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Expanding the COL7A1 mutation database: novel and recurrent mutations and unusual genotype-phenotype constellations in 41 patients with dystrophic epidermolysis bullosa.

Dystrophic epidermolysis bullosa (DEB), a heterogeneous hereditary skin disorder characterized by trauma-induced blistering and scarring, affects thousands of families worldwide. The clinical manifestations extend from minor nail dystrophy to severe life-threatening blistering, making early molecular diagnosis and prognostication of utmost importance for the affected families. DEB is caused by mutations in the COL7A1 gene encoding collagen VII in the skin. Molecular diagnostics and genotype-phenotype correlations in DEB remain complex owing to the gene structure, large variety of mutations, high rate of novel mutations, complex protein structure and assembly, and the heterogeneity of phenotypes. Here, we report an efficient strategy for COL7A1 mutation detection using direct automated DNA sequencing and implementation of software tools. With this approach, COL7A1 mutations of 41 DEB families were disclosed. Twenty-four mutations were novel and two recurrent. Elucidation of biological consequences of the mutations helped define disease mechanisms, but also revealed several unusual genotypic and/or phenotypic constellations, which impeded the diagnostics and prognostication. In addition, the studies disclosed a de novo mutation in recessive DEB and two new polymorphisms in the COL7A1 gene.

Collagen Type VII↗

Progression of maxillofacial squamous cell carcinoma evaluated using computer graphics with spiral computed tomography.

This report describes the appearance of maxillofacial squamous cell carcinoma in multiplanar (MPR) and three-dimensional (3D) images reconstructed from spiral CT using computer graphics and the importance of the computer software tools in permitting better visualization of the lesion. Two oral and maxillofacial radiologists and one neuroradiologist analysed the images. The usefulness of interactive reconstruction in the diagnosis, surgical planning and treatment evaluation, especially in the localization of the extent of these maxillofacial tumors, was demonstrated. Spiral CT-based computer graphics for displaying MPR and 3D images are an important adjunct in the evaluation of squamous cell carcinoma.

Aged↗

Searching the Porphyromonas gingivalis genome with peptide fragmentation mass spectra.

An approach is described for genomic database searching based on experimentally observed proteolytic fragments, e.g., isolated from 1D or 2D gels or analyzed directly, that can be applied to unfinished prokaryotic genomic data in the absence of annotations or previously assigned open reading frames (ORFs). This variation on the database search is in contrast to the more familiar use of peptide mass spectral fragmentation data to search fully annotated inferred protein databases, e.g., OWL or SWISS-PROT. We compared the SEQUEST search results from a six reading frame translation of the Porphyromonas gingivalis genome DNA sequence with those from computationally derived ORFs created using publicly available genomics software tools. The ORF approach eliminated many of the artifacts present in output from the six reading frame search. The method was applied to uninterpreted tandem mass spectrometric data derived from proteins secreted by the periodontal pathogen Porphyromonas gingivalis in response to the gingival epithelial cell environment, a model system for the study of host-pathogen interactions relevant to human periodontal disease.

Bacterial Proteins↗

Some characteristics and purification of anti-(human ovarian carcinoma)xanti-(human CD3) single-chain bispecific antibody.

To obtain high-quality AhOC x AhCD3 [anti-(human ovarian carcinoma)xanti-(human CD3)] with high biological activity economically and easily, some characteristics and purification of AhOC x AhCD3, a single chain bispecific antibody, were investigated. During the present study, some important properties of AhOC x AhCD3, such as molecular mass, pI, solubility, stability, hydrophobic ability, molecular status and bioactivity were primarily studied. The molecular mass of AhOC x AhCD3 was determined to be approx. 58.0 kDa by SDS/PAGE (theoretical molecular mass: 56972.5 Da, calculated on the basis of the primary structure) and the pI was approx. 7.5+/-0.4 by IEF (isoelectric focusing; theoretical pI: 8.5, predicted by the ProtParam software tool) respectively. Experiments showed that the solubility of AhOC x AhCD3 increased with the pH increase and that the AhOC x AhCD3 was easily degraded into several fragments during the storage time of samples and the mixtures of both fragment B and fragment C retained normal bioactivity. Particularly, the soluble aggregate/polymer status of AhOC x AhCD3 with bioactivity was verified by non-reducing SDS/PAGE. After optimization of purification process, AhOC x AhCD3 with electrophoretic homogeneity was successfully obtained and the yield was approx. 20%. Some important properties of AhOC x AhCD3 were first observed and a procedure for soluble AhOC x AhCD3 purification in scale-up was first established. Some characteristics of AhOC x AhCD3, especially the stability of AhOC x AhCD3, are critical for the development of this protein pharmaceutical and useful for reference to other proteins.

Antibodies, Bispecific↗

National sentinel clinical audit of evidence-based prescribing for older people: methodology and development.

RATIONALE, AIMS AND OBJECTIVES: This national clinical audit aimed to develop and implement a methodology to assess the appropriateness of prescribing for patients over the age of 65 in hospitals, general practice and nursing homes. METHODS: Organizations providing health care in the National Health Service in these three sectors were recruited into multi-disciplinary and inter-organizational local coalition teams. Prescription data and relevant clinical data were collected electronically on a customized database. The appropriateness of prescribing for specific conditions among the patients sampled was assessed by simple computerized algorithms, and users were provided with feedback to stimulate discussion and change. Use of the software tool was demonstrated to be feasible and its data reliable. Participants were re-audited, after a period of nationally guided and locally driven intervention, to evaluate levels of change. Local efforts to stimulate change and barriers to change were collected qualitatively. RESULTS AND CONCLUSIONS: The investigation revealed encouraging results and demonstrated the ability of audit to improve the quality of clinical services in given circumstances, although a multiplicity of questions relating to cost and methodology remain to be addressed.

Aged↗

Understanding mathematical models for breast cancer risk assessment and counseling.

Chemoprevention and prophylactic surgery are effective interventions for lowering breast cancer incidence. However, these approaches are associated with risks of their own. Accurate individualized breast cancer risk assessment is an essential component of the risk/benefit analysis that must take place prior to implementing either of these strategies. Several mathematical models for estimating individual breast cancer risk have been proposed over the last decade. The Gail model is the most generally applicable model; however, it neglects family history information in second-degree relatives, treats pre- and postmenopausal breast cancer the same, and ignores personal histories of lobular neoplasia. The Claus model is a better family history model, but it does not assign any special relevance to histories of bilateral breast cancer or ovarian cancer, and neglects all of the nonfamily history information accounted for by the Gail model. BRCAPRO is a Bayesian family history model that calculates individual breast cancer probabilities based on the probability that a family carries a mutation in one of the BRCA genes. Though its treatment of family history information is more thorough than the other models, it neglects the nonfamily history risk factors accounted for by the Gail model and may not appreciate familial clustering unrelated to BRCA gene mutation. A thorough understanding of the principles of risk analysis and the available mathematical models is essential for anyone wishing to perform intervention counseling. This review describes the basic components of risk analysis, explains how the mathematical models work and compares the strengths and weaknesses of the various models. CancerGene is a software tool for running all of these models. It may be obtained without charge at http://www.swmed.edu/home_pages/cancergene.

Breast Neoplasms↗

[New avenues to quality assurance--a model project for recording bedsore incidence].

Bedsores can usually be avoided by adequate care and preventive measures. In the context of the local agenda process a local district office (Landratsamt) and inspection units initiated a variety of activities to promote sensitisation in health institutions and contribute to an increase in life quality of the persons concerned. Nearly all nursing care homes, domiciliary services and hospitals participated in a pilot study which was accompanied by the Fraunhofer IAO in Stuttgart. Objectives of the pilot study were to implement internal quality assurance to sensitise for persons the topic and to collect comparable data to achieve benchmarking. Software-tool institutions recorded data on care days, days spent with bedsores according to care level from July till September 01. Major result was that - although institutions had already a decreasing incidence in bedsores since the start of discussing the project - bedsore quotas could be further decreased from 2.15 to 1.84 %.

Aged↗

[Quantification of atelectases in artificial respiration: spiral-CT versus dynamic single-slice CT].

PURPOSE: Dynamic CT (dCT) allows visualization and quantification of ventilated lung and atelectases with high temporal resolution during continuous ventilation. This study compares a quantitative image analysis in a subcarinal single slice dCT series versus a whole lung spiral-CT, in order to analyze, whether the distribution of atelectasis of a single dCT series is representative for the whole lung. MATERIALS AND METHODS: dCT in sliding windows technique (slice thickness 1 mm, temporal increment 100 ms) was performed in 8 healthy pigs 3 cm caudal to the carina during continuous mechanical ventilation. Subsequently, a spiral-CT of the whole lung (slice thickness 2 mm; pitch 1.5; increment 2 mm) was acquired during inspiratory breath hold (airway pressure 20 mbar). Lung segmentation and planimetry of predefined density ranges were achieved using a dedicated software tool in both data-sets. Thus, the fractions of the following functional lung compartments were averaged over time: hyperinflated lung (- 1024 to - 910 HE), normal ventilated lung -900 to -300 HE) and atelectasis (-300 to +200 HE). RESULTS: Quantitative analysis of dCT-series during continuous respiration correlated with the density analysis in spiral-CT as follows: hyperinflated lung r = 0.56; normal ventilated lung r = 0.83 and atelectases r = 0.84. Analysis of spiral-CT showed the following distribution of functional lung compartments: hyperinflated lung 3.1% normal ventilated lung 77.9% and atelectasis 19.0%. In dCT, hyperinflated lung represented 6.4%, normal ventilated lung 65.2% and atelectasis 28.4% of total the lung area. CONCLUSION: The results of our study demonstrate that dCT allows monitoring of atelectasis formation in response to different ventilatory strategies. However, a deviation between dCT and spiral-CT has to be taken into account. In subcarinal dCT series, hyperinflated lung areas and atelectases were overestimated due to a craniocaudal gradient of atelectases, whereas normal ventilated lung was underestimated.

Animals↗

Oxidative stress is involved in the development of experimental abdominal aortic aneurysm: a study of the transcription profile with complementary DNA microarray.

BACKGROUND: The role of oxidative stress in the formation of aneurysms is not fully understood. We used the complementary DNA (cDNA) microarray technique to determine the transcription profile in the development of elastase-induced abdominal aortic aneurysm in rat models, with an emphasis on the oxidative stress-related genes. MATERIALS AND METHODS: In the experimental group, rat abdominal aortas were perfused with elastase to induce AAA. In the control group, a sham operation was performed with perfusion of the aortas with saline solution. Four or five animals were used for each time point for each of the elastase-treated or saline-treated groups. At day 2, day 7, and day 10 after surgery, the external aortic diameter was measured and AAA formation was estimated. Total RNA was isolated from aortas and subjected to cDNA microarray analysis with the use of the rat genome U34A high-density oligonucleotide DNA chip (Affymetrix, Santa Clara, Calif), which contains a total number of 8799 genes of which 2017 are expressed sequence tag (EST) genes. The data were analyzed with the GENECHIP Data Mining Tool software (Affymetrix). For genes of interest, reverse-transcription polymerase chain reaction was performed to confirm their expression level. RESULTS: Comparison ranking analysis revealed that during AAA development, the expression of 212 genes, including 46 of EST genes, increased by more than two-fold and 229 genes, including 95 of EST genes, decreased by more than two-fold in at least one of the three time points. The regulated genes included those encoding heme oxygenase, inducible nitric oxide synthase, some extracellular matrix proteins, members of the matrix metalloproteinase family, and those associated with prooxidant/antioxidant and inflammatory responses. Reverse-transcription polymerase chain reaction analysis confirmed the upregulation of genes involved in oxidative stress, such as heme oxygenase, inducible nitric oxide synthase, 12-lipoxygenase, and heart cytochrome c oxydase subunit VIa, and the downregulation of antioxidant genes, such as superoxide dismutase, reduced nicotinamide adenine dinucleotide-cytochrome b-5 reductase, and glutathion S-transferase. CONCLUSION: The cDNA microarray technique was useful for investigation of the transcription profiles during the development of AAA. Our results indicate that oxidative stress may play a pivotal role in the pathologic progression of AAA.

Animals↗

A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors.

The low rate of homologous recombination exhibited by wild-type strains of filamentous fungi has hindered development of high-throughput gene knockout procedures for this group of organisms. In this study, we describe a method for rapidly creating knockout mutants in which we make use of yeast recombinational cloning, Neurospora mutant strains deficient in nonhomologous end-joining DNA repair, custom-written software tools, and robotics. To illustrate our approach, we have created strains bearing deletions of 103 Neurospora genes encoding transcription factors. Characterization of strains during growth and both asexual and sexual development revealed phenotypes for 43% of the deletion mutants, with more than half of these strains possessing multiple defects. Overall, the methodology, which achieves high-throughput gene disruption at an efficiency >90% in this filamentous fungus, promises to be applicable to other eukaryotic organisms that have a low frequency of homologous recombination.

DNA Primers↗

Gene recognition via spliced sequence alignment.

Gene recognition is one of the most important problems in computational molecular biology. Previous attempts to solve this problem were based on statistics, and applications of combinatorial methods for gene recognition were almost unexplored. Recent advances in large-scale cDNA sequencing open a way toward a new approach to gene recognition that uses previously sequenced genes as a clue for recognition of newly sequenced genes. This paper describes a spliced alignment algorithm and software tool that explores all possible exon assemblies in polynomial time and finds the multiexon structure with the best fit to a related protein. Unlike other existing methods, the algorithm successfully recognizes genes even in the case of short exons or exons with unusual codon usage; we also report correct assemblies for genes with more than 10 exons. On a test sample of human genes with known mammalian relatives, the average correlation between the predicted and actual proteins was 99%. The algorithm correctly reconstructed 87% of genes and the rare discrepancies between the predicted and real exon-intron structures were caused either by short (less than 5 amino acids) initial/terminal exons or by alternative splicing. Moreover, the algorithm predicts human genes reasonably well when the homologous protein is nonvertebrate or even prokaryotic. The surprisingly good performance of the method was confirmed by extensive simulations: in particular, with target proteins at 160 accepted point mutations (PAM) (25% similarity), the correlation between the predicted and actual genes was still as high as 95%.

Algorithms↗

Predicting amino acid sequences of the antibody human VH chains from its first several residues.

A new method for classification of Ig sequences is suggested. The defining characteristic of a class is presence of particular residues at several class-determining positions. Sequences within a class follow the same amino acid pattern, i.e., residues at identical positions are, in an overwhelming majority of sequences of that class, identical or chemically related. Thus, once the class of a sequence is determined, one can predict the residue(s) at almost any position in the sequence. In this paper, results of analysis of 1,172 human heavy chains are presented. It was shown that a sequence can be assigned to one of six classes depending on which residues are found at its positions 1, 3, 5, 6, 7, 9, 10, 12, and 13. It is important to note that it is possible to achieve same six-class classification of the human heavy chains on the basis of a different set of positions found not at the beginning but near the end of the sequence (around position 80). For every class, an amino acid pattern of an entire sequence (complementarity determining regions excepting) has been determined. Our approach allowed us to reconstruct the incomplete human heavy chains in which residues at certain positions at the beginning or end of the chain are known. We developed a software tool for analysis, classification, and prediction of residues in sequences of the Ig family.

Algorithms↗

Tumor antigens and proteomics from the point of view of the major histocompatibility complex peptides.

The major histocompatibility complex (MHC) peptide repertoire of cancer cells serves both as a source for new tumor antigens for development of cancer immunotherapy and as a rich information resource about the protein content of the cancer cells (their proteome). Thousands of different MHC peptides are normally displayed by each cell, where most of them are derived from different proteins and thus represent most of the cellular proteome. However, in contrast to standard proteomics, which surveys the cellular protein contents, analyses of the MHC peptide repertoire correspond more to the rapidly degrading proteins in the cells (i.e. the transient proteome). MHC peptides can be efficiently purified by affinity chromatography from membranal MHC molecules, or preferably following transfection of vectors for expression of recombinant soluble MHC molecules. The purified peptides are resolved and analyzed by capillary high-pressure liquid chromatography-electrospray ionization-tandem mass spectrometry, and the data are deciphered with new software tools enabling the creation of large databanks of MHC peptides displayed by different cell types and by different MHC haplotypes. These lists of identified MHC peptides can now be used for searching new tumor antigens, and for identification of proteins whose rapid degradation is significant to cancer progression and metastasis. These lists can also be used for identification of new proteins of yet unknown function that are not detected by standard proteomics approaches. This review focuses on the presentation, identification and analysis of MHC peptides significant for cancer immunotherapy. It is also concerned with the aspects of human proteomics observed through large-scale analyses of MHC peptides.

Antigens, Neoplasm↗

Fast image acquisition and processing on a TV camera-based portal imaging system.

The present paper describes the fast acquisition and processing of portal images directly from a TV camera-based portal imaging device (Siemens Beamview Plus). This approach employs not only hard- and software included in the standard package installed by the manufacturer (in particular the frame grabber card and the Matrox Intellicam interpreter software), but also a software tool developed in-house for further processing and analysis of the images. The technical details are presented, including the source code for the Matrox interpreter script that enables the image capturing process. With this method it is possible to obtain raw images directly from the frame grabber card at an acquisition rate of 15 images per second. The original configuration by the manufacturer allows the acquisition of only a few images over the course of a treatment session. The approach has a wide range of applications, such as quality assurance (QA) of the radiation beam, real-time imaging, real-time verification of intensity-modulated radiation therapy (IMRT) fields, and generation of movies of the radiation field (fluoroscopy mode).

Humans↗

Prediction of protein structure by simulating coarse-grained folding pathways: a preliminary report.

A set of software tools designed to study protein structure and kinetics has been developed. The core of these tools is a program called Folding Machine (FM) which is able to generate low resolution folding pathways using modest computational resources. The FM is based on a coarse-grained kinetic ab initio Monte-Carlo sampler that can optionally use information extracted from secondary structure prediction servers or from fragment libraries of local structure. The model underpinning this algorithm contains two novel elements: (a) the conformational space is discretized using the Ramachandran basins defined in the local phi-psi energy maps; and (b) the solvent is treated implicitly by rescaling the pairwise terms of the non-bonded energy function according to the local solvent environments. The purpose of this hybrid ab initio/knowledge-based approach is threefold: to cover the long time scales of folding, to generate useful 3-dimensional models of protein structures, and to gain insight on the protein folding kinetics. Even though the algorithm is not yet fully developed, it has been used in a recent blind test of protein structure prediction (CASP5). The FM generated models within 6 A backbone rmsd for fragments of about 60-70 residues of alpha-helical proteins. For a CASP5 target that turned out to be natively unfolded, the trajectory obtained for this sequence uniquely failed to converge. Also, a new measure to evaluate structure predictions is presented and used along the standard CASP assessment methods. Finally, recent improvements in the prediction of beta-sheet structures are briefly described.

Algorithms↗

The virtual courtroom: a view of justice. Project to prepare witnesses or victims with learning disabilities to give evidence.

PURPOSE: With the advent of 'The Youth Justice and Criminal Evidence Act 1999' passed by Parliament in August 1999, vulnerable witnesses can for the first time give evidence to the court with the support of 'special measures'. People with a learning disability fall into the category of vulnerable witnesses, and the purpose of this paper is to describe the development of the virtual courtroom, a virtual reality (VR) and multimedia based training platform to prepare this group of people for such an eventuality. METHOD: A user-centred design methodology was adopted, with a user group being formed of students and adults with learning disabilities. This group, working together with facilitators, experts on the new act, and experienced designers of VR based training systems, designed and implemented the virtual courtroom. RESULTS: The virtual courtroom model has been produced using the Realimation Virtual Reality software tool. The next stage of the project is to design and develop three multimedia-based scenarios showing a variety of situations in which a person with a learning disability could give evidence in court. CONCLUSION: One of the recommendations in the 'Speaking up for justice' report, suggested that the Home Office develop further material to assist vulnerable witnesses to prepare for their attendance at court. The virtual courtroom provides one of the first and most innovative of such solutions.

Adolescent↗

A proposed computational biomechanics cyber-infrastructure for multi-phase and multi-scale problems: delivering biomechanics to the surgeon.

This paper presents a new direction for practitioners of computational biomechanics. It provides a description of three prototype software platforms, which demonstrate how the cyber-infrastructure can be used to integrate the algorithms of computational biomechanics to solve multi-phase and multi-scale problems. Then, a development platform is presented. This platform can also deliver integrated biomechanics into the surgical ward for surgical planning. This platform performs these tasks without the need for advanced network software tools: an appendix provides all the simple and fundamental open source and CI technologies that are required. The overarching goal of this paper is to make the potential of the emerging cyber-infrastructure comprehensible and accessible to practitioners of computational biomechanics.

Biomechanical Phenomena↗

Quantification of variability and uncertainty in air pollutant emission inventories: method and case study for utility NOx emissions.

The quality of stationary source emission factors is typically described using data quality ratings, which provide no quantification of the precision of the emission factor for an average source, nor of the variability from one source to another within a category. Variability refers to actual differences caused by differences in feedstock composition, design, maintenance, and operation. Uncertainty refers to lack of knowledge regarding the true emissions. A general methodology for the quantification of variability and uncertainty in emission factors, activity factors, and emission inventories (EIs) is described, featuring the use of bootstrap simulation and related techniques. The methodology is demonstrated via a case study for a selected example of NOx emissions from coal-fired power plants. A prototype software tool was developed to implement the methodology. The range of interunit variability in selected activity and emission factors was shown to be as much as a factor of 4, and the range of uncertainty in mean emissions is shown to depend on the interunit variability and sample size. The uncertainty in the total inventory of -16 to +19% was attributed primarily to one technology group, suggesting priorities for collecting data and improving the inventory. The implications for decision-making are discussed.

Air Pollutants↗