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PubMed2004

Gene expression profiling of cultured human islet preparations.

The expression of functional and regulatory genes by islet cells is a key determinant for the success of islet transplantation. The aim of this study is twofold: first, to characterize the cluster of genes expressed in human islet isolations; and second, to validate the capability of gene array technology to assess with accuracy the expression of various transcripts. RNA from isolated islet preparations obtained from three independent donors was converted to cDNA and then transcribed to cRNA. Individual cRNA preparations were then hybridized to U133A microarrays carrying approximately 23,000 genes, and analyzed using GeneSpring (SiliconGenetics, Redwood City, CA) software. Real-time reverse transcription-polymerase chain reaction was performed to validate results obtained by microarray analysis. Microarray analysis identified the expression of about 7,000 genes transcribed in cultured human islet preparations. Enzymes represented the most abundant class of genes identified, followed by nuclear binding proteins, signal transduction molecules, transport proteins, and growth factor receptors and their ligands. Real-time polymerase chain reaction confirmed the identification of various islet-specific genes detected by microarray analysis, but also showed that such genes as pancreatic duodenal homeobox 1 protein and glucagon-like peptide 1 receptor, which were not detected by gene array, can be readily identified and quantified. In addition, gene array produced a suboptimal quantification of genes expressed in large amounts by islet cells. Indeed, the abundance of mRNA for insulin when compared with the level of somatostatin mRNA was not as different as one would have predicated based on the classic knowledge of islet physiology. Gene array analysis appears to be a valuable tool to obtain preliminary information of genes expressed by a given tissue. The expression levels of transcripts expressed in very low or very high quantities need to be confirmed by an independent technique.

Base Sequence↗

PubMed2001

Use of real time control modelling on the urban sewage system of Nancy.

Since 1991, European Legislation on the urban treatment of wastewater requires local authorities to take into account the treatment of polluted water transported by the sewerage system and this during dry and wet weather conditions. In the seventies, the urban Community of Grand Nancy constructed storage tanks in its sewerage system in order to prevent flooding and wish today to use them to reduce and control the pollution discharges into the receiving water. This action is a part of a European LIFE project 1996-2000. The main aim of this project was to assess the effectiveness of reducing pollution of one particular retention basin, the 12,000 m3 Gentilly tank. This one has two operating modes: protection against floods during heavy rain and reduction of pollutant overflows during lighter rain. To assess its effect on the pollutant discharge, the HYDROWORKS DM software and its Real Time Control Module have been used, calibrated and validated. As this study is still in progress, this paper describes the studied site and the modelling results under different weather conditions and shows that the mathematical model can be used to simulate the operation of the catchment area and its associated sewerage system realistically.

Cities↗

PubMed2004

The application of an automated allele concordance analysis system (CompareCalls) to ensure the accuracy of single-source STR DNA profiles.

A powerful method for validating a scientific result is to confirm specific results utilizing independent methodologies and processing pathways. Thus, we have designed, developed and validated an automated allele concordance analysis system (CompareCalls, patent pending) that performs comparisons between two independent DNA analysis platforms to ensure the highest accuracy for allele calls. Application of this system in a quality assurance role has shown the potential to eliminate greater than 90% of the STR analysis required of a DNA data analyst. While this system is broadly applicable for use with any two independent STR analysis programs, either prior to or following human data review, we are presenting its application to data generated with the ABI Prism Genotyper software system versus data generated with the SurelockID system. With the automated allele concordance analysis system, the GeneScan DNA fragment data generated from an ABI 377 gel image are analyzed in two independent pathways. In one analysis pathway, the GeneScan data are imported into Genotyper software where STR labels are assigned to the fragment data based upon the criteria of the Kazam 20% macro. The "Kazam" macro provided with the Genotyper program works by labeling all peaks in a category (or locus) and then filtering (or removing) the labels from peaks, such as those in stutter positions, that meet predefined criteria. In the second pathway, the GeneScan data are imported into the SurelockID analysis platform where STR labels and error messages are assigned to the fragment data based upon hard-coded allele calling criteria and quality parameters. The resulting STR allele calls for each analysis platform are then compared, utilizing the automated allele concordance analysis system. Any differences in the STR allele calls between the two systems are flagged in a discordance report for further review by a qualified DNA data analyst. The automated allele concordance analysis system guides the DNA data analyst to the discordant data generated by either analysis platform. Additionally, the analyst is also directed to data that are of less than pristine quality which may have an increased potential for errors in interpretation by either analysis platform or by a human DNA data analyst. Implementation of an automated allele concordance analysis system will yield high-quality data for CODIS and free the human DNA data analyst to perform other critical duties within the laboratory.

Alleles↗

PubMed2006

Universal metrics for quality assessment of protein identifications by mass spectrometry.

Increasing numbers of large proteomic datasets are becoming available. As attempts are made to interpret these datasets and integrate them with other forms of genomic data, researchers are becoming more aware of the importance of data quality with respect to protein identification. We present three simple and universal metrics that describe different aspects of the quality of protein identifications by peptide mass fingerprinting. Hit ratio gives an indication of the signal-to-noise ratio in a mass spectrum, mass coverage measures the amount of protein sequence matched, and excess of limit-digested peptides reflects the completeness of the digestion that precedes the peptide mass fingerprinting. Receiver-operating characteristic plots show that the novel metric, excess of limit-digested peptides, can discriminate between correct and random matches more accurately than search score when validating the results from a state-of-the-art protein identification software system (Mascot) especially when combined with the two other metrics, hit ratio and mass coverage. Recommendations are made regarding the use of the metrics when reporting protein identification experiments.

Mass Spectrometry↗

PubMed2006

GNU polyxmass: a software framework for mass spectrometric simulations of linear (bio-)polymeric analytes.

BACKGROUND: Nowadays, a variety of (bio-)polymers can be analyzed by mass spectrometry. The detailed interpretation of the spectra requires a huge number of "hypothesis cycles", comprising the following three actions 1) put forth a structural hypothesis, 2) test it, 3) (in)validate it. This time-consuming and painstaking data scrutiny is alleviated by using specialized software tools. However, all the software tools available to date are polymer chemistry-specific. This imposes a heavy overhead to researchers who do mass spectrometry on a variety of (bio-)polymers, as each polymer type will require a different software tool to perform data simulations and analyses. We developed a software to address the lack of an integrated software framework able to deal with different polymer chemistries. RESULTS: The GNU polyxmass software framework performs common (bio-)chemical simulations-along with simultaneous mass spectrometric calculations-for any kind of linear bio-polymeric analyte (DNA, RNA, saccharides or proteins). The framework is organized into three modules, all accessible from one single binary program. The modules let the user to 1) define brand new polymer chemistries, 2) perform quick mass calculations using a desktop calculator paradigm, 3) graphically edit polymer sequences and perform (bio-)chemical/mass spectrometric simulations. Any aspect of the mass calculations, polymer chemistry reactions or graphical polymer sequence editing is configurable. CONCLUSION: The scientist who uses mass spectrometry to characterize (bio-)polymeric analytes of different chemistries is provided with a single software framework for his data prediction/analysis needs, whatever the polymer chemistry being involved.

Biopolymers↗

PubMed1999

Development and validation of an automated, microscopy-based method for enumeration of groups of intestinal bacteria.

An automated microscopy-based method using fluorescently labelled 16S rRNA-targeted oligonucleotide probes directed against the predominant groups of intestinal bacteria was developed and validated. The method makes use of the Leica 600HR image analysis system, a Kodak MegaPlus camera model 1.4 and a servo-controlled Leica DM/RXA ultra-violet microscope. Software for automated image acquisition and analysis was developed and tested. The performance of the method was validated using a set of four fluorescent oligonucleotide probes: a universal probe for the detection of all bacterial species, one probe specific for Bifidobacterium spp., a digenus-probe specific for Bacteroides spp. and Prevotella spp. and a trigenus-probe specific for Ruminococcus spp., Clostridium spp. and Eubacterium spp. A nucleic acid stain, 4',6-diamidino-2-phenylindole (DAPI), was also included in the validation. In order to quantify the assay-error, one faecal sample was measured 20 times using each separate probe. Thereafter faecal samples of 20 different volunteers were measured following the same procedure in order to quantify the error due to individual-related differences in gut flora composition. It was concluded that the combination of automated microscopy and fluorescent whole-cell hybridisation enables distinction in gut flora-composition between volunteers at a significant level. With this method it is possible to process 48 faecal samples overnight, with coefficients of variation ranging from 0.07 to 0.30.

Adult↗

PubMedDate not supplied

Agreement between Medline searches using the Medline-CD-Rom and Internet Pubmed, BioMedNet, Medscape and Gateway search-engines.

OBJECTIVE: To compare the information obtained from the Medline database using Internet commercial search engines with that obtained from a compact disc (Medline-CD). METHODS: An agreement study was carried out based on 101 clinical scenarios provided by specialists in internal medicine, pharmacy, gynaecology-obstetrics, surgery and paediatrics. 175 search strategies were employed using the connector AND plus text within quotation marks. The search was limited to 1991-1999. Internet search-engines were selected by common criteria. Identical search strategies were independently applied to and masked from Internet search engines, as well as the Medline-CD. RESULTS: 3,488 articles were obtained using 129 search strategies. Agreement with the Medline-CD was 54% for PubMed, 57% for Gateway, 54% for Medscape and 65% for BioMedNet. The highest agreement rate for a given speciality (paediatrics) was 78.1% for BioMedNet, having greater -/- than +/+ agreement. CONCLUSIONS: Even though free access to Medline has encouraged the boom and growth of evidence-based medicine, these results must be considered within the context of which search engine was selected for doing the searches. The Internet search engines studied showed a poor agreement with the Medline-CD, the rate of agreement differing according to speciality, thus significantly affecting searches and their reproducibility. Software designed for conducting Medline database searches, including the Medline-CD, must be standardised and validated.

Databases as Topic↗

PubMed2001

Preventing medical errors in point-of-care testing: security, validation, safeguards, and connectivity..

OBJECTIVES: o prevent medical errors, improve user performance, and enhance the quality, safety, and connectivity (bidirectional communication) of point-of-care testing. PARTICIPANTS: Group A included 37 multidisciplinary experts in point-of-care testing programs in critical care and other hospital disciplines. Group B included 175 professional point-of-care managers, specialists, clinicians, and researchers. The total number of participants equaled 212. EVIDENCE: This study followed a systems approach. Expert specifications for prevention of medical errors were incorporated into the designs of security, validation, performance, and emergency systems. Additional safeguards need to be implemented through instrument software options and point-of-care coordinators. Connectivity will be facilitated by standards that eliminate deficiencies in instrument communication and device compatibility. Assessment of control features on handheld, portable, and transportable point-of-care instruments shows that current error reduction features lag behind needs. CONCENSUS PROCESS: Step 1: United States national survey and collation of group A expert requirements for security, validation, and performance. Step 2: Design of parallel systems for these functions. Step 3: Written critique and improvement of the error-prevention systems during 4 successive presentations to group B participants over 9 months until system designs stabilized into final consensus form. CONCLUSIONS: The consensus process produced 6 conclusions for preventing medical errors in point-of-care testing: (1) adopt operator certification and validation in point-of-care testing programs; (2) implement security, validation, performance, and emergency systems on existing and new devices; (3) require flexible, user-defined error-prevention system options on instruments as a prerequisite to federal licensing of new diagnostic tests and devices; (4) integrate connectivity standards for bidirectional information exchange; (5) preserve fast therapeutic turnaround time of point-of-care test results; and (6) monitor invalid use, operator competence, quality compliance, and other performance improvement indices to reduce errors, thereby focusing on patient outcomes.(Arch Pathol Lab Med. 2001;1307-1315)

Consensus Statements as Topic↗

PubMed2025

Analysis of differentially expressed genes in schizophrenia based on bioinformatics and corresponding mRNA expression levels.

OBJECTIVE: This study aimed to use bioinformatics analysis to identify differentially expressed genes (DEGs) involved in the pathogenesis of schizophrenia and validate their mRNA expression levels through real-time quantitative PCR (qPCR). MATERIAL/METHODS: Datasets from the publicly available Gene Expression Omnibus (GEO) database were analyzed using R software to identify DEGs. Functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, were conducted. A protein-protein interaction (PPI) network was constructed using Cytoscape software to identify key genes with notable expression changes. The expression levels of these key genes were subsequently validated in schizophrenia patients using qPCR to assess potential susceptibility genes. RESULTS: In total, 813 DEGs were identified, with six key genes highlighted through GO analysis and PPI network screening. Among these, HDAC1, UBA52, and FYN demonstrated statistically significant differences in mRNA expression between schizophrenia patients and healthy controls (P < 0.05). CONCLUSIONS: This study identified several DEGs potentially linked to the pathogenesis of schizophrenia, suggesting that HDAC1, UBA52, and FYN could serve as candidate susceptibility genes and diagnostic biomarkers. These findings provide new insights and directions for future schizophrenia research.

Humans↗

PubMed2006

Effectiveness of educational interventions in improving detection and management of dementia in primary care: cluster randomised controlled study.

OBJECTIVE: To test the effectiveness of educational interventions in improving detection rates and management of dementia in primary care. DESIGN: Unblinded, cluster randomised, before and after controlled study. SETTING: General practices in the United Kingdom (central Scotland and London) between 1999 and 2002. INTERVENTIONS: Three educational interventions: an electronic tutorial carried on a CD Rom; decision support software built into the electronic medical record; and practice based workshops. PARTICIPANTS: 36 practices participated in the study. Eight practices were randomly assigned to the electronic tutorial; eight to decision support software; 10 to practice based workshops; and 10 to control. Electronic and manual searches yielded 450 valid and usable medical records. MAIN OUTCOME MEASURES: Rates of detection of dementia and the extent to which medical records showed evidence of improved concordance with guidelines regarding diagnosis and management. RESULTS: Decision support software (P = 0.01) and practice based workshops (P = 0.01) both significantly improved rates of detection compared with control. There were no significant differences by intervention in the measures of concordance with guidelines. CONCLUSIONS: Decision support systems and practice based workshops are effective educational approaches in improving detection rates in dementia.

Aged↗

PubMed2006

An automated method for rapid identification of putative gene family members in plants.

BACKGROUND: Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families has become increasingly important. Subfunctionalization via changes in regulatory sequences following duplication (adaptive selection) appears to be a common mechanism of evolution in plants and can be accompanied by purifying selection on the coding region. Such negative selection can be detected by a bias toward synonymous over nonsynonymous substitutions. However, the process of identifying this bias requires many steps usually employing several different software programs. We have simplified the process and significantly shortened the time required by condensing many steps into a few scripts or programs to rapidly identify putative gene family members beginning with a single query sequence. RESULTS: In this report we 1) describe the software tools (SimESTs, PCAT, and SCAT) developed to automate the gene family identification, 2) demonstrate the validity of the method by correctly identifying 3 of 4 PAL gene family members from Arabidopsis using EST data alone, 3) identify 2 to 6 CAD gene family members from Glycine max (previously unidentified), and 4) identify 2 members of a putative Glycine max gene family previously unidentified in any plant species. CONCLUSION: Gene families in plants, particularly that subset where purifying selection has occurred in the coding region, can be identified quickly and easily by integrating our software tools and commonly available contig assembly and ORF identification programs.

Arabidopsis↗

PubMed2005

[Clinical gait analysis].

Clinical gait analysis comprises a well defined repertoire of various methods for valid and reliable assessment. The rapid development of corresponding hardware and software has substantially decreased the efforts necessary for data processing and has promoted the clinical applicability of the procedures. The clinical question defines the amount of methodological input. Clinical gait analysis may provide diagnostic insight into the pathobiomechanics and the pathophysiology of complex gait disorders for which a profound understanding of the underlying causes is a prerequisite for adequate treatment. The methods may help in the screening of gait function following reconstructive surgery as a measure of quality control, the assessment of the severity of a gait disturbance, the evaluation of a rehabilitation process, or the quantification of the effect of orthoses, insoles or specific shoe ware. Simple procedures of gait analysis may suffice to obtain information on gait function which can not be derived by mere clinical observation and which can be incorporated into a clinical concept.

Activities of Daily Living↗

PubMed1990

Review of Q-FAST interactive testing system.

The administration and scoring of paper and pencil measures present a host of logistical problems to clinicians, researchers and educators who rely heavily on these techniques. In addition to the expense of producing and reproducing these materials, the completed measures must be scored, the results must be reduced and recorded and the data must be analyzed. The introduction of human error at any of these steps may compromise the reliability of the obtained data and obstruct its valid interpretation. The Q-FAST computerized testing system is a software package which could improve the efficiency of collection, scoring and analysis of data obtained through such procedures.

Humans↗

PubMed2005

Implementation of a simple semi-quantitative near-infrared method for the classification of clinical trial tablets.

Near infrared transmission spectroscopy combined with chemometrical methods can be applied for identity confirmation of double-blind clinical trial tablets. Samples of two clinical studies, investigating the dose and placebo effect of an experimental drug, were studied. The identity of the blistered tablets was checked using partial least squares beta classification (PLSBC) applied to their NIR transmission spectra. PLSBC is a new supervised classification approach based on partial least squares (PLS) regression combined with beta-error driven class boundaries. It has the ability to limit the probability for misclassification to a known number and therefore providing the method developer a tool for deciding whether the NIR spectra of the different strengths of tablets are specific enough to obtain a robust classification model. The presented approach has the advantage to be applicable on most commercial available near infrared spectroscopy (NIRS) instrumentation software and it can be applied in a GMP environment since validation according to the ICH Q2A and Q2B guidelines on analytical method validation is fast and relatively easy.

Clinical Trials as Topic↗

PubMed2005

Use of AFLP markers in surveys of plant diversity.

The collection of the available range of genetic variation in a gene pool, usually made of the cultivated species and their undomesticated relatives, is referred to as a germplasm collection. Increasingly, discriminator data generated using molecular genetic markers are either complementing or completely replacing those from morphological characters (known as descriptors) in surveys of genetic diversity. In addition to highlighting the state of knowledge on the specific applications of amplified fragment length polymorphisms (AFLPs) in surveys of plant genetic diversity, an attempt at a brief description and comparison of the different marker systems in use has also been made in this chapter. We have also attempted a description of the AFLP marker technology, its strengths and weaknesses, methodologies for generating reliable AFLP data, available resources (hardware, software, consumables); the kinds of questions for which AFLP data provide valid answers; and data management options. This chapter also highlights salient considerations that would guide decisions on the adoption of molecular marker assays.

DNA, Complementary↗

PubMed2005

Novel ligands for the chemokine receptor-3 (CCR3): a receptor-modeling study based on 5D-QSAR.

We recently reported the development of a receptor-modeling concept based on 5D-QSAR (quantitative structure-activity relationships) and which explicitly allows for the simulation of induced fit. In this account, we report its utilization toward the design of novel compounds able to inhibit the chemokine receptor-3 (CCR3). The study was based on a total of 141 compounds, representing four different substance classes. Using the Quasar software, we built two receptor surrogates that yielded a cross-validated r(2) value of 0.950/0.861 and a predictive r(2) of 0.879/0.798, respectively. The model was then employed to predict the activity of 58 hypothetical compounds featuring two variation patterns: lipophilic substitutions and amphiphilic H-bond acceptors. Eleven of the proposed ligands show a calculated binding affinity lower than any compound within the training set; the most potent candidate molecule is expected to bind at an IC(50) of 0.3 nM.

Benzene Derivatives↗

PubMed2002

A digital model for the venous junctions.

The venous network in the lower limbs is composed of a considerable number of confluent junctions. Each of these singularities introduces some blood flow disturbances. Each physiological junction is unique, in terms of its geometry as well as the blood flow rate. In order to account for this great variability, we developed a numerical model based on the use of the N3S code (a software package for solving Navier-Stokes equations). To test the validity of the model, one of the numerical simulations is compared with the data obtained in the corresponding experimental configuration. The velocity measurements were carried out with an ultrasonic pulsed Doppler velocimeter. We also measured pressure differences using differential sensors. The numerical computations were then used to obtain the values of the flow variables at any point, with various geometrical and flow configurations. As far as the velocity field is concerned, a very marked three-dimensional pattern with swirls was observed. The pressure evolution was also strongly disturbed, with a non-linear decrease. All these data indicate that confluence effects cannot be neglected when evaluating pressure decreases. With a tool of this kind, it is possible to accurately predict the disturbances associated with any geometrical configuration or any flow rate.

Blood Flow Velocity↗

PubMed1995

Laser profiling: a technique for the study of prosthetic heart valve leaflet motion.

A detailed understanding of the stresses and strains developed in functioning flexible-leaflet valves is necessary if a durable, non-thrombogenic heart valve replacement is to be realized. A new experimental tool, laser profiling, is presented for the study of flexible-leaflet heart valve dynamics. Profiles of moving leaflet surfaces are obtained by projecting parallel sheets of laser light onto valve leaflets as the valves open and close in a mock circulatory loop. Two versions of laser profiling have been developed. In two-dimensional mode multiple profiles are generated on a fixed plane in space but at discrete intervals in time, whereas in three-dimensional mode multiple profiles are generated across the leaflet surface at (effectively) a single instant in time. Highlighted leaflet profiles are captured by camera and transferred to an image processing system for analysis. A simple algorithm permits digitized profiles to be reconstructed within a computer-aided design software package, providing detailed visualization and quantification of valve motion. Extensive validation studies have been performed using the Medtronic-Hall mechanical prosthetic heart valve. Laser profiling enables computer reconstruction of the rigid occluder to an accuracy of +/- 200 microns from a 0.7 ms exposure taken during the period at which the occluder moves with greatest velocity. The technique has been applied to investigate the leaflet dynamics of a bovine pericardial heart valve prosthesis.

Acoustic Stimulation↗