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At least 1,009 records · Page 56Linked to original sources
PubMed2002

PGAAS: a prokaryotic genome assembly assistant system.

MOTIVATION: In order to accelerate the finishing phase of genome assembly, especially for the whole genome shotgun approach of prokaryotic species, we have developed a software package designated prokaryotic genome assembly assistant system (PGAAS). The approach upon which PGAAS is based is to confirm the order of contigs and fill gaps between contigs through peptide links obtained by searching each contig end with BLASTX against protein databases. RESULTS: We used the contig dataset of the cyanobacterium Synechococcus sp. strain PCC7002 (PCC7002), which was sequenced with six-fold coverage and assembled using the Phrap package. The subject database is the protein database of the cyanobacterium, Synechocystis sp. strain PCC6803 (PCC6803). We found more than 100 non-redundant peptide segments which can link at least 2 contigs. We tested one pair of linked contigs by sequencing and obtained satisfactory result. PGAAS provides a graphic user interface to show the bridge peptides and pier contigs. We integrated Primer3 into our package to design PCR primers at the adjacent ends of the pier contigs. AVAILABILITY: We tested PGAAS on a Linux (Redhat 6.2) PC machine. It is developed with free software (MySQL, PHP and Apache). The whole package is distributed freely and can be downloaded as UNIX compress file: ftp://ftp.cbi.pku.edu.cn/pub/software/unix/pgaas1.0.tar.gz. The package is being continually updated.

Algorithms↗
PubMed1988

POEMS: program for outliers elimination in multidimensional space.

A Program for Outliers Elimination in Multidimensional Space (POEMS), which allows the user to eliminate outliers from training spaces as a prior step to any statistical study, is presented. Even though the program can be applied to any scientific field, the characteristics of POEMS makes it particularly suitable for 'series design' on Quantitative Structure-Activity Relationships studies.

Algorithms↗
PubMedDate not supplied

Designing an information technology application for use in community-focused nursing education. Nightingale Tracker Field Test Nurse Team.

Changes in healthcare are highlighting the need for nurse educators to include more community-focused clinical experiences in the nursing curriculum. Because community experiences often require students to travel to clinics and patients' homes at multiple distant sites, nurse educators are concerned about how to best supervise their students and maintain reliable communication links. In light of these needs, FITNE (formerly the Fuld Institute for Technology in Nursing Education) undertook a 3-year information technology research and development project known as the Nightingale Tracker. The design for the Nightingale Tracker included activities aimed toward analyzing the unique communication needs faced by practitioners in community settings. It incorporated multiple forms of user input, including requirements-gathering focus groups, nurse educator surveys, and feedback from two user tests. Subject feedback from using Tracker prototypes in the field was invaluable in the design of the final product.

Community Health Nursing↗
PubMed2005

Structural flexibility of laparoscopic instruments: implication for the design of virtual reality simulators.

In accordance with the Practice Specificity Theory, training on models that closely resemble real life scenarios is most beneficial to learning. Research in the virtual reality (VR) simulation, as a potential teaching and evaluation tool, concentrated on the design of trainers to resemble operating room (OR) conditions. The purpose of the present investigation was to determine the structural flexibility of laparoscopic instruments of different materials and diameters under a wide range of stresses. Incorporating the mechanical properties of these instruments into the algorithms can prove to further increase the fidelity of VR simulators. The amount of deviation from pre-stress position in the instruments' shaft was measured with infrared markers and used as the index of structural flexibility. All instruments deviated considerably with the largest deviations observed for the small disposable, and lowest for the large reusable instruments. There was a linear relation between the stress and deviation for all instruments, which varied as a function of diameter. Similar instrument deviations were observed during cholecystectomy performed on porcine liver. Our findings show that laparoscopic instruments are not rigid bodies and are prone to significant deviations during standard laparoscopic procedures. This suggests that the structural flexibility of laparoscopic instruments should be modeled in the design of VR simulators.

Canada↗
PubMed1986

Computer-assisted measurements in pacemaker follow-up.

The application of increasingly sophisticated engineering techniques to cardiac pacemaker design has resulted in substantially greater complexity of follow-up which requires that more complicated measurements be made and interpreted. A feasibility study was conducted in which microcomputer software was designed to permit direct electronic communication between the computer and a commercial follow-up measurement device. This technique eliminates human error in reading or copying measurement data, and facilitates the application of computerized error-trapping, predictive interpretation of measurements, and database-management methods to pacemaker follow-up.

Computers↗
PubMed1993

The Habitability Mini-Laboratory: testing the tools of space habitat architecture.

Living in the closed, confined environment of a space station for a long period and under microgravity conditions, crew members can encounter problems of a physiological and also a psychological nature. The architecture of their living quarters can greatly influence their well-being and their efficiency. Simulation of a proposed architecture and of human movement within that architecture is the most effective way to evaluate the design. Two simulation tools, Computer-Aided Design (CAD) software tools and a mock-up on a smaller scale, were used to 'construct' several proposed architectures. Those models were then evaluated to determine the investigation methods that should be used in future architectural development projects.

Computer Simulation↗
PubMed2004

Improved and automated prediction of effective siRNA.

Short interfering RNAs are used in functional genomics studies to knockdown a single gene in a reversible manner. The results of siRNA experiments are highly dependent on the choice of siRNA sequence. In order to evaluate siRNA design rules, we collected a database of 398 siRNAs of known efficacy from 92 genes. We used this database to evaluate previously proposed rules from smaller datasets, and to find a new set of rules that are optimal for the entire database. We also trained a regression tree with full cross-validation. It was however difficult to obtain the same precision as methods previously tested on small datasets from one or two genes. We show that those methods are overfitting as they work poorly on independent validation datasets from multiple genes. Our new design rules can predict siRNAs with efficacy >/= 50% in 91% of cases, and with efficacy >/=90% in 52% of cases, which is more than a twofold improvement over random selection. Software for designing siRNAs is available online via a web server at or as a standalone version for high-throughput applications.

Algorithms↗
PubMed1995

Pediatric parenteral nutrition mixtures design program: validity and stability study.

The formulation and elaboration of a correct parenteral nutrition (PN) in infancy requires the use of many parameters, the realization of complicated mathematical calculations, and repeated and individualized adjustments of the final constituents. The use of computer programs in the confection of PN has simplified the whole process, but, to our understanding, the programs being used at the moment lack the flexibility needed to generalize its use in the pediatric age. The aim of this work is to present a new computer program able to make up complete pediatric units of PN by itself, which follow the nutritional requirements and the marketed preparations established for each clinical situation. The program provides, automatically, standard amounts for each nutrient, according to age, water needs, and route of administration. The program turns these amounts, which can be modified before or after knowing the final composition, into milliliters of each commercial product and provides a complete analysis of the PN solution. It is also possible to adapt the basic configuration of the program to the needs of each patient, modifying the nutritional requirements and the products that the program will use. In order to assess the validity of the program, we made up a series of PN solutions, for a simulated sample of patients, which represented different clinical situations and age groups. We analyzed the composition of the mixtures and its physical-chemical stability. No problems in the PN solutions generated by the program when using our standard configuration were found. A study of reproducibility was carried out and no difficulties of execution, errors, or differences in the composition of the PN solutions designed by the different physicians were found. Average time needed for the design of a PN was less than 5 min. The use of computer programs in the design of mixtures of PN reduces errors and time, allowing a better use of this technique of nutritional support.

Adolescent↗
PubMedDate not supplied

Genetic algorithm for the design of molecules with desired properties.

The design of molecules with desired properties is still a challenge because of the largely unpredictable end results. Computational methods can be used to assist and speed up this process. In particular, genetic algorithms have proved to be powerful tools with a wide range of applications, e.g. in the field of drug development. Here, we propose a new genetic algorithm that has been tailored to meet the demands of de novo drug design, i.e. efficient optimization based on small training sets that are analyzed in only a small number of design cycles. The efficiency of the design algorithm was demonstrated in the context of several different applications. First, RNA molecules were optimized with respect to folding energy. Second, a spinglass was optimized as a model system for the optimization of multiletter alphabet biopolymers such as peptides. Finally, the feasibility of the computer-assisted molecular design approach was demonstrated for the de novo construction of peptidic thrombin inhibitors using an iterative process of 4 design cycles of computer-guided optimization. Synthesis and experimental fitness determination of only 600 different compounds from a virtual library of more than 10(17) molecules was necessary to achieve this goal.

Algorithms↗
PubMed1997

[A comprehensive detection and psocessing system of visual electrophysiological information based on interconnected computers].

This paper introduce a novel comprehensive system of visual electrophysiological information processing. The weak-light stimulator and surface-electrode are used to overcome the subject's unfitted sense led by Ganzifield stimulator and the cornea-touch electrode. Based on two computers which are interconnected, this system can work on pan-character picture stimulating mode. While working on line, it can dynamically display the process of test in real-time. It also offers a clear interface and integrated modules of information processing and analysis.

Adult↗
PubMed2001

[Development and clinical application of the full automatic animal rearing cabin of low oxygen and high carbon dioxide].

This paper introduces a kind of automatic animal rearing cabin of low oxygen and high carbon dioxide. It can mimic the environment of low oxygen and high carbon dioxide at atmospheric pressure and automatically measure and control the concentrations of oxygen and carbon dioxide as well as temperature and humidity in the cabin. The system may provide the equipment support for clinical COPD study. The clinical applications show that the cabin with accurate measurement and control is practical and reliable.

Air Conditioning↗
PubMed2000

Relational database design.

Relational databases are the predominant method for storing repetitive data in computers because they allow efficient and flexible storage of that data. While medical directors and underwriters are more likely to use a spreadsheet than a database program to analyze their business, the data they wish to study are often stored in corporate databases. Or the data may be complex enough to require being keyed into or downloaded into a personal computer (PC) database program for storage, even if the data are then output to a spread-sheet for numerical analysis. In many circumstances, one can benefit from an understanding of efficient database design. After a brief overview, the reader is led step-by-step through a practical explanation of database design, from a flat file to a relational model.

Database Management Systems↗
PubMed1998

Automated interpretation of high-energy collision-induced dissociation spectra of singly protonated peptides by 'SeqMS', a software aid for de novo sequencing by tandem mass spectrometry.

SeqMS, a software program designed for the automated interpretation of high-energy collision-induced dissociation (CID) mass spectra of singly protonated peptides ionized by fast atom bombardment, has been developed. The software is capable of probing the sequence of an unknown peptide, and even of certain modified peptides. The program, compiled for WINDOWS95 or NT, also permits the retrieval of raw data and the reconstruction of the spectra on a user-friendly graphical interface with the aid of several tools for processing the spectra, which include setting multiple threshold levels and automatic peak detection. SeqMS is capable of generating candidate sequences, based on the detected peaks, and of displaying the resulting assignments for each candidate in a spectrum or in tabular form. The software has the following capabilities: 1) the ions derived from backbone and side-chain fragmentations, internal and immonium ions, and side-chain loss ions can be used for calculation; 2) 18O-labeling of a peptide at the C terminus, a methodology which was developed to differentiate N-terminal from C-terminal ions, is applicable as an optional setting; 3) modified amino acids and N- or C-terminal blocking groups are taken into account for calculation according to the user's setting in a library; 4) amino acid composition and partial or complete amino acid sequence of a peptide can be used as input for calculation; 5) the assignments of signal output in a spectrum can be graphically edited, and then re-calculated based on the edited peaks. The efficacy of the program is demonstrated by testing 74 high-energy CID spectra, obtained using a four-sector instrument, of synthetic, proteolytic, and biologically active peptides, some of which contain modified groups.

Algorithms↗
PubMed2004

A novel method for visualizing nuclear hormone receptor networks relevant to drug metabolism.

The increasing generation of biological data represents a challenge to understanding the complexity of systems, resulting in scientists increasingly focused on a relatively narrow area of study, thereby limiting insight that can be gained from a broader perspective. In the field of drug metabolism and toxicology we are witnessing the characterization of many proteins. Most of the key enzymes and transporters are recognized as transcriptionally regulated by the nuclear hormone receptors such as pregnane X receptor, constitutive androstane receptor, vitamin D receptor, glucocorticoid receptor, and others. There is apparent cross talk in regulation, since multiple receptors may modulate expression of a single enzyme or transporter, representing one of many areas of active research interest. We have used published data on nuclear hormone receptors, enzymes, ligands, and other biological information to manually annotate an Oracle database, forming the basis of a platform for querying (MetaDrug). Using algorithms, we have demonstrated how nuclear hormone receptors alone can form a network of direct interactions, and when expanded, this network increases in complexity to describe the interactions with target genes as well as small molecules known to bind a receptor, enzyme, or transporter. We have also described how the database can be used for visualizing high-throughput microarray data derived from a published study of MCF-7 cells treated with 4-hydroxytamoxifen, to highlight potential downstream effects of molecule treatment. The database represents a novel knowledge mining and analytical tool that, to be relevant, requires continual updating to evolve alongside other key storage systems and sources of biological knowledge.

Databases, Factual↗