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PubMedDate not supplied

[Recurrent relationship for the characteristic polynom of a system of enzymatic catalysis of nonbranched monomolecular reactions].

A new mode is proposed to represent the characteristics equation for the system of monomolecular reaction on the basis of directed graphs method. A characteristic equation can be represented as a sum of weights of spanning trees derived from some graph which is connected with the initial graph of reaction. The recurrent relationship for the characteristic polynom of the system of nonbranched monomolecular reaction was obtained on the basis of this representation. A new proof on the matrix theorem about trees formulated by Volkenstein and Goldstein was established.

Chemical Phenomena↗

PubMed1982

[Use of the free venous auto-transplant of the "patch" type in the prevention and treatment of ureteral stenoses. Experimental study with emphasis on the functional value of the operation].

The author analyze the problems of transplantation of the free venous auto-transplant which they implant in the milieu of the urinary system at the location of a previously intentionally performed defect on the side of the ureter. Distinctively, they examine the functional value of such an operation. The experimental model was chosen as the ureter of a dog. A free venous auto-transplant, elliptical in shape (patch) with standard dimensions 2cm-6mm is built in a defect of the ureter side. Fifteen days after the operation an intravenous urography is done, while is repeated after four months. The findings of the urography show consistent values. Four months after the operation in order to check the functional value of the operation a dynamic scintigraphy of the kidneys together with computer data processing is done. An intravenous injection is given to the dogs of 25 micro Curie Hipurin (ortho-iod-hippuric acid labeled with J131). Following this, the dogs are put under a Gamma camera (LFOV - Searle), while registers a accumulation of activity. The results are expressed by a dynamic graph; from which it is easily seen that part of the graph, which relates to the disappearance of activity is almost identical with the graph of the non-operated half of the urinary system. This shows the functional equivalence of the operated and non-operated sides. Such good functional results are obtained in all trials. All together 6 dogs are operated and a total of 8 operations are performed. The results of this work, as well as the clinical experience of other author allow us to propose the application of the free venous auto-transplant (patch), in the cure and prevention of the stenosis of the ureter of the shorter segment at specific indications.

Animals↗

PubMedDate not supplied

[Regulation of two-substrate reaction by substrate analog, as analyzed by graphic methods].

The regulatory action of a substrate analogue on the two-substrate reaction has been analysed by the method of graphs. It was shown that the analogue can act not only as inhibitor but also as activator in an ordered mechanism of the two-substrate reaction. Activation of the reaction by the analogue is a consequence of its random mechanism in regard to substrates and products. This random mechanism tends to the appearance of another route in the enzymic reaction and by this route the activation of the reaction may be obtained. It was also shown, that substrate inhibition may be abolished by the analogue, if the reaction rate via analogue route is large enough. On this case the analogue competes with the substrate-inhibitor in the non-active ternary complex. For the analysis of kinetic schemes the cyclic algorithm of the graph method was applied because of its convenience for multiroute reactions. Some simplifications were proposed for the structure of graphs. The results of this analysis are applicable for interpretation of abolishing the substrate inhibition by monovalent anions for some dehydrogenases.

Enzymes↗

PubMed1995

A model for medical knowledge representation application to the analysis of descriptive pathology reports.

A new knowledge-representation system is presented, designed for medical knowledge-based applications and in particular for the analysis of descriptive medical reports. Knowledge is represented at two levels. A definitional level uses a concept-type hierarchy, a relation-type hierarchy, and a set of schematic graphs to define the concepts used and the relations between them, as well as different types of cardinality restrictions on these relations. A set of compositional hierarchies using the classic "has-part" relation as well as a new set-inclusion relation allows concept composition to be precisely defined. An assertional level allows the creation and manipulation of empirical data, in the form of graphs using the concepts, relations, and constraints defined at the definition level. The use of cardinality constraints in graph unification is considered in the context of descriptive medical discourse analysis.

Artificial Intelligence↗

PubMed1995

Identification of human gene structure using linear discriminant functions and dynamic programming.

Development of advanced technique to identify gene structure is one of the main challenges of the Human Genome Project. Discriminant analysis was applied to the construction of recognition functions for various components of gene structure. Linear discriminant functions for splice sites, 5'-coding, internal exon, and 3'-coding region recognition have been developed. A gene structure prediction system FGENE has been developed based on the exon recognition functions. We compute a graph of mutual compatibility of different exons and present a gene structure models as paths of this directed acyclic graph. For an optimal model selection we apply a variant of dynamic programming algorithm to search for the path in the graph with the maximal value of the corresponding discriminant functions. Prediction by FGENE for 185 complete human gene sequences has 81% exact exon recognition accuracy and 91% accuracy at the level of individual exon nucleotides with the correlation coefficient (C) equals 0.90. Testing FGENE on 35 genes not used in the development of discriminant functions shows 71% accuracy of exact exon prediction and 89% at the nucleotide level (C = 0.86). FGENE compares very favorably with the other programs currently used to predict protein-coding regions. Analysis of uncharacterized human sequences based on our methods for splice site (HSPL, RNASPL), internal exons (HEXON), all type of exons (FEXH) and human (FGENEH) and bacterial (CDSB) gene structure prediction and recognition of human and bacterial sequences (HBR) (to test a library for E. coli contamination) is available through the University of Houston, Weizmann Institute of Science network server and a WWW page of the Human Genome Center at Baylor College of Medicine.

Algorithms↗

PubMed1994

[A comparative evaluation of three commercially available peak flowmeters before and after being used 1000 times].

The differences in values, accuracy, reproducibility and interdevice variability of three models of portable peak flowmeters (standard and low range of Assess, mini-Wright, Pulmo-Graph) before use and after they had been used 1000 times. A computerized standard flow generator was used to evaluate. Standard range; The three models showed differences in values before and after 100 uses of less than 3 percent at flow rates below 480 L/min. However, the used flowmeters, especially the Assess, showed higher values compared with the new ones at higher flow ranges. There was no significant difference in accuracy between the new and used mini-Wright and Pulmo-Graph models. The used Assess, howevers, showed higher values at higher ranges, thus demonstrating improved accuracy over the new ones. The reproducibilities of the three models deteriorated at high flow rates. The interdevice variability of the used Pulmo-Graph flowmeter was better than that the new one. No significant changes were observed in the mini-Wright, while the Assess showed deteriorated interdevice variability. Low range; The three models showed no significant differences in values, accuracy, reproducibility or interdevice variability before and after use.

Evaluation Studies as Topic↗

PubMed1994

[An evaluation of three commercially available peak flowmeters].

The accuracy, reproducibility and interdevice variability of three models of portable peak flowmeters (standard and low range) were evaluated by using a computerized standard flow generator. Standard range; The mini-Wright peak flow meter generally overestimated peak flow from 120 L/min to 540 L/min and the Assess peak flowmeter underestimated peak flow at full range. The Pulmo-Graph peak flowmeter showed a similar pattern to the mini-Wright but with more accuracy. The Assess showed the best linearity. The reproducibilities of the three models deteriorated over 20 L/min at high flow rates. The interdevice variability of the mini-Wright was better than those of the Assess or the Pulmo-Graph. Low range: The accuracy and interdevice variability of the Pulmo-Graph were better than those of the Assess or the mini-Wright. The reproducibility of Assess seemed to be inferior to the other's. The measured flow from the low ranges was not the same as that of the standard ranges. The three peak flowmeter models have different spring mechanisms for their readings, and the measured flows by one model should not be compared with other models.

Evaluation Studies as Topic↗

PubMed1994

[TNM system: presentation of graphic classification of T laryngeal cancer].

Using the most recent TNM revision as a basic framework to build upon, the Authors set up a graphic representation of the larynx on the basis of data gathered using clinical-instrumental examination. This graph, which allows automatic extrapolation of the degree of T, represents various sites and subsites of the larynx (including the pre-epiglottic area, the retro-cricoid area and the piriform sinus) which are divided by different coloured lines. This simple graphic representation of cancerous tumours, whose various colours indicate tumor extension in depth (data had with CT and RM), allows for automatic T classification of larynx cancer on the basis of T extension as well as on that of the degree of vocal cord impairment. Particularly useful for students in memorizing TNM classification, this graph, furthermore, groves to be a means of facilitating under standing the disease as well as opinion exchange among members of the medical staff. As furthermore proves of utmost value in patient management in that it may be fed into computerized management programmes containing individual patient's records thereby permitting a more rapid classification of the tumor. Moreover, the data easily stored in the programme are readily accessible for eventual statistical elaboration. The Authors conclude with a proposal of the eventual use of a similar graph of other sites in the body which may be adapted in the event of future TNM revisions.

Glottis↗

PubMed1993

Defining normality--art or science?

The problem of defining normality, and in particular the establishment of reference ranges, is discussed. A so-called "objective" method of determining such ranges is described. It is suggested, however, that all currently used methods for defining "normal" ranges rely ultimately on a subjective choice. We propose the use of "How Often That Happens" (HOTH) graphs as an alternative to the conventional reference range. Such graphs show the frequency of results at least as extreme as any observed value. We have used such graphs, along with computer simulation models, in an attempt to describe how the frequency distribution of a given parameter changes as a population ages. Finally, an analogy is drawn between the states of "health", "illness" and "death", and the attractors which arise in non-linear dynamic systems. We conclude that the definition of normality is in fact more of an art than a science.

Adult↗

PubMed1993

[A serum cholesterol study in a consulting population and its implications in clinical practice].

OBJECTIVE: To investigate serious cholesterol levels in the population seeking medical attention, utilising HOTH (How Often That High) graphs, and to look at implications these results have for recording of cholesterol incidence. DESIGN: This was a non-longitudinal, retrospective, observational study. SETTING: Carried out at the general practice level, in the Valdefierro Basic Health Area (Zaragoza Province). PATIENTS: 742 subjects aged between 18 and 65 years with no previous history of dyslipemia. MEASUREMENTS AND MAIN RESULTS: After obtaining the figures on cholesterolemia, the HOTH graph was drawn from which, for a given cholesterol value, the percentage of the population with a given value can be seen. The mean cholesterol value was 201 mg/dl. A total of 54% of male subjects and 40% of female subjects were situated above the threshold figure of 200 mg/dl. Furthermore, 15% of male subjects and 10% of female subjects were situated above 250 mg/dl. CONCLUSIONS: The application of recording procedures for cholesterol, based on a globally discriminatory score, reveals a startling number of patients who need tests and treatment. We suggest a strategy based on the different levels according to age, sex, bloodstream cholesterol level, and the existence or otherwise of other cardiovascular risk factors. Lastly, we would mention the usefulness of the HOTH graphs in improving our knowledge of the cholesterol levels in a population.

Adolescent↗

PubMed1995

Current trends with natural language processing.

Natural Language Processing in the medical domain becomes more and more powerful, efficient, and ready to be used in daily practice. The needs for such tools are enormous in the medical field, due to the vast amount of written texts for medical records. In the authors' point of view, the Electronic Patient Record (EPR) is achieved neither with Information Systems of all kinds nor with commercially available word processing systems. Natural Language Processing (NLP) is one dimension of the EPR, as well as Image Processing and Decision Support Systems. Analysis of medical texts to facilitate indexing and retrieval is well known. The need for a generation tool is to produce progress notes from menu driven systems. The computer systems of tomorrow cannot miss any single dimension. Since 1988, we've been developing an NLP system; it is supported by the European program AIM (Advanced Informatics in Medicine) within the GALEN and HELIOS consortium and the CERS (Commission d'Encouragement á la Recherche Scientifique) in Switzerland. The main directions of development are: a medical language analyzer, a language generator, a query processor, and dictionary building tools to support the Medical Linguistic Knowledge Base (MLKB). The knowledge representation schema is essentially based on Sowa's conceptual graphs, and the MLKB is multilingual from its design phase; it currently incorporates the English and the French languages; it will also continue using German. The goal of this demonstration is to provide evidence of what exists today, what will be soon available, and what is planned for the long term. Complete sentences will be processed in real time, and the browsing capabilities of the MLKB will be exercised. In particular, the following features will be presented: Analysis of complete sentences with verbs and relatives, as extracted from clinical narratives, with special attention to the method of "proximity processing" as developed in our group and the rule based approach to language description to resolve the specific surface language problems as well as the language independent semantic situations. Comparison of results for English, French, and German sentences, showing the commonalities between these languages and, therefore, the re-usable features and the language specific aspects. Generation of noun phrases in English and French, showing the opportunities for translation between these two languages. Application of the analyzer to build a knowledge representation of ICD under the form of conceptual graphs and presentation of the possibilities of a natural language encoding of diagnosis. Strategies for query processing through a sample of abdominal ultrasonography reports, which have been analyzed and stored under the form of conceptual graphs. Feeding in and browsing of the Medical Linguistic Knowledge Base and other Dictionary Building Tools, using the perspective of an international initiative to converge towards a multilingual universal solution, valid for the medical domain. The demonstration platform is Microsoft Windows 4 on a PC, with Microsoft Visual Basic as the GUI and Quintus Prolog as NLP tools language. The same programs were originally developed for Unix-based workstations and are available on multiple platforms under Motif and X11. .

European Union↗

PubMed1996

Knowledge on collection and analysis of health information of state certified nurses from rural health centres, Masvingo Province.

OBJECTIVE: To assess the knowledge on collection and analysis of health information of State Certified Nurses (SCNs) from Rural Health Centres (RHCs), Masvingo Province. DESIGN: Three methods were employed during the assessment: a questionnaire, observation, and practical exercises (calculations). SETTINGS: 19 RHCs in Chiredzi and Bikita Districts, Masvingo Province. SUBJECTS: 19 SCNs in charge of Rural Health Centres. MAIN OUTCOME MEASURES: Ability to analyze and utilize health information, availability of graphs, master cards summaries (health diaries) and minutes. Presence or absence of catchment maps, charts on population breakdown and immunization coverage charts. Ability to calculate some rates and percentages. RESULTS: Of 19 SCNs in charge who said they do school health programmes, only six had any evidence that they do so; of nine SCNs in charge who reported that they have graphs on weekly reported diseases, only four had graphs displayed. Of 18 SCNs in charge who said they had immunization coverage targets only 11 had charts displayed; of 18 SCNs in charge who reported that they discuss health problems in their areas, only one had minutes documenting the discussion. Only six of 19 SCNs at rural centres could calculate coverage rates and only one of 19 SCNs at health centres could calculate dropout rates. CONCLUSION: Comparing the questionnaire responses with the findings from observations, it can be seen that more is reported than is actually done. From the practical exercises it was evident that the ability to do basic calculations was often lacking.

Data Collection↗

PubMed1997

Adaptive sampling in behavioral surveys.

Studies of populations such as drug users encounter difficulties because the members of the populations are rare, hidden, or hard to reach. Conventionally designed large-scale surveys detect relatively few members of the populations so that estimates of population characteristics have high uncertainty. Ethnographic studies, on the other hand, reach suitable numbers of individuals only through the use of link-tracing, chain referral, or snowball sampling procedures that often leave the investigators unable to make inferences from their sample to the hidden population as a whole. In adaptive sampling, the procedure for selecting people or other units to be in the sample depends on variables of interest observed during the survey, so the design adapts to the population as encountered. For example, when self-reported drug use is found among members of the sample, sampling effort may be increased in nearby areas. Types of adaptive sampling designs include ordinary sequential sampling, adaptive allocation in stratified sampling, adaptive cluster sampling, and optimal model-based designs. Graph sampling refers to situations with nodes (for example, people) connected by edges (such as social links or geographic proximity). An initial sample of nodes or edges is selected and edges are subsequently followed to bring other nodes into the sample. Graph sampling designs include network sampling, snowball sampling, link-tracing, chain referral, and adaptive cluster sampling. A graph sampling design is adaptive if the decision to include linked nodes depends on variables of interest observed on nodes already in the sample. Adjustment methods for nonsampling errors such as imperfect detection of drug users in the sample apply to adaptive as well as conventional designs.

Behavior↗

PubMed1998

Visualization based on the Enzyme Commission nomenclature.

We developed a tool for visualizing data related to protein function, based on the nomenclature defined by the International Enzyme Commission. The method represents the 1327 specific reaction types and three additional levels of abstract classifications in the nomenclature as an interactive graph. Each node and link in the graph can have associated with it stored or computed data values of various types, each of which can be assigned to any of a set of visualization methods, including color, size, various chart types and text. Visualizations can then be interactively created for single nodes, groups of nodes or the entire graph. This visualization tool is particularly useful for exploring the distribution of quantitative attributes across protein function classes. As a test of this tool, we developed a visualization of data measuring the effectiveness of sequence similarity for prediction of EC class. Using this tool, it was possible to rapidly scan hundreds of functional classes, and to correlate predictability from sequence with other attributes, facilitating the generation of hypotheses about the causes of predictive failure.

Amino Acid Sequence↗

PubMed1998

A map of the protein space--an automatic hierarchical classification of all protein sequences.

We investigate the space of all protein sequences. We combine the standard measures of similarity (SW, FASTA, BLAST), to associate with each sequence an exhaustive list of neighboring sequences. These lists induce a (weighted directed) graph whose vertices are the sequences. The weight of an edge connecting two sequences represents their degree of similarity. This graph encodes much of the fundamental properties of the sequence space. We look for clusters of related proteins in this graph. These clusters correspond to strongly connected sets of vertices. Two main ideas underlie our work: i) Interesting homologies among proteins can be deduced by transitivity. ii) Transitivity should be applied restrictively in order to prevent unrelated proteins from clustering together. Our analysis starts from a very conservative classification, based on very significant similarities, that has many classes. Subsequently, classes are merged to include less significant similarities. Merging is performed via a novel two phase algorithm. First, the algorithm identifies groups of possibly related clusters (based on transitivity and strong connectivity) using local considerations, and merges them. Then, a global test is applied to identify nuclei of strong relationships within these groups of clusters, and the classification is refined accordingly. This process takes place at varying thresholds of statistical significance, where at each step the algorithm is applied on the classes of the previous classification, to obtain the next one, at the more permissive threshold. Consequently, a hierarchical organization of all proteins is obtained. The resulting classification splits the space of all protein sequences into well defined groups of proteins. The results show that the automatically induced sets of proteins are closely correlated with natural biological families and super families. The hierarchical organization reveals finer sub-families that make up known families of proteins as well as many interesting relations between protein families. The hierarchical organization proposed may be considered as the first map of the space of all protein sequences. An interactive web site including the results of our analysis has been constructed, and is now accessible through http:/(/)www.protomap.cs.huji.ac.il

Algorithms↗

PubMed2026

Artificial Intelligence-Driven Multi-Omics Analysis Reveals Hydroxytyrosol Targeting of the TXNIP-NLRP3 Inflammasome Axis in Traumatic Brain Injury.

Traumatic brain injury (TBI) induces secondary neuroinflammation driven by oxidative stress, inflammasome activation, and immune remodeling, yet specific mechanism-guided pharmacological interventions remain limited. This study established an artificial intelligence (AI)-integrated network pharmacology and multi-omics framework to evaluate whether hydroxytyrosol (HT), an olive-derived natural polyphenol, may regulate TBI-related neuroinflammatory targets centered on the TXNIP/NLRP3 inflammasome axis. Starting from the SMILES structure of HT, potential targets were predicted using PharmMapper, SwissTargetPrediction, and the Similarity Ensemble Approach and were standardized to UniProt identifiers. TBI-associated genes were integrated from GeneCards, DisGeNET, OMIM, and the Therapeutic Target Database. The overlapping target set was analyzed using STRING-based protein-protein interaction (PPI) networks, MCODE, CytoHubba, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Public GEO transcriptomic datasets (GSE123831 and GSE104687) were used for cross-platform expression validation, differential expression analysis, and exploratory CIBERSORT-based immune infiltration estimation. Random forest (RF), multilayer perceptron (MLP), graph convolutional network (GCN), graph attention network (GAT), SHAP/LIME explainability analysis, LASSO inflammatory-risk scoring, and two-sample Mendelian randomization (MR) were further applied for target prioritization, immune phenotype mapping, and genetic association analysis. Seventy-three overlapping HT-TBI targets were identified. PPI and topology analyses prioritized TXNIP, NLRP3, CASP1, MAPK1, and TP53 as key hubs enriched in inflammasome activation, oxidative stress, apoptosis, and NOD-like receptor signaling. TXNIP, NLRP3, and CASP1 were consistently upregulated in both TBI transcriptomic datasets. LM22-based immune deconvolution suggested increased pro-inflammatory immune signatures and a positive TXNIP-M1 macrophage association (r = 0.63, p < 0.001), which should be interpreted as a transcriptome-derived hypothesis rather than validated murine immune-cell proportions. AI-based models consistently ranked TXNIP/NLRP3 as high-contribution features under internal validation, and removal of these targets reduced model performance. A five-gene inflammatory score achieved an internally evaluated AUC of 0.87, while two-sample MR supported positive genetic associations involving TXNIP expression, TBI risk, NLRP3 and IL-1β expression. Collectively, these findings prioritize the TXNIP/NLRP3/CASP1 module as a computationally supported candidate mechanism through which HT may influence oxidative stress-inflammasome-immune coupling in TBI. This study provides an interpretable drug-target-pathway-phenotype framework and identifies TXNIP, NLRP3, and CASP1 as priority nodes for future experimental validation.

Artificial Intelligence↗

PubMed1998

Kidneys of the killerwhale and significance of reniculism.

BACKGROUND: The kidneys of all Cetacea are composed of many small relatively independent kidneys (renicules) containing considerable interrenicular tissue. Although reniculism is not entirely confined to the Cetacea, it is desirable to consider the possible advantage of reniculism to mammals of gigantic size. The kidneys of the killerwhale, Orcinus orca, are compared from this standpoint to the kidneys of diverse mammals. METHODS: The specific renal parenchymal mass, glomerular counts, glomerular size, and specific glomerular mass of the killerwhale are measured and compared quantitatively (statistically) with similar data from numerous diverse mammals. Simultaneously, a method is described for enumerating the renicules of a cetacean kidney. RESULTS: Specific parenchymal mass of a killerwhale adult's two kidneys (0.33%) is close to the expected value for mammals of its adult body mass (2,087 kg). The diameter of the adult's glomerular capsules (153 microm) is strikingly less than that expected from its body mass (regression equation and graph for mammals in general). However, the number of glomeruli per kidney (approximately 100 x 10[6]) is markedly greater than that for mammals of its body mass (regression equation and graph for mammals in general) and is the first such count for a cetacean. The total glomerular mass relative to parenchymal renal mass of the O. orca infant and adult is, nevertheless, 5.5% and 6.0%, respectively, and is thus close to the general mammalian value of approximately 5%. CONCLUSIONS: Organization of a cetacean kidney into numerous renicules does not increase specific renal parenchymal mass or specific glomerular mass. The apparent advantage of numerous independent renicules is the limit that is afforded for length of tubules in the necessarily large kidneys of gigantic mammals.

Animals↗

PubMed1999

Energy-resolved mass spectrometry: a comparison of quadrupole cell and cone-voltage collision-induced dissociation.

Collision-induced dissociation (CID) can be effected in the interface region between atmospheric pressure ionization sources and single quadrupole mass analyzers. By varying the electric field in these cone-voltage CID experiments energy-resolved mass spectra can be obtained leading to breakdown graphs exploring the energy evolution of the fragmentation pathways. The breakdown graphs obtained from these cone-voltage CID studies are very comparable to those obtained by varying the collision energy in the quadrupole collision cell of a BEqQ mass spectrometer. The comparison has been made for the protonated peptides H-Leu-Gly-Gly-OH, H-Gly-Leu-Gly-OH, H-Gly-Gly-Leu-OH and Leu-enkephalin

Animals↗