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Structure of the colcemid-treated PtK1 kinetochore outer plate as determined by high voltage electron microscopic tomography.

High voltage electron microscopic tomography was used to determine the organization of the kinetochore plate and its attachment to the underlying chromosome. Six reconstructions were computed from thick sections of Colcemid-treated PtK1 cells and analyzed by a number of computer graphics methods including extensive thin slicing, three-dimensional masking, and volume rendering. When viewed en-face the kinetochore plate appeared to be constructed from a scaffold of numerous 10-20-nm thick fibers or rods. Although the fibers exhibited regions of parallel alignment and hints of a lattice, they were highly variable in length, orientation and spacing. When viewed in stereo, groups of these fibers were often seen oriented in different directions at different depths to give an overall matted appearance to the structure. When viewed "on edge," the plate was 35-40 nm thick, and in thin slices many regions were tripartite with electron-opaque domains, separated by a more translucent middle layer, forming the inner and outer plate boundaries. These domains were joined at irregular intervals. In some slices, each domain appeared as a linear array of 10-20-nm dots or rods embedded in a less electron-opaque matrix, and adjacent dots within or between domains often appeared fused to form larger blocks. The plate was connected to the underlying chromosome by less densely arrayed 10-20-nm thick fibers that contacted the chromosome-facing (i.e., inner) surface of the plate in numerous patches. These patches tended to be arrayed in parallel rows perpendicular to the long axis of the chromosome. In contrast to connecting fibers, corona fibers were more uniformly distributed over the cytoplasmic-facing (i.e., outer) surface of the plate. When large portions of the reconstructions were viewed, either en-face or in successive slices parallel to the long axis of the chromosome, the edges of the plate appeared splayed into multiple "fingers" that partly encircled the primary constriction. Together these observations reveal that regions of the kinetochore outer plate contain separate structural domains, which we hypothesize to serve separate functional roles. Our three-dimensional images of the kinetochore are largely consistent with the hypothesis that the outer plate is composed of multiple identical subunits (Zinkowski, R. P., J. Meyne, and B. R. Brinkley. 1991. J. Cell Biol. 113:1091-1110).

Animals↗

The perinucleolar compartment and transcription.

The perinucleolar compartment (PNC) is a unique nuclear structure localized at the periphery of the nucleolus. Several small RNAs transcribed by RNA polymerase III and two hnRNP proteins have been localized in the PNC (Ghetti, A., S. Piñol-Roma, W.M. Michael, C. Morandi, and G. Dreyfuss. 1992. Nucleic Acids Res. 20:3671-3678; Matera, A.G., M.R. Frey, K. Margelot, and S.L. Wolin. 1995. J. Cell Biol. 129:1181- 1193; Timchenko, L.T., J.W. Miller, N.A. Timchenko, D.R. DeVore, K.V. Datar, L. Lin, R. Roberts, C.T. Caskey, and M.S. Swanson. 1996. Nucleic Acids Res. 24: 4407-4414; Huang, S., T. Deerinck, M.H. Ellisman, and D.L. Spector. 1997. J. Cell Biol. 137:965-974). In this report, we show that the PNC incorporates Br-UTP and FITC-conjugated CTP within 5 min of pulse labeling. Selective inhibition of RNA polymerase I does not appreciably affect the nucleotide incorporation in the PNC. Inhibition of all RNA polymerases by actinomycin D blocks the incorporation completely, suggesting that Br-UTP incorporation in the PNC is due to transcription by RNA polymerases II and/or III. Treatment of cells with an RNA polymerase II and III inhibitor induces a significant reorganization of the PNC. In addition, double labeling experiments showed that poly(A) RNA and some of the factors required for pre-mRNA processing were localized in the PNC in addition to being distributed in their previously characterized nucleoplasmic domains. Fluorescence recovery after photobleaching (FRAP) analysis revealed a rapid turnover of polypyrimidine tract binding protein within the PNC, demonstrating the dynamic nature of the structure. Together, these findings suggest that the PNC is a functional compartment involved in RNA metabolism in the cell nucleus.

Cell Nucleolus↗

Golgi structure in three dimensions: functional insights from the normal rat kidney cell.

Three-dimensional reconstructions of portions of the Golgi complex from cryofixed, freeze-substituted normal rat kidney cells have been made by dual-axis, high-voltage EM tomography at approximately 7-nm resolution. The reconstruction shown here ( approximately 1 x 1 x 4 microm3) contains two stacks of seven cisternae separated by a noncompact region across which bridges connect some cisternae at equivalent levels, but none at nonequivalent levels. The rest of the noncompact region is filled with both vesicles and polymorphic membranous elements. All cisternae are fenestrated and display coated buds. They all have about the same surface area, but they differ in volume by as much as 50%. The trans-most cisterna produces exclusively clathrin-coated buds, whereas the others display only nonclathrin coated buds. This finding challenges traditional views of where sorting occurs within the Golgi complex. Tubules with budding profiles extend from the margins of both cis and trans cisternae. They pass beyond neighboring cisternae, suggesting that these tubules contribute to traffic to and/or from the Golgi. Vesicle-filled "wells" open to both the cis and lateral sides of the stacks. The stacks of cisternae are positioned between two types of ER, cis and trans. The cis ER lies adjacent to the ER-Golgi intermediate compartment, which consists of discrete polymorphic membranous elements layered in front of the cis-most Golgi cisterna. The extensive trans ER forms close contacts with the two trans-most cisternae; this apposition may permit direct transfer of lipids between ER and Golgi membranes. Within 0.2 microm of the cisternae studied, there are 394 vesicles (8 clathrin coated, 190 nonclathrin coated, and 196 noncoated), indicating considerable vesicular traffic in this Golgi region. Our data place structural constraints on models of trafficking to, through, and from the Golgi complex.

Animals↗

A software tool for 2D/3D visualization and analysis of phase-space data generated by Monte Carlo modelling of medical linear accelerators.

A computer program has been developed for novel 2D/3D visualization and analysis of the phase-space parameters of Monte Carlo simulations of medical accelerator radiation beams. The software is written in the IDL language and reads the phase-space data generated in the BEAMnrc/BEAM Monte Carlo code format. Contour and colour-wash plots of the fluence, mean energy, energy fluence, mean angle, spectra distribution, energy fluence distribution, angular distribution, and slices and projections of the 3D ZLAST distribution can be calculated and displayed. Based on our experience of using it at Massachusetts General Hospital, the software has proven to be a useful tool for analysis and verification of the Monte Carlo generated phase-space files. The software is in the public domain.

Computer Graphics↗

Elucidation of causal relationships for multi-sourced activities in the human brain by directed transinformation between time series of equivalent dipoles.

Visualizing the causal relationships among multi-sourced activities in the human brain non-invasively is important for the elucidation of the processing mechanism and for clinical application of the diagnosis of disease. We will show our preliminary results of estimating equivalent dipoles to show the multi-sourced brain activities and analyse directed transinformation through time series of dipoles with three-dimensional display. First, we estimated the equivalent dipoles from evoked potentials via a three-layered concentric spherical model and two-dipole estimation. Second, we analysed the directed transinformation between two time series of the first and second dipole moments by use of the derived two dipole positions and moments as the loci and magnitude of brain activities. Therefore, we obtained bi-directional information flow between the neuronal activities localized in three-dimensional space of the brain with respect to 21-ch somatosensory evoked potentials (SEPs). Our preliminary results can be interpreted as showing that the information, calculated based on our method, flows from the first dipole cluster located in the thalamus, to the second dipole cluster located in the somatosensory area. This does not go against the neurophysiological knowledge of SEPs that the activities move from the thalamus to the somatosensory area. With the above, we show the potential possibility of realizing the elucidation of causal relationships.

Action Potentials↗

Use of runs statistics for pattern recognition in genomic DNA sequences.

In this article, the use of the finite Markov chain imbedding (FMCI) technique to study patterns in DNA under a hidden Markov model (HMM) is introduced. With a vision of studying multiple runs-related statistics simultaneously under an HMM through the FMCI technique, this work establishes an investigation of a bivariate runs statistic under a binary HMM for DNA pattern recognition. An FMCI-based recursive algorithm is derived and implemented for the determination of the exact distribution of this bivariate runs statistic under an independent identically distributed (IID) framework, a Markov chain (MC) framework, and a binary HMM framework. With this algorithm, we have studied the distributions of the bivariate runs statistic under different binary HMM parameter sets; probabilistic profiles of runs are created and shown to be useful for trapping HMM maximum likelihood estimates (MLEs). This MLE-trapping scheme offers good initial estimates to jump-start the expectation-maximization (EM) algorithm in HMM parameter estimation and helps prevent the EM estimates from landing on a local maximum or a saddle point. Applications of the bivariate runs statistic and the probabilistic profiles in conjunction with binary HMMs for pattern recognition in genomic DNA sequences are illustrated via case studies on DNA bendability signals using human DNA data.

Algorithms↗

Avatars in clinical psychology: a framework for the clinical use of virtual humans.

Early applications of virtual reality (VR) technology in psychological assessment, treatment, and research have yielded promising results. In particular, an increasing number of studies analyze the unique features of the experience made by patients during their exposure to virtual environments. However, the majority of these studies explore how patients navigate in the virtual spaces and interact with virtual objects. Only a few of them investigate the features of inhabited virtual environments, where real people and autonomous virtual humans are able to interact and to cooperate. In particular, there is a lack of discussion of the role that such autonomous virtual humans could have in VR-aided psychotherapy. The main goal of this paper is to identify a framework for future research in this area. Three levels of analysis are identified. The purpose of the first two levels is the identification of the key "physical" features (e.g., appearance, structure) and "internal" characteristics (e.g., behavior, degree of autonomy, perceptual capabilities) needed by an effective simulation. The third level is concerned with the evaluation of the interaction characteristics required for a successful relationship between the patient and the virtual human.

Behavior Therapy↗

The illusion of presence in immersive virtual reality during an fMRI brain scan.

The essence of immersive virtual reality (VR) is the illusion it gives users that they are inside the computer-generated virtual environment. This unusually strong illusion is theorized to contribute to the successful pain reduction observed in burn patients who go into VR during woundcare (www.vrpain.com) and to successful VR exposure therapy for phobias and post-traumatic stress disorder (PTSD). The present study demonstrated for the first time that subjects could experience a strong illusion of presence during an fMRI despite the constraints of the fMRI magnet bore (i.e., immobilized head and loud ambient noise).

Adult↗

How does schema theory apply to real versus virtual memories?

Schemas are cognitive frameworks that guide memory, aide in the interpretation of events, and influence how we retrieve stored memories. The purpose of this study was to explore how schemas operate in a well-known environment and to examine whether or not schemas operate differently in real versus virtual environments. Twenty-four undergraduate students from a small liberal arts college in the northeast participated for course credit. Two identical offices (a real office and a virtual office) were created and filled with eight consistent and eight inconsistent items. Each participant explored either the real office or the virtual office for 20 seconds without any knowledge that their memory would be tested. After leaving the office, participants completed a recognition task and a short demographic questionnaire. Overall sensitivity and higher confidence in recognition memory scores was found for inconsistent compared to consistent items. Greater support for the consistency effect was observed in this study and interpreted in terms of the dynamic memory model and the schema-plus-correction model. The results also demonstrate that virtual reality paradigms may produce similar outcomes compared to the real world in terms of some memory processes, but additional design factors must be considered if the researcher's goal is to create equivalent paradigms.

Adolescent↗

Three-year follow-up for virtual reality exposure for fear of flying.

Thirty participants who had been treated for aviophobia with virtual reality graded exposure therapy with physiological monitoring and visual feedback (VRGETpm), virtual reality graded exposure therapy with physiological monitoring only (VRGETno), or imaginal exposure therapy (visualization) with physiological monitoring only (IET) between January 1998 and January 1999 were contacted in January 2002 for a 3-year posttreatment follow-up assessment. Of the participants in the VRGETpm group who had flown successfully by the end of treatment, all had maintained their ability to fly at follow-up. Of the participants in the VRGETno group who had flown successfully by the end of treatment, two were no longer able to fly. Of the participants in the IET group who had flown successfully, all were still able to fly. It appears that the addition of teaching self-control via visual feedback of physiological signals may serve to maintain treatment gains in long-term follow-up.

Adult↗

Virtual reality as a pediatric pain modulation technique: a case study.

Post-surgical pain has been consistently reported in pediatrics as being difficult to manage and limiting to surgical outcomes. Pain management of children is not ideal, and some children unable to tolerate traditional pharmacological agents. Virtual reality (VR) is a new and promising form of non-pharmacologic analgesia. This case study explored the use of VR analgesia with a 16-year-old patient with cerebral palsy participating in a twice-daily physiotherapy program following Single Event Multi-Level Surgery. Over 6 days, the patient spent half of his physiotherapy sessions using VR and the other half without (order randomized). Traditional pharmacological pain management was administered throughout the trial. Using a subjective pain scale (five faces denoting levels of pain), the patient's overall pain ratings whilst in the VR (experimental) condition were 41.2% less than those in the no-VR (control) condition. This case report provides the first evidence that VR may serve as a powerful non-pharmacologic analgesic for children following surgery.

Adolescent↗

A magnet-friendly virtual reality fiberoptic image delivery system.

A custom display was built into the MR radiofrequency headcoil to project high-resolution, wide field-of-view stereographic images. Advanced stimulus presentation technologies such as the one described could potentially contribute to a better understanding of the relation between what people are thinking or experiencing, and their associated patterns of brain activity (www.vrpain.com).

Computer Graphics↗

Use of virtual reality as a distractor for painful procedures in a patient with pediatric cancer: a case study.

Virtual reality (VR) has been demonstrated as an effective tool to help people overcome a variety of anxiety disorders. In this case study, the use of VR as a distractor to alleviate pain and anxiety associated with an invasive medical procedure for a pediatric cancer patient was explored. An A-B-C-A design during four consecutive medical appointments in an outpatient oncology clinic compared no distraction (A), non-VR distraction on a computer screen (B), and VR distraction with a head set (C). Behavioral observations of distress by the researcher and reports of pain and anxiety by the patient, parent, and nurse were taken before and during the procedure. The child's pulse was monitored throughout the procedure. The findings from this case study suggest benefit from using VR distraction, as indicated by lower pain and anxiety ratings, reduced pulse, and fewer observed behavioral indices of distress. The need for larger scale studies and application of VR with younger children is discussed in the context of confirming effectiveness of this technique and providing more generalizable information about efficacy.

Analgesia↗

The role of flow experience in cyber-game addiction.

Consumer habit, an important key to repetitive consumption, is an interesting yet puzzling phenomenon. Sometimes this consumption becomes obsessive--consumers will continue to act a certain way even when they feel it is not in their best interests. However, not all consumers develop such addictions. This study uses cyber-game addiction syndrome as an analogue to trace the possible causes of consumer addiction. Results from structure equation modeling show that repetition of favorite activities has a moderate effect upon addiction, which is in line with the assertion of rational addiction theory. However, flow experience--the emotional state embracing perceptional distortion and enjoyment--shows a much stronger impact on addiction. This suggests that consumers who have experienced flow are more likely to be addicted.

Behavior, Addictive↗

Capturing behaviour for the use of avatars in virtual environments.

Avatars, representations of people in virtual environments, are subject to human control. However, for most applications, it is impractical for a person to directly control each joint in a complex avatar. Rather, people must be allowed to specify complex behaviours with simple instructions and the avatar permitted to select the correct movements in sequence to execute the instruction. This requires a variety of technologies that are currently available. Human behaviour must be captured and stored it so that it can be retrieved at a later time for use by the avatar. This has been done successfully with a variety of haptic interfaces, with visual observation of human head movements, and with verbal behaviour in natural language applications. The behaviour must be broken into atomic actions that can be sequenced with a regular grammar, and an appropriate grammar developed. Finally, a user interface must be developed so that a person can deliver instructions to the avatar.

Behavior↗

Extremal problems for topological indices in combinatorial chemistry.

Topological indices of molecular graphs are related to several physicochemical characteristics; recently, the inverse problem for some of these indices has been studied, and it has some applications in the design of combinatorial libraries for drug discovery. It is thus very natural to study also extremal problems for these indices, i.e., finding graphs having minimal or maximal index. In this paper, these questions will be discussed for three different indices, namely the sigma-index, the c-index and the Z-index, with emphasis on the sigma-index.

Combinatorial Chemistry Techniques↗

Constructing minimal ancestral recombination graphs.

By viewing the ancestral recombination graph as defining a sequence of trees, we show how possible evolutionary histories consistent with given data can be constructed using the minimum number of recombination events. In contrast to previously known methods, which yield only estimated lower bounds, our method of detecting recombination always gives the minimum number of recombination events if the right kind of rooted trees are used in our algorithm. A new lower bound can be defined if rooted trees with fewer constraints are used. As well as studying how often it actually is equal to the minimum, we test how this new lower bound performs in comparison to some other lower bounds. Our study indicates that the new lower bound is an improvement on earlier bounds. Also, using simulated data, we investigate how well our method can recover the actual site-specific evolutionary relationships. In the presence of recombination, using a single tree to describe the evolution of the entire locus clearly leads to lower average recovery percentages than does our method. Our study shows that recovering the actual local tree topologies can be done more accurately than estimating the actual number of recombination events.

Algorithms↗

Mixing realities? An application of augmented reality for the treatment of cockroach phobia.

Augmented reality (AR) refers to the introduction of virtual elements in the real world. That is, the person is seeing an image composed of a visualization of the real world, and a series of virtual elements that, at that same moment, are super-imposed on the real world. The most important aspect of AR is that the virtual elements supply to the person relevant and useful information that is not contained in the real world. AR has notable potential, and has already been used in diverse fields, such as medicine, the army, coaching, engineering, design, and robotics. Until now, AR has never been used in the scope of psychological treatment. Nevertheless, AR presents various advantages. Just like in the classical systems of virtual reality, it is possible to have total control over the virtual elements that are super-imposed on the real world, and how one interacts with those elements. AR could involve additional advantages; on one side it could be less expensive since it also uses the real world (this does not need to be modeled), and it could facilitate the feeling of presence (the sensation of being there), and reality judgment (the fact of judging the experience as real) of the person since the environment he or she is in, and what he or she is seeing is, in fact the "reality." In this paper, we present the data of the first case study in which AR has been used for the treatment of a specific phobia, cockroaches phobia. It addresses a system of AR that permits exposure to virtual cockroaches super-imposed on the real world. In order to carry out the exposure, the guidelines of Ost with respect to "one-session treatment" were followed. The results are promising. The participant demonstrated notable fear and avoidance in the behavioral avoidance test before the treatment, and not only was an important decrease in the scores of fear and avoidance observed after the treatment, but also the participant was capable of approaching, interacting, and killing live cockroaches immediately following the treatment. The results are maintained in a follow-up conducted 1 month after the termination of the treatment.

Adult↗