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PubMed1998

Development and validation of an evaluation tool for multimedia resources in health education.

The last decade saw a rapid increase in the use of multimedia in health education. Easy availability, accessibility, low cost of technological resources and the expanding body of research on the role of multimedia in student learning, among others, have all contributed to this increase in usage. Since one of the roles of educators is to assess and select learning resources based on curriculum goals and student needs, the development of standardized methods for multimedia evaluation becomes vital. To the learner, it is important for reviews of the quality of the resource to be readily available. An evaluation too was developed based on the recognition of this need. The validity of the tool was tested using experts in technology and education. Reliability was determined using faculty and students who reviewed the same software, using the tool. In addition, graduate students reviewed two versions of a nursing program, of varying quality. The results indicate that the tool is reliable and valid. It is envisaged that this tool can be utilized by health educators for evaluating multimedia resources and setting up a much needed clearinghouse for health education resources.

CD-ROM↗
PubMed1999

HOLON/CADSE: integrating open software standards and formal methods to generate guideline-based decision support agents.

This paper describes the efforts of a consortium that is trying to develop and validate formal methods and a meta-environment for authoring, checking, and maintaining a large repository of machine executable practice guidelines. The goal is to integrate and extend a number of open software standards so that guidelines in the meta-environment become a resource that any vendor can plug their applications into and run in their proprietary environment provided they conform to the interface standards.

Computer Communication Networks↗
PubMed2006

The psychometric properties of the Chinese version of the Fagerstrom Test for Nicotine Dependence.

This study examined the psychometric properties of the Chinese version of the Fagerstrom Test for Nicotine Dependence (FTND). Criterion validity, factorial structure, and construct reliability were conducted using PRELIS 2 and LISREL 8.7 software. Two hundred and forty-five adult smokers were recruited from April to August 2005 in Taiwan. Because some items of the FTND are dichotomous and ordinal, biserial and polyserial correlations between the items and saliva cotinine levels were utilized. Confirmatory factor analyses (CFA) were performed to compare the relative fit of three competing models. Computation of the construct reliability was necessitated by a lack of tau-equivalence. The results demonstrated that the Chinese version has satisfactory validity and reliability. One item, "Smoke more in the morning," had low correlations with saliva cotinine. CFA found the items of the Chinese version were best modeled as two correlated factors without a cross-loading. These findings differ from the previous research testing the English version. Studies addressing the specific features of cigarette dependence in different socio-cultural contexts are needed.

Adolescent↗
PubMed1998

Are you using data to build valid comparisons? Here's how.

In the quest for needed data and benchmarks under capitation, providers are discovering comparative analysis software to examine their internal costs, model a proposed contract, or determine what clinical programs are needed in the community.

Benchmarking↗
PubMed1995

[Validation of a computer-assisted procedure for producing blood and blood component transfusions].

BACKGROUND: The validation of computer-aided methods in the production of stored blood and blood components represents for a pharmaceutical institution a basic condition for the carrying out of the decrees of pharmaceutical companies. When validating computer-aided methods in medicine or pharmacy, the fields of informatics and technology have to be linked to applications in medicine and pharmacy. METHOD: In many cases the methods for the documented proof that a system achieves the expected capacity are too complex, so that a validation is only practicable in module groups. This is shown with an example of the blood typing on microtiter plates. RESULTS: After the selection of the hard- and software according to the safety criteria of information technology taking into consideration functional classes and degrees of quality, a complete documentation of the validation of blood typing on the microtiter plate was carried out.

Blood Banks↗
PubMed1997

Detection of intra- and cross-cultural non-equivalence by simple methods in cross-cultural research: evidence from a study of eating attitudes in Nigeria and Britain.

The desiderata for cross-cultural research are reviewed showing how this is dominated by the presumption of transcultural equivalence hidden by the technical problems of translation. This model requires intensive translation work on measures to preserve "equivalence". This work can be prohibitively intensive, might lead to spurious evidence of "equivalence" and has not produced much evidence of equivalence to date. A psychometric axiom--that a measure with low reliability cannot have validity--suggests a pragmatic way to explore these issues and current statistical software and personal computers make this feasible. We recommend that all cross-cultural research should present the internal reliability of the data as this will expose all but one theoretical problem in the detection of "equivalence". We also suggest that non-equivalence may indicate cross-cultural differences in the dimensionality of eating and body image concerns rather than just a problem to be exorcised by more translation work or to be hidden by not reporting reliability. These issues are not specific to work across languages but also apply to comparisons between any social groups within cultures. This is shown using data from questionnaires in their original English with respondents who were fluent in that language.

Adult↗
PubMed2003

Vertical cup-to-disc ratio: agreement between direct ophthalmoscopic estimation, fundus biomicroscopic estimation, and scanning laser ophthalmoscopic measurement.

PURPOSE: Ophthalmoscopic estimation of the vertical cup-to-disc ratio (VCDR) of the optic nerve head is important in the management of patients with glaucoma or who are glaucoma suspects. The purpose of this study was to compare the accuracy of estimation of VCDR obtained with direct ophthalmoscopy with that obtained with fundus biomicroscopy through undilated pupils. Measurements of VCDR obtained with the Heidelberg Retina Tomograph (HRT), a confocal scanning laser ophthalmoscope, were used as a standard. METHODS: Thirty young, healthy adults had their optic discs photographed and then imaged and analyzed with the HRT. Due to HRT software limitations, the VCDR could not be calculated automatically, and so a validated VCDR measurement was derived. This was used as the standard against which ophthalmoscopic estimations were compared. Two months later, the subjects had their VCDRs estimated using direct ophthalmoscopy and fundus biomicroscopy performed in random order after varying time intervals. Agreement between ophthalmoscopic VCDR estimation and HRT-derived VCDR measurement was assessed by means of bias plots and the weighted kappa statistic. RESULTS: Compared with the HRT-derived VCDR measurement, both ophthalmoscopic techniques tended to underestimate VCDR. The bias with direct ophthalmoscopy was statistically significant. There were also wide variations in VCDR estimation with direct ophthalmoscopy and fundus biomicroscopy, which were more pronounced with direct ophthalmoscopy. The weighted kappa statistic indicated moderate agreement between fundus biomicroscopy and HRT-derived VCDR measurement. There was poor to fair agreement between direct ophthalmoscopy and HRT-derived VCDR measurement. The level of disagreement was independent of HRT-derived VCDR, optic nerve head size and pupil size for both direct ophthalmoscopy and fundus biomicroscopy. CONCLUSIONS: Fundus biomicroscopy enables more accurate, less variable VCDR estimation than direct ophthalmoscopy. The clinician should record which method they used to examine the optic nerve head so that subsequent clinical decisions are not influenced by apparent VCDR changes.

Adult↗
PubMed2005

Differential gene expression during capillary morphogenesis in a microcarrier-based three-dimensional in vitro model of angiogenesis with focus on chemokines and chemokine receptors.

AIM: To globally compare the gene expression profiles during the capillary morphogenesis of human microvascular endothelial cells (HMVECs) in an in vitro angiogenesis system with affymetrix oligonucleotide array. METHODS: A microcarrier-based in vitro angiogenesis system was developed, in which ECs migrated into the matrix, proliferated, and formed capillary sprouts. The sprouts elongated, branched and formed networks. The total RNA samples from the HMVECs at the selected time points (0.5, 24, and 72 h) during the capillary morphogenesis were used for microarray analyses, and the data were processed with the softwares provided by the manufacturers. The expression patterns of some genes were validated and confirmed by semi-quantitative RT-PCR. The regulated genes were grouped based on their molecular functions and expression patterns, and among them the expression of chemokines and chemokine receptors was specially examined and their functional implications were analyzed. RESULTS: A total of 1 961 genes were up- or down-regulated two-folds or above, and among them, 468 genes were up- or down-regulated three-folds or above. The regulated genes could be grouped into categories based on their molecular functions, and were also clustered into six groups based on their patterns of expression. As for chemokines and chemokine receptors, CXCL1/GRO-alpha, CXCL2/GRO-beta, CXCL5/ENA-78, CXCL6/GCP2, IL-8/CXCL8, CXCL12/SDF-1, CXCL9/Mig, CXC11/ITAC, CX3CL1/fractalkine, CCL2/MCP-1, CCL3, CCL5/RANTES, CCL7, CCL15, CCL21, CCL23, CCL28, and CCR1, CCR9, CXCR4 were identified. Moreover, these genes demonstrated different changing patterns during the capillary morphogenesis, which implied that they might have different roles in the sequential process. Among the chemokines identified, CCL2/MCP-1, CCL5/RANTES and CX3CL1 were specially up-regulated at the 24-h time point when the sprouting characterized the morphological change. It was thus suggested that they might exert crucial roles at the early stage of angiogenesis. CONCLUSION: The present study demonstrates a global profile of gene expression during endothelial capillary morphogenesis, and the results provide us much information about the molecular mechanisms of angiogenesis, with which further evaluation of individual genes can be conducted.

Cell Culture Techniques↗
PubMed2005

[Gene expression profiling of microvascular endothelial cells during capillary morphogenesis in an in vitro model of angiogenesis].

OBJECTIVE: To globally compare the gene expression profiles during the capillary morphogenesis of human microvascular endothelial cells (HMVECs) in an in vitro angiogenesis system with Affymetrix oligonucleotide array. METHODS: A microcarrier-based in vitro angiogenesis system was developed, in which endothelial cells (ECs) migrated into the matrix, proliferated, and formed capillary sprouts. The sprouts elongated, branched and formed network. The total RNA samples from the HMVECs at the selected time points (0.5 h, 24 h, and 72 h) during the capillary morphogenesis were used for microarray analyses, and the data were processed with the software provided by the manufactory. The expression patterns of some genes were validated and confirmed by Semi-quantitative RT-PCR. The regulated genes were grouped based on their molecular functions and expression patterns, and among them the expression of chemokines/chemokine receptors were specially examined and their functional implications were analyzed. RESULTS: About 1500 genes were found up- or down- regulated 2-folds or above detected by the arrays, and among them, about 400 genes regulated 3-folds or above. The regulated genes could be grouped into categories based on their molecular functions such as growth factor and receptor, cell proliferation, extracellular matrix, cell cycle and apoptosis, signaling molecule and transcription factor, and so on, using the Gene Ontology Mining Tool in The NetAffx Analysis Center. The regulated genes were also clustered into six groups based on their patterns of expression. As for chemokines, the CCL2/MCP-1, CCL5/RANTES and CX3CL1 were identified to be specially upregulated at 24 h time point when the sprouting characterized the morphological change. It was thus suggested that they might exert crucial roles at the early stage of angiogenesis. CONCLUSIONS: Based on our angiogenesis model, and by oligonucleotide arrays, the present study demonstrates global profiles of the gene expression during endothelial capillary morphogenesis, and the results provide us much information about the molecular mechanisms of angiogenesis, with which further evaluation of individual genes can be encouraged.

Capillaries↗
PubMed2005

Gene expression profile of human Down syndrome leukocytes.

AIM: Identification of differences in the gene expression patterns of Down syndrome and normal leukocytes. METHODS: We constructed the first Down syndrome leukocyte serial analysis of gene expression (SAGE) library from a 28 year-old patient. This library was analyzed and compared with a normal leukocyte SAGE library using the eSAGE software. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to validate the results. RESULTS: We found that a large number of unidentified transcripts were overexpressed in Down syndrome leukocytes and some transcripts coding for growth factors (e.g. interleukin 8, IL-8), ribosomaproteins (e.g. L13a, L29, and L37), and transcription factors (e.g., Jun B, Jun D, and C/EBP beta) were underexpressed. The SAGE data were successfully validated for the genes IL-8, CXCR4, BCL2A1, L13a, L29, L37, and GTF3A using RT-PCR. CONCLUSION: Our analysis identified significant changes in the expression pattern of Down syndrome leukocytes compared with normal ones, including key regulators of growth and proliferation, ribosomal proteins, and a large number of overexpressed transcripts that were not matched in UniGene clusters and that may represent novel genes related to Down syndrome. This study offers a new insight into transcriptional changes in Down syndrome leukocytes and indicates candidate genes for further investigations into the molecular mechanism of Down syndrome pathology.

Adult↗
PubMed2003

PipeAlign: A new toolkit for protein family analysis.

PipeAlign is a protein family analysis tool integrating a five step process ranging from the search for sequence homologues in protein and 3D structure databases to the definition of the hierarchical relationships within and between subfamilies. The complete, automatic pipeline takes a single sequence or a set of sequences as input and constructs a high-quality, validated MACS (multiple alignment of complete sequences) in which sequences are clustered into potential functional subgroups. For the more experienced user, the PipeAlign server also provides numerous options to run only a part of the analysis, with the possibility to modify the default parameters of each software module. For example, the user can choose to enter an existing multiple sequence alignment for refinement, validation and subsequent clustering of the sequences. The aim is to provide an interactive workbench for the validation, integration and presentation of a protein family, not only at the sequence level, but also at the structural and functional levels. PipeAlign is available at http://igbmc.u-strasbg.fr/PipeAlign/.

Internet↗
PubMed2003

Can transcriptome size be estimated from SAGE catalogs?

MOTIVATION: SAGE (Serial Analysis of Gene Expression) can be used to estimate the number of unique transcripts in a transcriptome. A simple estimator that corrects for sequencing and sampling errors was applied to a SAGE library (137 832 tags) obtained from mouse embryonic stem cells, and also to Monte Carlo simulated libraries generated using assumed distributions of 'true' expression levels consistent with the data. RESULTS: When the corrected data themselves were taken as the underlying model of 'ground truth', the estimator converged to the 'true' value (53 535) only after counting 300 000 simulated tags, more than twice the number in the experiment. The SAGE data could also be well fit by a Monte Carlo model based on a truncated inverse-square distribution of expression levels, with 130 000 'true' transcripts and 10(6) samples needed for convergence. We conclude that the size of a transcriptome is ill-determined from SAGE libraries of even moderately large size. In order to obtain a valid estimate, one must sample a number of tags inversely proportional to the lowest abundance level, which is not known a priori. This constrains the design of SAGE experiments intended to determine biological complexity. AVAILABILITY: The 'homemade' software used for this analysis was not designed for general or 'production' use, but the authors will be happy to share Fortran sourcecode with interested parties. CONTACT: sternm@grc.nia.nih.gov

Algorithms↗
PubMed2003

AMIDE: a free software tool for multimodality medical image analysis.

Amide's a Medical Image Data Examiner (AMIDE) has been developed as a user-friendly, open-source software tool for displaying and analyzing multimodality volumetric medical images. Central to the package's abilities to simultaneously display multiple data sets (e.g., PET, CT, MRI) and regions of interest is the on-demand data reslicing implemented within the program. Data sets can be freely shifted, rotated, viewed, and analyzed with the program automatically handling interpolation as needed from the original data. Validation has been performed by comparing the output of AMIDE with that of several existing software packages. AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License.

Costs and Cost Analysis↗
PubMed2006

AceView: a comprehensive cDNA-supported gene and transcripts annotation.

BACKGROUND: Regions covering one percent of the genome, selected by ENCODE for extensive analysis, were annotated by the HAVANA/Gencode group with high quality transcripts, thus defining a benchmark. The ENCODE Genome Annotation Assessment Project (EGASP) competition aimed at reproducing Gencode and finding new genes. The organizers evaluated the protein predictions in depth. We present a complementary analysis of the mRNAs, including alternative transcript variants. RESULTS: We evaluate 25 gene tracks from the University of California Santa Cruz (UCSC) genome browser. We either distinguish or collapse the alternative splice variants, and compare the genomic coordinates of exons, introns and nucleotides. Whole mRNA models, seen as chains of introns, are sorted to find the best matching pairs, and compared so that each mRNA is used only once. At the mRNA level, AceView is by far the closest to Gencode: the vast majority of transcripts of the two methods, including alternative variants, are identical. At the protein level, however, due to a lack of experimental data, our predictions differ: Gencode annotates proteins in only 41% of the mRNAs whereas AceView does so in virtually all. We describe the driving principles of AceView, and how, by performing hand-supervised automatic annotation, we solve the combinatorial splicing problem and summarize all of GenBank, dbEST and RefSeq into a genome-wide non-redundant but comprehensive cDNA-supported transcriptome. AceView accuracy is now validated by Gencode. CONCLUSION: Relative to a consensus mRNA catalog constructed from all evidence-based annotations, Gencode and AceView have 81% and 84% sensitivity, and 74% and 73% specificity, respectively. This close agreement validates a richer view of the human transcriptome, with three to five times more transcripts than in UCSC Known Genes (sensitivity 28%), RefSeq (sensitivity 21%) or Ensembl (sensitivity 19%).

Computational Biology↗
PubMed2005

Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.

Chromatin immunoprecipitation combined with microarray technology (Chip2) allows genome-wide determination of protein-DNA binding sites. The current standard method for analyzing Chip2 data requires additional control experiments that are subject to systematic error. We developed methods to assess significance using variance stabilization, learning error-model parameters without external control experiments. The method was validated experimentally, shows greater sensitivity than the current standard method, and incorporates false-discovery rate analysis. The corresponding software ('Chipper') is freely available. The method described here should help reveal an organism's transcription-regulatory 'wiring diagram'.

Analysis of Variance↗
PubMed2003

A declarative implementation of the DICOM-3 network protocol.

We describe a new design for programs using the Digital Imaging and Communications in Medicine (DICOM) protocol, which we have implemented in a DICOM image storage server and a radiation treatment plan transfer facility for our locally developed radiation treatment planning system, Prism. This design is declarative, representing DICOM as a language for describing messages and sequencing of messages. The coding involved implementing an interpreter for this language. The DICOM protocol specifies messages, message formats, and sequencing. In our design, the specification translates almost directly into computer-readable declarative expressions that closely resemble the relevant tabulated DICOM specifications. The resulting programs are small, simple, and extensible, because most of the details of the DICOM protocol are not coded in the procedural control statements but are in the expressions and state table that the interpreter uses to perform all its functions. This approach provides a way to validate the consistency of a specification and the correctness of the implementation. The same method can be generalized to other such protocols. It may also be used to assist the design of new protocols.

Algorithms↗
PubMed2003

Automatic three-dimensional model for protontherapy of the eye: preliminary results.

Recently, radiotherapy possibilities have been dramatically increased by software and hardware developments. Improvements in medical imaging devices have increased the importance of three-dimensional (3D) images as the complete examination of these data by a physician is not possible. Computer techniques are needed to present only the pertinent information for clinical applications. We describe a technique for an automatic 3D reconstruction of the eye and CT scan merging with fundus photographs (retinography). The final result is a "virtual eye" to guide ocular tumor protontherapy. First, we make specific software to automatically detect the position of the eyeball, the optical nerve, and the lens in the CT scan. We obtain a 3D eye reconstruction using this automatic method. Second, we describe the retinography and demonstrate the projection of this modality. Then we combine retinography with a reconstructed eye, using a CT scan to get a virtual eye. The result is a computer 3D scene rendering a virtual eye into a skull reconstruction. The virtual eye can be useful for the simulation, the planning, and the control of ocular tumor protontherapy. It can be adapted to treatment planning to automatically detect eye and organs at risk position. It should be highlighted that all the image processing is fully automatic to allow the reproduction of results, this is a useful property to conduct a consistent clinical validation. The automatic localization of the organ at risk in a CT scan or an MRI by automatic software could be of great interest for radiotherapy in the future for comparison of one patient at different times, the comparison of different treatments centers, the possibility of pooling results of different treatments centers, the automatic generation of doses-volumes histograms, the comparison between different treatment planning for the same patient and the comparison between different patients at the same time. It will also be less time consuming.

Eye↗
PubMed2003

A reassessment of normal cervical range of motion.

STUDY DESIGN: Intraexaminer and interexaminer/procedure reliability and error analysis using a repeated-measures design. OBJECTIVE: To quantify sources of discrepancies in cervical range of motion values between two procedures that use the same potentiometric technology. SUMMARY OF BACKGROUND DATA: Studies using an early version of an electrogoniometer system, which was connected between a helmet worn by the study participant and a chair on which they sat, reported unusually high values for active and passive cervical range of motion, although measurements were reliable. To understand the sources of the discrepancies between that study and later studies (using upgraded software), the current study was designed to quantify possible sources of error contributed by various components of the procedures: helmet, thoracic reference, chair, and software. METHODS: A total of 22 asymptomatic study participants were evaluated in two separate sessions, 1-3 days apart. Components of two procedures were changed systematically in a series of repeated measurements to provide concurrent reliability and to assess sources of error between the two procedures. RESULTS: The reliabilities of both procedures were generally high with no systematic trends, except for lower values for flexion-extension studies with Procedure 2. Procedure 2 also provided systematically greater range of motion values (2-8 degrees ) than Procedure 1, except for flexion (half-cycle). The source of the greatest discrepancy between the two procedures was the software, when comparing the original with the updated versions. With regard to the instrumentation, the greatest source of variability was in the thoracic reference post; next was the helmet, and least significant was the type of seat used. A comparison of overall procedure discrepancies and summation of individual elements of the procedures accounted for virtually all of the observed error. CONCLUSION: The potentiometer-based electrogoniometer is a reliable instrument for determining cervical range of motion. Measurements appear to be more valid when the thoracic reference point is physically attached to the study participant's body. The original software provided with the system appears to have contributed to systematic overestimation of ranges of motion, but current units provide measurements that are both reliable and valid.

Adult↗