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At least 415 records · Page 23Linked to original sources

PubMed2002

The EBI SRS server-new features.

MOTIVATION: Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. The new additions include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in 'Nice views', SRSQuickSearch bookmarklets. AVAILABILITY: SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.

Computer Communication Networks↗

PubMed2003

Methods for optimizing antiviral combination therapies.

MOTIVATION: Despite some progress with antiretroviral combination therapies, therapeutic success in the management of HIV-infected patients is limited. The evolution of drug-resistant genetic variants in response to therapy plays a key role in treatment failure and finding a new potent drug combination after therapy failure is considered challenging. RESULTS: To estimate the activity of a drug combination against a particular viral strain, we develop a scoring function whose independent variables describe a set of antiviral agents and viral DNA sequences coding for the molecular targets of the respective drugs. The construction of this activity score involves (1) predicting phenotypic drug resistance from genotypes for each drug individually, (2) probabilistic modeling of predicted resistance values and integration into a score for drug combinations, and (3) searching through the mutational neighborhood of the considered strain in order to estimate activity on nearby mutants. For a clinical data set, we determine the optimal search depth and show that the scoring scheme is predictive of therapeutic outcome. Properties of the activity score and applications are discussed.

Algorithms↗

PubMed2006

P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R.

UNLABELLED: The software tool P2BAT provides a massive parallel and user friendly implementation of the PBAT-analysis tools for family-based association tests (FBATs) in large-scale studies, including genome-wide association studies with several thousand subjects. Built on the original PBAT-implementation of the Lange-Van Steen algorithm to bypass the multiple testing problem in family-based association studies, P2BAT integrates all PBAT-analysis tools for binary and complex traits into R and makes them accessible through a user-friendly GUI. The genome-wide analysis tools are fully automated and can be ran massively parallel directly through the GUI. P2BAT is fully documented and contains graphical output tools for time-to-onset analysis. P2BAT also features the ability to test for gene and environment/drug interaction. AVAILABILITY: The P2BAT package is available as the R package 'pbatR' which can be downloaded from http://cran.r-project.org/. The PBAT-software is available at http://www.biostat.harvard.edu/~clange/.

Algorithms↗

PubMed2005

Asymmetric subsethood-product fuzzy neural inference system (ASuPFuNIS).

This paper presents an asymmetric subsethood-product fuzzy neural inference system (ASuPFuNIS) that directly extends the SuPFuNIS model by permitting signal and weight fuzzy sets to be modeled by asymmetric Gaussian membership functions. The asymmetric subsethood-product network admits both numeric as well as linguistic inputs. Input nodes, which act as tunable feature fuzzifiers, fuzzify numeric inputs with asymmetric Gaussian fuzzy sets; and linguistic inputs are presented as is. The antecedent and consequent labels of standard fuzzy if-then rules are represented as asymmetric Gaussian fuzzy connection weights of the network. The model uses mutual subsethood based activation spread and a product aggregation operator that works in conjunction with volume defuzzification in a gradient descent learning framework. Despite the increase in the number of free parameters, the proposed model performs better than SuPFuNIS, on various benchmarking problems, both in terms of the performance accuracy and architectural economy and compares excellently with other various existing models with a performance better than most of them.

Algorithms↗

PubMed2005

Self-organizing topological tree for online vector quantization and data clustering.

The self-organizing Maps (SOM) introduced by Kohonen implement two important operations: vector quantization (VQ) and a topology-preserving mapping. In this paper, an online self-organizing topological tree (SOTT) with faster learning is proposed. A new learning rule delivers the efficiency and topology preservation, which is superior of other structures of SOMs. The computational complexity of the proposed SOTT is O(log N) rather than O(N) as for the basic SOM. The experimental results demonstrate that the reconstruction performance of SOTT is comparable to the full-search SOM and its computation time is much shorter than the full-search SOM and other vector quantizers. In addition, SOTT delivers the hierarchical mapping of codevectors and the progressive transmission and decoding property, which are rarely supported by other vector quantizers at the same time. To circumvent the shortcomings of clustering performance of classical partition clustering algorithms, a hybrid clustering algorithm that fully exploit the online learning and multiresolution characteristics of SOTT is devised. A new linkage metric is proposed which can be updated online to accelerate the time consuming agglomerative hierarchical clustering stage. Besides the enhanced clustering performance, due to the online learning capability, the memory requirement of the proposed SOTT hybrid clustering algorithm is independent of the size of the data set, making it attractive for large database.

Algorithms↗

PubMedDate not supplied

Using UNIX, Part 2.

We talked about using 3 UNIX commands. In UNIX, there are many other options for using them. But for the most part, if you can use them like I have shown, you will be able to do everything you need. If you can learn these few points well, I think you will be better off than if I give you 50 options and leave you totally confused about when to do what. On some UNIX systems, an electronic version of the UNIX manual is on the system. This gives a lot more information about each command. However, it is a bit difficult to understand. If you want more information about any command, you can type man COMMAND, e.g., man ls. This will give you more ways to use the ls command. And remember, the command pwd tells what directory you are in, cd/directory changes to another directory, ls lists the contents of the directory you are in, ls more displays the directory contents 1 page at a time (the space bar gives you the next page), ls-al gives a detailed listing of the contents of the directory you are in, ls-al more displays them 1 page at a time (the space bar gives you the next page).

Biomedical Engineering↗

PubMed2004

Simulation of branching blood flows on parallel computers.

We present a fully parallel nonlinearly implicit algorithm for the numerical simulation of some branching blood flow problems, which require efficient and robust solver technologies in order to handle the high nonlinearity and the complex geometry. Parallel processing is necessary because of the large number of mesh points needed to accurately discretize the system of differential equations. In this paper we introduce a parallel Newton-Krylov-Schwarz based implicit method, and software for distributed memory parallel computers, for solving the nonlinear algebraic systems arising from a Q2-Q1 finite element discretization of the incompressible Navier-Stokes equations that we use to model the blood flow in the left anterior descending coronary artery.

Arteries↗

PubMedDate not supplied

A practical approach to the balance between acid production and renal acid excretion in humans.

Precise measurements of net endogenous acid production (NEAP) to determine net acid balance require labor and laboratory intensive steady-state measurements of dietary nutrient intakes and urine and stool composition. In an effort to simplify the task, investigators have devised several alternative methodologies, especially computational predictive models based on diet composition. This paper describes the so-called gold standard, and the details of each alternative methodology, discussing their strengths and potential pitfalls. We also briefly discuss what we believe the optimal NEAP for adult humans, and how to achieve that through diet.

Acid-Base Equilibrium↗

PubMedDate not supplied

MAP: an iterative experimental design methodology for the optimization of catalytic search space structure modeling.

One of the main problems in high-throughput research for materials is still the design of experiments. At early stages of discovery programs, purely exploratory methodologies coupled with fast screening tools should be employed. This should lead to opportunities to find unexpected catalytic results and identify the "groups" of catalyst outputs, providing well-defined boundaries for future optimizations. However, very few new papers deal with strategies that guide exploratory studies. Mostly, traditional designs, homogeneous covering, or simple random samplings are exploited. Typical catalytic output distributions exhibit unbalanced datasets for which an efficient learning is hardly carried out, and interesting but rare classes are usually unrecognized. Here is suggested a new iterative algorithm for the characterization of the search space structure, working independently of learning processes. It enhances recognition rates by transferring catalysts to be screened from "performance-stable" space zones to "unsteady" ones which necessitate more experiments to be well-modeled. The evaluation of new algorithm attempts through benchmarks is compulsory due to the lack of past proofs about their efficiency. The method is detailed and thoroughly tested with mathematical functions exhibiting different levels of complexity. The strategy is not only empirically evaluated, the effect or efficiency of sampling on future Machine Learning performances is also quantified. The minimum sample size required by the algorithm for being statistically discriminated from simple random sampling is investigated.

Algorithms↗

PubMed2005

Adjoint acceleration of Monte Carlo simulations using TORT/MCNP coupling approach: a case study on the shielding improvement for the cyclotron room of the Buddhist Tzu Chi General Hospital.

Full-scale Monte Carlo simulations of the cyclotron room of the Buddhist Tzu Chi General Hospital were carried out to improve the original inadequate maze design. Variance reduction techniques are indispensable in this study to facilitate the simulations for testing a variety of configurations of shielding modification. The TORT/MCNP manual coupling approach based on the Consistent Adjoint Driven Importance Sampling (CADIS) methodology has been used throughout this study. The CADIS utilises the source and transport biasing in a consistent manner. With this method, the computational efficiency was increased significantly by more than two orders of magnitude and the statistical convergence was also improved compared to the unbiased Monte Carlo run. This paper describes the shielding problem encountered, the procedure for coupling the TORT and MCNP codes to accelerate the calculations and the calculation results for the original and improved shielding designs. In order to verify the calculation results and seek additional accelerations, sensitivity studies on the space-dependent and energy-dependent parameters were also conducted.

Algorithms↗

PubMed1995

Methodological aspects of a computer-assisted telephone interview survey of oral health.

Despite the reported benefits of computer-assisted telephone interview (CATI) methods, experiences from their use in Australian oral health surveys have not been described. This report aimed to present methodological aspects of a CATI survey conducted in the five mainland states. A response rate of 66 per cent was obtained, yielding 4050 completed interviews. Analysis revealed generally small levels of non-response bias: persons who avoided or delayed dental treatment because of cost and non-health card holders were harder to contact, while non-English speakers and persons aged 20-29 years were less likely to participate. A total of 1770 person hours of interview time was spent on the survey: 64.5 per cent of that time was spent on the telephone with an average of 10 minutes 17 seconds per call (13 minutes 37 seconds per completed call). Only seven questions had missing data for more than 1 per cent of respondents. Comprehension of questions and cooperation with the interview was rated by interviewers as 'good' or 'very good' for more than 90 per cent of respondents. The CATI method was highly efficient and yielded good quality data for the survey.

Adolescent↗

PubMed1998

SHARE: a tool to analyze and assess strategies in health care organization management.

In health care organizations, management of both human and material resources implies decision making. When seemingly equivalent strategies are possible, simulation can help to make a decision on better grounds. The SHARE workframe was designed to address the specificities of health care and to provide a comprehensive environment for modelling and simulating health care processes. The typology of objects is defined as Actors, subdivided in Clients and Resources and Elementary Operations. Graphical tools allow us to build processes from these objects and to create their relationships. Various strategies based on either clinical or managerial changes may be investigated. After a simulation, graphical tools allow us to display summary information on the utilization of all actors, waiting times, and goodness of execution. The use of SHARE is exemplified with the analysis and simulation of changes in the Pulmonary Function Testing Laboratory of the Saint-Antoine Hospital, Paris.

Computer Simulation↗

PubMed2004

Super-proximity routing in structured peer-to-peer overlay networks.

Peer-to-Peer systems are emerging as one of the most popular Internet applications. Structured Peer-to-Peer overlay networks use identifier based routing algorithms to allow robustness, load balancing, and distributed lookup needed in this environment. However, identifier based routing that is independent of Internet topology tends to be of low efficiency. Aimed at improving the routing efficiency, the super-proximity routing algorithms presented in this paper combine Internet topology and overlay routing table in choosing the next hop. Experimental results showed that the algorithms greatly improve the efficiency of Peer-to-Peer routing.

Algorithms↗

PubMed2004

A hierarchical architecture of centralized monitoring and controlling system and its high-performance and interoperability protocol.

This paper describes a hierarchical architecture and a high-performance and interoperability protocol for centralized monitoring and controlling systems (CMCS). The protocol we proposed can interoperate different monitoring and controlling systems constructed by different companies, each with different functions and communication protocols. The protocol reduces the amount of traffic and has real-time and high-performance advantages. The protocol was implemented in CMCS for telecommunication power supply and air-conditioner used by the Telecommunication Bureau of Zhejiang Province. This paper deals with the hierarchical architecture and function of CMCS and packet format, command ID, and SDL description of its protocol. We also discuss the properties of the interoperability and performance of the protocol in this paper.

Algorithms↗

PubMed2004

Simulation of emission tomography using grid middleware for distributed computing.

SimSET is Monte Carlo simulation software for emission tomography. This paper describes a simple but effective scheme for parallel execution of SimSET using NetSolve, a client-server system for distributed computation. NetSolve (version 1.4.1) is "grid middleware" which enables a user (the client) to run specific computations remotely and simultaneously on a grid of networked computers (the servers). Since the servers do not have to be identical machines, computation may take place in a heterogeneous environment. To take advantage of diversity in machines and their workloads, a client-side scheduler was implemented for the Monte Carlo simulation. The scheduler partitions the total decay events by taking into account the inherent compute-speeds and recent average workloads, i.e., the scheduler assigns more decay events to processors expected to give faster service and fewer decay events to those expected to give slower service. When compute-speeds and sustained workloads are taken into account, the speed-up is essentially linear in the number of equivalent "maximum-service" processors. One modification in the SimSET code (version 2.6.2.3) was made to ensure that the total number of decay events specified by the user is maintained in the distributed simulation. No other modifications in the standard SimSET code were made. Each processor runs complete SimSET code for its assignment of decay events, independently of others running simultaneously. Empirical results are reported for simulation of a clinical-quality lung perfusion study.

Computer Communication Networks↗

PubMed1984

Clinical interpretation of maternal serum alpha-fetoprotein concentrations.

Concentrations of maternal serum alpha-fetoprotein provide the basis for decisions to proceed to ultrasonography and amniocentesis in the multistaged screening/diagnostic process used for the prenatal detection of open neural tube defects, abdominal wall defects, and twins. The concentration of maternal serum alpha-fetoprotein at or above which women should be advised that amniocentesis is available (cutoff levels for amniocentesis) varies, depending upon a number of factors, such as maternal weight, race, residence, and gestational age. We briefly describe a methodology for computing the predicted risks of fetal conditions associated with a given concentration of maternal serum alpha-fetoprotein adjusted for important variables. This adjustment methodology provides a straightforward means for clinical laboratories to report results of assays of maternal serum alpha-fetoprotein in terms of predicted risks, to facilitate understanding by the physician and patient of the clinical meaning of the results of maternal serum alpha-fetoprotein testing.

Amniocentesis↗

PubMed1997

Coarse-grain parallel computing for very large scale neural simulations in the NEXUS simulation environment.

We describe a neural simulator designed for simulating very large scale models of cortical architectures. This simulator, NEXUS, uses coarse-grain parallel computing by distributing computation and data onto multiple conventional workstations connected via a local area network. Coarse-grain parallel computing offers natural advantages in simulating functionally segregated neural processes. We partition a complete model into modules with locally dense connections--a module may represent a cortical area, column, layer, or functional entity. Asynchronous data communications among workstations are established through the Network File System, which, together with the implicit modularity, decreases communications overhead, and increases overall performance. Coarse-grain parallelism also benefits from the standardization of conventional workstations and LAN, including portability between generations and vendors.

Computer Communication Networks↗

PubMed2004

A new computational efficient approach for trabecular bone analysis using beam models generated with skeletonized graph technique.

Micro-finite element (FE) analysis is a well established technique for the evaluation of the elastic properties of trabecular bone, but is limited in its application due to the large number of elements that it requires to represent the complex internal structure of the bone. In this paper, we present an alternative FE approach that makes use of a recently developed 3D-Line Skeleton Graph Analysis (LSGA) technique to represent the complex internal structure of trabecular bone as a network of simple straight beam elements in which the beams are assigned geometrical properties of the trabeculae that they represent. Since an enormous reduction of cputime can be obtained with this beam modeling approach, ranging from approximately 1,200 to 3,600 for the problems investigated here, we think that the FE modeling technique that we introduced could potentially constitute an interesting alternative for the evaluation of the elastic mechanical properties of trabecular bone.

Algorithms↗