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PubMed2006

Towards systemic theories in biological psychiatry.

Although still rather controversial, empirical data on the neurobiology of schizophrenia have reached a degree of complexity that makes it hard to obtain a coherent picture of the malfunctions of the brain in schizophrenia. Theoretical neuropsychiatry should therefore use the tools of theoretical sciences like cybernetics, informatics, computational neuroscience or systems science. The methodology of systems science permits the modeling of complex dynamic nonlinear systems. Such procedures might help us to understand brain functions and the disorders and actions of psychiatric drugs better.

Antipsychotic Agents↗
PubMed2006

[Evaluation of therapeutic effects of Chinese materia medica by tongue image analysis software 1.0 based on tongue colors].

OBJECTIVE: To evaluate the therapeutic effects of Chinese materia medica in treating patients with different syndromes by tongue image analysis software 1.0 based on tongue colors, and to discuss the feasibility of applying this computer science-based techniques into drug evaluation. METHODS: The tongue colors and the areas of tongue fur were examined and analyzed by the tongue image analysis software 1.0 in healthy persons and the patients with different syndromes before and after treatment. The parameters of tongue colors consisted of the followings: the hue (H), the lightness (L), the saturation (S), and the values of red (R), green (G) and blue (B). RESULTS: Obvious differences could be revealed in tongue color index between the healthy persons and the patients in five groups of different syndromes. There also existed some significant differences in those index between patients before and after treatment. CONCLUSION: The tongue image analysis software 1.0 based on tongue colors is helpful to evaluate the therapeutic effects of Chinese materia medica.

Adolescent↗
PubMed1996

Mental models and temporal reasoning.

We report five experiments investigating reasoning based on temporal relations, such as: "John takes a shower before he drinks coffee". How individuals make temporal inferences has not been studied hitherto, but we conjectured that they construct mental models of events, and we developed a computer program that reasons in this way. As the program shows, a problem of the form: a before b b before c d while b e while c What is the relation between d and e? where a, b, c, etc. refer to everyday events, calls for just one model, whereas a problem in which the second premise is modified to c before b calls for multiple models because a may occur before c, after c, or at the same time as c. Experiments 1-3 showed that problems requiring one mental model elicited more correct responses than problems requiring multiple models, which in turn elicited more correct answers than multiple model problems with no valid answers. Experiment 4 contrasted the predictions of the model theory with those based on formal rules of inference; its results corroborated the model theory. Experiment 5 confirmed that a premise leading to multiple models took longer to read than the corresponding premise in one-model problems, and that latency to respond correctly was greater for multiple-model problems than for one-model problems. We conclude that the experiments corroborate the mental model theory.

Adolescent↗
PubMed2005

In silico prediction of harmful effects triggered by drugs and chemicals.

While the computer-assisted discovery and optimization of drug candidates based on the known three-dimensional structure of the macromolecular target (structure-based design) or a binding-site surrogate (receptor modeling) is doubtless one of the more potent approaches in rational drug design, the simulation and quantification of side effects triggered by drugs and chemicals are still in their infancy. Major obstacles include the often not available 3D structure of the molecular target, the low specificity of the involved bioregulators and the identification of the controlling metabolic pathways. In the recent past, our laboratory has explored concepts allowing to simulate receptor-mediated toxic phenomena by developing algorithms, allowing to construct realistic 3D binding-site surrogates of receptors known or assumed triggering adverse effects and validating them against large batches of molecular data. The underlying technology (software Quasar and Raptor, respectively) specifically allows for induced fit, solvation phenomena and entropic effects. It has been applied to various systems both of pharmacological and toxicological interest including the neurokinin-1, chemokine-3, bradykinin B(2), steroid, 5 HT(2A), aryl hydrocarbon, estrogen and androgen receptor, respectively. In this account, we describe the design of a virtual laboratory allowing for a reliable estimation of harmful effects triggered by drugs, chemicals and their metabolites in silico. In the recent past, the Biographics Laboratory 3R has compiled a 3D database including the surrogates of three major receptor systems known to mediate adverse effects (the aryl hydrocarbon, the estrogen and the androgen receptor, respectively) and validated them against a total of 345 compounds (drugs, chemicals, toxins) using multidimensional QSAR technologies. Within this pilot project, we could demonstrate that our virtual laboratory is able to both recognize toxic compounds substantially different from those used in the training set as well as to classify harmless compounds as being nontoxic. This suggests that our approach may be used for the prediction of adverse effects of drug molecules and chemicals. It is the aim to provide cost-covering access to this technology--particularly to universities, hospitals and regulatory bodies--as it bears a significant potential to recognize hazardous compounds early in the development process and hence improve resource and waste management as well as reduce animal testing. The Biographics Laboratory 3R is a non-profit-oriented organization aimed at reducing animal experimentation in the biomedical sciences by computational approaches (cf. http://www.biograf.ch).

Computer Simulation↗
PubMed2005

External cross-validation for unbiased evaluation of protein family detectors: application to allergens.

Key issues in protein science and computational biology are design and evaluation of algorithms aimed at detection of proteins that belong to a specific family, as defined by structural, evolutionary, or functional criteria. In this context, several validation techniques are often used to compare different parameter settings of the detector, and to subsequently select the setting that yields the smallest error rate estimate. A frequently overlooked problem associated with this approach is that this smallest error rate estimate may have a large optimistic bias. Based on computer simulations, we show that a detector's error rate estimate can be overly optimistic and propose a method to obtain unbiased performance estimates of a detector design procedure. The method is founded on an external 10-fold cross-validation (CV) loop that embeds an internal validation procedure used for parameter selection in detector design. The designed detector generated in each of the 10 iterations are evaluated on held-out examples exclusively available in the external CV iterations. Notably, the average of these 10 performance estimates is not associated with a final detector, but rather with the average performance of the design procedure used. We apply the external CV loop to the particular problem of detecting potentially allergenic proteins, using a previously reported design procedure. Unbiased performance estimates of the allergen detector design procedure are presented together with information about which algorithms and parameter settings that are most frequently selected.

Allergens↗
PubMed2006

Operational Noology as a new methodology for the study of thought and language: theoretical aspects and possible practical applications.

In this article, the author presents a new methodology for the study of two fundamental components of consciousness, that is thought and language. The fundamental presupposition that forms the basis of this methodology is that thought is not simply a passive "reflection" of an external "reality", but also (and especially) something active, i.e. that the fundamental components of thought are sequences of operations, amongst which the ones of attention play a key role. These sequences of elementary mental operations are called mental categories, and are the meanings of all the words that do not seem to indicate something physical (first of all, all the "grammatical" words, that is conjunctions, prepositions, articles, pronouns, fundamental verbs like "to be", "to have" etc., the main adverbs, and, in the large number of languages that have a more or less rich morphology, all morphemes (the ones which indicate cases, in languages that have cases, the number and the gender of nouns and adjectives, moods and tenses of the verb etc.). The author proposes a list of these elementary mental operations and he shows how it is possible, basing ourselves on them, to identify the meanings of these words, which are indispensable for any linguistic expression. The author also mentions a possible short-term practical application of these theories, i.e. a device in order to improve the quality of machine translation. He also formulates the hypothesis that these theories could allow us to look in a new way at the problem of the (partial) artificial reproduction of the human activity of thought and language.

Attention↗
PubMed1986

A microcomputer-based system for detailed analysis of rat behavior.

A microcomputer-based system that can measure rotational behavior and moving velocity is described. Infrared photobeams detect the animal behavior. One advantage of this system is that data can be stored on floppy disks and analyzed in arbitrary time intervals. This system may be useful for detailed analysis of rat behavior in physiological or psychopharmacological experiments.

Animals↗
PubMed2004

Influence of spectacle-related changes in retinal image size on contrast sensitivity function after laser in situ keratomileusis.

PURPOSE: To evaluate changes in contrast sensitivity after laser in situ keratomileusis (LASIK) for the correction of myopia using a monitor-based method and considering the preoperative minification effect of high-diopter spectacles. SETTING: Department of Ophthalmology, University of Vienna Medical School, Vienna, Austria. METHODS: Fifteen eyes of 11 patients had LASIK to correct myopia. The best corrected visual acuity (BCVA) and contrast sensitivity function (CSF) were measured preoperatively and 1, 3, and 6 months postoperatively using the AcuityMax (Science 2020) computer program. The error in contrast sensitivity measurement due to different angular sizes of the test figures deriving from the spectacle refractions before and after LASIK were considered. RESULTS: Preoperatively, and at 1, 3, and 6 months, the mean Snellen BCVA was 0.93 +/- 0.19 (SD), 0.80 +/- 0.26, 0.85 +/- 0.21, and 0.84 +/- 0.27, respectively. The best mean CS (measured at 1.1 logMAR) was 1.17 +/- 0.05, 1.12 +/- 0.07, 1.13 +/- 0.08, and 1.18 +/- 0.04, respectively. The strongest CS changes were observed at 0.7 logMAR (6 cycles per degree), where CS was 1.10 +/- 0.07 preoperatively and 1.06 +/- 0.09, 1.07 +/- 0.12, and 1.14 +/- 0.07, at 1 month, 3 months, and 6 months, respectively. With correction for the spectacle effect, the preoperative CS was approximately 3% higher and CS at 3 months for intermediate optotype sizes was significantly inferior to preoperatively. CONCLUSIONS: With correction of different retinal image sizes before and after LASIK (due to different spectacle refraction), the CS was significantly below the preoperative values at 1 and 3 months and approached the preoperative values at 6 months. The proposed method is potentially capable of quality monitoring and method comparisons after photorefractive surgery.

Adult↗
PubMed2005

Contrast sensitivity function in eyes with diffractive bifocal intraocular lenses.

PURPOSE: To evaluate the image quality of asymmetric Acri. Twin bifocal intraocular lenses (IOLs) (Acri.Tec) by comparing distance and near black-white contrast sensitivity function with that of the Pharmacia 811E IOL. SETTING: Department of Ophthalmology, Medical University of Vienna, Vienna, Austria. METHODS: Thirty-two eyes of 16 patients were examined after contralateral implantation of 1 Acri. Twin near-weighted 733D IOL and 1 Acri. Twin distance-weighted 737D IOL. Twenty eyes in 10 patients were examined after binocular Pharmacia 811E IOL implantation. Best corrected distance and near visual acuities were determined. Individual reading distance was recorded and corrected to 40 cm for the near contrast test (Holladay Contrast Acuity Test). Distance contrast sensitivity function was evaluated using the Acuity Max (Science 2020) computer program. RESULTS: Best corrected distance visual acuity was significantly better in patients with the 737D IOL than in those with the 733D or 811E IOLs. For distance reading with best distance correction, the 733D IOL performed better than the 737D and the 811E. Individual reading distance with the Acri. Twin IOL and 811E IOL was 33.6 cm and 34.0 cm, respectively. Best distance-corrected near contrast sensitivity function was better in eyes with the near-weighted 733D IOL. Binocular testing showed a significant difference between the 2 groups only at low-contrast values. At distance, contrast sensitivity function was better with the 737D IOL, whereas no difference was found between the 733D and the 811E IOLs. Binocular contrast sensitivity function at distance revealed statistically significantly better results in the Acri. Twin group. CONCLUSION: An asymmetric diffractive bifocal lens system was advantageous in terms of vision quality when implanted binocularly and superior to monocular stronger weighted focus compared with conventional bifocal IOLs.

Adult↗
PubMed2024

Protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique.

The advent of single-cell multi-omics sequencing technology makes it possible for researchers to leverage multiple modalities for individual cells. Here, we present a protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique called moETM. We describe steps for data preprocessing, multi-omics integration, inclusion of prior pathway knowledge, and cross-omics imputation. As a demonstration, we used the single-cell multi-omics data collected from bone marrow mononuclear cells (GSE194122) as in our original study. For complete details on the use and execution of this protocol, please refer to Zhou et al.1.

Deep Learning↗
PubMed1999

The Zavanelli maneuver: 12 years of recorded experience.

OBJECTIVE: To evaluate the applicability and safety of the Zavanelli maneuver (manual return to the vagina of the partially born but undeliverable fetus with subsequent extraction by cesarean). DATA SOURCES: MEDLINE computer database, Science Citation Index, and Index Medicus, 1985 through 1997 using the search terms Zavanelli maneuver, cephalic replacement, abdominal rescue, head entrapment, and shoulder dystocia. METHOD OF STUDY SELECTION: Efforts to return 103 partially born but undeliverable fetuses to the uterus have been reported in 30 publications since the first case was reported in 1985. All cases were accepted for review, successful or not. TABULATION, INTEGRATION, AND RESULTS: Clinically relevant features were extracted from each case report. In 92 cases, fetuses presented by the vertex. Cephalic replacement was successful in 84 of those. In 11 cases, the fetus presented by the breech. Podalic replacement was successful in all of those. Seven women suffered tissue-disruptive trauma. There were no maternal deaths or fetal injuries ascribed to the maneuver. CONCLUSION: The 92% overall success rate is remarkable for a new procedure; even more noteworthy, in most cases it was applied by operators with no experience with it, and for cephalic replacement, it was used only after conventional maneuvers had failed. Using it early in the treatment of obstructed partial vaginal delivery is recommended.

Cesarean Section↗
PubMed2000

Nanobiotechnology: the fabrication and applications of chemical and biological nanostructures.

Biology can teach the physical world of electronics, computing, materials science and manufacturing how to assemble complex functional devices and systems that operate at the molecular level. Our present capability to fabricate simple molecular tools, devices, materials and machines is primitive compared with the sophistication of nature. Nevertheless, the nanomanufacturing of 'biomimetic' devices is moving ahead strongly. Recent developments have been made in the use of biological systems in molecular self-assembly, spatial positioning, microconstruction, biocomposite fabrication, nanomachines and biocomputing.

Animals↗
PubMed2002

Representations of health concepts: a cognitive perspective.

OBJECTIVE: This paper studies the differences between controlled medical vocabularies that are designed as external artifacts and the mental concepts that are inside users' heads and used by users for reasoning, decision making, diagnosis, and treatment. DESIGN: The major theories of concept representations developed in cognitive science were reviewed, analyzed, and compared with the major controlled medical vocabularies developed in medicine. RESULTS: It was found that there are significant mismatches between controlled medical vocabularies that are designed as external artifacts and the mental concepts that are inside users' heads and used by users for reasoning, decision making, diagnosis, and treatment. CONCLUSIONS: Controlled medical vocabularies should be designed with systematical considerations of the cognitive structures and processes of the users. Without such considerations, the designed vocabularies will not be appropriate for people because they are hard to use, although they may or may not be appropriate for machine processing.

Attitude to Health↗
PubMed2002

Emerging paradigms of cognition in medical decision-making.

The limitations of the classical or traditional paradigm of decision research are increasingly apparent, even though there has been a substantial body of empirical research on medical decision-making over the past 40 years. As decision-support technology continues to proliferate in medical settings, it is imperative that "basic science" decision research develop a broader-based and more valid foundation for the study of medical decision-making as it occurs in the natural setting. This paper critically reviews both traditional and recent approaches to medical decision making, considering the integration of problem-solving and decision-making research paradigms, the role of conceptual knowledge in decision-making, and the emerging paradigm of naturalistic decision-making. We also provide an examination of technology-mediated decision-making. Expanding the scope of decision research will better enable us to understand optimal decision processes, suitable coping mechanisms under suboptimal conditions, the development of expertise in decision-making, and ways in which decision-support technology can successfully mediate decision processes.

Cognitive Science↗
PubMed2000

Transition states for surface-catalyzed chemistry.

Fluorine substituent effects have been used to probe the nature of the transition states for the several elementary reaction steps occurring on metal surfaces. The reactions described include beta-hydrogen elimination in adsorbed alkoxide and alkyl groups, coupling of alkyl groups, and dehalogenation of alkyl chloride and iodides. The substituent effect method can provide a connection between heterogeneous catalysis, surface science, and computational molecular simulation of surface reactions.

Catalysis↗
PubMed2005

Theoretical study of the interaction between selected adhesives and oxide surfaces.

We investigate the competition of the various organic components of two representative adhesive systems for reactive defect sites at model surfaces of both SiO2 and Al2O3. The reaction energies of resin monomers, curing agents, and in some cases also of additional adhesion promoters with the defects are calculated. We applied a density-functional based tight-binding method including a self-consistent correction of the Mulliken charges, which has already proven to be a useful tool for computational materials science, delivering reliable structural and energetic information.

Journal Article↗