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PubMed2005

On the use of error propagation for statistical validation of computer vision software.

Computer vision software is complex, involving many tens of thousands of lines of code. Coding mistakes are not uncommon. When the vision algorithms are run on controlled data which meet all the algorithm assumptions, the results are often statistically predictable. This renders it possible to statistically validate the computer vision software and its associated theoretical derivations. In this paper, we review the general theory for some relevant kinds of statistical testing and then illustrate this experimental methodology to validate our building parameter estimation software. This software estimates the 3D positions of buildings vertices based on the input data obtained from multi-image photogrammetric resection calculations and 3D geometric information relating some of the points, lines and planes of the buildings to each other.

Algorithms↗
PubMed1998

Towards a biocatalyst for (S)-styrene oxide production: characterization of the styrene degradation pathway of Pseudomonas sp. strain VLB120.

In order to design a biocatalyst for the production of optically pure styrene oxide, an important building block in organic synthesis, the metabolic pathway and molecular biology of styrene degradation in Pseudomonas sp. strain VLB120 was investigated. A 5.7-kb XhoI fragment, which contained on the same strand of DNA six genes involved in styrene degradation, was isolated from a gene library of this organism in Escherichia coli by screening for indigo formation. T7 RNA polymerase expression experiments indicated that this fragment coded for at least five complete polypeptides, StyRABCD, corresponding to five of the six genes. The first two genes encoded the potential carboxy-terminal part of a sensor, named StySc, and the complete response regulator StyR. Fusion of the putative styAp promoter to a lacZ reporter indicated that StySc and StyR together regulate expression of the structural genes at the transcriptional level. Expression of styScR also alleviated a block that prevented translation of styA mRNA when a heterologous promoter was used. The structural genes styA and styB produced a styrene monooxygenase that converted styrene to styrene oxide, which was then converted to phenylacetaldehyde by StyC. Sequence homology analysis of StyD indicated a probable function as a phenylacetaldehyde dehydrogenase. To assess the usefulness of the enzymes for the production of enantiomerically pure styrene oxide, we investigated the enantiospecificities of the reactions involved. Kinetic resolution of racemic styrene oxide by styrene oxide isomerase was studied with E. coli recombinants carrying styC, which converted styrene oxide at a very high rate but with only a slight preference for the S enantiomer. However, recombinants producing styrene monooxygenase catalyzed the formation of (S)-styrene oxide from inexpensive styrene with an excellent enantiomeric excess of more than 99% at rates up to 180 U g (dry weight) of cells-1.

Base Sequence↗
PubMed2000

A Monte Carlo simulation of background characteristics of low-level HPGe detectors

The radionuclide levels observed at present in the marine environment are very low, therefore high sensitive spectrometric systems are required for carrying out oceanographic investigations. The present-state-of-the-art carefully designed low-level HPGe gamma-spectrometers, which do not operate underground, have a dominating background component induced by cosmic rays, mostly by cosmic muons. High energy cosmic rays can initiate a large number of physical processes leading to background induction. Analytic solutions for describing these processes are not available and therefore, a Monte Carlo simulation is necessary. The development of a simulation code for background induction is useful for the optimisation of a counting system in respect to its background characteristics. It enables to assert the background before the system is built and also to perform systematic investigation of the influence of various parameters on the background of the detector. The GEANT code has been selected from the codes systems facilitating the simulation of the passage of particles through matter, as it best meets the requirements for simulations with high-energy muons. The obtained results show that the background depends most significantly on the thickness, the size and lining of the shield. Lead shielding of 15 cm thick has been found to be the optimum shielding for most applications. It is not advisable to build an unnecessarily large shield. A shield with removable lining would be the best as the lining can be removed from applications where the lead X-rays are not a disturbing influence.

Journal Article↗
PubMed1997

Using structured text and templates to capture health status outcomes in the electronic health record.

BACKGROUND: Because of the difficulty of implementing clinical outcomes-focused quality improvement (QI) projects, most organizations' efforts and comparative quality report cards have centered on structure and process indicators or on outcomes captured in administrative data systems. Ultimately, however, health care is intended to improve health. Health status is now frequently included in the set of quality of care information requested by purchasers of health care, accrediting and governmental agencies, and consumer groups. Subsequently, users of electronic health record (EHR) systems are demanding that the EHR support the collection and comparative analysis of health status information over time and by clinical population and provider. APPROACH: As opposed to the current practice in most organizations of collecting health status data via an annual mail survey, the approach discussed in this article utilizes standardized coding and classification (SCC) systems and standardized surveys to capture health status information in the EHR during the routine course of care delivery through the use of templates built on structured text. This method is illustrated with examples from the WAVE EHR. The EHR-based structured text and template approach facilitates the incorporation of health status measurement into the documentation of the patient-provider encounter, builds on recognized SCC systems and standardized surveys, and enables information retrieval for a variety of analyses, including those focused on QI. CONCLUSIONS: Health status outcomes are an essential component of an information set focused on health care quality. To routinely capture and analyze health status variables, SCC systems and standardized health status surveys are necessary.

Forms and Records Control↗
PubMed1994

M.phi 3TII: a new monospecific DNA (cytosine-C5) methyltransferase with pronounced amino acid sequence similarity to a family of adenine-N6-DNA-methyltransferases.

The temperate B.subtilis phages phi 3T and rho 11s code, in addition to the multispecific DNA (cytosine-C5) methyltransferases (C5-MTases) M.phi 3TI and M.rho 11sI, which were previously characterized, for the identical monospecific C5-MTases M.phi 3TII and M.rho 11sII. These enzymes modify the C to TCGA sites, a novel target specificity among C5-MTases. The primary sequence of M.phi 3TII (326 amino acids) shows all conserved motifs typical of the building plan of C5-MTases. The degree of relatedness between M.phi 3TII and all other mono- or multispecific C5-MTases ranges from 30-40% amino acid identity. Particularly M.phi 3TII does not show pronounced similarity to M.phi 3TI indicating that both MTase genes were not generated from one another but were acquired independently by the phage. The amino terminal part of the M.phi 3TII (preceding the variable region 'V'), which predominantly constitutes the catalytic domain of the enzyme, exhibits pronounced sequence similarity to the amino termini of a family of A-N6-MTases, which--like M.Taql--recognize the general sequence TNNA. This suggests that recently described similarities in the general three dimensional organization of C5- and A-N6-MTases imply divergent evolution of these enzymes originating from a common molecular ancestor.

Amino Acid Sequence↗
PubMed2006

Gadolinium neutron capture brachytherapy (GdNCB), a new treatment method for intravascular brachytherapy.

Restenosis is a major problem after balloon angioplasty and stent implantation. The aim of this study is to introduce gadolinium neutron capture brachytherapy (GdNCB) as a suitable modality for treatment of stenosis. The utility of GdNCB in intravascular brachytherapy (IVBT) of stent stenosis is investigated by using the GEANT4 and MCNP4B Monte Carlo radiation transport codes. To study capture rate, Kerma, absorbed dose and absorbed dose rate around a Gd-containing stent activated with neutrons, a 30 mm long, 5 mm diameter gadolinium foil is chosen. The input data is a neutron spectrum used for clinical neutron capture therapy in Studsvik, Sweden. Thermal neutron capture in gadolinium yields a spectrum of high-energy gamma photons, which due to the build-up effect gives an almost flat dose delivery pattern to the first 4 mm around the stent. The absorbed dose rate is 1.33 Gy/min, 0.25 mm from the stent surface while the dose to normal tissue is in order of 0.22 Gy/min, i.e., a factor of 6 lower. To spare normal tissue further fractionation of the dose is also possible. The capture rate is relatively high at both ends of the foil. The dose distribution from gamma and charge particle radiation at the edges and inside the stent contributes to a nonuniform dose distribution. This will lead to higher doses to the surrounding tissue and may prevent stent edge and in-stent restenosis. The position of the stent can be verified and corrected by the treatment plan prior to activation. Activation of the stent by an external neutron field can be performed days after catherization when the target cells start to proliferate and can be expected to be more radiation sensitive. Another advantage of the nonradioactive gadolinium stent is the possibility to avoid radiation hazard to personnel.

Blood Vessel Prosthesis↗
PubMed1994

Lessons learned while building an integrated ICU workstation.

The project LUCY (Linked Ulm Care sYstem) is described. The goal of this project was to build a research workstation in an Intensive Care Unit which enables evaluation of data/information processing and presentation concepts. Also evaluation of new devices and functions considering not only one device but the workplace as an entirety was an aim of the project. We describe the complete process of building from the stage of design until its testing in clinical routine. LUCY includes a patient monitor, a ventilator, 4 infusion pumps and 8 syringe pumps. All devices are connected to a preprocessing computer via serial interfaces. A high performance graphic workstation is used for central display of physiological and therapeutic variables. A versatile user interface provides touch screen, keyboard and mouse interaction. For fluid administration a bar code based control and documentation facility was included. While our scheduled development efforts were below 4 man-years, the overall man-power needed until the first routine test amounts to 8 man-years. Costs of devices and software sum up to 160,000 US$. First experiences in clinical routine show good general acceptance of the workplace concept. Analysing the recorded data we found 90% of the items to be redundant: individual filtering algorithms are necessary for each of nowaday's devices. The flexibility of the system concerning the implementation of new features is far from our expectations. Technical maintenance of the system during clinical operation requires continuous effort which we cannot afford in the current situation.

Algorithms↗
PubMed2002

Characterization, heterologous expression and functional analysis of mevalonate diphosphate decarboxylase gene (MVD) of Candida albicans.

Mevalonate diphosphate decarboxylase (MVD) catalyzes the conversion of mevalonate diphosphate to isopentenyl diphosphate, a key building block for a large family of functionally important biomolecules. We have cloned the gene encoding MVD from Candida albicans, and report the first characterization of such a gene from an opportunistic fungal pathogen. Sequence analysis revealed that the MVD comprises 362 amino acid residues with a predicted molecular weight of 39.5 kDa, sharing minimal identity with the human analogue. Analysis of the genomic sequence indicated that the coding frame is interrupted by a small intron of 51 bp. Southern analysis of genomic DNA demonstrated that MVD is a single-copy gene. Furthermore, Southern analysis of electrophoretic karyotypes of C. albicans obtained by pulsed-field gel electrophoresis showed that MVD is located on chromosome 1. Northern analysis revealed that the level of MVD expression is affected by (1) the carbon source in the growth medium, (2) the growth phase, and (3) the growth form of the fungus (yeast-like or hyphal). To demonstrate the biological function of C. albicans MVD, complementation experiments were carried out with an S. cerevisiae strain (erg19(ts)) that is temperature-sensitive for MVD activity. A single copy of the C. albicans MVD gene, under the control of the NOP1 promoter, was able fully to complement the erg19(ts) phenotype, and expression of the epitope-tagged C. albicans MVD was detectable by Western analysis. Furthermore, the low degree of sequence identity between C. albicans MVD and its human analogue raises the possibility that fungal-specific inhibitors can be developed for the enzyme. Thus, C. albicans MVD appears to be an interesting candidate that could be targeted for the development of anti-fungal agents.

Amino Acid Sequence↗
PubMed2000

Molecular phylogeography of western Mediterranean dusky grouper Epinephelus marginatus.

Intraspecific sequence variation in a portion of the gene coding for cytochrome b in the dusky grouper (Epinephelus marginatus Lowe 1834), an endangered fish species in various regions of the Mediterranean sea, was examined in 29 individuals from the western Mediterranean sea. Sixty-four phylogenetically informative nucleotide positions were present in a 353-base pair cytochrome b sequence, amplified using the polymerase chain reaction. Statistical analysis of the sequence data using a variety of tree-building algorithms separated the taxa into one group of dusky groupers corresponding to some of the Algerian individuals and another regrouped set of fishes originating in France, Tunisia and the remaining Algerian specimens. Although, on the basis of their morphology, E. marginatus are now considered as a single species, our results suggest that a subgroup of the Algerian dusky grouper constitutes a cryptic (undescribed) species. These results suggest that morphological and genetic evolution may be uncoupled in dusky grouper, resulting in morphological similarity between species despite extensive genetic divergence. In addition, we cannot rule out the possibility of gene introgression with other species of grouper. A more in depth phylogenetic analysis (i.e. between and within the different Epinephelus species) would likely affect many conservation management decisions about this assemblage of groupers.

Animals↗
PubMed2004

Use of an innovative video feedback technique to enhance communication skills training.

CONTEXT: Despite growing interest in medical communication by certification bodies, significant methodological and logistic challenges are evident in experiential methods of instruction. OBJECTIVE: There were three study objectives: 1) to explore the acceptability of an innovative video feedback programme to residents and faculty; 2) to evaluate a brief teaching intervention comprising the video feedback innovation when linked to a one-hour didactic and role-play teaching session on paediatric residents' communication with a simulated patient; and 3) to explore the impact of resident gender on communication change. DESIGN: Pre/post comparison of residents' performance in videotaped interviews with simulated patients before and after the teaching intervention. Individually tailored feedback on targeted communication skills was facilitated by embedding the Roter Interaction Analysis System (RIAS) within a software platform that presents a fully coded interview with instant search and review features. SETTING/PARTICIPANTS: 28 first year residents in a large, urban, paediatric residency programme. RESULTS: Communication changes following the teaching intervention were demonstrated through significant improvements in residents' performance with simulated patients pre and post teaching and feedback. Using paired t-tests, differences include: reduced verbal dominance; increased use of open-ended questions; increased use of empathy; and increased partnership building and problem solving for therapeutic regimen adherence. Female residents demonstrated greater communication change than males. CONCLUSIONS: The RIAS embedded CD-ROM provides a flexible structure for individually tailoring feedback of targeted communication skills that is effective in facilitating communication change as part of a very brief teaching intervention.

Adult↗
PubMed2025

Genome editing in the green alga Chlamydomonas: past, present practice and future prospects.

The green alga Chlamydomonas is an important and versatile model organism for research topics ranging from photosynthesis and metabolism, cilia, and basal bodies to cellular communication and the cellular cycle and is of significant interest for green bioengineering processes. The genome in this unicellular green alga is contained in 17 haploid chromosomes and codes for 16 883 protein coding genes. Functional genomics, as well as biotechnological applications, rely on the ability to remove, add, and change these genes in a controlled and efficient manner. In this review, the history of gene editing in Chlamydomonas is put in the context of the wider developments in genetics to demonstrate how many of the key developments to engineer these algae follow the global trends and the availability of technology. Building on this background, an overview of the state of the art in Chlamydomonas engineering is given, focusing primarily on the practical aspects while giving examples of recent applications. Commonly encountered Chlamydomonas-specific challenges, recent developments, and community resources are presented, and finally, a comprehensive discussion on the emergence and evolution of CRISPR/Cas-based precision gene editing is given. An outline of possible future paths for gene editing based on current global trends in genetic engineering and tools for gene editing is presented.

Gene Editing↗
PubMed2006

Fold classification based on secondary structure--how much is gained by including loop topology?

BACKGROUND: It has been proposed that secondary structure information can be used to classify (to some extend) protein folds. Since this method utilizes very limited information about the protein structure, it is not surprising that it has a higher error rate than the approaches that use full 3D fold description. On the other hand, the comparing of 3D protein structures is computing intensive. This raises the question to what extend the error rate can be decreased with each new source of information, especially if the new information can still be used with simple alignment algorithms. We consider the question whether the information about closed loops can improve the accuracy of this approach. While the answer appears to be obvious, we had to overcome two challenges. First, how to code and to compare topological information in such a way that local alignment of strings will properly identify similar structures. Second, how to properly measure the effect of new information in a large data sample. We investigate alternative ways of computing and presenting this information. RESULTS: We used the set of beta proteins with at most 30% pairwise identity to test the approach; local alignment scores were used to build a tree of clusters which was evaluated using a new log-odd cluster scoring function. In particular, we derive a closed formula for the probability of obtaining a given score by chance. Parameters of local alignment function were optimized using a genetic algorithm. Of 81 folds that had more than one representative in our data set, log-odds scores registered significantly better clustering in 27 cases and significantly worse in 6 cases, and small differences in the remaining cases. Various notions of the significant change or average change were considered and tried, and the results were all pointing in the same direction. CONCLUSION: We found that, on average, properly presented information about the loop topology improves noticeably the accuracy of the method but the benefits vary between fold families as measured by log-odds cluster score.

Algorithms↗
PubMed2002

Genetic polymorphisms of XRCC1 and risk of gastric cancer.

Coding polymorphisms of the DNA repair gene XRCC1 have been shown to affect the DNA repair capacity and to be associated with genetic susceptibility to carcinogenesis. In our association study between three amino acid substitution polymorphisms of XRCC1 (Arg194Trp, Arg280His, and Arg399Gln) and the risk of gastric cancer in the Korean population, none of the polymorphisms were associated with increased risk of gastric cancer. We then extended our study by building haplotypes of the entire XRCC1 gene with six single neuclotide polymorphisms (SNPs), including two novel polymorphisms at the 5'-flanking sequence. When haplotype frequencies in cases and controls and haplotype-specific odds ratios (ORs) were estimated, haplotype A (194Trp, 280Arg, and 399Arg) was associated with significant reduction in gastric cancer risk (adjusted OR=0.65, 95% CI=0.43-0.99) whereas haplotype D (194Arg, 280Arg, and 399Arg alleles) was a risk type for gastric cancer (adjusted OR=1.57, 95% CI=0.93-2.65). The association with the haplotype D was more pronounced in the cancers of antrum (adjusted OR=2.06, 95% CI=1.03-2.00). Our results suggest that the haplotype estimation is advantageous for association studies of such a complex disease as gastric cancer.

Aged↗
PubMed2000

The language of covalent histone modifications.

Histone proteins and the nucleosomes they form with DNA are the fundamental building blocks of eukaryotic chromatin. A diverse array of post-translational modifications that often occur on tail domains of these proteins has been well documented. Although the function of these highly conserved modifications has remained elusive, converging biochemical and genetic evidence suggests functions in several chromatin-based processes. We propose that distinct histone modifications, on one or more tails, act sequentially or in combination to form a 'histone code' that is, read by other proteins to bring about distinct downstream events.

Acetylation↗
PubMed2005

Genomics in C. elegans: so many genes, such a little worm.

The Caenorhabditis elegans genome sequence is now complete, fully contiguous telomere to telomere and totaling 100,291,840 bp. The sequence has catalyzed the collection of systematic data sets and analyses, including a curated set of 19,735 protein-coding genes--with >90% directly supported by experimental evidence--and >1300 noncoding RNA genes. High-throughput efforts are under way to complete the gene sets, along with studies to characterize gene expression, function, and regulation on a genome-wide scale. The success of the worm project has had a profound effect on genome sequencing and on genomics more broadly. We now have a solid platform on which to build toward the lofty goal of a true molecular understanding of worm biology with all its implications including those for human health.

Animals↗
PubMed2004

Prediction of DtxR regulon: identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae.

BACKGROUND: The diphtheria toxin repressor, DtxR, of Corynebacterium diphtheriae has been shown to be an iron-activated transcription regulator that controls not only the expression of diphtheria toxin but also of iron uptake genes. This study aims to identify putative binding sites and operons controlled by DtxR to understand the role of DtxR in patho-physiology of Corynebacterium diphtheriae. RESULT: Positional Shannon relative entropy method was used to build the DtxR-binding site recognition profile and the later was used to identify putative regulatory sites of DtxR within C. diphtheriae genome. In addition, DtxR-regulated operons were also identified taking into account the predicted DtxR regulatory sites and genome annotation. Few of the predicted motifs were experimentally validated by electrophoretic mobility shift assay. The analysis identifies motifs upstream to the novel iron-regulated genes that code for Formamidopyrimidine-DNA glycosylase (FpG), an enzyme involved in DNA-repair and starvation inducible DNA-binding protein (Dps) which is involved in iron storage and oxidative stress defense. In addition, we have found the DtxR motifs upstream to the genes that code for sortase which catalyzes anchoring of host-interacting proteins to the cell wall of pathogenic bacteria and the proteins of secretory system which could be involved in translocation of various iron-regulated virulence factors including diphtheria toxin. CONCLUSIONS: We have used an in silico approach to identify the putative binding sites and genes controlled by DtxR in Corynebacterium diphtheriae. Our analysis shows that DtxR could provide a molecular link between Fe+2-induced Fenton's reaction and protection of DNA from oxidative damage. DtxR-regulated Dps prevents lethal combination of Fe+2 and H2O2 and also protects DNA by nonspecific DNA-binding. In addition DtxR could play an important role in host interaction and virulence by regulating the levels of sortase, a potential vaccine candidate and proteins of secretory system.

Bacterial Proteins↗
PubMedDate not supplied

Enhance your team-based qualitative research.

PURPOSE: Qualitative research projects often involve the collaborative efforts of a research team. Challenges inherent in teamwork include changes in membership and differences in analytical style, philosophy, training, experience, and skill. This article discusses teamwork issues and tools and techniques used to improve team-based qualitative research. METHODS: We drew on our experiences in working on numerous projects of varying, size, duration, and purpose. Through trials of different tools and techniques, expert consultation, and review of the literature, we learned to improve how we build teams, manage information, and disseminate results. RESULTS: Attention given to team members and team processes is as important as choosing appropriate analytical tools and techniques. Attentive team leadership, commitment to early and regular team meetings, and discussion of roles, responsibilities, and expectations all help build more effective teams and establish clear norms. As data are collected and analyzed, it is important to anticipate potential problems from differing skills and styles, and how information and files are managed. Discuss analytical preferences and biases and set clear guidelines and practices for how data will be analyzed and handled. As emerging ideas and findings disperse across team members, common tools (such as summary forms and data grids), coding conventions, intermediate goals or products, and regular documentation help capture essential ideas and insights. CONCLUSIONS: In a team setting, little should be left to chance. This article identifies ways to improve team-based qualitative research with more a considered and systematic approach. Qualitative researchers will benefit from further examination and discussion of effective, field-tested, team-based strategies.

Biomedical Research↗
PubMed1997

Does case mix matter for substance abuse treatment? A comparison of observed and case mix-adjusted readmission rates for inpatient substance abuse treatment in the Department of Veterans Affairs.

OBJECTIVE: To develop a case mix model for inpatient substance abuse treatment to assess the effect of case mix on readmission across Veterans Affairs Medical Centers (VAMCs). DATA SOURCES/STUDY SETTING: The computerized patient records from the 116 VAMCs with inpatient substance abuse treatment programs between 1987 and 1992. STUDY DESIGN: Logistic regression was used on patient data to model the effect of demographic, psychiatric, medical, and substance abuse factors on readmission to VAMCs for substance abuse treatment within six months of discharge. The model predictions were aggregated for each VAMC to produce an expected number of readmissions. The observed number of readmissions for each VAMC was divided by its expected number to create a measure of facility performance. Confidence intervals and rankings were used to examine how case mix adjustment changed relative performance among VAMCs. DATA COLLECTION/EXTRACTION METHODS: Ward where care was provided and ICD-9-CM diagnosis codes were used to identify patients receiving treatment for substance abuse (N = 313,886). PRINCIPAL FINDINGS: The case mix model explains 36 percent of the observed facility level variation in readmission. Over half of the VAMCs had numbers of readmissions that were significantly different than expected. There were also noticeable differences between the rankings based on actual and case mix-adjusted readmissions. CONCLUSIONS: Secondary data can be used to build a reasonably stable case mix model for substance abuse treatment that will identify meaningful variation across facilities. Further, case mix has a large effect on facility level readmission rates for substance abuse treatment. Uncontrolled facility comparisons can be misleading. Case mix models are potentially useful for quality assurance efforts.

Adult↗