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PubMed2004

Validation of alternative methods of data normalization in gene co-expression studies.

MOTIVATION: Clusters of genes encoding proteins with related functions, or in the same regulatory network, often exhibit expression patterns that are correlated over a large number of conditions. Protein associations and gene regulatory networks can be modelled from expression data. We address the question of which of several normalization methods is optimal prior to computing the correlation of the expression profiles between every pair of genes. RESULTS: We use gene expression data from five experiments with a total of 78 hybridizations and 23 diverse conditions. Nine methods of data normalization are explored based on all possible combinations of normalization techniques according to between and within gene and experiment variation. We compare the resulting empirical distribution of gene x gene correlations with the expectations and apply cross-validation to test the performance of each method in predicting accurate functional annotation. We conclude that normalization methods based on mixed-model equations are optimal.

Algorithms↗
PubMed1984

Computer software design for pediatric practice. A modular approach.

Practical applications for using computers in everyday medical practice have not kept pace with the technical developments that now make this tool available to the pediatric practitioner. A modular approach to user-developed applications software is presented as a model for computerizing the pediatric office. Benefits have included lower cost, greater data reliability and validity, standardization of office and medical procedures, and automation of jobs formerly requiring much personnel time. Some patient services have improved, and other new services have become possible, through the application of computer software designed in accordance with our practice philosophy.

Computers↗
PubMed2005

Generation and validation of a shielding library based on ENDF/B-VI.8.

For various shielding and reactor pressure vessel dosimetry applications, a pseudo-problem-independent neutron-photon coupled MATXS-format library, based on the last release of ENDF/B-VI, has been generated as a part of the update program for KASHIL-E6, which was based on ENDF/B-VI.5. It has a VITAMIN-B6 neutron and photon energy group structures, i.e. 199 groups for the neutron and 42 groups for the photon. The neutron and photon weighting functions and the Legendre orders of scattering are the same as in KASHIL-E6. The library has been validated through some benchmarks: the PCA-REPLICA and NESDIP-2 experiments for the light-water reactor (LWR) pressure vessel facility benchmark, the Winfrith Iron 88 experiment for the validation of the iron data and the Winfrith Graphite experiment for the validation of the graphite data. These calculations were performed by the TRANSX/DANTSYS code system. In addition, the substitutions of the JENDL-3.3 and JEFF-3.0 data for Fe, Cr, Cu and Ni, which are very important nuclides for shielding analyses, were investigated to estimate the effects on the benchmark calculation results.

Algorithms↗
PubMed2002

CHOMPER: a bioinformatic tool for rapid validation of tandem mass spectrometry search results associated with high-throughput proteomic strategies.

Current efforts aimed at developing high-throughput proteomics focus on increasing the speed of protein identification. Although improvements in sample separation, enrichment, automated handling, mass spectrometric analysis, as well as data reduction and database interrogation strategies have done much to increase the quality, quantity and efficiency of data collection, significant bottlenecks still exist. Various separation techniques have been coupled with tandem mass spectrometric (MS/MS) approaches to allow a quicker analysis of complex mixtures of proteins, especially where a high number of unambiguous protein identifications are the exception, rather than the rule. MS/MS is required to provide structural / amino acid sequence information on a peptide and thus allow protein identity to be inferred from individual peptides. Currently these spectra need to be manually validated because: (a) the potential of false positive matches i.e., protein not in database, and (b) observed fragmentation trends may not be incorporated into current MS/MS search algorithms. This validation represents a significant bottleneck associated with high-throughput proteomic strategies. We have developed CHOMPER, a software program which reduces the time required to both visualize and confirm MS/MS search results and generate post-analysis reports and protein summary tables. CHOMPER extracts the identification information from SEQUEST MS/MS search result files, reproduces both the peptide and protein identification summaries, provides a more interactive visualization of the MS/MS spectra and facilitates the direct submission of manually validated identifications to a database.

Algorithms↗
PubMed1999

Is the coefficient of variation a valid measure for detecting sincerity of effort of grip strength?

The wide use of the coefficient of variation in detecting sincerity of effort is puzzling since existing research findings regarding its effectiveness are contradictory. The lack of empirical support in the literature raises the question of whether or not the coefficient of variation is a valid measure for detecting sincerity of effort. Many clinicians, especially those who use a computer software to calculate the coefficient of variation, may not understand how the coefficient of variation is derived and what it is based on. The coefficient of variation is a measure of relative variability and would be used correctly only if the average and the standard deviation of grip strength trials increased proportionally. This case study, however, demonstrated that the average and standard deviation of grip strength are independent. Thus, the coefficient of variation is not a valid measure of sincerity of effort. In addition, this study indicated that the coefficient of variation may be inflated in individuals after carpal tunnel release surgery. The author, therefore, cautions clinicians against the use of the coefficient of variation as a measure of sincerity of effort especially in injured individuals with compromised hand strength.

Journal Article↗
PubMed2006

Identification and stoichiometry of glycosylphosphatidylinositol-anchored membrane proteins of the human malaria parasite Plasmodium falciparum.

Most proteins that coat the surface of the extracellular forms of the human malaria parasite Plasmodium falciparum are attached to the plasma membrane via glycosylphosphatidylinositol (GPI) anchors. These proteins are exposed to neutralizing antibodies, and several are advanced vaccine candidates. To identify the GPI-anchored proteome of P. falciparum we used a combination of proteomic and computational approaches. Focusing on the clinically relevant blood stage of the life cycle, proteomic analysis of proteins labeled with radioactive glucosamine identified GPI anchoring on 11 proteins (merozoite surface protein (MSP)-1, -2, -4, -5, -10, rhoptry-associated membrane antigen, apical sushi protein, Pf92, Pf38, Pf12, and Pf34). These proteins represent approximately 94% of the GPI-anchored schizont/merozoite proteome and constitute by far the largest validated set of GPI-anchored proteins in this organism. Moreover MSP-1 and MSP-2 were present in similar copy number, and we estimated that together these proteins comprise approximately two-thirds of the total membrane-associated surface coat. This is the first time the stoichiometry of MSPs has been examined. We observed that available software performed poorly in predicting GPI anchoring on P. falciparum proteins where such modification had been validated by proteomics. Therefore, we developed a hidden Markov model (GPI-HMM) trained on P. falciparum sequences and used this to rank all proteins encoded in the completed P. falciparum genome according to their likelihood of being GPI-anchored. GPI-HMM predicted GPI modification on all validated proteins, on several known membrane proteins, and on a number of novel, presumably surface, proteins expressed in the blood, insect, and/or pre-erythrocytic stages of the life cycle. Together this work identified 11 and predicted a further 19 GPI-anchored proteins in P. falciparum.

Animals↗
PubMed2004

Determining sociability, social space, and social presence in (a)synchronous collaborative groups.

The effectiveness of group learning in asynchronous distributed learning groups depends on the social interaction that takes place. This social interaction affects both cognitive and socioemotional processes that take place during learning, group forming, establishment of group structures, and group dynamics. Though now known to be important, this aspect is often ignored, denied or forgotten by educators and researchers who tend to concentrate on cognitive processes and on-task contexts. This "one-sided" educational focus largely determines the set of requirements in the design of computer-supported collaborative learning (CSCL) environments resulting in functional CSCL environments. In contrast, our research is aimed at the design and implementation of sociable CSCL environments which may increase the likelihood that a sound social space will emerge. We use a theoretical framework that is based upon an ecological approach to social interaction, centering on the concept of social affordances, the concept of the sociability of CSCL environments, and social presence theory. The hypothesis is that the higher the sociability, the more likely that social interaction will take place or will increase, and the more likely that this will result in an emerging sound social space. In the present research, the variables of interest are sociability, social space, and social presence. This study deals with the construction and validation of three instruments to determine sociability, social space, and social presence in (a)synchronous collaborating groups. The findings suggest that the instruments have potential to be useful as measures for the respective variables. However, it must be realized that these measures are "first steps."

Adult↗
PubMed1985

Automating the purchasing and inventory control functions.

Factors involved in computerizing the purchasing and inventory control functions in hospital pharmacies are described. When initiating an automated purchasing and inventory control system, a feasibility study should first be conducted to determine the extent of automation needed to develop a cost-effective system. The design of the system will depend on the extent to which the department of materials management is involved with other hospital departments. The advantages and disadvantages of decentralized versus centralized systems are discussed, and criteria for selecting hardware and software vendors are presented. A return-on-investment analysis should be performed to validate the benefits or savings expected from implementing the new automated system. Factors to consider during implementation of the new system and future developments affecting purchasing and inventory control systems, such as bar coding, are discussed. With the current concern about rapidly rising health-care costs and the need to enhance productivity, the development and implementation of automated purchasing and inventory control systems are important strategies for institutions to pursue now.

Computers↗
PubMed2005

Semi-automated ultrasound facial soft tissue depth registration: method and validation.

A mobile and fast, semi-automatic ultrasound (US) system was developed for facial soft tissue depth registration. The system consists of an A-Scan ultrasound device connected to a portable PC with interfacing and controlling software. For 52 cephalometric landmarks, the system was tested for repeatability and accuracy by evaluating intra-observer agreement and comparing ultrasound and CT-scan results on 12 subjects planned for craniofacial surgery, respectively. A paired t-test evaluating repeatability of the ultrasound measurements showed 5.7% (n = 3) of the landmarks being significantly different (p < 0.01). US and CT-scan results showed significant differences (p < 0.01) using a Wilcoxon signed rank test analysis for 11.5% (n = 6) of the landmarks. This is attributed to a difference in the volunteer's head position between lying (CT) and sitting (US). Based on these tests, we conclude that the proposed registration system and measurement protocol allows relatively fast (52 landmarks/20 min), non-invasive, repeatable and accurate acquisition of facial soft tissue depth measurements.

Adult↗
PubMed1986

Design and validation of an automated hydrostatic weighing system.

The purpose of this study was to design and evaluate the validity of an automated technique to assess body density using a computerized hydrostatic weighing system. An existing hydrostatic tank was modified and interfaced with a microcomputer equipped with an analog-to-digital converter. Software was designed to input variables, control the collection of data, calculate selected measurements, and provide a summary of the results of each session. Validity of the data obtained utilizing the automated hydrostatic weighing system was estimated by: evaluating the reliability of the transducer/computer interface to measure objects of known underwater weight; comparing the data against a criterion measure; and determining inter-session subject reliability. Values obtained from the automated system were found to be highly correlated with known underwater weights (r = 0.99, SEE = 0.0060 kg). Data concurrently obtained utilizing the automated system and a manual chart recorder were also found to be highly correlated (r = 0.99, SEE = 0.0606 kg). Inter-session subject reliability was determined utilizing data collected on subjects (N = 16) tested on two occasions approximately 24 h apart. Correlations revealed high relationships between measures of underwater weight (r = 0.99, SEE = 0.1399 kg) and body density (r = 0.98, SEE = 0.00244 g X cm-1). Results indicate that a computerized hydrostatic weighing system is a valid and reliable method for determining underwater weight.

Adult↗
PubMed2006

Model-based estimation of muscle forces exerted during movements.

Estimation of individual muscle forces during human movement can provide insight into neural control and tissue loading and can thus contribute to improved diagnosis and management of both neurological and orthopaedic conditions. Direct measurement of muscle forces is generally not feasible in a clinical setting, and non-invasive methods based on musculoskeletal modeling should therefore be considered. The current state of the art in clinical movement analysis is that resultant joint torques can be reliably estimated from motion data and external forces (inverse dynamic analysis). Static optimization methods to transform joint torques into estimates of individual muscle forces using musculoskeletal models, have been known for several decades. To date however, none of these methods have been successfully translated into clinical practice. The main obstacles are the lack of studies reporting successful validation of muscle force estimates, and the lack of user-friendly and efficient computer software. Recent advances in forward dynamics methods have opened up new opportunities. Forward dynamic optimization can be performed such that solutions are less dependent on measured kinematics and ground reaction forces, and are consistent with additional knowledge, such as the force-length-velocity-activation relationships of the muscles, and with observed electromyography signals during movement. We conclude that clinical applications of current research should be encouraged, supported by further development of computational tools and research into new algorithms for muscle force estimation and their validation.

Algorithms↗
PubMedDate not supplied

The CAREPLAN knowledge base. A prototype expert system for postpartum nursing care.

With the growth of scientific knowledge in the health care disciplines, it has become increasingly difficult for practicing health care professionals to store and manipulate the information required to make clinical decisions. Where the decision making process can be defined and validated, expert systems will be able to assist beginning professionals to learn appropriate patterns of decision making. This article discusses the rationale for utilization of expert systems in a nursing environment. A prototype expert system called CAREPLAN, developed for use in an obstetrical environment, was built using Personal Consultant Plus, a software tool based on the LISP language. The project demonstrates that it is feasible to develop and validate an expert system for a specialized clinical environment in a relatively short period of time in comparison to traditional development methods. Graphics were used to enhance textual information and to increase user appeal. Strategies for future implementation and evaluation are outlined.

Expert Systems↗
PubMed2004

Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data.

MOTIVATION: Despite the growing literature devoted to finding differentially expressed genes in assays probing different tissues types, little attention has been paid to the combinatorial nature of feature selection inherent to large, high-dimensional gene expression datasets. New flexible data analysis approaches capable of searching relevant subgroups of genes and experiments are needed to understand multivariate associations of gene expression patterns with observed phenotypes. RESULTS: We present in detail a deterministic algorithm to discover patterns of multivariate gene associations in gene expression data. The patterns discovered are differential with respect to a control dataset. The algorithm is exhaustive and efficient, reporting all existent patterns that fit a given input parameter set while avoiding enumeration of the entire pattern space. The value of the pattern discovery approach is demonstrated by finding a set of genes that differentiate between two types of lymphoma. Moreover, these genes are found to behave consistently in an independent dataset produced in a different laboratory using different arrays, thus validating the genes selected using our algorithm. We show that the genes deemed significant in terms of their multivariate statistics will be missed using other methods. AVAILABILITY: Our set of pattern discovery algorithms including a user interface is distributed as a package called Genes@Work. This package is freely available to non-commercial users and can be downloaded from our website (http://www.research.ibm.com/FunGen).

Algorithms↗
PubMed2005

Development and validation of XML-based calculations within order sets.

We have developed two XML Schemas to support the implementation of calculations within XML-based order sets. The models support the representation of variable-based algorithms and include data elements designed to support ancillary functions such as input range checking, rounding, and minimum/maximum value constraints. Two clinicians successfully authored 57 unique calculated orders derived from a set of 11 calculations using the models within our authoring environment. The resultant knowledge base content was subsequently tested and found to produce the desired results within the electronic physician order entry environment.

Algorithms↗
PubMed2005

Automated image analysis methods for 3-D quantification of the neurovascular unit from multichannel confocal microscope images.

BACKGROUND: There is a need for integrative and quantitative methods to investigate the structural and functional relations among elements of complex systems, such as the neurovascular unit (NVU), that involve multiple cell types, microvasculatures, and various genomic/proteomic/ionic functional entities. METHODS: Vascular casting and selective labeling enabled simultaneous three-dimensional imaging of the microvasculature, cell nuclei, and cytoplasmic stains. Multidimensional segmentation was achieved by (i) bleed-through removal and attenuation correction; (ii) independent segmentation and morphometry for each corrected channel; and (iii) spatially associative feature computation across channels. The combined measurements enabled cell classification based on nuclear morphometry, cytoplasmic signals, and distance from vascular elements. Specific spatial relations among the NVU elements could be quantified. RESULTS: A software system combining nuclear and vessel segmentation codes and associative features was constructed and validated. Biological variability contributed to misidentified nuclei (9.3%), undersegmentation of nuclei (3.7%), hypersegmentation of nuclei (14%), and missed nuclei (4.7%). Microvessel segmentation errors occurred rarely, mainly due to nonuniform lumen staining. CONCLUSIONS: Associative features across fluorescence channels, in combination with standard features, enable integrative structural and functional analysis of the NVU. By labeling additional structural and functional entities, this method can be scaled up to larger-scale systems biology studies that integrate spatial and molecular information.

Animals↗
PubMed2004

Validation study of the TrueAllele automated data review system.

The New York State Convicted Offender DNA Databank is the first U.S. lab to complete an internal validation of the TrueAllele expert data review system. TrueAllele is designed to assess short tandem repeat (STR) DNA data based on several key features such as peak height, shape, area, and position relative to a standard ladder and use this information to make accurate allele calls. The software then prioritizes the allele calls based on several user-defined rules. As a result, the user need only review low-quality data. The validation of this system consisted of an extensive optimization phase and a large concordance phase. During optimization, the rule settings were tailored to minimize the amount of high-quality data viewed by the user. In the concordance phase, a large dataset was typed in parallel with the ABI software Gene Scan and Genotyper (manual review) and TrueAllele (automated review) for comparison of allele calls and sample state assignment. Only one significant difference was discovered out of 2048 samples in the concordance study. In this case, TrueAllele revealed a spike in the profile that was interpreted as a DNA peak by the analyst in Genotyper. TrueAllele was designed to focus the review on poor data and to eliminate the need for complete reanalysis technical review. This validation project proved TrueAllele to be dependable for use at the NYS Convicted Offender DNA Databank.

Alleles↗
PubMed2004

Application of the BioMek 2000 Laboratory Automation Workstation and the DNA IQ System to the extraction of forensic casework samples.

Robotic systems are commonly utilized for the extraction of database samples. However, the application of robotic extraction to forensic casework samples is a more daunting task. Such a system must be versatile enough to accommodate a wide range of samples that may contain greatly varying amounts of DNA, but it must also pose no more risk of contamination than the manual DNA extraction methods. This study demonstrates that the BioMek 2000 Laboratory Automation Workstation, used in combination with the DNA IQ System, is versatile enough to accommodate the wide range of samples typically encountered by a crime laboratory. The use of a silica coated paramagnetic resin, as with the DNA IQ System, facilitates the adaptation of an open well, hands off, robotic system to the extraction of casework samples since no filtration or centrifugation steps are needed. Moreover, the DNA remains tightly coupled to the silica coated paramagnetic resin for the entire process until the elution step. A short pre-extraction incubation step is necessary prior to loading samples onto the robot and it is at this step that most modifications are made to accommodate the different sample types and substrates commonly encountered with forensic evidentiary samples. Sexual assault (mixed stain) samples, cigarette butts, blood stains, buccal swabs, and various tissue samples were successfully extracted with the BioMek 2000 Laboratory Automation Workstation and the DNA IQ System, with no evidence of contamination throughout the extensive validation studies reported here.

Automation↗
PubMedDate not supplied

Non-linear mixed effects modeling of sparse concentration data from rats: application to a glycogen phosphorylase inhibitor.

We investigated the use of non-linear mixed effects modeling in two preclinical studies of the glycogen phosphorylase inhibitor 1,4-dideoxy-1,4-imino-D-arabinitol (DAB). In a 28-day repeated-dose toxicity study rats were dosed once daily p.o. with 0, 20, 45, 100, or 470 mg/kg of DAB in aqueous solutions by oral gavage. Three blood samples were obtained from each animal using a staggered sampling scheme. During the cause of model development, data were included from a safety pharmacological cardiovascular study, in which rats were dosed once orally with 0, 4, 40, or 400 mg/kg of DAB thereby enabling an extension of the dose range of the model. DAB was assayed in plasma using a validated LC/MS/MS method. Non-linear mixed effects modeling was performed using the software NONMEM. The covariate analysis comprised dose, sex and time. Exposure results (Cmax, AUC) obtained by mixed effects modeling were compared to results from noncompartmental analysis using naïve pooling of data. The final model was a one-compartment model with first order absorption and a saturation-like dose dependent increase of the (oral) clearance (CL/f) and volume of distribution (V/f). Furthermore, V/f increased (by 55%) from Day 1 to Day 28. The dose dependencies of CL/f and V/f were most likely due to dose dependent decreases of the fraction systemically absorbed (f). The mechanism behind the dose dependencies may be saturation of a (putative) carrier mediated transport or modulation of tight junctions causing a reduced paracellular transport across the intestinal epithelium. Exposure results obtained from the model compared well with results obtained using noncompartmental analysis. An analysis of the data requirements for non-linear mixed effects modeling showed that at least three concentration values per animal were required for model development. We conclude that non-linear mixed effects modeling is feasible even with dose dependent pharmacokinetics in preclinical studies, such as 28-day toxicity studies in rodents. Supplementing data from additional preclinical studies may be required in order to extend the dose range. Non-linear mixed effects models may prove to be valuable tools in early PK and PK-PD modeling during drug development.

Animals↗