Computer simulations of sample preconcentration in carrier-free systems and isoelectric focusing in microchannels using simple ampholytes.

In this work, electrophoretic preconcentration of protein and peptide samples in microchannels was studied theoretically using the 1D dynamic simulator GENTRANS, and experimentally combined with MS. In all configurations studied, the sample was uniformly distributed throughout the channel before power application, and driving electrodes were used as microchannel ends. In the first part, previously obtained experimental results from carrier-free systems are compared to simulation results, and the effects of atmospheric carbon dioxide and impurities in the sample solution are examined. Simulation provided insight into the dynamics of the transport of all components under the applied electric field and revealed the formation of a pure water zone in the channel center. In the second part, the use of an IEF procedure with simple well defined amphoteric carrier components, i.e. amino acids, for concentration and fractionation of peptides was investigated. By performing simulations a qualitative description of the analyte behavior in this system was obtained. Neurotensin and [Glu1]-Fibrinopeptide B were separated by IEF in microchannels featuring a liquid lid for simple sample handling and placement of the driving electrodes. Component distributions in the channel were detected using MALDI- and nano-ESI-MS and data were in agreement with those obtained by simulation. Dynamic simulations are demonstrated to represent an effective tool to investigate the electrophoretic behavior of all components in the microchannel.

Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling

Rho guanosine triphosphatases (GTPases) control the cytoskeletal dynamics that power neurite outgrowth. This process consists of dynamic neurite initiation, elongation, retraction, and branching cycles that are likely to be regulated by specific spatiotemporal signaling networks, which cannot be resolved with static, steady-state assays. We present NeuriteTracker, a computer-vision approach to automatically segment and track neuronal morphodynamics in time-lapse datasets. Feature extraction then quantifies dynamic neurite outgrowth phenotypes. We identify a set of stereotypic neurite outgrowth morphodynamic behaviors in a cultured neuronal cell system. Systematic RNA interference perturbation of a Rho GTPase interactome consisting of 219 proteins reveals a limited set of morphodynamic phenotypes. As proof of concept, we show that loss of function of two distinct RhoA-specific GTPase-activating proteins (GAPs) leads to opposite neurite outgrowth phenotypes. Imaging of RhoA activation dynamics indicates that both GAPs regulate different spatiotemporal Rho GTPase pools, with distinct functions. Our results provide a starting point to dissect spatiotemporal Rho GTPase signaling networks that regulate neurite outgrowth.

Computer Simulation of Crowd Dynamics and Destructive Crowd Behavior

The social processes that lead to destructive behavior in celebratory crowds can be studied through an agent-based computer simulation. Riots are an increasingly common outcome of sports celebrations, and pose the potential for harm to participants, bystanders, property, and the reputation of the groups with whom participants are associated. Rioting cannot necessarily be attributed to the negative emotions of individuals, such as anger, rage, frustration and despair. For instance, the celebratory behavior (e.g., chanting, cheering, singing) during UConn’s “Spring Weekend” and after the 2004 NCAA Championships resulted in several small fires and overturned cars. Further, not every individual in the area of a riot engages in violence, and those who do, do not do so continuously. Instead, small groups carry out the majority of violent acts in relatively short-lived episodes. Agent-based computer simulations are an ideal method for modeling complex group-level social phenomena, such as celebratory gatherings and riots, which emerge from the interaction of relatively “simple” individuals. By making simple assumptions about individuals’ decision-making and behaviors and allowing actors to affect one another, behavioral patterns emerge that cannot be predicted by the characteristics of individuals. The computer simulation developed here models celebratory riot behavior by repeatedly evaluating a single algorithm for each individual, the inputs of which are affected by the characteristics of nearby actors. Specifically, the simulation assumes that (a) actors possess 1 of 5 distinct social identities (group memberships), (b) actors will congregate with actors who possess the same identity, (c) the degree of social cohesion generated in the social context determines the stability of relationships within groups, and (d) actors’ level of aggression is affected by the aggression of other group members. Not only does this simulation provide a systematic investigation of the effects of the initial distribution of aggression, social identification, and cohesiveness on riot outcomes, but also an analytic tool others may use to investigate, visualize and predict how various individual characteristics affect emergent crowd behavior.

Advanced Protein Modeling Method: Benchmarking and Applications in Computer-Aided Drug Discovery

Development of homology modeling methods will remain an area of active research. These methods aim to develop and model increasingly accurate three-dimensional structures of yet uncrystallized therapeutically relevant proteins e.g. Class A G-Protein Coupled Receptors. Incorporating protein flexibility is one way to achieve this goal. Here, I will discuss the enhancement and validation of the ligand-steered modeling, originally developed by Dr. Claudio Cavasotto, via cross modeling of the newly crystallized GPCR structures. This method uses known ligands and known experimental information to optimize relevant protein binding sites by incorporating protein flexibility. The ligand-steered models were able to model, reasonably reproduce binding sites and the co-crystallized native ligand poses of the β2 adrenergic and Adenosine 2A receptors using a single template structure. They also performed better than the choice of template, and crude models in a small scale high-throughput docking experiments and compound selectivity studies. Next, the application of this method to develop high-quality homology models of Cannabinoid Receptor 2, an emerging non-psychotic pain management target, is discussed. These models were validated by their ability to rationalize structure activity relationship data of two, inverse agonist and agonist, series of compounds. The method was also applied to improve the virtual screening performance of the β2 adrenergic crystal structure by optimizing the binding site using β2 specific compounds. These results show the feasibility of optimizing only the pharmacologically relevant protein binding sites and applicability to structure-based drug design projects.

Decomposition of $\rm R\times C$ contingency table chi -square: Application to binned DNA fragment size data and population structure analysis

The purpose of this research is to develop a new statistical method to determine the minimum set of rows (R) in a R x C contingency table of discrete data that explains the dependence of observations. The statistical power of the method will be empirically determined by computer simulation to judge its efficiency over the presently existing methods. The method will be applied to data on DNA fragment length variation at six VNTR loci in over 72 populations from five major racial groups of human (total sample size is over 15,000 individuals; each sample having at least 50 individuals). DNA fragment lengths grouped in bins will form the basis of studying inter-population DNA variation within the racial groups are significant, will provide a rigorous re-binning procedure for forensic computation of DNA profile frequencies that takes into account intra-racial DNA variation among populations. ^

The computer paradigm in vocational guidance

The technological advances in last decades have transformed the external resources of Vocational Counseling, Occupational Information and assessment of clients. Most computer systems follow a behaviorist-cognitive approach. However, the use of vocational counseling software is not exclusive to one conceptual approach. Computers are introduced in education from primary school; counselors and other educators are expected to use those systems. The attitude of counselors ranges from enthusiastic acceptance to complete refusal. Many counselors fear that computers will replace them. An underlying theory holds that counseling is based on the counselor-client interaction. A computer- client interaction cannot be considered vocational counseling. Counseling has five basic aims: prevention, assistance, education and development, service of diverse groups and research. The most relevant trends in computer-based counseling are: tests and questionnaires based on computers, adaptive development, computarized information, vocational counseling systems and research. Basic aims and the potential role of computers in achieving them are discussed. Present vocational counselors can use the technology of computers to link the past of our profession to its promising future. In view of these premises we have developed two computer systems that assist the vocational counseling process: "Professional Interests Questionnaire, Computer Version", and "Computer-based System of Vocational Counseling".

The computer paradigm in vocational guidance

The technological advances in last decades have transformed the external resources of Vocational Counseling, Occupational Information and assessment of clients. Most computer systems follow a behaviorist-cognitive approach. However, the use of vocational counseling software is not exclusive to one conceptual approach. Computers are introduced in education from primary school; counselors and other educators are expected to use those systems. The attitude of counselors ranges from enthusiastic acceptance to complete refusal. Many counselors fear that computers will replace them. An underlying theory holds that counseling is based on the counselor-client interaction. A computer- client interaction cannot be considered vocational counseling. Counseling has five basic aims: prevention, assistance, education and development, service of diverse groups and research. The most relevant trends in computer-based counseling are: tests and questionnaires based on computers, adaptive development, computarized information, vocational counseling systems and research. Basic aims and the potential role of computers in achieving them are discussed. Present vocational counselors can use the technology of computers to link the past of our profession to its promising future. In view of these premises we have developed two computer systems that assist the vocational counseling process: "Professional Interests Questionnaire, Computer Version", and "Computer-based System of Vocational Counseling".

The computer paradigm in vocational guidance

The technological advances in last decades have transformed the external resources of Vocational Counseling, Occupational Information and assessment of clients. Most computer systems follow a behaviorist-cognitive approach. However, the use of vocational counseling software is not exclusive to one conceptual approach. Computers are introduced in education from primary school; counselors and other educators are expected to use those systems. The attitude of counselors ranges from enthusiastic acceptance to complete refusal. Many counselors fear that computers will replace them. An underlying theory holds that counseling is based on the counselor-client interaction. A computer- client interaction cannot be considered vocational counseling. Counseling has five basic aims: prevention, assistance, education and development, service of diverse groups and research. The most relevant trends in computer-based counseling are: tests and questionnaires based on computers, adaptive development, computarized information, vocational counseling systems and research. Basic aims and the potential role of computers in achieving them are discussed. Present vocational counselors can use the technology of computers to link the past of our profession to its promising future. In view of these premises we have developed two computer systems that assist the vocational counseling process: "Professional Interests Questionnaire, Computer Version", and "Computer-based System of Vocational Counseling".

How Blended Learning Reduce Underachievement in Higher Education: An Experience in Teaching Computer Sciences.

This paper presents a blended learning approach and a study evaluating instruction in a software engineering-related course unit as part of an undergraduate engineering degree program in computing. In the past, the course unit had a lecture-based format. In view of student underachievement and the high course unit dropout rate, a distance-learning system was deployed, where students were allowed to choose between a distance-learning approach driven by a moderate constructivist instructional model or a blended-learning approach. The results of this experience are presented, with the aim of showing the effectiveness of the teaching/learning system deployed compared to the lecture-based system previously in place. The grades earned by students under the new system, following the distance-learning and blended-learning courses, are compared statistically to the grades attained in earlier years in the traditional face-to-face classroom (lecture-based) learning.

Application of virtual certification techniques to vehicle design and track maintenance

Virtual certification partially substitutes by computer simulations the experimental techniques required for rail vehicle certification. In this paper, several works were these techniques were used in the vehicle design and track maintenance processes are presented. Dynamic simulation of multibody systems was used to virtually apply the EN14363 standard to certify the dynamic behaviour of vehicles. The works described are: assessment of a freight bogie design adapted to meter-gauge, assessment of a railway track layout for a subway network, freight bogie design with higher speed and axle load, and processing of the data acquired by a track recording vehicle for track maintenance.

Integrated learning of computer applications for production engineering

A high productivity rate in Engineering is related to an efficient management of the flow of the large quantities of information and associated decision making activities that are consubstantial to the Engineering processes both in design and production contexts. Dealing with such problems from an integrated point of view and mimicking real scenarios is not given much attention in Engineering degrees. In the context of Engineering Education, there are a number of courses designed for developing specific competencies, as required by the academic curricula, but not that many in which integration competencies are the main target. In this paper, a course devoted to that aim is discussed. The course is taught in a Marine Engineering degree but the philosophy could be used in any Engineering field. All the lessons are given in a computer room in which every student can use each all the treated software applications. The first part of the course is dedicated to Project Management: the students acquire skills in defining, using Ms-PROJECT, the work breakdown structure (WBS), and the organization breakdown structure (OBS) in Engineering projects, through a series of examples of increasing complexity, ending up with the case of vessel construction. The second part of the course is dedicated to the use of a database manager, Ms-ACCESS, for managing production related information. A series of increasing complexity examples is treated ending up with the management of the pipe database of a real vessel. This database consists of a few thousand of pipes, for which a production timing frame is defined, which connects this part of the course with the first one. Finally, the third part of the course is devoted to the work with FORAN, an Engineering Production package of widespread use in the shipbuilding industry. With this package, the frames and plates where all the outfitting will be carried out are defined through cooperative work by the studens, working simultaneously in the same 3D model. In the paper, specific details about the learning process are given. Surveys have been posed to the students in order to get feed-back from their experience as well as to assess their satisfaction with the learning process. Results from these surveys are discussed in the paper

A computer vision approach for weeds identification through Support Vector Machines

This paper outlines an automatic computervision system for the identification of avena sterilis which is a special weed seed growing in cereal crops. The final goal is to reduce the quantity of herbicide to be sprayed as an important and necessary step for precision agriculture. So, only areas where the presence of weeds is important should be sprayed. The main problems for the identification of this kind of weed are its similar spectral signature with respect the crops and also its irregular distribution in the field. It has been designed a new strategy involving two processes: image segmentation and decision making. The image segmentation combines basic suitable image processing techniques in order to extract cells from the image as the low level units. Each cell is described by two area-based attributes measuring the relations among the crops and weeds. The decision making is based on the SupportVectorMachines and determines if a cell must be sprayed. The main findings of this paper are reflected in the combination of the segmentation and the SupportVectorMachines decision processes. Another important contribution of this approach is the minimum requirements of the system in terms of memory and computation power if compared with other previous works. The performance of the method is illustrated by comparative analysis against some existing strategies.

An abstract machine based execution model for computer architecture design and efficient implementation of logic programs in parallel.

The term "Logic Programming" refers to a variety of computer languages and execution models which are based on the traditional concept of Symbolic Logic. The expressive power of these languages offers promise to be of great assistance in facing the programming challenges of present and future symbolic processing applications in Artificial Intelligence, Knowledge-based systems, and many other areas of computing. The sequential execution speed of logic programs has been greatly improved since the advent of the first interpreters. However, higher inference speeds are still required in order to meet the demands of applications such as those contemplated for next generation computer systems. The execution of logic programs in parallel is currently considered a promising strategy for attaining such inference speeds. Logic Programming in turn appears as a suitable programming paradigm for parallel architectures because of the many opportunities for parallel execution present in the implementation of logic programs. This dissertation presents an efficient parallel execution model for logic programs. The model is described from the source language level down to an "Abstract Machine" level suitable for direct implementation on existing parallel systems or for the design of special purpose parallel architectures. Few assumptions are made at the source language level and therefore the techniques developed and the general Abstract Machine design are applicable to a variety of logic (and also functional) languages. These techniques offer efficient solutions to several areas of parallel Logic Programming implementation previously considered problematic or a source of considerable overhead, such as the detection and handling of variable binding conflicts in AND-Parallelism, the specification of control and management of the execution tree, the treatment of distributed backtracking, and goal scheduling and memory management issues, etc. A parallel Abstract Machine design is offered, specifying data areas, operation, and a suitable instruction set. This design is based on extending to a parallel environment the techniques introduced by the Warren Abstract Machine, which have already made very fast and space efficient sequential systems a reality. Therefore, the model herein presented is capable of retaining sequential execution speed similar to that of high performance sequential systems, while extracting additional gains in speed by efficiently implementing parallel execution. These claims are supported by simulations of the Abstract Machine on sample programs.