfamiliarity with available CPT codes were by far the most common perceived barriers to accuracy. Survey results also indicated that most residents (74%) believe that they code accurately most of the time and agree that their case log would accurately represent their operative experience (66.6%). This is the first study to evaluate correctness of residents' ACGME case logs in general surgery. The degree of inaccuracy found here necessitates further investigation into the etiology of these discrepancies. Instruction on coding practices should also benefit the residents after graduation. Optimizing communication among attendings and residents, improving ACGME coding search interface, and implementing consistent coding practices could improve accuracy giving a more realistic view of residents' operative experience. Published by Elsevier Inc.

A Low-Storage-Consumption XML Labeling Method for Efficient Structural Information Extraction

NASA Astrophysics Data System (ADS)

Liang, Wenxin; Takahashi, Akihiro; Yokota, Haruo

Recently, labeling methods to extract and reconstruct the structural information of XML data, which are important for many applications such as XPath query and keyword search, are becoming more attractive. To achieve efficient structural information extraction, in this paper we propose C-DO-VLEI code, a novel update-friendly bit-vector encoding scheme, based on register-length bit operations combining with the properties of Dewey Order numbers, which cannot be implemented in other relevant existing schemes such as ORDPATH. Meanwhile, the proposed method also achieves lower storage consumption because it does not require either prefix schema or any reserved codes for node insertion. We performed experiments to evaluate and compare the performance and storage consumption of the proposed method with those of the ORDPATH method. Experimental results show that the execution times for extracting depth information and parent node labels using the C-DO-VLEI code are about 25% and 15% less, respectively, and the average label size using the C-DO-VLEI code is about 24% smaller, comparing with ORDPATH.

SOC-DS computer code provides tool for design evaluation of homogeneous two-material nuclear shield

NASA Technical Reports Server (NTRS)

Disney, R. K.; Ricks, L. O.

1967-01-01

SOC-DS Code /Shield Optimization Code-Direc Search/, selects a nuclear shield material of optimum volume, weight, or cost to meet the requirments of a given radiation dose rate or energy transmission constraint. It is applicable to evaluating neutron and gamma ray shields for all nuclear reactors.

Visual Tracking via Sparse and Local Linear Coding.

PubMed

Wang, Guofeng; Qin, Xueying; Zhong, Fan; Liu, Yue; Li, Hongbo; Peng, Qunsheng; Yang, Ming-Hsuan

2015-11-01

The state search is an important component of any object tracking algorithm. Numerous algorithms have been proposed, but stochastic sampling methods (e.g., particle filters) are arguably one of the most effective approaches. However, the discretization of the state space complicates the search for the precise object location. In this paper, we propose a novel tracking algorithm that extends the state space of particle observations from discrete to continuous. The solution is determined accurately via iterative linear coding between two convex hulls. The algorithm is modeled by an optimal function, which can be efficiently solved by either convex sparse coding or locality constrained linear coding. The algorithm is also very flexible and can be combined with many generic object representations. Thus, we first use sparse representation to achieve an efficient searching mechanism of the algorithm and demonstrate its accuracy. Next, two other object representation models, i.e., least soft-threshold squares and adaptive structural local sparse appearance, are implemented with improved accuracy to demonstrate the flexibility of our algorithm. Qualitative and quantitative experimental results demonstrate that the proposed tracking algorithm performs favorably against the state-of-the-art methods in dynamic scenes.

The diagnosis related groups enhanced electronic medical record.

PubMed

Müller, Marcel Lucas; Bürkle, Thomas; Irps, Sebastian; Roeder, Norbert; Prokosch, Hans-Ulrich

2003-07-01

The introduction of Diagnosis Related Groups as a basis for hospital payment in Germany announced essential changes in the hospital reimbursement practice. A hospital's economical survival will depend vitally on the accuracy and completeness of the documentation of DRG relevant data like diagnosis and procedure codes. In order to enhance physicians' coding compliance, an easy-to-use interface integrating coding tasks seamlessly into clinical routine had to be developed. A generic approach should access coding and clinical guidelines from different information sources. Within the Electronic Medical Record (EMR) a user interface ('DRG Control Center') for all DRG relevant clinical and administrative data has been built. A comprehensive DRG-related web site gives online access to DRG grouping software and an electronic coding expert. Both components are linked together using an application supporting bi-directional communication. Other web based services like a guideline search engine can be integrated as well. With the proposed method, the clinician gains quick access to context sensitive clinical guidelines for appropriate treatment of his/her patient and administrative guidelines for the adequate coding of the diagnoses and procedures. This paper describes the design and current implementation and discusses our experiences.

Development and Validation of a Natural Language Processing Tool to Identify Patients Treated for Pneumonia across VA Emergency Departments.

PubMed

Jones, B E; South, B R; Shao, Y; Lu, C C; Leng, J; Sauer, B C; Gundlapalli, A V; Samore, M H; Zeng, Q

2018-01-01

Identifying pneumonia using diagnosis codes alone may be insufficient for research on clinical decision making. Natural language processing (NLP) may enable the inclusion of cases missed by diagnosis codes. This article (1) develops a NLP tool that identifies the clinical assertion of pneumonia from physician emergency department (ED) notes, and (2) compares classification methods using diagnosis codes versus NLP against a gold standard of manual chart review to identify patients initially treated for pneumonia. Among a national population of ED visits occurring between 2006 and 2012 across the Veterans Affairs health system, we extracted 811 physician documents containing search terms for pneumonia for training, and 100 random documents for validation. Two reviewers annotated span- and document-level classifications of the clinical assertion of pneumonia. An NLP tool using a support vector machine was trained on the enriched documents. We extracted diagnosis codes assigned in the ED and upon hospital discharge and calculated performance characteristics for diagnosis codes, NLP, and NLP plus diagnosis codes against manual review in training and validation sets. Among the training documents, 51% contained clinical assertions of pneumonia; in the validation set, 9% were classified with pneumonia, of which 100% contained pneumonia search terms. After enriching with search terms, the NLP system alone demonstrated a recall/sensitivity of 0.72 (training) and 0.55 (validation), and a precision/positive predictive value (PPV) of 0.89 (training) and 0.71 (validation). ED-assigned diagnostic codes demonstrated lower recall/sensitivity (0.48 and 0.44) but higher precision/PPV (0.95 in training, 1.0 in validation); the NLP system identified more "possible-treated" cases than diagnostic coding. An approach combining NLP and ED-assigned diagnostic coding classification achieved the best performance (sensitivity 0.89 and PPV 0.80). System-wide application of NLP to clinical text can increase capture of initial diagnostic hypotheses, an important inclusion when studying diagnosis and clinical decision-making under uncertainty. Schattauer GmbH Stuttgart.

Query-Adaptive Hash Code Ranking for Large-Scale Multi-View Visual Search.

PubMed

Liu, Xianglong; Huang, Lei; Deng, Cheng; Lang, Bo; Tao, Dacheng

2016-10-01

Hash-based nearest neighbor search has become attractive in many applications. However, the quantization in hashing usually degenerates the discriminative power when using Hamming distance ranking. Besides, for large-scale visual search, existing hashing methods cannot directly support the efficient search over the data with multiple sources, and while the literature has shown that adaptively incorporating complementary information from diverse sources or views can significantly boost the search performance. To address the problems, this paper proposes a novel and generic approach to building multiple hash tables with multiple views and generating fine-grained ranking results at bitwise and tablewise levels. For each hash table, a query-adaptive bitwise weighting is introduced to alleviate the quantization loss by simultaneously exploiting the quality of hash functions and their complement for nearest neighbor search. From the tablewise aspect, multiple hash tables are built for different data views as a joint index, over which a query-specific rank fusion is proposed to rerank all results from the bitwise ranking by diffusing in a graph. Comprehensive experiments on image search over three well-known benchmarks show that the proposed method achieves up to 17.11% and 20.28% performance gains on single and multiple table search over the state-of-the-art methods.

A geo-coded inventory of anophelines in the Afrotropical Region south of the Sahara: 1898-2016.

PubMed

Kyalo, David; Amratia, Punam; Mundia, Clara W; Mbogo, Charles M; Coetzee, Maureen; Snow, Robert W

2017-01-01

Background : Understanding the distribution of anopheline vectors of malaria is an important prelude to the design of national malaria control and elimination programmes. A single, geo-coded continental inventory of anophelines using all available published and unpublished data has not been undertaken since the 1960s. Methods : We have searched African, European and World Health Organization archives to identify unpublished reports on anopheline surveys in 48 sub-Saharan Africa countries. This search was supplemented by identification of reports that formed part of post-graduate theses, conference abstracts, regional insecticide resistance databases and more traditional bibliographic searches of peer-reviewed literature. Finally, a check was made against two recent repositories of dominant malaria vector species locations ( circa 2,500). Each report was used to extract information on the survey dates, village locations (geo-coded to provide a longitude and latitude), sampling methods, species identification methods and all anopheline species found present during the survey. Survey records were collapsed to a single site over time.    Results : The search strategy took years and resulted in 13,331 unique, geo-coded survey locations of anopheline vector occurrence between 1898 and 2016. A total of 12,204 (92%) sites reported the presence of 10 dominant vector species/sibling species; 4,473 (37%) of these sites were sampled since 2005. 4,442 (33%) sites reported at least one of 13 possible secondary vector species; 1,107 (25%) of these sites were sampled since 2005. Distributions of dominant and secondary vectors conform to previous descriptions of the ecological ranges of these vectors. Conclusion : We have assembled the largest ever geo-coded database of anophelines in Africa, representing a legacy dataset for future updating and identification of knowledge gaps at national levels. The geo-coded database is available on Harvard Dataverse as a reference source for African national malaria control programmes planning their future control and elimination strategies.

A geo-coded inventory of anophelines in the Afrotropical Region south of the Sahara: 1898-2016

PubMed Central

Kyalo, David; Amratia, Punam; Mundia, Clara W.; Mbogo, Charles M.; Coetzee, Maureen; Snow, Robert W.

2017-01-01

Background: Understanding the distribution of anopheline vectors of malaria is an important prelude to the design of national malaria control and elimination programmes. A single, geo-coded continental inventory of anophelines using all available published and unpublished data has not been undertaken since the 1960s. Methods: We have searched African, European and World Health Organization archives to identify unpublished reports on anopheline surveys in 48 sub-Saharan Africa countries. This search was supplemented by identification of reports that formed part of post-graduate theses, conference abstracts, regional insecticide resistance databases and more traditional bibliographic searches of peer-reviewed literature. Finally, a check was made against two recent repositories of dominant malaria vector species locations ( circa 2,500). Each report was used to extract information on the survey dates, village locations (geo-coded to provide a longitude and latitude), sampling methods, species identification methods and all anopheline species found present during the survey. Survey records were collapsed to a single site over time.    Results: The search strategy took years and resulted in 13,331 unique, geo-coded survey locations of anopheline vector occurrence between 1898 and 2016. A total of 12,204 (92%) sites reported the presence of 10 dominant vector species/sibling species; 4,473 (37%) of these sites were sampled since 2005. 4,442 (33%) sites reported at least one of 13 possible secondary vector species; 1,107 (25%) of these sites were sampled since 2005. Distributions of dominant and secondary vectors conform to previous descriptions of the ecological ranges of these vectors. Conclusion: We have assembled the largest ever geo-coded database of anophelines in Africa, representing a legacy dataset for future updating and identification of knowledge gaps at national levels. The geo-coded database is available on Harvard Dataverse as a reference source for African national malaria control programmes planning their future control and elimination strategies. PMID:28884158

OHD - OHD Staff

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Site Map News Organization Search NWS All NOAA Go Local forecast by "City, St" Search by city or zip code. Press enter or select the go button to submit request City, St Go Front Office OWP

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36 CFR 404.9 - Miscellaneous fee provisions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... United States Code and will accrue from the date of the billing. (b) Charges for unsuccessful search. ABMC may assess charges for time spent searching, even if it fails to locate the records or if records located are determined to be exempt from disclosure. If ABMC estimates that search charges are likely to...

36 CFR § 404.9 - Miscellaneous fee provisions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... United States Code and will accrue from the date of the billing. (b) Charges for unsuccessful search. ABMC may assess charges for time spent searching, even if it fails to locate the records or if records located are determined to be exempt from disclosure. If ABMC estimates that search charges are likely to...

36 CFR 404.9 - Miscellaneous fee provisions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... United States Code and will accrue from the date of the billing. (b) Charges for unsuccessful search. ABMC may assess charges for time spent searching, even if it fails to locate the records or if records located are determined to be exempt from disclosure. If ABMC estimates that search charges are likely to...

36 CFR 404.9 - Miscellaneous fee provisions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... United States Code and will accrue from the date of the billing. (b) Charges for unsuccessful search. ABMC may assess charges for time spent searching, even if it fails to locate the records or if records located are determined to be exempt from disclosure. If ABMC estimates that search charges are likely to...

MMAB Developmental Products

Science.gov Websites

Skip Navigation Links www.nws.noaa.gov NOAA logo - Click to go to the NOAA homepage National Weather Service NWS logo - Click to go to the NWS homepage Environmental Modeling Center Home News Organization Search Search Search by city or zip code. Press enter or select the go button to submit request

Sierra Toolkit Manual Version 4.48.

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

Sierra Toolkit Team

This report provides documentation for the SIERRA Toolkit (STK) modules. STK modules are intended to provide infrastructure that assists the development of computational engineering soft- ware such as finite-element analysis applications. STK includes modules for unstructured-mesh data structures, reading/writing mesh files, geometric proximity search, and various utilities. This document contains a chapter for each module, and each chapter contains overview descriptions and usage examples. Usage examples are primarily code listings which are generated from working test programs that are included in the STK code-base. A goal of this approach is to ensure that the usage examples will not fall outmore » of date. This page intentionally left blank.« less

Influence of Interpretation Aids on Attentional Capture, Visual Processing, and Understanding of Front-of-Package Nutrition Labels.

PubMed

Antúnez, Lucía; Giménez, Ana; Maiche, Alejandro; Ares, Gastón

2015-01-01

To study the influence of 2 interpretational aids of front-of-package (FOP) nutrition labels (color code and text descriptors) on attentional capture and consumers' understanding of nutritional information. A full factorial design was used to assess the influence of color code and text descriptors using visual search and eye tracking. Ten trained assessors participated in the visual search study and 54 consumers completed the eye-tracking study. In the visual search study, assessors were asked to indicate whether there was a label high in fat within sets of mayonnaise labels with different FOP labels. In the eye-tracking study, assessors answered a set of questions about the nutritional content of labels. The researchers used logistic regression to evaluate the influence of interpretational aids of FOP nutrition labels on the percentage of correct answers. Analyses of variance were used to evaluate the influence of the studied variables on attentional measures and participants' response times. Response times were significantly higher for monochromatic FOP labels compared with color-coded ones (3,225 vs 964 ms; P < .001), which suggests that color codes increase attentional capture. The highest number and duration of fixations and visits were recorded on labels that did not include color codes or text descriptors (P < .05). The lowest percentage of incorrect answers was observed when the nutrient level was indicated using color code and text descriptors (P < .05). The combination of color codes and text descriptors seems to be the most effective alternative to increase attentional capture and understanding of nutritional information. Copyright © 2015 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

New variable stars discovered in the fields of three Galactic open clusters using the VVV survey

NASA Astrophysics Data System (ADS)

Palma, T.; Minniti, D.; Dékány, I.; Clariá, J. J.; Alonso-García, J.; Gramajo, L. V.; Ramírez Alegría, S.; Bonatto, C.

2016-11-01

This project is a massive near-infrared (NIR) search for variable stars in highly reddened and obscured open cluster (OC) fields projected on regions of the Galactic bulge and disk. The search is performed using photometric NIR data in the J-, H- and Ks- bands obtained from the Vista Variables in the Vía Láctea (VVV) Survey. We performed in each cluster field a variability search using Stetson's variability statistics to select the variable candidates. Later, those candidates were subjected to a frequency analysis using the Generalized Lomb-Scargle and the Phase Dispersion Minimization algorithms. The number of independent observations range between 63 and 73. The newly discovered variables in this study, 157 in total in three different known OCs, are classified based on their light curve shapes, periods, amplitudes and their location in the corresponding color-magnitude (J -Ks ,Ks) and color-color (H -Ks , J - H) diagrams. We found 5 possible Cepheid stars which, based on the period-luminosity relation, are very likely type II Cepheids located behind the bulge. Among the newly discovered variables, there are eclipsing binaries, δ Scuti, as well as background RR Lyrae stars. Using the new version of the Wilson & Devinney code as well as the "Physics Of Eclipsing Binaries" (PHOEBE) code, we analyzed some of the best eclipsing binaries we discovered. Our results show that these studied systems turn out to be ranging from detached to double-contact binaries, with low eccentricities and high inclinations of approximately 80°. Their surface temperatures range between 3500 K and 8000 K.

Environmental Dataset Gateway (EDG) Search Widget

EPA Pesticide Factsheets

Use the Environmental Dataset Gateway (EDG) to find and access EPA's environmental resources. Many options are available for easily reusing EDG content in other other applications. This allows individuals to provide direct access to EPA's metadata outside the EDG interface. The EDG Search Widget makes it possible to search the EDG from another web page or application. The search widget can be included on your website by simply inserting one or two lines of code. Users can type a search term or lucene search query in the search field and retrieve a pop-up list of records that match that search.

A Novel Method of Building Functional Brain Network Using Deep Learning Algorithm with Application in Proficiency Detection.

PubMed

Hua, Chengcheng; Wang, Hong; Wang, Hong; Lu, Shaowen; Liu, Chong; Khalid, Syed Madiha

2018-04-11

Functional brain network (FBN) has become very popular to analyze the interaction between cortical regions in the last decade. But researchers always spend a long time to search the best way to compute FBN for their specific studies. The purpose of this study is to detect the proficiency of operators during their mineral grinding process controlling based on FBN. To save the search time, a novel semi-data-driven method of computing functional brain connection based on stacked autoencoder (BCSAE) is proposed in this paper. This method uses stacked autoencoder (SAE) to encode the multi-channel EEG data into codes and then computes the dissimilarity between the codes from every pair of electrodes to build FBN. The highlight of this method is that the SAE has a multi-layered structure and is semi-supervised, which means it can dig deeper information and generate better features. Then an experiment was performed, the EEG of the operators were collected while they were operating and analyzed to detect their proficiency. The results show that the BCSAE method generated more number of separable features with less redundancy, and the average accuracy of classification (96.18%) is higher than that of the control methods: PLV (92.19%) and PLI (78.39%).

Evolutionary pattern search algorithms

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

Hart, W.E.

1995-09-19

This paper defines a class of evolutionary algorithms called evolutionary pattern search algorithms (EPSAs) and analyzes their convergence properties. This class of algorithms is closely related to evolutionary programming, evolutionary strategie and real-coded genetic algorithms. EPSAs are self-adapting systems that modify the step size of the mutation operator in response to the success of previous optimization steps. The rule used to adapt the step size can be used to provide a stationary point convergence theory for EPSAs on any continuous function. This convergence theory is based on an extension of the convergence theory for generalized pattern search methods. An experimentalmore » analysis of the performance of EPSAs demonstrates that these algorithms can perform a level of global search that is comparable to that of canonical EAs. We also describe a stopping rule for EPSAs, which reliably terminated near stationary points in our experiments. This is the first stopping rule for any class of EAs that can terminate at a given distance from stationary points.« less

Analysing patent landscapes in plant biotechnology and new plant breeding techniques.

PubMed

Parisi, Claudia; Rodríguez-Cerezo, Emilio; Thangaraj, Harry

2013-02-01

This article aims to inform the reader of the importance of searching patent landscapes in plant biotechnology and the use of basic tools to perform a patent search. The recommendations for a patent search strategy are illustrated with the specific example of zinc finger nuclease technology for genetic engineering in plants. Within this scope, we provide a general introduction to searching using two online and free-access patent databases esp@cenet and PatentScope. The essential features of the two databases, and their functionality is described, together with short descriptions to enable the reader to understand patents, searching, their content, patent families, and their territorial scope. We mostly stress the value of patent searching for mining scientific, rather than legal information. Search methods through the use of keywords and patent codes are elucidated together with suggestions about how to search with or combine codes with keywords and we also comment on limitations of each method. We stress the importance of patent literature to complement more mainstream scientific literature, and the relative complexities and difficulties in searching patents compared to the latter. A parallel online resource where we describe detailed search exercises is available through reference for those intending further exploration. In essence this is aimed at a novice patent searcher who may want to examine accessory patent literature to complement knowledge gained from mainstream journal resources.

Compiling a register of patients with moderate or severe learning disabilities: experience at one United Kingdom general practice.

PubMed

Lodge, Keri-Michèle; Milnes, David; Gilbody, Simon M

2011-03-01

Background Identifying patients with learning disabilities within primary care is central to initiatives for improving the health of this population. UK general practitioners (GPs) receive additional income for maintaining registers of patients with learning disabilities as part of the Quality and Outcomes Framework (QOF), and may opt to provide Directed Enhanced Services (DES), which requires practices to maintain registers of patients with moderate or severe learning disabilities and offer them annual health checks.Objectives This paper describes the development of a register of patients with moderate or severe learning disabilities at one UK general practice.Methods A Read code search of one UK general practice's electronic medical records was conducted in order to identify patients with learning disabilities. Confirmation of diagnoses was sought by scrutinising records and GP verification. Cross-referencing with the practice QOF register of patients with learning disabilities of any severity, and the local authority's list of clients with learning disabilities, was performed.Results Of 15 001 patients, 229 (1.5%) were identified by the Read code search as possibly having learning disabilities. Scrutiny of records and GP verification confirmed 64 had learning disabilities and 24 did not, but the presence or absence of learning disability remained unclear in 141 cases. Cross-referencing with the QOF register (n=81) and local authority list (n=49) revealed little overlap.Conclusion Identifying learning disability and assessing its severity are tasks GPs may be unfamiliar with, and relying on Read code searches may result in under-detection. Further research is needed to define optimum strategies for identifying, cross-referencing and validating practice-based registers of patients with learning disabilities.

Compiling a register of patients with moderate or severe learning disabilities: experience at one United Kingdom general practice

PubMed Central

2011-01-01

Background Identifying patients with learning disabilities within primary care is central to initiatives for improving the health of this population. UK general practitioners (GPs) receive additional income for maintaining registers of patients with learning disabilities as part of the Quality and Outcomes Framework (QOF), and may opt to provide Directed Enhanced Services (DES), which requires practices to maintain registers of patients with moderate or severe learning disabilities and offer them annual health checks. Objectives This paper describes the development of a register of patients with moderate or severe learning disabilities at one UK general practice. Methods A Read code search of one UK general practice's electronic medical records was conducted in order to identify patients with learning disabilities. Confirmation of diagnoses was sought by scrutinising records and GP verification. Cross-referencing with the practice QOF register of patients with learning disabilities of any severity, and the local authority's list of clients with learning disabilities, was performed. Results Of 15 001 patients, 229 (1.5%) were identified by the Read code search as possibly having learning disabilities. Scrutiny of records and GP verification confirmed 64 had learning disabilities and 24 did not, but the presence or absence of learning disability remained unclear in 141 cases. Cross-referencing with the QOF register (n=81) and local authority list (n=49) revealed little overlap. Conclusion Identifying learning disability and assessing its severity are tasks GPs may be unfamiliar with, and relying on Read code searches may result in under-detection. Further research is needed to define optimum strategies for identifying, cross-referencing and validating practice-based registers of patients with learning disabilities. PMID:22479290

[Algorithms for the identification of hospital stays due to osteoporotic femoral neck fractures in European medical administrative databases using ICD-10 codes: A non-systematic review of the literature].

PubMed

Caillet, P; Oberlin, P; Monnet, E; Guillon-Grammatico, L; Métral, P; Belhassen, M; Denier, P; Banaei-Bouchareb, L; Viprey, M; Biau, D; Schott, A-M

2017-10-01

Osteoporotic hip fractures (OHF) are associated with significant morbidity and mortality. The French medico-administrative database (SNIIRAM) offers an interesting opportunity to improve the management of OHF. However, the validity of studies conducted with this database relies heavily on the quality of the algorithm used to detect OHF. The aim of the REDSIAM network is to facilitate the use of the SNIIRAM database. The main objective of this study was to present and discuss several OHF-detection algorithms that could be used with this database. A non-systematic literature search was performed. The Medline database was explored during the period January 2005-August 2016. Furthermore, a snowball search was then carried out from the articles included and field experts were contacted. The extraction was conducted using the chart developed by the REDSIAM network's "Methodology" task force. The ICD-10 codes used to detect OHF are mainly S72.0, S72.1, and S72.2. The performance of these algorithms is at best partially validated. Complementary use of medical and surgical procedure codes would affect their performance. Finally, few studies described how they dealt with fractures of non-osteoporotic origin, re-hospitalization, and potential contralateral fracture cases. Authors in the literature encourage the use of ICD-10 codes S72.0 to S72.2 to develop algorithms for OHF detection. These are the codes most frequently used for OHF in France. Depending on the study objectives, other ICD10 codes and medical and surgical procedures could be usefully discussed for inclusion in the algorithm. Detection and management of duplicates and non-osteoporotic fractures should be considered in the process. Finally, when a study is based on such an algorithm, all these points should be precisely described in the publication. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Interactive Exploration for Continuously Expanding Neuron Databases.

PubMed

Li, Zhongyu; Metaxas, Dimitris N; Lu, Aidong; Zhang, Shaoting

2017-02-15

This paper proposes a novel framework to help biologists explore and analyze neurons based on retrieval of data from neuron morphological databases. In recent years, the continuously expanding neuron databases provide a rich source of information to associate neuronal morphologies with their functional properties. We design a coarse-to-fine framework for efficient and effective data retrieval from large-scale neuron databases. In the coarse-level, for efficiency in large-scale, we employ a binary coding method to compress morphological features into binary codes of tens of bits. Short binary codes allow for real-time similarity searching in Hamming space. Because the neuron databases are continuously expanding, it is inefficient to re-train the binary coding model from scratch when adding new neurons. To solve this problem, we extend binary coding with online updating schemes, which only considers the newly added neurons and update the model on-the-fly, without accessing the whole neuron databases. In the fine-grained level, we introduce domain experts/users in the framework, which can give relevance feedback for the binary coding based retrieval results. This interactive strategy can improve the retrieval performance through re-ranking the above coarse results, where we design a new similarity measure and take the feedback into account. Our framework is validated on more than 17,000 neuron cells, showing promising retrieval accuracy and efficiency. Moreover, we demonstrate its use case in assisting biologists to identify and explore unknown neurons. Copyright © 2017 Elsevier Inc. All rights reserved.

Rural School District Dress Code Implementation: Perceptions of Stakeholders after First Year

ERIC Educational Resources Information Center

Wright, Krystal M.

2012-01-01

Schools are continuously searching for solutions to solve truancy, academic, behavioral, safety, and climate issues. One of the latest trends in education is requiring students to adhere to dress codes as a solution to these issues. Dress codes can range from slightly restrictive clothing to the requiring of a uniform. Many school district…

Helping the police with their inquiries

NASA Astrophysics Data System (ADS)

Kitson, Anthony J.

1995-09-01

The UK Home Office has held a long term interest in facial recognition. Work has concentrated upon providing the UK police with facilities to improve the use that can be made of the memory of victims and witnesses rather than automatically matching images. During the 1970s a psychological coding scheme and a search method were developed by Aberdeen University and Home Office. This has been incorporated into systems for searching prisoner photographs both experimentally and operationally. The coding scheme has also been incorporated in a facial likeness composition system. The Home Office is currenly implementing a national criminal record system (Phoenix) and work has been conducted to define and demonstrate standards for image enabled terminals for this application. Users have been consulted to establish suitable picture quality for the purpose, and a study of compression methods is in hand. Recently there has been increased use made by UK courts of expert testimony based upon the measurement of facial images. We are currently working with a group of practitioners to examine and improve the quality of such evidence and to develop a national standard.

An investigation of messy genetic algorithms

NASA Technical Reports Server (NTRS)

Goldberg, David E.; Deb, Kalyanmoy; Korb, Bradley

1990-01-01

Genetic algorithms (GAs) are search procedures based on the mechanics of natural selection and natural genetics. They combine the use of string codings or artificial chromosomes and populations with the selective and juxtapositional power of reproduction and recombination to motivate a surprisingly powerful search heuristic in many problems. Despite their empirical success, there has been a long standing objection to the use of GAs in arbitrarily difficult problems. A new approach was launched. Results to a 30-bit, order-three-deception problem were obtained using a new type of genetic algorithm called a messy genetic algorithm (mGAs). Messy genetic algorithms combine the use of variable-length strings, a two-phase selection scheme, and messy genetic operators to effect a solution to the fixed-coding problem of standard simple GAs. The results of the study of mGAs in problems with nonuniform subfunction scale and size are presented. The mGA approach is summarized, both its operation and the theory of its use. Experiments on problems of varying scale, varying building-block size, and combined varying scale and size are presented.

Multidimensional incremental parsing for universal source coding.

PubMed

Bae, Soo Hyun; Juang, Biing-Hwang

2008-10-01

A multidimensional incremental parsing algorithm (MDIP) for multidimensional discrete sources, as a generalization of the Lempel-Ziv coding algorithm, is investigated. It consists of three essential component schemes, maximum decimation matching, hierarchical structure of multidimensional source coding, and dictionary augmentation. As a counterpart of the longest match search in the Lempel-Ziv algorithm, two classes of maximum decimation matching are studied. Also, an underlying behavior of the dictionary augmentation scheme for estimating the source statistics is examined. For an m-dimensional source, m augmentative patches are appended into the dictionary at each coding epoch, thus requiring the transmission of a substantial amount of information to the decoder. The property of the hierarchical structure of the source coding algorithm resolves this issue by successively incorporating lower dimensional coding procedures in the scheme. In regard to universal lossy source coders, we propose two distortion functions, the local average distortion and the local minimax distortion with a set of threshold levels for each source symbol. For performance evaluation, we implemented three image compression algorithms based upon the MDIP; one is lossless and the others are lossy. The lossless image compression algorithm does not perform better than the Lempel-Ziv-Welch coding, but experimentally shows efficiency in capturing the source structure. The two lossy image compression algorithms are implemented using the two distortion functions, respectively. The algorithm based on the local average distortion is efficient at minimizing the signal distortion, but the images by the one with the local minimax distortion have a good perceptual fidelity among other compression algorithms. Our insights inspire future research on feature extraction of multidimensional discrete sources.

A MPEG-4 encoder based on TMS320C6416

NASA Astrophysics Data System (ADS)

Li, Gui-ju; Liu, Wei-ning

2013-08-01

Engineering and products need to achieve real-time video encoding by DSP, but the high computational complexity and huge amount of data requires that system has high data throughput. In this paper, a real-time MPEG-4 video encoder is designed based on TMS320C6416 platform. The kernel is the DSP of TMS320C6416T and FPGA chip f as the organization and management of video data. In order to control the flow of input and output data. Encoded stream is output using the synchronous serial port. The system has the clock frequency of 1GHz and has up to 8000 MIPS speed processing capacity when running at full speed. Due to the low coding efficiency of MPEG-4 video encoder transferred directly to DSP platform, it is needed to improve the program structure, data structures and algorithms combined with TMS320C6416T characteristics. First: Design the image storage architecture by balancing the calculation spending, storage space cost and EDMA read time factors. Open up a more buffer in memory, each buffer cache 16 lines of video data to be encoded, reconstruction image and reference image including search range. By using the variable alignment mode of the DSP, modifying the definition of structure variables and change the look-up table which occupy larger space with a direct calculation array to save memory space. After the program structure optimization, the program code, all variables, buffering buffers and the interpolation image including the search range can be placed in memory. Then, as to the time-consuming process modules and some functions which are called many times, the corresponding modules are written in parallel assembly language of TMS320C6416T which can increase the running speed. Besides, the motion estimation algorithm is improved by using a cross-hexagon search algorithm, The search speed can be increased obviously. Finally, the execution time, signal-to-noise ratio and compression ratio of a real-time image acquisition sequence is given. The experimental results show that the designed encoder in this paper can accomplish real-time encoding of a 768× 576, 25 frames per second grayscale video. The code rate is 1.5M bits per second.

Large-scale Exploration of Neuronal Morphologies Using Deep Learning and Augmented Reality.

PubMed

Li, Zhongyu; Butler, Erik; Li, Kang; Lu, Aidong; Ji, Shuiwang; Zhang, Shaoting

2018-02-12

Recently released large-scale neuron morphological data has greatly facilitated the research in neuroinformatics. However, the sheer volume and complexity of these data pose significant challenges for efficient and accurate neuron exploration. In this paper, we propose an effective retrieval framework to address these problems, based on frontier techniques of deep learning and binary coding. For the first time, we develop a deep learning based feature representation method for the neuron morphological data, where the 3D neurons are first projected into binary images and then learned features using an unsupervised deep neural network, i.e., stacked convolutional autoencoders (SCAEs). The deep features are subsequently fused with the hand-crafted features for more accurate representation. Considering the exhaustive search is usually very time-consuming in large-scale databases, we employ a novel binary coding method to compress feature vectors into short binary codes. Our framework is validated on a public data set including 58,000 neurons, showing promising retrieval precision and efficiency compared with state-of-the-art methods. In addition, we develop a novel neuron visualization program based on the techniques of augmented reality (AR), which can help users take a deep exploration of neuron morphologies in an interactive and immersive manner.

OHD/HL - National Weather Hydrology Laboratory

Science.gov Websites

Organization Search NWS All NOAA Go Local forecast by "City, St" Search by city or zip code. Press enter or select the go button to submit request City, St Go Science Research and Collaboration Hydrology

A VLSI chip set for real time vector quantization of image sequences

NASA Technical Reports Server (NTRS)

Baker, Richard L.

1989-01-01

The architecture and implementation of a VLSI chip set that vector quantizes (VQ) image sequences in real time is described. The chip set forms a programmable Single-Instruction, Multiple-Data (SIMD) machine which can implement various vector quantization encoding structures. Its VQ codebook may contain unlimited number of codevectors, N, having dimension up to K = 64. Under a weighted least squared error criterion, the engine locates at video rates the best code vector in full-searched or large tree searched VQ codebooks. The ability to manipulate tree structured codebooks, coupled with parallelism and pipelining, permits searches in as short as O (log N) cycles. A full codebook search results in O(N) performance, compared to O(KN) for a Single-Instruction, Single-Data (SISD) machine. With this VLSI chip set, an entire video code can be built on a single board that permits realtime experimentation with very large codebooks.

Interactive searching of facial image databases

NASA Astrophysics Data System (ADS)

Nicholls, Robert A.; Shepherd, John W.; Shepherd, Jean

1995-09-01

A set of psychological facial descriptors has been devised to enable computerized searching of criminal photograph albums. The descriptors have been used to encode image databased of up to twelve thousand images. Using a system called FACES, the databases are searched by translating a witness' verbal description into corresponding facial descriptors. Trials of FACES have shown that this coding scheme is more productive and efficient than searching traditional photograph albums. An alternative method of searching the encoded database using a genetic algorithm is currenly being tested. The genetic search method does not require the witness to verbalize a description of the target but merely to indicate a degree of similarity between the target and a limited selection of images from the database. The major drawback of FACES is that is requires a manual encoding of images. Research is being undertaken to automate the process, however, it will require an algorithm which can predict human descriptive values. Alternatives to human derived coding schemes exist using statistical classifications of images. Since databases encoded using statistical classifiers do not have an obvious direct mapping to human derived descriptors, a search method which does not require the entry of human descriptors is required. A genetic search algorithm is being tested for such a purpose.

The Maximal C³ Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses.

PubMed

Michel, Christian J

2017-04-18

In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C 3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses. The method was based on the preferential occurrence of trinucleotides among the three frames at the gene population level. We extend here this definition at the gene level. This new statistical approach considers all the genes, i.e., of large and small lengths, with the same weight for searching the circular code X . As a consequence, the concept of circular code, in particular the reading frame retrieval, is directly associated to each gene. At the gene level, the circular code X is strengthened in the genes of bacteria, eukaryotes, plasmids, and viruses, and is now also identified in the genes of archaea. The genes of mitochondria and chloroplasts contain a subset of the circular code X . Finally, by studying viral genes, the circular code X was found in DNA genomes, RNA genomes, double-stranded genomes, and single-stranded genomes.

A Comparison of the Incidence of Cricothyrotomy in the Deployed Setting to the Emergency Department at a Level 1 Military Trauma Center: A Descriptive Analysis

DTIC Science & Technology

2015-03-01

the providers in the deployed setting and include the Tactical Combat Casualty Care casualty card. Data are then coded for query and analysis. All...intubate, can’t ventilate” and disruption of head/neck anatomy. Of the four procedures performed in the ED setting, three patients survived to hospital...data from SAMMC are limited by the search methods and data extraction. We searched by Current Procedural Ter- minology code , which requires that the

Quality of online information on type 2 diabetes: a cross-sectional study.

PubMed

Weymann, Nina; Härter, Martin; Dirmaier, Jörg

2015-12-01

Evidence-based health information is a prerequisite for patients with type 2 diabetes to engage in self-management and to make informed medical decisions. The Internet is an important source of health information. In the present study, we systematically assessed formal quality, quality of decision support and usability of German and English language websites on type 2 diabetes. The search term 'type 2 diabetes' was entered in the two most popular search engines. Descriptive data on website quality are presented. Additionally, associations between website quality and affiliation (commercial vs. non-commercial), presence of the HON code quality seal and website traffic were explored. Forty-six websites were included. Most websites provided basic information necessary for decision-making, while only one website also provided decision support. Websites with a HON code had significantly better formal quality than websites without HON code. We found a highly significant correlation between usability and website traffic and a significant correlation between formal quality and website traffic. Most websites do not provide sufficient information to support patients in medical decision-making. Our finding that usability and website traffic are tightly associated is consistent with previous research indicating that design is the most important cue for users assessing website credibility. © The Author (2014). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

FAMA: Fast Automatic MOOG Analysis

NASA Astrophysics Data System (ADS)

Magrini, Laura; Randich, Sofia; Friel, Eileen; Spina, Lorenzo; Jacobson, Heather; Cantat-Gaudin, Tristan; Donati, Paolo; Baglioni, Roberto; Maiorca, Enrico; Bragaglia, Angela; Sordo, Rosanna; Vallenari, Antonella

2014-02-01

FAMA (Fast Automatic MOOG Analysis), written in Perl, computes the atmospheric parameters and abundances of a large number of stars using measurements of equivalent widths (EWs) automatically and independently of any subjective approach. Based on the widely-used MOOG code, it simultaneously searches for three equilibria, excitation equilibrium, ionization balance, and the relationship between logn(FeI) and the reduced EWs. FAMA also evaluates the statistical errors on individual element abundances and errors due to the uncertainties in the stellar parameters. Convergence criteria are not fixed "a priori" but instead are based on the quality of the spectra.

Progress in Search for Antihelium with BESS

NASA Technical Reports Server (NTRS)

Sasaki, M.; Matsumoto, H.; Nozaki, M.; Saeki, T.; Abe, K.; Anraku, K.; Asoka, Y.; Fujikawa, M.; Fuke, H.; Imori, M.

2002-01-01

We have searched for antihelium nuclei in cosmic rays using the data obtained from balloon flights of the BESS magnetic spectrometer. The search was mainly based on track-quality selection, followed by rigidity analysis, and on the time-of-flight and dE/dx measurements by the scintillation counter hodoscope. We analysed all the data collected during 1993-2000 with a common analysis procedure. No antihelium nuclei events were found in the energy range from 1 to 14 GV. In order to determine a new upper limit, we have simulated the loss in the air and in the instrument of He (He-bar) using the GEANT/GHEISHA code. Combined with the data collected in 1993 through 2000, a new 95 % confidence upper limit for the ratio of He-bar/He at the top of the atmosphere of 6.8 x 10(exp -7) has been obtained to be after correcting for the interactions in the air and in the instruments.

The Spatial Coding Strategies of One-Year-Old Infants in a Locomotor Search Task.

ERIC Educational Resources Information Center

Bushnell, Emily W.; And Others

1995-01-01

Examined the ability of 1-year olds to remember the location of nonvisible targets. Found that infants were able to associate a nonvisible target with a direct landmark and to code its distance and direction with respect to themselves or the larger framework. Difficulty of coding with indirect landmarks was associated with cognitive complexity and…

Redundant Coding in Visual Search Displays: Effects of Shape and Colour.

DTIC Science & Technology

1997-02-01

results for refining color selection algorithms and for color coding in situations where the gamut of available colors is limited. In a secondary set of analyses, we note large performance differences as a function of target shape.

Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns

PubMed Central

2007-01-01

We have converted genome-encoded protein sequences into musical notes to reveal auditory patterns without compromising musicality. We derived a reduced range of 13 base notes by pairing similar amino acids and distinguishing them using variations of three-note chords and codon distribution to dictate rhythm. The conversion will help make genomic coding sequences more approachable for the general public, young children, and vision-impaired scientists. PMID:17477882

Engineering calculations for communications satellite systems planning

NASA Technical Reports Server (NTRS)

Reilly, C. H.; Levis, C. A.; Mount-Campbell, C.; Gonsalvez, D. J.; Wang, C. W.; Yamamura, Y.

1985-01-01

Computer-based techniques for optimizing communications-satellite orbit and frequency assignments are discussed. A gradient-search code was tested against a BSS scenario derived from the RARC-83 data. Improvement was obtained, but each iteration requires about 50 minutes of IBM-3081 CPU time. Gradient-search experiments on a small FSS test problem, consisting of a single service area served by 8 satellites, showed quickest convergence when the satellites were all initially placed near the center of the available orbital arc with moderate spacing. A transformation technique is proposed for investigating the surface topography of the objective function used in the gradient-search method. A new synthesis approach is based on transforming single-entry interference constraints into corresponding constraints on satellite spacings. These constraints are used with linear objective functions to formulate the co-channel orbital assignment task as a linear-programming (LP) problem or mixed integer programming (MIP) problem. Globally optimal solutions are always found with the MIP problems, but not necessarily with the LP problems. The MIP solutions can be used to evaluate the quality of the LP solutions. The initial results are very encouraging.

Towards iconic language for patient records, drug monographs, guidelines and medical search engines.

PubMed

Lamy, Jean-Baptiste; Duclos, Catherine; Hamek, Saliha; Beuscart-Zéphir, Marie-Catherine; Kerdelhué, Gaetan; Darmoni, Stefan; Favre, Madeleine; Falcoff, Hector; Simon, Christian; Pereira, Suzanne; Serrot, Elisabeth; Mitouard, Thierry; Hardouin, Etienne; Kergosien, Yannick; Venot, Alain

2010-01-01

Practicing physicians have limited time for consulting medical knowledge and records. We have previously shown that using icons instead of text to present drug monographs may allow contraindications and adverse effects to be identified more rapidly and more accurately. These findings were based on the use of an iconic language designed for drug knowledge, providing icons for many medical concepts, including diseases, antecedents, drug classes and tests. In this paper, we describe a new project aimed at extending this iconic language, and exploring the possible applications of these icons in medicine. Based on evaluators' comments, focus groups of physicians and opinions of academic, industrial and associative partners, we propose iconic applications related to patient records, for example summarizing patient conditions, searching for specific clinical documents and helping to code structured data. Other applications involve the presentation of clinical practice guidelines and improving the interface of medical search engines. These new applications could use the same iconic language that was designed for drug knowledge, with a few additional items that respect the logic of the language.

High Frequency Scattering Code in a Distributed Processing Environment

DTIC Science & Technology

1991-06-01

Block 6. Author(s). Name(s) of person (s) Block 14. Subiect Terms. Keywords or phrases responsible for writing the report, performing identifying major...use of auttomated analysis tools is indicated. One tool developed by Pacific-Sierra Re- 22 search Corporation and marketed by Intel Corporation for...XQ: EXECUTE CODE EN : END CODE This input deck differs from that in the manual because the "PP" option is disabled in the modified code. 45 A.3

A fuzzy-match search engine for physician directories.

PubMed

Rastegar-Mojarad, Majid; Kadolph, Christopher; Ye, Zhan; Wall, Daniel; Murali, Narayana; Lin, Simon

2014-11-04

A search engine to find physicians' information is a basic but crucial function of a health care provider's website. Inefficient search engines, which return no results or incorrect results, can lead to patient frustration and potential customer loss. A search engine that can handle misspellings and spelling variations of names is needed, as the United States (US) has culturally, racially, and ethnically diverse names. The Marshfield Clinic website provides a search engine for users to search for physicians' names. The current search engine provides an auto-completion function, but it requires an exact match. We observed that 26% of all searches yielded no results. The goal was to design a fuzzy-match algorithm to aid users in finding physicians easier and faster. Instead of an exact match search, we used a fuzzy algorithm to find similar matches for searched terms. In the algorithm, we solved three types of search engine failures: "Typographic", "Phonetic spelling variation", and "Nickname". To solve these mismatches, we used a customized Levenshtein distance calculation that incorporated Soundex coding and a lookup table of nicknames derived from US census data. Using the "Challenge Data Set of Marshfield Physician Names," we evaluated the accuracy of fuzzy-match engine-top ten (90%) and compared it with exact match (0%), Soundex (24%), Levenshtein distance (59%), and fuzzy-match engine-top one (71%). We designed, created a reference implementation, and evaluated a fuzzy-match search engine for physician directories. The open-source code is available at the codeplex website and a reference implementation is available for demonstration at the datamarsh website.

Rate-Compatible Protograph LDPC Codes

NASA Technical Reports Server (NTRS)

Nguyen, Thuy V. (Inventor); Nosratinia, Aria (Inventor); Divsalar, Dariush (Inventor)

2014-01-01

Digital communication coding methods resulting in rate-compatible low density parity-check (LDPC) codes built from protographs. Described digital coding methods start with a desired code rate and a selection of the numbers of variable nodes and check nodes to be used in the protograph. Constraints are set to satisfy a linear minimum distance growth property for the protograph. All possible edges in the graph are searched for the minimum iterative decoding threshold and the protograph with the lowest iterative decoding threshold is selected. Protographs designed in this manner are used in decode and forward relay channels.

A character string scanner

NASA Technical Reports Server (NTRS)

Enison, R. L.

1971-01-01

A computer program called Character String Scanner (CSS), is presented. It is designed to search a data set for any specified group of characters and then to flag this group. The output of the CSS program is a listing of the data set being searched with the specified group of characters being flagged by asterisks. Therefore, one may readily identify specific keywords, groups of keywords or specified lines of code internal to a computer program, in a program output, or in any other specific data set. Possible applications of this program include the automatic scan of an output data set for pertinent keyword data, the editing of a program to change the appearance of a certain word or group of words, and the conversion of a set of code to a different set of code.

Performance Analysis of a De-correlated Modified Code Tracking Loop for Synchronous DS-CDMA System under Multiuser Environment

NASA Astrophysics Data System (ADS)

Wu, Ya-Ting; Wong, Wai-Ki; Leung, Shu-Hung; Zhu, Yue-Sheng

This paper presents the performance analysis of a De-correlated Modified Code Tracking Loop (D-MCTL) for synchronous direct-sequence code-division multiple-access (DS-CDMA) systems under multiuser environment. Previous studies have shown that the imbalance of multiple access interference (MAI) in the time lead and time lag portions of the signal causes tracking bias or instability problem in the traditional correlating tracking loop like delay lock loop (DLL) or modified code tracking loop (MCTL). In this paper, we exploit the de-correlating technique to combat the MAI at the on-time code position of the MCTL. Unlike applying the same technique to DLL which requires an extensive search algorithm to compensate the noise imbalance which may introduce small tracking bias under low signal-to-noise ratio (SNR), the proposed D-MCTL has much lower computational complexity and exhibits zero tracking bias for the whole range of SNR, regardless of the number of interfering users. Furthermore, performance analysis and simulations based on Gold codes show that the proposed scheme has better mean square tracking error, mean-time-to-lose-lock and near-far resistance than the other tracking schemes, including traditional DLL (T-DLL), traditional MCTL (T-MCTL) and modified de-correlated DLL (MD-DLL).

Spotted star light curve numerical modeling technique and its application to HII 1883 surface imaging

NASA Astrophysics Data System (ADS)

Kolbin, A. I.; Shimansky, V. V.

2014-04-01

We developed a code for imaging the surfaces of spotted stars by a set of circular spots with a uniform temperature distribution. The flux from the spotted surface is computed by partitioning the spots into elementary areas. The code takes into account the passing of spots behind the visible stellar limb, limb darkening, and overlapping of spots. Modeling of light curves includes the use of recent results of the theory of stellar atmospheres needed to take into account the temperature dependence of flux intensity and limb darkening coefficients. The search for spot parameters is based on the analysis of several light curves obtained in different photometric bands. We test our technique by applying it to HII 1883.

Differences in reported sepsis incidence according to study design: a literature review.

PubMed

Mariansdatter, Saga Elise; Eiset, Andreas Halgreen; Søgaard, Kirstine Kobberøe; Christiansen, Christian Fynbo

2016-10-12

Sepsis and severe sepsis are common conditions in hospital settings, and are associated with high rates of morbidity and mortality, but reported incidences vary considerably. In this literature review, we describe the variation in reported population-based incidences of sepsis and severe sepsis. We also examine methodological and demographic differences between studies that may explain this variation. We carried out a literature review searching three major databases and reference lists of relevant articles, to identify all original studies reporting the incidence of sepsis or severe sepsis in the general population. Two authors independently assessed all articles, and the final decision to exclude an article was reached by consensus. We extracted data according to predetermined variables, including study country, sepsis definition, and data source. We then calculated descriptive statistics for the reported incidences of sepsis and severe sepsis. The studies were classified according to the method used to identify cases of sepsis or severe sepsis: chart-based (i.e. review of patient charts) or code-based (i.e. predetermined International Classification of Diseases [ICD] codes). Among 482 articles initially screened, we identified 23 primary publications reporting incidence of sepsis and/or severe sepsis in the general population. The reported incidences ranged from 74 to 1180 per 100,000 person-years and 3 to 1074 per 100,000 person-years for sepsis and severe sepsis, respectively. Most chart-based studies used the Bone criteria (or a modification hereof) and Protein C Worldwide Evaluation in Severe Sepsis (PROWESS) study criteria to identify cases of sepsis and severe sepsis. Most code-based studies used ICD-9 codes, but the number of codes used ranged from 1 to more than 1200. We found that the incidence varied according to how sepsis was identified (chart-based vs. code-based), calendar year, data source, and world region. The reported incidences of sepsis and severe sepsis in the general population varied greatly between studies. Such differences may be attributable to differences in the methods used to collect the data, the study period, or the world region where the study was undertaken. This finding highlights the importance of standardised definitions and acquisition of data regarding sepsis and severe sepsis.

Data engineering systems: Computerized modeling and data bank capabilities for engineering analysis

NASA Technical Reports Server (NTRS)

Kopp, H.; Trettau, R.; Zolotar, B.

1984-01-01

The Data Engineering System (DES) is a computer-based system that organizes technical data and provides automated mechanisms for storage, retrieval, and engineering analysis. The DES combines the benefits of a structured data base system with automated links to large-scale analysis codes. While the DES provides the user with many of the capabilities of a computer-aided design (CAD) system, the systems are actually quite different in several respects. A typical CAD system emphasizes interactive graphics capabilities and organizes data in a manner that optimizes these graphics. On the other hand, the DES is a computer-aided engineering system intended for the engineer who must operationally understand an existing or planned design or who desires to carry out additional technical analysis based on a particular design. The DES emphasizes data retrieval in a form that not only provides the engineer access to search and display the data but also links the data automatically with the computer analysis codes.

The availability of web sites offering to sell opioid medications without prescriptions.

PubMed

Forman, Robert F; Woody, George E; McLellan, Thomas; Lynch, Kevin G

2006-07-01

This study was designed to determine the availability of web sites offering to sell opioid medications without prescriptions. Forty-seven Internet searches were conducted with a variety of opioid medication terms, including "codeine," "no prescription Vicodin," and "OxyContin." Two independent raters examined the links generated in each search and resolved any coding disagreements. The resulting links were coded as "no prescription web sites" (NPWs) if they offered to sell opioid medications without prescriptions. In searches with terms such as "no prescription codeine" and "Vicodin," over 50% of the links obtained were coded as "NPWs." The proportion of links yielding NPWs was greater when the phrase "no prescription" was added to the opioid term. More than 300 opioid NPWs were identified and entered into a database. Three national drug-use monitoring studies have cited significant increases in prescription opioid use over the past 5 years, particularly among young people. The emergence of NPWs introduces a new vector for unregulated access to opioids. Research is needed to determine the effect of NPWs on prescription opioid use initiation, misuse, and dependence.

Stimulus information contaminates summation tests of independent neural representations of features

NASA Technical Reports Server (NTRS)

Shimozaki, Steven S.; Eckstein, Miguel P.; Abbey, Craig K.

2002-01-01

Many models of visual processing assume that visual information is analyzed into separable and independent neural codes, or features. A common psychophysical test of independent features is known as a summation study, which measures performance in a detection, discrimination, or visual search task as the number of proposed features increases. Improvement in human performance with increasing number of available features is typically attributed to the summation, or combination, of information across independent neural coding of the features. In many instances, however, increasing the number of available features also increases the stimulus information in the task, as assessed by an optimal observer that does not include the independent neural codes. In a visual search task with spatial frequency and orientation as the component features, a particular set of stimuli were chosen so that all searches had equivalent stimulus information, regardless of the number of features. In this case, human performance did not improve with increasing number of features, implying that the improvement observed with additional features may be due to stimulus information and not the combination across independent features.

Identification of pneumonia and influenza deaths using the death certificate pipeline

PubMed Central

2012-01-01

Background Death records are a rich source of data, which can be used to assist with public surveillance and/or decision support. However, to use this type of data for such purposes it has to be transformed into a coded format to make it computable. Because the cause of death in the certificates is reported as free text, encoding the data is currently the single largest barrier of using death certificates for surveillance. Therefore, the purpose of this study was to demonstrate the feasibility of using a pipeline, composed of a detection rule and a natural language processor, for the real time encoding of death certificates using the identification of pneumonia and influenza cases as an example and demonstrating that its accuracy is comparable to existing methods. Results A Death Certificates Pipeline (DCP) was developed to automatically code death certificates and identify pneumonia and influenza cases. The pipeline used MetaMap to code death certificates from the Utah Department of Health for the year 2008. The output of MetaMap was then accessed by detection rules which flagged pneumonia and influenza cases based on the Centers of Disease and Control and Prevention (CDC) case definition. The output from the DCP was compared with the current method used by the CDC and with a keyword search. Recall, precision, positive predictive value and F-measure with respect to the CDC method were calculated for the two other methods considered here. The two different techniques compared here with the CDC method showed the following recall/ precision results: DCP: 0.998/0.98 and keyword searching: 0.96/0.96. The F-measure were 0.99 and 0.96 respectively (DCP and keyword searching). Both the keyword and the DCP can run in interactive form with modest computer resources, but DCP showed superior performance. Conclusion The pipeline proposed here for coding death certificates and the detection of cases is feasible and can be extended to other conditions. This method provides an alternative that allows for coding free-text death certificates in real time that may increase its utilization not only in the public health domain but also for biomedical researchers and developers. Trial Registration This study did not involved any clinical trials. PMID:22569097

Decoding Crucial LncRNAs Implicated in Neurogenesis and Neurological Disorders.

PubMed

Ayana, R; Singh, Shailja; Pati, Soumya

2017-04-15

Unraveling transcriptional heterogeneity and the labyrinthine nature of neurodevelopment can probe insights into neuropsychiatric disorders. It is noteworthy that adult neurogenesis is restricted to the subventricular and subgranular zones of the brain. Recent studies suggest long non-coding RNAs (lncRNAs) as an avant-garde class of regulators implicated in neurodevelopment. But, paucity exists in the knowledge regarding lncRNAs in neurogenesis and their associations with neurodevelopmental defects. To address this, we extensively reviewed the existing literature databases as well as performed relevant in-silico analysis. We utilized Allen Brain Atlas (ABA) differential search module and generated a catalogue of ∼30,000 transcripts specific to the neurogenic zones, including coding and non-coding transcripts. To explore the existing lncRNAs reported in neurogenesis, we performed extensive literature mining and identified 392 lncRNAs. These degenerate lncRNAs were mapped onto the ABA transcript list leading to detection of 20 lncRNAs specific to neurogenic zones (Dentate gyrus/Lateral ventricle), among which 10 showed associations to several neurodevelopmental disorders following in-silico mapping onto brain disease databases like Simons Foundation Autism Research Initiative, AutDB, and lncRNADisease. Notably, using ABA correlation module, we could establish lncRNA-to-mRNA coexpression networks for the above 10 candidate lncRNAs. Finally, pathway prediction revealed physical, biochemical, or regulatory interactions for nine lncRNAs. In addition, ABA differential search also revealed 54 novel significant lncRNAs from the null set (∼30,000). Conclusively, this review represents an updated catalogue of lncRNAs in neurogenesis and neurological diseases, and overviews the field of OMICs-based data analysis for understanding lncRNome-based regulation in neurodevelopment.

Sensitivity curves for searches for gravitational-wave backgrounds

NASA Astrophysics Data System (ADS)

Thrane, Eric; Romano, Joseph D.

2013-12-01

We propose a graphical representation of detector sensitivity curves for stochastic gravitational-wave backgrounds that takes into account the increase in sensitivity that comes from integrating over frequency in addition to integrating over time. This method is valid for backgrounds that have a power-law spectrum in the analysis band. We call these graphs “power-law integrated curves.” For simplicity, we consider cross-correlation searches for unpolarized and isotropic stochastic backgrounds using two or more detectors. We apply our method to construct power-law integrated sensitivity curves for second-generation ground-based detectors such as Advanced LIGO, space-based detectors such as LISA and the Big Bang Observer, and timing residuals from a pulsar timing array. The code used to produce these plots is available at https://dcc.ligo.org/LIGO-P1300115/public for researchers interested in constructing similar sensitivity curves.

Clinical code set engineering for reusing EHR data for research: A review.

PubMed

Williams, Richard; Kontopantelis, Evangelos; Buchan, Iain; Peek, Niels

2017-06-01

The construction of reliable, reusable clinical code sets is essential when re-using Electronic Health Record (EHR) data for research. Yet code set definitions are rarely transparent and their sharing is almost non-existent. There is a lack of methodological standards for the management (construction, sharing, revision and reuse) of clinical code sets which needs to be addressed to ensure the reliability and credibility of studies which use code sets. To review methodological literature on the management of sets of clinical codes used in research on clinical databases and to provide a list of best practice recommendations for future studies and software tools. We performed an exhaustive search for methodological papers about clinical code set engineering for re-using EHR data in research. This was supplemented with papers identified by snowball sampling. In addition, a list of e-phenotyping systems was constructed by merging references from several systematic reviews on this topic, and the processes adopted by those systems for code set management was reviewed. Thirty methodological papers were reviewed. Common approaches included: creating an initial list of synonyms for the condition of interest (n=20); making use of the hierarchical nature of coding terminologies during searching (n=23); reviewing sets with clinician input (n=20); and reusing and updating an existing code set (n=20). Several open source software tools (n=3) were discovered. There is a need for software tools that enable users to easily and quickly create, revise, extend, review and share code sets and we provide a list of recommendations for their design and implementation. Research re-using EHR data could be improved through the further development, more widespread use and routine reporting of the methods by which clinical codes were selected. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Optimal periodic binary codes of lengths 28 to 64

NASA Technical Reports Server (NTRS)

Tyler, S.; Keston, R.

1980-01-01

Results from computer searches performed to find repeated binary phase coded waveforms with optimal periodic autocorrelation functions are discussed. The best results for lengths 28 to 64 are given. The code features of major concern are where (1) the peak sidelobe in the autocorrelation function is small and (2) the sum of the squares of the sidelobes in the autocorrelation function is small.

Injury in China: a systematic review of injury surveillance studies conducted in Chinese hospital emergency departments

PubMed Central

2011-01-01

Background Injuries represent a significant and growing public health concern in China. This Review was conducted to document the characteristics of injured patients presenting to the emergency department of Chinese hospitals and to assess of the nature of information collected and reported in published surveillance studies. Methods A systematic search of MEDLINE and China Academic Journals supplemented with a hand search of journals was performed. Studies published in the period 1997 to 2007 were included and research published in Chinese was the focus. Search terms included emergency, injury, medical care. Results Of the 268 studies identified, 13 were injury surveillance studies set in the emergency department. Nine were collaborative studies of which eight were prospective studies. Of the five single centre studies only one was of a prospective design. Transport, falls and industrial injuries were common mechanisms of injury. Study strengths were large patient sample sizes and for the collaborative studies a large number of participating hospitals. There was however limited use of internationally recognised injury classification and severity coding indices. Conclusion Despite the limited number of studies identified, the scope of each highlights the willingness and the capacity to conduct surveillance studies in the emergency department. This Review highlights the need for the adoption of standardized injury coding indices in the collection and reporting of patient health data. While high level injury surveillance systems focus on population-based priority setting, this Review demonstrates the need to establish an internationally comparable trauma registry that would permit monitoring of the trauma system and would by extension facilitate the optimal care of the injured patient through the development of informed quality assurance programs and the implementation of evidence-based health policy. PMID:22029774

Moving Object Detection Using a Parallax Shift Vector Algorithm

NASA Astrophysics Data System (ADS)

Gural, Peter S.; Otto, Paul R.; Tedesco, Edward F.

2018-07-01

There are various algorithms currently in use to detect asteroids from ground-based observatories, but they are generally restricted to linear or mildly curved movement of the target object across the field of view. Space-based sensors in high inclination, low Earth orbits can induce significant parallax in a collected sequence of images, especially for objects at the typical distances of asteroids in the inner solar system. This results in a highly nonlinear motion pattern of the asteroid across the sensor, which requires a more sophisticated search pattern for detection processing. Both the classical pattern matching used in ground-based asteroid search and the more sensitive matched filtering and synthetic tracking techniques, can be adapted to account for highly complex parallax motion. A new shift vector generation methodology is discussed along with its impacts on commonly used detection algorithms, processing load, and responsiveness to asteroid track reporting. The matched filter, template generator, and pattern matcher source code for the software described herein are available via GitHub.

A fast method for finding bound systems in numerical simulations: Results from the formation of asteroid binaries

NASA Astrophysics Data System (ADS)

Leinhardt, Zoë M.; Richardson, Derek C.

2005-08-01

We present a new code ( companion) that identifies bound systems of particles in O(NlogN) time. Simple binaries consisting of pairs of mutually bound particles and complex hierarchies consisting of collections of mutually bound particles are identifiable with this code. In comparison, brute force binary search methods scale as O(N) while full hierarchy searches can be as expensive as O(N), making analysis highly inefficient for multiple data sets with N≳10. A simple test case is provided to illustrate the method. Timing tests demonstrating O(NlogN) scaling with the new code on real data are presented. We apply our method to data from asteroid satellite simulations [Durda et al., 2004. Icarus 167, 382-396; Erratum: Icarus 170, 242; reprinted article: Icarus 170, 243-257] and note interesting multi-particle configurations. The code is available at http://www.astro.umd.edu/zoe/companion/ and is distributed under the terms and conditions of the GNU Public License.

Parallel database search and prime factorization with magnonic holographic memory devices

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

Khitun, Alexander

In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploitmore » wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.« less

Parallel database search and prime factorization with magnonic holographic memory devices

NASA Astrophysics Data System (ADS)

Khitun, Alexander

2015-12-01

In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.

78 FR 52607 - Unified Registration System

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-23

...'' and click ``Search.'' Next, click ``Open Docket Folder'' in the ``Actions'' column. Finally, in the... comments received are posted without change to http://www.regulations.gov . Anyone is able to search the... License CFR Code of Federal Regulations CMV Commercial Motor Vehicle CR Compliance Review CSA Compliance...

A Dual-Channel Acquisition Method Based on Extended Replica Folding Algorithm for Long Pseudo-Noise Code in Inter-Satellite Links.

PubMed

Zhao, Hongbo; Chen, Yuying; Feng, Wenquan; Zhuang, Chen

2018-05-25

Inter-satellite links are an important component of the new generation of satellite navigation systems, characterized by low signal-to-noise ratio (SNR), complex electromagnetic interference and the short time slot of each satellite, which brings difficulties to the acquisition stage. The inter-satellite link in both Global Positioning System (GPS) and BeiDou Navigation Satellite System (BDS) adopt the long code spread spectrum system. However, long code acquisition is a difficult and time-consuming task due to the long code period. Traditional folding methods such as extended replica folding acquisition search technique (XFAST) and direct average are largely restricted because of code Doppler and additional SNR loss caused by replica folding. The dual folding method (DF-XFAST) and dual-channel method have been proposed to achieve long code acquisition in low SNR and high dynamic situations, respectively, but the former is easily affected by code Doppler and the latter is not fast enough. Considering the environment of inter-satellite links and the problems of existing algorithms, this paper proposes a new long code acquisition algorithm named dual-channel acquisition method based on the extended replica folding algorithm (DC-XFAST). This method employs dual channels for verification. Each channel contains an incoming signal block. Local code samples are folded and zero-padded to the length of the incoming signal block. After a circular FFT operation, the correlation results contain two peaks of the same magnitude and specified relative position. The detection process is eased through finding the two largest values. The verification takes all the full and partial peaks into account. Numerical results reveal that the DC-XFAST method can improve acquisition performance while acquisition speed is guaranteed. The method has a significantly higher acquisition probability than folding methods XFAST and DF-XFAST. Moreover, with the advantage of higher detection probability and lower false alarm probability, it has a lower mean acquisition time than traditional XFAST, DF-XFAST and zero-padding.

Automated identification of patients with pulmonary nodules in an integrated health system using administrative health plan data, radiology reports, and natural language processing.

PubMed

Danforth, Kim N; Early, Megan I; Ngan, Sharon; Kosco, Anne E; Zheng, Chengyi; Gould, Michael K

2012-08-01

Lung nodules are commonly encountered in clinical practice, yet little is known about their management in community settings. An automated method for identifying patients with lung nodules would greatly facilitate research in this area. Using members of a large, community-based health plan from 2006 to 2010, we developed a method to identify patients with lung nodules, by combining five diagnostic codes, four procedural codes, and a natural language processing algorithm that performed free text searches of radiology transcripts. An experienced pulmonologist reviewed a random sample of 116 radiology transcripts, providing a reference standard for the natural language processing algorithm. With the use of an automated method, we identified 7112 unique members as having one or more incident lung nodules. The mean age of the patients was 65 years (standard deviation 14 years). There were slightly more women (54%) than men, and Hispanics and non-whites comprised 45% of the lung nodule cohort. Thirty-six percent were never smokers whereas 11% were current smokers. Fourteen percent of the patients were subsequently diagnosed with lung cancer. The sensitivity and specificity of the natural language processing algorithm for identifying the presence of lung nodules were 96% and 86%, respectively, compared with clinician review. Among the true positive transcripts in the validation sample, only 35% were solitary and unaccompanied by one or more associated findings, and 56% measured 8 to 30 mm in diameter. A combination of diagnostic codes, procedural codes, and a natural language processing algorithm for free text searching of radiology reports can accurately and efficiently identify patients with incident lung nodules, many of whom are subsequently diagnosed with lung cancer.

The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses

PubMed Central

Michel, Christian J.

2017-01-01

In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses. The method was based on the preferential occurrence of trinucleotides among the three frames at the gene population level. We extend here this definition at the gene level. This new statistical approach considers all the genes, i.e., of large and small lengths, with the same weight for searching the circular code X. As a consequence, the concept of circular code, in particular the reading frame retrieval, is directly associated to each gene. At the gene level, the circular code X is strengthened in the genes of bacteria, eukaryotes, plasmids, and viruses, and is now also identified in the genes of archaea. The genes of mitochondria and chloroplasts contain a subset of the circular code X. Finally, by studying viral genes, the circular code X was found in DNA genomes, RNA genomes, double-stranded genomes, and single-stranded genomes. PMID:28420220

Cloud4Psi: cloud computing for 3D protein structure similarity searching.

PubMed

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

2014-10-01

Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. © The Author 2014. Published by Oxford University Press.

Cloud4Psi: cloud computing for 3D protein structure similarity searching

PubMed Central

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

2014-01-01

Summary: Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Availability and implementation: Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. Contact: dariusz.mrozek@polsl.pl PMID:24930141

Distributed Learning, Recognition, and Prediction by ART and ARTMAP Neural Networks.

PubMed

Carpenter, Gail A.

1997-11-01

A class of adaptive resonance theory (ART) models for learning, recognition, and prediction with arbitrarily distributed code representations is introduced. Distributed ART neural networks combine the stable fast learning capabilities of winner-take-all ART systems with the noise tolerance and code compression capabilities of multilayer perceptrons. With a winner-take-all code, the unsupervised model dART reduces to fuzzy ART and the supervised model dARTMAP reduces to fuzzy ARTMAP. With a distributed code, these networks automatically apportion learned changes according to the degree of activation of each coding node, which permits fast as well as slow learning without catastrophic forgetting. Distributed ART models replace the traditional neural network path weight with a dynamic weight equal to the rectified difference between coding node activation and an adaptive threshold. Thresholds increase monotonically during learning according to a principle of atrophy due to disuse. However, monotonic change at the synaptic level manifests itself as bidirectional change at the dynamic level, where the result of adaptation resembles long-term potentiation (LTP) for single-pulse or low frequency test inputs but can resemble long-term depression (LTD) for higher frequency test inputs. This paradoxical behavior is traced to dual computational properties of phasic and tonic coding signal components. A parallel distributed match-reset-search process also helps stabilize memory. Without the match-reset-search system, dART becomes a type of distributed competitive learning network.

Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures.

PubMed

Campbell, J R; Carpenter, P; Sneiderman, C; Cohn, S; Chute, C G; Warren, J

1997-01-01

To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for "parent" and "child" codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p < .00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56, UMLS 3.17; READ 2.14, *p < .005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p < .00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p < .004) associated with a loss of clarity. No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. Is suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record.

Sum of the Magnitude for Hard Decision Decoding Algorithm Based on Loop Update Detection.

PubMed

Meng, Jiahui; Zhao, Danfeng; Tian, Hai; Zhang, Liang

2018-01-15

In order to improve the performance of non-binary low-density parity check codes (LDPC) hard decision decoding algorithm and to reduce the complexity of decoding, a sum of the magnitude for hard decision decoding algorithm based on loop update detection is proposed. This will also ensure the reliability, stability and high transmission rate of 5G mobile communication. The algorithm is based on the hard decision decoding algorithm (HDA) and uses the soft information from the channel to calculate the reliability, while the sum of the variable nodes' (VN) magnitude is excluded for computing the reliability of the parity checks. At the same time, the reliability information of the variable node is considered and the loop update detection algorithm is introduced. The bit corresponding to the error code word is flipped multiple times, before this is searched in the order of most likely error probability to finally find the correct code word. Simulation results show that the performance of one of the improved schemes is better than the weighted symbol flipping (WSF) algorithm under different hexadecimal numbers by about 2.2 dB and 2.35 dB at the bit error rate (BER) of 10 -5 over an additive white Gaussian noise (AWGN) channel, respectively. Furthermore, the average number of decoding iterations is significantly reduced.

Minimum Standards for Student Conduct and Discipline, Including Suggested Guidelines and Model Codes. Oregon Administrative Rules 21-050 -- 21-085.

ERIC Educational Resources Information Center

Parnell, Dale

The guidelines and codes in this booklet were written to assist teachers and administrators strengthen their positions in times of legal and social confusion and in the face of challenges to administrative and staff authority. Model codes are provided for student (1) assembly, (2) dress and grooming, (3) motor vehicles, (4) search and seizure, (5)…

Facilitators and barriers to the delivery of school-based smoking prevention interventions for children and young people: a protocol for a systematic review of qualitative studies.

PubMed

Dobbie, Fiona; Angus, Kathryn; Littlecott, Hannah; Allum, Karen; Wells, Valerie; Amos, Amanda; Haw, Sally; Bauld, Linda

2018-04-06

Despite a decline in child and adult smoking prevalence, young people who smoke (even occasionally) can rapidly become addicted to nicotine, with most adult smokers initiating smoking before they are 18. Schools have long been a popular setting to deliver youth smoking prevention interventions, but evidence of the effectiveness of school-based prevention programmes is mixed, and outcomes vary by the type of programme delivered. Existing systematic reviews that explore the factors contributing to the success or failure of school-based smoking prevention programmes often exclude qualitative studies, due to a focus on intervention effectiveness which qualitative research cannot answer. Instead, qualitative research is focussed on the experiences and perceptions of those involved in the programmes. This systematic review will address this gap by updating a 2009 review to examine qualitative studies. The aim is to generate deeper insight to help target resources which have the potential to save lives by preventing smoking initiation among children and young people. This systematic review will be searching the following databases: the Cochrane Library, MEDLINE, EMBASE, PsycINFO, HMIC, ERIC, ASSIA, Web of Science and CINAHL. In order to identify additional references, we will consult the reference lists of a sample of systematic reviews and search relevant organizational websites in order to identify appropriate grey literature. The search strategy will include key words and database-specific subject headings relating to smoking, children and young people, health promotion and school. Authors will independently screen, assess data quality and extract data for synthesis. Study findings will be synthesised thematically using 'best-fit framework syntheses'. This allows for an existing set of themes to be used as a starting point to map or code included studies. These themes are then adapted as coding takes place to accommodate new emerging themes. This review will focus on qualitative studies that seek to examine the barriers and facilitators to the delivery of school-based smoking prevention programmes in order to inform the design of future theory-based interventions in schools to prevent children and young people from smoking. PROSPERO CRD42014015483.

Lessons learned from a pilot implementation of the UMLS information sources map.

PubMed

Miller, P L; Frawley, S J; Wright, L; Roderer, N K; Powsner, S M

1995-01-01

To explore the software design issues involved in implementing an operational information sources map (ISM) knowledge base (KB) and system of navigational tools that can help medical users access network-based information sources relevant to a biomedical question. A pilot biomedical ISM KB and associated client-server software (ISM/Explorer) have been developed to help students, clinicians, researchers, and staff access network-based information sources, as part of the National Library of Medicine's (NLM) multi-institutional Unified Medical Language System (UMLS) project. The system allows the user to specify and constrain a search for a biomedical question of interest. The system then returns a list of sources matching the search. At this point the user may request 1) further information about a source, 2) that the list of sources be regrouped by different criteria to allow the user to get a better overall appreciation of the set of retrieved sources as a whole, or 3) automatic connection to a source. The pilot system operates in client-server mode and currently contains coded information for 121 sources. It is in routine use from approximately 40 workstations at the Yale School of Medicine. The lessons that have been learned are that: 1) it is important to make access to different versions of a source as seamless as possible, 2) achieving seamless, cross-platform access to heterogeneous sources is difficult, 3) significant differences exist between coding the subject content of an electronic information resource versus that of an article or a book, 4) customizing the ISM to multiple institutions entails significant complexities, and 5) there are many design trade-offs between specifying searches and viewing sets of retrieved sources that must be taken into consideration. An ISM KB and navigational tools have been constructed. In the process, much has been learned about the complexities of development and evaluation in this new environment, which are different from those for Gopher, wide area information servers (WAIS), World-Wide-Web (WWW), and MOSAIC resources.

Multimodal Discriminative Binary Embedding for Large-Scale Cross-Modal Retrieval.

PubMed

Wang, Di; Gao, Xinbo; Wang, Xiumei; He, Lihuo; Yuan, Bo

2016-10-01

Multimodal hashing, which conducts effective and efficient nearest neighbor search across heterogeneous data on large-scale multimedia databases, has been attracting increasing interest, given the explosive growth of multimedia content on the Internet. Recent multimodal hashing research mainly aims at learning the compact binary codes to preserve semantic information given by labels. The overwhelming majority of these methods are similarity preserving approaches which approximate pairwise similarity matrix with Hamming distances between the to-be-learnt binary hash codes. However, these methods ignore the discriminative property in hash learning process, which results in hash codes from different classes undistinguished, and therefore reduces the accuracy and robustness for the nearest neighbor search. To this end, we present a novel multimodal hashing method, named multimodal discriminative binary embedding (MDBE), which focuses on learning discriminative hash codes. First, the proposed method formulates the hash function learning in terms of classification, where the binary codes generated by the learned hash functions are expected to be discriminative. And then, it exploits the label information to discover the shared structures inside heterogeneous data. Finally, the learned structures are preserved for hash codes to produce similar binary codes in the same class. Hence, the proposed MDBE can preserve both discriminability and similarity for hash codes, and will enhance retrieval accuracy. Thorough experiments on benchmark data sets demonstrate that the proposed method achieves excellent accuracy and competitive computational efficiency compared with the state-of-the-art methods for large-scale cross-modal retrieval task.

Are all sport activities equal? A systematic review of how youth psychosocial experiences vary across differing sport activities.

PubMed

Evans, M Blair; Allan, Veronica; Erickson, Karl; Martin, Luc J; Budziszewski, Ross; Côté, Jean

2017-02-01

Models of sport development often support the assumption that young athletes' psychosocial experiences differ as a result of seemingly minor variations in how their sport activities are designed (eg, participating in team or individual sport; sampling many sports or specialising at an early age). This review was conducted to systematically search sport literature and explore how the design of sport activities relates to psychosocial outcomes. Systematic search, followed by data extraction and synthesis. The Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines were applied and a coding sheet was used to extract article information and code for risk of bias. Academic databases and manual search of peer-reviewed journals. Search criteria determined eligibility primarily based on the sample (eg, ages 7 through 17 years) and study design (eg, measured psychosocial constructs). 35 studies were located and were classified within three categories: (1) sport types, (2) sport settings, and (3) individual patterns of sport involvement. These studies represented a wide range of scores when assessed for risk of bias and involved an array of psychosocial constructs, with the most prevalent investigations predicting outcomes such as youth development, self-esteem and depression by comparing (1) team or individual sport participants and (2) youth with varying amounts of sport involvement. As variations in sport activities impact youth sport experiences, it is vital for researchers to carefully describe and study these factors, while practitioners may use the current findings when designing youth sport programmes. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

A Framework for Debugging Geoscience Projects in a High Performance Computing Environment

NASA Astrophysics Data System (ADS)

Baxter, C.; Matott, L.

2012-12-01

High performance computing (HPC) infrastructure has become ubiquitous in today's world with the emergence of commercial cloud computing and academic supercomputing centers. Teams of geoscientists, hydrologists and engineers can take advantage of this infrastructure to undertake large research projects - for example, linking one or more site-specific environmental models with soft computing algorithms, such as heuristic global search procedures, to perform parameter estimation and predictive uncertainty analysis, and/or design least-cost remediation systems. However, the size, complexity and distributed nature of these projects can make identifying failures in the associated numerical experiments using conventional ad-hoc approaches both time- consuming and ineffective. To address these problems a multi-tiered debugging framework has been developed. The framework allows for quickly isolating and remedying a number of potential experimental failures, including: failures in the HPC scheduler; bugs in the soft computing code; bugs in the modeling code; and permissions and access control errors. The utility of the framework is demonstrated via application to a series of over 200,000 numerical experiments involving a suite of 5 heuristic global search algorithms and 15 mathematical test functions serving as cheap analogues for the simulation-based optimization of pump-and-treat subsurface remediation systems.

7 CFR 271.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... to an amendment published at 75 FR 78153, Dec. 15, 2010. Access device means any card, plate, code... evaluation of employability skills coupled with counseling on how and where to search for employment. If combined with work experience, employment search or training, an assessment of this nature could constitute...

Object Identity in Infancy: The Interaction of Spatial Location Codes in Determining Search Errors

ERIC Educational Resources Information Center

Butterworth, George

1975-01-01

Reports two experiments which were designed to establish whether errors in infants' manual searches for objects are caused by changes in the location of an object or by the change in the relation between old and new hiding places. (JMB)

Finding collaborators: toward interactive discovery tools for research network systems.

PubMed

Borromeo, Charles D; Schleyer, Titus K; Becich, Michael J; Hochheiser, Harry

2014-11-04

Research networking systems hold great promise for helping biomedical scientists identify collaborators with the expertise needed to build interdisciplinary teams. Although efforts to date have focused primarily on collecting and aggregating information, less attention has been paid to the design of end-user tools for using these collections to identify collaborators. To be effective, collaborator search tools must provide researchers with easy access to information relevant to their collaboration needs. The aim was to study user requirements and preferences for research networking system collaborator search tools and to design and evaluate a functional prototype. Paper prototypes exploring possible interface designs were presented to 18 participants in semistructured interviews aimed at eliciting collaborator search needs. Interview data were coded and analyzed to identify recurrent themes and related software requirements. Analysis results and elements from paper prototypes were used to design a Web-based prototype using the D3 JavaScript library and VIVO data. Preliminary usability studies asked 20 participants to use the tool and to provide feedback through semistructured interviews and completion of the System Usability Scale (SUS). Initial interviews identified consensus regarding several novel requirements for collaborator search tools, including chronological display of publication and research funding information, the need for conjunctive keyword searches, and tools for tracking candidate collaborators. Participant responses were positive (SUS score: mean 76.4%, SD 13.9). Opportunities for improving the interface design were identified. Interactive, timeline-based displays that support comparison of researcher productivity in funding and publication have the potential to effectively support searching for collaborators. Further refinement and longitudinal studies may be needed to better understand the implications of collaborator search tools for researcher workflows.

Finding Collaborators: Toward Interactive Discovery Tools for Research Network Systems

PubMed Central

Schleyer, Titus K; Becich, Michael J; Hochheiser, Harry

2014-01-01

Background Research networking systems hold great promise for helping biomedical scientists identify collaborators with the expertise needed to build interdisciplinary teams. Although efforts to date have focused primarily on collecting and aggregating information, less attention has been paid to the design of end-user tools for using these collections to identify collaborators. To be effective, collaborator search tools must provide researchers with easy access to information relevant to their collaboration needs. Objective The aim was to study user requirements and preferences for research networking system collaborator search tools and to design and evaluate a functional prototype. Methods Paper prototypes exploring possible interface designs were presented to 18 participants in semistructured interviews aimed at eliciting collaborator search needs. Interview data were coded and analyzed to identify recurrent themes and related software requirements. Analysis results and elements from paper prototypes were used to design a Web-based prototype using the D3 JavaScript library and VIVO data. Preliminary usability studies asked 20 participants to use the tool and to provide feedback through semistructured interviews and completion of the System Usability Scale (SUS). Results Initial interviews identified consensus regarding several novel requirements for collaborator search tools, including chronological display of publication and research funding information, the need for conjunctive keyword searches, and tools for tracking candidate collaborators. Participant responses were positive (SUS score: mean 76.4%, SD 13.9). Opportunities for improving the interface design were identified. Conclusions Interactive, timeline-based displays that support comparison of researcher productivity in funding and publication have the potential to effectively support searching for collaborators. Further refinement and longitudinal studies may be needed to better understand the implications of collaborator search tools for researcher workflows. PMID:25370463

An MPI + $X$ implementation of contact global search using Kokkos

DOE PAGES

Hansen, Glen A.; Xavier, Patrick G.; Mish, Sam P.; ...

2015-10-05

This paper describes an approach that seeks to parallelize the spatial search associated with computational contact mechanics. In contact mechanics, the purpose of the spatial search is to find “nearest neighbors,” which is the prelude to an imprinting search that resolves the interactions between the external surfaces of contacting bodies. In particular, we are interested in the contact global search portion of the spatial search associated with this operation on domain-decomposition-based meshes. Specifically, we describe an implementation that combines standard domain-decomposition-based MPI-parallel spatial search with thread-level parallelism (MPI-X) available on advanced computer architectures (those with GPU coprocessors). Our goal ismore » to demonstrate the efficacy of the MPI-X paradigm in the overall contact search. Standard MPI-parallel implementations typically use a domain decomposition of the external surfaces of bodies within the domain in an attempt to efficiently distribute computational work. This decomposition may or may not be the same as the volume decomposition associated with the host physics. The parallel contact global search phase is then employed to find and distribute surface entities (nodes and faces) that are needed to compute contact constraints between entities owned by different MPI ranks without further inter-rank communication. Key steps of the contact global search include computing bounding boxes, building surface entity (node and face) search trees and finding and distributing entities required to complete on-rank (local) spatial searches. To enable source-code portability and performance across a variety of different computer architectures, we implemented the algorithm using the Kokkos hardware abstraction library. While we targeted development towards machines with a GPU accelerator per MPI rank, we also report performance results for OpenMP with a conventional multi-core compute node per rank. Results here demonstrate a 47 % decrease in the time spent within the global search algorithm, comparing the reference ACME algorithm with the GPU implementation, on an 18M face problem using four MPI ranks. As a result, while further work remains to maximize performance on the GPU, this result illustrates the potential of the proposed implementation.« less

A systematic review of validated methods for identifying erythema multiforme major/minor/not otherwise specified, Stevens-Johnson Syndrome, or toxic epidermal necrolysis using administrative and claims data.

PubMed

Schneider, Gary; Kachroo, Sumesh; Jones, Natalie; Crean, Sheila; Rotella, Philip; Avetisyan, Ruzan; Reynolds, Matthew W

2012-01-01

The Food and Drug Administration's (FDA) Mini-Sentinel pilot program aims to conduct active surveillance to refine safety signals that emerge for marketed medical products. A key facet of this surveillance is to develop and understand the validity of algorithms for identifying health outcomes of interest (HOIs) from administrative and claims data. This paper summarizes the process and findings of the algorithm review of erythema multiforme and related conditions. PubMed and Iowa Drug Information Service searches were conducted to identify citations applicable to the erythema multiforme HOI. Level 1 abstract reviews and Level 2 full-text reviews were conducted to find articles that used administrative and claims data to identify erythema multiforme, Stevens-Johnson syndrome, or toxic epidermal necrolysis and that included validation estimates of the coding algorithms. Our search revealed limited literature focusing on erythema multiforme and related conditions that provided administrative and claims data-based algorithms and validation estimates. Only four studies provided validated algorithms and all studies used the same International Classification of Diseases code, 695.1. Approximately half of cases subjected to expert review were consistent with erythema multiforme and related conditions. Updated research needs to be conducted on designing validation studies that test algorithms for erythema multiforme and related conditions and that take into account recent changes in the diagnostic coding of these diseases. Copyright © 2012 John Wiley & Sons, Ltd.

Eye-Movements During Search for Coded and Uncoded Targets

DTIC Science & Technology

1974-06-28

effective a coding system as solor . Subjects did not exhibit a reliable, characteristic scan-path, except for two subjects in the uncoded condition...Psychophysics 8, 171- 172, 1970. 31. Clarke, S. E. Retrieval of color information from the pre-perceptu- al storage system . J Exp Psychol 82, 263

Holland Code, Job Satisfaction and Productivity in Clothing Factory Workers.

ERIC Educational Resources Information Center

Heesacker, Martin; And Others

Published research on vocational interests and personality has not often assessed the characteristics of workers and the work environment in blue-collar, women-dominated industries. This study administered the Self-Directed Search (Form E) to 318 sewing machine operators in three clothing factories. Holland codes, productivity, job satisfaction,…

Phase II Evaluation of Clinical Coding Schemes

PubMed Central

Campbell, James R.; Carpenter, Paul; Sneiderman, Charles; Cohn, Simon; Chute, Christopher G.; Warren, Judith

1997-01-01

Abstract Objective: To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). Methods: The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for “parent” and “child” codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. Results: SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p <.00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56; UMLS 3.17; READ 2.14, *p <.005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p <. 00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p <. 004) associated with a loss of clarity. Conclusion: No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. It suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record. PMID:9147343

Non-US data compression and coding research. FASAC Technical Assessment Report

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

Gray, R.M.; Cohn, M.; Craver, L.W.

1993-11-01

This assessment of recent data compression and coding research outside the United States examines fundamental and applied work in the basic areas of signal decomposition, quantization, lossless compression, and error control, as well as application development efforts in image/video compression and speech/audio compression. Seven computer scientists and engineers who are active in development of these technologies in US academia, government, and industry carried out the assessment. Strong industrial and academic research groups in Western Europe, Israel, and the Pacific Rim are active in the worldwide search for compression algorithms that provide good tradeoffs among fidelity, bit rate, and computational complexity,more » though the theoretical roots and virtually all of the classical compression algorithms were developed in the United States. Certain areas, such as segmentation coding, model-based coding, and trellis-coded modulation, have developed earlier or in more depth outside the United States, though the United States has maintained its early lead in most areas of theory and algorithm development. Researchers abroad are active in other currently popular areas, such as quantizer design techniques based on neural networks and signal decompositions based on fractals and wavelets, but, in most cases, either similar research is or has been going on in the United States, or the work has not led to useful improvements in compression performance. Because there is a high degree of international cooperation and interaction in this field, good ideas spread rapidly across borders (both ways) through international conferences, journals, and technical exchanges. Though there have been no fundamental data compression breakthroughs in the past five years--outside or inside the United State--there have been an enormous number of significant improvements in both places in the tradeoffs among fidelity, bit rate, and computational complexity.« less

Decomposing experience-driven attention: Opposite attentional effects of previously predictive cues.

PubMed

Lin, Zhicheng; Lu, Zhong-Lin; He, Sheng

2016-10-01

A central function of the brain is to track the dynamic statistical regularities in the environment - such as what predicts what over time. How does this statistical learning process alter sensory and attentional processes? Drawing upon animal conditioning and predictive coding, we developed a learning procedure that revealed two distinct components through which prior learning-experience controls attention. During learning, a visual search task was used in which the target randomly appeared at one of several locations but always inside an encloser of a particular color - the learned color served to direct attention to the target location. During test, the color no longer predicted the target location. When the same search task was used in the subsequent test, we found that the learned color continued to attract attention despite the behavior being counterproductive for the task and despite the presence of a completely predictive cue. However, when tested with a flanker task that had minimal location uncertainty - the target was at the fixation surrounded by a distractor - participants were better at ignoring distractors in the learned color than other colors. Evidently, previously predictive cues capture attention in the same search task but can be better suppressed in a flanker task. These results demonstrate opposing components - capture and inhibition - in experience-driven attention, with their manifestations crucially dependent on task context. We conclude that associative learning enhances context-sensitive top-down modulation while it reduces bottom-up sensory drive and facilitates suppression, supporting a learning-based predictive coding account.

Decomposing experience-driven attention: opposite attentional effects of previously predictive cues

PubMed Central

Lin, Zhicheng; Lu, Zhong-Lin; He, Sheng

2016-01-01

A central function of the brain is to track the dynamic statistical regularities in the environment—such as what predicts what over time. How does this statistical learning process alter sensory and attentional processes? Drawing upon animal conditioning and predictive coding, we developed a learning procedure that revealed two distinct components through which prior learning-experience controls attention. During learning, a visual search task was used in which the target randomly appeared at one of several locations but always inside an encloser of a particular color—the learned color served to direct attention to the target location. During test, the color no longer predicted the target location. When the same search task was used in the subsequent test, we found that the learned color continued to attract attention despite the behavior being counterproductive for the task and despite the presence of a completely predictive cue. However, when tested with a flanker task that had minimal location uncertainty—the target was at the fixation surrounded by a distractor—participants were better at ignoring distractors in the learned color than other colors. Evidently, previously predictive cues capture attention in the same search task but can be better suppressed in a flanker task. These results demonstrate opposing components—capture and inhibition—in experience-driven attention, with their manifestations crucially dependent on task context. We conclude that associative learning enhances context-sensitive top-down modulation while reduces bottom-up sensory drive and facilitates suppression, supporting a learning-based predictive coding account. PMID:27068051

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

Defining traumatic brain injury in children and youth using international classification of diseases version 10 codes: a systematic review protocol.

PubMed

Chan, Vincy; Thurairajah, Pravheen; Colantonio, Angela

2013-11-13

Although healthcare administrative data are commonly used for traumatic brain injury research, there is currently no consensus or consistency on using the International Classification of Diseases version 10 codes to define traumatic brain injury among children and youth. This protocol is for a systematic review of the literature to explore the range of International Classification of Diseases version 10 codes that are used to define traumatic brain injury in this population. The databases MEDLINE, MEDLINE In-Process, Embase, PsychINFO, CINAHL, SPORTDiscus, and Cochrane Database of Systematic Reviews will be systematically searched. Grey literature will be searched using Grey Matters and Google. Reference lists of included articles will also be searched. Articles will be screened using predefined inclusion and exclusion criteria and all full-text articles that meet the predefined inclusion criteria will be included for analysis. The study selection process and reasons for exclusion at the full-text level will be presented using a PRISMA study flow diagram. Information on the data source of included studies, year and location of study, age of study population, range of incidence, and study purpose will be abstracted into a separate table and synthesized for analysis. All International Classification of Diseases version 10 codes will be listed in tables and the codes that are used to define concussion, acquired traumatic brain injury, head injury, or head trauma will be identified. The identification of the optimal International Classification of Diseases version 10 codes to define this population in administrative data is crucial, as it has implications for policy, resource allocation, planning of healthcare services, and prevention strategies. It also allows for comparisons across countries and studies. This protocol is for a review that identifies the range and most common diagnoses used to conduct surveillance for traumatic brain injury in children and youth. This is an important first step in reaching an appropriate definition using International Classification of Diseases version 10 codes and can inform future work on reaching consensus on the codes to define traumatic brain injury for this vulnerable population.

Static Stretching of the Hamstring Muscle for Injury Prevention in Football Codes: a Systematic Review

PubMed Central

Rogan, Slavko; Wüst, Dirk; Schwitter, Thomas; Schmidtbleicher, Dietmar

2012-01-01

Purpose Hamstring injuries are common among football players. There is still disagreement regarding prevention. The aim of this review is to determine whether static stretching reduces hamstring injuries in football codes. Methods A systematic literature search was conducted on the online databases PubMed, PEDro, Cochrane, Web of Science, Bisp and Clinical Trial register. Study results were presented descriptively and the quality of the studies assessed were based on Cochrane's ‘risk of bias’ tool. Results The review identified 35 studies, including four analysis studies. These studies show deficiencies in the quality of study designs. Conclusion The study protocols are varied in terms of the length of intervention and follow-up. No RCT studies are available, however, RCT studies should be conducted in the near future. PMID:23785569

Linear chirp phase perturbing approach for finding binary phased codes

NASA Astrophysics Data System (ADS)

Li, Bing C.

2017-05-01

Binary phased codes have many applications in communication and radar systems. These applications require binary phased codes to have low sidelobes in order to reduce interferences and false detection. Barker codes are the ones that satisfy these requirements and they have lowest maximum sidelobes. However, Barker codes have very limited code lengths (equal or less than 13) while many applications including low probability of intercept radar, and spread spectrum communication, require much higher code lengths. The conventional techniques of finding binary phased codes in literatures include exhaust search, neural network, and evolutionary methods, and they all require very expensive computation for large code lengths. Therefore these techniques are limited to find binary phased codes with small code lengths (less than 100). In this paper, by analyzing Barker code, linear chirp, and P3 phases, we propose a new approach to find binary codes. Experiments show that the proposed method is able to find long low sidelobe binary phased codes (code length >500) with reasonable computational cost.

NOAA Weather Radio

Science.gov Websites

Station Search Coverage Maps Outages View Outages Report Outages Information General Information Receiver Information Reception Problems NWR Alarms Automated Voices FIPS Codes NWR - Special Needs SAME USING SAME SAME Search For Go NWS All NOAA Frequently Asked Questions This site offers a wealth of information on NOAA

Genetic learning in rule-based and neural systems

NASA Technical Reports Server (NTRS)

Smith, Robert E.

1993-01-01

The design of neural networks and fuzzy systems can involve complex, nonlinear, and ill-conditioned optimization problems. Often, traditional optimization schemes are inadequate or inapplicable for such tasks. Genetic Algorithms (GA's) are a class of optimization procedures whose mechanics are based on those of natural genetics. Mathematical arguments show how GAs bring substantial computational leverage to search problems, without requiring the mathematical characteristics often necessary for traditional optimization schemes (e.g., modality, continuity, availability of derivative information, etc.). GA's have proven effective in a variety of search tasks that arise in neural networks and fuzzy systems. This presentation begins by introducing the mechanism and theoretical underpinnings of GA's. GA's are then related to a class of rule-based machine learning systems called learning classifier systems (LCS's). An LCS implements a low-level production-system that uses a GA as its primary rule discovery mechanism. This presentation illustrates how, despite its rule-based framework, an LCS can be thought of as a competitive neural network. Neural network simulator code for an LCS is presented. In this context, the GA is doing more than optimizing and objective function. It is searching for an ecology of hidden nodes with limited connectivity. The GA attempts to evolve this ecology such that effective neural network performance results. The GA is particularly well adapted to this task, given its naturally-inspired basis. The LCS/neural network analogy extends itself to other, more traditional neural networks. Conclusions to the presentation discuss the implications of using GA's in ecological search problems that arise in neural and fuzzy systems.

Astrophysics Source Code Library -- Now even better!

NASA Astrophysics Data System (ADS)

Allen, Alice; Schmidt, Judy; Berriman, Bruce; DuPrie, Kimberly; Hanisch, Robert J.; Mink, Jessica D.; Nemiroff, Robert J.; Shamir, Lior; Shortridge, Keith; Taylor, Mark B.; Teuben, Peter J.; Wallin, John F.

2015-01-01

The Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. Indexed by ADS, it now contains nearly 1,000 codes and with recent major changes, is better than ever! The resource has a new infrastructure that offers greater flexibility and functionality for users, including an easier submission process, better browsing, one-click author search, and an RSS feeder for news. The new database structure is easier to maintain and offers new possibilities for collaboration. Come see what we've done!

Improvement of the cruise performances of a wing by means of aerodynamic optimization. Validation with a Far-Field method

NASA Astrophysics Data System (ADS)

Jiménez-Varona, J.; Ponsin Roca, J.

2015-06-01

Under a contract with AIRBUS MILITARY (AI-M), an exercise to analyze the potential of optimization techniques to improve the wing performances at cruise conditions has been carried out by using an in-house design code. The original wing was provided by AI-M and several constraints were posed for the redesign. To maximize the aerodynamic efficiency at cruise, optimizations were performed using the design techniques developed internally at INTA under a research program (Programa de Termofluidodinámica). The code is a gradient-based optimizaa tion code, which uses classical finite differences approach for gradient computations. Several techniques for search direction computation are implemented for unconstrained and constrained problems. Techniques for geometry modifications are based on different approaches which include perturbation functions for the thickness and/or mean line distributions and others by Bézier curves fitting of certain degree. It is very e important to afford a real design which involves several constraints that reduce significantly the feasible design space. And the assessment of the code is needed in order to check the capabilities and the possible drawbacks. Lessons learnt will help in the development of future enhancements. In addition, the validation of the results was done using also the well-known TAU flow solver and a far-field drag method in order to determine accurately the improvement in terms of drag counts.

A new method to improve network topological similarity search: applied to fold recognition

PubMed Central

Lhota, John; Hauptman, Ruth; Hart, Thomas; Ng, Clara; Xie, Lei

2015-01-01

Motivation: Similarity search is the foundation of bioinformatics. It plays a key role in establishing structural, functional and evolutionary relationships between biological sequences. Although the power of the similarity search has increased steadily in recent years, a high percentage of sequences remain uncharacterized in the protein universe. Thus, new similarity search strategies are needed to efficiently and reliably infer the structure and function of new sequences. The existing paradigm for studying protein sequence, structure, function and evolution has been established based on the assumption that the protein universe is discrete and hierarchical. Cumulative evidence suggests that the protein universe is continuous. As a result, conventional sequence homology search methods may be not able to detect novel structural, functional and evolutionary relationships between proteins from weak and noisy sequence signals. To overcome the limitations in existing similarity search methods, we propose a new algorithmic framework—Enrichment of Network Topological Similarity (ENTS)—to improve the performance of large scale similarity searches in bioinformatics. Results: We apply ENTS to a challenging unsolved problem: protein fold recognition. Our rigorous benchmark studies demonstrate that ENTS considerably outperforms state-of-the-art methods. As the concept of ENTS can be applied to any similarity metric, it may provide a general framework for similarity search on any set of biological entities, given their representation as a network. Availability and implementation: Source code freely available upon request Contact: lxie@iscb.org PMID:25717198

Computer search for binary cyclic UEP codes of odd length up to 65

NASA Technical Reports Server (NTRS)

Lin, Mao-Chao; Lin, Chi-Chang; Lin, Shu

1990-01-01

Using an exhaustive computation, the unequal error protection capabilities of all binary cyclic codes of odd length up to 65 that have minimum distances at least 3 are found. For those codes that can only have upper bounds on their unequal error protection capabilities computed, an analytic method developed by Dynkin and Togonidze (1976) is used to show that the upper bounds meet the exact unequal error protection capabilities.

Resource Management In Peer-To-Peer Networks: A Nadse Approach

NASA Astrophysics Data System (ADS)

Patel, R. B.; Garg, Vishal

2011-12-01

This article presents a common solution to Peer-to-Peer (P2P) network problems and distributed computing with the help of "Neighbor Assisted Distributed and Scalable Environment" (NADSE). NADSE supports both device and code mobility. In this article mainly we focus on the NADSE based resource management technique. How information dissemination and searching is speedup when using the NADSE service provider node in large network. Results show that performance of the NADSE network is better in comparison to Gnutella, and Freenet.

VENTURE: a code block for solving multigroup neutronics problems applying the finite-difference diffusion-theory approximation to neutron transport

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

Vondy, D.R.; Fowler, T.B.; Cunningham, G.W.

1975-10-01

The computer code block VENTURE, designed to solve multigroup neutronics problems with application of the finite-difference diffusion-theory approximation to neutron transport (or alternatively simple P$sub 1$) in up to three- dimensional geometry is described. A variety of types of problems may be solved: the usual eigenvalue problem, a direct criticality search on the buckling, on a reciprocal velocity absorber (prompt mode), or on nuclide concentrations, or an indirect criticality search on nuclide concentrations, or on dimensions. First- order perturbation analysis capability is available at the macroscopic cross section level. (auth)

Validated methods for identifying tuberculosis patients in health administrative databases: systematic review.

PubMed

Ronald, L A; Ling, D I; FitzGerald, J M; Schwartzman, K; Bartlett-Esquilant, G; Boivin, J-F; Benedetti, A; Menzies, D

2017-05-01

An increasing number of studies are using health administrative databases for tuberculosis (TB) research. However, there are limitations to using such databases for identifying patients with TB. To summarise validated methods for identifying TB in health administrative databases. We conducted a systematic literature search in two databases (Ovid Medline and Embase, January 1980-January 2016). We limited the search to diagnostic accuracy studies assessing algorithms derived from drug prescription, International Classification of Diseases (ICD) diagnostic code and/or laboratory data for identifying patients with TB in health administrative databases. The search identified 2413 unique citations. Of the 40 full-text articles reviewed, we included 14 in our review. Algorithms and diagnostic accuracy outcomes to identify TB varied widely across studies, with positive predictive value ranging from 1.3% to 100% and sensitivity ranging from 20% to 100%. Diagnostic accuracy measures of algorithms using out-patient, in-patient and/or laboratory data to identify patients with TB in health administrative databases vary widely across studies. Use solely of ICD diagnostic codes to identify TB, particularly when using out-patient records, is likely to lead to incorrect estimates of case numbers, given the current limitations of ICD systems in coding TB.

Computation of the Genetic Code

NASA Astrophysics Data System (ADS)

Kozlov, Nicolay N.; Kozlova, Olga N.

2018-03-01

One of the problems in the development of mathematical theory of the genetic code (summary is presented in [1], the detailed -to [2]) is the problem of the calculation of the genetic code. Similar problems in the world is unknown and could be delivered only in the 21st century. One approach to solving this problem is devoted to this work. For the first time provides a detailed description of the method of calculation of the genetic code, the idea of which was first published earlier [3]), and the choice of one of the most important sets for the calculation was based on an article [4]. Such a set of amino acid corresponds to a complete set of representations of the plurality of overlapping triple gene belonging to the same DNA strand. A separate issue was the initial point, triggering an iterative search process all codes submitted by the initial data. Mathematical analysis has shown that the said set contains some ambiguities, which have been founded because of our proposed compressed representation of the set. As a result, the developed method of calculation was limited to the two main stages of research, where the first stage only the of the area were used in the calculations. The proposed approach will significantly reduce the amount of computations at each step in this complex discrete structure.

Cauda equina syndrome: assessing the readability and quality of patient information on the Internet.

PubMed

O'Neill, Shane Ciaran; Baker, Joseph Frederick; Fitzgerald, Conall; Fleming, Christina; Rowan, Fiachra; Byrne, Damien; Synnott, Keith

2014-05-01

A readability and quality control Internet-based study using recognized quality scoring systems. To assess the readability and quality of Internet information relating to cauda equina syndrome accessed through common search engines. Access to health-related Internet information has increased dramatically during the past decade. A significant proportion of this information has been demonstrated to be set at too high a level for general comprehension. Despite this, searching for health-related information is now the third most popular online activity. A total of 125 cauda equina syndrome Web sites were analyzed from the 5 most popular Internet search engines: Google, Bing, Yahoo, Ask, and AOL. Web site authorship was classified: academic, physician, medico-legal, commercial, or discussion/social media. Readability of each Web site was assessed using the Flesch Reading Ease score, the Flesch-Kincaid grade level, and the Gunning Fog Index. Quality was calculated using the DISCERN instrument and The Journal of the American Medical Association benchmark criteria. The presence of HON-code certification was also assessed. Fifty-two individual Web sites were identified and assessed. The majority of Web sites were academic or physician compiled (53.8%; 28/52); however, a significant minority of Web sites were medico-legal related (19.2%; 10/52). Just 13.5% (7/52) of Web sites were at or below the recommended sixth-grade readability level. HON-code certified Web sites achieved significantly greater DISCERN (P = 0.0006) and The Journal of the American Medical Association (P = 0.0002) scores. Internet information relating to cauda equina syndrome is of variable quality and largely set at an inappropriate readability level. Given this variability in quality, health care providers should direct patients to known sources of reliable, readable online information. Identification of reliable sources may be aided by known markers of quality such as HON-code certification.

Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV) processing speed scores as measures of noncredible responding: The third generation of embedded performance validity indicators.

PubMed

Erdodi, Laszlo A; Abeare, Christopher A; Lichtenstein, Jonathan D; Tyson, Bradley T; Kucharski, Brittany; Zuccato, Brandon G; Roth, Robert M

2017-02-01

Research suggests that select processing speed measures can also serve as embedded validity indicators (EVIs). The present study examined the diagnostic utility of Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV) subtests as EVIs in a mixed clinical sample of 205 patients medically referred for neuropsychological assessment (53.3% female, mean age = 45.1). Classification accuracy was calculated against 3 composite measures of performance validity as criterion variables. A PSI ≤79 produced a good combination of sensitivity (.23-.56) and specificity (.92-.98). A Coding scaled score ≤5 resulted in good specificity (.94-1.00), but low and variable sensitivity (.04-.28). A Symbol Search scaled score ≤6 achieved a good balance between sensitivity (.38-.64) and specificity (.88-.93). A Coding-Symbol Search scaled score difference ≥5 produced adequate specificity (.89-.91) but consistently low sensitivity (.08-.12). A 2-tailed cutoff on the Coding/Symbol Search raw score ratio (≤1.41 or ≥3.57) produced acceptable specificity (.87-.93), but low sensitivity (.15-.24). Failing ≥2 of these EVIs produced variable specificity (.81-.93) and sensitivity (.31-.59). Failing ≥3 of these EVIs stabilized specificity (.89-.94) at a small cost to sensitivity (.23-.53). Results suggest that processing speed based EVIs have the potential to provide a cost-effective and expedient method for evaluating the validity of cognitive data. Given their generally low and variable sensitivity, however, they should not be used in isolation to determine the credibility of a given response set. They also produced unacceptably high rates of false positive errors in patients with moderate-to-severe head injury. Combining evidence from multiple EVIs has the potential to improve overall classification accuracy. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

An Integrative Model of Patient-Centeredness – A Systematic Review and Concept Analysis

PubMed Central

Scholl, Isabelle; Zill, Jördis M.; Härter, Martin; Dirmaier, Jörg

2014-01-01

Background Existing models of patient-centeredness reveal a lack of conceptual clarity. This results in a heterogeneous use of the term, unclear measurement dimensions, inconsistent results regarding the effectiveness of patient-centered interventions, and finally in difficulties in implementing patient-centered care. The aim of this systematic review was to identify the different dimensions of patient-centeredness described in the literature and to propose an integrative model of patient-centeredness based on these results. Methods Protocol driven search in five databases, combined with a comprehensive secondary search strategy. All articles that include a definition of patient-centeredness were eligible for inclusion in the review and subject to subsequent content analysis. Two researchers independently first screened titles and abstracts, then assessed full texts for eligibility. In each article the given definition of patient-centeredness was coded independently by two researchers. We discussed codes within the research team and condensed them into an integrative model of patient-centeredness. Results 4707 records were identified through primary and secondary search, of which 706 were retained after screening of titles and abstracts. 417 articles (59%) contained a definition of patient-centeredness and were coded. 15 dimensions of patient-centeredness were identified: essential characteristics of clinician, clinician-patient relationship, clinician-patient communication, patient as unique person, biopsychosocial perspective, patient information, patient involvement in care, involvement of family and friends, patient empowerment, physical support, emotional support, integration of medical and non-medical care, teamwork and teambuilding, access to care, coordination and continuity of care. In the resulting integrative model the dimensions were mapped onto different levels of care. Conclusions The proposed integrative model of patient-centeredness allows different stakeholders to speak the same language. It provides a foundation for creating better measures and interventions. It can also be used to inform the development of clinical guidance documents and health policy directives, and through this support the shift towards patient-centered health care. PMID:25229640

BrainLiner: A Neuroinformatics Platform for Sharing Time-Aligned Brain-Behavior Data

PubMed Central

Takemiya, Makoto; Majima, Kei; Tsukamoto, Mitsuaki; Kamitani, Yukiyasu

2016-01-01

Data-driven neuroscience aims to find statistical relationships between brain activity and task behavior from large-scale datasets. To facilitate high-throughput data processing and modeling, we created BrainLiner as a web platform for sharing time-aligned, brain-behavior data. Using an HDF5-based data format, BrainLiner treats brain activity and data related to behavior with the same salience, aligning both behavioral and brain activity data on a common time axis. This facilitates learning the relationship between behavior and brain activity. Using a common data file format also simplifies data processing and analyses. Properties describing data are unambiguously defined using a schema, allowing machine-readable definition of data. The BrainLiner platform allows users to upload and download data, as well as to explore and search for data from the web platform. A WebGL-based data explorer can visualize highly detailed neurophysiological data from within the web browser, and a data-driven search feature allows users to search for similar time windows of data. This increases transparency, and allows for visual inspection of neural coding. BrainLiner thus provides an essential set of tools for data sharing and data-driven modeling. PMID:26858636

De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris

PubMed Central

Niu, Shan-Ce; Xu, Qing; Zhang, Guo-Qiang; Zhang, Yong-Qiang; Tsai, Wen-Chieh; Hsu, Jui-Ling; Liang, Chieh-Kai; Luo, Yi-Bo; Liu, Zhong-Jian

2016-01-01

Orchids are renowned for their spectacular flowers and ecological adaptations. After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris, we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues representing the root, stem, leaf, flower buds, column, lip, petal, sepal and three developmental stages of seeds. Our aims were to contribute to a better understanding of the molecular mechanisms driving the analysed tissue characteristics and to enrich the available data for P. equestris. Here, we present three databases. The first dataset is the RNA-Seq raw reads, which can be used to execute new experiments with different analysis approaches. The other two datasets allow different types of searches for candidate homologues. The second dataset includes the sets of assembled unigenes and predicted coding sequences and proteins, enabling a sequence-based search. The third dataset consists of the annotation results of the aligned unigenes versus the Nonredundant (Nr) protein database, Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) databases with low e-values, enabling a name-based search. PMID:27673730

Study on user interface of pathology picture archiving and communication system.

PubMed

Kim, Dasueran; Kang, Peter; Yun, Jungmin; Park, Sung-Hye; Seo, Jeong-Wook; Park, Peom

2014-01-01

It is necessary to improve the pathology workflow. A workflow task analysis was performed using a pathology picture archiving and communication system (pathology PACS) in order to propose a user interface for the Pathology PACS considering user experience. An interface analysis of the Pathology PACS in Seoul National University Hospital and a task analysis of the pathology workflow were performed by observing recorded video. Based on obtained results, a user interface for the Pathology PACS was proposed. Hierarchical task analysis of Pathology PACS was classified into 17 tasks including 1) pre-operation, 2) text, 3) images, 4) medical record viewer, 5) screen transition, 6) pathology identification number input, 7) admission date input, 8) diagnosis doctor, 9) diagnosis code, 10) diagnosis, 11) pathology identification number check box, 12) presence or absence of images, 13) search, 14) clear, 15) Excel save, 16) search results, and 17) re-search. And frequently used menu items were identified and schematized. A user interface for the Pathology PACS considering user experience could be proposed as a preliminary step, and this study may contribute to the development of medical information systems based on user experience and usability.

Standardized mappings--a framework to combine different semantic mappers into a standardized web-API.

PubMed

Neuhaus, Philipp; Doods, Justin; Dugas, Martin

2015-01-01

Automatic coding of medical terms is an important, but highly complicated and laborious task. To compare and evaluate different strategies a framework with a standardized web-interface was created. Two UMLS mapping strategies are compared to demonstrate the interface. The framework is a Java Spring application running on a Tomcat application server. It accepts different parameters and returns results in JSON format. To demonstrate the framework, a list of medical data items was mapped by two different methods: similarity search in a large table of terminology codes versus search in a manually curated repository. These mappings were reviewed by a specialist. The evaluation shows that the framework is flexible (due to standardized interfaces like HTTP and JSON), performant and reliable. Accuracy of automatically assigned codes is limited (up to 40%). Combining different semantic mappers into a standardized Web-API is feasible. This framework can be easily enhanced due to its modular design.

Image management research

NASA Technical Reports Server (NTRS)

Watson, Andrew B.

1988-01-01

Two types of research issues are involved in image management systems with space station applications: image processing research and image perception research. The image processing issues are the traditional ones of digitizing, coding, compressing, storing, analyzing, and displaying, but with a new emphasis on the constraints imposed by the human perceiver. Two image coding algorithms have been developed that may increase the efficiency of image management systems (IMS). Image perception research involves a study of the theoretical and practical aspects of visual perception of electronically displayed images. Issues include how rapidly a user can search through a library of images, how to make this search more efficient, and how to present images in terms of resolution and split screens. Other issues include optimal interface to an IMS and how to code images in a way that is optimal for the human perceiver. A test-bed within which such issues can be addressed has been designed.

GSAC - Generic Seismic Application Computing

NASA Astrophysics Data System (ADS)

Herrmann, R. B.; Ammon, C. J.; Koper, K. D.

2004-12-01

With the success of the IRIS data management center, the use of large data sets in seismological research has become common. Such data sets, and especially the significantly larger data sets expected from EarthScope, present challenges for analysis with existing tools developed over the last 30 years. For much of the community, the primary format for data analysis is the Seismic Analysis Code (SAC) format developed by Lawrence Livermore National Laboratory. Although somewhat restrictive in meta-data storage, the simplicity and stability of the format has established it as an important component of seismological research. Tools for working with SAC files fall into two categories - custom research quality processing codes and shared display - processing tools such as SAC2000, MatSeis,etc., which were developed primarily for the needs of individual seismic research groups. While the current graphics display and platform dependence of SAC2000 may be resolved if the source code is released, the code complexity and the lack of large-data set analysis or even introductory tutorials could preclude code improvements and development of expertise in its use. We believe that there is a place for new, especially open source, tools. The GSAC effort is an approach that focuses on ease of use, computational speed, transportability, rapid addition of new features and openness so that new and advanced students, researchers and instructors can quickly browse and process large data sets. We highlight several approaches toward data processing under this model. gsac - part of the Computer Programs in Seismology 3.30 distribution has much of the functionality of SAC2000 and works on UNIX/LINUX/MacOS-X/Windows (CYGWIN). This is completely programmed in C from scratch, is small, fast, and easy to maintain and extend. It is command line based and is easily included within shell processing scripts. PySAC is a set of Python functions that allow easy access to SAC files and enable efficient manipulation of SAC files under a variety of operating systems. PySAC has proven to be valuable in organizing large data sets. An array processing package includes standard beamforming algorithms and a search based method for inference of slowness vectors. The search results can be visualized using GMT scripts output by the C programs, and the resulting snapshots can be combined into an animation of the time evolution of the 2D slowness field.

Network effects across the earnings distribution: payoffs to visible and invisible job finding assistance.

PubMed

McDonald, Steve

2015-01-01

This study makes three critical contributions to the "Do Contacts Matter?" debate. First, the widely reported null relationship between informal job searching and wages is shown to be mostly the artifact of a coding error and sample selection restrictions. Second, previous analyses examined only active informal job searching without fully considering the benefits derived from unsolicited network assistance (the "invisible hand of social capital") - thereby underestimating the network effect. Third, wage returns to networks are examined across the earnings distribution. Longitudinal data from the NLSY reveal significant wage returns for network-based job finding over formal job searching, especially for individuals who were informally recruited into their jobs (non-searchers). Fixed effects quantile regression analyses show that contacts generate wage premiums among middle and high wage jobs, but not low wage jobs. These findings challenge conventional wisdom on contact effects and advance understanding of how social networks affect wage attainment and inequality. Copyright © 2014 Elsevier Inc. All rights reserved.

Optimization of a Boiling Water Reactor Loading Pattern Using an Improved Genetic Algorithm

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

Kobayashi, Yoko; Aiyoshi, Eitaro

2003-08-15

A search method based on genetic algorithms (GA) using deterministic operators has been developed to generate optimized boiling water reactor (BWR) loading patterns (LPs). The search method uses an Improved GA operator, that is, crossover, mutation, and selection. The handling of the encoding technique and constraint conditions is designed so that the GA reflects the peculiar characteristics of the BWR. In addition, some strategies such as elitism and self-reproduction are effectively used to improve the search speed. LP evaluations were performed with a three-dimensional diffusion code that coupled neutronic and thermal-hydraulic models. Strong axial heterogeneities and three-dimensional-dependent constraints have alwaysmore » necessitated the use of three-dimensional core simulators for BWRs, so that an optimization method is required for computational efficiency. The proposed algorithm is demonstrated by successfully generating LPs for an actual BWR plant applying the Haling technique. In test calculations, candidates that shuffled fresh and burned fuel assemblies within a reasonable computation time were obtained.« less

Characterizing the Processes for Navigating Internet Health Information Using Real-Time Observations: A Mixed-Methods Approach.

PubMed

Perez, Susan L; Paterniti, Debora A; Wilson, Machelle; Bell, Robert A; Chan, Man Shan; Villareal, Chloe C; Nguyen, Hien Huy; Kravitz, Richard L

2015-07-20

Little is known about the processes people use to find health-related information on the Internet or the individual characteristics that shape selection of information-seeking approaches. Our aim was to describe the processes by which users navigate the Internet for information about a hypothetical acute illness and to identify individual characteristics predictive of their information-seeking strategies. Study participants were recruited from public settings and agencies. Interested individuals were screened for eligibility using an online questionnaire. Participants listened to one of two clinical scenarios—consistent with influenza or bacterial meningitis—and then conducted an Internet search. Screen-capture video software captured Internet search mouse clicks and keystrokes. Each step of the search was coded as hypothesis testing (etiology), evidence gathering (symptoms), or action/treatment seeking (behavior). The coded steps were used to form a step-by-step pattern of each participant's information-seeking process. A total of 78 Internet health information seekers ranging from 21-35 years of age and who experienced barriers to accessing health care services participated. We identified 27 unique patterns of information seeking, which were grouped into four overarching classifications based on the number of steps taken during the search, whether a pattern consisted of developing a hypothesis and exploring symptoms before ending the search or searching an action/treatment, and whether a pattern ended with action/treatment seeking. Applying dual-processing theory, we categorized the four overarching pattern classifications as either System 1 (41%, 32/78), unconscious, rapid, automatic, and high capacity processing; or System 2 (59%, 46/78), conscious, slow, and deliberative processing. Using multivariate regression, we found that System 2 processing was associated with higher education and younger age. We identified and classified two approaches to processing Internet health information. System 2 processing, a methodical approach, most resembles the strategies for information processing that have been found in other studies to be associated with higher-quality decisions. We conclude that the quality of Internet health-information seeking could be improved through consumer education on methodical Internet navigation strategies and the incorporation of decision aids into health information websites.

Characterizing the Processes for Navigating Internet Health Information Using Real-Time Observations: A Mixed-Methods Approach

PubMed Central

Paterniti, Debora A; Wilson, Machelle; Bell, Robert A; Chan, Man Shan; Villareal, Chloe C; Nguyen, Hien Huy; Kravitz, Richard L

2015-01-01

Background Little is known about the processes people use to find health-related information on the Internet or the individual characteristics that shape selection of information-seeking approaches. Objective Our aim was to describe the processes by which users navigate the Internet for information about a hypothetical acute illness and to identify individual characteristics predictive of their information-seeking strategies. Methods Study participants were recruited from public settings and agencies. Interested individuals were screened for eligibility using an online questionnaire. Participants listened to one of two clinical scenarios—consistent with influenza or bacterial meningitis—and then conducted an Internet search. Screen-capture video software captured Internet search mouse clicks and keystrokes. Each step of the search was coded as hypothesis testing (etiology), evidence gathering (symptoms), or action/treatment seeking (behavior). The coded steps were used to form a step-by-step pattern of each participant’s information-seeking process. A total of 78 Internet health information seekers ranging from 21-35 years of age and who experienced barriers to accessing health care services participated. Results We identified 27 unique patterns of information seeking, which were grouped into four overarching classifications based on the number of steps taken during the search, whether a pattern consisted of developing a hypothesis and exploring symptoms before ending the search or searching an action/treatment, and whether a pattern ended with action/treatment seeking. Applying dual-processing theory, we categorized the four overarching pattern classifications as either System 1 (41%, 32/78), unconscious, rapid, automatic, and high capacity processing; or System 2 (59%, 46/78), conscious, slow, and deliberative processing. Using multivariate regression, we found that System 2 processing was associated with higher education and younger age. Conclusions We identified and classified two approaches to processing Internet health information. System 2 processing, a methodical approach, most resembles the strategies for information processing that have been found in other studies to be associated with higher-quality decisions. We conclude that the quality of Internet health-information seeking could be improved through consumer education on methodical Internet navigation strategies and the incorporation of decision aids into health information websites. PMID:26194787

Towards a semantic medical Web: HealthCyberMap's tool for building an RDF metadata base of health information resources based on the Qualified Dublin Core Metadata Set.

PubMed

Boulos, Maged N; Roudsari, Abdul V; Carson, Ewart R

2002-07-01

HealthCyberMap (http://healthcybermap.semanticweb.org/) aims at mapping Internet health information resources in novel ways for enhanced retrieval and navigation. This is achieved by collecting appropriate resource metadata in an unambiguous form that preserves semantics. We modelled a qualified Dublin Core (DC) metadata set ontology with extra elements for resource quality and geographical provenance in Prot g -2000. A metadata collection form helps acquiring resource instance data within Prot g . The DC subject field is populated with UMLS terms directly imported from UMLS Knowledge Source Server using UMLS tab, a Prot g -2000 plug-in. The project is saved in RDFS/RDF. The ontology and associated form serve as a free tool for building and maintaining an RDF medical resource metadata base. The UMLS tab enables browsing and searching for concepts that best describe a resource, and importing them to DC subject fields. The resultant metadata base can be used with a search and inference engine, and have textual and/or visual navigation interface(s) applied to it, to ultimately build a medical Semantic Web portal. Different ways of exploiting Prot g -2000 RDF output are discussed. By making the context and semantics of resources, not merely their raw text and formatting, amenable to computer 'understanding,' we can build a Semantic Web that is more useful to humans than the current Web. This requires proper use of metadata and ontologies. Clinical codes can reliably describe the subjects of medical resources, establish the semantic relationships (as defined by underlying coding scheme) between related resources, and automate their topical categorisation.

Evaluation of hospital staff’s perceived quality of librarian-mediated literature searching services*,†

PubMed Central

McKeown, Sandra; Konrad, Shauna-Lee; McTavish, Jill; Boyce, Erin

2017-01-01

Objective The research evaluated the perceived quality of librarian-mediated literature searching services at one of Canada’s largest acute care teaching hospitals for the purpose of continuous quality improvement and investigation of relationships between variables that can impact user satisfaction. Methods An online survey was constructed using evidence-based methodologies. A systematic sample of staff and physicians requesting literature searches at London Health Sciences Centre were invited to participate in the study over a one-year period. Data analyses included descriptive statistics of closed-ended questions and coding of open-ended questions. Results A range of staff including clinicians, researchers, educators, leaders, and analysts submitted a total of 137 surveys, representing a response rate of 71%. Staff requested literature searches for the following “primary” purposes: research or publication (34%), teaching or training (20%), informing a policy or standard practice (16%), patient care (15%), and “other” purposes (15%). While the majority of staff (76%) submitted search requests using methods of written communication, including email and search request forms, staff using methods of verbal communication, including face-to-face and telephone conversations, were significantly more likely to be extremely satisfied with the librarian’s interpretation of the search request (p=0.004) and to rate the perceived quality of the search results as excellent (p=0.005). In most cases, librarians followed up with staff to clarify the details of their search requests (72%), and these staff were significantly more likely to be extremely satisfied with the librarian’s interpretation of the search request (p=0.002). Conclusions Our results demonstrate the limitations of written communication in the context of librarian-mediated literature searching and suggest a multifaceted approach to quality improvement efforts. PMID:28377674

Evaluation of hospital staff's perceived quality of librarian-mediated literature searching services.

PubMed

McKeown, Sandra; Konrad, Shauna-Lee; McTavish, Jill; Boyce, Erin

2017-04-01

The research evaluated the perceived quality of librarian-mediated literature searching services at one of Canada's largest acute care teaching hospitals for the purpose of continuous quality improvement and investigation of relationships between variables that can impact user satisfaction. An online survey was constructed using evidence-based methodologies. A systematic sample of staff and physicians requesting literature searches at London Health Sciences Centre were invited to participate in the study over a one-year period. Data analyses included descriptive statistics of closed-ended questions and coding of open-ended questions. A range of staff including clinicians, researchers, educators, leaders, and analysts submitted a total of 137 surveys, representing a response rate of 71%. Staff requested literature searches for the following "primary" purposes: research or publication (34%), teaching or training (20%), informing a policy or standard practice (16%), patient care (15%), and "other" purposes (15%). While the majority of staff (76%) submitted search requests using methods of written communication, including email and search request forms, staff using methods of verbal communication, including face-to-face and telephone conversations, were significantly more likely to be extremely satisfied with the librarian's interpretation of the search request ( p =0.004) and to rate the perceived quality of the search results as excellent ( p =0.005). In most cases, librarians followed up with staff to clarify the details of their search requests (72%), and these staff were significantly more likely to be extremely satisfied with the librarian's interpretation of the search request ( p =0.002). Our results demonstrate the limitations of written communication in the context of librarian-mediated literature searching and suggest a multifaceted approach to quality improvement efforts.

Efficiency of International Classification of Diseases, Ninth Revision, Billing Code Searches to Identify Emergency Department Visits for Blood or Body Fluid Exposures through a Statewide Multicenter Database

PubMed Central

Rosen, Lisa M.; Liu, Tao; Merchant, Roland C.

2016-01-01

BACKGROUND Blood and body fluid exposures are frequently evaluated in emergency departments (EDs). However, efficient and effective methods for estimating their incidence are not yet established. OBJECTIVE Evaluate the efficiency and accuracy of estimating statewide ED visits for blood or body fluid exposures using International Classification of Diseases, Ninth Revision (ICD-9), code searches. DESIGN Secondary analysis of a database of ED visits for blood or body fluid exposure. SETTING EDs of 11 civilian hospitals throughout Rhode Island from January 1, 1995, through June 30, 2001. PATIENTS Patients presenting to the ED for possible blood or body fluid exposure were included, as determined by prespecified ICD-9 codes. METHODS Positive predictive values (PPVs) were estimated to determine the ability of 10 ICD-9 codes to distinguish ED visits for blood or body fluid exposure from ED visits that were not for blood or body fluid exposure. Recursive partitioning was used to identify an optimal subset of ICD-9 codes for this purpose. Random-effects logistic regression modeling was used to examine variations in ICD-9 coding practices and styles across hospitals. Cluster analysis was used to assess whether the choice of ICD-9 codes was similar across hospitals. RESULTS The PPV for the original 10 ICD-9 codes was 74.4% (95% confidence interval [CI], 73.2%–75.7%), whereas the recursive partitioning analysis identified a subset of 5 ICD-9 codes with a PPV of 89.9% (95% CI, 88.9%–90.8%) and a misclassification rate of 10.1%. The ability, efficiency, and use of the ICD-9 codes to distinguish types of ED visits varied across hospitals. CONCLUSIONS Although an accurate subset of ICD-9 codes could be identified, variations across hospitals related to hospital coding style, efficiency, and accuracy greatly affected estimates of the number of ED visits for blood or body fluid exposure. PMID:22561713

Methods for Coding Tobacco-Related Twitter Data: A Systematic Review

PubMed Central

Unger, Jennifer B; Cruz, Tess Boley; Chu, Kar-Hai

2017-01-01

Background As Twitter has grown in popularity to 313 million monthly active users, researchers have increasingly been using it as a data source for tobacco-related research. Objective The objective of this systematic review was to assess the methodological approaches of categorically coded tobacco Twitter data and make recommendations for future studies. Methods Data sources included PsycINFO, Web of Science, PubMed, ABI/INFORM, Communication Source, and Tobacco Regulatory Science. Searches were limited to peer-reviewed journals and conference proceedings in English from January 2006 to July 2016. The initial search identified 274 articles using a Twitter keyword and a tobacco keyword. One coder reviewed all abstracts and identified 27 articles that met the following inclusion criteria: (1) original research, (2) focused on tobacco or a tobacco product, (3) analyzed Twitter data, and (4) coded Twitter data categorically. One coder extracted data collection and coding methods. Results E-cigarettes were the most common type of Twitter data analyzed, followed by specific tobacco campaigns. The most prevalent data sources were Gnip and Twitter’s Streaming application programming interface (API). The primary methods of coding were hand-coding and machine learning. The studies predominantly coded for relevance, sentiment, theme, user or account, and location of user. Conclusions Standards for data collection and coding should be developed to be able to more easily compare and replicate tobacco-related Twitter results. Additional recommendations include the following: sample Twitter’s databases multiple times, make a distinction between message attitude and emotional tone for sentiment, code images and URLs, and analyze user profiles. Being relatively novel and widely used among adolescents and black and Hispanic individuals, Twitter could provide a rich source of tobacco surveillance data among vulnerable populations. PMID:28363883

Simulated Raman Spectral Analysis of Organic Molecules

NASA Astrophysics Data System (ADS)

Lu, Lu

The advent of the laser technology in the 1960s solved the main difficulty of Raman spectroscopy, resulted in simplified Raman spectroscopy instruments and also boosted the sensitivity of the technique. Up till now, Raman spectroscopy is commonly used in chemistry and biology. As vibrational information is specific to the chemical bonds, Raman spectroscopy provides fingerprints to identify the type of molecules in the sample. In this thesis, we simulate the Raman Spectrum of organic and inorganic materials by General Atomic and Molecular Electronic Structure System (GAMESS) and Gaussian, two computational codes that perform several general chemistry calculations. We run these codes on our CPU-based high-performance cluster (HPC). Through the message passing interface (MPI), a standardized and portable message-passing system which can make the codes run in parallel, we are able to decrease the amount of time for computation and increase the sizes and capacities of systems simulated by the codes. From our simulations, we will set up a database that allows search algorithm to quickly identify N-H and O-H bonds in different materials. Our ultimate goal is to analyze and identify the spectra of organic matter compositions from meteorites and compared these spectra with terrestrial biologically-produced amino acids and residues.

NWS Marine, Tropical, and Tsunami Services Branch Feedback

Science.gov Websites

Service NWS logo - Click to go to the NWS homepage Marine Forecasts Marine Forecasts Home News Organization Search Landlubber's forecast: "City, St" or zip code (Pan/Zoom for Marine) Search by Office Marine, Tropical, and Tsunami Services Branch Items of Interest Marine Forecasts Text, Graphic

A Semiotic Analysis of Icons on the World Wide Web.

ERIC Educational Resources Information Center

Ma, Yan

The World Wide Web allows users to interact with a graphic interface to search information in a hypermedia and multimedia environment. Graphics serve as reference points on the World Wide Web for searching and retrieving information. This study analyzed the culturally constructed syntax patterns, or codes, embedded in the icons of library…

NCO Systems Integration

Science.gov Websites

: AWC CPC EMC NCO NHC OPC SPC SWPC WPC Search by city or zip code. Press enter or select the go button to submit request Local forecast by "City, St" City, St Go Search NCEP Go NCEP Quarterly Surface Analysis Product Loops Environmental Models Product Info Current Status Model Analyses &

NCEP Decoder Web Site

Science.gov Websites

: AWC CPC EMC NCO NHC OPC SPC SWPC WPC Search by city or zip code. Press enter or select the go button to submit request Local forecast by "City, St" City, St Go Search NCEP Go NCEP Quarterly Surface Analysis Product Loops Environmental Models Product Info Current Status Model Analyses &

NCO Mail Webmaster

Science.gov Websites

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Design of two-dimensional zero reference codes with cross-entropy method.

PubMed

Chen, Jung-Chieh; Wen, Chao-Kai

2010-06-20

We present a cross-entropy (CE)-based method for the design of optimum two-dimensional (2D) zero reference codes (ZRCs) in order to generate a zero reference signal for a grating measurement system and achieve absolute position, a coordinate origin, or a machine home position. In the absence of diffraction effects, the 2D ZRC design problem is known as the autocorrelation approximation. Based on the properties of the autocorrelation function, the design of the 2D ZRC is first formulated as a particular combination optimization problem. The CE method is then applied to search for an optimal 2D ZRC and thus obtain the desirable zero reference signal. Computer simulation results indicate that there are 15.38% and 14.29% reductions in the second maxima value for the 16x16 grating system with n(1)=64 and the 100x100 grating system with n(1)=300, respectively, where n(1) is the number of transparent pixels, compared with those of the conventional genetic algorithm.

SinEx DB: a database for single exon coding sequences in mammalian genomes.

PubMed

Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

2016-01-01

Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl. © The Author(s) 2016. Published by Oxford University Press.

Multi-fidelity and multi-disciplinary design optimization of supersonic business jets

NASA Astrophysics Data System (ADS)

Choi, Seongim

Supersonic jets have been drawing great attention after the end of service for the Concorde was announced on April of 2003. It is believed, however, that civilian supersonic aircraft may make a viable return in the business jet market. This thesis focuses on the design optimization of feasible supersonic business jet configurations. Preliminary design techniques for mitigation of ground sonic boom are investigated while ensuring that all relevant disciplinary constraints are satisfied (including aerodynamic performance, propulsion, stability & control and structures.) In order to achieve reasonable confidence in the resulting designs, high-fidelity simulations are required, making the entire design process both expensive and complex. In order to minimize the computational cost, surrogate/approximate models are constructed using a hierarchy of different fidelity analysis tools including PASS, A502/Panair and Euler/NS codes. Direct search methods such as Genetic Algorithms (GAs) and a nonlinear SIMPLEX are employed to designs in searches of large and noisy design spaces. A local gradient-based search method can be combined with these global search methods for small modifications of candidate optimum designs. The Mesh Adaptive Direct Search (MADS) method can also be used to explore the design space using a solution-adaptive grid refinement approach. These hybrid approaches, both in search methodology and surrogate model construction, are shown to result in designs with reductions in sonic boom and improved aerodynamic performance.

MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data.

PubMed

Yang, Chunguang G; Granite, Stephen J; Van Eyk, Jennifer E; Winslow, Raimond L

2006-11-01

Protein identification using MS is an important technique in proteomics as well as a major generator of proteomics data. We have designed the protein identification data object model (PDOM) and developed a parser based on this model to facilitate the analysis and storage of these data. The parser works with HTML or XML files saved or exported from MASCOT MS/MS ions search in peptide summary report or MASCOT PMF search in protein summary report. The program creates PDOM objects, eliminates redundancy in the input file, and has the capability to output any PDOM object to a relational database. This program facilitates additional analysis of MASCOT search results and aids the storage of protein identification information. The implementation is extensible and can serve as a template to develop parsers for other search engines. The parser can be used as a stand-alone application or can be driven by other Java programs. It is currently being used as the front end for a system that loads HTML and XML result files of MASCOT searches into a relational database. The source code is freely available at http://www.ccbm.jhu.edu and the program uses only free and open-source Java libraries.

Effects of data quality vetoes on a search for compact binary coalescences in Advanced LIGO’s first observing run

NASA Astrophysics Data System (ADS)

Abbott, B. P.; Abbott, R.; Abbott, T. D.; Abernathy, M. R.; Acernese, F.; Ackley, K.; Adams, C.; Adams, T.; Addesso, P.; Adhikari, R. X.; Adya, V. B.; Affeldt, C.; Agathos, M.; Agatsuma, K.; Aggarwal, N.; Aguiar, O. D.; Aiello, L.; Ain, A.; Allen, B.; Allocca, A.; Altin, P. A.; Anderson, S. B.; Anderson, W. G.; Arai, K.; Araya, M. C.; Arceneaux, C. C.; Areeda, J. S.; Arnaud, N.; Arun, K. G.; Ascenzi, S.; Ashton, G.; Ast, M.; Aston, S. M.; Astone, P.; Aufmuth, P.; Aulbert, C.; Babak, S.; Bacon, P.; Bader, M. K. M.; Baker, P. T.; Baldaccini, F.; Ballardin, G.; Ballmer, S. W.; Barayoga, J. C.; Barclay, S. E.; Barish, B. C.; Barker, D.; Barone, F.; Barr, B.; Barsotti, L.; Barsuglia, M.; Barta, D.; Bartlett, J.; Bartos, I.; Bassiri, R.; Basti, A.; Batch, J. C.; Baune, C.; Bavigadda, V.; Bazzan, M.; Bejger, M.; Bell, A. S.; Berger, B. K.; Bergmann, G.; Berry, C. P. L.; Bersanetti, D.; Bertolini, A.; Betzwieser, J.; Bhagwat, S.; Bhandare, R.; Bilenko, I. A.; Billingsley, G.; Birch, J.; Birney, R.; Biscans, S.; Bisht, A.; Bitossi, M.; Biwer, C.; Bizouard, M. A.; Blackburn, J. K.; Blair, C. D.; Blair, D. G.; Blair, R. M.; Bloemen, S.; Bock, O.; Boer, M.; Bogaert, G.; Bogan, C.; Bohe, A.; Bond, C.; Bondu, F.; Bonnand, R.; Boom, B. A.; Bork, R.; Boschi, V.; Bose, S.; Bouffanais, Y.; Bozzi, A.; Bradaschia, C.; Brady, P. R.; Braginsky, V. B.; Branchesi, M.; Brau, J. E.; Briant, T.; Brillet, A.; Brinkmann, M.; Brisson, V.; Brockill, P.; Broida, J. E.; Brooks, A. F.; Brown, D. A.; Brown, D. D.; Brown, N. M.; Brunett, S.; Buchanan, C. C.; Buikema, A.; Bulik, T.; Bulten, H. J.; Buonanno, A.; Buskulic, D.; Buy, C.; Byer, R. L.; Cabero, M.; Cadonati, L.; Cagnoli, G.; Cahillane, C.; Calderón Bustillo, J.; Callister, T.; Calloni, E.; Camp, J. B.; Cannon, K. C.; Cao, J.; Capano, C. D.; Capocasa, E.; Carbognani, F.; Caride, S.; Casanueva Diaz, J.; Casentini, C.; Caudill, S.; Cavaglià, M.; Cavalier, F.; Cavalieri, R.; Cella, G.; Cepeda, C. B.; Cerboni Baiardi, L.; Cerretani, G.; Cesarini, E.; Chamberlin, S. J.; Chan, M.; Chao, S.; Charlton, P.; Chassande-Mottin, E.; Cheeseboro, B. D.; Chen, H. Y.; Chen, Y.; Cheng, C.; Chincarini, A.; Chiummo, A.; Cho, H. S.; Cho, M.; Chow, J. H.; Christensen, N.; Chu, Q.; Chua, S.; Chung, S.; Ciani, G.; Clara, F.; Clark, J. A.; Cleva, F.; Coccia, E.; Cohadon, P.-F.; Colla, A.; Collette, C. G.; Cominsky, L.; Constancio, M.; Conte, A.; Conti, L.; Cook, D.; Corbitt, T. R.; Cornish, N.; Corsi, A.; Cortese, S.; Costa, C. A.; Coughlin, M. W.; Coughlin, S. B.; Coulon, J.-P.; Countryman, S. T.; Couvares, P.; Cowan, E. E.; Coward, D. M.; Cowart, M. J.; Coyne, D. C.; Coyne, R.; Craig, K.; Creighton, J. D. E.; Cripe, J.; Crowder, S. G.; Cumming, A.; Cunningham, L.; Cuoco, E.; Dal Canton, T.; Danilishin, S. L.; D’Antonio, S.; Danzmann, K.; Darman, N. S.; Dasgupta, A.; Da Silva Costa, C. F.; Dattilo, V.; Dave, I.; Davier, M.; Davies, G. S.; Daw, E. J.; Day, R.; De, S.; DeBra, D.; Debreczeni, G.; Degallaix, J.; De Laurentis, M.; Deléglise, S.; Del Pozzo, W.; Denker, T.; Dent, T.; Dergachev, V.; De Rosa, R.; DeRosa, R. T.; DeSalvo, R.; Devine, R. C.; Dhurandhar, S.; Díaz, M. C.; Di Fiore, L.; Di Giovanni, M.; Di Girolamo, T.; Di Lieto, A.; Di Pace, S.; Di Palma, I.; Di Virgilio, A.; Dolique, V.; Donovan, F.; Dooley, K. L.; Doravari, S.; Douglas, R.; Downes, T. P.; Drago, M.; Drever, R. W. P.; Driggers, J. C.; Ducrot, M.; Dwyer, S. E.; Edo, T. B.; Edwards, M. C.; Effler, A.; Eggenstein, H.-B.; Ehrens, P.; Eichholz, J.; Eikenberry, S. S.; Engels, W.; Essick, R. C.; Etzel, T.; Evans, M.; Evans, T. M.; Everett, R.; Factourovich, M.; Fafone, V.; Fair, H.; Fairhurst, S.; Fan, X.; Fang, Q.; Farinon, S.; Farr, B.; Farr, W. M.; Favata, M.; Fays, M.; Fehrmann, H.; Fejer, M. M.; Fenyvesi, E.; Ferrante, I.; Ferreira, E. C.; Ferrini, F.; Fidecaro, F.; Fiori, I.; Fiorucci, D.; Fisher, R. P.; Flaminio, R.; Fletcher, M.; Fournier, J.-D.; Frasca, S.; Frasconi, F.; Frei, Z.; Freise, A.; Frey, R.; Frey, V.; Fritschel, P.; Frolov, V. V.; Fulda, P.; Fyffe, M.; Gabbard, H. A. G.; Gair, J. R.; Gammaitoni, L.; Gaonkar, S. G.; Garufi, F.; Gaur, G.; Gehrels, N.; Gemme, G.; Geng, P.; Genin, E.; Gennai, A.; George, J.; Gergely, L.; Germain, V.; Ghosh, Abhirup; Ghosh, Archisman; Ghosh, S.; Giaime, J. A.; Giardina, K. D.; Giazotto, A.; Gill, K.; Glaefke, A.; Goetz, E.; Goetz, R.; Gondan, L.; González, G.; Gonzalez Castro, J. M.; Gopakumar, A.; Gordon, N. A.; Gorodetsky, M. L.; Gossan, S. E.; Gosselin, M.; Gouaty, R.; Grado, A.; Graef, C.; Graff, P. B.; Granata, M.; Grant, A.; Gras, S.; Gray, C.; Greco, G.; Green, A. C.; Groot, P.; Grote, H.; Grunewald, S.; Guidi, G. M.; Guo, X.; Gupta, A.; Gupta, M. K.; Gushwa, K. E.; Gustafson, E. K.; Gustafson, R.; Hacker, J. J.; Hall, B. R.; Hall, E. D.; Hammond, G.; Haney, M.; Hanke, M. M.; Hanks, J.; Hannam, M. D.; Hanson, J.; Hardwick, T.; Harms, J.; Harry, G. M.; Harry, I. W.; Hart, M. J.; Hartman, M. T.; Haster, C.-J.; Haughian, K.; Heidmann, A.; Heintze, M. C.; Heitmann, H.; Hello, P.; Hemming, G.; Hendry, M.; Heng, I. S.; Hennig, J.; Henry, J.; Heptonstall, A. W.; Heurs, M.; Hild, S.; Hoak, D.; Hofman, D.; Holt, K.; Holz, D. E.; Hopkins, P.; Hough, J.; Houston, E. A.; Howell, E. J.; Hu, Y. M.; Huang, S.; Huerta, E. A.; Huet, D.; Hughey, B.; Husa, S.; Huttner, S. H.; Huynh-Dinh, T.; Indik, N.; Ingram, D. R.; Inta, R.; Isa, H. N.; Isac, J.-M.; Isi, M.; Isogai, T.; Iyer, B. R.; Izumi, K.; Jacqmin, T.; Jang, H.; Jani, K.; Jaranowski, P.; Jawahar, S.; Jian, L.; Jiménez-Forteza, F.; Johnson, W. W.; Jones, D. I.; Jones, R.; Jonker, R. J. G.; Ju, L.; Haris, K.; Kalaghatgi, C. V.; Kalogera, V.; Kandhasamy, S.; Kang, G.; Kanner, J. B.; Kapadia, S. J.; Karki, S.; Karvinen, K. S.; Kasprzack, M.; Katsavounidis, E.; Katzman, W.; Kaufer, S.; Kaur, T.; Kawabe, K.; Kéfélian, F.; Kehl, M. S.; Keitel, D.; Kelley, D. B.; Kells, W.; Kennedy, R.; Key, J. S.; Khalili, F. Y.; Khan, I.; Khan, S.; Khan, Z.; Khazanov, E. A.; Kijbunchoo, N.; Kim, Chi-Woong; Kim, Chunglee; Kim, J.; Kim, K.; Kim, N.; Kim, W.; Kim, Y.-M.; Kimbrell, S. J.; King, E. J.; King, P. J.; Kissel, J. S.; Klein, B.; Kleybolte, L.; Klimenko, S.; Koehlenbeck, S. M.; Koley, S.; Kondrashov, V.; Kontos, A.; Korobko, M.; Korth, W. Z.; Kowalska, I.; Kozak, D. B.; Kringel, V.; Krishnan, B.; Królak, A.; Krueger, C.; Kuehn, G.; Kumar, P.; Kumar, R.; Kuo, L.; Kutynia, A.; Lackey, B. D.; Landry, M.; Lange, J.; Lantz, B.; Lasky, P. D.; Laxen, M.; Lazzarini, A.; Lazzaro, C.; Leaci, P.; Leavey, S.; Lebigot, E. O.; Lee, C. H.; Lee, H. K.; Lee, H. M.; Lee, K.; Lenon, A.; Leonardi, M.; Leong, J. R.; Leroy, N.; Letendre, N.; Levin, Y.; Lewis, J. B.; Li, T. G. F.; Libson, A.; Littenberg, T. B.; Lockerbie, N. A.; Lombardi, A. L.; London, L. T.; Lord, J. E.; Lorenzini, M.; Loriette, V.; Lormand, M.; Losurdo, G.; Lough, J. D.; Lück, H.; Lundgren, A. P.; Lynch, R.; Ma, Y.; Machenschalk, B.; MacInnis, M.; Macleod, D. M.; Magaña-Sandoval, F.; Magaña Zertuche, L.; Magee, R. M.; Majorana, E.; Maksimovic, I.; Malvezzi, V.; Man, N.; Mandic, V.; Mangano, V.; Mansell, G. L.; Manske, M.; Mantovani, M.; Marchesoni, F.; Marion, F.; Márka, S.; Márka, Z.; Markosyan, A. S.; Maros, E.; Martelli, F.; Martellini, L.; Martin, I. W.; Martynov, D. V.; Marx, J. N.; Mason, K.; Masserot, A.; Massinger, T. J.; Masso-Reid, M.; Mastrogiovanni, S.; Matichard, F.; Matone, L.; Mavalvala, N.; Mazumder, N.; McCarthy, R.; McClelland, D. E.; McCormick, S.; McGuire, S. C.; McIntyre, G.; McIver, J.; McManus, D. J.; McRae, T.; McWilliams, S. T.; Meacher, D.; Meadors, G. D.; Meidam, J.; Melatos, A.; Mendell, G.; Mercer, R. A.; Merilh, E. L.; Merzougui, M.; Meshkov, S.; Messenger, C.; Messick, C.; Metzdorff, R.; Meyers, P. M.; Mezzani, F.; Miao, H.; Michel, C.; Middleton, H.; Mikhailov, E. E.; Milano, L.; Miller, A. L.; Miller, A.; Miller, B. B.; Miller, J.; Millhouse, M.; Minenkov, Y.; Ming, J.; Mirshekari, S.; Mishra, C.; Mitra, S.; Mitrofanov, V. P.; Mitselmakher, G.; Mittleman, R.; Moggi, A.; Mohan, M.; Mohapatra, S. R. P.; Montani, M.; Moore, B. C.; Moore, C. J.; Moraru, D.; Moreno, G.; Morriss, S. R.; Mossavi, K.; Mours, B.; Mow-Lowry, C. M.; Mueller, G.; Muir, A. W.; Mukherjee, Arunava; Mukherjee, D.; Mukherjee, S.; Mukund, N.; Mullavey, A.; Munch, J.; Murphy, D. J.; Murray, P. G.; Mytidis, A.; Nardecchia, I.; Naticchioni, L.; Nayak, R. K.; Nedkova, K.; Nelemans, G.; Nelson, T. J. N.; Neri, M.; Neunzert, A.; Newton, G.; Nguyen, T. T.; Nielsen, A. B.; Nissanke, S.; Nitz, A.; Nocera, F.; Nolting, D.; Normandin, M. E. N.; Nuttall, L. K.; Oberling, J.; Ochsner, E.; O’Dell, J.; Oelker, E.; Ogin, G. H.; Oh, J. J.; Oh, S. H.; Ohme, F.; Oliver, M.; Oppermann, P.; Oram, Richard J.; O’Reilly, B.; O’Shaughnessy, R.; Ottaway, D. J.; Overmier, H.; Owen, B. J.; Pai, A.; Pai, S. A.; Palamos, J. R.; Palashov, O.; Palomba, C.; Pal-Singh, A.; Pan, H.; Pankow, C.; Pannarale, F.; Pant, B. C.; Paoletti, F.; Paoli, A.; Papa, M. A.; Paris, H. R.; Parker, W.; Pascucci, D.; Pasqualetti, A.; Passaquieti, R.; Passuello, D.; Patricelli, B.; Patrick, Z.; Pearlstone, B. L.; Pedraza, M.; Pedurand, R.; Pekowsky, L.; Pele, A.; Penn, S.; Perreca, A.; Perri, L. M.; Phelps, M.; Piccinni, O. J.; Pichot, M.; Piergiovanni, F.; Pierro, V.; Pillant, G.; Pinard, L.; Pinto, I. M.; Pitkin, M.; Poe, M.; Poggiani, R.; Popolizio, P.; Post, A.; Powell, J.; Prasad, J.; Pratt, J.; Predoi, V.; Prestegard, T.; Price, L. R.; Prijatelj, M.; Principe, M.; Privitera, S.; Prix, R.; Prodi, G. A.; Prokhorov, L.; Puncken, O.; Punturo, M.; Puppo, P.; Pürrer, M.; Qi, H.; Qin, J.; Qiu, S.; Quetschke, V.; Quintero, E. A.; Quitzow-James, R.; Raab, F. J.; Rabeling, D. S.; Radkins, H.; Raffai, P.; Raja, S.; Rajan, C.; Rakhmanov, M.; Rapagnani, P.; Raymond, V.; Razzano, M.; Re, V.; Read, J.; Reed, C. M.; Regimbau, T.; Rei, L.; Reid, S.; Reitze, D. H.; Rew, H.; Reyes, S. D.; Ricci, F.; Riles, K.; Rizzo, M.; Robertson, N. A.; Robie, R.; Robinet, F.; Rocchi, A.; Rolland, L.; Rollins, J. G.; Roma, V. J.; Romano, J. D.; Romano, R.; Romanov, G.; Romie, J. H.; Rosińska, D.; Rowan, S.; Rüdiger, A.; Ruggi, P.; Ryan, K.; Sachdev, S.; Sadecki, T.; Sadeghian, L.; Sakellariadou, M.; Salconi, L.; Saleem, M.; Salemi, F.; Samajdar, A.; Sammut, L.; Sanchez, E. J.; Sandberg, V.; Sandeen, B.; Sanders, J. R.; Sassolas, B.; Sathyaprakash, B. S.; Saulson, P. R.; Sauter, O. E. S.; Savage, R. L.; Sawadsky, A.; Schale, P.; Schilling, R.; Schmidt, J.; Schmidt, P.; Schnabel, R.; Schofield, R. M. S.; Schönbeck, A.; Schreiber, E.; Schuette, D.; Schutz, B. F.; Scott, J.; Scott, S. M.; Sellers, D.; Sengupta, A. S.; Sentenac, D.; Sequino, V.; Sergeev, A.; Setyawati, Y.; Shaddock, D. A.; Shaffer, T.; Shahriar, M. S.; Shaltev, M.; Shapiro, B.; Shawhan, P.; Sheperd, A.; Shoemaker, D. H.; Shoemaker, D. M.; Siellez, K.; Siemens, X.; Sieniawska, M.; Sigg, D.; Silva, A. D.; Singer, A.; Singer, L. P.; Singh, A.; Singh, R.; Singhal, A.; Sintes, A. M.; Slagmolen, B. J. J.; Smith, J. R.; Smith, N. D.; Smith, R. J. E.; Son, E. J.; Sorazu, B.; Sorrentino, F.; Souradeep, T.; Srivastava, A. K.; Staley, A.; Steinke, M.; Steinlechner, J.; Steinlechner, S.; Steinmeyer, D.; Stephens, B. C.; Stone, R.; Strain, K. A.; Straniero, N.; Stratta, G.; Strauss, N. A.; Strigin, S.; Sturani, R.; Stuver, A. L.; Summerscales, T. Z.; Sun, L.; Sunil, S.; Sutton, P. J.; Swinkels, B. L.; Szczepańczyk, M. J.; Tacca, M.; Talukder, D.; Tanner, D. B.; Tápai, M.; Tarabrin, S. P.; Taracchini, A.; Taylor, R.; Theeg, T.; Thirugnanasambandam, M. P.; Thomas, E. G.; Thomas, M.; Thomas, P.; Thorne, K. A.; Thrane, E.; Tiwari, S.; Tiwari, V.; Tokmakov, K. V.; Toland, K.; Tomlinson, C.; Tonelli, M.; Tornasi, Z.; Torres, C. V.; Torrie, C. I.; Töyrä, D.; Travasso, F.; Traylor, G.; Trifirò, D.; Tringali, M. C.; Trozzo, L.; Tse, M.; Turconi, M.; Tuyenbayev, D.; Ugolini, D.; Unnikrishnan, C. S.; Urban, A. L.; Usman, S. A.; Vahlbruch, H.; Vajente, G.; Valdes, G.; van Bakel, N.; van Beuzekom, M.; van den Brand, J. F. J.; Van Den Broeck, C.; Vander-Hyde, D. C.; van der Schaaf, L.; van Heijningen, J. V.; van Veggel, A. A.; Vardaro, M.; Vass, S.; Vasúth, M.; Vaulin, R.; Vecchio, A.; Vedovato, G.; Veitch, J.; Veitch, P. J.; Venkateswara, K.; Verkindt, D.; Vetrano, F.; Viceré, A.; Vinciguerra, S.; Vine, D. J.; Vinet, J.-Y.; Vitale, S.; Vo, T.; Vocca, H.; Vorvick, C.; Voss, D. V.; Vousden, W. D.; Vyatchanin, S. P.; Wade, A. R.; Wade, L. E.; Wade, M.; Walker, M.; Wallace, L.; Walsh, S.; Wang, G.; Wang, H.; Wang, M.; Wang, X.; Wang, Y.; Ward, R. L.; Warner, J.; Was, M.; Weaver, B.; Wei, L.-W.; Weinert, M.; Weinstein, A. J.; Weiss, R.; Wen, L.; Weßels, P.; Westphal, T.; Wette, K.; Whelan, J. T.; Whiting, B. F.; Williams, R. D.; Williamson, A. R.; Willis, J. L.; Willke, B.; Wimmer, M. H.; Winkler, W.; Wipf, C. C.; Wittel, H.; Woan, G.; Woehler, J.; Worden, J.; Wright, J. L.; Wu, D. S.; Wu, G.; Yablon, J.; Yam, W.; Yamamoto, H.; Yancey, C. C.; Yu, H.; Yvert, M.; Zadrożny, A.; Zangrando, L.; Zanolin, M.; Zendri, J.-P.; Zevin, M.; Zhang, L.; Zhang, M.; Zhang, Y.; Zhao, C.; Zhou, M.; Zhou, Z.; Zhu, X. J.; Zucker, M. E.; Zuraw, S. E.; Zweizig, J.; LIGO Scientific Collaboration; Virgo Collaboration

2018-03-01

The first observing run of Advanced LIGO spanned 4 months, from 12 September 2015 to 19 January 2016, during which gravitational waves were directly detected from two binary black hole systems, namely GW150914 and GW151226. Confident detection of gravitational waves requires an understanding of instrumental transients and artifacts that can reduce the sensitivity of a search. Studies of the quality of the detector data yield insights into the cause of instrumental artifacts and data quality vetoes specific to a search are produced to mitigate the effects of problematic data. In this paper, the systematic removal of noisy data from analysis time is shown to improve the sensitivity of searches for compact binary coalescences. The output of the PyCBC pipeline, which is a python-based code package used to search for gravitational wave signals from compact binary coalescences, is used as a metric for improvement. GW150914 was a loud enough signal that removing noisy data did not improve its significance. However, the removal of data with excess noise decreased the false alarm rate of GW151226 by more than two orders of magnitude, from 1 in 770 yr to less than 1 in 186 000 yr.

The quality of patient-orientated Internet information on oral lichen planus: a pilot study.

PubMed

López-Jornet, Pía; Camacho-Alonso, Fabio

2010-10-01

This study examines the accessibility and quality Web pages related with oral lichen planus. Sites were identified using two search engines (Google and Yahoo!) and the search terms 'oral lichen planus' and 'oral lesion lichenoid'. The first 100 sites in each search were visited and classified. The web sites were evaluated for content quality by using the validated DISCERN rating instrument. JAMA benchmarks and 'Health on the Net' seal (HON). A total of 109,000 sites were recorded in Google using the search terms and 520,000 in Yahoo! A total of 19 Web pages considered relevant were examined on Google and 20 on Yahoo! As regards the JAMA benchmarks, only two pages satisfied the four criteria in Google (10%), and only three (15%) in Yahoo! As regards DISCERN, the overall quality of web site information was poor, no site reaching the maximum score. In Google 78.94% of sites had important deficiencies, and 50% in Yahoo!, the difference between the two search engines being statistically significant (P = 0.031). Only five pages (17.2%) on Google and eight (40%) on Yahoo! showed the HON code. Based on our review, doctors must assume primary responsibility for educating and counselling their patients. © 2010 Blackwell Publishing Ltd.

Association between Search Behaviors and Disease Prevalence Rates at 18 U.S. Children's Hospitals.

PubMed

Daniel, Dennis; Wolbrink, Traci; Logvinenko, Tanya; Harper, Marvin; Burns, Jeffrey

2017-10-01

Background Usage of online resources by clinicians in training and practice can provide insight into knowledge gaps and inform development of decision support tools. Although online information seeking is often driven by encountered patient problems, the relationship between disease prevalence and search rate has not been previously characterized. Objective This article aimed to (1) identify topics frequently searched by pediatric clinicians using UpToDate (http://www.uptodate.com) and (2) explore the association between disease prevalence rate and search rate using data from the Pediatric Health Information System. Methods We identified the most common search queries and resources most frequently accessed on UpToDate for a cohort of 18 children's hospitals during calendar year 2012. We selected 64 of the most frequently searched diseases and matched ICD-9 data from the PHIS database during the same time period. Using linear regression, we explored the relationship between clinician query rate and disease prevalence rate. Results The hospital cohort submitted 1,228,138 search queries across 592,454 sessions. The majority of search sessions focused on a single search topic. We identified no consistent overall association between disease prevalence and search rates. Diseases where search rate was substantially higher than prevalence rate were often infectious or immune/rheumatologic conditions, involved potentially complex diagnosis or management, and carried risk of significant morbidity or mortality. None of the examined diseases showed a decrease in search rate associated with increased disease prevalence rates. Conclusion This is one of the first medical learning needs assessments to use large-scale, multisite data to identify topics of interest to pediatric clinicians, and to examine the relationship between disease prevalence and search rate for a set of pediatric diseases. Overall, disease search rate did not appear to be associated with hospital disease prevalence rates based on ICD-9 codes. However, some diseases were consistently searched at a higher rate than their prevalence rate; many of these diseases shared common features.

Accelerating execution of the integrated TIGER series Monte Carlo radiation transport codes

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

Smith, L.M.; Hochstedler, R.D.

1997-02-01

Execution of the integrated TIGER series (ITS) of coupled electron/photon Monte Carlo radiation transport codes has been accelerated by modifying the FORTRAN source code for more efficient computation. Each member code of ITS was benchmarked and profiled with a specific test case that directed the acceleration effort toward the most computationally intensive subroutines. Techniques for accelerating these subroutines included replacing linear search algorithms with binary versions, replacing the pseudo-random number generator, reducing program memory allocation, and proofing the input files for geometrical redundancies. All techniques produced identical or statistically similar results to the original code. Final benchmark timing of themore » accelerated code resulted in speed-up factors of 2.00 for TIGER (the one-dimensional slab geometry code), 1.74 for CYLTRAN (the two-dimensional cylindrical geometry code), and 1.90 for ACCEPT (the arbitrary three-dimensional geometry code).« less

PDB-Explorer: a web-based interactive map of the protein data bank in shape space.

PubMed

Jin, Xian; Awale, Mahendra; Zasso, Michaël; Kostro, Daniel; Patiny, Luc; Reymond, Jean-Louis

2015-10-23

The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.cheminfo.org/pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB. ᅟ

Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing.

PubMed

Palkowski, Marek; Bielecki, Wlodzimierz

2017-06-02

RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maximization, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. Polyhedral compilation techniques have proven to be a powerful tool for optimization of dense array codes. However, classical affine loop nest transformations used with these techniques do not optimize effectively codes of dynamic programming of RNA structure predictions. The purpose of this paper is to present a novel approach allowing for generation of a parallel tiled Nussinov RNA loop nest exposing significantly higher performance than that of known related code. This effect is achieved due to improving code locality and calculation parallelization. In order to improve code locality, we apply our previously published technique of automatic loop nest tiling to all the three loops of the Nussinov loop nest. This approach first forms original rectangular 3D tiles and then corrects them to establish their validity by means of applying the transitive closure of a dependence graph. To produce parallel code, we apply the loop skewing technique to a tiled Nussinov loop nest. The technique is implemented as a part of the publicly available polyhedral source-to-source TRACO compiler. Generated code was run on modern Intel multi-core processors and coprocessors. We present the speed-up factor of generated Nussinov RNA parallel code and demonstrate that it is considerably faster than related codes in which only the two outer loops of the Nussinov loop nest are tiled.

Development of the ICD-10 simplified version and field test.

PubMed

Paoin, Wansa; Yuenyongsuwan, Maliwan; Yokobori, Yukiko; Endo, Hiroyoshi; Kim, Sukil

2018-05-01

The International Statistical Classification of Diseases and Related Health Problems, 10th Revision (ICD-10) has been used in various Asia-Pacific countries for more than 20 years. Although ICD-10 is a powerful tool, clinical coding processes are complex; therefore, many developing countries have not been able to implement ICD-10-based health statistics (WHO-FIC APN, 2007). This study aimed to simplify ICD-10 clinical coding processes, to modify index terms to facilitate computer searching and to provide a simplified version of ICD-10 for use in developing countries. The World Health Organization Family of International Classifications Asia-Pacific Network (APN) developed a simplified version of the ICD-10 and conducted field testing in Cambodia during February and March 2016. Ten hospitals were selected to participate. Each hospital sent a team to join a training workshop before using the ICD-10 simplified version to code 100 cases. All hospitals subsequently sent their coded records to the researchers. Overall, there were 1038 coded records with a total of 1099 ICD clinical codes assigned. The average accuracy rate was calculated as 80.71% (66.67-93.41%). Three types of clinical coding errors were found. These related to errors relating to the coder (14.56%), those resulting from the physician documentation (1.27%) and those considered system errors (3.46%). The field trial results demonstrated that the APN ICD-10 simplified version is feasible for implementation as an effective tool to implement ICD-10 clinical coding for hospitals. Developing countries may consider adopting the APN ICD-10 simplified version for ICD-10 code assignment in hospitals and health care centres. The simplified version can be viewed as an introductory tool which leads to the implementation of the full ICD-10 and may support subsequent ICD-11 adoption.

Contextual cueing of tactile search is coded in an anatomical reference frame.

PubMed

Assumpção, Leonardo; Shi, Zhuanghua; Zang, Xuelian; Müller, Hermann J; Geyer, Thomas

2018-04-01

This work investigates the reference frame(s) underlying tactile context memory, a form of statistical learning in a tactile (finger) search task. In this task, if a searched-for target object is repeatedly encountered within a stable spatial arrangement of task-irrelevant distractors, detecting the target becomes more efficient over time (relative to nonrepeated arrangements), as learned target-distractor spatial associations come to guide tactile search, thus cueing attention to the target location. Since tactile search displays can be represented in several reference frames, including multiple external and an anatomical frame, in Experiment 1 we asked whether repeated search displays are represented in tactile memory with reference to an environment-centered or anatomical reference frame. In Experiment 2, we went on examining a hand-centered versus anatomical reference frame of tactile context memory. Observers performed a tactile search task, divided into a learning and test session. At the transition between the two sessions, we introduced postural manipulations of the hands (crossed ↔ uncrossed in Expt. 1; palm-up ↔ palm-down in Expt. 2) to determine the reference frame of tactile contextual cueing. In both experiments, target-distractor associations acquired during learning transferred to the test session when the placement of the target and distractors was held constant in anatomical, but not external, coordinates. In the latter, RTs were even slower for repeated displays. We conclude that tactile contextual learning is coded in an anatomical reference frame. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Surveillance of contrast-media-induced hypersensitivity reactions using signals from an electronic medical recording system.

PubMed

Kim, Min-Hye; Park, Chang-Han; Kim, Duk-In; Kim, Kyung-Mook; Kim, Hui-Kyu; Lim, Kyu-Hyoung; Song, Woo-Jung; Lee, Sang-Min; Kim, Sae-Hoon; Kwon, Hyouk-Soo; Park, Heung-Woo; Yoon, Chang-Jin; Cho, Sang-Heon; Min, Kyung-Up; Kim, You-Young; Chang, Yoon-Seok

2012-03-01

Contrast-media (CM) hypersensitivity is a well-known adverse drug reaction. Surveillance of adverse drug reactions usually depends on spontaneous reports. However, the rate of spontaneous reports is low. Recent progress in information technology enables the electronic search on signals of adverse drug reactions from electronic medical recording (EMR) systems. To analyze the incidence and clinical characteristics of CM hypersensitivity using an EMR-based surveillance system. The surveillance system used signals from standardized terms within the international classification of nursing practice terms that can indicate symptoms of CM hypersensitivity and from the order codes for procedures that used contrast media, antihistamine, and epinephrine. The search strategy was validated by allergists comparing the electronic search strategy versus manually reviewing medical charts over one month. The main study covered for one year period. Detection rate of the electronic search method was 0.9% (7/759), while that of the manual search method was 0.8% (6/759). EMR-based electronic search method was highly efficient: reduced the charts that needed to be reviewed by 96% (28/759). The sensitivity of electronic screening was 66.7%, specificity was 99.6%, and the negative predictive value was 99.7%. CM hypersensitivity reactions were noted in 266 among 12,483 cases (2.1%). Urticaria was the most frequent symptom (74.4%). CT was the most frequent procedure (3.6%) that induced CM hypersensitivity. A surveillance system using EMR may be a useful tool in the study of drug hypersensitivity epidemiology and may be used in an adverse drug reaction alarm system and as a clinical, decision making support system. Copyright © 2012 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Strategies for searching medical natural language text. Distribution of words in the anatomic diagnoses of 7000 autopsy subjects.

PubMed Central

Moore, G. W.; Hutchins, G. M.; Miller, R. E.

1984-01-01

Computerized indexing and retrieval of medical records is increasingly important; but the use of natural language versus coded languages (SNOP, SNOMED) for this purpose remains controversial. In an effort to develop search strategies for natural language text, the authors examined the anatomic diagnosis reports by computer for 7000 consecutive autopsy subjects spanning a 13-year period at The Johns Hopkins Hospital. There were 923,657 words, 11,642 of them distinct. The authors observed an average of 1052 keystrokes, 28 lines, and 131 words per autopsy report, with an average 4.6 words per line and 7.0 letters per word. The entire text file represented 921 hours of secretarial effort. Words ranged in frequency from 33,959 occurrences of "and" to one occurrence for each of 3398 different words. Searches for rare diseases with unique names or for representative examples of common diseases were most readily performed with the use of computer-printed key word in context (KWIC) books. For uncommon diseases designated by commonly used terms (such as "cystic fibrosis"), needs were best served by a computerized search for logical combinations of key words. In an unbalanced word distribution, each conjunction (logical and) search should be performed in ascending order of word frequency; but each alternation (logical inclusive or) search should be performed in descending order of word frequency. Natural language text searches will assume a larger role in medical records analysis as the labor-intensive procedure of translation into a coded language becomes more costly, compared with the computer-intensive procedure of text searching. PMID:6546837

Applying graphics user interface ot group technology classification and coding at the Boeing aerospace company

NASA Astrophysics Data System (ADS)

Ness, P. H.; Jacobson, H.

1984-10-01

The thrust of 'group technology' is toward the exploitation of similarities in component design and manufacturing process plans to achieve assembly line flow cost efficiencies for small batch production. The systematic method devised for the identification of similarities in component geometry and processing steps is a coding and classification scheme implemented by interactive CAD/CAM systems. This coding and classification scheme has led to significant increases in computer processing power, allowing rapid searches and retrievals on the basis of a 30-digit code together with user-friendly computer graphics.

Adapting the coping in deliberation (CODE) framework: a multi-method approach in the context of familial ovarian cancer risk management.

PubMed

Witt, Jana; Elwyn, Glyn; Wood, Fiona; Rogers, Mark T; Menon, Usha; Brain, Kate

2014-11-01

To test whether the coping in deliberation (CODE) framework can be adapted to a specific preference-sensitive medical decision: risk-reducing bilateral salpingo-oophorectomy (RRSO) in women at increased risk of ovarian cancer. We performed a systematic literature search to identify issues important to women during deliberations about RRSO. Three focus groups with patients (most were pre-menopausal and untested for genetic mutations) and 11 interviews with health professionals were conducted to determine which issues mattered in the UK context. Data were used to adapt the generic CODE framework. The literature search yielded 49 relevant studies, which highlighted various issues and coping options important during deliberations, including mutation status, risks of surgery, family obligations, physician recommendation, peer support and reliable information sources. Consultations with UK stakeholders confirmed most of these factors as pertinent influences on deliberations. Questions in the generic framework were adapted to reflect the issues and coping options identified. The generic CODE framework was readily adapted to a specific preference-sensitive medical decision, showing that deliberations and coping are linked during deliberations about RRSO. Adapted versions of the CODE framework may be used to develop tailored decision support methods and materials in order to improve patient-centred care. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.

PubMed

Caldas, José; Gehlenborg, Nils; Kettunen, Eeva; Faisal, Ali; Rönty, Mikko; Nicholson, Andrew G; Knuutila, Sakari; Brazma, Alvis; Kaski, Samuel

2012-01-15

Genome-wide measurement of transcript levels is an ubiquitous tool in biomedical research. As experimental data continues to be deposited in public databases, it is becoming important to develop search engines that enable the retrieval of relevant studies given a query study. While retrieval systems based on meta-data already exist, data-driven approaches that retrieve studies based on similarities in the expression data itself have a greater potential of uncovering novel biological insights. We propose an information retrieval method based on differential expression. Our method deals with arbitrary experimental designs and performs competitively with alternative approaches, while making the search results interpretable in terms of differential expression patterns. We show that our model yields meaningful connections between biological conditions from different studies. Finally, we validate a previously unknown connection between malignant pleural mesothelioma and SIM2s suggested by our method, via real-time polymerase chain reaction in an independent set of mesothelioma samples. Supplementary data and source code are available from http://www.ebi.ac.uk/fg/research/rex.

Sum of the Magnitude for Hard Decision Decoding Algorithm Based on Loop Update Detection

PubMed Central

Meng, Jiahui; Zhao, Danfeng; Tian, Hai; Zhang, Liang

2018-01-01

In order to improve the performance of non-binary low-density parity check codes (LDPC) hard decision decoding algorithm and to reduce the complexity of decoding, a sum of the magnitude for hard decision decoding algorithm based on loop update detection is proposed. This will also ensure the reliability, stability and high transmission rate of 5G mobile communication. The algorithm is based on the hard decision decoding algorithm (HDA) and uses the soft information from the channel to calculate the reliability, while the sum of the variable nodes’ (VN) magnitude is excluded for computing the reliability of the parity checks. At the same time, the reliability information of the variable node is considered and the loop update detection algorithm is introduced. The bit corresponding to the error code word is flipped multiple times, before this is searched in the order of most likely error probability to finally find the correct code word. Simulation results show that the performance of one of the improved schemes is better than the weighted symbol flipping (WSF) algorithm under different hexadecimal numbers by about 2.2 dB and 2.35 dB at the bit error rate (BER) of 10−5 over an additive white Gaussian noise (AWGN) channel, respectively. Furthermore, the average number of decoding iterations is significantly reduced. PMID:29342963

New Directions in Giant Planet Formation

NASA Astrophysics Data System (ADS)

Youdin, Andrew

The proposed research will explore the limits of the core accretion mechanism for forming giant planets, both in terms of timescale and orbital distance. This theoretical research will be useful in interpreting the results of ongoing exoplanet searches. The effects of radiogenic heating and aerodynamic accretion of pebbles and boulders will be included in time-dependent models of atmospheric structure and growth. To investigate these issues, we will develop and publicly share a protoplanet atmospheric evolution code as an extension of the MESA stellar evolution code. By focusing on relevant processes in the early stages of giant planet formation, we can refine model predictions for exoplanet searches at a wide range of stellar ages and distances from the host star.

Problem Management Module: An Innovative System to Improve Problem List Workflow

PubMed Central

Hodge, Chad M.; Kuttler, Kathryn G.; Bowes, Watson A.; Narus, Scott P.

2014-01-01

Electronic problem lists are essential to modern health record systems, with a primary goal to serve as the repository of a patient’s current health issues. Additionally, coded problems can be used to drive downstream activities such as decision support, evidence-based medicine, billing, and cohort generation for research. Meaningful Use also requires use of a coded problem list. Over the course of three years, Intermountain Healthcare developed a problem management module (PMM) that provided innovative functionality to improve clinical workflow and boost problem list adoption, e.g. smart search, user customizable views, problem evolution, and problem timelines. In 23 months of clinical use, clinicians entered over 70,000 health issues, the percentage of free-text items dropped to 1.2%, completeness of problem list items increased by 14%, and more collaborative habits were initiated. PMID:25954372

Software Security Knowledge: CWE. Knowing What Could Make Software Vulnerable to Attack

DTIC Science & Technology

2011-05-01

shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. 1...Buffer • CWE-642: External Control of Critical State Data • CWE-73: External Control of File Name or Path • CWE-426: Untrusted Search Path • CWE...94: Failure to Control Generation of Code (aka ’Code Injection’) • CWE-494: Download of Code Without Integrity Check • CWE-404: Improper Resource

A return mapping algorithm for isotropic and anisotropic plasticity models using a line search method

DOE PAGES

Scherzinger, William M.

2016-05-01

The numerical integration of constitutive models in computational solid mechanics codes allows for the solution of boundary value problems involving complex material behavior. Metal plasticity models, in particular, have been instrumental in the development of these codes. Here, most plasticity models implemented in computational codes use an isotropic von Mises yield surface. The von Mises, of J 2, yield surface has a simple predictor-corrector algorithm - the radial return algorithm - to integrate the model.

Accuracy of Binary Black Hole waveforms for Advanced LIGO searches

NASA Astrophysics Data System (ADS)

Kumar, Prayush; Barkett, Kevin; Bhagwat, Swetha; Chu, Tony; Fong, Heather; Brown, Duncan; Pfeiffer, Harald; Scheel, Mark; Szilagyi, Bela

2015-04-01

Coalescing binaries of compact objects are flagship sources for the first direct detection of gravitational waves with LIGO-Virgo observatories. Matched-filtering based detection searches aimed at binaries of black holes will use aligned spin waveforms as filters, and their efficiency hinges on the accuracy of the underlying waveform models. A number of gravitational waveform models are available in literature, e.g. the Effective-One-Body, Phenomenological, and traditional post-Newtonian ones. While Numerical Relativity (NR) simulations provide for the most accurate modeling of gravitational radiation from compact binaries, their computational cost limits their application in large scale searches. In this talk we assess the accuracy of waveform models in two regions of parameter space, which have only been explored cursorily in the past: the high mass-ratio regime as well as the comparable mass-ratio + high spin regime.s Using the SpEC code, six q = 7 simulations with aligned-spins and lasting 60 orbits, and tens of q ∈ [1,3] simulations with high black hole spins were performed. We use them to study the accuracy and intrinsic parameter biases of different waveform families, and assess their viability for Advanced LIGO searches.

Utility of rapid database searching for quality assurance: 'detective work' in uncovering radiology coding and billing errors

NASA Astrophysics Data System (ADS)

Horii, Steven C.; Kim, Woojin; Boonn, William; Iyoob, Christopher; Maston, Keith; Coleman, Beverly G.

2011-03-01

When the first quarter of 2010 Department of Radiology statistics were provided to the Section Chiefs, the authors (SH, BC) were alarmed to discover that Ultrasound showed a decrease of 2.5 percent in billed examinations. This seemed to be in direct contradistinction to the experience of the ultrasound faculty members and sonographers. Their experience was that they were far busier than during the same quarter of 2009. The one exception that all acknowledged was the month of February, 2010 when several major winter storms resulted in a much decreased Hospital admission and Emergency Department visit rate. Since these statistics in part help establish priorities for capital budget items, professional and technical staffing levels, and levels of incentive salary, they are taken very seriously. The availability of a desktop, Web-based RIS database search tool developed by two of the authors (WK, WB) and built-in database functions of the ultrasound miniPACS, made it possible for us very rapidly to develop and test hypotheses for why the number of billable examinations was declining in the face of what experience told the authors was an increasing number of examinations being performed. Within a short time, we identified the major cause as errors on the part of the company retained to verify billable Current Procedural Terminology (CPT) codes against ultrasound reports. This information is being used going forward to recover unbilled examinations and take measures to reduce or eliminate the types of coding errors that resulted in the problem.

Database Resources of the BIG Data Center in 2018.

PubMed

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

DOE Research and Development Accomplishments QR Code

Science.gov Websites

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The Influence of Item Response Indecision on the Self-Directed Search

ERIC Educational Resources Information Center

Sampson, James P., Jr.; Shy, Jonathan D.; Hartley, Sarah Lucas; Reardon, Robert C.; Peterson, Gary W.

2009-01-01

Students (N = 247) responded to Self-Directed Search (SDS) per the standard response format and were also instructed to record a question mark (?) for items about which they were uncertain (item response indecision [IRI]). The initial responses of the 114 participants with a (?) were then reversed and a second SDS summary code was obtained and…

Schroedinger’s code: Source code availability and transparency in astrophysics

NASA Astrophysics Data System (ADS)

Ryan, PW; Allen, Alice; Teuben, Peter

2018-01-01

Astronomers use software for their research, but how many of the codes they use are available as source code? We examined a sample of 166 papers from 2015 for clearly identified software use, then searched for source code for the software packages mentioned in these research papers. We categorized the software to indicate whether source code is available for download and whether there are restrictions to accessing it, and if source code was not available, whether some other form of the software, such as a binary, was. Over 40% of the source code for the software used in our sample was not available for download.As URLs have often been used as proxy citations for software, we also extracted URLs from one journal’s 2015 research articles, removed those from certain long-term, reliable domains, and tested the remainder to determine what percentage of these URLs were still accessible in September and October, 2017.

JSPAM: A restricted three-body code for simulating interacting galaxies

NASA Astrophysics Data System (ADS)

Wallin, J. F.; Holincheck, A. J.; Harvey, A.

2016-07-01

Restricted three-body codes have a proven ability to recreate much of the disturbed morphology of actual interacting galaxies. As more sophisticated n-body models were developed and computer speed increased, restricted three-body codes fell out of favor. However, their supporting role for performing wide searches of parameter space when fitting orbits to real systems demonstrates a continuing need for their use. Here we present the model and algorithm used in the JSPAM code. A precursor of this code was originally described in 1990, and was called SPAM. We have recently updated the software with an alternate potential and a treatment of dynamical friction to more closely mimic the results from n-body tree codes. The code is released publicly for use under the terms of the Academic Free License ("AFL") v. 3.0 and has been added to the Astrophysics Source Code Library.

Pharmer: efficient and exact pharmacophore search.

PubMed

Koes, David Ryan; Camacho, Carlos J

2011-06-27

Pharmacophore search is a key component of many drug discovery efforts. Pharmer is a new computational approach to pharmacophore search that scales with the breadth and complexity of the query, not the size of the compound library being screened. Two novel methods for organizing pharmacophore data, the Pharmer KDB-tree and Bloom fingerprints, enable Pharmer to perform an exact pharmacophore search of almost two million structures in less than a minute. In general, Pharmer is more than an order of magnitude faster than existing technologies. The complete source code is available under an open-source license at http://pharmer.sourceforge.net .

Pupil measures of alertness and mental load

NASA Technical Reports Server (NTRS)

Backs, Richard W.; Walrath, Larry C.

1988-01-01

A study of eight adults given active and passive search tasks showed that evoked pupillary response was sensitive to information processing demands. In particular, large pupillary diameter was observed in the active search condition where subjects were actively processing information relevant to task performance, as opposed to the passive search (control) condition where subjects passively viewed the displays. However, subjects may have simply been more aroused in the active search task. Of greater importance was that larger pupillary diameter, corresponding to longer search time, was observed for noncoded than for color-coded displays in active search. In the control condition, pupil diameter was larger with the color displays. The data indicate potential usefulness of pupillary responses in evaluating the information processing requirements of visual displays.

Evaluation of Diagnostic Codes in Morbidity and Mortality Data Sources for Heat-Related Illness Surveillance

PubMed Central

Watkins, Sharon

2017-01-01

Objectives: The primary objective of this study was to identify patients with heat-related illness (HRI) using codes for heat-related injury diagnosis and external cause of injury in 3 administrative data sets: emergency department (ED) visit records, hospital discharge records, and death certificates. Methods: We obtained data on ED visits, hospitalizations, and deaths for Florida residents for May 1 through October 31, 2005-2012. To identify patients with HRI, we used codes from the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) to search data on ED visits and hospitalizations and codes from the International Classification of Diseases, Tenth Revision (ICD-10) to search data on deaths. We stratified the results by data source and whether the HRI was work related. Results: We identified 23 981 ED visits, 4816 hospitalizations, and 140 deaths in patients with non–work-related HRI and 2979 ED visits, 415 hospitalizations, and 23 deaths in patients with work-related HRI. The most common diagnosis codes among patients were for severe HRI (heat exhaustion or heatstroke). The proportion of patients with a severe HRI diagnosis increased with data source severity. If ICD-9-CM code E900.1 and ICD-10 code W92 (excessive heat of man-made origin) were used as exclusion criteria for HRI, 5.0% of patients with non–work-related deaths, 3.0% of patients with work-related ED visits, and 1.7% of patients with work-related hospitalizations would have been removed. Conclusions: Using multiple data sources and all diagnosis fields may improve the sensitivity of HRI surveillance. Future studies should evaluate the impact of converting ICD-9-CM to ICD-10-CM codes on HRI surveillance of ED visits and hospitalizations. PMID:28379784

A Repository of Codes of Ethics and Technical Standards in Health Informatics

PubMed Central

Zaïane, Osmar R.

2014-01-01

We present a searchable repository of codes of ethics and standards in health informatics. It is built using state-of-the-art search algorithms and technologies. The repository will be potentially beneficial for public health practitioners, researchers, and software developers in finding and comparing ethics topics of interest. Public health clinics, clinicians, and researchers can use the repository platform as a one-stop reference for various ethics codes and standards. In addition, the repository interface is built for easy navigation, fast search, and side-by-side comparative reading of documents. Our selection criteria for codes and standards are two-fold; firstly, to maintain intellectual property rights, we index only codes and standards freely available on the internet. Secondly, major international, regional, and national health informatics bodies across the globe are surveyed with the aim of understanding the landscape in this domain. We also look at prevalent technical standards in health informatics from major bodies such as the International Standards Organization (ISO) and the U. S. Food and Drug Administration (FDA). Our repository contains codes of ethics from the International Medical Informatics Association (IMIA), the iHealth Coalition (iHC), the American Health Information Management Association (AHIMA), the Australasian College of Health Informatics (ACHI), the British Computer Society (BCS), and the UK Council for Health Informatics Professions (UKCHIP), with room for adding more in the future. Our major contribution is enhancing the findability of codes and standards related to health informatics ethics by compilation and unified access through the health informatics ethics repository. PMID:25422725

Epidemiology of angina pectoris: role of natural language processing of the medical record

PubMed Central

Pakhomov, Serguei; Hemingway, Harry; Weston, Susan A.; Jacobsen, Steven J.; Rodeheffer, Richard; Roger, Véronique L.

2007-01-01

Background The diagnosis of angina is challenging as it relies on symptom descriptions. Natural language processing (NLP) of the electronic medical record (EMR) can provide access to such information contained in free text that may not be fully captured by conventional diagnostic coding. Objective To test the hypothesis that NLP of the EMR improves angina pectoris (AP) ascertainment over diagnostic codes. Methods Billing records of in- and out-patients were searched for ICD-9 codes for AP, chronic ischemic heart disease and chest pain. EMR clinical reports were searched electronically for 50 specific non-negated natural language synonyms to these ICD-9 codes. The two methods were compared to a standardized assessment of angina by Rose questionnaire for three diagnostic levels: unspecified chest pain, exertional chest pain, and Rose angina. Results Compared to the Rose questionnaire, the true positive rate of EMR-NLP for unspecified chest pain was 62% (95%CI:55–67) vs. 51% (95%CI:44–58) for diagnostic codes (p<0.001). For exertional chest pain, the EMR-NLP true positive rate was 71% (95%CI:61–80) vs. 62% (95%CI:52–73) for diagnostic codes (p=0.10). Both approaches had 88% (95%CI:65–100) true positive rate for Rose angina. The EMR-NLP method consistently identified more patients with exertional chest pain over 28-month follow-up. Conclusion EMR-NLP method improves the detection of unspecified and exertional chest pain cases compared to diagnostic codes. These findings have implications for epidemiological and clinical studies of angina pectoris. PMID:17383310

Surging Seas Risk Finder: A Simple Search-Based Web Tool for Local Sea Level Rise Projections, Coastal Flood Risk Forecasts, and Inundation Exposure Analysis

NASA Astrophysics Data System (ADS)

Strauss, B.; Dodson, D.; Kulp, S. A.; Rizza, D. H.

2016-12-01

Surging Seas Risk Finder (riskfinder.org) is an online tool for accessing extensive local projections and analysis of sea level rise; coastal floods; and land, populations, contamination sources, and infrastructure and other assets that may be exposed to inundation. Risk Finder was first published in 2013 for Florida, New York and New Jersey, expanding to all states in the contiguous U.S. by 2016, when a major new version of the tool was released with a completely new interface. The revised tool was informed by hundreds of survey responses from and conversations with planners, local officials and other coastal stakeholders, plus consideration of modern best practices for responsive web design and user interfaces, and social science-based principles for science communication. Overarching design principles include simplicity and ease of navigation, leading to a landing page with Google-like sparsity and focus on search, and to an architecture based on search, so that each coastal zip code, city, county, state or other place type has its own webpage gathering all relevant analysis in modular, scrollable units. Millions of users have visited the Surging Seas suite of tools to date, and downloaded thousands of files, for stated purposes ranging from planning to business to education to personal decisions; and from institutions ranging from local to federal government agencies, to businesses, to NGOs, and to academia.

Combined Wavelet Video Coding and Error Control for Internet Streaming and Multicast

NASA Astrophysics Data System (ADS)

Chu, Tianli; Xiong, Zixiang

2003-12-01

This paper proposes an integrated approach to Internet video streaming and multicast (e.g., receiver-driven layered multicast (RLM) by McCanne) based on combined wavelet video coding and error control. We design a packetized wavelet video (PWV) coder to facilitate its integration with error control. The PWV coder produces packetized layered bitstreams that are independent among layers while being embedded within each layer. Thus, a lost packet only renders the following packets in the same layer useless. Based on the PWV coder, we search for a multilayered error-control strategy that optimally trades off source and channel coding for each layer under a given transmission rate to mitigate the effects of packet loss. While both the PWV coder and the error-control strategy are new—the former incorporates embedded wavelet video coding and packetization and the latter extends the single-layered approach for RLM by Chou et al.—the main distinction of this paper lies in the seamless integration of the two parts. Theoretical analysis shows a gain of up to 1 dB on a channel with 20% packet loss using our combined approach over separate designs of the source coder and the error-control mechanism. This is also substantiated by our simulations with a gain of up to 0.6 dB. In addition, our simulations show a gain of up to 2.2 dB over previous results reported by Chou et al.

Scoliosis-specific information on the internet: has the "information highway" led to better information provision?

PubMed

Nason, Gregory J; Baker, Joseph F; Byrne, Damien P; Noel, Jacques; Moore, David; Kiely, Patrick J

2012-10-01

A quality-control Internet-based study using recognized quality scoring systems. To evaluate the quality of information available on the Internet. The quality of information available is of poor quality and unreliable, and this study was to determine if it has improved in line with the exponential increase in Internet-based information since the last time it was reviewed in 2005. To identify potential Web sites, the 5 most commonly accessed search engines were identified and a search for "scoliosis" was performed on each. The top 100 Web sites were reviewed. Each Web site was categorized according to its authorship and assessed using recognized scoring systems (Journal of American Medical Association [JAMA] and DISCERN criteria, scoliosis-specific content quality). The presence of the Health on the Net code, a reported quality-assurance marker, was noted. Forty-one unique Web sites were identified and analyzed. Five were academic, 11 were produced by physicians, 5 were commercial, 3 were nonphysician sites, 6 were attached to discussion groups or social media sites, 3 were media related, and 8 were not otherwise classifiable. There were significant differences noted between the authorship categories on the DISCERN score, JAMA benchmark criteria, and scoliosis-specific content quality score, (P = 0.001, <0.0001, and 0.009, respectively) with academic- and physician-related Web sites containing better-quality information. Internet sites with a Health on the Net code demonstrated higher-quality scoliosis-specific information than those without the code (P = 0.1368). The overall quality of information regarding scoliosis remains poor despite an exponential increase in the number of sites available. Patients need to be educated about appropriate Internet use-academic- and physician-provided sites have been shown to contain better-quality information. We have a potential role as clinicians to not only direct patients to appropriate sites but also to help in developing content on the Internet.

Disclosure of terminal illness to patients and families: diversity of governing codes in 14 Islamic countries.

PubMed

Abdulhameed, Hunida E; Hammami, Muhammad M; Mohamed, Elbushra A Hameed

2011-08-01

The consistency of codes governing disclosure of terminal illness to patients and families in Islamic countries has not been studied until now. To review available codes on disclosure of terminal illness in Islamic countries. DATA SOURCE AND EXTRACTION: Data were extracted through searches on Google and PubMed. Codes related to disclosure of terminal illness to patients or families were abstracted, and then classified independently by the three authors. Codes for 14 Islamic countries were located. Five codes were silent regarding informing the patient, seven allowed concealment, one mandated disclosure and one prohibited disclosure. Five codes were silent regarding informing the family, four allowed disclosure and five mandated/recommended disclosure. The Islamic Organization for Medical Sciences code was silent on both issues. Codes regarding disclosure of terminal illness to patients and families differed markedly among Islamic countries. They were silent in one-third of the codes, and tended to favour a paternalistic/utilitarian, family-centred approach over an autonomous, patient-centred approach.

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.

PubMed

Shankar, Ravi; Parkinson, Helen; Burdett, Tony; Hastings, Emma; Liu, Junmin; Miller, Michael; Srinivasa, Rashmi; White, Joseph; Brazma, Alvis; Sherlock, Gavin; Stoeckert, Christian J; Ball, Catherine A

2010-10-01

Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis. Annotare is available from http://code.google.com/p/annotare/ under the terms of the open-source MIT License (http://www.opensource.org/licenses/mit-license.php). It has been tested on both Mac and Windows.

The Future of ECHO: Evaluating Open Source Possibilities

NASA Astrophysics Data System (ADS)

Pilone, D.; Gilman, J.; Baynes, K.; Mitchell, A. E.

2012-12-01

NASA's Earth Observing System ClearingHOuse (ECHO) is a format agnostic metadata repository supporting over 3000 collections and 100M science granules. ECHO exposes FTP and RESTful Data Ingest APIs in addition to both SOAP and RESTful search and order capabilities. Built on top of ECHO is a human facing search and order web application named Reverb. ECHO processes hundreds of orders, tens of thousands of searches, and 1-2M ingest actions each week. As ECHO's holdings, metadata format support, and visibility have increased, the ECHO team has received requests by non-NASA entities for copies of ECHO that can be run locally against their data holdings. ESDIS and the ECHO Team have begun investigations into various deployment and Open Sourcing models that can balance the real constraints faced by the ECHO project with the benefits of providing ECHO capabilities to a broader set of users and providers. This talk will discuss several release and Open Source models being investigated by the ECHO team along with the impacts those models are expected to have on the project. We discuss: - Addressing complex deployment or setup issues for potential users - Models of vetting code contributions - Balancing external (public) user requests versus our primary partners - Preparing project code for public release, including navigating licensing issues related to leveraged libraries - Dealing with non-free project dependencies such as commercial databases - Dealing with sensitive aspects of project code such as database passwords, authentication approaches, security through obscurity, etc. - Ongoing support for the released code including increased testing demands, bug fixes, security fixes, and new features.

Beyond terrestrial biology: charting the chemical universe of α-amino acid structures.

PubMed

Meringer, Markus; Cleaves, H James; Freeland, Stephen J

2013-11-25

α-Amino acids are fundamental to biochemistry as the monomeric building blocks with which cells construct proteins according to genetic instructions. However, the 20 amino acids of the standard genetic code represent a tiny fraction of the number of α-amino acid chemical structures that could plausibly play such a role, both from the perspective of natural processes by which life emerged and evolved, and from the perspective of human-engineered genetically coded proteins. Until now, efforts to describe the structures comprising this broader set, or even estimate their number, have been hampered by the complex combinatorial properties of organic molecules. Here, we use computer software based on graph theory and constructive combinatorics in order to conduct an efficient and exhaustive search of the chemical structures implied by two careful and precise definitions of the α-amino acids relevant to coded biological proteins. Our results include two virtual libraries of α-amino acid structures corresponding to these different approaches, comprising 121 044 and 3 846 structures, respectively, and suggest a simple approach to exploring much larger, as yet uncomputed, libraries of interest.

A user's manual for DELSOL3: A computer code for calculating the optical performance and optimal system design for solar thermal central receiver plants

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

Kistler, B.L.

DELSOL3 is a revised and updated version of the DELSOL2 computer program (SAND81-8237) for calculating collector field performance and layout and optimal system design for solar thermal central receiver plants. The code consists of a detailed model of the optical performance, a simpler model of the non-optical performance, an algorithm for field layout, and a searching algorithm to find the best system design based on energy cost. The latter two features are coupled to a cost model of central receiver components and an economic model for calculating energy costs. The code can handle flat, focused and/or canted heliostats, and externalmore » cylindrical, multi-aperture cavity, and flat plate receivers. The program optimizes the tower height, receiver size, field layout, heliostat spacings, and tower position at user specified power levels subject to flux limits on the receiver and land constraints for field layout. DELSOL3 maintains the advantages of speed and accuracy which are characteristics of DELSOL2.« less

U. S. statutes of general interest to safeguards and security officers

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

Cadwell, J.J.

1988-01-01

A handbook of enforcement provisions of Federal law and regulations was prepared for use by U.S. DOE Security Inspectors. This handbook provides security inspectors for the U.S. Department of Energy, security officers at Nuclear Regulatory Licensee facilities, and others with a single document containing most of the Federal law provisions available to assist them in enforcing agency regulations. The handbook contains selected enforcement provisions of Titles 18, 42 and 50 of the United States Code (USC). Topical coverage of Title 18 includes Espionage and Misrepresentation or Impersonation; Theft and Embezzlement; Malicious Mischief; Conspiracy; Search and Seizure. A miscellaneous section dealsmore » with explosives, blackmail, firearms, and other subjects. Certain enforcement sections of Title 42 of the USC (The Atomic Energy Act) and of the Internal Security Act of the United States Code (Title 50) are also provided. Finally, relevant parts of the Federal Property Management Regulations of Title 50, Chapter 101 of the Code of Federal Regulations are presented. A comprehensive index is provided based on key words.« less

Choices in the use of ICD-9 codes to identify stroke risk factors can affect the apparent population-level risk factor prevalence and distribution of CHADS2 scores

PubMed Central

Rothendler, James A; Rose, Adam J; Reisman, Joel I; Berlowitz, Dan R; Kazis, Lewis E

2012-01-01

While developed for managing individuals with atrial fibrillation, risk stratification schemes for stroke, such as CHADS2, may be useful in population-based studies, including those assessing process of care. We investigated how certain decisions in identifying diagnoses from administrative data affect the apparent prevalence of CHADS2-associated diagnoses and distribution of scores. Two sets of ICD-9 codes (more restrictive/ more inclusive) were defined for each CHADS2-associated diagnosis. For stroke/transient ischemic attack (TIA), the more restrictive set was applied to only inpatient data. We varied the number of years (1-3) in searching for relevant codes, and, except for stroke/TIA, the number of instances (1 vs. 2) that diagnoses were required to appear. The impact of choices on apparent disease prevalence varied by type of choice and condition, but was often substantial. Choices resulting in substantial changes in prevalence also tended to be associated with more substantial effects on the distribution of CHADS2 scores. PMID:22937488

A systematic review of validated methods for identifying acute respiratory failure using administrative and claims data.

PubMed

Jones, Natalie; Schneider, Gary; Kachroo, Sumesh; Rotella, Philip; Avetisyan, Ruzan; Reynolds, Matthew W

2012-01-01

The Food and Drug Administration's (FDA) Mini-Sentinel pilot program initially aims to conduct active surveillance to refine safety signals that emerge for marketed medical products. A key facet of this surveillance is to develop and understand the validity of algorithms for identifying health outcomes of interest (HOIs) from administrative and claims data. This paper summarizes the process and findings of the algorithm review of acute respiratory failure (ARF). PubMed and Iowa Drug Information Service searches were conducted to identify citations applicable to the anaphylaxis HOI. Level 1 abstract reviews and Level 2 full-text reviews were conducted to find articles using administrative and claims data to identify ARF, including validation estimates of the coding algorithms. Our search revealed a deficiency of literature focusing on ARF algorithms and validation estimates. Only two studies provided codes for ARF, each using related yet different ICD-9 codes (i.e., ICD-9 codes 518.8, "other diseases of lung," and 518.81, "acute respiratory failure"). Neither study provided validation estimates. Research needs to be conducted on designing validation studies to test ARF algorithms and estimating their predictive power, sensitivity, and specificity. Copyright © 2012 John Wiley & Sons, Ltd.

Migration to Current Open Source Technologies by MagIC Enables a More Responsive Website, Quicker Development Times, and Increased Community Engagement

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Koppers, A.; Constable, C.; Tauxe, L.; Jonestrask, L.

2017-12-01

The Magnetics Information Consortium (MagIC) supports an online database for the paleo, geo, and rock magnetic communities ( https://earthref.org/MagIC ). Researchers can upload data into the archive and download data as selected with a sophisticated search system. MagIC has completed the transition from an Oracle backed, Perl based, server oriented website to an ElasticSearch backed, Meteor based thick client website technology stack. Using JavaScript on both the sever and the client enables increased code reuse and allows easy offloading many computational operations to the client for faster response. On-the-fly data validation, column header suggestion, and spreadsheet online editing are some new features available with the new system. The 3.0 data model, method codes, and vocabulary lists can be browsed via the MagIC website and more easily updated. Source code for MagIC is publicly available on GitHub ( https://github.com/earthref/MagIC ). The MagIC file format is natively compatible with the PmagPy ( https://github.com/PmagPy/PmagPy) paleomagnetic analysis software. MagIC files can now be downloaded from the database and viewed and interpreted in the PmagPy GUI based tool, pmag_gui. Changes or interpretations of the data can then be saved by pmag_gui in the MagIC 3.0 data format and easily uploaded to the MagIC database. The rate of new contributions to the database has been increasing with many labs contributing measurement level data for the first time in the last year. Over a dozen file format conversion scripts are available for translating non-MagIC measurement data files into the MagIC format for easy uploading. We will continue to work with more labs until the whole community has a manageable workflow for contributing their measurement level data. MagIC will continue to provide a global repository for archiving and retrieving paleomagnetic and rock magnetic data and, with the new system in place, be able to more quickly respond to the community's requests for changes and improvements.

The development of automaticity in short-term memory search: Item-response learning and category learning.

PubMed

Cao, Rui; Nosofsky, Robert M; Shiffrin, Richard M

2017-05-01

In short-term-memory (STM)-search tasks, observers judge whether a test probe was present in a short list of study items. Here we investigated the long-term learning mechanisms that lead to the highly efficient STM-search performance observed under conditions of consistent-mapping (CM) training, in which targets and foils never switch roles across trials. In item-response learning, subjects learn long-term mappings between individual items and target versus foil responses. In category learning, subjects learn high-level codes corresponding to separate sets of items and learn to attach old versus new responses to these category codes. To distinguish between these 2 forms of learning, we tested subjects in categorized varied mapping (CV) conditions: There were 2 distinct categories of items, but the assignment of categories to target versus foil responses varied across trials. In cases involving arbitrary categories, CV performance closely resembled standard varied-mapping performance without categories and departed dramatically from CM performance, supporting the item-response-learning hypothesis. In cases involving prelearned categories, CV performance resembled CM performance, as long as there was sufficient practice or steps taken to reduce trial-to-trial category-switching costs. This pattern of results supports the category-coding hypothesis for sufficiently well-learned categories. Thus, item-response learning occurs rapidly and is used early in CM training; category learning is much slower but is eventually adopted and is used to increase the efficiency of search beyond that available from item-response learning. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Discectomy-related information on the internet: does the quality follow the surge?

PubMed

Elhassan, Yahya; Sheridan, Gerard; Nassiri, Mujtaba; Osman, Mugtaba; Kiely, Pat; Noel, Jacques

2015-01-15

A quality-control Internet-based study using recognized quality-scoring systems. To evaluate the quality of information available on the Internet. Quality of health information on the Internet is of much concern and the emphasis for appraisal of Internet Web sites is needed. This study is to determine if it has improved with the surge in Internet usage. The 3 most commonly used search engines were identified and a search for "Discectomy" was performed on each. Two reviewers categorized the Web sites according to their types and the quality of each was assessed using recognized scoring systems including the Journal of the American Medical Association (JAMA) benchmark, DISCERN score, and discectomy-specific content score. The quality of the information was also assessed according to the presence and absence of the Health on the Net code. Fifty-three Web sites were identified, and analyzed. Commercial Web sites were predominant, 24 of them were identified, 7 were governmental, 6 were produced by physicians, none were produced by allied health professionals, 3 were academic, 4 were public health information Web sites, 4 were attached to social media and discussion groups, 3 were related to media, and 2 were unspecified. Internet sites with a Health on the Net code demonstrated significantly higher quality than those without the code (P < 0.0001). Public health information Web sites attained the highest overall DISCERN and discectomy-specific scores followed by Web sites of the government and nonprofit organizations. The overall quality of information regarding discectomy remains poor and variable despite an exponential increase in the number of users and Web sites, with a slight trend toward improvement, only 20% to 30% are of good quality, compared with that 10 years ago (<10%). Presence of Health on the Net code is a very reliable marker for health information quality.

Document image retrieval through word shape coding.

PubMed

Lu, Shijian; Li, Linlin; Tan, Chew Lim

2008-11-01

This paper presents a document retrieval technique that is capable of searching document images without OCR (optical character recognition). The proposed technique retrieves document images by a new word shape coding scheme, which captures the document content through annotating each word image by a word shape code. In particular, we annotate word images by using a set of topological shape features including character ascenders/descenders, character holes, and character water reservoirs. With the annotated word shape codes, document images can be retrieved by either query keywords or a query document image. Experimental results show that the proposed document image retrieval technique is fast, efficient, and tolerant to various types of document degradation.

Googling suicide: surfing for suicide information on the Internet.

PubMed

Recupero, Patricia R; Harms, Samara E; Noble, Jeffrey M

2008-06-01

This study examined the types of resources a suicidal person might find through search engines on the Internet. We were especially interested in determining the accessibility of potentially harmful resources, such as prosuicide forums, as such resources have been implicated in completed suicides and are known to exist on the Web. Using 5 popular search engines (Google, Yahoo!, Ask.com, Lycos, and Dogpile) and 4 suicide-related search terms (suicide, how to commit suicide, suicide methods, and how to kill yourself), we collected quantitative and qualitative data about the search results. The searches were conducted in August and September 2006. Several coraters assigned codes and characterizations to the first 30 Web sites per search term combination (and "sponsored links" on those pages), which were then confirmed by consensus ratings. Search results were classified as being prosuicide, antisuicide, suicide-neutral, not a suicide site, or error (i.e., page would not load). Additional information was collected to further characterize the nature of the information on these Web sites. Suicide-neutral and anti-suicide pages occurred most frequently (of 373 unique Web pages, 115 were coded as suicide-neutral, and 109 were anti-suicide). While pro-suicide resources were less frequent (41 Web pages), they were nonetheless easily accessible. Detailed how-to instructions for unusual and lethal suicide methods were likewise easily located through the searches. Mental health professionals should ask patients about their Internet use. Depressed, suicidal, or potentially suicidal patients who use the Internet may be especially at risk. Clinicians may wish to assist patients in locating helpful, supportive resources online so that patients' Internet use may be more therapeutic than harmful.

PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results.

PubMed

He, Ji; Dai, Xinbin; Zhao, Xuechun

2007-02-09

BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at http://bioinfo.noble.org/plan/. The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users.

PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results

PubMed Central

He, Ji; Dai, Xinbin; Zhao, Xuechun

2007-01-01

Background BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. Results Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. Conclusion PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at . The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users. PMID:17291345

Dual representation of item positions in verbal short-term memory: Evidence for two access modes.

PubMed

Lange, Elke B; Verhaeghen, Paul; Cerella, John

Memory sets of N = 1~5 digits were exposed sequentially from left-to-right across the screen, followed by N recognition probes. Probes had to be compared to memory list items on identity only (Sternberg task) or conditional on list position. Positions were probed randomly or in left-to-right order. Search functions related probe response times to set size. Random probing led to ramped, "Sternbergian" functions whose intercepts were elevated by the location requirement. Sequential probing led to flat search functions-fast responses unaffected by set size. These results suggested that items in STM could be accessed either by a slow search-on-identity followed by recovery of an associated location tag, or in a single step by following item-to-item links in study order. It is argued that this dual coding of location information occurs spontaneously at study, and that either code can be utilised at retrieval depending on test demands.

Applications of statistical physics and information theory to the analysis of DNA sequences

NASA Astrophysics Data System (ADS)

Grosse, Ivo

2000-10-01

DNA carries the genetic information of most living organisms, and the of genome projects is to uncover that genetic information. One basic task in the analysis of DNA sequences is the recognition of protein coding genes. Powerful computer programs for gene recognition have been developed, but most of them are based on statistical patterns that vary from species to species. In this thesis I address the question if there exist universal statistical patterns that are different in coding and noncoding DNA of all living species, regardless of their phylogenetic origin. In search for such species-independent patterns I study the mutual information function of genomic DNA sequences, and find that it shows persistent period-three oscillations. To understand the biological origin of the observed period-three oscillations, I compare the mutual information function of genomic DNA sequences to the mutual information function of stochastic model sequences. I find that the pseudo-exon model is able to reproduce the mutual information function of genomic DNA sequences. Moreover, I find that a generalization of the pseudo-exon model can connect the existence and the functional form of long-range correlations to the presence and the length distributions of coding and noncoding regions. Based on these theoretical studies I am able to find an information-theoretical quantity, the average mutual information (AMI), whose probability distributions are significantly different in coding and noncoding DNA, while they are almost identical in all studied species. These findings show that there exist universal statistical patterns that are different in coding and noncoding DNA of all studied species, and they suggest that the AMI may be used to identify genes in different living species, irrespective of their taxonomic origin.

Mapping the Color Space of Saccadic Selectivity in Visual Search

ERIC Educational Resources Information Center

Xu, Yun; Higgins, Emily C.; Xiao, Mei; Pomplun, Marc

2007-01-01

Color coding is used to guide attention in computer displays for such critical tasks as baggage screening or air traffic control. It has been shown that a display object attracts more attention if its color is more similar to the color for which one is searching. However, what does "similar" precisely mean? Can we predict the amount of attention…

Establishing and Maintaining Trust for an Airborne Network. Search and Rescue Enterprise: Security Assessment Report

DTIC Science & Technology

2014-12-01

Area Code) (937) 528-8142 Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. Z39-18 1 MITCHELL, LOLITA V CIV USAF AFMC AFRL/RYOX To...MITCHELL, LOLITA V CIV USAF AFMC AFRL/RYOX Subject: FW: Final Report Change - Search and Rescue Security Assessment From: J M Schlesselman [mailto:joe

Trellis coding with multidimensional QAM signal sets

NASA Technical Reports Server (NTRS)

Pietrobon, Steven S.; Costello, Daniel J.

1993-01-01

Trellis coding using multidimensional QAM signal sets is investigated. Finite-size 2D signal sets are presented that have minimum average energy, are 90-deg rotationally symmetric, and have from 16 to 1024 points. The best trellis codes using the finite 16-QAM signal set with two, four, six, and eight dimensions are found by computer search (the multidimensional signal set is constructed from the 2D signal set). The best moderate complexity trellis codes for infinite lattices with two, four, six, and eight dimensions are also found. The minimum free squared Euclidean distance and number of nearest neighbors for these codes were used as the selection criteria. Many of the multidimensional codes are fully rotationally invariant and give asymptotic coding gains up to 6.0 dB. From the infinite lattice codes, the best codes for transmitting J, J + 1/4, J + 1/3, J + 1/2, J + 2/3, and J + 3/4 bit/sym (J an integer) are presented.

Nonlinear inversion of potential-field data using a hybrid-encoding genetic algorithm

USGS Publications Warehouse

Chen, C.; Xia, J.; Liu, J.; Feng, G.

2006-01-01

Using a genetic algorithm to solve an inverse problem of complex nonlinear geophysical equations is advantageous because it does not require computer gradients of models or "good" initial models. The multi-point search of a genetic algorithm makes it easier to find the globally optimal solution while avoiding falling into a local extremum. As is the case in other optimization approaches, the search efficiency for a genetic algorithm is vital in finding desired solutions successfully in a multi-dimensional model space. A binary-encoding genetic algorithm is hardly ever used to resolve an optimization problem such as a simple geophysical inversion with only three unknowns. The encoding mechanism, genetic operators, and population size of the genetic algorithm greatly affect search processes in the evolution. It is clear that improved operators and proper population size promote the convergence. Nevertheless, not all genetic operations perform perfectly while searching under either a uniform binary or a decimal encoding system. With the binary encoding mechanism, the crossover scheme may produce more new individuals than with the decimal encoding. On the other hand, the mutation scheme in a decimal encoding system will create new genes larger in scope than those in the binary encoding. This paper discusses approaches of exploiting the search potential of genetic operations in the two encoding systems and presents an approach with a hybrid-encoding mechanism, multi-point crossover, and dynamic population size for geophysical inversion. We present a method that is based on the routine in which the mutation operation is conducted in the decimal code and multi-point crossover operation in the binary code. The mix-encoding algorithm is called the hybrid-encoding genetic algorithm (HEGA). HEGA provides better genes with a higher probability by a mutation operator and improves genetic algorithms in resolving complicated geophysical inverse problems. Another significant result is that final solution is determined by the average model derived from multiple trials instead of one computation due to the randomness in a genetic algorithm procedure. These advantages were demonstrated by synthetic and real-world examples of inversion of potential-field data. ?? 2005 Elsevier Ltd. All rights reserved.

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

PubMed

Huang, Jingshan; Gutierrez, Fernando; Strachan, Harrison J; Dou, Dejing; Huang, Weili; Smith, Barry; Blake, Judith A; Eilbeck, Karen; Natale, Darren A; Lin, Yu; Wu, Bin; Silva, Nisansa de; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming; Ruttenberg, Alan

2016-01-01

As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs regulate specific target genes. It is therefore critical to identify, analyze, and cross-reference miRNA-target interactions to better explore and delineate miRNA functions. Semantic technologies can help in this regard. We previously developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), whose goal was to serve as a foundation for semantic annotation, data integration, and semantic search in the miRNA field. In this paper we describe our continuing effort to develop the OMIT, and demonstrate its use within a semantic search system, OmniSearch, designed to facilitate knowledge capture of miRNA-target interaction data. Important changes in the current version OMIT are summarized as: (1) following a modularized ontology design (with 2559 terms imported from the NCRO ontology); (2) encoding all 1884 human miRNAs (vs. 300 in previous versions); and (3) setting up a GitHub project site along with an issue tracker for more effective community collaboration on the ontology development. The OMIT ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/omit.owl. The OmniSearch system is also free and open to all users, accessible at: http://omnisearch.soc.southalabama.edu/index.php/Software.

Differentiation of ileostomy from colostomy procedures: assessing the accuracy of current procedural terminology codes and the utility of natural language processing.

PubMed

Vo, Elaine; Davila, Jessica A; Hou, Jason; Hodge, Krystle; Li, Linda T; Suliburk, James W; Kao, Lillian S; Berger, David H; Liang, Mike K

2013-08-01

Large databases provide a wealth of information for researchers, but identifying patient cohorts often relies on the use of current procedural terminology (CPT) codes. In particular, studies of stoma surgery have been limited by the accuracy of CPT codes in identifying and differentiating ileostomy procedures from colostomy procedures. It is important to make this distinction because the prevalence of complications associated with stoma formation and reversal differ dramatically between types of stoma. Natural language processing (NLP) is a process that allows text-based searching. The Automated Retrieval Console is an NLP-based software that allows investigators to design and perform NLP-assisted document classification. In this study, we evaluated the role of CPT codes and NLP in differentiating ileostomy from colostomy procedures. Using CPT codes, we conducted a retrospective study that identified all patients undergoing a stoma-related procedure at a single institution between January 2005 and December 2011. All operative reports during this time were reviewed manually to abstract the following variables: formation or reversal and ileostomy or colostomy. Sensitivity and specificity for validation of the CPT codes against the mastery surgery schedule were calculated. Operative reports were evaluated by use of NLP to differentiate ileostomy- from colostomy-related procedures. Sensitivity and specificity for identifying patients with ileostomy or colostomy procedures were calculated for CPT codes and NLP for the entire cohort. CPT codes performed well in identifying stoma procedures (sensitivity 87.4%, specificity 97.5%). A total of 664 stoma procedures were identified by CPT codes between 2005 and 2011. The CPT codes were adequate in identifying stoma formation (sensitivity 97.7%, specificity 72.4%) and stoma reversal (sensitivity 74.1%, specificity 98.7%), but they were inadequate in identifying ileostomy (sensitivity 35.0%, specificity 88.1%) and colostomy (75.2% and 80.9%). NLP performed with greater sensitivity, specificity, and accuracy than CPT codes in identifying stoma procedures and stoma types. Major differences where NLP outperformed CPT included identifying ileostomy (specificity 95.8%, sensitivity 88.3%, and accuracy 91.5%) and colostomy (97.6%, 90.5%, and 92.8%, respectively). CPT codes can identify effectively patients who have had stoma procedures and are adequate in distinguishing between formation and reversal; however, CPT codes cannot differentiate ileostomy from colostomy. NLP can be used to differentiate between ileostomy- and colostomy-related procedures. The role of NLP in conjunction with electronic medical records in data retrieval warrants further investigation. Published by Mosby, Inc.

The annotation-enriched non-redundant patent sequence databases.

PubMed

Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

2013-01-01

The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/

The Annotation-enriched non-redundant patent sequence databases

PubMed Central

Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

2013-01-01

The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/ PMID:23396323

GPU-accelerated low-latency real-time searches for gravitational waves from compact binary coalescence

NASA Astrophysics Data System (ADS)

Liu, Yuan; Du, Zhihui; Chung, Shin Kee; Hooper, Shaun; Blair, David; Wen, Linqing

2012-12-01

We present a graphics processing unit (GPU)-accelerated time-domain low-latency algorithm to search for gravitational waves (GWs) from coalescing binaries of compact objects based on the summed parallel infinite impulse response (SPIIR) filtering technique. The aim is to facilitate fast detection of GWs with a minimum delay to allow prompt electromagnetic follow-up observations. To maximize the GPU acceleration, we apply an efficient batched parallel computing model that significantly reduces the number of synchronizations in SPIIR and optimizes the usage of the memory and hardware resource. Our code is tested on the CUDA ‘Fermi’ architecture in a GTX 480 graphics card and its performance is compared with a single core of Intel Core i7 920 (2.67 GHz). A 58-fold speedup is achieved while giving results in close agreement with the CPU implementation. Our result indicates that it is possible to conduct a full search for GWs from compact binary coalescence in real time with only one desktop computer equipped with a Fermi GPU card for the initial LIGO detectors which in the past required more than 100 CPUs.

ESTEST: A Framework for the Verification and Validation of Electronic Structure Codes

NASA Astrophysics Data System (ADS)

Yuan, Gary; Gygi, Francois

2011-03-01

ESTEST is a verification and validation (V& V) framework for electronic structure codes that supports Qbox, Quantum Espresso, ABINIT, the Exciting Code and plans support for many more. We discuss various approaches to the electronic structure V& V problem implemented in ESTEST, that are related to parsing, formats, data management, search, comparison and analyses. Additionally, an early experiment in the distribution of V& V ESTEST servers among the electronic structure community will be presented. Supported by NSF-OCI 0749217 and DOE FC02-06ER25777.

Methods for Coding Tobacco-Related Twitter Data: A Systematic Review.

PubMed

Lienemann, Brianna A; Unger, Jennifer B; Cruz, Tess Boley; Chu, Kar-Hai

2017-03-31

As Twitter has grown in popularity to 313 million monthly active users, researchers have increasingly been using it as a data source for tobacco-related research. The objective of this systematic review was to assess the methodological approaches of categorically coded tobacco Twitter data and make recommendations for future studies. Data sources included PsycINFO, Web of Science, PubMed, ABI/INFORM, Communication Source, and Tobacco Regulatory Science. Searches were limited to peer-reviewed journals and conference proceedings in English from January 2006 to July 2016. The initial search identified 274 articles using a Twitter keyword and a tobacco keyword. One coder reviewed all abstracts and identified 27 articles that met the following inclusion criteria: (1) original research, (2) focused on tobacco or a tobacco product, (3) analyzed Twitter data, and (4) coded Twitter data categorically. One coder extracted data collection and coding methods. E-cigarettes were the most common type of Twitter data analyzed, followed by specific tobacco campaigns. The most prevalent data sources were Gnip and Twitter's Streaming application programming interface (API). The primary methods of coding were hand-coding and machine learning. The studies predominantly coded for relevance, sentiment, theme, user or account, and location of user. Standards for data collection and coding should be developed to be able to more easily compare and replicate tobacco-related Twitter results. Additional recommendations include the following: sample Twitter's databases multiple times, make a distinction between message attitude and emotional tone for sentiment, code images and URLs, and analyze user profiles. Being relatively novel and widely used among adolescents and black and Hispanic individuals, Twitter could provide a rich source of tobacco surveillance data among vulnerable populations. ©Brianna A Lienemann, Jennifer B Unger, Tess Boley Cruz, Kar-Hai Chu. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 31.03.2017.

SeisCode: A seismological software repository for discovery and collaboration

NASA Astrophysics Data System (ADS)

Trabant, C.; Reyes, C. G.; Clark, A.; Karstens, R.

2012-12-01

SeisCode is a community repository for software used in seismological and related fields. The repository is intended to increase discoverability of such software and to provide a long-term home for software projects. Other places exist where seismological software may be found, but none meet the requirements necessary for an always current, easy to search, well documented, and citable resource for projects. Organizations such as IRIS, ORFEUS, and the USGS have websites with lists of available or contributed seismological software. Since the authors themselves do often not maintain these lists, the documentation often consists of a sentence or paragraph, and the available software may be outdated. Repositories such as GoogleCode and SourceForge, which are directly maintained by the authors, provide version control and issue tracking but do not provide a unified way of locating geophysical software scattered in and among countless unrelated projects. Additionally, projects are hosted at language-specific sites such as Mathworks and PyPI, in FTP directories, and in websites strewn across the Web. Search engines are only partially effective discovery tools, as the desired software is often hidden deep within the results. SeisCode provides software authors a place to present their software, codes, scripts, tutorials, and examples to the seismological community. Authors can choose their own level of involvement. At one end of the spectrum, the author might simply create a web page that points to an existing site. At the other extreme, an author may choose to leverage the many tools provided by SeisCode, such as a source code management tool with integrated issue tracking, forums, news feeds, downloads, wikis, and more. For software development projects with multiple authors, SeisCode can also be used as a central site for collaboration. SeisCode provides the community with an easy way to discover software, while providing authors a way to build a community around their software packages. IRIS invites the seismological community to browse and to submit projects to https://seiscode.iris.washington.edu/

Genetic Local Search for Optimum Multiuser Detection Problem in DS-CDMA Systems

NASA Astrophysics Data System (ADS)

Wang, Shaowei; Ji, Xiaoyong

Optimum multiuser detection (OMD) in direct-sequence code-division multiple access (DS-CDMA) systems is an NP-complete problem. In this paper, we present a genetic local search algorithm, which consists of an evolution strategy framework and a local improvement procedure. The evolution strategy searches the space of feasible, locally optimal solutions only. A fast iterated local search algorithm, which employs the proprietary characteristics of the OMD problem, produces local optima with great efficiency. Computer simulations show the bit error rate (BER) performance of the GLS outperforms other multiuser detectors in all cases discussed. The computation time is polynomial complexity in the number of users.

Rapid code acquisition algorithms employing PN matched filters

NASA Technical Reports Server (NTRS)

Su, Yu T.

1988-01-01

The performance of four algorithms using pseudonoise matched filters (PNMFs), for direct-sequence spread-spectrum systems, is analyzed. They are: parallel search with fix dwell detector (PL-FDD), parallel search with sequential detector (PL-SD), parallel-serial search with fix dwell detector (PS-FDD), and parallel-serial search with sequential detector (PS-SD). The operation characteristic for each detector and the mean acquisition time for each algorithm are derived. All the algorithms are studied in conjunction with the noncoherent integration technique, which enables the system to operate in the presence of data modulation. Several previous proposals using PNMF are seen as special cases of the present algorithms.

Effects of Mode of Target Task Selection on Learning about Plants in a Mobile Learning Environment: Effortful Manual Selection versus Effortless QR-Code Selection

ERIC Educational Resources Information Center

Gao, Yuan; Liu, Tzu-Chien; Paas, Fred

2016-01-01

This study compared the effects of effortless selection of target plants using quick respond (QR) code technology to effortful manual search and selection of target plants on learning about plants in a mobile device supported learning environment. In addition, it was investigated whether the effectiveness of the 2 selection methods was…

A Modified Artificial Bee Colony Algorithm for p-Center Problems

PubMed Central

Yurtkuran, Alkın

2014-01-01

The objective of the p-center problem is to locate p-centers on a network such that the maximum of the distances from each node to its nearest center is minimized. The artificial bee colony algorithm is a swarm-based meta-heuristic algorithm that mimics the foraging behavior of honey bee colonies. This study proposes a modified ABC algorithm that benefits from a variety of search strategies to balance exploration and exploitation. Moreover, random key-based coding schemes are used to solve the p-center problem effectively. The proposed algorithm is compared to state-of-the-art techniques using different benchmark problems, and computational results reveal that the proposed approach is very efficient. PMID:24616648

Characterizing internet health information seeking strategies by socioeconomic status: a mixed methods approach.

PubMed

Perez, Susan L; Kravitz, Richard L; Bell, Robert A; Chan, Man Shan; Paterniti, Debora A

2016-08-09

The Internet is valuable for those with limited access to health care services because of its low cost and wealth of information. Our objectives were to investigate how the Internet is used to obtain health-related information and how individuals with differing socioeconomic resources navigate it when presented with a health decision. Study participants were recruited from public settings and social service agencies. Participants listened to one of two clinical scenarios - consistent with influenza or bacterial meningitis - and then conducted an Internet search. Screen-capture video software captured the Internet search. Participant Internet search strategies were analyzed and coded for pre- and post-Internet search guess at diagnosis and information seeking patterns. Individuals who did not have a college degree and were recruited from locations offering social services were categorized as "lower socioeconomic status" (SES); the remainder was categorized as "higher SES." Participants were 78 Internet health information seekers, ranging from 21-35 years of age, who experienced barriers to accessing health care services. Lower-SES individuals were more likely to use an intuitive, rather than deliberative, approach to Internet health information seeking. Lower- and higher-SES participants did not differ in the tendency to make diagnostic guesses based on Internet searches. Lower-SES participants were more likely than their higher-SES counterparts to narrow the scope of their search. Our findings suggest that individuals with different levels of socioeconomic status vary in the heuristics and search patterns they rely upon to direct their searches. The influence and use of credible information in the process of making a decision is associated with education and prior experiences with healthcare services. Those with limited resources may be disadvantaged when turning to the Internet to make a health decision.

A systematic review of validated methods for identifying transfusion-related ABO incompatibility reactions using administrative and claims data.

PubMed

Carnahan, Ryan M; Kee, Vicki R

2012-01-01

This paper aimed to systematically review algorithms to identify transfusion-related ABO incompatibility reactions in administrative data, with a focus on studies that have examined the validity of the algorithms. A literature search was conducted using PubMed, Iowa Drug Information Service database, and Embase. A Google Scholar search was also conducted because of the difficulty identifying relevant studies. Reviews were conducted by two investigators to identify studies using data sources from the USA or Canada because these data sources were most likely to reflect the coding practices of Mini-Sentinel data sources. One study was found that validated International Classification of Diseases (ICD-9-CM) codes representing transfusion reactions. None of these cases were ABO incompatibility reactions. Several studies consistently used ICD-9-CM code 999.6, which represents ABO incompatibility reactions, and a technical report identified the ICD-10 code for these reactions. One study included the E-code E8760 for mismatched blood in transfusion in the algorithm. Another study reported finding no ABO incompatibility reaction codes in the Healthcare Cost and Utilization Project Nationwide Inpatient Sample database, which contains data of 2.23 million patients who received transfusions, raising questions about the sensitivity of administrative data for identifying such reactions. Two studies reported perfect specificity, with sensitivity ranging from 21% to 83%, for the code identifying allogeneic red blood cell transfusions in hospitalized patients. There is no information to assess the validity of algorithms to identify transfusion-related ABO incompatibility reactions. Further information on the validity of algorithms to identify transfusions would also be useful. Copyright © 2012 John Wiley & Sons, Ltd.

The search for person-related information in general practice: a qualitative study.

PubMed

Schrans, Diego; Avonts, Dirk; Christiaens, Thierry; Willems, Sara; de Smet, Kaat; van Boven, Kees; Boeckxstaens, Pauline; Kühlein, Thomas

2016-02-01

General practice is person-focused. Contextual information influences the clinical decision-making process in primary care. Currently, person-related information (PeRI) is neither recorded in a systematic way nor coded in the electronic medical record (EMR), and therefore not usable for scientific use. To search for classes of PeRI influencing the process of care. GPs, from nine countries worldwide, were asked to write down narrative case histories where personal factors played a role in decision-making. In an inductive process, the case histories were consecutively coded according to classes of PeRI. The classes found were deductively applied to the following cases and refined, until saturation was reached. Then, the classes were grouped into code-families and further clustered into domains. The inductive analysis of 32 case histories resulted in 33 defined PeRI codes, classifying all personal-related information in the cases. The 33 codes were grouped in the following seven mutually exclusive code-families: 'aspects between patient and formal care provider', 'social environment and family', 'functioning/behaviour', 'life history/non-medical experiences', 'personal medical information', 'socio-demographics' and 'work-/employment-related information'. The code-families were clustered into four domains: 'social environment and extended family', 'medicine', 'individual' and 'work and employment'. As PeRI is used in the process of decision-making, it should be part of the EMR. The PeRI classes we identified might form the basis of a new contextual classification mainly for research purposes. This might help to create evidence of the person-centredness of general practice. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Database extraction strategies for low-template evidence.

PubMed

Bleka, Øyvind; Dørum, Guro; Haned, Hinda; Gill, Peter

2014-03-01

Often in forensic cases, the profile of at least one of the contributors to a DNA evidence sample is unknown and a database search is needed to discover possible perpetrators. In this article we consider two types of search strategies to extract suspects from a database using methods based on probability arguments. The performance of the proposed match scores is demonstrated by carrying out a study of each match score relative to the level of allele drop-out in the crime sample, simulating low-template DNA. The efficiency was measured by random man simulation and we compared the performance using the SGM Plus kit and the ESX 17 kit for the Norwegian population, demonstrating that the latter has greatly enhanced power to discover perpetrators of crime in large national DNA databases. The code for the database extraction strategies will be prepared for release in the R-package forensim. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

The (De-)evolution of Evolution Games: A Content Analysis of the Representation of Evolution Through Natural Selection in Digital Games

NASA Astrophysics Data System (ADS)

Leith, Alex P.; Ratan, Rabindra A.; Wohn, Donghee Yvette

2016-08-01

Given the diversity and complexity of education game mechanisms and topics, this article contributes to a theoretical understanding of how game mechanisms "map" to educational topics through inquiry-based learning. Namely, the article examines the presence of evolution through natural selection (ENS) in digital games. ENS is a fundamentally important and widely misunderstood theory. This analysis of ENS portrayal in digital games provides insight into the use of games in teaching ENS. Systematic database search results were coded for the three principles of ENS: phenotypic variation, differential fitness, and fitness heritability. Though thousands of games use the term evolution, few presented elements of evolution, and even fewer contained all principles of ENS. Games developed to specifically teach evolution were difficult to find through Web searches. These overall deficiencies in ENS games reflect the inherent incompatibility between game control elements and the automatic process of ENS.

Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods.

PubMed

Brandt, C; Nadkarni, P

2001-01-01

The Web is increasingly the medium of choice for multi-user application program delivery. Yet selection of an appropriate programming environment for rapid prototyping, code portability, and maintainability remain issues. We summarize our experience on the conversion of a LISP Web application, Search/SR to a new, functionally identical application, Search/SR-ASP using a relational database and active server pages (ASP) technology. Our results indicate that provision of easy access to database engines and external objects is almost essential for a development environment to be considered viable for rapid and robust application delivery. While LISP itself is a robust language, its use in Web applications may be hard to justify given that current vendor implementations do not provide such functionality. Alternative, currently available scripting environments for Web development appear to have most of LISP's advantages and few of its disadvantages.

FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes

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

Borziak, Kirill; Jouline, Igor B

2007-01-01

Motivation: Sensory domains that are conserved among Bacteria, Archaea and Eucarya are important detectors of common signals detected by living cells. Due to their high sequence divergence, sensory domains are difficult to identify. We systematically look for novel sensory domains using sensitive profile-based searches initi-ated with regions of signal transduction proteins where no known domains can be identified by current domain models. Results: Using profile searches followed by multiple sequence alignment, structure prediction, and domain architecture analysis, we have identified a novel sensory domain termed FIST, which is present in signal transduction proteins from Bacteria, Archaea and Eucarya. Remote similaritymore » to a known ligand-binding fold and chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids.« less

Optimizing event selection with the random grid search

NASA Astrophysics Data System (ADS)

Bhat, Pushpalatha C.; Prosper, Harrison B.; Sekmen, Sezen; Stewart, Chip

2018-07-01

The random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector boson fusion events in the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.

Web-Based Environment for Maintaining Legacy Software

NASA Technical Reports Server (NTRS)

Tigges, Michael; Thompson, Nelson; Orr, Mark; Fox, Richard

2007-01-01

Advanced Tool Integration Environment (ATIE) is the name of both a software system and a Web-based environment created by the system for maintaining an archive of legacy software and expertise involved in developing the legacy software. ATIE can also be used in modifying legacy software and developing new software. The information that can be encapsulated in ATIE includes experts documentation, input and output data of tests cases, source code, and compilation scripts. All of this information is available within a common environment and retained in a database for ease of access and recovery by use of powerful search engines. ATIE also accommodates the embedment of supporting software that users require for their work, and even enables access to supporting commercial-off-the-shelf (COTS) software within the flow of the experts work. The flow of work can be captured by saving the sequence of computer programs that the expert uses. A user gains access to ATIE via a Web browser. A modern Web-based graphical user interface promotes efficiency in the retrieval, execution, and modification of legacy code. Thus, ATIE saves time and money in the support of new and pre-existing programs.

Population mixtures and searches of lensed and extended quasars across photometric surveys

NASA Astrophysics Data System (ADS)

Williams, Peter; Agnello, Adriano; Treu, Tommaso

2017-04-01

Wide-field photometric surveys enable searches of rare yet interesting objects, such as strongly lensed quasars or quasars with a bright host galaxy. Past searches for lensed quasars based on their optical and near-infrared properties have relied on photometric cuts and spectroscopic preselection (as in the Sloan Quasar Lens Search), or neural networks applied to photometric samples. These methods rely on cuts in morphology and colours, with the risk of losing many interesting objects due to scatter in their population properties, restrictive training sets, systematic uncertainties in catalogue-based magnitudes and survey-to-survey photometric variations. Here, we explore the performance of a Gaussian mixture model to separate point-like quasars, quasars with an extended host and strongly lensed quasars using griz psf and model magnitudes and WISE W1, W2. The choice of optical magnitudes is due to their presence in all current and upcoming releases of wide-field surveys, whereas UV information is not always available. We then assess the contamination from blue galaxies and the role of additional features such as W3 magnitudes or psf-model terms as morphological information. As a demonstration, we conduct a search in a random 10 per cent of the SDSS footprint, and provide the catalogue of the 43 SDSS object with the highest 'lens' score in our selection that survive visual inspection, and are spectroscopically confirmed to host active nuclei. We inspect archival data and find images of 5/43 objects in the Hubble Legacy Archive, including two known lenses. The code and materials are available to facilitate follow-up.

A nationwide register-based survey of baclofen toxicity.

PubMed

Kiel, Louise Bendix; Hoegberg, Lotte Christine Groth; Jansen, Tejs; Petersen, John Asger; Dalhoff, Kim Peder

2015-05-01

To study the use and misuse (poisonings) of baclofen in the time period of 2007-2012 and to evaluate the severity and clinical symptoms of poisonings including ingested baclofen. The National Patient Register (NPR) was searched for admissions due to baclofen poisonings from 2007 to 2012. The search was conducted with ICD-10 codes for poisoning, self-harm and suicide, and coupled with the baclofen ATC code. All enquiries about baclofen to the Danish Poison Information Centre (DPIC) in the same period were evaluated. Demographic and clinical data were extracted, and the poisonings were classified according to the Poison Severity Score. The number of baclofen poisonings did not increase from 2007 to 2012. Thirty-eight admissions with baclofen poisoning were registered at the NPR; however, only one-third of the reviewed DPIC cases were registered at the NPR with the correct coding. In the group of severely poisoned patients (PSS 3), three patients had only ingested baclofen (mean 2000 mg; SD 500 mg) and eight patients had ingested baclofen together with alcohol or psychotropic drugs (mean 900 mg; SD 641 mg). All patients presented with deep coma and respiratory depression. Additionally, seizures and cardiovascular events (mild hypo- or hypertension and bradycardia) occurred. There is a substantial degree of underreporting of baclofen poisonings in Denmark. Symptoms of baclofen poisoning progress very fast, and toxicity was observed even with doses as low as 150 mg. We therefore recommend that observation and treatment of these patients should be carried out in an intermediate- or intensive care unit. The most important treatment is the maintenance of a protected airway and respiration. © 2014 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).

Facebook Apps for Smoking Cessation: A Review of Content and Adherence to Evidence-Based Guidelines

PubMed Central

2014-01-01

Background Facebook is the most popular social network site, with over 1 billion users globally. There are millions of apps available within Facebook, many of which address health and health behavior change. Facebook may represent a promising channel to reach smokers with cessation interventions via apps. To date, there have been no published reports about Facebook apps for smoking cessation. Objective The purpose of this study was to review the features and functionality of Facebook apps for smoking cessation and to determine the extent to which they adhere to evidence-based guidelines for tobacco dependence treatment. Methods In August 2013, we searched Facebook and three top Internet search engines using smoking cessation keywords to identify relevant Facebook apps. Resultant apps were screened for eligibility (smoking cessation-related, English language, and functioning). Eligible apps were reviewed by 2 independent coders using a standardized coding scheme. Coding included content features (interactive, informational, and social) and adherence to an established 20-item index (possible score 0-40) derived from the US Public Health Service’s Clinical Practice Guidelines for Treating Tobacco Use and Dependence. Results We screened 22 apps for eligibility; of these, 12 underwent full coding. Only 9 apps were available on Facebook. Facebook apps fell into three broad categories: public pledge to quit (n=3), quit-date–based calculator/tracker (n=4), or a multicomponent quit smoking program (n=2). All apps incorporated interactive, informational, and social features except for two quit-date–based calculator/trackers apps (lacked informational component). All apps allowed app-related posting within Facebook (ie, on self/other Facebook profile), and four had a within-app “community” feature to enable app users to communicate with each other. Adherence index summary scores among Facebook apps were low overall (mean 15.1, SD 7.8, range 7-30), with multicomponent apps scoring the highest. Conclusions There are few smoking cessation apps available within Facebook. Among those available, adherence to cessation treatment guidelines was low. Smoking cessation interventions provided via the Facebook platform are a unique and as yet untapped treatment strategy that can harness existing social support and social networks for quitting. Research is needed to examine whether apps that adhere to clinical practice guidelines for tobacco dependence treatment are more effective in promoting cessation than those that do not. PMID:25205129

Facebook apps for smoking cessation: a review of content and adherence to evidence-based guidelines.

PubMed

Jacobs, Megan A; Cobb, Caroline O; Abroms, Lorien; Graham, Amanda L

2014-09-09

Facebook is the most popular social network site, with over 1 billion users globally. There are millions of apps available within Facebook, many of which address health and health behavior change. Facebook may represent a promising channel to reach smokers with cessation interventions via apps. To date, there have been no published reports about Facebook apps for smoking cessation. The purpose of this study was to review the features and functionality of Facebook apps for smoking cessation and to determine the extent to which they adhere to evidence-based guidelines for tobacco dependence treatment. In August 2013, we searched Facebook and three top Internet search engines using smoking cessation keywords to identify relevant Facebook apps. Resultant apps were screened for eligibility (smoking cessation-related, English language, and functioning). Eligible apps were reviewed by 2 independent coders using a standardized coding scheme. Coding included content features (interactive, informational, and social) and adherence to an established 20-item index (possible score 0-40) derived from the US Public Health Service's Clinical Practice Guidelines for Treating Tobacco Use and Dependence. We screened 22 apps for eligibility; of these, 12 underwent full coding. Only 9 apps were available on Facebook. Facebook apps fell into three broad categories: public pledge to quit (n=3), quit-date-based calculator/tracker (n=4), or a multicomponent quit smoking program (n=2). All apps incorporated interactive, informational, and social features except for two quit-date-based calculator/trackers apps (lacked informational component). All apps allowed app-related posting within Facebook (ie, on self/other Facebook profile), and four had a within-app "community" feature to enable app users to communicate with each other. Adherence index summary scores among Facebook apps were low overall (mean 15.1, SD 7.8, range 7-30), with multicomponent apps scoring the highest. There are few smoking cessation apps available within Facebook. Among those available, adherence to cessation treatment guidelines was low. Smoking cessation interventions provided via the Facebook platform are a unique and as yet untapped treatment strategy that can harness existing social support and social networks for quitting. Research is needed to examine whether apps that adhere to clinical practice guidelines for tobacco dependence treatment are more effective in promoting cessation than those that do not.

Microlensing observations rapid search for exoplanets: MORSE code for GPUs

NASA Astrophysics Data System (ADS)

McDougall, Alistair; Albrow, Michael D.

2016-02-01

The rapid analysis of ongoing gravitational microlensing events has been integral to the successful detection and characterization of cool planets orbiting low-mass stars in the Galaxy. In this paper, we present an implementation of search and fit techniques on graphical processing unit (GPU) hardware. The method allows for the rapid identification of candidate planetary microlensing events and their subsequent follow-up for detailed characterization.

Identifying patients with hypertension: a case for auditing electronic health record data.

PubMed

Baus, Adam; Hendryx, Michael; Pollard, Cecil

2012-01-01

Problems in the structure, consistency, and completeness of electronic health record data are barriers to outcomes research, quality improvement, and practice redesign. This nonexperimental retrospective study examines the utility of importing de-identified electronic health record data into an external system to identify patients with and at risk for essential hypertension. We find a statistically significant increase in cases based on combined use of diagnostic and free-text coding (mean = 1,256.1, 95% CI 1,232.3-1,279.7) compared to diagnostic coding alone (mean = 1,174.5, 95% CI 1,150.5-1,198.3). While it is not surprising that significantly more patients are identified when broadening search criteria, the implications are critical for quality of care, the movement toward the National Committee for Quality Assurance's Patient-Centered Medical Home program, and meaningful use of electronic health records. Further, we find a statistically significant increase in potential cases based on the last two or more blood pressure readings greater than or equal to 140/90 mm Hg (mean = 1,353.9, 95% CI 1,329.9-1,377.9).

Indoor high precision three-dimensional positioning system based on visible light communication using modified genetic algorithm

NASA Astrophysics Data System (ADS)

Chen, Hao; Guan, Weipeng; Li, Simin; Wu, Yuxiang

2018-04-01

To improve the precision of indoor positioning and actualize three-dimensional positioning, a reversed indoor positioning system based on visible light communication (VLC) using genetic algorithm (GA) is proposed. In order to solve the problem of interference between signal sources, CDMA modulation is used. Each light-emitting diode (LED) in the system broadcasts a unique identity (ID) code using CDMA modulation. Receiver receives mixed signal from every LED reference point, by the orthogonality of spreading code in CDMA modulation, ID information and intensity attenuation information from every LED can be obtained. According to positioning principle of received signal strength (RSS), the coordinate of the receiver can be determined. Due to system noise and imperfection of device utilized in the system, distance between receiver and transmitters will deviate from the real value resulting in positioning error. By introducing error correction factors to global parallel search of genetic algorithm, coordinates of the receiver in three-dimensional space can be determined precisely. Both simulation results and experimental results show that in practical application scenarios, the proposed positioning system can realize high precision positioning service.

Locating Biodiversity Data Through The Global Change Master Directory

NASA Technical Reports Server (NTRS)

Olsen, Lola M.

1998-01-01

The Global Change Master Directory (GCMD) presently holds descriptions for almost 7000 data sets held worldwide. The directory's primary purpose is for data discovery. The information provided through the GCMD's Directory Interchange Format (DIF) is the set of information that a researcher would need to determine if a particular data set could be of value. By offering data set descriptions worldwide in many scientific disciplines - including meteorology, oceanography, ecology, geology, hydrology, geophysics, remote sensing, paleoclimate, solar-terrestrial physics, and human dimensions of climate change - the GCMD simplifies the discovery of data sources. Direct linkages to many of the data sets are also provided. In addition, several data set registration tools are offered for populating the directory. To search the directory, one may choose the Guided Search or Free-Text Search. Two experimental interfaces were also made available with the latest software release - one based on a keyword search and another based on a graphical interface. The graphical interface was designed in collaboration with the Human Computer Interaction Laboratory at the University of Maryland. The latest version of the software, Version 6, was released in April, 1998. It features the implementation of a scheme to handle hierarchical data set collections (parent-child relationships); a hierarchical geospatial location search scheme; a Java-based geographic map for conducting geospatial searches; a Related-URL field for project-related data set collections, metadata extensions (such as more detailed inventory information), etc.; a new implementation of the Isite software; a new dataset language field; hyperlinked email addresses, and more. The key to the continued evolution of the GCMD is in the flexibility of the GCMD database, allowing modifications and additions to made relatively easily to maintain currency, thus providing the ability to capitalize on current technology while importing all existing records. Changes are discussed and approved through an online "interoperability" forum. The next major release of the GCMD is scheduled for early 1999 and will include the incorporation of a new matrix-based interface, a rapid valids-based query system; improvement in the operations facility - important for future distributed options; new streamlined code for greater performance and maintainability; improvements in the handling of seven current fields proposed through the interoperability forum (at no expense to the data providers); and the release of DOCmorph, a more robust version of DIFmorph to translate many 'standards' multi-directionally. Issues and actions will also be addressed.

A simple approach to improve recording of concerns about childmaltreatment in primary care records: developing a quality improvement intervention

PubMed Central

Woodman, Jenny; Allister, Janice; Rafi, Imran; de Lusignan, Simon; Belsey, Jonathan; Petersen, Irene; Gilbert, Ruth

2012-01-01

Background Information is lacking on how concerns about child maltreatment are recorded in primary care records. Aim To determine how the recording of child maltreatment concerns can be improved. Design and setting Development of a quality improvement intervention involving: clinical audit, a descriptive survey, telephone interviews, a workshop, database analyses, and consensus development in UK general practice. Method Descriptive analyses and incidence estimates were carried out based on 11 study practices and 442 practices in The Health Improvement Network (THIN). Telephone interviews, a workshop, and a consensus development meeting were conducted with lead GPs from 11 study practices. Results The rate of children with at least one maltreatment-related code was 8.4/1000 child years (11 study practices, 2009–2010), and 8.0/1000 child years (THIN, 2009–2010). Of 25 patients with known maltreatment, six had no maltreatment-related codes recorded, but all had relevant free text, scanned documents, or codes. When stating their reasons for undercoding maltreatment concerns, GPs cited damage to the patient relationship, uncertainty about which codes to use, and having concerns about recording information on other family members in the child’s records. Consensus recommendations are to record the code ‘child is cause for concern’ as a red flag whenever maltreatment is considered, and to use a list of codes arranged around four clinical concepts, with an option for a templated short data entry form. Conclusion GPs under-record maltreatment-related concerns in children’s electronic medical records. As failure to use codes makes it impossible to search or audit these cases, an approach designed to be simple and feasible to implement in UK general practice was recommended. PMID:22781996

Building a High Performance Metadata Broker using Clojure, NoSQL and Message Queues

NASA Astrophysics Data System (ADS)

Truslove, I.; Reed, S.

2013-12-01

In practice, Earth and Space Science Informatics often relies on getting more done with less: fewer hardware resources, less IT staff, fewer lines of code. As a capacity-building exercise focused on rapid development of high-performance geoinformatics software, the National Snow and Ice Data Center (NSIDC) built a prototype metadata brokering system using a new JVM language, modern database engines and virtualized or cloud computing resources. The metadata brokering system was developed with the overarching goals of (i) demonstrating a technically viable product with as little development effort as possible, (ii) using very new yet very popular tools and technologies in order to get the most value from the least legacy-encumbered code bases, and (iii) being a high-performance system by using scalable subcomponents, and implementation patterns typically used in web architectures. We implemented the system using the Clojure programming language (an interactive, dynamic, Lisp-like JVM language), Redis (a fast in-memory key-value store) as both the data store for original XML metadata content and as the provider for the message queueing service, and ElasticSearch for its search and indexing capabilities to generate search results. On evaluating the results of the prototyping process, we believe that the technical choices did in fact allow us to do more for less, due to the expressive nature of the Clojure programming language and its easy interoperability with Java libraries, and the successful reuse or re-application of high performance products or designs. This presentation will describe the architecture of the metadata brokering system, cover the tools and techniques used, and describe lessons learned, conclusions, and potential next steps.

Bilingual and Home Language Interventions With Young Dual Language Learners: A Research Synthesis.

PubMed

Durán, Lillian K; Hartzheim, Daphne; Lund, Emily M; Simonsmeier, Vicki; Kohlmeier, Theresa L

2016-10-01

The purpose of this systematic review was to determine what bilingual or home language interventions have been found to be effective for 2- to 6-year-old dual language learners who have language impairment (LI) or are at risk for LI. We conducted ancestral searches and searches of electronic databases, hand-searched article bibliographies, and searched 19 journals for experimental, quasiexperimental, or single-subject studies. The review yielded 26 studies that were coded for quality, frequency and duration of the intervention, number of participants, location of intervention, interventionist, language(s) of intervention, and reported or calculated effect sizes. Studies were grouped by those that focused specifically on at-risk populations and those that focused on children with LI. Emerging trends provide support for bilingual and/or home language interventions for both children with LI and those at risk for LI. There were relatively few studies that met inclusion criteria, and the average quality rating for a study was 6.8 out of 9.0 possible points. More high-quality research is needed, particularly with populations that speak languages other than Spanish. Clinicians need more evidence-based recommendations to improve the language and literacy outcomes of the diverse range of dual language learners served in the United States and abroad.

A master-slave parallel hybrid multi-objective evolutionary algorithm for groundwater remediation design under general hydrogeological conditions

NASA Astrophysics Data System (ADS)

Wu, J.; Yang, Y.; Luo, Q.; Wu, J.

2012-12-01

This study presents a new hybrid multi-objective evolutionary algorithm, the niched Pareto tabu search combined with a genetic algorithm (NPTSGA), whereby the global search ability of niched Pareto tabu search (NPTS) is improved by the diversification of candidate solutions arose from the evolving nondominated sorting genetic algorithm II (NSGA-II) population. Also, the NPTSGA coupled with the commonly used groundwater flow and transport codes, MODFLOW and MT3DMS, is developed for multi-objective optimal design of groundwater remediation systems. The proposed methodology is then applied to a large-scale field groundwater remediation system for cleanup of large trichloroethylene (TCE) plume at the Massachusetts Military Reservation (MMR) in Cape Cod, Massachusetts. Furthermore, a master-slave (MS) parallelization scheme based on the Message Passing Interface (MPI) is incorporated into the NPTSGA to implement objective function evaluations in distributed processor environment, which can greatly improve the efficiency of the NPTSGA in finding Pareto-optimal solutions to the real-world application. This study shows that the MS parallel NPTSGA in comparison with the original NPTS and NSGA-II can balance the tradeoff between diversity and optimality of solutions during the search process and is an efficient and effective tool for optimizing the multi-objective design of groundwater remediation systems under complicated hydrogeologic conditions.

Robust watermarking scheme for binary images using a slice-based large-cluster algorithm with a Hamming Code

NASA Astrophysics Data System (ADS)

Chen, Wen-Yuan; Liu, Chen-Chung

2006-01-01

The problems with binary watermarking schemes are that they have only a small amount of embeddable space and are not robust enough. We develop a slice-based large-cluster algorithm (SBLCA) to construct a robust watermarking scheme for binary images. In SBLCA, a small-amount cluster selection (SACS) strategy is used to search for a feasible slice in a large-cluster flappable-pixel decision (LCFPD) method, which is used to search for the best location for concealing a secret bit from a selected slice. This method has four major advantages over the others: (a) SBLCA has a simple and effective decision function to select appropriate concealment locations, (b) SBLCA utilizes a blind watermarking scheme without the original image in the watermark extracting process, (c) SBLCA uses slice-based shuffling capability to transfer the regular image into a hash state without remembering the state before shuffling, and finally, (d) SBLCA has enough embeddable space that every 64 pixels could accommodate a secret bit of the binary image. Furthermore, empirical results on test images reveal that our approach is a robust watermarking scheme for binary images.

An overview of Aboriginal health research in the social sciences: current trends and future directions.

PubMed

Wilson, Kathi; Young, T Kue

2008-06-01

To examine if Aboriginal health research conducted within the field of social sciences reflects the population and geographic diversity of the Aboriginal population. Review. We searched the Web of Science Social Science Citation Index, the Arts and Humanities Citation Index and Scholars Portal for the time period 1995-2005 using search terms to reflect different names used to refer to Canada's Aboriginal peoples. Citations that did not focus on health or Canada were eliminated. Each paper was coded according to 7 broad categories: Aboriginal identity group; geography; age; health status; health determinants; health services; and methods. Based on the 96 papers reviewed, the results show an under-representation of Métis and urban Aboriginal peoples. Most of the papers are on health status and non-medical determinants of health, with a particular focus on chronic conditions and life-style behaviours. Only 6 papers examined traditional approaches to healing and/or access to traditional healers/medicines. A small number involved the use of community-based research methods. Further research is required to address gaps in the current body of literature. Community-based research studies are necessary to address gaps that are most relevant to Aboriginal peoples.

Parallel algorithm for solving Kepler’s equation on Graphics Processing Units: Application to analysis of Doppler exoplanet searches

NASA Astrophysics Data System (ADS)

Ford, Eric B.

2009-05-01

We present the results of a highly parallel Kepler equation solver using the Graphics Processing Unit (GPU) on a commercial nVidia GeForce 280GTX and the "Compute Unified Device Architecture" (CUDA) programming environment. We apply this to evaluate a goodness-of-fit statistic (e.g., χ2) for Doppler observations of stars potentially harboring multiple planetary companions (assuming negligible planet-planet interactions). Given the high-dimensionality of the model parameter space (at least five dimensions per planet), a global search is extremely computationally demanding. We expect that the underlying Kepler solver and model evaluator will be combined with a wide variety of more sophisticated algorithms to provide efficient global search, parameter estimation, model comparison, and adaptive experimental design for radial velocity and/or astrometric planet searches. We tested multiple implementations using single precision, double precision, pairs of single precision, and mixed precision arithmetic. We find that the vast majority of computations can be performed using single precision arithmetic, with selective use of compensated summation for increased precision. However, standard single precision is not adequate for calculating the mean anomaly from the time of observation and orbital period when evaluating the goodness-of-fit for real planetary systems and observational data sets. Using all double precision, our GPU code outperforms a similar code using a modern CPU by a factor of over 60. Using mixed precision, our GPU code provides a speed-up factor of over 600, when evaluating nsys > 1024 models planetary systems each containing npl = 4 planets and assuming nobs = 256 observations of each system. We conclude that modern GPUs also offer a powerful tool for repeatedly evaluating Kepler's equation and a goodness-of-fit statistic for orbital models when presented with a large parameter space.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome.

PubMed

Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

2010-11-27

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome

PubMed Central

Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

2010-01-01

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs. PMID:21364831

Comparing NEO Search Telescopes

NASA Astrophysics Data System (ADS)

Myhrvold, Nathan

2016-04-01

Multiple terrestrial and space-based telescopes have been proposed for detecting and tracking near-Earth objects (NEOs). Detailed simulations of the search performance of these systems have used complex computer codes that are not widely available, which hinders accurate cross-comparison of the proposals and obscures whether they have consistent assumptions. Moreover, some proposed instruments would survey infrared (IR) bands, whereas others would operate in the visible band, and differences among asteroid thermal and visible-light models used in the simulations further complicate like-to-like comparisons. I use simple physical principles to estimate basic performance metrics for the ground-based Large Synoptic Survey Telescope and three space-based instruments—Sentinel, NEOCam, and a Cubesat constellation. The performance is measured against two different NEO distributions, the Bottke et al. distribution of general NEOs, and the Veres et al. distribution of Earth-impacting NEO. The results of the comparison show simplified relative performance metrics, including the expected number of NEOs visible in the search volumes and the initial detection rates expected for each system. Although these simplified comparisons do not capture all of the details, they give considerable insight into the physical factors limiting performance. Multiple asteroid thermal models are considered, including FRM, NEATM, and a new generalized form of FRM. I describe issues with how IR albedo and emissivity have been estimated in previous studies, which may render them inaccurate. A thermal model for tumbling asteroids is also developed and suggests that tumbling asteroids may be surprisingly difficult for IR telescopes to observe.

A new code for Galileo

NASA Technical Reports Server (NTRS)

Dolinar, S.

1988-01-01

Over the past six to eight years, an extensive research effort was conducted to investigate advanced coding techniques which promised to yield more coding gain than is available with current NASA standard codes. The delay in Galileo's launch due to the temporary suspension of the shuttle program provided the Galileo project with an opportunity to evaluate the possibility of including some version of the advanced codes as a mission enhancement option. A study was initiated last summer to determine if substantial coding gain was feasible for Galileo and, is so, to recommend a suitable experimental code for use as a switchable alternative to the current NASA-standard code. The Galileo experimental code study resulted in the selection of a code with constant length 15 and rate 1/4. The code parameters were chosen to optimize performance within cost and risk constraints consistent with retrofitting the new code into the existing Galileo system design and launch schedule. The particular code was recommended after a very limited search among good codes with the chosen parameters. It will theoretically yield about 1.5 dB enhancement under idealizing assumptions relative to the current NASA-standard code at Galileo's desired bit error rates. This ideal predicted gain includes enough cushion to meet the project's target of at least 1 dB enhancement under real, non-ideal conditions.

A Qualitative Analysis of the Navy’s HSI Billet Structure

DTIC Science & Technology

2008-06-01

of information is estimated to average 1 hour per response, including the time for reviewing instruction, searching existing data sources, gathering...and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other...subspecialty code. The research results support the hypothesis that the work requirements of the July 2007 data set of 4600P-coded billets (billets

Binary encoding of multiplexed images in mixed noise.

PubMed

Lalush, David S

2008-09-01

Binary coding of multiplexed signals and images has been studied in the context of spectroscopy with models of either purely constant or purely proportional noise, and has been shown to result in improved noise performance under certain conditions. We consider the case of mixed noise in an imaging system consisting of multiple individually-controllable sources (X-ray or near-infrared, for example) shining on a single detector. We develop a mathematical model for the noise in such a system and show that the noise is dependent on the properties of the binary coding matrix and on the average number of sources used for each code. Each binary matrix has a characteristic linear relationship between the ratio of proportional-to-constant noise and the noise level in the decoded image. We introduce a criterion for noise level, which is minimized via a genetic algorithm search. The search procedure results in the discovery of matrices that outperform the Hadamard S-matrices at certain levels of mixed noise. Simulation of a seven-source radiography system demonstrates that the noise model predicts trends and rank order of performance in regions of nonuniform images and in a simple tomosynthesis reconstruction. We conclude that the model developed provides a simple framework for analysis, discovery, and optimization of binary coding patterns used in multiplexed imaging systems.

References that anyone can edit: review of Wikipedia citations in peer reviewed health science literature.

PubMed

Bould, M Dylan; Hladkowicz, Emily S; Pigford, Ashlee-Ann E; Ufholz, Lee-Anne; Postonogova, Tatyana; Shin, Eunkyung; Boet, Sylvain

2014-03-06

To examine indexed health science journals to evaluate the prevalence of Wikipedia citations, identify the journals that publish articles with Wikipedia citations, and determine how Wikipedia is being cited. Bibliometric analysis. Publications in the English language that included citations to Wikipedia were retrieved using the online databases Scopus and Web of Science. To identify health science journals, results were refined using Ulrich's database, selecting for citations from journals indexed in Medline, PubMed, or Embase. Using Thomson Reuters Journal Citation Reports, 2011 impact factors were collected for all journals included in the search. Resulting citations were thematically coded, and descriptive statistics were calculated. 1433 full text articles from 1008 journals indexed in Medline, PubMed, or Embase with 2049 Wikipedia citations were accessed. The frequency of Wikipedia citations has increased over time; most citations occurred after December 2010. More than half of the citations were coded as definitions (n = 648; 31.6%) or descriptions (n=482; 23.5%). Citations were not limited to journals with a low or no impact factor; the search found Wikipedia citations in many journals with high impact factors. Many publications are citing information from a tertiary source that can be edited by anyone, although permanent, evidence based sources are available. We encourage journal editors and reviewers to use caution when publishing articles that cite Wikipedia.

Utilization of the Discrete Differential Evolution for Optimization in Multidimensional Point Clouds.

PubMed

Uher, Vojtěch; Gajdoš, Petr; Radecký, Michal; Snášel, Václav

2016-01-01

The Differential Evolution (DE) is a widely used bioinspired optimization algorithm developed by Storn and Price. It is popular for its simplicity and robustness. This algorithm was primarily designed for real-valued problems and continuous functions, but several modified versions optimizing both integer and discrete-valued problems have been developed. The discrete-coded DE has been mostly used for combinatorial problems in a set of enumerative variants. However, the DE has a great potential in the spatial data analysis and pattern recognition. This paper formulates the problem as a search of a combination of distinct vertices which meet the specified conditions. It proposes a novel approach called the Multidimensional Discrete Differential Evolution (MDDE) applying the principle of the discrete-coded DE in discrete point clouds (PCs). The paper examines the local searching abilities of the MDDE and its convergence to the global optimum in the PCs. The multidimensional discrete vertices cannot be simply ordered to get a convenient course of the discrete data, which is crucial for good convergence of a population. A novel mutation operator utilizing linear ordering of spatial data based on the space filling curves is introduced. The algorithm is tested on several spatial datasets and optimization problems. The experiments show that the MDDE is an efficient and fast method for discrete optimizations in the multidimensional point clouds.

Utilization of the Discrete Differential Evolution for Optimization in Multidimensional Point Clouds

PubMed Central

Radecký, Michal; Snášel, Václav

2016-01-01

The Differential Evolution (DE) is a widely used bioinspired optimization algorithm developed by Storn and Price. It is popular for its simplicity and robustness. This algorithm was primarily designed for real-valued problems and continuous functions, but several modified versions optimizing both integer and discrete-valued problems have been developed. The discrete-coded DE has been mostly used for combinatorial problems in a set of enumerative variants. However, the DE has a great potential in the spatial data analysis and pattern recognition. This paper formulates the problem as a search of a combination of distinct vertices which meet the specified conditions. It proposes a novel approach called the Multidimensional Discrete Differential Evolution (MDDE) applying the principle of the discrete-coded DE in discrete point clouds (PCs). The paper examines the local searching abilities of the MDDE and its convergence to the global optimum in the PCs. The multidimensional discrete vertices cannot be simply ordered to get a convenient course of the discrete data, which is crucial for good convergence of a population. A novel mutation operator utilizing linear ordering of spatial data based on the space filling curves is introduced. The algorithm is tested on several spatial datasets and optimization problems. The experiments show that the MDDE is an efficient and fast method for discrete optimizations in the multidimensional point clouds. PMID:27974884

Genebanks: a comparison of eight proposed international genetic databases.

PubMed

Austin, Melissa A; Harding, Sarah; McElroy, Courtney

2003-01-01

To identify and compare population-based genetic databases, or "genebanks", that have been proposed in eight international locations between 1998 and 2002. A genebank can be defined as a stored collection of genetic samples in the form of blood or tissue, that can be linked with medical and genealogical or lifestyle information from a specific population, gathered using a process of generalized consent. Genebanks were identified by searching Medline and internet search engines with key words such as "genetic database" and "biobank" and by reviewing literature on previously identified databases such as the deCode project. Collection of genebank characteristics was by an electronic and literature search, augmented by correspondence with informed individuals. The proposed genebanks are located in Iceland, the United Kingdom, Estonia, Latvia, Sweden, Singapore, the Kingdom of Tonga, and Quebec, Canada. Comparisons of the genebanks were based on the following criteria: genebank location and description of purpose, role of government, commercial involvement, consent and confidentiality procedures, opposition to the genebank, and current progress. All of the groups proposing the genebanks plan to search for susceptibility genes for complex diseases while attempting to improve public health and medical care in the region and, in some cases, stimulating the local economy through expansion of the biotechnology sector. While all of the identified plans share these purposes, they differ in many aspects, including funding, subject participation, and organization. The balance of government and commercial involvement in the development of each project varies. Genetic samples and health information will be collected from participants and coded in all of the genebanks, but consent procedures range from presumed consent of the entire eligible population to recruitment of volunteers with informed consent. Issues regarding confidentiality and consent have resulted in opposition to some of the more publicized projects. None of the proposed databases are currently operational and at least one project was terminated due to opposition. Ambitious genebank projects have been proposed in numerous countries and provinces. The characteristics of the projects vary, but all intend to map genes for common diseases and hope to improve the health of the populations involved. The impact of these projects on understanding genetic susceptibility to disease will be increasingly apparent if the projects become operational. The ethical, legal, and social implications of the projects should be carefully considered during their development. Copyright 2003 S. Karger AG, Basel

Maximum-likelihood soft-decision decoding of block codes using the A* algorithm

NASA Technical Reports Server (NTRS)

Ekroot, L.; Dolinar, S.

1994-01-01

The A* algorithm finds the path in a finite depth binary tree that optimizes a function. Here, it is applied to maximum-likelihood soft-decision decoding of block codes where the function optimized over the codewords is the likelihood function of the received sequence given each codeword. The algorithm considers codewords one bit at a time, making use of the most reliable received symbols first and pursuing only the partially expanded codewords that might be maximally likely. A version of the A* algorithm for maximum-likelihood decoding of block codes has been implemented for block codes up to 64 bits in length. The efficiency of this algorithm makes simulations of codes up to length 64 feasible. This article details the implementation currently in use, compares the decoding complexity with that of exhaustive search and Viterbi decoding algorithms, and presents performance curves obtained with this implementation of the A* algorithm for several codes.

Semantic representations in the temporal pole predict false memories

PubMed Central

Chadwick, Martin J.; Anjum, Raeesa S.; Kumaran, Dharshan; Schacter, Daniel L.; Spiers, Hugo J.; Hassabis, Demis

2016-01-01

Recent advances in neuroscience have given us unprecedented insight into the neural mechanisms of false memory, showing that artificial memories can be inserted into the memory cells of the hippocampus in a way that is indistinguishable from true memories. However, this alone is not enough to explain how false memories can arise naturally in the course of our daily lives. Cognitive psychology has demonstrated that many instances of false memory, both in the laboratory and the real world, can be attributed to semantic interference. Whereas previous studies have found that a diverse set of regions show some involvement in semantic false memory, none have revealed the nature of the semantic representations underpinning the phenomenon. Here we use fMRI with representational similarity analysis to search for a neural code consistent with semantic false memory. We find clear evidence that false memories emerge from a similarity-based neural code in the temporal pole, a region that has been called the “semantic hub” of the brain. We further show that each individual has a partially unique semantic code within the temporal pole, and this unique code can predict idiosyncratic patterns of memory errors. Finally, we show that the same neural code can also predict variation in true-memory performance, consistent with an adaptive perspective on false memory. Taken together, our findings reveal the underlying structure of neural representations of semantic knowledge, and how this semantic structure can both enhance and distort our memories. PMID:27551087

Toward Optimal Manifold Hashing via Discrete Locally Linear Embedding.

PubMed

Rongrong Ji; Hong Liu; Liujuan Cao; Di Liu; Yongjian Wu; Feiyue Huang

2017-11-01

Binary code learning, also known as hashing, has received increasing attention in large-scale visual search. By transforming high-dimensional features to binary codes, the original Euclidean distance is approximated via Hamming distance. More recently, it is advocated that it is the manifold distance, rather than the Euclidean distance, that should be preserved in the Hamming space. However, it retains as an open problem to directly preserve the manifold structure by hashing. In particular, it first needs to build the local linear embedding in the original feature space, and then quantize such embedding to binary codes. Such a two-step coding is problematic and less optimized. Besides, the off-line learning is extremely time and memory consuming, which needs to calculate the similarity matrix of the original data. In this paper, we propose a novel hashing algorithm, termed discrete locality linear embedding hashing (DLLH), which well addresses the above challenges. The DLLH directly reconstructs the manifold structure in the Hamming space, which learns optimal hash codes to maintain the local linear relationship of data points. To learn discrete locally linear embeddingcodes, we further propose a discrete optimization algorithm with an iterative parameters updating scheme. Moreover, an anchor-based acceleration scheme, termed Anchor-DLLH, is further introduced, which approximates the large similarity matrix by the product of two low-rank matrices. Experimental results on three widely used benchmark data sets, i.e., CIFAR10, NUS-WIDE, and YouTube Face, have shown superior performance of the proposed DLLH over the state-of-the-art approaches.

Semantic representations in the temporal pole predict false memories.

PubMed

Chadwick, Martin J; Anjum, Raeesa S; Kumaran, Dharshan; Schacter, Daniel L; Spiers, Hugo J; Hassabis, Demis

2016-09-06

Recent advances in neuroscience have given us unprecedented insight into the neural mechanisms of false memory, showing that artificial memories can be inserted into the memory cells of the hippocampus in a way that is indistinguishable from true memories. However, this alone is not enough to explain how false memories can arise naturally in the course of our daily lives. Cognitive psychology has demonstrated that many instances of false memory, both in the laboratory and the real world, can be attributed to semantic interference. Whereas previous studies have found that a diverse set of regions show some involvement in semantic false memory, none have revealed the nature of the semantic representations underpinning the phenomenon. Here we use fMRI with representational similarity analysis to search for a neural code consistent with semantic false memory. We find clear evidence that false memories emerge from a similarity-based neural code in the temporal pole, a region that has been called the "semantic hub" of the brain. We further show that each individual has a partially unique semantic code within the temporal pole, and this unique code can predict idiosyncratic patterns of memory errors. Finally, we show that the same neural code can also predict variation in true-memory performance, consistent with an adaptive perspective on false memory. Taken together, our findings reveal the underlying structure of neural representations of semantic knowledge, and how this semantic structure can both enhance and distort our memories.

The NCEP Mission

Science.gov Websites

code. Press enter or select the go button to submit request Local forecast by "City, St" City , St Go Search NCEP Go Current Hazards Watches/Warnings Outlooks National Current Conditions

Content Analysis of Virtual Reference Data: Reshaping Library Website Design.

PubMed

Fan, Suhua Caroline; Welch, Jennifer M

2016-01-01

An academic health sciences library wanted to redesign its website to provide better access to health information in the community. Virtual reference data were used to provide information about user searching behavior. This study analyzed three years (2012-2014) of virtual reference data, including e-mail questions, text messaging, and live chat transcripts, to evaluate the library website for redesigning, especially in areas such as the home page, patrons' terminology, and issues prompting patrons to ask for help. A coding system based on information links in the current library website was created to analyze the data.

Annotare—a tool for annotating high-throughput biomedical investigations and resulting data

PubMed Central

Shankar, Ravi; Parkinson, Helen; Burdett, Tony; Hastings, Emma; Liu, Junmin; Miller, Michael; Srinivasa, Rashmi; White, Joseph; Brazma, Alvis; Sherlock, Gavin; Stoeckert, Christian J.; Ball, Catherine A.

2010-01-01

Summary: Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis. Availability and Implementation: Annotare is available from http://code.google.com/p/annotare/ under the terms of the open-source MIT License (http://www.opensource.org/licenses/mit-license.php). It has been tested on both Mac and Windows. Contact: rshankar@stanford.edu PMID:20733062

Care management and nursing governance in a maternity ward: grounded theory.

PubMed

Copelli, Fernanda Hannah da Silva; Oliveira, Roberta Juliane Tono de; Santos, José Luís Guedes Dos; Magalhães, Aline Lima Pestana; Gregório, Vitória Regina Petters; Erdmann, Alacoque Lorenzini

2017-01-01

To understand the care management strategies used by nurses in the governance of nursing practice in a maternity ward. Qualitative study based on grounded theory conducted with 27 participants, partitioned into four sample groups. The data were collected through semi-structured interviews and analyzed through open, axial, and selective coding. The care management strategies used by the nurses were: planning professional practice, leading the nursing team, search for scientific knowledge, and training inthe best practices in obstetric care. Associating care management with nursing governance can foster better care outcomes and strengthen nursing autonomy when coordinating nursing work in maternity wards.

A Bell-Curved Based Algorithm for Mixed Continuous and Discrete Structural Optimization

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.; Weber, Michael; Sobieszczanski-Sobieski, Jaroslaw

2001-01-01

An evolutionary based strategy utilizing two normal distributions to generate children is developed to solve mixed integer nonlinear programming problems. This Bell-Curve Based (BCB) evolutionary algorithm is similar in spirit to (mu + mu) evolutionary strategies and evolutionary programs but with fewer parameters to adjust and no mechanism for self adaptation. First, a new version of BCB to solve purely discrete optimization problems is described and its performance tested against a tabu search code for an actuator placement problem. Next, the performance of a combined version of discrete and continuous BCB is tested on 2-dimensional shape problems and on a minimum weight hub design problem. In the latter case the discrete portion is the choice of the underlying beam shape (I, triangular, circular, rectangular, or U).

Formal specification and verification of Ada software

NASA Technical Reports Server (NTRS)

Hird, Geoffrey R.

1991-01-01

The use of formal methods in software development achieves levels of quality assurance unobtainable by other means. The Larch approach to specification is described, and the specification of avionics software designed to implement the logic of a flight control system is given as an example. Penelope is described which is an Ada-verification environment. The Penelope user inputs mathematical definitions, Larch-style specifications and Ada code and performs machine-assisted proofs that the code obeys its specifications. As an example, the verification of a binary search function is considered. Emphasis is given to techniques assisting the reuse of a verification effort on modified code.

Inhibition of Pancreatic Cancer Cell Proliferation by LRH-1 Inhibitors

DTIC Science & Technology

2014-12-01

coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org [ PDB ID codes 4QJR (SF-1/PIP3) and 4QK4 (SF-1/PIP2)]. 1To whom...with Rfree/Rcryst values of 23/19% (Table S2). The structure was deposited with the PDB ID code 4QJR. SF 1/PIP3 (Fig. 1C) adopts the classic NR LBD...PIP2) was solved by molecular replacement, using PDB ID code 1YOW as the search model, and compared with the SF 1/PIP3 structure (Table S2). The

Efficient biprediction decision scheme for fast high efficiency video coding encoding

NASA Astrophysics Data System (ADS)

Park, Sang-hyo; Lee, Seung-ho; Jang, Euee S.; Jun, Dongsan; Kang, Jung-Won

2016-11-01

An efficient biprediction decision scheme of high efficiency video coding (HEVC) is proposed for fast-encoding applications. For low-delay video applications, bidirectional prediction can be used to increase compression performance efficiently with previous reference frames. However, at the same time, the computational complexity of the HEVC encoder is significantly increased due to the additional biprediction search. Although a some research has attempted to reduce this complexity, whether the prediction is strongly related to both motion complexity and prediction modes in a coding unit has not yet been investigated. A method that avoids most compression-inefficient search points is proposed so that the computational complexity of the motion estimation process can be dramatically decreased. To determine if biprediction is critical, the proposed method exploits the stochastic correlation of the context of prediction units (PUs): the direction of a PU and the accuracy of a motion vector. Through experimental results, the proposed method showed that the time complexity of biprediction can be reduced to 30% on average, outperforming existing methods in view of encoding time, number of function calls, and memory access.

The Breakthrough Listen Search for Intelligent Life: Data Calibration using Pulsars

NASA Astrophysics Data System (ADS)

Brinkman-Traverse, Casey Lynn; Gajjar, Vishal; BSRC

2018-01-01

The ability to distinguish ET signals requires a deep understanding of the radio telescopes with which we search; therefore, before we observe stars of interest, the Breathrough Listen scientists at Berkeley SETI Research Center first observe a Pulsar with well-documented flux and polarization properties. The process of calibrating the flux and polarization is a lengthy process by hand, so we produced a pipeline code that will automatically calibrate the pulsar in under an hour. Using PSRCHIVE the code coherently dedisperses the pulsed radio signals, and then calibrates the flux using observation files with a noise diode turning on and off. The code was developed using PSR B1937+ 21 and is primarily used on PSR B0329+54. This will expedite the process of assessing the quality of data collected from the Green Bank Telescope in West Virginia and will allow us to more efficiently find life beyond Planet Earth. Additionally, the stability of the B0329+54 calibration data will allow us to analyze data taken on FRB's with confidence of its cosmic origin.

Optimizing event selection with the random grid search

DOE PAGES

Bhat, Pushpalatha C.; Prosper, Harrison B.; Sekmen, Sezen; ...

2018-02-27

In this paper, the random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector bosonmore » fusion events in the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.« less

Optimizing Event Selection with the Random Grid Search

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

Bhat, Pushpalatha C.; Prosper, Harrison B.; Sekmen, Sezen

2017-06-29

The random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector boson fusion events inmore » the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.« less

Optimizing event selection with the random grid search

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

Bhat, Pushpalatha C.; Prosper, Harrison B.; Sekmen, Sezen

In this paper, the random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector bosonmore » fusion events in the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.« less

Generalized serial search code acquisition - The equivalent circular state diagram approach

NASA Technical Reports Server (NTRS)

Polydoros, A.; Simon, M. K.

1984-01-01

A transform-domain method for deriving the generating function of the acquisition process resulting from an arbitrary serial search strategy is presented. The method relies on equivalent circular state diagrams, uses Mason's formula from flow-graph theory, and employs a minimum number of required parameters. The transform-domain approach is briefly described and the concept of equivalent circular state diagrams is introduced and exploited to derive the generating function and resulting mean acquisition time for three particular cases of interest, the continuous/center Z search, the broken/center Z search, and the expanding window search. An optimization of the latter technique is performed whereby the number of partial windows which minimizes the mean acquisition time is determined. The numerical results satisfy certain intuitive predictions and provide useful design guidelines for such systems.

A Search for Kilonovae in the Dark Energy Survey

DOE PAGES

Doctor, Z.; Kessler, R.; Chen, H. Y.; ...

2017-03-01

The coalescence of a binary neutron star pair is expected to produce gravitational waves (GW) and electromagnetic radiation, both of which may be detectable with currently available instruments. In this paper, we describe a search for a predicted r-process optical transient from these mergers, dubbed the “kilonova” (KN), using griz broadband data from the Dark Energy Survey Supernova Program (DES-SN). Some models predict KNe to be redder, shorter-lived, and dimmer than supernovae (SNe), but the event rate of KNe is poorly constrained. We simulate KN and SN light curves with the Monte-Carlo simulation code SNANA to optimize selection requirements, determine search efficiency, and predict SN backgrounds. Our analysis of the first two seasons of DES-SN data results in 0 events, and is consistent with our prediction of 1.1 ± 0.2 background events based on simulations of SNe. From our prediction, there is a 33% chance of finding 0 events in the data. Assuming no underlying galaxy flux, our search sets 90% upper limits on the KN volumetric rate of 1.0 x 10more » $$^{7}$$ Gpc $-$3 yr $-$1 for the dimmest KN model we consider (peak i-band absolute magnitude $${M}_{i}=-11.4$$ mag) and 2.4x 10$$^{4}$$ Gpc $-$3 yr $-$1 for the brightest ($${M}_{i}=-16.2$$ mag). Accounting for anomalous subtraction artifacts on bright galaxies, these limits are ~3 times higher. This analysis is the first untriggered optical KN search and informs selection requirements and strategies for future KN searches. Finally, our upper limits on the KN rate are consistent with those measured by GW and gamma-ray burst searches.« less

A Search for Kilonovae in the Dark Energy Survey

NASA Astrophysics Data System (ADS)

Doctor, Z.; Kessler, R.; Chen, H. Y.; Farr, B.; Finley, D. A.; Foley, R. J.; Goldstein, D. A.; Holz, D. E.; Kim, A. G.; Morganson, E.; Sako, M.; Scolnic, D.; Smith, M.; Soares-Santos, M.; Spinka, H.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Bechtol, K.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Drlica-Wagner, A.; Eifler, T. F.; Frieman, J.; García-Bellido, J.; Gaztanaga, E.; Gerdes, D. W.; Gruendl, R. A.; Gschwend, J.; Gutierrez, G.; James, D. J.; Krause, E.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; Maia, M. A. G.; March, M.; Marshall, J. L.; Menanteau, F.; Miquel, R.; Neilsen, E.; Nichol, R. C.; Nord, B.; Plazas, A. A.; Romer, A. K.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Walker, A. R.; Wester, W.; DES Collaboration

2017-03-01

The coalescence of a binary neutron star pair is expected to produce gravitational waves (GW) and electromagnetic radiation, both of which may be detectable with currently available instruments. We describe a search for a predicted r-process optical transient from these mergers, dubbed the “kilonova” (KN), using griz broadband data from the Dark Energy Survey Supernova Program (DES-SN). Some models predict KNe to be redder, shorter-lived, and dimmer than supernovae (SNe), but the event rate of KNe is poorly constrained. We simulate KN and SN light curves with the Monte-Carlo simulation code SNANA to optimize selection requirements, determine search efficiency, and predict SN backgrounds. Our analysis of the first two seasons of DES-SN data results in 0 events, and is consistent with our prediction of 1.1 ± 0.2 background events based on simulations of SNe. From our prediction, there is a 33% chance of finding 0 events in the data. Assuming no underlying galaxy flux, our search sets 90% upper limits on the KN volumetric rate of 1.0 × {10}7 Gpc-3 yr-1 for the dimmest KN model we consider (peak I-band absolute magnitude {M}I=-11.4 mag) and 2.4 × {10}4 Gpc-3 yr-1 for the brightest ({M}I=-16.2 mag). Accounting for anomalous subtraction artifacts on bright galaxies, these limits are ˜3 times higher. This analysis is the first untriggered optical KN search and informs selection requirements and strategies for future KN searches. Our upper limits on the KN rate are consistent with those measured by GW and gamma-ray burst searches.

Determination of in vivo regulation kinetics of small non-coding RNA in bacteria

NASA Astrophysics Data System (ADS)

Fei, Jingyi

Small RNAs (sRNAs) play important roles in regulating gene expression through a variety of mechanisms. As one of the most common strategies, sRNA induced target messenger RNA (mRNA) includes two major steps: target search by base-pairing interactions with the and downstream execution by modulating translation or the stability of the mRNA. Here we describe a new imaging and analysis platform based on super-resolution fluorescence microscopy, which enabled the first in vivo kinetic measurement of sRNA-mediated gene regulation. Specifically, this platform was used to investigate a sugar-phosphate stress-induced bacterial sRNA that induces the degradation of target mRNAs. The data reveal that the sRNA binds to a primary target mRNA in a reversible and dynamic fashion, and that formation of the sRNA-mRNA complexes is the rate-limiting step, dictating the overall efficiency of regulation in vivo; whereas the downstream co-degradation of sRNA-mRNA complex can kinetically compete with the fast complex disassembly. Examination of a secondary target of this sRNA indicated that differences in the target search kinetics contribute to setting the regulation priority among different target mRNAs. This super-resolution imaging and analysis approach provides a conceptual framework that can be generalized to other sRNA systems and other target search processes.

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

PubMed Central

Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny

2015-01-01

Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular—no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site. PMID:25940619

National Centers for Environmental Prediction

Science.gov Websites

code. Press enter or select the go button to submit request Local forecast by "City, St" City , St Go Search NCEP Go Current Hazards Watches/Warnings Outlooks National Current Conditions

PEGASUS 5: An Automated Pre-Processor for Overset-Grid CFD

NASA Technical Reports Server (NTRS)

Suhs, Norman E.; Rogers, Stuart E.; Dietz, William E.; Kwak, Dochan (Technical Monitor)

2002-01-01

An all new, automated version of the PEGASUS software has been developed and tested. PEGASUS provides the hole-cutting and connectivity information between overlapping grids, and is used as the final part of the grid generation process for overset-grid computational fluid dynamics approaches. The new PEGASUS code (Version 5) has many new features: automated hole cutting; a projection scheme for fixing gaps in overset surfaces; more efficient interpolation search methods using an alternating digital tree; hole-size optimization based on adding additional layers of fringe points; and an automatic restart capability. The new code has also been parallelized using the Message Passing Interface standard. The parallelization performance provides efficient speed-up of the execution time by an order of magnitude, and up to a factor of 30 for very large problems. The results of three example cases are presented: a three-element high-lift airfoil, a generic business jet configuration, and a complete Boeing 777-200 aircraft in a high-lift landing configuration. Comparisons of the computed flow fields for the airfoil and 777 test cases between the old and new versions of the PEGASUS codes show excellent agreement with each other and with experimental results.

Comprehensive Reconstruction and Visualization of Non-Coding Regulatory Networks in Human

PubMed Central

Bonnici, Vincenzo; Russo, Francesco; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba

2014-01-01

Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape. PMID:25540777

Metabolic basis for the self-referential genetic code.

PubMed

Guimarães, Romeu Cardoso

2011-08-01

An investigation of the biosynthesis pathways producing glycine and serine was necessary to clarify an apparent inconsistency between the self-referential model (SRM) for the formation of the genetic code and the model of coevolution of encodings and of amino acid biosynthesis routes. According to the SRM proposal, glycine was the first amino acid encoded, followed by serine. The coevolution model does not state precisely which the first encodings were, only presenting a list of about ten early assignments including the derivation of glycine from serine-this being derived from the glycolysis intermediate glycerate, which reverses the order proposed by the self-referential model. Our search identified the glycine-serine pathway of syntheses based on one-carbon sources, involving activities of the glycine decarboxylase complex and its associated serine hydroxymethyltransferase, which is consistent with the order proposed by the self-referential model and supports its rationale for the origin of the genetic code: protein synthesis was developed inside an early metabolic system, serving the function of a sink of amino acids; the first peptides were glycine-rich and fit for the function of building the early ribonucleoproteins; glycine consumption in proteins drove the fixation of the glycine-serine pathway.

Comprehensive reconstruction and visualization of non-coding regulatory networks in human.

PubMed

Bonnici, Vincenzo; Russo, Francesco; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba

2014-01-01

Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape.

DFT Performance Prediction in FFTW

NASA Astrophysics Data System (ADS)

Gu, Liang; Li, Xiaoming

Fastest Fourier Transform in the West (FFTW) is an adaptive FFT library that generates highly efficient Discrete Fourier Transform (DFT) implementations. It is one of the fastest FFT libraries available and it outperforms many adaptive or hand-tuned DFT libraries. Its success largely relies on the huge search space spanned by several FFT algorithms and a set of compiler generated C code (called codelets) for small size DFTs. FFTW empirically finds the best algorithm by measuring the performance of different algorithm combinations. Although the empirical search works very well for FFTW, the search process does not explain why the best plan found performs best, and the search overhead grows polynomially as the DFT size increases. The opposite of empirical search is model-driven optimization. However, it is widely believed that model-driven optimization is inferior to empirical search and is particularly powerless to solve problems as complex as the optimization of DFT.

Quality of Web-based Information for the 10 Most Common Fractures.

PubMed

Memon, Muzammil; Ginsberg, Lydia; Simunovic, Nicole; Ristevski, Bill; Bhandari, Mohit; Kleinlugtenbelt, Ydo Vincent

2016-06-17

In today's technologically advanced world, 75% of patients have used Google to search for health information. As a result, health care professionals fear that patients may be misinformed. Currently, there is a paucity of data on the quality and readability of Web-based health information on fractures. In this study, we assessed the quality and readability of Web-based health information related to the 10 most common fractures. Using the Google search engine, we assessed websites from the first results page for the 10 most common fractures using lay search terms. Website quality was measured using the DISCERN instrument, which scores websites as very poor (15-22.5), poor (22.5-37.5), fair (37.5-52.5), good (52.5-67.5), or excellent (67.5-75). The presence of Health on the Net code (HONcode) certification was assessed for all websites. Website readability was measured using the Flesch Reading Ease Score (0-100), where 60-69 is ideal for the general public, and the Flesch-Kincaid Grade Level (FKGL; -3.4 to ∞), where the mean FKGL of the US adult population is 8. Overall, website quality was "fair" for all fractures, with a mean (standard deviation) DISCERN score of 50.3 (5.8). The DISCERN score correlated positively with a higher website position on the search results page (r(2)=0.1, P=.002) and with HONcode certification (P=.007). The mean (standard deviation) Flesch Reading Ease Score and FKGL for all fractures were 62.2 (9.1) and 6.7 (1.6), respectively. The quality of Web-based health information on fracture care is fair, and its readability is appropriate for the general public. To obtain higher quality information, patients should select HONcode-certified websites. Furthermore, patients should select websites that are positioned higher on the results page because the Google ranking algorithms appear to rank the websites by quality.

Quality of Web-based Information for the 10 Most Common Fractures

PubMed Central

Ginsberg, Lydia; Simunovic, Nicole; Ristevski, Bill; Bhandari, Mohit; Kleinlugtenbelt, Ydo Vincent

2016-01-01

Background In today's technologically advanced world, 75% of patients have used Google to search for health information. As a result, health care professionals fear that patients may be misinformed. Currently, there is a paucity of data on the quality and readability of Web-based health information on fractures. Objectives In this study, we assessed the quality and readability of Web-based health information related to the 10 most common fractures. Methods Using the Google search engine, we assessed websites from the first results page for the 10 most common fractures using lay search terms. Website quality was measured using the DISCERN instrument, which scores websites as very poor (15-22.5), poor (22.5-37.5), fair (37.5-52.5), good (52.5-67.5), or excellent (67.5-75). The presence of Health on the Net code (HONcode) certification was assessed for all websites. Website readability was measured using the Flesch Reading Ease Score (0-100), where 60-69 is ideal for the general public, and the Flesch-Kincaid Grade Level (FKGL; −3.4 to ∞), where the mean FKGL of the US adult population is 8. Results Overall, website quality was “fair” for all fractures, with a mean (standard deviation) DISCERN score of 50.3 (5.8). The DISCERN score correlated positively with a higher website position on the search results page (r2=0.1, P=.002) and with HONcode certification (P=.007). The mean (standard deviation) Flesch Reading Ease Score and FKGL for all fractures were 62.2 (9.1) and 6.7 (1.6), respectively. Conclusion The quality of Web-based health information on fracture care is fair, and its readability is appropriate for the general public. To obtain higher quality information, patients should select HONcode-certified websites. Furthermore, patients should select websites that are positioned higher on the results page because the Google ranking algorithms appear to rank the websites by quality. PMID:27317159

High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network.

PubMed

Maleki, Ehsan; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra

2017-07-01

This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the basic local alignment search tool.

Drupal as the platform of choice for the Skolr digital meeting poster service

NASA Astrophysics Data System (ADS)

Caron, B. R.

2011-12-01

In the Winter of 2011, a small team received funding from the Alfred P. Sloan Foundation to build a pilot digital science meeting poster service (working name: Skolr). Skolr was successfully tested at the summer ESIP Federation meeting in Santa Fe. This talk will outline the issues for building out this service within Drupal. The use of Drupal as the framework/platform for Skolr is expected to facilitate the rapid development of the code base, an ability to then develop a mobile device application for meetings, and improved data-mining and searching. Each year in the USA (and elsewhere), professional academic societies host academic meetings where they provide for a poster session. Collectively, it is not difficult to imagine upwards of a quarter-million posters created, displayed, and discarded in a single year in the U.S. The Skolr service does not propose to replace the current poster activity with a digital activity, the direct person-to-person conversational aspects of these events remain worthwhile. When fully built, Skolr promises to enhance current poster session activities at academic meetings in several ways. For the poster presenter, Skolr offers the following opportunities: 1. Easy upload into an archive where the poster can be viewed by researchers across the globe. 2. Support for a wide range of metadata to improve search-ability. 3. Search and browse capabilities, combined with ratings and other user-generated value added capabilities (tagging and commenting). 4. The poster remains visible and findable for as long as the presenter wishes. 5. The presenter's profile and other information becomes available to those who view her poster, increasing the networking potential. 6. The presenter can activate their own RSS feeds to view similar posters from meetings across the planet and over years. For the meeting host organization, Skolr offers the following opportunities: 1. Social networking for meeting attendees/organizataion members. 2. Poster session recruitment, abstract posting, room scheduling, and judging are supported. 3. Poster browsing and poster ratings for meeting attendees; also personal scheduling for larger meetings. 4. Organizational branding of poster content for broader markets. For science and engineering communities, Skolr offers the following opportunities: 1. A searchable open-source archival repository for hundreds of thousands (eventually, millions) of posters. 2. Planet-wide access to science/engineering meeting content, and poster presenters. 3. A mine of collective information about the state-of-the-science in its up-to-date, pre-published form. 4. An ability to search across disciplines and organizations to connect research efforts and results. The Skolr service will be designed to scale up to a level that would encompass any/all science/engineering meetings. The use of Drupal creates specific affordances for sharing the code base. The open-source Skolr software code can be used by anyone to create other similar services.

GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii).

PubMed

Xu, Zhenzhen; Liu, Jing; Ni, Wanchao; Peng, Zhen; Guo, Yue; Ye, Wuwei; Huang, Fang; Zhang, Xianggui; Xu, Peng; Guo, Qi; Shen, Xinlian; Du, Jianchang

2017-01-01

Although several diploid and tetroploid Gossypium species genomes have been sequenced, the well annotated web-based transposable elements (TEs) database is lacking. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the cotton genome, a comprehensive, specific, and user-friendly web-based database, Gossypium raimondii transposable elements database (GrTEdb), was constructed. A total of 14 332 TEs were structurally annotated and clearly categorized in G. raimondii genome, and these elements have been classified into seven distinct superfamilies based on the order of protein-coding domains, structures and/or sequence similarity, including 2929 Copia-like elements, 10 368 Gypsy-like elements, 299 L1 , 12 Mutators , 435 PIF-Harbingers , 275 CACTAs and 14 Helitrons . Meanwhile, the web-based sequence browsing, searching, downloading and blast tool were implemented to help users easily and effectively to annotate the TEs or TE fragments in genomic sequences from G. raimondii and other closely related Gossypium species. GrTEdb provides resources and information related with TEs in G. raimondii , and will facilitate gene and genome analyses within or across Gossypium species, evaluating the impact of TEs on their host genomes, and investigating the potential interaction between TEs and protein-coding genes in Gossypium species. http://www.grtedb.org/. © The Author(s) 2017. Published by Oxford University Press.

Vascular Cures

MedlinePlus

... SV Gives Search ©2017 Vascular Cures is a tax-exempt, nonprofit organization tax ID#: 94-2825216 as described in the Section ... 3) of the Internal Revenue Code. Donations are tax deductible. 274 Redwood Shores Parkway, #717, Redwood City, ...

Find a Diabetes Prevention Program Near You

MedlinePlus

... throughout the country. Find an In-person Class Select From List Find a class near you by ... some locations. Search by ZIP ZIP Code: Distance: Select Location Location: Find an Online Program Online programs ...

The circulating transcriptome as a source of non-invasive cancer biomarkers: concepts and controversies of non-coding and coding RNA in body fluids

PubMed Central

Fernandez-Mercado, Marta; Manterola, Lorea; Larrea, Erika; Goicoechea, Ibai; Arestin, María; Armesto, María; Otaegui, David; Lawrie, Charles H

2015-01-01

The gold standard for cancer diagnosis remains the histological examination of affected tissue, obtained either by surgical excision, or radiologically guided biopsy. Such procedures however are expensive, not without risk to the patient, and require consistent evaluation by expert pathologists. Consequently, the search for non-invasive tools for the diagnosis and management of cancer has led to great interest in the field of circulating nucleic acids in plasma and serum. An additional benefit of blood-based testing is the ability to carry out screening and repeat sampling on patients undergoing therapy, or monitoring disease progression allowing for the development of a personalized approach to cancer patient management. Despite having been discovered over 60 years ago, the clear clinical potential of circulating nucleic acids, with the notable exception of prenatal diagnostic testing, has yet to translate into the clinic. The recent discovery of non-coding (nc) RNA (in particular micro(mi)RNAs) in the blood has provided fresh impetuous for the field. In this review, we discuss the potential of the circulating transcriptome (coding and ncRNA), as novel cancer biomarkers, the controversy surrounding their origin and biology, and most importantly the hurdles that remain to be overcome if they are really to become part of future clinical practice. PMID:26119132

Parametric color coding of digital subtraction angiography.

PubMed

Strother, C M; Bender, F; Deuerling-Zheng, Y; Royalty, K; Pulfer, K A; Baumgart, J; Zellerhoff, M; Aagaard-Kienitz, B; Niemann, D B; Lindstrom, M L

2010-05-01

Color has been shown to facilitate both visual search and recognition tasks. It was our purpose to examine the impact of a color-coding algorithm on the interpretation of 2D-DSA acquisitions by experienced and inexperienced observers. Twenty-six 2D-DSA acquisitions obtained as part of routine clinical care from subjects with a variety of cerebrovascular disease processes were selected from an internal data base so as to include a variety of disease states (aneurysms, AVMs, fistulas, stenosis, occlusions, dissections, and tumors). Three experienced and 3 less experienced observers were each shown the acquisitions on a prerelease version of a commercially available double-monitor workstation (XWP, Siemens Healthcare). Acquisitions were presented first as a subtracted image series and then as a single composite color-coded image of the entire acquisition. Observers were then asked a series of questions designed to assess the value of the color-coded images for the following purposes: 1) to enhance their ability to make a diagnosis, 2) to have confidence in their diagnosis, 3) to plan a treatment, and 4) to judge the effect of a treatment. The results were analyzed by using 1-sample Wilcoxon tests. Color-coded images enhanced the ease of evaluating treatment success in >40% of cases (P < .0001). They also had a statistically significant impact on treatment planning, making planning easier in >20% of the cases (P = .0069). In >20% of the examples, color-coding made diagnosis and treatment planning easier for all readers (P < .0001). Color-coding also increased the confidence of diagnosis compared with the use of DSA alone (P = .056). The impact of this was greater for the naïve readers than for the expert readers. At no additional cost in x-ray dose or contrast medium, color-coding of DSA enhanced the conspicuity of findings on DSA images. It was particularly useful in situations in which there was a complex flow pattern and in evaluation of pre- and posttreatment acquisitions. Its full potential remains to be defined.

Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline*

PubMed Central

Zhu, Xun; Xie, Shangbo; Armengaud, Jean; Xie, Wen; Guo, Zhaojiang; Kang, Shi; Wu, Qingjun; Wang, Shaoli; Xia, Jixing; He, Rongjun; Zhang, Youjun

2016-01-01

The diamondback moth, Plutella xylostella (L.), is the major cosmopolitan pest of brassica and other cruciferous crops. Its larval midgut is a dynamic tissue that interfaces with a wide variety of toxicological and physiological processes. The draft sequence of the P. xylostella genome was recently released, but its annotation remains challenging because of the low sequence coverage of this branch of life and the poor description of exon/intron splicing rules for these insects. Peptide sequencing by computational assignment of tandem mass spectra to genome sequence information provides an experimental independent approach for confirming or refuting protein predictions, a concept that has been termed proteogenomics. In this study, we carried out an in-depth proteogenomic analysis to complement genome annotation of P. xylostella larval midgut based on shotgun HPLC-ESI-MS/MS data by means of a multialgorithm pipeline. A total of 876,341 tandem mass spectra were searched against the predicted P. xylostella protein sequences and a whole-genome six-frame translation database. Based on a data set comprising 2694 novel genome search specific peptides, we discovered 439 novel protein-coding genes and corrected 128 existing gene models. To get the most accurate data to seed further insect genome annotation, more than half of the novel protein-coding genes, i.e. 235 over 439, were further validated after RT-PCR amplification and sequencing of the corresponding transcripts. Furthermore, we validated 53 novel alternative splicings. Finally, a total of 6764 proteins were identified, resulting in one of the most comprehensive proteogenomic study of a nonmodel animal. As the first tissue-specific proteogenomics analysis of P. xylostella, this study provides the fundamental basis for high-throughput proteomics and functional genomics approaches aimed at deciphering the molecular mechanisms of resistance and controlling this pest. PMID:26902207

Design search and optimization in aerospace engineering.

PubMed

Keane, A J; Scanlan, J P

2007-10-15

In this paper, we take a design-led perspective on the use of computational tools in the aerospace sector. We briefly review the current state-of-the-art in design search and optimization (DSO) as applied to problems from aerospace engineering, focusing on those problems that make heavy use of computational fluid dynamics (CFD). This ranges over issues of representation, optimization problem formulation and computational modelling. We then follow this with a multi-objective, multi-disciplinary example of DSO applied to civil aircraft wing design, an area where this kind of approach is becoming essential for companies to maintain their competitive edge. Our example considers the structure and weight of a transonic civil transport wing, its aerodynamic performance at cruise speed and its manufacturing costs. The goals are low drag and cost while holding weight and structural performance at acceptable levels. The constraints and performance metrics are modelled by a linked series of analysis codes, the most expensive of which is a CFD analysis of the aerodynamics using an Euler code with coupled boundary layer model. Structural strength and weight are assessed using semi-empirical schemes based on typical airframe company practice. Costing is carried out using a newly developed generative approach based on a hierarchical decomposition of the key structural elements of a typical machined and bolted wing-box assembly. To carry out the DSO process in the face of multiple competing goals, a recently developed multi-objective probability of improvement formulation is invoked along with stochastic process response surface models (Krigs). This approach both mitigates the significant run times involved in CFD computation and also provides an elegant way of balancing competing goals while still allowing the deployment of the whole range of single objective optimizers commonly available to design teams.

Line-Editor Computer Program

NASA Technical Reports Server (NTRS)

Scott, Peter J.

1989-01-01

ZED editing program for DEC VAX computer simple, powerful line editor for text, program source code, and nonbinary data. Excels in processing of text by use of procedure files. Also features versatile search qualifiers, global changes, conditionals, online help, hexadecimal mode, space compression, looping, logical combinations of search strings, journaling, visible control characters, and automatic detabbing. Users of Cambridge implementation devised such ZED procedures as chess games, calculators, and programs for evaluating pi. Written entirely in C.

Schroedinger’s Code: A Preliminary Study on Research Source Code Availability and Link Persistence in Astrophysics

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter J.; Ryan, P. Wesley

2018-05-01

We examined software usage in a sample set of astrophysics research articles published in 2015 and searched for the source codes for the software mentioned in these research papers. We categorized the software to indicate whether the source code is available for download and whether there are restrictions to accessing it, and if the source code is not available, whether some other form of the software, such as a binary, is. We also extracted hyperlinks from one journal’s 2015 research articles, as links in articles can serve as an acknowledgment of software use and lead to the data used in the research, and tested them to determine which of these URLs are still accessible. For our sample of 715 software instances in the 166 articles we examined, we were able to categorize 418 records as according to whether source code was available and found that 285 unique codes were used, 58% of which offered the source code for download. Of the 2558 hyperlinks extracted from 1669 research articles, at best, 90% of them were available over our testing period.

Positional priming of visual pop-out search is supported by multiple spatial reference frames

PubMed Central

Gokce, Ahu; Müller, Hermann J.; Geyer, Thomas

2015-01-01

The present study investigates the representations(s) underlying positional priming of visual ‘pop-out’ search (Maljkovic and Nakayama, 1996). Three search items (one target and two distractors) were presented at different locations, in invariant (Experiment 1) or random (Experiment 2) cross-trial sequences. By these manipulations it was possible to disentangle retinotopic, spatiotopic, and object-centered priming representations. Two forms of priming were tested: target location facilitation (i.e., faster reaction times – RTs– when the trial n target is presented at a trial n-1 target relative to n-1 blank location) and distractor location inhibition (i.e., slower RTs for n targets presented at n-1 distractor compared to n-1 blank locations). It was found that target locations were coded in positional short-term memory with reference to both spatiotopic and object-centered representations (Experiment 1 vs. 2). In contrast, distractor locations were maintained in an object-centered reference frame (Experiments 1 and 2). We put forward the idea that the uncertainty induced by the experiment manipulation (predictable versus random cross-trial item displacements) modulates the transition from object- to space-based representations in cross-trial memory for target positions. PMID:26136718

Final Report A Multi-Language Environment For Programmable Code Optimization and Empirical Tuning

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

Yi, Qing; Whaley, Richard Clint; Qasem, Apan

This report summarizes our effort and results of building an integrated optimization environment to effectively combine the programmable control and the empirical tuning of source-to-source compiler optimizations within the framework of multiple existing languages, specifically C, C++, and Fortran. The environment contains two main components: the ROSE analysis engine, which is based on the ROSE C/C++/Fortran2003 source-to-source compiler developed by Co-PI Dr.Quinlan et. al at DOE/LLNL, and the POET transformation engine, which is based on an interpreted program transformation language developed by Dr. Yi at University of Texas at San Antonio (UTSA). The ROSE analysis engine performs advanced compiler analysis,more » identifies profitable code transformations, and then produces output in POET, a language designed to provide programmable control of compiler optimizations to application developers and to support the parameterization of architecture-sensitive optimizations so that their configurations can be empirically tuned later. This POET output can then be ported to different machines together with the user application, where a POET-based search engine empirically reconfigures the parameterized optimizations until satisfactory performance is found. Computational specialists can write POET scripts to directly control the optimization of their code. Application developers can interact with ROSE to obtain optimization feedback as well as provide domain-specific knowledge and high-level optimization strategies. The optimization environment is expected to support different levels of automation and programmer intervention, from fully-automated tuning to semi-automated development and to manual programmable control.« less

dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts

PubMed Central

Vincent, Jonathan; Dai, Zhanwu; Ravel, Catherine; Choulet, Frédéric; Mouzeyar, Said; Bouzidi, M. Fouad; Agier, Marie; Martre, Pierre

2013-01-01

The functional annotation of genes based on sequence homology with genes from model species genomes is time-consuming because it is necessary to mine several unrelated databases. The aim of the present work was to develop a functional annotation database for common wheat Triticum aestivum (L.). The database, named dbWFA, is based on the reference NCBI UniGene set, an expressed gene catalogue built by expressed sequence tag clustering, and on full-length coding sequences retrieved from the TriFLDB database. Information from good-quality heterogeneous sources, including annotations for model plant species Arabidopsis thaliana (L.) Heynh. and Oryza sativa L., was gathered and linked to T. aestivum sequences through BLAST-based homology searches. Even though the complexity of the transcriptome cannot yet be fully appreciated, we developed a tool to easily and promptly obtain information from multiple functional annotation systems (Gene Ontology, MapMan bin codes, MIPS Functional Categories, PlantCyc pathway reactions and TAIR gene families). The use of dbWFA is illustrated here with several query examples. We were able to assign a putative function to 45% of the UniGenes and 81% of the full-length coding sequences from TriFLDB. Moreover, comparison of the annotation of the whole T. aestivum UniGene set along with curated annotations of the two model species assessed the accuracy of the annotation provided by dbWFA. To further illustrate the use of dbWFA, genes specifically expressed during the early cell division or late storage polymer accumulation phases of T. aestivum grain development were identified using a clustering analysis and then annotated using dbWFA. The annotation of these two sets of genes was consistent with previous analyses of T. aestivum grain transcriptomes and proteomes. Database URL: urgi.versailles.inra.fr/dbWFA/ PMID:23660284

Alien Mindscapes—A Perspective on the Search for Extraterrestrial Intelligence

NASA Astrophysics Data System (ADS)

Cabrol, Nathalie A.

2016-09-01

Advances in planetary and space sciences, astrobiology, and life and cognitive sciences, combined with developments in communication theory, bioneural computing, machine learning, and big data analysis, create new opportunities to explore the probabilistic nature of alien life. Brought together in a multidisciplinary approach, they have the potential to support an integrated and expanded Search for Extraterrestrial Intelligence (SETI1), a search that includes looking for life as we do not know it. This approach will augment the odds of detecting a signal by broadening our understanding of the evolutionary and systemic components in the search for extraterrestrial intelligence (ETI), provide more targets for radio and optical SETI, and identify new ways of decoding and coding messages using universal markers.

High-performance metadata indexing and search in petascale data storage systems

NASA Astrophysics Data System (ADS)

Leung, A. W.; Shao, M.; Bisson, T.; Pasupathy, S.; Miller, E. L.

2008-07-01

Large-scale storage systems used for scientific applications can store petabytes of data and billions of files, making the organization and management of data in these systems a difficult, time-consuming task. The ability to search file metadata in a storage system can address this problem by allowing scientists to quickly navigate experiment data and code while allowing storage administrators to gather the information they need to properly manage the system. In this paper, we present Spyglass, a file metadata search system that achieves scalability by exploiting storage system properties, providing the scalability that existing file metadata search tools lack. In doing so, Spyglass can achieve search performance up to several thousand times faster than existing database solutions. We show that Spyglass enables important functionality that can aid data management for scientists and storage administrators.

Critical Limb Ischemia (CLI)

MedlinePlus

... re human: Search ©2017 Vascular Cures is a tax-exempt, nonprofit organization tax ID#: 94-2825216 as described in the Section ... 3) of the Internal Revenue Code. Donations are tax deductible. 274 Redwood Shores Parkway, #717, Redwood City, ...

What Is Vascular Disease?

MedlinePlus

... re human: Search ©2017 Vascular Cures is a tax-exempt, nonprofit organization tax ID#: 94-2825216 as described in the Section ... 3) of the Internal Revenue Code. Donations are tax deductible. 274 Redwood Shores Parkway, #717, Redwood City, ...

Alternative Fuels Data Center: Natural Gas Fueling Station Locations

Science.gov Websites

or ZIP code or along a route in the United States. Loading alternative fueling station locator Fleet Rightsizing System Efficiency Locate Stations Search by Location Map a Route Laws & Incentives

Systematic review of validated case definitions for diabetes in ICD-9-coded and ICD-10-coded data in adult populations.

PubMed

Khokhar, Bushra; Jette, Nathalie; Metcalfe, Amy; Cunningham, Ceara Tess; Quan, Hude; Kaplan, Gilaad G; Butalia, Sonia; Rabi, Doreen

2016-08-05

With steady increases in 'big data' and data analytics over the past two decades, administrative health databases have become more accessible and are now used regularly for diabetes surveillance. The objective of this study is to systematically review validated International Classification of Diseases (ICD)-based case definitions for diabetes in the adult population. Electronic databases, MEDLINE and Embase, were searched for validation studies where an administrative case definition (using ICD codes) for diabetes in adults was validated against a reference and statistical measures of the performance reported. The search yielded 2895 abstracts, and of the 193 potentially relevant studies, 16 met criteria. Diabetes definition for adults varied by data source, including physician claims (sensitivity ranged from 26.9% to 97%, specificity ranged from 94.3% to 99.4%, positive predictive value (PPV) ranged from 71.4% to 96.2%, negative predictive value (NPV) ranged from 95% to 99.6% and κ ranged from 0.8 to 0.9), hospital discharge data (sensitivity ranged from 59.1% to 92.6%, specificity ranged from 95.5% to 99%, PPV ranged from 62.5% to 96%, NPV ranged from 90.8% to 99% and κ ranged from 0.6 to 0.9) and a combination of both (sensitivity ranged from 57% to 95.6%, specificity ranged from 88% to 98.5%, PPV ranged from 54% to 80%, NPV ranged from 98% to 99.6% and κ ranged from 0.7 to 0.8). Overall, administrative health databases are useful for undertaking diabetes surveillance, but an awareness of the variation in performance being affected by case definition is essential. The performance characteristics of these case definitions depend on the variations in the definition of primary diagnosis in ICD-coded discharge data and/or the methodology adopted by the healthcare facility to extract information from patient records. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

FAMA: An automatic code for stellar parameter and abundance determination

NASA Astrophysics Data System (ADS)

Magrini, Laura; Randich, Sofia; Friel, Eileen; Spina, Lorenzo; Jacobson, Heather; Cantat-Gaudin, Tristan; Donati, Paolo; Baglioni, Roberto; Maiorca, Enrico; Bragaglia, Angela; Sordo, Rosanna; Vallenari, Antonella

2013-10-01

Context. The large amount of spectra obtained during the epoch of extensive spectroscopic surveys of Galactic stars needs the development of automatic procedures to derive their atmospheric parameters and individual element abundances. Aims: Starting from the widely-used code MOOG by C. Sneden, we have developed a new procedure to determine atmospheric parameters and abundances in a fully automatic way. The code FAMA (Fast Automatic MOOG Analysis) is presented describing its approach to derive atmospheric stellar parameters and element abundances. The code, freely distributed, is written in Perl and can be used on different platforms. Methods: The aim of FAMA is to render the computation of the atmospheric parameters and abundances of a large number of stars using measurements of equivalent widths (EWs) as automatic and as independent of any subjective approach as possible. It is based on the simultaneous search for three equilibria: excitation equilibrium, ionization balance, and the relationship between log n(Fe i) and the reduced EWs. FAMA also evaluates the statistical errors on individual element abundances and errors due to the uncertainties in the stellar parameters. The convergence criteria are not fixed "a priori" but are based on the quality of the spectra. Results: In this paper we present tests performed on the solar spectrum EWs that assess the method's dependency on the initial parameters and we analyze a sample of stars observed in Galactic open and globular clusters. The current version of FAMA is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/558/A38

Performance Analysis of the Link-16/JTIDS Waveform with Concatenated Coding, Soft Decision Reed-Solomon Decoding, and Noise-Normalization

DTIC Science & Technology

2010-09-01

the time for reviewing instruction, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the...Col Terry Smith for his time spent serving as the second reader of this thesis. xxii THIS PAGE INTENTIONALLY LEFT BLANK 1 I. INTRODUCTION...However, this is the first time that concatenated coding in combination with noise- normalization has been considered. 2 B. THESIS OUTLINE The thesis

JavaGenes Molecular Evolution

NASA Technical Reports Server (NTRS)

Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

2007-01-01

JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.

PubMed

He, Yi; Xiao, Yi; Liwo, Adam; Scheraga, Harold A

2009-10-01

We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal alpha-helical and a minimal beta-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with alpha or alpha + beta structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. Copyright 2009 Wiley Periodicals, Inc.

The Use of Automated SNOMED CT Clinical Coding in Clinical Decision Support Systems for Preventive Care.

PubMed

Al-Hablani, Bader

2017-01-01

The objective of this study is to discuss and analyze the use of automated SNOMED CT clinical coding in clinical decision support systems (CDSSs) for preventive care. The central question that this study seeks to answer is whether the utilization of SNOMED CT in CDSSs can improve preventive care. PubMed, Google Scholar, and Cochrane Library were searched for articles published in English between 2001 and 2012 on SNOMED CT, CDSS, and preventive care. Outcome measures were the sensitivity or specificity of SNOMED CT coded data and the positive predictive value or negative predictive value of SNOMED CT coded data. Additionally, we documented the publication year, research question, study design, results, and conclusions of these studies. The reviewed studies suggested that SNOMED CT successfully represents clinical terms and negated clinical terms. The use of SNOMED CT in CDSS can be considered to provide an answer to the problem of medical errors as well as for preventive care in general. Enhancement of the modifiers and synonyms found in SNOMED CT will be necessary to improve the expected outcome of the integration of SNOMED CT with CDSS. Moreover, the application of the tree-augmented naïve (TAN) Bayesian network method can be considered the best technique to search SNOMED CT data and, consequently, to help improve preventive health services.

The Use of Automated SNOMED CT Clinical Coding in Clinical Decision Support Systems for Preventive Care

PubMed Central

Al-Hablani, Bader

2017-01-01

Objective The objective of this study is to discuss and analyze the use of automated SNOMED CT clinical coding in clinical decision support systems (CDSSs) for preventive care. The central question that this study seeks to answer is whether the utilization of SNOMED CT in CDSSs can improve preventive care. Method PubMed, Google Scholar, and Cochrane Library were searched for articles published in English between 2001 and 2012 on SNOMED CT, CDSS, and preventive care. Outcome Measures Outcome measures were the sensitivity or specificity of SNOMED CT coded data and the positive predictive value or negative predictive value of SNOMED CT coded data. Additionally, we documented the publication year, research question, study design, results, and conclusions of these studies. Results The reviewed studies suggested that SNOMED CT successfully represents clinical terms and negated clinical terms. Conclusion The use of SNOMED CT in CDSS can be considered to provide an answer to the problem of medical errors as well as for preventive care in general. Enhancement of the modifiers and synonyms found in SNOMED CT will be necessary to improve the expected outcome of the integration of SNOMED CT with CDSS. Moreover, the application of the tree-augmented naïve (TAN) Bayesian network method can be considered the best technique to search SNOMED CT data and, consequently, to help improve preventive health services. PMID:28566995

GRay: A Massively Parallel GPU-based Code for Ray Tracing in Relativistic Spacetimes

NASA Astrophysics Data System (ADS)

Chan, Chi-kwan; Psaltis, Dimitrios; Özel, Feryal

2013-11-01

We introduce GRay, a massively parallel integrator designed to trace the trajectories of billions of photons in a curved spacetime. This graphics-processing-unit (GPU)-based integrator employs the stream processing paradigm, is implemented in CUDA C/C++, and runs on nVidia graphics cards. The peak performance of GRay using single-precision floating-point arithmetic on a single GPU exceeds 300 GFLOP (or 1 ns per photon per time step). For a realistic problem, where the peak performance cannot be reached, GRay is two orders of magnitude faster than existing central-processing-unit-based ray-tracing codes. This performance enhancement allows more effective searches of large parameter spaces when comparing theoretical predictions of images, spectra, and light curves from the vicinities of compact objects to observations. GRay can also perform on-the-fly ray tracing within general relativistic magnetohydrodynamic algorithms that simulate accretion flows around compact objects. Making use of this algorithm, we calculate the properties of the shadows of Kerr black holes and the photon rings that surround them. We also provide accurate fitting formulae of their dependencies on black hole spin and observer inclination, which can be used to interpret upcoming observations of the black holes at the center of the Milky Way, as well as M87, with the Event Horizon Telescope.

The EMBL-EBI bioinformatics web and programmatic tools framework.

PubMed

Li, Weizhong; Cowley, Andrew; Uludag, Mahmut; Gur, Tamer; McWilliam, Hamish; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Lopez, Rodrigo

2015-07-01

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Spatial Pyramid Covariance based Compact Video Code for Robust Face Retrieval in TV-series.

PubMed

Li, Yan; Wang, Ruiping; Cui, Zhen; Shan, Shiguang; Chen, Xilin

2016-10-10

We address the problem of face video retrieval in TV-series which searches video clips based on the presence of specific character, given one face track of his/her. This is tremendously challenging because on one hand, faces in TV-series are captured in largely uncontrolled conditions with complex appearance variations, and on the other hand retrieval task typically needs efficient representation with low time and space complexity. To handle this problem, we propose a compact and discriminative representation for the huge body of video data, named Compact Video Code (CVC). Our method first models the face track by its sample (i.e., frame) covariance matrix to capture the video data variations in a statistical manner. To incorporate discriminative information and obtain more compact video signature suitable for retrieval, the high-dimensional covariance representation is further encoded as a much lower-dimensional binary vector, which finally yields the proposed CVC. Specifically, each bit of the code, i.e., each dimension of the binary vector, is produced via supervised learning in a max margin framework, which aims to make a balance between the discriminability and stability of the code. Besides, we further extend the descriptive granularity of covariance matrix from traditional pixel-level to more general patchlevel, and proceed to propose a novel hierarchical video representation named Spatial Pyramid Covariance (SPC) along with a fast calculation method. Face retrieval experiments on two challenging TV-series video databases, i.e., the Big Bang Theory and Prison Break, demonstrate the competitiveness of the proposed CVC over state-of-the-art retrieval methods. In addition, as a general video matching algorithm, CVC is also evaluated in traditional video face recognition task on a standard Internet database, i.e., YouTube Celebrities, showing its quite promising performance by using an extremely compact code with only 128 bits.

Development, dissemination, and applications of a new terminological resource, the Q-Code taxonomy for professional aspects of general practice/family medicine.

PubMed

Jamoulle, Marc; Resnick, Melissa; Grosjean, Julien; Ittoo, Ashwin; Cardillo, Elena; Vander Stichele, Robert; Darmoni, Stefan; Vanmeerbeek, Marc

2018-12-01

While documentation of clinical aspects of General Practice/Family Medicine (GP/FM) is assured by the International Classification of Primary Care (ICPC), there is no taxonomy for the professional aspects (context and management) of GP/FM. To present the development, dissemination, applications, and resulting face validity of the Q-Codes taxonomy specifically designed to describe contextual features of GP/FM, proposed as an extension to the ICPC. The Q-Codes taxonomy was developed from Lamberts' seminal idea for indexing contextual content (1987) by a multi-disciplinary team of knowledge engineers, linguists and general practitioners, through a qualitative and iterative analysis of 1702 abstracts from six GP/FM conferences using Atlas.ti software. A total of 182 concepts, called Q-Codes, representing professional aspects of GP/FM were identified and organized in a taxonomy. Dissemination: The taxonomy is published as an online terminological resource, using semantic web techniques and web ontology language (OWL) ( http://www.hetop.eu/Q ). Each Q-Code is identified with a unique resource identifier (URI), and provided with preferred terms, and scope notes in ten languages (Portuguese, Spanish, English, French, Dutch, Korean, Vietnamese, Turkish, Georgian, German) and search filters for MEDLINE and web searches. This taxonomy has already been used to support queries in bibliographic databases (e.g., MEDLINE), to facilitate indexing of grey literature in GP/FM as congress abstracts, master theses, websites and as an educational tool in vocational teaching, Conclusions: The rapidly growing list of practical applications provides face-validity for the usefulness of this freely available new terminological resource.

NDEC: A NEA platform for nuclear data testing, verification and benchmarking

NASA Astrophysics Data System (ADS)

Díez, C. J.; Michel-Sendis, F.; Cabellos, O.; Bossant, M.; Soppera, N.

2017-09-01

The selection, testing, verification and benchmarking of evaluated nuclear data consists, in practice, in putting an evaluated file through a number of checking steps where different computational codes verify that the file and the data it contains complies with different requirements. These requirements range from format compliance to good performance in application cases, while at the same time physical constraints and the agreement with experimental data are verified. At NEA, the NDEC (Nuclear Data Evaluation Cycle) platform aims at providing, in a user friendly interface, a thorough diagnose of the quality of a submitted evaluated nuclear data file. Such diagnose is based on the results of different computational codes and routines which carry out the mentioned verifications, tests and checks. NDEC also searches synergies with other existing NEA tools and databases, such as JANIS, DICE or NDaST, including them into its working scheme. Hence, this paper presents NDEC, its current development status and its usage in the JEFF nuclear data project.

Non-Coding RNA Analysis Using the Rfam Database.

PubMed

Kalvari, Ioanna; Nawrocki, Eric P; Argasinska, Joanna; Quinones-Olvera, Natalia; Finn, Robert D; Bateman, Alex; Petrov, Anton I

2018-06-01

Rfam is a database of non-coding RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. Using a combination of manual and literature-based curation and a custom software pipeline, Rfam converts descriptions of RNA families found in the scientific literature into computational models that can be used to annotate RNAs belonging to those families in any DNA or RNA sequence. Valuable research outputs that are often locked up in figures and supplementary information files are encapsulated in Rfam entries and made accessible through the Rfam Web site. The data produced by Rfam have a broad application, from genome annotation to providing training sets for algorithm development. This article gives an overview of how to search and navigate the Rfam Web site, and how to annotate sequences with RNA families. The Rfam database is freely available at http://rfam.org. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.

SAM: String-based sequence search algorithm for mitochondrial DNA database queries

PubMed Central

Röck, Alexander; Irwin, Jodi; Dür, Arne; Parsons, Thomas; Parson, Walther

2011-01-01

The analysis of the haploid mitochondrial (mt) genome has numerous applications in forensic and population genetics, as well as in disease studies. Although mtDNA haplotypes are usually determined by sequencing, they are rarely reported as a nucleotide string. Traditionally they are presented in a difference-coded position-based format relative to the corrected version of the first sequenced mtDNA. This convention requires recommendations for standardized sequence alignment that is known to vary between scientific disciplines, even between laboratories. As a consequence, database searches that are vital for the interpretation of mtDNA data can suffer from biased results when query and database haplotypes are annotated differently. In the forensic context that would usually lead to underestimation of the absolute and relative frequencies. To address this issue we introduce SAM, a string-based search algorithm that converts query and database sequences to position-free nucleotide strings and thus eliminates the possibility that identical sequences will be missed in a database query. The mere application of a BLAST algorithm would not be a sufficient remedy as it uses a heuristic approach and does not address properties specific to mtDNA, such as phylogenetically stable but also rapidly evolving insertion and deletion events. The software presented here provides additional flexibility to incorporate phylogenetic data, site-specific mutation rates, and other biologically relevant information that would refine the interpretation of mitochondrial DNA data. The manuscript is accompanied by freeware and example data sets that can be used to evaluate the new software (http://stringvalidation.org). PMID:21056022

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions.

PubMed

Liu, Yongchao; Wirawan, Adrianto; Schmidt, Bertil

2013-04-04

The maximal sensitivity for local alignments makes the Smith-Waterman algorithm a popular choice for protein sequence database search based on pairwise alignment. However, the algorithm is compute-intensive due to a quadratic time complexity. Corresponding runtimes are further compounded by the rapid growth of sequence databases. We present CUDASW++ 3.0, a fast Smith-Waterman protein database search algorithm, which couples CPU and GPU SIMD instructions and carries out concurrent CPU and GPU computations. For the CPU computation, this algorithm employs SSE-based vector execution units as accelerators. For the GPU computation, we have investigated for the first time a GPU SIMD parallelization, which employs CUDA PTX SIMD video instructions to gain more data parallelism beyond the SIMT execution model. Moreover, sequence alignment workloads are automatically distributed over CPUs and GPUs based on their respective compute capabilities. Evaluation on the Swiss-Prot database shows that CUDASW++ 3.0 gains a performance improvement over CUDASW++ 2.0 up to 2.9 and 3.2, with a maximum performance of 119.0 and 185.6 GCUPS, on a single-GPU GeForce GTX 680 and a dual-GPU GeForce GTX 690 graphics card, respectively. In addition, our algorithm has demonstrated significant speedups over other top-performing tools: SWIPE and BLAST+. CUDASW++ 3.0 is written in CUDA C++ and PTX assembly languages, targeting GPUs based on the Kepler architecture. This algorithm obtains significant speedups over its predecessor: CUDASW++ 2.0, by benefiting from the use of CPU and GPU SIMD instructions as well as the concurrent execution on CPUs and GPUs. The source code and the simulated data are available at http://cudasw.sourceforge.net.

PSEUDO-CODEWORD LANDSCAPE

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

CHERTKOV, MICHAEL; STEPANOV, MIKHAIL

2007-01-10

The authors discuss performance of Low-Density-Parity-Check (LDPC) codes decoded by Linear Programming (LP) decoding at moderate and large Signal-to-Noise-Ratios (SNR). Frame-Error-Rate (FER) dependence on SNR and the noise space landscape of the coding/decoding scheme are analyzed by a combination of the previously introduced instanton/pseudo-codeword-search method and a new 'dendro' trick. To reduce complexity of the LP decoding for a code with high-degree checks, {ge} 5, they introduce its dendro-LDPC counterpart, that is the code performing identifically to the original one under Maximum-A-Posteriori (MAP) decoding but having reduced (down to three) check connectivity degree. Analyzing number of popular LDPC codes andmore » their dendro versions performing over the Additive-White-Gaussian-Noise (AWGN) channel, they observed two qualitatively different regimes: (i) error-floor sets early, at relatively low SNR, and (ii) FER decays with SNR increase faster at moderate SNR than at the largest SNR. They explain these regimes in terms of the pseudo-codeword spectra of the codes.« less

Hard x ray imaging graphics development and literature search

NASA Technical Reports Server (NTRS)

Emslie, A. Gordon

1991-01-01

This report presents work performed between June 1990 and June 1991 and has the following objectives: (1) a comprehensive literature search of imaging technology and coded aperture imaging as well as relevant topics relating to solar flares; (2) an analysis of random number generators; and (3) programming simulation models of hard x ray telescopes. All programs are compatible with NASA/MSFC Space Science LAboratory VAX Cluster and are written in VAX FORTRAN and VAX IDL (Interactive Data Language).

Object-Location-Aware Hashing for Multi-Label Image Retrieval via Automatic Mask Learning.

PubMed

Huang, Chang-Qin; Yang, Shang-Ming; Pan, Yan; Lai, Han-Jiang

2018-09-01

Learning-based hashing is a leading approach of approximate nearest neighbor search for large-scale image retrieval. In this paper, we develop a deep supervised hashing method for multi-label image retrieval, in which we propose to learn a binary "mask" map that can identify the approximate locations of objects in an image, so that we use this binary "mask" map to obtain length-limited hash codes which mainly focus on an image's objects but ignore the background. The proposed deep architecture consists of four parts: 1) a convolutional sub-network to generate effective image features; 2) a binary "mask" sub-network to identify image objects' approximate locations; 3) a weighted average pooling operation based on the binary "mask" to obtain feature representations and hash codes that pay most attention to foreground objects but ignore the background; and 4) the combination of a triplet ranking loss designed to preserve relative similarities among images and a cross entropy loss defined on image labels. We conduct comprehensive evaluations on four multi-label image data sets. The results indicate that the proposed hashing method achieves superior performance gains over the state-of-the-art supervised or unsupervised hashing baselines.

Evaluation of the Intel Xeon Phi 7120 and NVIDIA K80 as accelerators for two-dimensional panel codes

PubMed Central

2017-01-01

To optimize the geometry of airfoils for a specific application is an important engineering problem. In this context genetic algorithms have enjoyed some success as they are able to explore the search space without getting stuck in local optima. However, these algorithms require the computation of aerodynamic properties for a significant number of airfoil geometries. Consequently, for low-speed aerodynamics, panel methods are most often used as the inner solver. In this paper we evaluate the performance of such an optimization algorithm on modern accelerators (more specifically, the Intel Xeon Phi 7120 and the NVIDIA K80). For that purpose, we have implemented an optimized version of the algorithm on the CPU and Xeon Phi (based on OpenMP, vectorization, and the Intel MKL library) and on the GPU (based on CUDA and the MAGMA library). We present timing results for all codes and discuss the similarities and differences between the three implementations. Overall, we observe a speedup of approximately 2.5 for adding an Intel Xeon Phi 7120 to a dual socket workstation and a speedup between 3.4 and 3.8 for adding a NVIDIA K80 to a dual socket workstation. PMID:28582389

Evaluation of the Intel Xeon Phi 7120 and NVIDIA K80 as accelerators for two-dimensional panel codes.

PubMed

Einkemmer, Lukas

2017-01-01

To optimize the geometry of airfoils for a specific application is an important engineering problem. In this context genetic algorithms have enjoyed some success as they are able to explore the search space without getting stuck in local optima. However, these algorithms require the computation of aerodynamic properties for a significant number of airfoil geometries. Consequently, for low-speed aerodynamics, panel methods are most often used as the inner solver. In this paper we evaluate the performance of such an optimization algorithm on modern accelerators (more specifically, the Intel Xeon Phi 7120 and the NVIDIA K80). For that purpose, we have implemented an optimized version of the algorithm on the CPU and Xeon Phi (based on OpenMP, vectorization, and the Intel MKL library) and on the GPU (based on CUDA and the MAGMA library). We present timing results for all codes and discuss the similarities and differences between the three implementations. Overall, we observe a speedup of approximately 2.5 for adding an Intel Xeon Phi 7120 to a dual socket workstation and a speedup between 3.4 and 3.8 for adding a NVIDIA K80 to a dual socket workstation.

Identifying Patients with Hypertension: A Case for Auditing Electronic Health Record Data

PubMed Central

Baus, Adam; Hendryx, Michael; Pollard, Cecil

2012-01-01

Problems in the structure, consistency, and completeness of electronic health record data are barriers to outcomes research, quality improvement, and practice redesign. This nonexperimental retrospective study examines the utility of importing de-identified electronic health record data into an external system to identify patients with and at risk for essential hypertension. We find a statistically significant increase in cases based on combined use of diagnostic and free-text coding (mean = 1,256.1, 95% CI 1,232.3–1,279.7) compared to diagnostic coding alone (mean = 1,174.5, 95% CI 1,150.5—1,198.3). While it is not surprising that significantly more patients are identified when broadening search criteria, the implications are critical for quality of care, the movement toward the National Committee for Quality Assurance's Patient-Centered Medical Home program, and meaningful use of electronic health records. Further, we find a statistically significant increase in potential cases based on the last two or more blood pressure readings greater than or equal to 140/90 mm Hg (mean = 1,353.9, 95% CI 1,329.9—1,377.9). PMID:22737097

Methods and pitfalls in searching drug safety databases utilising the Medical Dictionary for Regulatory Activities (MedDRA).

PubMed

Brown, Elliot G

2003-01-01

The Medical Dictionary for Regulatory Activities (MedDRA) is a unified standard terminology for recording and reporting adverse drug event data. Its introduction is widely seen as a significant improvement on the previous situation, where a multitude of terminologies of widely varying scope and quality were in use. However, there are some complexities that may cause difficulties, and these will form the focus for this paper. Two methods of searching MedDRA-coded databases are described: searching based on term selection from all of MedDRA and searching based on terms in the safety database. There are several potential traps for the unwary in safety searches. There may be multiple locations of relevant terms within a system organ class (SOC) and lack of recognition of appropriate group terms; the user may think that group terms are more inclusive than is the case. MedDRA may distribute terms relevant to one medical condition across several primary SOCs. If the database supports the MedDRA model, it is possible to perform multiaxial searching: while this may help find terms that might have been missed, it is still necessary to consider the entire contents of the SOCs to find all relevant terms and there are many instances of incomplete secondary linkages. It is important to adjust for multiaxiality if data are presented using primary and secondary locations. Other sources for errors in searching are non-intuitive placement and the selection of terms as preferred terms (PTs) that may not be widely recognised. Some MedDRA rules could also result in errors in data retrieval if the individual is unaware of these: in particular, the lack of multiaxial linkages for the Investigations SOC, Social circumstances SOC and Surgical and medical procedures SOC and the requirement that a PT may only be present under one High Level Term (HLT) and one High Level Group Term (HLGT) within any single SOC. Special Search Categories (collections of PTs assembled from various SOCs by searching all of MedDRA) are limited by the small number available and by lack of clarity about criteria applied in their construction. Difficulties in database searching may be addressed by suitable user training and experience, and by central reporting of detected deficiencies in MedDRA. Other remedies may include regulatory guidance on implementation and use of MedDRA. Further systematic review of MedDRA is needed and generation of standardised searches that may be used 'off the shelf' will help, particularly where the same search is performed repeatedly on multiple data sets. Until these enhancements are widely available, MedDRA users should take great care when searching a safety database to ensure that cases are not inadvertently missed.

A Multiuser Detector Based on Artificial Bee Colony Algorithm for DS-UWB Systems

PubMed Central

Liu, Xiaohui

2013-01-01

Artificial Bee Colony (ABC) algorithm is an optimization algorithm based on the intelligent behavior of honey bee swarm. The ABC algorithm was developed to solve optimizing numerical problems and revealed premising results in processing time and solution quality. In ABC, a colony of artificial bees search for rich artificial food sources; the optimizing numerical problems are converted to the problem of finding the best parameter which minimizes an objective function. Then, the artificial bees randomly discover a population of initial solutions and then iteratively improve them by employing the behavior: moving towards better solutions by means of a neighbor search mechanism while abandoning poor solutions. In this paper, an efficient multiuser detector based on a suboptimal code mapping multiuser detector and artificial bee colony algorithm (SCM-ABC-MUD) is proposed and implemented in direct-sequence ultra-wideband (DS-UWB) systems under the additive white Gaussian noise (AWGN) channel. The simulation results demonstrate that the BER and the near-far effect resistance performances of this proposed algorithm are quite close to those of the optimum multiuser detector (OMD) while its computational complexity is much lower than that of OMD. Furthermore, the BER performance of SCM-ABC-MUD is not sensitive to the number of active users and can obtain a large system capacity. PMID:23983638

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts

PubMed Central

Naito, Yuki; Bono, Hidemasa

2012-01-01

GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly returns relevant RefSeq transcripts. A typical search takes just a few seconds, which dramatically enhances the usability of routine searching. In particular, GGRNA can search sequences as short as 10 nt or 4 amino acids, which cannot be handled easily by popular sequence analysis tools. Nucleotide sequences can be searched allowing up to three mismatches, or the query sequences may contain degenerate nucleotide codes (e.g. N, R, Y, S). Furthermore, Gene Ontology annotations, Enzyme Commission numbers and probe sequences of catalog microarrays are also incorporated into GGRNA, which may help users to conduct searches by various types of keywords. GGRNA web server will provide a simple and powerful interface for finding genes and transcripts for a wide range of users. All services at GGRNA are provided free of charge to all users. PMID:22641850

A Real-Time All-Atom Structural Search Engine for Proteins

PubMed Central

Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

2014-01-01

Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.

PubMed

Naito, Yuki; Bono, Hidemasa

2012-07-01

GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly returns relevant RefSeq transcripts. A typical search takes just a few seconds, which dramatically enhances the usability of routine searching. In particular, GGRNA can search sequences as short as 10 nt or 4 amino acids, which cannot be handled easily by popular sequence analysis tools. Nucleotide sequences can be searched allowing up to three mismatches, or the query sequences may contain degenerate nucleotide codes (e.g. N, R, Y, S). Furthermore, Gene Ontology annotations, Enzyme Commission numbers and probe sequences of catalog microarrays are also incorporated into GGRNA, which may help users to conduct searches by various types of keywords. GGRNA web server will provide a simple and powerful interface for finding genes and transcripts for a wide range of users. All services at GGRNA are provided free of charge to all users.

A real-time all-atom structural search engine for proteins.

PubMed

Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F

2014-07-01

Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

Supersonic and hypersonic shock/boundary-layer interaction database

NASA Technical Reports Server (NTRS)

Settles, Gary S.; Dodson, Lori J.

1994-01-01

An assessment is given of existing shock wave/tubulent boundary-layer interaction experiments having sufficient quality to guide turbulence modeling and code validation efforts. Although the focus of this work is hypersonic, experiments at Mach numbers as low as 3 were considered. The principal means of identifying candidate studies was a computerized search of the AIAA Aerospace Database. Several hundred candidate studies were examined and over 100 of these were subjected to a rigorous set of acceptance criteria for inclusion in the data-base. Nineteen experiments were found to meet these criteria, of which only seven were in the hypersonic regime (M is greater than 5).

Development and Implementation of Kumamoto Technopolis Regional Database T-KIND

NASA Astrophysics Data System (ADS)

Onoue, Noriaki

T-KIND (Techno-Kumamoto Information Network for Data-Base) is a system for effectively searching information of technology, human resources and industries which are necessary to realize Kumamoto Technopolis. It is composed of coded database, image database and LAN inside technoresearch park which is the center of R & D in the Technopolis. It constructs on-line system by networking general-purposed computers, minicomputers, optical disk file systems and so on, and provides the service through public telephone line. Two databases are now available on enterprise information and human resource information. The former covers about 4,000 enterprises, and the latter does about 2,000 persons.

Experiments with a small behaviour controlled planetary rover

NASA Technical Reports Server (NTRS)

Miller, David P.; Desai, Rajiv S.; Gat, Erann; Ivlev, Robert; Loch, John

1993-01-01

A series of experiments that were performed on the Rocky 3 robot is described. Rocky 3 is a small autonomous rover capable of navigating through rough outdoor terrain to a predesignated area, searching that area for soft soil, acquiring a soil sample, and depositing the sample in a container at its home base. The robot is programmed according to a reactive behavior control paradigm using the ALFA programming language. This style of programming produces robust autonomous performance while requiring significantly less computational resources than more traditional mobile robot control systems. The code for Rocky 3 runs on an eight bit processor and uses about ten k of memory.

Garbage in, Garbage Out: Data Collection, Quality Assessment and Reporting Standards for Social Media Data Use in Health Research, Infodemiology and Digital Disease Detection.

PubMed

Kim, Yoonsang; Huang, Jidong; Emery, Sherry

2016-02-26

Social media have transformed the communications landscape. People increasingly obtain news and health information online and via social media. Social media platforms also serve as novel sources of rich observational data for health research (including infodemiology, infoveillance, and digital disease detection detection). While the number of studies using social data is growing rapidly, very few of these studies transparently outline their methods for collecting, filtering, and reporting those data. Keywords and search filters applied to social data form the lens through which researchers may observe what and how people communicate about a given topic. Without a properly focused lens, research conclusions may be biased or misleading. Standards of reporting data sources and quality are needed so that data scientists and consumers of social media research can evaluate and compare methods and findings across studies. We aimed to develop and apply a framework of social media data collection and quality assessment and to propose a reporting standard, which researchers and reviewers may use to evaluate and compare the quality of social data across studies. We propose a conceptual framework consisting of three major steps in collecting social media data: develop, apply, and validate search filters. This framework is based on two criteria: retrieval precision (how much of retrieved data is relevant) and retrieval recall (how much of the relevant data is retrieved). We then discuss two conditions that estimation of retrieval precision and recall rely on--accurate human coding and full data collection--and how to calculate these statistics in cases that deviate from the two ideal conditions. We then apply the framework on a real-world example using approximately 4 million tobacco-related tweets collected from the Twitter firehose. We developed and applied a search filter to retrieve e-cigarette-related tweets from the archive based on three keyword categories: devices, brands, and behavior. The search filter retrieved 82,205 e-cigarette-related tweets from the archive and was validated. Retrieval precision was calculated above 95% in all cases. Retrieval recall was 86% assuming ideal conditions (no human coding errors and full data collection), 75% when unretrieved messages could not be archived, 86% assuming no false negative errors by coders, and 93% allowing both false negative and false positive errors by human coders. This paper sets forth a conceptual framework for the filtering and quality evaluation of social data that addresses several common challenges and moves toward establishing a standard of reporting social data. Researchers should clearly delineate data sources, how data were accessed and collected, and the search filter building process and how retrieval precision and recall were calculated. The proposed framework can be adapted to other public social media platforms.

Engineering calculations for communications satellite systems planning

NASA Technical Reports Server (NTRS)

Levis, C. A.; Martin, C. H.; Reilly, C. H.; Gonsalvez, D. J.; Yamaura, Y.

1985-01-01

An extended gradient search code for broadcasting satellite service (BSS) spectrum/orbit assignment synthesis is discussed. Progress is also reported on both single-entry and full synthesis computational aids for fixed satellite service (FSS) spectrum/orbit assignment purposes.

Searching for Planning and Design Solutions.

ERIC Educational Resources Information Center

Roark, Steven

2001-01-01

Presents the fourth article in a series on the Longview Community College (Kansas City, Missouri) Liberal Arts building project. How architects are revising floor plans, evaluating building systems, deciding on furniture, and dealing with building codes are discussed. (GR)

Alternative Fuels Data Center: Propane Fueling Station Locations

Science.gov Websites

petroleum gas (propane) fueling stations near an address or ZIP code or along a route in the United States Location Map a Route Laws & Incentives Search Federal State Key Legislation Data & Tools Widgets

Accuracy of Binary Black Hole Waveform Models for Advanced LIGO

NASA Astrophysics Data System (ADS)

Kumar, Prayush; Fong, Heather; Barkett, Kevin; Bhagwat, Swetha; Afshari, Nousha; Chu, Tony; Brown, Duncan; Lovelace, Geoffrey; Pfeiffer, Harald; Scheel, Mark; Szilagyi, Bela; Simulating Extreme Spacetimes (SXS) Team

2016-03-01

Coalescing binaries of compact objects, such as black holes and neutron stars, are the primary targets for gravitational-wave (GW) detection with Advanced LIGO. Accurate modeling of the emitted GWs is required to extract information about the binary source. The most accurate solution to the general relativistic two-body problem is available in numerical relativity (NR), which is however limited in application due to computational cost. Current searches use semi-analytic models that are based in post-Newtonian (PN) theory and calibrated to NR. In this talk, I will present comparisons between contemporary models and high-accuracy numerical simulations performed using the Spectral Einstein Code (SpEC), focusing at the questions: (i) How well do models capture binary's late-inspiral where they lack a-priori accurate information from PN or NR, and (ii) How accurately do they model binaries with parameters outside their range of calibration. These results guide the choice of templates for future GW searches, and motivate future modeling efforts.

A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction.

PubMed

Edvardsson, Sverker; Gardner, Paul P; Poole, Anthony M; Hendy, Michael D; Penny, David; Moulton, Vincent

2003-05-01

Noncoding RNA genes produce functional RNA molecules rather than coding for proteins. One such family is the H/ACA snoRNAs. Unlike the related C/D snoRNAs these have resisted automated detection to date. We develop an algorithm to screen the yeast genome for novel H/ACA snoRNAs. To achieve this, we introduce some new methods for facilitating the search for noncoding RNAs in genomic sequences which are based on properties of predicted minimum free-energy (MFE) secondary structures. The algorithm has been implemented and can be generalized to enable screening of other eukaryote genomes. We find that use of primary sequence alone is insufficient for identifying novel H/ACA snoRNAs. Only the use of secondary structure filters reduces the number of candidates to a manageable size. From genomic context, we identify three strong H/ACA snoRNA candidates. These together with a further 47 candidates obtained by our analysis are being experimentally screened.

Conserved syntenic clusters of protein coding genes are missing in birds.

PubMed

Lovell, Peter V; Wirthlin, Morgan; Wilhelm, Larry; Minx, Patrick; Lazar, Nathan H; Carbone, Lucia; Warren, Wesley C; Mello, Claudio V

2014-01-01

Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood. Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian sauropsids and in humans. These genes are located in regions associated with chromosomal rearrangements, and are largely present in crocodiles, suggesting that their loss occurred subsequent to the split of dinosaurs/birds from crocodilians. Many of these genes are associated with lethality in rodents, human genetic disorders, or biological functions targeting various tissues. Functional enrichment analysis combined with orthogroup analysis and paralog searches revealed enrichments that were shared by non-avian species, present only in birds, or shared between all species. Together these results provide a clearer definition of the genetic background of extant birds, extend the findings of previous studies on missing avian genes, and provide clues about molecular events that shaped avian evolution. They also have implications for fields that largely benefit from avian studies, including development, immune system, oncogenesis, and brain function and cognition. With regards to the missing genes, birds can be considered ‘natural knockouts’ that may become invaluable model organisms for several human diseases.

Sinbase: an integrated database to study genomics, genetics and comparative genomics in Sesamum indicum.

PubMed

Wang, Linhai; Yu, Jingyin; Li, Donghua; Zhang, Xiurong

2015-01-01

Sesame (Sesamum indicum L.) is an ancient and important oilseed crop grown widely in tropical and subtropical areas. It belongs to the gigantic order Lamiales, which includes many well-known or economically important species, such as olive (Olea europaea), leonurus (Leonurus japonicus) and lavender (Lavandula spica), many of which have important pharmacological properties. Despite their importance, genetic and genomic analyses on these species have been insufficient due to a lack of reference genome information. The now available S. indicum genome will provide an unprecedented opportunity for studying both S. indicum genetic traits and comparative genomics. To deliver S. indicum genomic information to the worldwide research community, we designed Sinbase, a web-based database with comprehensive sesame genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes, protein-coding genes (27,148), transposable elements (372,167) and non-coding RNAs (1,748). In particular, Sinbase provides unique and valuable information on colinear regions with various plant genomes, including Arabidopsis thaliana, Glycine max, Vitis vinifera and Solanum lycopersicum. Sinbase also provides a useful search function and data mining tools, including a keyword search and local BLAST service. Sinbase will be updated regularly with new features, improvements to genome annotation and new genomic sequences, and is freely accessible at http://ocri-genomics.org/Sinbase/. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

FastBit Reference Manual

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

Wu, Kesheng

2007-08-02

An index in a database system is a data structure that utilizes redundant information about the base data to speed up common searching and retrieval operations. Most commonly used indexes are variants of B-trees, such as B+-tree and B*-tree. FastBit implements a set of alternative indexes call compressed bitmap indexes. Compared with B-tree variants, these indexes provide very efficient searching and retrieval operations by sacrificing the efficiency of updating the indexes after the modification of an individual record. In addition to the well-known strengths of bitmap indexes, FastBit has a special strength stemming from the bitmap compression scheme used. Themore » compression method is called the Word-Aligned Hybrid (WAH) code. It reduces the bitmap indexes to reasonable sizes and at the same time allows very efficient bitwise logical operations directly on the compressed bitmaps. Compared with the well-known compression methods such as LZ77 and Byte-aligned Bitmap code (BBC), WAH sacrifices some space efficiency for a significant improvement in operational efficiency. Since the bitwise logical operations are the most important operations needed to answer queries, using WAH compression has been shown to answer queries significantly faster than using other compression schemes. Theoretical analyses showed that WAH compressed bitmap indexes are optimal for one-dimensional range queries. Only the most efficient indexing schemes such as B+-tree and B*-tree have this optimality property. However, bitmap indexes are superior because they can efficiently answer multi-dimensional range queries by combining the answers to one-dimensional queries.« less

References that anyone can edit: review of Wikipedia citations in peer reviewed health science literature

PubMed Central

Hladkowicz, Emily S; Pigford, Ashlee-Ann E; Ufholz, Lee-Anne; Postonogova, Tatyana; Shin, Eunkyung; Boet, Sylvain

2014-01-01

Objectives To examine indexed health science journals to evaluate the prevalence of Wikipedia citations, identify the journals that publish articles with Wikipedia citations, and determine how Wikipedia is being cited. Design Bibliometric analysis. Study selection Publications in the English language that included citations to Wikipedia were retrieved using the online databases Scopus and Web of Science. Data sources To identify health science journals, results were refined using Ulrich’s database, selecting for citations from journals indexed in Medline, PubMed, or Embase. Using Thomson Reuters Journal Citation Reports, 2011 impact factors were collected for all journals included in the search. Data extraction Resulting citations were thematically coded, and descriptive statistics were calculated. Results 1433 full text articles from 1008 journals indexed in Medline, PubMed, or Embase with 2049 Wikipedia citations were accessed. The frequency of Wikipedia citations has increased over time; most citations occurred after December 2010. More than half of the citations were coded as definitions (n=648; 31.6%) or descriptions (n=482; 23.5%). Citations were not limited to journals with a low or no impact factor; the search found Wikipedia citations in many journals with high impact factors. Conclusions Many publications are citing information from a tertiary source that can be edited by anyone, although permanent, evidence based sources are available. We encourage journal editors and reviewers to use caution when publishing articles that cite Wikipedia. PMID:24603564

Scalable gamma-ray camera for wide-area search based on silicon photomultipliers array

NASA Astrophysics Data System (ADS)

Jeong, Manhee; Van, Benjamin; Wells, Byron T.; D'Aries, Lawrence J.; Hammig, Mark D.

2018-03-01

Portable coded-aperture imaging systems based on scintillators and semiconductors have found use in a variety of radiological applications. For stand-off detection of weakly emitting materials, large volume detectors can facilitate the rapid localization of emitting materials. We describe a scalable coded-aperture imaging system based on 5.02 × 5.02 cm2 CsI(Tl) scintillator modules, each partitioned into 4 × 4 × 20 mm3 pixels that are optically coupled to 12 × 12 pixel silicon photo-multiplier (SiPM) arrays. The 144 pixels per module are read-out with a resistor-based charge-division circuit that reduces the readout outputs from 144 to four signals per module, from which the interaction position and total deposited energy can be extracted. All 144 CsI(Tl) pixels are readily distinguishable with an average energy resolution, at 662 keV, of 13.7% FWHM, a peak-to-valley ratio of 8.2, and a peak-to-Compton ratio of 2.9. The detector module is composed of a SiPM array coupled with a 2 cm thick scintillator and modified uniformly redundant array mask. For the image reconstruction, cross correlation and maximum likelihood expectation maximization methods are used. The system shows a field of view of 45° and an angular resolution of 4.7° FWHM.

Particle swarm optimization-based automatic parameter selection for deep neural networks and its applications in large-scale and high-dimensional data

PubMed Central

2017-01-01

In this paper, we propose a new automatic hyperparameter selection approach for determining the optimal network configuration (network structure and hyperparameters) for deep neural networks using particle swarm optimization (PSO) in combination with a steepest gradient descent algorithm. In the proposed approach, network configurations were coded as a set of real-number m-dimensional vectors as the individuals of the PSO algorithm in the search procedure. During the search procedure, the PSO algorithm is employed to search for optimal network configurations via the particles moving in a finite search space, and the steepest gradient descent algorithm is used to train the DNN classifier with a few training epochs (to find a local optimal solution) during the population evaluation of PSO. After the optimization scheme, the steepest gradient descent algorithm is performed with more epochs and the final solutions (pbest and gbest) of the PSO algorithm to train a final ensemble model and individual DNN classifiers, respectively. The local search ability of the steepest gradient descent algorithm and the global search capabilities of the PSO algorithm are exploited to determine an optimal solution that is close to the global optimum. We constructed several experiments on hand-written characters and biological activity prediction datasets to show that the DNN classifiers trained by the network configurations expressed by the final solutions of the PSO algorithm, employed to construct an ensemble model and individual classifier, outperform the random approach in terms of the generalization performance. Therefore, the proposed approach can be regarded an alternative tool for automatic network structure and parameter selection for deep neural networks. PMID:29236718

Planetary Data Systems (PDS) Imaging Node Atlas II

NASA Technical Reports Server (NTRS)

Stanboli, Alice; McAuley, James M.

2013-01-01

The Planetary Image Atlas (PIA) is a Rich Internet Application (RIA) that serves planetary imaging data to the science community and the general public. PIA also utilizes the USGS Unified Planetary Coordinate system (UPC) and the on-Mars map server. The Atlas was designed to provide the ability to search and filter through greater than 8 million planetary image files. This software is a three-tier Web application that contains a search engine backend (MySQL, JAVA), Web service interface (SOAP) between server and client, and a GWT Google Maps API client front end. This application allows for the search, retrieval, and download of planetary images and associated meta-data from the following missions: 2001 Mars Odyssey, Cassini, Galileo, LCROSS, Lunar Reconnaissance Orbiter, Mars Exploration Rover, Mars Express, Magellan, Mars Global Surveyor, Mars Pathfinder, Mars Reconnaissance Orbiter, MESSENGER, Phoe nix, Viking Lander, Viking Orbiter, and Voyager. The Atlas utilizes the UPC to translate mission-specific coordinate systems into a unified coordinate system, allowing the end user to query across missions of similar targets. If desired, the end user can also use a mission-specific view of the Atlas. The mission-specific views rely on the same code base. This application is a major improvement over the initial version of the Planetary Image Atlas. It is a multi-mission search engine. This tool includes both basic and advanced search capabilities, providing a product search tool to interrogate the collection of planetary images. This tool lets the end user query information about each image, and ignores the data that the user has no interest in. Users can reduce the number of images to look at by defining an area of interest with latitude and longitude ranges.

Side effects of radiotherapy in breast cancer patients : The Internet as an information source.

PubMed

Janssen, S; Käsmann, L; Fahlbusch, F B; Rades, D; Vordermark, D

2018-02-01

Breast cancer is the most common cancer type among women necessitating adjuvant radiotherapy. As the Internet has become a major source of information for cancer patients, this study aimed to evaluate the quality of websites giving information on side effects of radiotherapy for breast cancer patients. A patients' search for the English terms "breast cancer - radiotherapy - side effects" and the corresponding German terms "Brustkrebs - Strahlentherapie - Nebenwirkungen" was carried out twice (5 months apart) using the search engine Google. The first 30 search results each were evaluated using the validated 16-question DISCERN Plus instrument, the Health on the Net Code of Conduct (HONcode) certification and the Journal of the American Medical Association (JAMA) benchmark criteria. The overall quality (DISCERN score) of the retrieved websites was further compared to queries via Bing and Yahoo search engines. The DISCERN score showed a great range, with the majority of websites ranking fair to poor. Significantly superior results were found for English websites, particularly for webpages run by hospitals/universities and nongovernmental organizations (NGO), when compared to the respective German categories. In general, only a minority of websites met all JAMA benchmarks and was HONcode certified (both languages). We did not determine a relevant temporal change in website ranking among the top ten search hits, while significant variation occurred thereafter. Mean overall DISCERN score was similar between the various search engines. The Internet can give breast cancer patients seeking information on side effects of radiotherapy an overview. However, based on the currently low overall quality of websites and the lack of transparency for the average layperson, we emphasize the value of personal contact with the treating radio-oncologist in order to integrate and interpret the information found online.

Can people find patient decision aids on the Internet?

PubMed

Morris, Debra; Drake, Elizabeth; Saarimaki, Anton; Bennett, Carol; O'Connor, Annette

2008-12-01

To determine if people could find patient decision aids (PtDAs) on the Internet using the most popular general search engines. We chose five medical conditions for which English language PtDAs were available from at least three different developers. The search engines used were: Google (www.google.com), Yahoo! (www.yahoo.com), and MSN (www.msn.com). For each condition and search engine we ran six searches using a combination of search terms. We coded all non-sponsored Web pages that were linked from the first page of the search results. Most first page results linked to informational Web pages about the condition, only 16% linked to PtDAs. PtDAs were more readily found for the breast cancer surgery decision (our searches found seven of the nine developers). The searches using Yahoo and Google search engines were more likely to find PtDAs. The following combination of search terms: condition, treatment, decision (e.g. breast cancer surgery decision) was most successful across all search engines (29%). While some terms and search engines were more successful, few resulted in direct links to PtDAs. Finding PtDAs would be improved with use of standardized labelling, providing patients with specific Web site addresses or access to an independent PtDA clearinghouse.

"Research protocol: a synthesis of qualitative studies on the process of adaptation to dependency in elderly persons and their families"

PubMed Central

2010-01-01

Background Dealing with dependency in the elderly and their families leads us to explore the life experience of those involved together with the processes of adaptation to this condition. A number of original studies have been published which, following a qualitative methodology, have dealt with both dimensions. Methods/Design Objectives: 1) To present a synthesis of the qualitative evidence available on the process of adaptation to dependency in elderly persons and their families; 2) to conduct an in-depth study into the experiences and strategies developed by both to optimise their living conditions; 3) to enable standards of action/intervention to be developed in the caregiving environment. A synthesis of qualitative studies is projected with an extensive and inclusive bibliography search strategy. The primary search will focus on the major databases (CINAHL, MEDLINE, EMBASE, PsycInfo, PSICODOC, Cochrane Library, JBI, EMBASE, LILACS, CUIDEN, CUIDEN qualitative, CUIDATGE, British Nursing Index, SSCI). The secondary search will be conducted in articles taken from the references to studies identified in the articles and reports and the manual search in congresses and foundation papers. Article quality will be assessed by the guide proposed by Sandelowski & Barroso and data extraction done using the QARI data extraction form proposed by the Joanna Briggs Institute for Evidence-Based Practice. The synthesis of the findings will be based on the principles and procedures of grounded theory: coding, identification and relationship between categories, and synthesis using constant comparison as a strategy. Discussion This synthesis of qualitative evidence will enable us to detect health needs as perceived by the receivers in their own interaction contexts. PMID:20738846

BRAD, the genetics and genomics database for Brassica plants.

PubMed

Cheng, Feng; Liu, Shengyi; Wu, Jian; Fang, Lu; Sun, Silong; Liu, Bo; Li, Pingxia; Hua, Wei; Wang, Xiaowu

2011-10-13

Brassica species include both vegetable and oilseed crops, which are very important to the daily life of common human beings. Meanwhile, the Brassica species represent an excellent system for studying numerous aspects of plant biology, specifically for the analysis of genome evolution following polyploidy, so it is also very important for scientific research. Now, the genome of Brassica rapa has already been assembled, it is the time to do deep mining of the genome data. BRAD, the Brassica database, is a web-based resource focusing on genome scale genetic and genomic data for important Brassica crops. BRAD was built based on the first whole genome sequence and on further data analysis of the Brassica A genome species, Brassica rapa (Chiifu-401-42). It provides datasets, such as the complete genome sequence of B. rapa, which was de novo assembled from Illumina GA II short reads and from BAC clone sequences, predicted genes and associated annotations, non coding RNAs, transposable elements (TE), B. rapa genes' orthologous to those in A. thaliana, as well as genetic markers and linkage maps. BRAD offers useful searching and data mining tools, including search across annotation datasets, search for syntenic or non-syntenic orthologs, and to search the flanking regions of a certain target, as well as the tools of BLAST and Gbrowse. BRAD allows users to enter almost any kind of information, such as a B. rapa or A. thaliana gene ID, physical position or genetic marker. BRAD, a new database which focuses on the genetics and genomics of the Brassica plants has been developed, it aims at helping scientists and breeders to fully and efficiently use the information of genome data of Brassica plants. BRAD will be continuously updated and can be accessed through http://brassicadb.org.