SEARCH · PubMed Health

Results for “Experimental validation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 379 records · Page 21Linked to original sources

PubMed2004

Reflections on an unsolved problem of biology: the evolution of senescence and death.

The evolutionary theory of senescence is based largely on principles first outlined by Williams in 1957, and consists of two relatively independent parts. The first part builds on ideas first put forward by Medawar, Haldane and others, to explain how something as negative as senescence could have been positively selected in evolution, particularly since most animals in the wild do not reach an age where senescence is expressed. Williams proposed that the genes responsible for the negative effects of senecence (senescence effector genes) were fixed in evolution by a process he called antagonistic pleiotropy, wherein a subset of genes selected because they confer a reproductive advantage early in life may have harmful effects in the post-reproductive period; negative selection against these harmful effects fails because, as pointed out by Medawar, the force of natural selection declines with age. The evolutionary history of senescence-causing genes is seen as a nondirected accumulation of genes selected on a basis independent of senescence per se. In the second portion of his paper, Williams made a series of predictions about how the age of organisms at reproductive maturity, fecundity, lifespan and the timing of the onset of senescence would all interact in the life history of a species. These latter predictions, which do not depend at all on details of the mechanisms of selection of senescence effector genes, have been validated by numerous experiments over the past several decades. On the other hand, it has become increasingly evident that the senescence effector genes did not, as would be predicted by antagonistic pleiotropy, accumulate in a random, non-directed fashion in various species over evolutionary time. Rather, everything we know about these genes suggests they were present in eukaryotic founder cells shortly after, or even congruent with, the emergence of eukaryotes from their prokaryotic ancestors, and have been stringently conserved ever since. Complicated explanations of how so-called "death genes" may have evolved in eukaryotes are thus not required. It is suggested that the evolutionary theory of senescence should be focused on those evolutionary principles that have been validated experimentally, and that the notion of antagonistic pleiotropy--which cannot be experimentally validated--be dropped from our thinking about the evolution of senescence.

Aging↗

PubMed2004

Development and validation of experimental protocols for use of cardinal models for prediction of microorganism growth in food products.

An experimental protocol to validate secondary-model application to foods was suggested. Escherichia coli, Listeria monocytogenes, Bacillus cereus, Clostridium perfringens, and Salmonella were observed in various food categories, such as meat, dairy, egg, or seafood products. The secondary model validated in this study was based on the gamma concept, in which the environmental factors temperature, pH, and water activity (aw) were introduced as individual terms with microbe-dependent parameters, and the effect of foodstuffs on the growth rates of these species was described with a food- and microbe-dependent parameter. This food-oriented approach was carried out by challenge testing, generally at 15 and 10 degrees C for L. monocytogenes, E. coli, B. cereus, and Salmonella and at 25 and 20 degrees C for C. perfringens. About 222 kinetics in foods were generated. The results were compared to simulations generated by existing software, such as PMP. The bias factor was also calculated. The methodology to obtain a food-dependent parameter (fitting step) and therefore to compare results given by models with new independent data (validation step) is discussed in regard to its food safety application. The proposed methods were used within the French national program of predictive microbiology, Sym'Previus, to include challenge test results in the database and to obtain predictive models designed for microbial growth in food products.

Animals↗

PubMed2001

Establishing the internal and external validity of experimental studies.

The information needed to determine the internal and external validity of an experimental study is discussed. Internal validity is the degree to which a study establishes the cause-and-effect relationship between the treatment and the observed outcome. Establishing the internal validity of a study is based on a logical process. For a research report, the logical framework is provided by the report's structure. The methods section describes what procedures were followed to minimize threats to internal validity, the results section reports the relevant data, and the discussion section assesses the influence of bias. Eight threats to internal validity have been defined: history, maturation, testing, instrumentation, regression, selection, experimental mortality, and an interaction of threats. A cognitive map may be used to guide investigators when addressing validity in a research report. The map is based on the premise that information in the report evolves from one section to the next to provide a complete logical description of each internal-validity problem. The map addresses experimental mortality, randomization, blinding, placebo effects, and adherence to the study protocol. Threats to internal validity may be a source of extraneous variance when the findings are not significant. External validity is addressed by delineating inclusion and exclusion criteria, describing subjects in terms of relevant variables, and assessing generalizability. By using a cognitive map, investigators reporting an experimental study can systematically address internal and external validity so that the effects of the treatment are accurately portrayed and generalization of the findings is appropriate.

Double-Blind Method↗

PubMed1999

Finite element modeling of the cervical spine: role of intervertebral disc under axial and eccentric loads.

An anatomically accurate, three-dimensional, nonlinear finite element model of the human cervical spine was developed using computed tomography images and cryomicrotome sections. The detailed model included the cortical bone, cancellous core, endplate, lamina, pedicle, transverse processes and spinous processes of the vertebrae; the annulus fibrosus and nucleus pulposus of the intervertebral discs; the uncovertebral joints; the articular cartilage, the synovial fluid and synovial membrane of the facet joints; and the anterior and posterior longitudinal ligaments, interspinous ligaments, capsular ligaments and ligamentum flavum. The finite element model was validated with experimental results: force-displacement and localized strain responses of the vertebral body and lateral masses under pure compression, and varying eccentric anterior-compression and posterior-compression loading modes. This experimentally validated finite element model was used to study the biomechanics of the cervical spine intervertebral disc by quantifying the internal axial and shear forces resisted by the ventral, middle, and dorsal regions of the disc under the above axial and eccentric loading modes. Results indicated that higher axial forces (compared to shear forces) were transmitted through different regions of the disc under all loading modes. While the ventral region of the disc resisted higher variations in axial force, the dorsal region transmitted higher shear forces under all loading modes. These findings may offer an insight to better understand the biomechanical role of the human cervical spine intervertebral disc.

Adult↗

PubMed2006

Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies.

We report the development and validation of experimental methods, study designs, and analysis software for pooling-based genomewide association (GWA) studies that use high-throughput single-nucleotide-polymorphism (SNP) genotyping microarrays. We first describe a theoretical framework for establishing the effectiveness of pooling genomic DNA as a low-cost alternative to individually genotyping thousands of samples on high-density SNP microarrays. Next, we describe software called "GenePool," which directly analyzes SNP microarray probe intensity data and ranks SNPs by increased likelihood of being genetically associated with a trait or disorder. Finally, we apply these methods to experimental case-control data and demonstrate successful identification of published genetic susceptibility loci for a rare monogenic disease (sudden infant death with dysgenesis of the testes syndrome), a rare complex disease (progressive supranuclear palsy), and a common complex disease (Alzheimer disease) across multiple SNP genotyping platforms. On the basis of these theoretical calculations and their experimental validation, our results suggest that pooling-based GWA studies are a logical first step for determining whether major genetic associations exist in diseases with high heritability.

Alzheimer Disease↗

PubMed2004

Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression.

Gene-specific oligonucleotide probes are currently used in microarrays to avoid cross-hybridization of highly similar sequences. We developed an approach to determine the optimal number and length of gene-specific probes for accurate transcriptional profiling studies. The study surveyed probe lengths from 25 to 1000 nt. Long probes yield better signal intensity than short probes. The signal intensity of short probes can be improved by addition of spacers or using higher probe concentration for spotting. We also found that accurate gene expression measurement can be achieved with multiple probes per gene and fewer probes are needed if longer probes rather than shorter probes are used. Based on theoretical considerations that were confirmed experimentally, our results showed that 150mer is the optimal probe length for expression measurement. Gene-specific probes can be identified using a computational approach for 150mer probes and they can be treated like long cDNA probes in terms of the hybridization reaction for high sensitivity detection. Our experimental data also show that probes which do not generate good signal intensity give erroneous expression ratio measurement results. To use microarray probes without experimental validation, gene-specific probes approximately 150mer in length are necessary. However, shorter oligonucleotide probes also work well in gene expression analysis if the probes are validated by experimental selection or if multiple probes per gene are used for expression measurement.

Escherichia coli↗

PubMed2004

Numerical evaluation of heating of the human head due to magnetic resonance imaging.

In this paper, we present a numerical model for evaluating tissue heating during magnetic resonance imaging (MRI). Our method, which included a detailed anatomical model of a human head, calculated both the electromagnetic power deposition and the associated temperature elevations during an MRI head examination. Numerical studies were conducted using a realistic birdcage coil excited at frequencies ranging from 63 to 500 MHz. The model was validated both experimentally and analytically. The experimental validation was performed at the MR test facility located at the Food and Drug Administration's Center for Devices and Radiological Health.

Body Burden↗

PubMedDate not supplied

Lessons learned from validation of in vitro toxicity test: from failure to acceptance into regulatory practice.

As no scientific approach or regulatory guidelines existed for the experimental validation of in vitro toxicity tests, in 1990 a US/European validation workshop agreed in Amden (Switzerland) on a simple definition of the validation process. Several international validation studies failed, although they were conducted according to these recommendations. Taking into account the lessons learned from this experience, a second validation workshop was held by ECVAM in Amden in 1994 to develop a more precisely defined validation concept. Prevalidation and the development of biostatistically defined prediction models were added as essential elements to the validation process. In 1995/1996 the ECVAM validation procedure was officially accepted by EU member countries and at the international level by the US regulatory agencies and the OECD. The improved validation concept was immediately introduced into ongoing validation studies. In 1996 the ECVAM/COLIPA validation study of the in vitro phototoxicity test, which was conducted according to the ECVAM/OECD validation concept, was finished successfully and in 1998 a supporting study on UV-filter chemicals was undertaken. In 1998 the 3T3 NRU PT in vitro phototoxicity test was the first experimentally validated in vitro toxicity test that was recommended for regulatory purposes by ESAC, the ECVAM Scientific Advisory Committee, and by the DG ENV of the EU Commission. Meanwhile, two in vitro skin corrosivity tests have successfully been validated by ECVAM. Finally, in June 2000 the three experimentally validated tests were accepted by EU member states for regulatory purposes as the first in vitro toxicity tests. In addition, ECVAM has funded a successful validation study of three in vitro embryotoxicity tests, which was conducted in 12 European laboratories and finished in July 2000. The three tests validated in this study were the whole embryo culture (WEC) test applied to rat embryos, the micromass (MM) test employing primary cultures of dissociated mouse limb bud cells and the mouse embryonic stem cell test (EST). Examples will be given of successful validation studies during the past decade with particular reference to in vitro toxicity tests that were evaluated for regulatory purposes either by the US validation centre ICCVAM or ECVAM in the fields of sensitisation, phototoxicity and embryotoxicity

Animal Testing Alternatives↗

PubMed2025

Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol-Related Liver Disease.

BACKGROUND: Skeletal muscle is a major target for ethanol-induced perturbations, leading to sarcopenia in alcohol-related liver disease (ALD). The complex interactions and pathways involved in adaptive and maladaptive responses to ethanol in skeletal muscle are not well understood. Unlike hypothesis-driven experiments, an integrated multiomics-experimental validation approach provides a comprehensive view of these interactions. METHODS: We performed multiomics analyses with experimental validation to identify novel regulatory mechanisms of sarcopenia in ALD. Studies were done in a comprehensive array of models including ethanol-treated (ET) murine and human-induced pluripotent stem cell-derived myotubes (hiPSCm), skeletal muscle from a mouse model of ALD (mALD) and human patients with alcohol-related cirrhosis and controls. We generated 13 untargeted datasets, including chromatin accessibility (assay for transposase accessible chromatin), RNA sequencing, proteomics, phosphoproteomics, acetylomics and metabolomics, and conducted integrated multiomics analyses using UpSet plots and feature extraction. Key findings were validated using immunoblots, redox measurements (NAD+/NADH ratio), imaging and senescence-associated molecular phenotype (SAMP) assays. Mechanistic studies included mitochondrial-targeted Lactobacillus brevis NADH oxidase (MitoLbNOX) to increase redox ratio and MitoTempo as a mitochondrial free radical scavenger. RESULTS: Multiomics analyses revealed enrichment in mitochondrial oxidative function, protein synthesis and senescence pathways consistent with the known effects of hypoxia-inducible factor 1α (HIF1α) during normoxia. Across preclinical and clinical models, HIF1α targets (n = 32 genes) and signalling genes (n > 100 genes) (n = 3 ATACseq, n = 65 phosphoproteomics, n = 10 acetylomics, n = 6 C2C12 proteomics, n = 106 C2C12 RNAseq, n = 64 hiPSC RNAseq, n = 30 hiPSC proteomics, n = 3 mouse proteomics, n = 25 mouse RNAseq, n = 8 human RNAseq, n = 3 human proteomics) were increased. Stabilization of HIF1α (C2C12, 6hEtOH 0.24 ± 0.09; p = 0.043; mALD 0.32 ± 0.074; p = 0.005; data shown as mean difference ± standard error mean) was accompanied by enrichment in the early transient and late change clusters, -log(p-value) = 1.5-3.8, of the HIF1α signalling pathway. Redox ratio was reduced in ET myotubes (C2C12: 15512 ± 872.1, p < 0.001) and mALD muscle, with decreased expression of electron transport chain components (CI-V, p < 0.05) and Sirt3 (C2C12: 0.067 ± 0.023, p = 0.025; mALD: 0.41 ± 0.12, p = 0.013). Acetylation of mitochondrial proteins was increased in both models (C2C12: 107364 ± 4558, p = 0.03; mALD: 40036 ± 18 987, p = 0.049). Ethanol-induced SAMP was observed across models (P16: C2C12: 0.2845 ± 0.1145, p < 0.05; hiPSCm: 0.2591, p = 0.041). MitoLbNOX treatment reversed redox imbalance, HIF1α stabilization, global acetylation and myostatin expression (p < 0.05). CONCLUSIONS: An integrated multiomics approach, combined with experimental validation, identifies HIF1α stabilization and accelerated post-mitotic senescence as novel mechanisms of sarcopenia in ALD. These findings show the complex molecular interactions leading to mitochondrial dysfunction and progressive sarcopenia in ALD.

Sarcopenia↗

PubMed2000

On the design of optimal dynamic experiments for parameter estimation of a Ratkowsky-type growth kinetics at suboptimal temperatures.

It is generally known that accurate model building, i.e., proper model structure selection and reliable parameter estimation, constitutes an essential matter in the field of predictive microbiology, in particular, when integrating these predictive models in food safety systems. In this context, Versyck et al. (1999) have introduced the methodology of optimal experimental design techniques for parameter estimation within the field. Optimal experimental design focuses on the development of optimal input profiles such that the resulting rich (i.e., highly informative) experimental data enable unique model parameter estimation. As a case study, Versyck et al. (1999) [Versyck, K., Bernaerts, K., Geeraerd, A.H., Van Impe, J.F., 1999. Introducing optimal experimental design in predictive modeling: a motivating example. Int. J. Food Microbiol., 51(1), 39-51] have elaborated the estimation of Bigelow inactivation kinetics parameters (in a numerical way). Opposed to the classic (static) experimental approach in predictive modelling, an optimal dynamic experimental setup is presented. In this paper, the methodology of optimal experimental design or parameter estimation is applied to obtain uncorrelated estimates of the square root model parameters [Ratkowsky, D.A., Olley, J., McMeekin, T.A., Ball, A., 1982. Relationship between temperature and growth rate of bacterial cultures. J. Bacteriol. 149, 1-5] describing the effect of suboptimal growth temperatures on the maximum specific growth rate of microorganisms. These estimates are the direct result of fitting a primary growth model to cell density measurements as a function of time. Apart from the design of an optimal time-varying temperature profile based on a sensitivity study of the model output, an important contribution of this publication is a first experimental validation of this innovative dynamic experimental approach for uncorrelated parameter identification. An optimal step temperature profile, within the range of model validity and practical feasibility, is developed for Escherichia coli K12 and successfully applied in practice. The presented experimental validation result illustrates the large potential of the dynamic experimental approach in the context of uncorrelated parameter estimation. Based on the experimental validation result, additional remarks are formulated related to future research in the field of optimal experimental design.

Escherichia coli↗

PubMed1998

Quantitative cardiac SPECT in three dimensions: validation by experimental phantom studies.

A mathematical framework for quantitative SPECT (single photon emission computed tomography) reconstruction of the heart is presented. An efficient simultaneous compensation approach to the reconstruction task is described. The implementation of the approach on a digital computer is delineated. The approach was validated by experimental data acquired from chest phantoms. The phantoms consisted of a cylindrical elliptical tank of Plexiglass, a cardiac insert made of Plexiglass, a spine insert of packed bone meal and lung inserts made of styrofoam beads alone. Water bags were added to simulate different body characteristics. Comparison between the quantitative reconstruction and the conventional FBP (filtered backprojection) method was performed. The FBP reconstruction had a poor quantitative accuracy and varied for different body configurations. Significant improvement in reconstruction accuracy by the quantitative approach was demonstrated with a moderate computing time on a currently available desktop computer. Furthermore, the quantitative reconstruction was robust for different body characteristics. Therefore, the quantitative approach has the potential for clinical use.

Body Composition↗

PubMed2007

Development of a three-dimensional finite element model of a human mandible containing endosseous dental implants. I. Mathematical validation and experimental verification.

The purpose of this study was to mathematically validate and clinically verify a finite element model (FEM) of the human mandible and to compare the functional deformation predicted by the model with that detected clinically. Mandibular surface strain, using 11 single strain gauges, and medial convergence (MC), using a custom-fabricated linear variable differential transformer (LVDT), were recorded in a dried human jaw. The mandible was treated with two endosseous implants, placed bilaterally in the premolar area, and mounted in a rig that simulated natural function of the jaw. Measurements were made in real time using a multichannel analogue/digital converter and a personal computer for data storage and analysis. A FEM of the mandible was constructed, using commercially available finite element software, based on CT scan images of the jaw. MC was predicted as the linear change in the orientation of the two implants in the horizontal plane. Predicted and measured values of MC ranged between 60 and 109 microm. The differences between the measured and predicted strain magnitudes were expressed as absolute percentages of the measured values and ranged between 3 and 18%. The limits of agreement between the predicted and measured strain values, as suggested by Bland and Altman (Lancet 1986; 1:307-310), were small enough for the predictions from the FEM to be considered clinically acceptable. The good agreement between the predicted and measured strain values indicates the accuracy of the present FEM. Finite element analysis is a powerful technique that provides a better insight into understanding the complex phenomena of mandibular functional deformation.

Computer Simulation↗

PubMed2006

Load-independent index of diastolic filling: model-based derivation with in vivo validation in control and diastolic dysfunction subjects.

Maximum elastance is an experimentally validated, load-independent systolic function index stemming from the time-varying elastance paradigm that decoupled extrinsic load from (intrinsic) contractility. Although Doppler echocardiography is the preferred method of diastolic function (DF) assessment, all echo-derived indexes are load dependent, and no invasive or noninvasive load-independent index of filling (LIIF) exists. In this study, we derived and experimentally validated a LIIF. We used a kinematic filling paradigm (the parameterized diastolic filling formalism) to predict and derive the (dimensionless) dynamic diastolic efficiency M, defined by the slope of the peak driving force [maximum driving force (kx(o)) proportional, variant peak atrioventricular (AV) gradient] to maximum viscoelastic resistive force [peak resistive force (cE(peak))] relation. To validate load independence, we analyzed E-waves recorded while load was varied via tilt table (head up, horizontal, and head down) in 16 healthy volunteers. For the group, linear regression of E-wave derived kx(o) vs. cE(peak) yielded kx(o) = M (cE(peak)) + B, r2 = 0.98; where M = 1.27 +/- 0.09 and B = 5.69 +/- 1.70. Effects of diastolic dysfunction (DD) on M were assessed by analysis of preexisting simultaneous cath-echo data in six DD vs. five control subjects. Average M for the DD group (M = 0.98 +/- 0.07) was significantly lower than controls (M = 1.17 +/- 0.05, P < 0.001). We conclude that M is a LIIF because it uncouples intrinsic DF (i.e., the pressure-flow relation) from extrinsic load (left ventricular end-diastolic pressure). Larger M values imply better DF in that increasing AV pressure gradient results in relatively smaller increases in peak resistive losses (cE(peak)). Conversely, lower M implies that increasing AV gradient leads to larger increases in resistive losses. Further prospective validation characterizing M in well-defined pathological states is warranted.

Adult↗

PubMed2026

MicroRNA-driven regulatory networks in aphid ecological adaptation: integrating stress tolerance, dispersal plasticity, and population expansion.

Aphids (Hemiptera: Aphididae) are important agricultural pests and exhibit strong ecological adaptability, allowing them to persist under stress, disperse to new habitats, and rapidly increase population size. Recent advances in functional genomics have identified microRNAs (miRNAs) as key post-transcriptional regulators involved in these processes, yet their roles have remained fragmented across studies. Here, we synthesize current evidence into a "three-stage framework", encompassing population maintenance under stress, dispersal to new habitats, and population expansion upon establishment. We highlight how miRNAs regulate detoxification pathways (e.g., P450s, UGTs, ABC transporters), mediate interactions with host plants and symbionts, and integrate hormonal signaling networks including insulin, juvenile hormone, and ecdysteroid pathways. This framework identifies candidate miRNAs, target genes, and signaling pathways that may recur across different ecological contexts, including stress responses, dispersal-related plasticity, and reproductive regulation. However, direct evidence demonstrating that candidate shared miRNA regulators coordinate multiple life-history stages remains limited and requires further experimental validation. We critically evaluate the strength of functional evidence, distinguishing experimentally validated miRNA-target interactions from prediction- or expression-based associations. Finally, we discuss emerging applications of miRNA-based pest control, including artificial miRNAs, RNAi technologies, and nanocarrier delivery systems. By linking molecular mechanisms with ecological outcomes, this review provides a synthesis and highlights miRNAs as important regulators of aphid adaptation and candidate targets for sustainable management strategies.

Aphids↗

PubMed1990

Assessing threats to the validity of experimental and observational designs.

Experimental designs, particularly the randomized trial, are viewed as the most scientifically rigorous methods by which knowledge is attained. Most clinical disciplines, however, use observational study designs more frequently than experimental designs. Nevertheless, the scientific rigor of experimental designs can be approximated by observational designs if common internal validity threats are recognized and addressed during the development of the research protocol. This paper presents a model of threats that can be applied to both types of designs to compare their scientific merits.

Case-Control Studies↗

PubMed2006

Cell proliferation drives neural crest cell invasion of the intestine.

A general mathematical model of cell invasion is developed and validated with an experimental system. The model incorporates two basic cell functions: non-directed (diffusive) motility and proliferation to a carrying capacity limit. The model is used here to investigate cell proliferation and motility differences along the axis of an invasion wave. Mathematical simulations yield surprising and counterintuitive predictions. In this general scenario, cells at the invasive front are proliferative and migrate into previously unoccupied tissues while those behind the front are essentially nonproliferative and do not directly migrate into unoccupied tissues. These differences are not innate to the cells, but are a function of proximity to uninvaded tissue. Therefore, proliferation at the invading front is the critical mechanism driving apparently directed invasion. An appropriate system to experimentally validate these predictions is the directional invasion and colonization of the gut by vagal neural crest cells that establish the enteric nervous system. An assay using gut organ culture with chick-quail grafting is used for this purpose. The experimental results are entirely concordant with the mathematical predictions. We conclude that proliferation at the wavefront is a key mechanism driving the invasive process. This has important implications not just for the neural crest, but for other invasion systems such as epidermal wound healing, carcinoma invasion and other developmental cell migrations.

Animals↗

PubMed1990

The validity of experimental evidence.

Commonly the assumption is held that correct data only and always will lead to valid deductions. However, analysis of the literature reveals striking examples of erroneous conclusions based upon correct data. The present article intends to show that meticulously performed research in itself is no guarantee for correct conclusions. It appears that investigators, together with the "scientific forum" of their time, interpret the results of experiments in the light of accepted viewpoints, without challenging other or less likely explanations. And since this has happened to the best of us in the past, it is also apt to happen to us today.

Animals↗

PubMedDate not supplied

[The combined use of electromagnetic decimeter waves and deresinated naphthalan in patients with vertebrogenic humeroscapular periarthrosis (its experimental and clinical validation)].

Physicochemical and experimental studies on pond snail neuron were made to validate combined or simultaneous usage of decimeter microwaves and deresinified naphthalane. Clinical and neurophysiological trials in 133 patients with vertebrogenic scapulohumeral periarthritis revealed that the above treatment is clinically beneficial and corrects functional activity of segmental-peripheral neuromotor system.

Animals↗