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[Protein folding: in vitro studies].

Protein folding is a topic of fundamental interest since it concerns the mechanisms by which the genetic information is translated into the three-dimensional and functional structure of proteins. In these post-genomic times, the knowledge of the fundamental principles is required in the exploitation of the information contained in the increasing number of sequenced genomes. Protein folding also has a practical application in the understanding of different pathologies associated with protein misfolding and aggregation. Significant advances have been made ranging from the Anfinsen postulate to the "new view" which describes the folding process in terms of an energy landscape. These insights arise from both theoretical and experimental studies. Unravelling the mechanisms of protein folding represents one of the most challenging problems to day. This is an extremely active field of research involving aspects of biology, chemistry, biochemistry, computer science and physics.

Kinetics↗

PubMed2006

On the origin of genetics and beginnings of medical genetics of diseases of the kidney.

The twentieth century has been termed the century of the gene. Although the term "gene" was introduced in 1909, interest in reproduction and heredity has occupied humankind since its transition from hunter-gatherers to farmers and herders. Heredity, as it applies to diseases, began with Greek medicine. The humoral theory of the Hippocratic Corpus provided an etiological explanation for susceptibility of individuals to certain diseases well into the nineteenth century and was variously termed diathesis, temperament, and constitution. The application of the new probability math to quantify the hybridization of sweet peas by Gregor Mendel (1822-1884) in 1866 provided a scientific basis to inheritance, which had theretofore been an amalgam of scattered empirical observations. The near simultaneous publication of Origin of Species by Charles Darwin (1809-1882) in 1859 was a key catalyst in the transfer of what had been studies in plant biology into studies of populations and humans. The subsequent growth of genetics has been the outcome of interplay of technological breakthroughs in statistical analysis, cytology, biochemistry, physics, and computer science, coupled with the insightful analysis of workers in the field, several of whom have been the recipients of the Nobel Prize in medicine or chemistry since 1933. Application of these techniques to molecular biology and medical genetics is just beginning to yield insight into diseases of the kidney and provide visions of their likely therapies in the future.

Genetics, Medical↗

PubMed2000

A neurobehavioral approach for treatment of complex partial epilepsy: efficacy.

This is a retrospective study of the efficacy of a short-term comprehensive multidisciplinary neurobehavioral treatment approach for complex partial epilepsy. Eleven patients were treated intensively for five consecutive days followed by 6 months of weekly telephone contact and an additional 6 months of monitoring of seizure logs and journals. Data was analysed at least 24 months after initiation of treatment. Pre-treatment seizure frequency ranged from 1 to 15 per month. Post-treatment seizure frequency was zero per month for the nine patients who experienced less than four seizures per month prior to treatment and less than two per month for the other two patients. Additional benefits of the treatment program were improved levels of professional achievement in the arts and computer sciences and reduction of medication dosages.

Adolescent↗

PubMed2003

Ability of different physical activity monitors to detect movement during treadmill walking.

This study assessed the ability of four different activity monitors to discriminate changes in treadmill walking velocity. The relationships between walking velocity and bodily movement and between bodily movement and energy expenditure determined by indirect calorimetry (IC-EE or METs) were determined. Twenty-eight subjects walked at 3.2, 4.0, 4.8, 5.6, and 6.4 km/h (0 % grade) for 30 min on separate occasions. The Tritrac-R3D (TT), Computer Science & Applications, Inc. (CSA), and Mini-Logger (ML) activity monitors that measure bodily acceleration in one or three planes, and a Yamax Digiwalker-500 (YX) that records footsteps, were secured at the waistline of each subject. CSA monitors were also worn at the wrist and ankle. Walking velocity and bodily movement were significantly related (r = 0.89 to 0.93) for TT, CSA, ML, and YX. Importantly, changing each walking velocity produced significant changes in bodily movement that was detected by each monitor. Bodily movement and IC-EE were significantly related for TT, CSA, ML, and YX (r = 0.47 to 0.94). Compared to IC-EE, and at all walking speeds, EE was significantly overestimated by the TT, and EE was significantly underestimated by the YX. These results indicate that the activity monitors can differentiate bodily movement associated with walking at slow speeds better than they can estimate energy expenditure associated with walking at slow speeds.

Acceleration↗

PubMed2006

High-accuracy extrapolated ab initio thermochemistry. II. Minor improvements to the protocol and a vital simplification.

The recently developed high-accuracy extrapolated ab initio thermochemistry method for theoretical thermochemistry, which is intimately related to other high-precision protocols such as the Weizmann-3 and focal-point approaches, is revisited. Some minor improvements in theoretical rigor are introduced which do not lead to any significant additional computational overhead, but are shown to have a negligible overall effect on the accuracy. In addition, the method is extended to completely treat electron correlation effects up to pentuple excitations. The use of an approximate treatment of quadruple and pentuple excitations is suggested; the former as a pragmatic approximation for standard cases and the latter when extremely high accuracy is required. For a test suite of molecules that have rather precisely known enthalpies of formation {as taken from the active thermochemical tables of Ruscic and co-workers [Lecture Notes in Computer Science, edited by M. Parashar (Springer, Berlin, 2002), Vol. 2536, pp. 25-38; J. Phys. Chem. A 108, 9979 (2004)]}, the largest deviations between theory and experiment are 0.52, -0.70, and 0.51 kJ mol(-1) for the latter three methods, respectively. Some perspective is provided on this level of accuracy, and sources of remaining systematic deficiencies in the approaches are discussed.

Journal Article↗

PubMed2005

Genomes, phylogeny, and evolutionary systems biology.

With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics, and computer science are now known as systems biology. Here, I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

Animals↗

PubMed2005

The hypergraph regularity method and its applications.

Szemeredi's regularity lemma asserts that every graph can be decomposed into relatively few random-like subgraphs. This random-like behavior enables one to find and enumerate subgraphs of a given isomorphism type, yielding the so-called counting lemma for graphs. The combined application of these two lemmas is known as the regularity method for graphs and has proved useful in graph theory, combinatorial geometry, combinatorial number theory, and theoretical computer science. Here, we report on recent advances in the regularity method for k-uniform hypergraphs, for arbitrary k > or = 2. This method, purely combinatorial in nature, gives alternative proofs of density theorems originally due to E. Szemeredi, H. Furstenberg, and Y. Katznelson. Further results in extremal combinatorics also have been obtained with this approach. The two main components of the regularity method for k-uniform hypergraphs, the regularity lemma and the counting lemma, have been obtained recently: Rodl and Skokan (based on earlier work of Frankl and Rodl) generalized Szemeredi's regularity lemma to k-uniform hypergraphs, and Nagle, Rodl, and Schacht succeeded in proving a counting lemma accompanying the Rodl-Skokan hypergraph regularity lemma. The counting lemma is proved by reducing the counting problem to a simpler one previously investigated by Kohayakawa, Rodl, and Skokan. Similar results were obtained independently by W. T. Gowers, following a different approach.

Journal Article↗

PubMed1997

Approximation algorithms.

Increasing global competition, rapidly changing markets, and greater consumer awareness have altered the way in which corporations do business. To become more efficient, many industries have sought to model some operational aspects by gigantic optimization problems. It is not atypical to encounter models that capture 10(6) separate "yes" or "no" decisions to be made. Although one could, in principle, try all 2(10(6)) possible solutions to find the optimal one, such a method would be impractically slow. Unfortunately, for most of these models, no algorithms are known that find optimal solutions with reasonable computation times. Typically, industry must rely on solutions of unguaranteed quality that are constructed in an ad hoc manner. Fortunately, for some of these models there are good approximation algorithms: algorithms that produce solutions quickly that are provably close to optimal. Over the past 6 years, there has been a sequence of major breakthroughs in our understanding of the design of approximation algorithms and of limits to obtaining such performance guarantees; this area has been one of the most flourishing areas of discrete mathematics and theoretical computer science.

Journal Article↗

PubMed2001

The structure of scientific collaboration networks.

The structure of scientific collaboration networks is investigated. Two scientists are considered connected if they have authored a paper together and explicit networks of such connections are constructed by using data drawn from a number of databases, including MEDLINE (biomedical research), the Los Alamos e-Print Archive (physics), and NCSTRL (computer science). I show that these collaboration networks form "small worlds," in which randomly chosen pairs of scientists are typically separated by only a short path of intermediate acquaintances. I further give results for mean and distribution of numbers of collaborators of authors, demonstrate the presence of clustering in the networks, and highlight a number of apparent differences in the patterns of collaboration between the fields studied.

Authorship↗

PubMed2003

Recognizing specialized terminology presented through different modes.

In the present study, the authors examined how previous experience and modes of presenting information affect the recognition of terms in new, specialized terminologies. The specialized terminology used was related to orienteering. Orienteering concepts representing features found in the woods may be communicated verbally (as definitions or words) or symbolically. There were 225 participants (101 reported no orienteering experience and 122 reported varying amounts of orienteering experience; 2 did not respond to that question) who tried to identify which of 5 entities was an orienteering definition, word, or symbol. Those with orienteering experience found that recognizing the specialized terminology was significantly easier than for those without experience. Recognizing symbols was significantly more difficult than recognizing definitions or words, particularly for non-orienteers. Performance of the orienteers was similar for the three modes. Within the orienteering group, the number of years of experience and usual course difficulty attempted were significant predictors of overall test success. Applications to training of both low-level specialized terminology (e.g., used in algebra), and higher level terminology (e.g., used in computer science) are discussed.

Adult↗

PubMed2001

Relative survival: comparison of regressive models and advice for the user.

BACKGROUND: Relative survival is a method of analysis of failure-time data used to estimate the net survival. Cancer registries frequently use this method. The main regressive models are the Hakulinen and Tenkanen model, and the Esteve et al. model, which are easily used in practice thanks to their specific software (SURV and RELSURV, respectively). An assessment of the behaviour of the models is made, with the aim of giving advice for users of lifetime data in practice. METHODS: Simulations were done by respecting, then violating, the basic hypothesis supporting the theoretical foundation of these two proportional hazard models (independence of the death and censor process, proportionality of risks). For each simulation, 100 files of either 100, 1,000, or 10,000 individuals were generated to assess the behaviour of the model. RESULTS: Moderate censor rates, with or without proportionality assumption, lead to the use of the Hakulinen and Tenkanen model, especially for studies with little information. Non-proportionality of risks in the Hakulinen and Tenkanen model could be tested and analysed. If assumptions underlying the models are respected, the Esteve et al. model seems to be more precise. DISCUSSION: The choice of a model in practice depends on its performance, and on the user's knowledge of statistics and computer science. Non-proportionality of risks is common in cancer registries. In theory, non-proportionality of risks could be taken into account for both relative survival models but, for the moment, it is feasible in routine only for the Hakulinen and Tenkanen model. Characteristics of the software should also be taken into account for routine relative survival analyses.

Data Interpretation, Statistical↗

PubMed2005

Design considerations for computer-based surgical simulators.

Computers will allow the creation of novel training environments in ways that can only be imagined at the present time. The design of computer-based simulators for training of surgical procedures is a highly complex and ever-more sophisticated process. A thorough understanding of human learning principles as well as the capabilities and limitations of simulation training is required. Only development teams with expertise in medicine and surgery, computer science, hardware engineering, and simulation training will be able to create the useful surgical simulators of tomorrow.

Journal Article↗

PubMed2006

Understanding spatial diagram structure: an analysis of hierarchies, matrices, and networks.

Abstract diagrams are powerful tools for comprehension and problem solving in diverse contexts. Two studies examined the structural properties of (i.e., applicability conditions for) three interrelated spatial diagrams--hierarchies, matrices, and networks. College students from two groups with distinct educational backgrounds and learning histories--advanced computer science students and representative undergraduates--rated the diagnosticity of the hypothesized applicability conditions for each of the 3 diagrams. The results validated 24-26 of the 30 hypothesized applicability conditions and provided evidence regarding the relative importance, or diagnosticity, of the validated properties for each type of diagram. A different set of properties was identified as most highly diagnostic for each type of diagram, indicating that the three spatial diagrams are optimized to serve different representational functions: The matrix stores static information about the kind of relation that exists between pairs of items in different sets, the network conveys dynamic information by showing the local connections and global routes connecting the items being represented, and the hierarchy depicts a rigid structure of power or precedence relations among items. The quantitative and qualitative differences in representational knowledge due to educational background are discussed.

Analysis of Variance↗

PubMed1994

An exponential example for a partial digest mapping algorithm.

The partial digest problem for small-scale DNA physical mapping is known is known in computer science as the turnpike reconstruction problem. Although no polynomial algorithm for this problem is known, a simple backtracking algorithm of Skiena et al. works well in practice. Weiss raises the question whether an exponential example exists for this algorithm. This paper presents such an exponential example for this backtracking algorithm.

Algorithms↗

PubMed1988

Optimal alignments in linear space.

Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed space-saving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the new proposals, both in theory and in practice. The goal of this paper is to give Hirschberg's idea the visibility it deserves by developing a linear-space version of Gotoh's algorithm, which accommodates affine gap penalties. A portable C-software package implementing this algorithm is available on the BIONET free of charge.

Algorithms↗

PubMed1991

The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars.

No one questions the important practical contributions of computer sciences to molecular biology. It may well be that one day theoretical contributions also will become useful. One example of this type of interdisciplinary research is the attempt to construct a grammatical theory of the regulation of gene expression. In this paper, I demonstrate that context-free grammars are inadequate for the description of regulatory properties coded in the DNA. This result is supported by data available in the literature that show changes in the specificity of the recognition between regulatory proteins and their DNA targets. This result is an important limitation for the use of statistical approaches such as information theory as a source of inspiration for a theory of gene regulation. Additionally, such a demonstration gives formal justification to the search for more elaborate grammatical models in the study of gene regulation. Some basic proposals for such grammatical approach have been presented previously.

DNA↗

PubMed2004

Designing and executing scientific workflows with a programmable integrator.

MOTIVATION: As in many other fields of science, computational methods in molecular biology need to intersperse information access and algorithm execution in a computational workflow. Users often find difficulties when transferring data between data sources and applications. In most cases there is no standard solution for workflow design and execution and tailored scripting mechanisms are implemented in a case by case basis. RESULTS: In this paper, we present a general purpose 'programmable integrator' that can access information from a variety of sources in a coordinated manner. Its usefulness in complex bioinformatics applications is claimed and supported by some application examples. AVAILABILITY: Tools are freely available to non-profit educations and research institutions. Usage by commercial organizations requires a license agreement. Software requirements: Java v1.3 (http://java.sun.com), Xerces XML Parser (http://xml.apache.org/xerces-j) and Kweelt implementation of XQuery (http://kweelt.sourceforge.net/).

Algorithms↗

PubMed2006

Innovative application of a multidimensional item response model in assessing the influence of social desirability on the pseudo-relationship between self-efficacy and behavior.

This study examined multidimensional item response theory (MIRT) modeling to assess social desirability (SocD) influences on self-reported physical activity self-efficacy (PASE) and fruit and vegetable self-efficacy (FVSE). The observed sample included 473 Houston-area adolescent males (10-14 years). SocD (nine items), PASE (19 items) and FVSE (21 items) were measured with previously validated self-report instruments containing Likert-type responses. Physical activity was objectively measured using the Computer Science Application Incorporated/Manufacturing Technology Incorporated (CSA/MTI) accelerometer. Total fruit, juice and vegetable consumption was measured with a food frequency questionnaire. Correlations between self-efficacy and behaviors were minimal, regardless of controlling for SocD. However, in a simulated sample derived to demonstrate the utility of MIRT when relationships exist, the pseudo-relationships between self-efficacy and behaviors were substantially weaker after controlling for SocD. MIRT provided disattenuated correlations between SocD and self-efficacy, thereby providing more precise estimates of the real influence of SocD on the relationship between self-efficacy and behavior. However, as shown in the observed sample, more research is needed to understand the influence of SocD on the relationship between self-efficacy and behaviors for different populations and for different degrees of SocD response bias.

Child↗