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At least 235 records · Page 13Linked to original sources

PubMed2006

Generating population data for the EMPOP database - an overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example.

The European DNA profiling group (EDNAP) mtDNA population database (EMPOP) is an international collaborative project between DNA laboratories performing mtDNA analysis and the DNA laboratory of the Institute of Legal Medicine (GMI) in Innsbruck, Austria. The goal is to set up a directly accessible mtDNA population database, which can be used in routine forensic casework for frequency investigations. Here we describe a safe laboratory scheme involving electronical data handling and computer-aided data transfer, which help to minimize errors originating from potential sample mix-up, data misinterpretation and incorrect transcription. The procedure is demonstrated by example of an mtDNA control region population study on 273 unrelated individuals from Austria. Our population sample was compared with five other European populations via an analysis of molecular variance (AMOVA). The inclusion of regions outside HVS-I and HVS-II increased the amount of information on the haplogroup diagnostic sites in the control region. Most of the haplotypes in Austrians fell into haplogroups H, J, K, T, and U. The random match probability in Austrians was 1:125; the average number of nucleotide differences between individuals in the Austrian database was 9.32.

Austria↗

PubMed2004

Cap-dependent and cap-independent translation in eukaryotic systems.

Unlike bacterial protein synthesis, eukaryotic protein synthesis has several mechanisms to initiate translation including cap-dependent initiation, re-initiation and internal initiation. While there is extensive biochemical characterization of the multiple steps in cap-dependent initiation, most of the information on the other two mechanisms is derived from studies on the nucleic acid sequences that influence their efficiency. However, even in the best of circumstances, both re-initiation and internal initiation are only 25% as efficient as cap-dependent initiation and more commonly, are only 1-10% as efficient. This general lack of efficiency leaves open possibilities for mis-interpretation/artifacts in vivo (cryptic promoters, alternate splicing) or in vitro (nuclease degradation). Two examples are cited from the author's laboratory as background for the development of a general set of guidelines to minimize errors and validate authenticity for internal initiation.

Animals↗

PubMed2006

Recommendations for quality assurance and improvement in surgical and autopsy pathology.

Current regulations require that departments of pathology have a structured and active program of quality assurance (QA) and quality improvement (QI), with the goals of enhancing patient safety, minimizing error, ensuring timely delivery of reports, and monitoring physician competence. Types of potential error may evolve over time and, as regulations become progressively more stringent, QA/QI programs need to be constantly updated. The Association of Directors of Anatomic and Surgical Pathology herein provides guidelines for QA and QI in surgical and autopsy pathology.

Humans↗

PubMed2005

Determination of patient-specific multi-joint kinematic models through two-level optimization.

Dynamic patient-specific musculoskeletal models have great potential for addressing clinical problems in orthopedics and rehabilitation. However, their predictive capability is limited by how well the underlying kinematic model matches the patient's structure. This study presents a general two-level optimization procedure for tuning any multi-joint kinematic model to a patient's experimental movement data. An outer level optimization modifies the model's parameters (joint position and orientations) while repeated inner level optimizations modify the model's degrees of freedom given the current parameters, with the goal of minimizing errors between model and experimental marker trajectories. The approach is demonstrated by fitting a 27 parameter, three-dimensional, 12 degree-of-freedom lower-extremity kinematic model to synthetic and experimental movement data for isolated joint (hip, knee, and ankle) and gait (full leg) motions. For noiseless synthetic data, the approach successfully recovered the known joint parameters to within an arbitrarily tight tolerance. When noise was added to the synthetic data, root-mean-square (RMS) errors between known and recovered joint parameters were within 10.4 degrees and 10 mm. For experimental data, RMS marker distance errors were reduced by up to 62% compared to methods that estimate joint parameters from anatomical landmarks. Optimized joint parameters found using a loaded full-leg gait motion differed significantly from those found using unloaded individual joint motions. In the future, this approach may facilitate the creation of dynamic patient-specific musculoskeletal models for predictive clinical applications.

Biomechanical Phenomena↗

PubMed2004

On-line coupling of sequential injection with liquid chromatography for the automated derivatization and determination of gamma-aminobutyric acid in human biological fluids.

The principle of sequential injection analysis (SIA) was exploited to develop a rapid fully automated and efficient pre-column derivatization procedure coupled on-line to liquid chromatography (HPLC). Using the SIA-HPLC derivatization protocol gamma-aminobutyric acid (GABA) was determined fluorimetrically in human biological fluids with o-phthaldialdehyde (OPA) as derivatization reagent and minimum sample pretreatment. A lab-built SIA system was used to handle samples, standard solutions and OPA reagent. Appropriate volumes of the reagents were introduced in the holding coil of the SIA system and were mixed on propulsion to the HPLC loop through a suitable reaction coil. The chemical (pH, c(OPA), c(mercaptoethanol)) and instrumental variables (volumes of sample and reagent, reaction time) of the reaction were studied and optimized in terms of maximum sensitivity. The chromatographic variables (gradient composition of the eluent and flow rate) were studied for optimum selectivity and peak characteristics. The developed experimental configuration facilitated fully-automated operation thus minimizing errors in handling. Additionally the method as a whole provided very satisfactory sensitivity, precision and accuracy. Direct determination of GABA in human urine and cerebrospinal fluid (CSF) at microg L(-1) (ppb) levels was accomplished, with minimum sample pretreatment.

Automation↗

PubMed2005

Effects of calibration on L-THIA GIS runoff and pollutant estimation.

Urbanization can result in alteration of a watershed's hydrologic response and water quality. To simulate hydrologic and water quality impacts of land use changes, the Long-Term Hydrologic Impact Assessment (L-THIA) system has been used. The L-THIA system estimates pollutant loading based on direct runoff quantity and land use based pollutant coefficients. The accurate estimation of direct runoff is important in assessing water quality impacts of land use changes. An automated program was developed to calibrate the L-THIA model using the millions of curve number (CN) combinations associated with land uses and hydrologic soil groups. L-THIA calibration for the Little Eagle Creek (LEC) watershed near Indianapolis, Indiana was performed using land use data for 1991 and daily rainfall data for six months of 1991 (January 1-June 30) to minimize errors associated with use of different temporal land use data and rainfall data. For the calibration period, the Nash-Sutcliffe coefficient was 0.60 for estimated and observed direct runoff. The calibrated CN values were used for validation of the model for the same year (July 1-December 31), and the Nash-Sutcliffe coefficient was 0.60 for estimated and observed direct runoff. The Nash-Sutcliffe coefficient was 0.52 for January 1, 1991 to December 31, 1991 using uncalibrated CN values. As shown in this study, the use of better input parameters for the L-THIA model can improve accuracy. The effects on direct runoff and pollutant estimation of the calibrated CN values in the L-THIA model were investigated for the LEC. Following calibration, the estimated average annual direct runoff for the LEC watershed increased by 34%, total nitrogen by 24%, total phosphorus by 22%, and total lead by 43%. This study demonstrates that the L-THIA model should be calibrated and validated prior to application in a particular watershed to more accurately assess the effects of land use changes on hydrology and water quality.

Calibration↗

PubMed2006

TaqMan PCR assay in the control of RNA normalization in human post-mortem brain tissue.

The brain tissue obtained after death is subjected to several circumstances that can affect RNA integrity. The present study has been directed to reveal possible pitfalls and to control RNA normalization in post-mortem samples in order to recognize the limitations and minimize errors when using TaqMan PCR technology. This has been carried out in samples of the frontal cortex in a series of control and diseased cases covering Parkinson's disease, dementia with Lewy bodies pure form and common form, and Alzheimer's disease. Special attention has been paid to the value of the agonal state, post-mortem delay and pH of the nervous tissue as approximate predictors of the quality of RNA, as well as to the use of the Bioanalyzer to confirm RNA preservation. In addition, since possible disease-modified mRNAs have to be normalized with ideal unaltered RNAs, TaqMan human endogenous control plates have been used to determine the endogenous control most appropriate for the study. beta-glucuronidase (GUS) and beta-actin were good endogenous controls because their expression levels showed a small variation across a representative number of control and pathological cases. RNA stability was also analysed in a paradigm mimicking cumulative delay in tissue processing. GUS mRNA levels were not modified although beta-actin mRNA levels showed degradation at 22 h. Finally, the control of RNA degradation for the normalization of genes of interest was also tested. mRNA expression levels for superoxide dismutase 1 (SOD1) and metalloproteinase domain 22 (ADAM22) were examined at several artificial post-mortem times, and their expression levels compared with those for putative controls beta-actin and GUS. In our paradigm, the expressions of SOD1 and ADAM22 were apparently not modified when normalized with beta-actin. Yet their expression levels were reduced with post-mortem delay when values were normalized with GUS. Taken together, these observations point to practical consequences in TaqMan PCR studies. Short post-mortem delays and acceptable pH of the brain are not sufficient to rule out RNA degradation. The selection of adequate endogenous controls is pivotal in the study. beta-actin and GUS are found to be good endogenous controls in these pathologies, although GUS but not beta-actin expression levels are preserved in samples with long post-mortem delay.

Aged↗

PubMedDate not supplied

Optimizing conductance parameters of cortical neural models via electrotonic partitions.

Development of automated methods for fitting computational models to observed biological data is an important challenge of neural modeling. Previous work has focused on generalized search techniques combined with distance measures tuned to specific neural morphologies. We propose general analysis techniques to guide construction of distance measures across a broader range of cell types. Specifically, we evaluate the use of multiple external stimuli to evoke characteristic behaviors of underlying active channel densities on a simple three-compartment model. We also examine the use of frequency analysis to smooth search space distortions induced by temporal shifts in recorded voltage traces. We propose a novel method of parameter optimization that is characterized by linear regression over the conductance densities using channel permissiveness as a basis of ionic current. We derive this method and demonstrate, given known anatomy and kinetics, it will solve all conductance densities in an N compartment model given N spatially distinct membrane potential traces with minimal error. We compare the regression method with the covariance matrix adaptation evolutionary strategy (CMA-ES) over a two-compartment cortical neuron and empirically show that regression over electrotonic partitions solves the cortical model near-optimally. We also show that electronic partitioning significantly improves search performance of CMA-ES on the cortical model.

Algorithms↗

PubMed2005

Activation of the precuneus is related to reduced reaction time in serial reaction time tasks.

Multiple brain areas are activated during serial reaction time (RT) tasks (SRTTs), but the part of the brain that facilitates reductions in RT remains unclear. The present study attempted to determine the brain region contributing most to improved RTs during explicit SRTTs. Subjects comprised 18 healthy volunteers who were instructed to press one of four buttons corresponding to visual stimuli as quickly as possible and with minimal errors during functional MRI. Stimuli were presented either in random order (control condition) or in a repeated six-item sequence (learning condition). Conventional analysis contrasting learning and control conditions revealed activation in the prefrontal-parietal area, which shifted to motor area. Subjects with high RT reduction showed more prominent activation in the precuneus than subjects with low RT reduction. Intra-subject correlation analysis revealed that time course of precuneus activation was unrelated to time-course of RT reduction. However, inter-subject correlation analysis revealed that RT changes correlate only with precuneus activation, meaning that subjects showing more prominent RT reduction revealed more prominent activation of the precuneus, which is known to play critical roles in controlling finger movements with reference to buffered memory.

Adult↗

PubMed2004

Quality assurance considerations for detection of waterborne zoonotic parasites using Cryptosporidium oocyst detection as the main example.

A laboratory quality assurance (QA) program can minimize errors and provide confidence in the validity of laboratory test results. The structure of a QA program varies somewhat among laboratories but usually requires addressing a QA manual, QA goals, quality of resources, standard operating procedures, internal quality control, and external QA procedures. This paper reviews these general components and discusses some of the more particular QA considerations specific to filtration, immunomagnetic separation (IMS), immunofluorescence microscopy (FA), vital dye staining, differential interference contrast (DIC) microscopy, and molecular methods, which are involved in the detection and enumeration of Cryptosporidium oocysts.

Animals↗

PubMed2006

Quantitative proteomics to study mitogen-activated protein kinases.

In the last several years, the impact of mass spectrometry (MS)-based proteomics on cell signaling research has increased dramatically. This development has been driven both by better instrumentation and by the progression of proteomics from mainly qualitative measurements towards quantitative analyses. In this regard, Stable Isotope Labeling by Amino acids in Cell culture (SILAC) has established itself as one of the most popular and useful quantitative proteomic methodologies to study signaling networks. SILAC relies on the metabolic incorporation of non-radioactive heavy isotopes in the whole proteome of desired cell line, making all proteins from these cells easily distinguishable in the mass spectrometers from the proteins originating from control cells. The procedure does not involve any chemical derivatization steps and, importantly, allows mixing of the two cell populations for combined additional sample manipulation, thus leading to highly reliable results with minimal errors. In this chapter, we describe in detail the SILAC labeling procedure and explain how to design SILAC experiments to examine the level and duration of phosphorylation of endogenous MAP kinases and their substrates in cell culture systems.

Amino Acids↗

PubMed2000

Designing a quality assurance system for dietary data in a multicenter clinical trial: Women's Intervention Nutrition Study.

Reliable dietary intake data are essential for determining outcomes in nutrition-related clinical trials. Nevertheless, systems for quality assurance of dietary intake data are often slighted in the design of such trials and not incorporated or monitored as the trials continue. The Women's Intervention Nutrition Study (WINS), a multicenter clinical trial investigating the effect of reduction of dietary fat intake together with adjuvant systemic therapy on recurrence rates in and survival of postmenopausal women with early stage, surgically treated, breast cancer, has developed a quality assurance system to minimize errors and to produce data that are complete and reliable. The system involves development of standardized procedures for data collection, a quality control program to evaluate the data collected, and continual monitoring and reevaluation. The WINS system is offered as a model for studies collecting dietary intake data, no matter how simple or complex the trial design.

Clinical Trials as Topic↗

PubMed1968

Estimating the median generation time of proliferating cell systems in steady state.

For proliferating cell systems in which the usual "labeled mitoses" method cannot be used to estimate generation times, an alternative scheme is derived. The method presented here is based on observation (by autoradiography) of the median grain count of labeled interphase cells following a pulse of labeled DNA precursor. It is shown that the median generation time of the labeled cells will be equal to the time required for the median grain count to halve, starting from the time when half the labeled cells have completed their first division. This starting time is determined from observation of the first wave of labeled mitoses. The procedure was designed to minimize error resulting from such factors as radiation damage, label reutilization, and the use of a nonzero grain counting threshold. The method is applied to the analysis of two cases of acute leukemia in man.

Autoradiography↗

PubMed1989

Cortical shell-liquid core model for passive flow of liquid-like spherical cells into micropipets.

Many nonadherent cells exist as spheres in suspension and when sucked into pipets, deform continuously like liquids within the fixed surface area limitation of a plasma membrane envelope. After release, these cells eventually recover their spherical form. Consequently, pipet aspiration test provides a useful method to assay the apparent viscosity of such cells. For this purpose, we have analyzed the inertialess flow of a liquid-like model cell into a tube at constant suction pressure. The cell is modeled as a uniform liquid core encapsulated by a distinct cortical shell. The method of analysis employs a variational approach that minimizes errors in boundary conditions defined by the equations of motion for the cortical shell where the trial functions are exact solutions for the flow field inside the liquid core. For the particular case of an anisotropic liquid cortex with persistent tension, we have determined universal predictions for flow rate scaled by the ratio of excess pressure (above the threshold established by the cortical tension) and core viscosity which is the reciprocal of the dynamic resistance to entry. The results depend on pipet to cell size ratio and a parameter that characterizes the ratio of viscous flow resistance in the cortex to that inside the cytoplasmic core. The rate of entry increases markedly as the pipet size approaches the outer segment diameter of the cell. Viscous dissipation in the cortex strongly influences the entry flow resistance for small tube sizes but has little effect for large tubes. This indicates that with sufficient experimental resolution, measurement of cell entry flow with different-size pipets could establish both the cortex to cell dissipation ratio as well as the apparent viscosity of the cytoplasmic core.

Cell Adhesion↗

PubMedDate not supplied

Models for assessing the relationship between drug concentration and drug effect in performance horses.

The actions of most drugs are dependent upon achieving adequate plasma concentrations. Plasma concentrations are influenced by the degree to which a drug is absorbed, distributed, metabolized and excreted. Pharmacokinetic assessment reflects changes in these variables as a function of time. Pharmacodynamics refers to specific drug effects or mechanisms of drug action. Individual drug pharmacokinetics provides information on which to base a therapeutic dose, route of administration and dosing interval. However, not all drug actions temporally correlate with plasma kinetics. To resolve this discrepancy, pharmacodynamic models of drug action have been developed. In this review several pharmacodynamic models of anti-inflammatory and central nervous system effects are discussed in relationship to individual drug pharmacokinetics in the horse. The use of appropriate statistical models can minimize error and maximize the detection of drug effects over time. Data are presented showing the value of pharmacodynamic models in assessing and predicting the onset, peak and duration of drug action. Penetration of drugs into inflamed tissue or the brain may not temporally correlate with plasma kinetics. Therefore, drug kinetics in tissues or compartments associated with a particular effect may be a better predictor of efficacy than plasma concentrations. Recent studies have shown that exercise can affect drug disposition and influence both pharmacokinetics and pharmacodynamics. In competitive athletes, plasma or urine concentrations of drugs are determined to regulate use. Some jurisdictions are advocating the establishment of specific drug thresholds based upon plasma or urine concentrations. However, drug effects may occur during low or undetectable plasma concentrations. Urine concentrations are often dissociated in time from those in plasma. Therefore, the use of appropriate pharmacodynamic models, and the exercising horse, can complement plasma pharmacokinetics in determining drug efficacy and drug thresholds.

Animals↗

PubMed1998

Glutathione measurement in human plasma. Evaluation of sample collection, storage and derivatization conditions for analysis of dansyl derivatives by HPLC.

Literature values for human plasma GSH vary over 10-fold despite the use of apparently valid analytical procedures for GSH measurement. The purpose of this study was to develop a procedure to minimize error in sample collection, processing and storage that could contribute to such differences. HPLC with fluorescence detection of dansyl derivatives was used for quantification. The results show that collection of blood with a butterfly needle and syringe reduces overestimation due to limited hemolysis and that use of a preservation solution designed to inhibit autooxidation and enzymatic degradation allows quantitative recovery of both GSH and GSSG. Stability tests showed that non-derivatized samples were stable for at least 2 months at - 80 degrees while dansyl derivatives were stable in the dark at 0-4 degrees for 12 months. Results from 59 healthy individuals (20-43 years) provided a mean (+/-1 SD) GSH value of 2.09+/-1.14 micromolar.

Blood Specimen Collection↗

PubMed2002

Ball stud inspection system using machine vision.

In this paper, a vision-based inspection system that measures the dimensions of a ball stud is designed and implemented. The system acquires silhouetted images by backlighting and extracts the outlines of the nearly dichotomized images in subpixel accuracy. The sets of boundary data are modeled with reasonable geometric primitives and the parameters of the models are estimated in a manner that minimizes error. Jig-fixtures and servo systems for the inspection are also contrived. The system rotates an inspected object to recognize the objects in space not on a plane. The system moves the object vertically so that it may take several pictures of different parts of the object, resulting in improvement of measuring resolution. The performance of the system is evaluated by measurement of the dimensions of a standard ball, a standard cylinder, and a ball stud.

Calibration↗

PubMed1995

Study of the acceptability of lateral interocclusal records by a modular articulator.

Semiadjustable articulators are extensively used for routine restorative procedures. The instruments may be adjusted by lateral interocclusal records. However, it has been reported that semiadjustable articulators do not accept lateral interocclusal records from all patients. The Hanau modular system 194 semiadjustable articulator was introduced to develop occlusion with minimal error. The manufacturer recommends that the instrument should be adjusted by means of lateral interocclusal records. This study investigated the acceptability of lateral interocclusal records. Sixty lateral interocclusal records were made for 30 edentulous subjects, and the acceptability of the records was evaluated by use of the split-cast mounting procedure. Out of 60 lateral interocclusal records, 52 (87%) records were accepted by the articulator. A Z test was used for two proportions and was statistically significant (p < 0.05).

Adult↗