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Results for “Experimental validation”

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At least 451 records · Page 25Linked to original sources

PubMed2005

Ketamine induces dopamine-dependent depression of evoked hippocampal activity in the nucleus accumbens in freely moving rats.

Noncompetitive NMDA receptor antagonists, such as ketamine, induce a transient schizophrenia-like state in healthy individuals and exacerbate psychosis in schizophrenic patients. In rodents, noncompetitive NMDA receptor antagonists induce a behavioral syndrome that represents an experimentally valid model of schizophrenia. Current experimental evidence has implicated the nucleus accumbens in the pathophysiology of schizophrenia and the psychomimetic actions of ketamine. In this study, we have demonstrated that acute systemic administration of ketamine, at a dose known to produce hyperlocomotion and stereotypy, depressed the amplitude of the monosynaptic component of fimbria-evoked field potentials recorded in the nucleus accumbens. A similar effect was observed using the more selective antagonist dizocilpine maleate, indicating the depression was NMDA receptor dependent. Paired-pulse facilitation was enhanced concomitantly with, and in proportion to, ketamine-induced depressed synaptic efficacy, indicative of a presynaptic mechanism of action. Notably, the depression of field potentials recorded in the nucleus accumbens was markedly reduced after a focal 6-hydroxydopamine lesioning procedure in the nucleus accumbens. More specifically, pretreatment with the D2/D4 antagonist haloperidol, but not the D1 antagonist SCH23390 blocked ketamine-induced depression of nucleus accumbens responses. Our findings provide supporting evidence for the contemporary theory of schizophrenia as aberrant excitatory neurotransmission at the level of the nucleus accumbens.

Animals↗

PubMed2006

GENCODE: producing a reference annotation for ENCODE.

BACKGROUND: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. RESULTS: The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. CONCLUSION: In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.

Chromosome Mapping↗

PubMed1994

EVA: European plans.

The current status of European EVA (extravehicular activity) plans is reviewed. The major difference to already existing EVA scenarios in U.S.A. and Soviet Union consists in the adoption of a higher suit pressure, namely 500 hPa. The results of a study concerned with the physiological consequences of this adoption are presented, including recommendations for protective procedures and their necessary experimental validation. A certain discrepancy between laboratory experimental decompression data and EVA operational results is discussed, leading to the identification of several items which may influence space decompression. Microgravity and the influence of the space suit itself are most likely factors in the explanation of this discrepancy, and both experimental procedures and technological developments are proposed to clarify their role for the future design of EVA procedures.

Aerospace Medicine↗

PubMed2026

Artificial Intelligence for Natural Products Discovery and Development.

Natural products (NPs) remain a cornerstone of modern drug discovery, offering stereochemical complexity and diverse bioactivities that precisely modulate therapeutic targets, refined through billions of years of evolution. However, their research has long been hindered by inefficient, empirical workflows, high resource consumption, structural complexity, and the "multicomponent, multi-target" nature of their mechanisms. The exponential growth of genomic, metabolomic, and spectral data has overwhelmed conventional analytical methods, exposing critical bottlenecks in handling high-dimensional, heterogeneous datasets that exceed human interpretive capacity. Artificial intelligence (AI) is emerging as a transformative paradigm to address these challenges, integrating multi-omics and chemical data to shift NP research from fragmented empiricism toward mechanism-driven, precision-oriented development. By leveraging deep learning architectures- including graph neural networks, Transformers, and diffusion-based generative models-AI enables systematic decoding of NP biosynthesis, automated structure elucidation, rational target identification, knowledge extraction from vast unstructured scientific literature, and de novo molecular design. This review comprehensively surveys recent advances in AI applications across the full NP discovery and development pipeline, encompassing genome mining, structure-based and ligand-based virtual screening, multimodal structural characterization, lead optimization, and biosynthetic pathway engineering. We further examine the emerging roles of protein-centric, molecule- centric, and multimodal foundation models, as well as large language models, in bridging genotype-to-chemotype gaps and unlocking unstructured scientific knowledge. Finally, we discuss critical challenges including data scarcity, representational limitations for complex stereochemistry, physical plausibility in generative models, and the urgent need for experimental validation, while outlining future directions toward autonomous experimentation, closed-loop optimization, and human-AI collaborative discovery.

Artificial intelligence↗

PubMed2026

Hepatic metabolic adaptation to endurance exercise: temporal and sex differences by multiomics integration and validation.

BACKGROUND: Although endurance exercise benefits liver health, sex-specific adaptive trajectories remain unclear. This study mapped dynamic liver adaptation in males and females during prolonged training and identified underlying molecular programs. METHODS: Using publicly available time-resolved liver multi-omics data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we established a computational pipeline for differential analysis of transcriptomic, proteomic, phosphoproteomic, and metabolomic data with FDR correction, followed by FGSEA pathway enrichment. Kinase activities were inferred through ortholog mapping and PhosphoSitePlus. Cross-omics co-expression networks were constructed using WGCNA and topological overlap to link omics features with physiological phenotypes. For experimental validation, liver tissues were collected from endurance-trained Sprague-Dawley rats, and key nodes were confirmed by Western blotting, qRT-PCR, and immunofluorescence/immunohistochemical staining. Public scRNA-seq data were further integrated to map multi-omics signals to single-cell resolution and assess functional changes in specific cell types. RESULTS: The hepatic response to exercise stress was stage-specific, shifting from early transcriptional activation to later proteomic and metabolic remodeling. Multi-omics integration revealed distinct sex-associated adaptive trajectories: males were more strongly associated with energy metabolism, redox-related programs, and amino acid/organic acid catabolism, whereas females showed prominent membrane lipid remodeling, proteostasis -related programs, and mitochondrial/ribosomal translational features. Single-cell analysis showed that tissue remodeling occurred without major lineage turnover, instead involving altered communication among pre-existing cell communities. Validation of PPP1R3G identified a protein-dominant exercise-responsive marker, supporting the contribution of post-transcriptional or protein-level regulation. CONCLUSIONS: Hepatic adaptation to endurance stress follows a cross-omics evolutionary pattern with sex-specific reprogramming of energy supply and homeostatic maintenance. This time-resolved framework clarifies how exercise improves liver function and supports sex-oriented metabolic interventions and therapeutic target discovery.

Animals↗

PubMed2001

Development and validation of a spatially explicit individual-based mixed crop growth model.

Spatial disposition of plants in intercrops, and differences in sowing time between species, can strongly affect their ecological interactions and, in consequence, the system's viability and performance. Empirical exploration of a wide range of spatial and temporal plant arrangements is costly and time-consuming. Modelling the growth of mixed crops is a tool which, combined with empirical tests, can greatly reduce the time and investment required for this task. Spatially explicit, individual-based dynamic models seem well suited for this purpose; their exploration and experimental validation for the case of simple, two-species, artificial plant communities, can also provide further insight as to how the spatial and temporal scales of a plant's multispecific neighbourhood affect its growth and performance. The aim of this investigation was to further develop a published spatially explicit individual-based mixed crop growth model [Vandermeer, J. H. (1989). The Ecology of Intercropping, Cambridge, U.K.: Cambridge University Press, p. 237], and to validate it experimentally. With this purpose in mind: (1) computer programs to simulate individual plant growth and to perform statistical analysis of both deterministic and stochastic versions of the model were developed; (2) the model was parametrized using a complex experimental diculture with several cohorts and spatial arrangements; (3) the predictive capacity of the model was tested using independent spatio-temporal experimental arrangements; (4) a modified version of the model was written, which abandons the assumption of linearity of the neighbourhood index at the cost of increasing the number of parameters; (5) The performance of stochastic versions of both Vandermeer's and our modified model were compared, employing a non-parametric measure of goodness of fit. We conclude that this approach to modelling plant growth subject to intra and interspecific competition is a remarkably efficient, general, conceptually elegant, heuristic tool whose predictive power can be further improved when nonlinear terms are introduced into the neighbourhood competition index, as done in our modified version of Vandermeer's model.

Agriculture↗

PubMed2001

Experimental annotation of the human genome using microarray technology.

The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

Algorithms↗

PubMed1989

Validation of single-sample doubly labeled water method.

We have experimentally validated a single-sample variant of the doubly labeled water method for measuring metabolic rate and water turnover in a very small passerine bird, the verdin (Auriparus flaviceps). We measured CO2 production using the Haldane gravimetric technique and compared these values with estimates derived from isotopic data. Doubly labeled water results based on the one-sample calculations differed from Haldane values by less than 0.5% on average (range -8.3 to 11.2%, n = 9). Water flux computed by the single-sample method differed by -1.5% on average from results for the same birds based on the standard, two-sample technique (range -13.7 to 2.0%, n = 9).

Animals↗

PubMed2002

AgeWa: an integrated approach for antisense experiment design.

One of the major fallouts of the human genome project relates to the investigation of the molecular mechanisms of diseases. Identification of genes which are involved in a specific pathological process and characterization of their interactions is of fundamental importance for supporting the drug design processes. Discovery of targets and the related experimental validation is a critical step in the development of new drugs. The new experimental methods for gene expression analysis, such as microarray technology, allows for the concurrent evaluation of the expression of multiple genes. The outcome of these new experimental methods requires a subsequent validation of the gene function by using in vitro or in vivo models. In the last decade, one of the most promising methodologies for the investigation of gene function relies upon antisense oligonucleotides (ASO). The crucial step in antisense experiment design is the characterization of the nucleotide domains that can efficiently be targeted by this kind of synthetic molecule. At present, no standardized procedures for target selection are available. In this paper, we propose an integrative approach to ASO target selection: the proposed tool Automatic Gene Walk (AgeWa) combines a neural filter with database mining for the prediction of the optimal target for antisense action.

Algorithms↗

PubMed2001

[Knee orthosis. First part : evaluation of physiological properties based on a review of the literature].

INTRODUCTION: The aim of this work was to proceed to a literature review to determine the physiological justifications underlying knee orthosis use in medical practice. METHOD: An analysis of the international literature relating to the years 1980-2000 was carried out with the Medline data bank. We added extra articles focusing on the validity of the protocols used in the different evaluations. RESULTS: Five hundred and twelve articles were selected and 46 articles of experimental validation were retained. The experimental protocols are divided into in vitro studies and clinical studies carried out in both healthy subject and patients. Only the in vitro experimental data allowed to reach strain values simulating traumatisms of the articular structures. They allowed to define the interest and limits of the orthosis according to articular physiology. Measurements carried out in vivo were effective to characterize the parameters of stability and proprioception and to discriminate between the orthosis. These studies correspond to experimental situations with related constraints that remain far below lesional constraints, focusing on their clinical validity. CONCLUSION: This work point out many studies focusing on the physiological characterization of the knee orthosis. This evaluation of the orthosis through a single methodology remains difficult and justifies confrontation with clinical trials data.

Biomechanical Phenomena↗

PubMed2004

Experimental and computational validation of BDTPS using a heterogeneous boron phantom.

The idea to couple the treatment planning system (TPS) to the information on the real boron distribution in the patient acquired by positron emission tomography (PET) is the main added value of the new methodology set-up at DIMNP (Dipartimento di Ingegneria Meccanica, Nucleare e della Produzione) of University of Pisa, in collaboration with the JRC (Joint Research Centre) at Petten (NL). This methodology has been implemented in a new TPS, called Boron Distribution Treatment Planning System (BDTPS), which takes into account the actual boron distribution in the patient's organ, as opposed to other TPSs used in BNCT that assume an ideal uniform boron distribution. BDTPS is based on the Monte Carlo technique and has been experimentally validated comparing the computed main parameters (thermal neutron flux, boron dose, etc.) to those measured during the irradiation of an ad hoc designed phantom (HEterogeneous BOron phantoM, HEBOM). The results are also in good agreement with those obtained by the standard TPS SERA and by reference calculations carried out using an analytical model with the MCNP code. In this paper, the methodology followed for both the experimental and the computational validation of BDTPS is described.

Boron↗

PubMed2006

A new organ transplantation location-allocation policy: a case study of Italy.

In this paper, we propose a location model for the optimal organization of transplant system. Instead of simulation approach, which is typical when facing many health care applications, our approach is distinctively based on a mathematical programming formulation of the relevant problem. In particular, we focus on the critical role of time in transplantation process as well as on a spatial distribution of transplant centers. The allocation of transplantable organs across regions with the objective of attaining regional equity in health care, is the aim of this paper. Our model differs from previous modeling approaches in that it considers the nationwide reorganization of the transplant system, identifying system barriers that may impair equity and efficiency. The demolition of these barriers may leads on a reduction of waiting lists and of wasted organs. We provide the basic structure and the properties of the model, and validate it on a real case study. The experimental validation of the model demonstrates the effectiveness and robustness of our proposal.

Efficiency, Organizational↗

PubMed2005

Development and validation of a solid phase micro-extraction-gas chromatography-mass spectrometry method for the determination of furan in baby-food.

An efficient and simple method for the determination of furan in baby-food (vegetables and fruits) by solid phase micro-extraction-gas chromatography-mass spectrometry (SPME-GC-MS) was developed and validated. Experimental design was used to investigate the effects of temperature and time of extraction. The calculated regression model was used to find the experimental conditions providing the optimal SPME extraction yield. Validation was carried out in terms of limit of detection (LOD), limit of quantitation (LOQ), linearity, precision and trueness. LOD and LOQ values in the low ngkg(-1) were achieved, whereas linearity was established over two order of magnitude. Good precision was obtained both in terms of intra-day repeatability and between-day precision on two concentration levels (RSD% lower than 3.6%). Recovery values of 91.5+/-6.2% and of 96.1+/-1.3% (n=3) were calculated at 75 ngkg(-1) and 75 microgkg(-1) level. Finally, the applicability of the method to the determination of furan in a number of commercial and home-made baby-food samples was demonstrated.

Furans↗

PubMedDate not supplied

[Body weight profile in acute mesenteric ischemia. Experimental study in New-Zealand rabbits].

INTRODUCTION AND OBJECTIVES: There are few investigation studies that relate acute mesenteric ischemia and body weight in animal experimentation. The aim is to studying whether initial weight loss is related to the magnitude of the aggression induced by clamps of the superior mesenteric artery for 30 and 60 minutes, and whether reperfusion ischemia may hinder weight recovery in surviving animals at the end of 11 weeks of experimental work with New Zealand rabbits through a valid experimental model. MATERIALS AND METHOD: 80 animals (rabbits) were distributed in four series of 20 each one: series I (control), animals were weighed for 11 weeks; series II (simulated surgery); series III (mesenteric ischemia for 30 minutes); series IV (mesenteric ischemia for 60 minutes). We induced ischemia by clamping the superior mesenteric artery. Animals from series II, III, and IV were weighed 24 hours before the surgical procedure and weekly after surgery along their survival, until completing 11 weeks. For weight analysis, an ANOVA test was used by confronting the percentage weight variation according to the series. All animals were necropsied to know the cause of death and histological lesions of the intestinal mucosa. RESULTS: Series I had a linear weight increase until the end of the observation period. Series II, III and IV had a significant initial decrease of the percentage weight during the first post-surgical week, with a recovery towards the end of the study, but significantly lower as compared to the control series. Significant differences have also been found in weight recovery at 11 weeks between series II and series III and IV, and between ischemic series. CONCLUSIONS: Animals in series II, III, and IV reached at the end of the study a percentage weight significantly lower to that obtained by series I. In the experimental animal mesenteric ischemia-reperfusion processes, the initial percentage weight loss in the postsurgical period is influenced not only by ischemia time but also by pre-and postsurgical manipulations; by contrast, the longer ischemia time is, the greater weight loss at the end of the study will be.

Acute Disease↗

PubMed1988

The validity of an experimental video examination.

This study investigated the validity of an experimental video examination that had previously been shown to be feasible and have reproducible scores for a sample of candidates taking the 1987 ABIM Cardiovascular Disease examination. Correlations of the three video formats of echocardiograms, ventriculograms, and arteriograms with traditional item formats, similar content multiple choice question scores, experience, and external measures suggest that the video formats could be a worthwhile addition to the examination.

Audiovisual Aids↗

PubMed1990

Antidotes to vesicant chemotherapy extravasations.

The foregoing sections have reviewed the experimental studies and clinical anecdotes describing potential pharmacologic antidotes to extravasations of vesicant anticancer agents. Numerous prior reviews have also suggested specific antidotes or very conservative, non-pharmacologic approaches. Many antidotal approaches to extravasation have not been experimentally validated and thus, few 'antidotes' share a rationale which is founded on positive experimental and clinical studies. However, using this criteria, a few active antidotes can be distilled from the literature. These are outlined in Table 6. These antidotes include isotonic (1/6 M) sodium thiosulfate for mechlorethamine (and optionally for cisplatin), hyaluronidase for the vinca alkaloids (and optionally for epipodophyllotoxins such as etoposide), and cooling with very topical DMSO and low dose hydrocortisone for the anthracyclines. For the alkylating agent mitomycin C, topical DMSO has been effective experimentally but has not yet received clinical validation, at least in published studies. Nonetheless, the severity of mitomycin C ulcerations and the documented safety of topical DMSO in the small series of doxorubicin extravasation patients argues for its use when mitomycin extravasates in the clinic. Furthermore, except for DMSO, all of these extravasation antidotes are listed in the official FDA-approved package inserts for each vesicant agent. Thus, the inserts for vincristine and vinblastine specify hyaluronidase, for doxorubicin, glucocorticosteroids, and for mechlorethamine, sodium thiosulfate. New studies are clearly needed to clarify the role of topical DMSO with anthracyclines and mitomycin C. In addition, efforts should be made to begin clinical development of radical dimers such as DHM3 which can directly inactivate quinone-containing vesicants like doxorubicin and mitomycin C. Although the incidence of chemotherapy extravasation may be lessened with vascular access devices, it nonetheless, continues to comprise a serious and highly litigious area of oncology practice. This commands continued extravasation intervention studies and diligent prevention when ever possible.

Animals↗

PubMed2002

Prediction of the generation of acoustic waves due to the penetration of pulsed microwaves in multilayer media.

The acoustic wave generation in a body irradiated by a pulsed microwave is predicted theoretically. The irradiated body is a viscoelastic multilayer rod inserted into a waveguide or an uniformly irradiated viscoelastic plate. The model is based on Maxwell's equations, the heat equation, and thermoviscoelasticity theory. It is validated experimentally by means of four tests performed on three different specimens. The two first specimens are homogeneous rods used to evaluate and verify the mechanical and electromagnetic characteristics of two different materials. The third specimen is a composite rod made up of these materials. Two tests are performed with this specimen. The comparison between the experimental results and the theoretical computations leads to the validation of the theoretical model.

Journal Article↗

PubMed1992

The mucosa of the rabbit vagina: a proposed experimental model for correlated morphofunctional studies in humans.

In order to suggest a valid experimental model for correlated studies regarding the complex phenomena of reproductive biology in humans, light (LM), transmission (TEM) and scanning electron microscopic (SEM) observations were carried out on vaginae of sexually mature New-Zealand albino rabbits, both in estrus and at 5 h after mating. To avoid artifacts depending upon the operative times for specimen removal and, in particular, to well visualize the inner surface of this organ, vaginal irrigation with fixative was performed prior to the surgical removal. Our data demonstrate that the upper 2/3 of the vaginal duct form a kind of 'cervico-vaginal canal' which shares many histological features with the human endocervix. In fact, this portion is lined within by a monostratified epithelium provided with tall microvillous and ciliated cells and often invaginated in crypts. After mating, the microvillous cells showed evidence of secretory activity, exhibiting dome-like luminal surfaces. Secretory droplets often contacted cilia and spermatozoa present in the mucosal furrows and crypts. Because of these singular features and the morphofunctional interactions between vaginal epithelium and male gametes, we believe the rabbit to be a helpful model for comparative biology in humans, concerning sperm capacitation and the general reactivity of the female genital tract during the reproductive cycle.

Animals↗