Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Dynamics of the Vimentin Coiled-coil Contact Regions Involved in Filament Assembly as Revealed by Hydrogen-Deuterium Exchange*

Intermediate filaments (IF) are major constituents of the cytoskeleton of metazoan cells. They are not only responsible for the mechanical properties but also for various physiological activities in different cells and tissues. The building blocks of IFs are extended coiled-coil-forming proteins exhibiting a characteristic central α-helical domain (“rod”). The fundamental principles of the filament assembly mechanism and the network formation have been widely elucidated for the cytoplasmic IF protein vimentin. Also, a comprehensive structural model for the tetrameric complex of vimentin has been obtained by X-ray crystallography in combination with various biochemical and biophysical techniques. To extend these static data and to investigate the dynamic properties of the full-length proteins in solution during the various assembly steps, we analyzed the patterns of hydrogen-deuterium exchange in vimentin and in four variants carrying point mutations in the IF consensus motifs present at either end of the α-helical rod that cause an assembly arrest at the unit-length filament (ULF) stage. The results yielded unique insights into the structural properties of subdomains within the full-length vimentin, in particular in regions of contact in α-helical and linker segments that stabilize different oligomeric forms such as tetramers, ULFs, and mature filaments. Moreover, hydrogen-deuterium exchange analysis of the point-mutated variants directly demonstrated the active role of the IF consensus motifs in the oligomerization mechanism of tetramers during ULF formation. Ultimately, using molecular dynamics simulation procedures, we provide a structural model for the subdomain-mediated tetramer/tetramer interaction via “cross-coiling” as the first step of the assembly process.
Simulation of Losses Due to Turbulence in the Time-Varying Vocal System

Flow separation in the vocal system at the outlet of a constriction causes turbulence and a fluid dynamic pressure loss. In articulatory synthesizers, the pressure drop associated with such a loss is usually assumed to be concentrated at one specific position near the constriction and is represented by a lumped nonlinear resistance to the flow. This paper highlights discontinuity problems of this simplified loss treatment when the constriction location changes during dynamic articulation. The discontinuities can manifest as undesirable acoustic artifacts in the synthetic speech signal that need to be avoided for high-quality articulatory synthesis. We present a solution to this problem based on a more realistic distributed consideration of fluid dynamic pressure changes. The proposed method was implemented in an articulatory synthesizer where it proved to prevent any acoustic artifacts
Teaching of Writing in Psychology: A Review of Sources

What role should psychologists take in teaching writing skills? Although the traditional response to this important question has amounted to silence, this journal has produced some controversy on how to begin. Calhoun and Selby (1 979) initiated the debate by proposing a separate course with supervised experience in library and writing skills. Spiegel, Cameron, Evans and Nodine (1980), while agreeing that psychology students need instruction in writing, argued against adding another course to already overloaded curricula. Instead, they urged an integration of teaching writing skills, such as list-making and rewriting, into existing courses. Whichever approach is taken, the result will almost certainly represent progress. Consider that many of our students become psychologists in a system where, despite the lack of formal training in its rudiments, publication remains the single most important factor in hiring, tenure, promotion, and granting (Cole, 1981 ; Mahoney, 1979). Even though we are at last beginning to take an interest in writing skills, two problems remain that could dissuade the most well-intentioned of psychology teachers. One is the uncertainty of how to proceed; few of us received any formal training in writing and so we may have no ready model on which to base our teaching. Second, many teachers approach the topic of writing with ambivalent attitudes at best. This paper is aimed, then, at providing solutions for those two problems-at reviewing the ideas and techniques relevant to teaching writing in psychology, and at dispelling some of the unproductive beliefs about writing.
Modulation of Training by Single-Session Transcranial Direct Current Stimulation to the Intact Motor Cortex Enhances Motor Skill Acquisition of the Paretic Hand

Background and Purpose— Mechanisms of skill learning are paramount components for stroke recovery. Recent noninvasive brain stimulation studies demonstrated that decreasing activity in the contralesional motor cortex might be beneficial, providing transient functional improvements after stroke. The more crucial question, however, is whether this intervention can also enhance the acquisition of complex motor tasks, yielding longer-lasting functional improvements. In the present study, we tested the capacity of cathodal transcranial direct current stimulation (tDCS) applied over the contralesional motor cortex during training to enhance the acquisition and retention of complex sequential finger movements of the paretic hand. Method— Twelve well-recovered chronic patients with subcortical stroke attended 2 training sessions during which either cathodal tDCS or a sham intervention were applied to the contralesional motor cortex in a double-blind, crossover design. Two different motor sequences, matched for their degree of complexity, were tested in a counterbalanced order during as well as 90 minutes and 24 hours after the intervention. Potential underlying mechanisms were evaluated with transcranial magnetic stimulation. Results— tDCS facilitated the acquisition of a new motor skill compared with sham stimulation (P=0.04) yielding better task retention results. A significant correlation was observed between the tDCS-induced improvement during training and the tDCS-induced changes of intracortical inhibition (R2=0.63). Conclusions— These results indicate that tDCS is a promising tool to improve not only motor behavior, but also procedural learning. They further underline the potential of noninvasive brain stimulation as an adjuvant treatment for long-term recovery, at least in patients with mild functional impairment after stroke.
Adopting the Scan Approach for a Fault Tolerant Asynchronous Clock Generation Circuit

We describe the test concept for a clock generation unit that implements one instance of a distributed agreement algorithm, in hardware. The challenge of testing this unit lies in its asynchronous nature. We propose a suitable partitioning of the self-timed circuit and the introduction of two scan chains whose operation is carefully interlocked. In this way we can achieve a coverage of 100% for single stuck-at faults with very low overheads in term of speed penalty and test pins.
Interactive Implicit Modelling Based on C1 Continuous Reconstruction of Regular Grids

Our goal is to provide a kernel to allow interactive and accurate modelling of volume objects. As a first step, we present a data structure for three-dimensional fields C1 continuous in the modelling space. Regular grids storing the field values discretely are combined with a triquadratic approximation filter to define volume objects. This association of a grid and an approximation/interpolation reconstruction allows the field to be defined by a C1 continuous real function and the surface to be directly visualised from its own equation. We show how accurate and high quality interactive visualisation is obtained during the modelling process, and we explain why the visualisation is faithful to the object definition. We also describe, as an example application of our data structure, how advanced Boolean operators realised with soft or free-form transitions are performed under the influence of an interactive modelling tool.
Integrating Fuzzy Geometric Maps and Topological Maps for Robot Navigation

Autonomous mobile robots need to use spatial information about the environment in order to effectively plan and execute navigation tasks. This information can be represented at different level of abstractions, ranging from detailed geometric maps to coarse topological maps. Each level is adequate for some sub-tasks, but not for others. In this paper, we propose to use hybrid maps, patchworks of local metric maps connected into a topological network. Our hybrid maps are peculiar in that they use fuzzy sets to represent the uncertainty that affects metric information. We show how a robot can build hybrid maps from sensor data, and how it can use them in autonomous indoor navigation. We also report experiments performed on a real mobile robot that demonstrate the robustness of our approach with respect to inaccuracies in the map and noise in the sensor data.
Reachable State Spaces of Distributed Deadlock Avoidance Protocols

We present a family of efficient distributed deadlock avoidance algorithms with applications to distributed real-time and embedded systems (DREs), which subsumes previously known solutions as special instances. Then we use this family to study the reachable set of states and the allocation sequences allowed by the different protocols. This result enables a new proof method for showing freedom from deadlock of variations of deadlock avoidance protocols. Distributed deadlock avoidance is a hard problem and general solutions are considered impractical due to the high communication overhead. In previous work, however, we showed that practical solutions exist when all possible sequences of resource requests are known a priori in the form of call graphs; in this case, protocols can be constructed that perform safe resource allocation based on local data only, that is, no communication between components is required. The most basic algorithm Basic-P, performs only one operation per request using one counter per site. The protocol Live-P, which also guarantees liveness globally, needs to performs a logarithmic number of operations per request, using a linear number of counters in each site (in terms of the total ammount of resources). The family of algorithms that we introduce here, called k-Efficient-P, subsumes these as special cases. This family allows us to compare the protocols according to the set of reachable states and their legal allocation sequences. We prove that, even though the more liberal algorithms allow more concurrency, all algorithms can reach the same set of states. We capture this set of states as a network invariant.
Towards linking normative theory, communication policy and audiences in South African communication research

Abstract In this article the need to revisit South African normative media theory and communication policy against the background of fundamental audience research is emphasised. This is done in view of the postmodemist argument that ‘classic’ normative media theory is no longer suitable as a yardstick for the measurement of media performance, quality and ethics in postmodern societies, in a changing media landscape. Bearing in mind that South Africa cannot be fully characterised as a postmodernist and advanced capitalist society, but based on the nature of its First World media system functioning in a multi-cultural, multi-racial, multi-ethnic and multi-linguistic society, the tendency to see ubuntuism as a point of departure for such revision is questioned. This is done in favour of an approach in which difference and diversity are acknowledged, including the different roles the media can play and the different forms in which it can (and do) contribute to social responsibility. As far as policy research is concerned, it is emphasised that such research should be based on normative theory about the role of the media in South African society. If not, South African communication policy will continue to be fragmented and responsive to mainly technological developments and opportunities, instead of being based on communicative goals and needs. This article concludes by emphasising that both normative theory and policy should be based on fundamental audience research, which is argued to be neglected in South African communication research.
The Effects of Iron Fertilization on Carbon Sequestration in the Southern Ocean

An unresolved issue in ocean and climate sciences is whether changes to the surface ocean input of the micronutrient iron can alter the flux of carbon to the deep ocean. During the Southern Ocean Iron Experiment, we measured an increase in the flux of particulate carbon from the surface mixed layer, as well as changes in particle cycling below the iron-fertilized patch. The flux of carbon was similar in magnitude to that of natural blooms in the Southern Ocean and thus small relative to global carbon budgets and proposed geoengineering plans to sequester atmospheric carbon dioxide in the deep sea.
Tracking the Frenet-Serret frame associated to a highly maneuvering target in 3D

In this paper we consider the problem of tracking a maneuvering aircraft. The dynamical model used is based on assumptions of nearly constant tangential velocity, curvature, and torsion, of the target trajectory. Using the Frenet-Serret frame, that is, an element of the special orthogonal group SO(3) we cast the tracking problem into a filtering on Lie groups framework. We then use an invariant extended Kalman filter to estimate the various quantities involved. The resulting filter is simple to implement, and gracefully accomodates some realistic target trajectories.
Object-oriented units of measurement

Programs that manipulate physical quantities typically represent these quantities as raw numbers corresponding to the quantities' measurements in particular units (e.g., a length represented as a number of meters). This approach eliminates the possibility of catching errors resulting from adding or comparing quantities expressed in different units (as in the Mars Climate Orbiter error [11]), and does not support the safe comparison and addition of quantities of the same dimension. We show how to formulate dimensions and units as classes in a nominally typed object-oriented language through the use of statically typed metaclasses. Our formulation allows both parametric and inheritance poly-morphism with respect to both dimension and unit types. It also allows for integration of encapsulated measurement systems, dynamic conversion factors, declarations of scales (including nonlinear scales) with defined zeros, and nonconstant exponents on dimension types. We also show how to encapsulate most of the "magic machinery" that handles the algebraic nature of dimensions and units in a single meta-class that allows us to treat select static types as generators of a free abelian group.
Modeling and control of rate-dependent hysteresis for a piezo-driven micropositioning stage

Piezoelectric hysteresis usually relies on the frequency of the input signal. Most of the existing rate-dependent models use a lot of parameters to capture the rate-dependent hysteresis. In this paper, a simple rate-dependent hysteresis model is proposed to describe the frequency dependency effect of a micropositioning stage driven by piezoelectric actuators. This model is extended from an enhanced Coleman-Hodgdon (C-H) model. It has only 9 parameters and exhibits an accuracy better than 97%. The dependencies of the model parameters on the input rate are derived based on open-loop experimental tests. As inverse rate-dependent C-H model is established to construct a feedforward compensation. Experimental results demonstrate the effectiveness of the rate-dependent model over the traditional rate-independent one. The feedforward in conjunction with a PID feedback control is constructed to further attenuate the modeling errors and creep effects. Results show that the combined control scheme suppresses the tracking error by more than 8 times compared to the stand-alone PID control. It provides a sound base of practical control of the micropositioning system for micro/nano scale manipulation.
Physical Disability, Stigma, and Physical Activity in Children

Using the stereotype content model as a guiding framework, this study explored whether the stigma that able‐bodied adults have towards children with a physical disability is reduced when the child is portrayed as being active. In a 2 (physical activity status) x 2 (ability status) study design, 178 university students rated a child described in one of four vignettes on 12 dimensions of perceived warmth and competence. Results revealed a main effect of ability status on warmth (p < 0.001) such that children with a physical disability were rated significantly higher in perceived warmth than able‐bodied children, regardless of activity status (d = 0.86). Also, there was a significant interaction (p = 0.02) of ability and activity status on perceived competence, indicating that ratings of perceived competence were significantly higher for active children with a physical disability than for all other children (d = 0.54–0.64). Results suggest that physical activity should be explored as a way to mitigate the stigmatisation of children with a physical disability.
Canonical TGF‐β Pathway Activity Is a Predictor of SHH‐Driven Medulloblastoma Survival and Delineates Putative Precursors in Cerebellar Development

Medulloblastoma (MB) is the most common malignant brain tumor of childhood. Very little is known about aggressive forms of this disease, such as metastatic or recurrent MBs. In order to identify pathways involved in aggressive MB pathophysiology, we performed unbiased, whole genome microarrays on MB tumors at both the human and murine levels. Primary human MBs were compared, transcriptomically, to their patient‐matched recurrent or metastatic tumors. Expression profiling was also performed on murine tumors from two spontaneously developing MB mouse models (Ptch+/− and Smo/Smo) that present with differing clinical severities. At both the human and murine levels we identified transforming growth factor‐beta (TGF‐β) as a potential contributor to MB progression/metastasis. Smad3, a major downstream component of the TGF‐β pathway, was also evaluated using immunohistochemistry in malignant human tissues and was shown to correlate with MB metastasis and survival. Similarly, Smad3 expression during development identified a subset of cerebellar neuronal precursors as putative cells of origin for the Smad3‐positive MBs. To our knowledge, this is the first study that links TGF‐β to MB pathogenesis. Our research suggests that canonical activation of this pathway leads to better prognosis for patients.
mRNA‐dependent yeast cell‐free translation systems: Theory and practice

Introduction Preparation of a cell-free lysate Cell disruption Centrifugal fractionation of lysate Chromatographic fractionation of lysate Isolation of a cell-free lysate by glass bead lysis Translation of homologous and heterologous mRNAs Removal of endogenous mRNAs-micrococcal nuclease Conditions for translation of natural mRNA Conditions for translation of synthetic templates Assay of translation in vitro: activity and products Comparison with other yeast cell-free systems Exploitation of the yeast cell-free system Analysis of initiation of translation Analysis of elongation of translation Analysis of termination of translation Antibiotic inhibitors of translation Summary and prospects Acknowledgements References
Models of Workplace Sexual Identity Disclosure and Management

This article advances the understanding of workplace sexual identity management for lesbian, gay, and bisexual individuals by examining three conceptual frameworks recently proposed in the organizational and psychological literature (Clair, Beatty, & MacLean, 2005; Lidderdale, Croteau, Anderson, Tovar-Murray, & Davis, 2007; Ragins, 2004, 2008). After exploring two of the models that are based in stigma theory and one that is based in social cognitive theory, the article addresses new directions for understanding and studying sexual identity in the workplace through expanding and clarifying the prior conceptual work in the three models. Specifically, directions for greater clarity in definitions of identity management are suggested, recommendations for the integration and extension of perspectives on the relationship of identity management and workplace climate are made, and the need for expanding notions of sexual identity itself is promoted.
PADAC⁁2: Real-time news recommendation system with heterogeneous social footprints

Everyday in Korea, more than hundred thousands of News articles and postings are generated by either writers or users. Many people read News articles and write their opinions on the articles through major News portal systems such as Naver or Daum. However, they are sometimes time-consuming, biased, and distracted by unnecessary information. We propose a realtime News recommendation system called PADACΛ2, that is more passive process for users to browse their interests from massive News media. We propose a recommendation algorithm called HeteRoCommender based on heterogeneous source of social footprints given.
Programmers: concrete women and abstract men?

Sherry Turkle and Seymour Papert have identified a hands-on and experimental 'concrete' approach to computer programming as feminine, and as a fully formed way of knowing how to program, rather than as either a learning style or as a stage in development. This paper differentiates between concrete styles of learning how to program, and the concrete style of programming. Learning strategy is decoupled from programming style, and the hypothesis that women are more likely than men to prefer a concrete style of programming is tested by means of examining responses to practical examples of concrete and abstract styles. The responses suggest that there is no significant difference between women and men in their attitude toward a concrete style of programming.
Migrating a Digital Library to a Private Cloud

A private cloud deployment of an infrastructure as a service (IaaS) cluster is a cost effective solution to many small and intermediate digital libraries and maybe companies. As a working online digital library search engine, the physical infrastructure of CiteSeerX represents many of the clusters for a typical digital library in terms of size and functionalities. CiteSeerX used to run on a cluster consisting of eighteen loosely coupled physical machines. In this work we share the experiences and lessons learned through migrating CiteSeerX into a private cloud environment using virtualization technique. We also discuss alternative solutions including a public cloud deployment using Amazon EC2 and EBS services. We found that the private cloud via virtualization is a better model for a digital library system like CiteSeerX. We also report system status, activities and proposed variations after the new system has been running for over half a year.
Novel drug delivery system for the vesicular delivery of drug by the niosomes

Non-ionic surfactant vesicles (or niosomes) are now widely studied as alternates to liposomes. An increasing number of nonionic surfactant has been found to form vesicles, capable of entrapping hydrophilic and hydrophobic molecules. Drug delivery system using colloidal particulate carrier such as liposomes or niosomes has distinct advantages over conventional dosage forms because the particles can act as drug containing reservoirs. Modification of the particle composition or surface can adjust the affinity for the target site and/or the drug release rate. Niosomes proved to be a promising drug carrier and has potential to reduce the side effects of drugs and increased therapeutic effectiveness in various diseases. © 2011 Universal Research Publications. All rights reserved