Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions

MyGV is an application to visualize (potentially genome-scale) gene structure annotation and prediction. The output of any external gene prediction program can be easily converted to a generalized format for input into MyGV. The application displays all input simultaneously in graphical representation, with a toggle option for a text-based view. Zooming capabilities allow detailed comparisons for specific genome locations. The tool is particularly helpful for refinement of ab initio predicted gene structures by spliced alignment with cDNA or protein homologs. AVAILABILITY: The program was written in Java and is freely available to non-commercial users by electronic download from http://bioinformatics.iastate.edu/bioinformatics2go/MyGV.     

BIOSITE: a program for the interactive comparison of aligned homologous protein sequences

A program, BIOSITE, providing for the interactive visual comparisonof aligned homologous amino-acid sequences is presented, includingan example of its application. The program allows for two typesof comparison sequence to be generated: an ‘identity’sequence and a ‘difference’ sequence. These maybe used on subsets of sequences and in further comparisons toidentify candidate sites involved in a distinct functional property.The program should prove a useful tool for biologists engagedin understanding sequence—function relationships.     

TreeSnatcher: coding trees from images

TreeSnatcher is a GUI-driven JAVA application for the semi-automatic recognition of multifurcating phylogenetic trees in pixel images. The program accepts an image file as input and analyzes the topology and the metrics of a tree depicted. The analysis is carried out in a multiple-stage process using algorithms from image analysis. In the end, TreeSnatcher produces a Newick tree code that represents the tree structure optionally including branch lengths. TreeSnatcher can process trees with 100 leaves or more in a few seconds. AVAILABILITY: TreeSnatcher was developed in JAVA under Mac OS X and is executable on UNIX/Linux, Windows and Mac OS X systems. The application and its documentation can be freely downloaded from http://www.cibiv.at/software/treesnatcher.     

Development of a program model to evaluate the potential for reuse of single-use medical devices: results of a pilot test study

Single-use medical devices (SUDs, or disposables) have become a major expense in hospital budgets. The need for cost reduction and the availability of sterilization technologies other than the autoclave have prompted hospitals worldwide to begin reusing disposables, in many cases without proper assessment of the true costs (time, personnel, etc) and ease/difficulty of implementation of an institutional reuse program. Our group has developed a rigorous program model to evaluate SUDs for reuse. The program comprises 3 sequential protocols: (1) device audit, (2) laboratory evaluation, and (3) clinical evaluation. Use of this model can produce scientific and financial data sufficient for any institution interested in reuse to reach an initial decision about its feasibility. In addition to the testing outcomes, regulatory requirements, the position of manufacturers and third-party reprocessors, and legal and ethical concerns must be considered. A successful reuse program must include ongoing evaluations to ensure that the safety levels and cost savings established during the initial audit and evaluation phases continue. Herein, we give the rationale and details of our program model and discuss results of our pilot application of the "ideal" protocol in a real-world context.     

Mass Survey—Its Future

Experience with a fast-tempo case finding survey in Seattle confirms the opinion expressed with regard to other areas, that the tools now are at hand to eradicate tuberculosis in Seattle in a 20-year period.The most important single factor in controlling tuberculosis is segregation and treatment of patients with active cases — sanatorium care that is sufficient in quantity and quality.Aggressive use of community-wide, mass x-ray program constitutes the second largest factor in controlling tuberculosis and has its greatest application in cities of over 100,000 population.The cost of such a mass survey program is trifling when compared with the cost of an adequate hospitalization program. The Seattle experience indicates that the cost of a mass survey program amortized over a five-year period is only 2 per cent of the cost of one year of hospital care.     

Mass survey--Its future

Experience with a fast-tempo case finding survey in Seattle confirms the opinion expressed with regard to other areas, that the tools now are at hand to eradicate tuberculosis in Seattle in a 20-year period. The most important single factor in controlling tuberculosis is segregation and treatment of patients with active cases - sanatorium care that is sufficient in quantity and quality. Aggressive use of community-wide, mass x-ray program constitutes the second largest factor in controlling tuberculosis and has its greatest application in cities of over 100,000 population. The cost of such a mass survey program is trifling when compared with the cost of an adequate hospitalization program. The Seattle experience indicates that the cost of a mass survey program amortized over a five-year period is only 2 per cent of the cost of one year of hospital care.     

SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs

Genome-wide analysis of single nucleotide polymorphism (SNP) markers is an extremely efficient means for genetic mapping of mutations or traits in mice. However, this approach often defines a relatively large recombinant interval. To facilitate the refinement of this interval, we developed the program SNP2RFLP. This program can be used to identify region-specific SNPs in which the polymorphic nucleotide creates a restriction fragment length polymorphism (RFLP) that can be readily assayed at the benchtop using restriction enzyme digestion of SNP-containing PCR products. The program permits user-defined queries that maximize the informative markers for a particular application. This facilitates fine-mapping in a region containing a mutation of interest, which should prove valuable to the mouse genetics community. SNP2RFLP and further details are publicly available at http://genetics.bwh.harvard.edu/snp2rflp/.     

SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs

Genome-wide analysis of single nucleotide polymorphism (SNP) markers is an extremely efficient means for genetic mapping of mutations or traits in mice. However, this approach often defines a relatively large recombinant interval. To facilitate the refinement of this interval, we developed the program SNP2RFLP. This program can be used to identify region-specific SNPs in which the polymorphic nucleotide creates a restriction fragment length polymorphism (RFLP) that can be readily assayed at the benchtop using restriction enzyme digestion of SNP-containing PCR products. The program permits user-defined queries that maximize the informative markers for a particular application. This facilitates fine-mapping in a region containing a mutation of interest, which should prove valuable to the mouse genetics community. SNP2RFLP and further details are publicly available at http://genetics.bwh.harvard.edu/snp2rflp/.

     

Diagnostic perspectives of mobile radiographic computerized tomography]

The authors assess mobile methods of x-ray computer-aided tomography (CAT) and suggest an organization and methodological scheme of its application. Their program of the first and up to now the only one in this country mobile CAT device is based on the new principles of mobile CAT application. It is realized in special hospitals of large regions, where the patients with the optimal indications for CAT are assembled. Over 15,000 examinations were carried out with the use of the suggested CAT program over 4 years, that resulted in detection of 1295 brain tumors, 804 cases with neoplastic involvement of the abdominal cavity and the retroperitoneal space. The authors claim that wide application of mobile CAT devices according to the program they suggest will help decide the problem of unavailability of such examinations, for it will rule out the principal cause of this unavailability--economic problems arising because of high price of this equipment. One mobile device may replace 3 permanent CAT devices, if used according to the program suggested by the authors.     

Effect of rhythmic gymnastics on the rhythm perception of children with deafness

This study was designed to examine the effect of a rhythmic gymnastics program on the rhythm perception of children with deafness. Two groups--control and experiment--of 12 and 17 children, respectively, coming from the same school for the deaf participated in this study. The duration of the program for the individuals in the experiment group was 16 weeks (at a frequency of 3 lessons per week, for 40 minutes each lesson), while children of both groups adhered to their regular school schedules. Five rhythmic patterns in 3 speeds (tempi) were reproduced both by a metronome and each child's performance and were recorded on a digital disk before and after the application of the program. The rate of time deviation (in seconds) between the 2 beats represented the score for each child. The average rate of the 5 rhythmic patterns in each tempo was calculated separately, giving 3 scores (one for every tempo) for each child. Significance was set at p < or = 0.05. The data revealed significant postexercise differences in favor of the experiment group, an improvement of the experiment group in all pre-post values, as well as an improved medium tempo with relation to the control group. The findings show the effectiveness of the specific program in terms of improving rhythm ability, thus indicating its use in educating children with deafness on rhythm instead of preferring the routine of the adapted school program.     

PhyloBLAST: facilitating phylogenetic analysis of BLAST results

PhyloBLAST is an internet-accessed application based on CGI/Perl programming that compares a users protein sequence to a SwissProt/TREMBL database using BLAST2 and then allows phylogenetic analyses to be performed on selected sequences from the BLAST output. Flexible features such as ability to input your own multiple sequence alignment and use PHYLIP program options provide additional web-based phylogenetic analysis functionality beyond the analysis of a BLAST result.     

Computer-assisted assignment of peptides with non-standard amino acids

Summary A comprehensive peptide assignment program and its application to a cyclic peptide, cyclosporin A, are presented in this paper. A group of graph theoretical algorithms using fuzzy logic are discussed with the aid of examples from cyclosporin A. The algorithms deal with heavily overlapped peaks, recover disjointed and distorted spin coupling networks, and include strategies for sequence-specific assignment. A procedure to extend the Protein Knowledge Base for automatically assigning non-standard amino acid residues is also presented. The program is capable of completely automated assignment for small peptides (20 residues). For such molecules, it is insensitive to whether the peptide chain is cyclic or acyclic, and to whether amide protons are present or absent. For larger peptides/proteins, more user interaction is required and the sequence-specific assignment step usually must proceed through fragments smaller than the full length to avoid problems due to occurrence of a combinatorial explosion. The program can be applied as a rigorous tool to check manual assignments. The fuzzy graph theoretical concepts built in the program are illustrated with 2D proton spectra of a peptide, but may be extended to higher-dimensional spectra, other biopolymers, natural products and other organic structures.     

GB2sequin - A file converter preparing custom GenBank files for database submission

The typical wet lab user often annotates smaller sequences in the GenBank format, but resulting files are not accepted for database submission by NCBI. This makes submission of such annotations a cumbersome task. Here we present “GB2sequin” an easy-to-use web application that converts custom annotations in the GenBank format into the NCBI direct submission format Sequin. Additionally, the program generates a “five-column, tab-delimited feature table” and a FASTA file. Those are required for submission through BankIt or the update of an existing GenBank entry. We specifically developed “GB2sequin” for the regular wet lab researcher with strong focus on user-friendliness and flexibility. The application is equipped with an intuitive graphical interface and a comprehensive documentation. It can be employed to prepare any GenBank file for database submission and is freely available online at https://chlorobox.mpimp-golm.mpg.de/GenBank2Sequin.html.     

A finite-difference computer model of solute diffusion in bacterial films with simultaneous metabolism and chemical reaction

This finite-difference computer model is designed to simulatecomplex diffusion/reaction events in bacterial films. It ismodular, each module mirroring closely a particular physical,chemical or biochemical factor. It is capable of handling >20 diffusing/reacting species, but can be easily expanded orsimplified to match particular systems. It was originally designedfor modelling the events in dental plaque leading to tooth decay,but should find application in other fields. It allows for ion-exchangeinteractions with, for example, fixed charges on bacterial surfaces,which can act as pH and cation buffer sites. pH-dependent utilizationof substrate is modelled implicitly, combining Michaelis-Mentenkinetics with diffusion in a single iterative procedure. Advantagesare given for computing diffusion of all other species explicitlyusing single-species diffusion coefficients, with charge-couplingby means of the algorithm Q-COUPLE. Activity corrections andenzyme pH-dependence are included. Chemical equilibria and mineraldeposition/dissolution are computed iteratively node by node.The program is tested against some problems having analyticalsolutions, and an example is given of its application to demineralizationof teeth as a result of bacterial action in dental plaque.     

gPGA: GPU Accelerated Population Genetics Analyses

Background

The isolation with migration (IM) model is important for studies in population genetics and phylogeography. IM program applies the IM model to genetic data drawn from a pair of closely related populations or species based on Markov chain Monte Carlo (MCMC) simulations of gene genealogies. But computational burden of IM program has placed limits on its application.

Methodology

With strong computational power, Graphics Processing Unit (GPU) has been widely used in many fields. In this article, we present an effective implementation of IM program on one GPU based on Compute Unified Device Architecture (CUDA), which we call gPGA.

Conclusions

Compared with IM program, gPGA can achieve up to 52.30X speedup on one GPU. The evaluation results demonstrate that it allows datasets to be analyzed effectively and rapidly for research on divergence population genetics. The software is freely available with source code at https://github.com/chunbaozhou/gPGA.     

Using Learning Outcome Measures to assess Doctoral Nursing Education

Education programs at all levels must be able to demonstrate successful program outcomes. Grades alone do not represent a comprehensive measurement methodology for assessing student learning outcomes at either the course or program level. The development and application of assessment rubrics provides an unequivocal measurement methodology to ensure a quality learning experience by providing a foundation for improvement based on qualitative and quantitatively measurable, aggregate course and program outcomes. Learning outcomes are the embodiment of the total learning experience and should incorporate assessment of both qualitative and quantitative program outcomes. The assessment of qualitative measures represents a challenge for educators in any level of a learning program. Nursing provides a unique challenge and opportunity as it is the application of science through the art of caring. Quantification of desired student learning outcomes may be enhanced through the development of assessment rubrics designed to measure quantitative and qualitative aspects of the nursing education and learning process. They provide a mechanism for uniform assessment by nursing faculty of concepts and constructs that are otherwise difficult to describe and measure. A protocol is presented and applied to a doctoral nursing education program with recommendations for application and transformation of the assessment rubric to other education programs. Through application of these specially designed rubrics, all aspects of an education program can be adequately assessed to provide information for program assessment that facilitates the closure of the gap between desired and actual student learning outcomes for any desired educational competency.     

Multi-query sequence BLAST output examination with MuSeqBox

SUMMARY: MuSeqBox is a program to parse BLAST output and store attributes of BLAST hits in tabular form. The user can apply a number of selection criteria to filter out hits with particular attributes. MuSeqBox provides a powerful annotation tool for large sets of query sequences that are simultaneously compared against a database with any of the standard stand-alone or network-client BLAST programs. We discuss such application to the problem of annotation and analysis of EST collections. AVAILABILITY: The program was written in standard C++ and is freely available to noncommercial users by request from the authors. The program is also available over the web at http://bioinformatics.iastate.edu/bioinformatics2go/mb/MuSeqBox.html.     

Results and harmonization guidelines from two large-scale international Elispot proficiency panels conducted by the Cancer Vaccine Consortium (CVC/SVI)

The Cancer Vaccine Consortium of the Sabin Vaccine Institute (CVC/SVI) is conducting an ongoing large-scale immune monitoring harmonization program through its members and affiliated associations. This effort was brought to life as an external validation program by conducting an international Elispot proficiency panel with 36 laboratories in 2005, and was followed by a second panel with 29 participating laboratories in 2006 allowing for application of learnings from the first panel. Critical protocol choices, as well as standardization and validation practices among laboratories were assessed through detailed surveys. Although panel participants had to follow general guidelines in order to allow comparison of results, each laboratory was able to use its own protocols, materials and reagents. The second panel recorded an overall significantly improved performance, as measured by the ability to detect all predefined responses correctly. Protocol choices and laboratory practices, which can have a dramatic effect on the overall assay outcome, were identified and lead to the following recommendations: (A) Establish a laboratory SOP for Elispot testing procedures including (A1) a counting method for apoptotic cells for determining adequate cell dilution for plating, and (A2) overnight rest of cells prior to plating and incubation, (B) Use only pre-tested serum optimized for low background: high signal ratio, (C) Establish a laboratory SOP for plate reading including (C1) human auditing during the reading process and (C2) adequate adjustments for technical artifacts, and (D) Only allow trained personnel, which is certified per laboratory SOPs to conduct assays. Recommendations described under (A) were found to make a statistically significant difference in assay performance, while the remaining recommendations are based on practical experiences confirmed by the panel results, which could not be statistically tested. These results provide initial harmonization guidelines to optimize Elispot assay performance to the immunotherapy community. Further optimization is in process with ongoing panels.