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PubMed2000

EmPLiCS: an empirical approach for structure-based design of natural peptide drugs.

The computer implementation of a peptide drug-design strategy has been developed. The system is named EmPLiCS (Empirical Peptide Ligand Construction System) according to the strategy of the system, which searches for peptide-ligand structures by referring to empirical rules that are derived from known protein 3D structures. The system was tested on several known peptide-protein complexes. The results demonstrated the ability of this system to detect key residues of peptides that are crucial for interaction with their specific proteins. The system also showed the ability to detect the main chain trace of these peptides. Some of the main chain atoms were detected even though the complete primary structures were not reproduced, suggesting that main chain structure is important in peptide-protein recognition. The results of the present study demonstrated that the empirical rules-based system can generate significant information for use in the design of natural peptide drugs.

Algorithms↗
PubMed2006

Theoretical and empirical approaches to express the mobility of small ions in capillary electrophoresis.

A discussion is given about the concepts of the ion mobility, the analyte property which governs migration and thus separation selectivity in CE. It deals with small organic and inorganic ions, not with charged polymers or large particles like colloids. The discussion is directed to two main concepts. (i) The first is based on physico-chemistry of ion conductance in solution, and distinguishes three types of mobility. The absolute mobility is the limiting mobility at zero ionic strength; it depends on the solvent and the temperature. It is obtained by extrapolation of the actual mobilities, those of the fully charged particles at finite ion concentration. The observed reduction of the absolute mobility with ionic concentration is related to an ion cloud, and is formulated by the established theories of ion conductance. It explains the actual mobility as function of (beside other factors) the ionic strength, the viscosity and relative permittivity of the solvent, the temperature, the relaxation time of solvent polarisation and the distance of closest approach between ion and counterion. The effective mobility, finally, is the mobility when association and dissociation equilibria play a role. Most important are acid-base reactions, but complexation, ion pairing and homo- and heteroconjugation were considered as well. (ii) The second approach treats mobility data with different mathematical methods, and formulates their dependence on variables like solvent composition with appropriate algorithms. These empirical methods mainly include least squares and neural network-based methods. The least square methods ranges from the simplest model, which uses only the molecular weight of the analyte, to more complicated model requiring three-dimensional structural descriptors of the solutes. Neural networks have been applied to model the mobility using different input variables and various architectures. Work comparing the accuracy of least squares and neural network methods was discussed; the results showed that the neural network method leads to a more accurate mobility calculation. However, the least squares methods could give some information to the factors affecting the mobility of the analytes. The resulting methods allow the prediction of mobilities under different experimental conditions with certain accuracy. It has been shown that using such models, it is possible to predict mobility of analytes after training the models by a minimum number of data to speed up the method development stage.

Algorithms↗
PubMed2004

Care needs among the dependent population in Spain: an empirical approach.

The objective of the present paper was to identify the profile and needs of social and healthcare users in Spain who required long-term care. To achieve this goal, an extensive empirical study was carried out in 2001 of a typical southern European region: the Valencia Autonomous Region in Spain. The method used was a questionnaire-based survey. The data collection instrument was a questionnaire comprising 119 questions grouped into seven sections: social and demographic data; clinical diagnosis and treatment; living environment; degree of dependence in activities of daily living (ADLs); cognitive state; social support; and the social, demographic and attendance data of the carer, if available. The sampling was carried out in two strata, i.e. social and healthcare: first, the authors randomly selected the centres and services as sampling points, and then they randomly selected the subjects. A total of 1265 people were interviewed. The results show different care profiles: users aged under 65 years were mostly mentally ill and/or drug users requiring short- and medium-term care from the health services, while those aged over 65 years had chronic illnesses for which they were actively receiving treatment, were functionally dependent for ADLs, and were normally receiving social care that basically provided company and resolved functional limitations.

Activities of Daily Living↗
PubMed1986

Population forecasts and confidence intervals for Sweden: a comparison of model-based and empirical approaches.

This paper compares several methods of generating confidence intervals for forecasts of population size. Two rest on a demographic model for age-structured populations with stochastic fluctuations in vital rates. Two rest on empirical analyses of past forecasts of population sizes of Sweden at five-year intervals from 1780 to 1980 inclusive. Confidence intervals produced by the different methods vary substantially. The relative sizes differ in the various historical periods. The narrowest intervals offer a lower bound on uncertainty about the future. Procedures for estimating a range of confidence intervals are tentatively recommended. A major lesson is that finitely many observations of the past and incomplete theoretical understanding of the present and future can justify at best a range of confidence intervals for population projections. Uncertainty attaches not only to the point forecasts of future population, but also to the estimates of those forecasts' uncertainty.

Forecasting↗
PubMed2005

The basic reproductive number of tick-borne encephalitis virus. An empirical approach.

Tick-borne encephalitis virus (TBEV) is reciprocally transmitted between Ixodes ricinus ticks and small mammals. Recently, transmission between co-feeding ticks has been postulated as an epidemiological by important mechanism of perpetuating the agent. To empirically examine the question whether the "traditional" mode of transmission is sufficient to maintain enzootic TBEV transmission, the basic reproductive number R(0) of TBEV could be estimated under this model for sites in which TBEV is enzootic. I propose an empirical estimator of R(0) for TBEV which is based on longitudinal stage-specific local tick infestation densities assessed by live trapping of small mammals. A Gibbs sampler-based 95%-credibility interval is presented. When applied to published field data from TBEV enzootic sites sub-critical R(0) estimates are obtained for both sites. I discuss potential shortcomings of this method and possible implications of these findings on the discussion of supplemental mechanisms of transmission.

Animals↗
PubMed2003

An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins.

A computer program system was developed to predict carbohydrate-binding sites on three-dimensional (3D) protein structures. The programs search for binding sites by referring to the empirical rules derived from the known 3D structures of carbohydrate-protein complexes. A total of 80 non-redundant carbohydrate-protein complex structures were selected from the Protein Data Bank for the empirical rule construction. The performance of the prediction system was tested on 50 known complex structures to determine whether the system could detect the known binding sites. The known monosaccharide-binding sites were detected among the best three predictions in 59% of the cases, which covered 69% of the polysaccharide-binding sites in the target proteins, when the performance was evaluated by the overlap between residue patches of predicted and known binding sites.

Animals↗
PubMed1988

An empirical approach to the study of defense mechanisms: I. Reliability and preliminary validity of the Rorschach Defense scales.

Despite widespread use of the Rorschach for the study of defense mechanisms, few recent Rorschach scales have been developed for the study of defensive functioning. We critically review previous empirical research and describe the Rorschach Defense scales. These scales provide criteria for rating both lower level defense mechanisms, such as splitting and primitive idealization, as well as higher level defenses, such as intellectualization and isolation. The scales utilize a broad range of content including all Rorschach responses, associative content, and verbalization of the tester-patient relationship. Data on interrater reliability and preliminary validity are presented.

Adolescent↗
PubMed2002

A fast empirical approach to binding free energy calculations based on protein interface information.

Three useful variables from the interfaces of 20 protein-protein complexes were investigated. These variables are the side-chain accessible number (N(b)), the number of hydrophilic pairs (N(pair)) and buried a polar solvent accessible surface areas (DeltaDeltaASA(apol)). An empirical model based on the three variables was developed to describe the free energy of protein associations. As the results show, the side-chain accessible numbers characterize the loss of side-chain conformational entropy of protein interactions and the effective empirical function presented here has great capability for estimating the binding free energy. It was found that the variables of interface information capture most of the significant features of protein-protein association. Also, we applied the model based on the variables as a rescoring function to docking simulations and found that it has the potential to distinguish the 'true' binding mode. It is clear that the simple and empirical scale developed here is an attractive target function for calculating binding free energy for various biological processes to rational protein design.

Algorithms↗
PubMed1992

[Empirical approaches to epidemiology of the Middle Ages].

Diseases result from hazards and influences originating in one's environment and could be described in evolutionary terms as maladaptations. Variations in the pattern of diseases throughout times and places can therefore indicate variations in the living conditions of ancient populations. Palaeopathology is the only way of gathering empirical data suitable for the reconstruction of epidemiological developments in the past. In spite of an abundance of material from the middle ages, only 25 series turned out to fulfill two crucial prerequisites, a certain minimal sizes and a palaeopathological analysis. Still a statistical comparison of those palaeopathological analyses proved impossible, because in most cases only casuistic details were available. This deficiency results from a lack of concept within palaeopathology. The ecosystem theory offers a basis for the development of a far-reaching concept. Widely accepted paradigms are indispensable for a prolific interdisciplinary cooperation on the highly relevant and complex phenomenon disease. Working with a standardized concept palaeopathology will be able to contribute to the solution of questions central to both, social history and environmental archaeology.

Germany↗
PubMed1991

Tufts assessment of motor performance: an empirical approach to identifying motor performance categories.

The Tufts Assessment of Motor Performance (TAMP) is a criterion-referenced test that measures motor performance capabilities of basic self-care skills, mobility and physical aspects of communication. Discrete motor performance tasks were identified within each of the 32 items. The purpose of this paper is to report the results of an empirical method of determining the factor structure underlying the motor performance tasks of the TAMP. Initially, motor performance tasks were categorized into a priori groupings based on previous literature and clinical judgment. The TAMP was administered to 206 children and adults (age range 6 to 86 years) with physical disabilities. Diagnoses included a variety of musculoskeletal and neurologic disorders. A principal-factor analysis was used to organize and cluster the item tasks into appropriate common factors. Seven factors were identified that accounted for 70.6% of the total variance for the assistance dimension; similar results were obtained for other measurement dimensions of the TAMP. The defined factor structure has patterns of similarity to the motor performance variables as defined by clinical judgment; however, the tasks were organized into factors that were more functionally oriented than expected. The results provide a framework for which the motor performance tasks of the TAMP might be organized into scales that identify essential performance constructs for rehabilitation. The results permit examination of the nature and clinical importance of these common motor performance factors for clinical evaluation and the description of functional disability.

Adolescent↗
PubMed1997

Personality and endogenous/major depression: an empirical approach to typus melancholicus. 1. Theoretical issues.

The concept of typus melancholicus (TM) was shaped by Tellenbach by means of phenomenological analysis in order to describe the premorbid and intermorbid personality of endogenous depressives. In this paper, the authors delineate the core properties of TM-i.e. orderliness, conscientiousness, norm orientation and intolerance of ambiguity-as a point of departure for empirical-statistical research. Qualitative and quantitative studies inquiring the characteristics of TM are reviewed in order to point out its well-established personality dimensions. Alternating methodological steps are proposed, combining phenomenological hypotheses with empirical-statistical tests (hermeneutic complementarity) in order to validate and differentiate the TM concept. The question whether TM should be considered as a personality disorder and the ethical attitude of subsiding appreciation of the TM in different generations of psychiatrists are discussed. It is emphasized that the TM concept brings otherwise unsystematized observations of depressives' intermorbid personality features into a coherent theoretical framework.

Depressive Disorder↗
PubMed2006

Supportive psychoanalytic psychotherapy for borderline patients: an empirical approach.

The author describes a reformulation for research purposes of a supportive psychoanalytic therapy for patients with borderline personality disorder. The major influences on the thinking that led to the modification of prior formulations and the historical background of treatment manuals are described. Supportive treatment is contrasted with transference-focused psychotherapy and dialectic behavior therapy in the interest of creating a clear comparison that lends itself to empirical study.

Borderline Personality Disorder↗
PubMed1988

Finding complex oscillatory phenomena in biochemical systems. An empirical approach.

Starting with a model for a product-activated enzymatic reaction proposed for glycolytic oscillations, we show how more complex oscillatory phenomena may develop when the basic model is modified by addition of product recycling into substrate or by coupling in parallel or in series two autocatalytic enzyme reactions. Among the new modes of behavior are the coexistence between two stable types of oscillations (birhythmicity), bursting, and aperiodic oscillations (chaos). On the basis of these results, we outline an empirical method for finding complex oscillatory phenomena in autonomous biochemical systems, not subjected to forcing by a periodic input. This procedure relies on finding in parameter space two domains of instability of the steady state and bringing them close to each other until they merge. Complex phenomena occur in or near the region where the two domains overlap. The method applies to the search for birhythmicity, bursting and chaos in a model for the cAMP signalling system of Dictyostelium discoideum amoebae.

Cyclic AMP↗
PubMed2005

PostDOCK: a structural, empirical approach to scoring protein ligand complexes.

In this work we introduce a postprocessing filter (PostDOCK) that distinguishes true binding ligand-protein complexes from docking artifacts (that are created by DOCK 4.0.1). PostDOCK is a pattern recognition system that relies on (1) a database of complexes, (2) biochemical descriptors of those complexes, and (3) machine learning tools. We use the protein databank (PDB) as the structural database of complexes and create diverse training and validation sets from it based on the "families of structurally similar proteins" (FSSP) hierarchy. For the biochemical descriptors, we consider terms from the DOCK score, empirical scoring, and buried solvent accessible surface area. For the machine-learners, we use a random forest classifier and logistic regression. Our results were obtained on a test set of 44 structurally diverse protein targets. Our highest performing descriptor combinations obtained approximately 19-fold enrichment (39 of 44 binding complexes were correctly identified, while only allowing 2 of 44 decoy complexes), and our best overall accuracy was 92%.

Ligands↗
PubMed2002

Regulation of bacterial assemblages in oligotrophic plankton systems: results from experimental and empirical approaches.

Bacteria are relevant members of planktonic food webs, both in terms of biomass and production share. The assessment and comprehension of the factors that control bacterial abundance and production are, thus, necessary to understand how carbon and nutrients circulate in planktonic food webs. It is commonly believed that bacterial abundance, activity and production are either determined by the available nutrient levels ('bottom-up' control) or by the effect of predators ('top-down'). These factors have also been shown to regulate the internal structure (the physiological and phylogenetic structure) of the bacterioplankton black box. We present here different empirical and experimental ways in which the factors that control bacterial communities are assessed, among them, the direct comparison of the rates of bacterial growth and losses to grazing. Application of several of these methods to open ocean data suggests that bacteria are regulated by resources at the largest scales of analysis, but that this overall regulation is strongly modulated by predators in all types of systems. In the most oligotrophic environments, bacterial abundance and growth are regulated by predators, while in the richest environments it is bacterial (phylogenetic, size, activity) community composition that is most affected by protist predators, while abundance can be influenced by metazoans. Because changes in bacterial community composition require that bacteria have enough nutrient supply, the overall effect of these regulations is that bacterial growth appears to be top-down regulated in the most nutrient-poor environments and bottom-up regulated in the richer ones.

Animals↗
PubMed2004

An empirical approach for thermal stability (Tm) prediction of PNA/DNA duplexes.

To predict the Tm value of PNA/DNA duplex, we performed to determine the melting temperature of several PNA oligomers. For Tm calculation model building, we searched the correlativity of measured Tm value and each base contents of PNA oligomer. Here, We propose a novel formula for thermal stability (Tm) prediction of PNA/DNA duplexes.

Base Composition↗
PubMed2005

Chronic fatigue syndrome--a clinically empirical approach to its definition and study.

BACKGROUND: The lack of standardized criteria for defining chronic fatigue syndrome (CFS) has constrained research. The objective of this study was to apply the 1994 CFS criteria by standardized reproducible criteria. METHODS: This population-based case control study enrolled 227 adults identified from the population of Wichita with: (1) CFS (n = 58); (2) non-fatigued controls matched to CFS on sex, race, age and body mass index (n = 55); (3) persons with medically unexplained fatigue not CFS, which we term ISF (n = 59); (4) CFS accompanied by melancholic depression (n = 27); and (5) ISF plus melancholic depression (n = 28). Participants were admitted to a hospital for two days and underwent medical history and physical examination, the Diagnostic Interview Schedule, and laboratory testing to identify medical and psychiatric conditions exclusionary for CFS. Illness classification at the time of the clinical study utilized two algorithms: (1) the same criteria as in the surveillance study; (2) a standardized clinically empirical algorithm based on quantitative assessment of the major domains of CFS (impairment, fatigue, and accompanying symptoms). RESULTS: One hundred and sixty-four participants had no exclusionary conditions at the time of this study. Clinically empirical classification identified 43 subjects as CFS, 57 as ISF, and 64 as not ill. There was minimal association between the empirical classification and classification by the surveillance criteria. Subjects empirically classified as CFS had significantly worse impairment (evaluated by the SF-36), more severe fatigue (documented by the multidimensional fatigue inventory), more frequent and severe accompanying symptoms than those with ISF, who in turn had significantly worse scores than the not ill; this was not true for classification by the surveillance algorithm. CONCLUSION: The empirical definition includes all aspects of CFS specified in the 1994 case definition and identifies persons with CFS in a precise manner that can be readily reproduced by both investigators and clinicians.

Adult↗