Miracle-dz/UniFAR-FTUs huggingface dataset:
UL54-Null Pseudorabies Virus Is Attenuated in Mice but Productively Infects Cells in Culture

ABSTRACT The pseudorabies virus (PRV) UL54 homologs are important multifunctional proteins with roles in shutoff of host protein synthesis, transactivation of virus and cellular genes, and regulation of splicing and translation. Here we describe the first genetic characterization of UL54. We constructed UL54 null mutations in a PRV bacterial artificial chromosome using sugar suicide and λRed allele exchange systems. Surprisingly, UL54 is dispensable for growth in tissue culture but exhibits a small-plaque phenotype that can be complemented in trans by both the herpes simplex virus type 1 ICP27 and varicella-zoster virus open reading frame 4 proteins. Deletion of UL54 in the virus vJSΔ54 had no effect on the ability of the virus to shut off host cell protein synthesis but did affect virus gene expression. The glycoprotein gC accumulated to lower levels in cells infected with vJSΔ54 compared to those infected with wild-type virus, while gK levels were undetectable. Other late gene products, gB, gE, and Us9, accumulated to higher levels than those seen in cells infected with wild-type virus in a multiplicity-dependent manner. DNA replication is also reduced in cells infected with vJSΔ54. UL54 appears to regulate UL53 and UL52 at the transcriptional level as their respective RNAs are decreased in cells infected with vJSΔ54. Interestingly, vJSΔ54 is highly attenuated in a mouse model of PRV infection. Animals infected with vJSΔ54 survive twice as long as animals infected with wild-type virus, and this results in delayed accumulation of virus-specific antigens in skin, dorsal root ganglia, and spinal cord tissues.
The Role of the University Supervisor

The purpose of this investigation was to examine perceptions of practicum students regarding the appropriate role of their university supervisor during a field-based experience. Seventy-nine seniors responded to several open-ended questions regarding their supervisor's behavior during the field-based experience. Responses to these questions were then analyzed through a content analysis. Results indicated that students perceived that superviors should fulfill two distinct roles: provider of evaluative feedback and support person.
sTeam - Designing an integrative infrastructure for Web-based computer-supported cooperative learning

Learning is a socially embedded design process. But most of today’s hypermedia systems fail to properly support both the design-related and the social aspects of learning. Authoring and web-publishing systems aim to support the authors’ design process. Consequently, learners’ activities are confined to selecting and reading. Based on some fundamental reflections on the role of technology in learning processes, we conclude that top priority must be given to the construction of infrastructures that support cooperative learning processes if we are to properly harness technology’s potential. We present a learner-centered – wholly web-based – approach for structuring information in teams (sTeam). The key concept in sTeam is virtual space. It draws together cooperation and communication, at the same time embodying the common external memory of a (virtual) learning group. The focus is not, then, on interactive systems for individual accessing of knowledge bases, but rather on the cooperative management and structuring of distributed knowledge bases.
Accurate Performance Evaluation ,-Modeling and-Prediction of a Molecular Simulation coded with Message Passing Middleware

In distributed and vectorized computing there is a large number of highly different supercomputing platforms an application could run on. Therefore most traditional parallel codes are ill equipped to collect data about their resource usage or their behavior at run time and the corresponding data are rarely published. Only few computational scientists explore the interactions of their target platforms with their application systematically. As an improvement over the current state of the art, we propose an integrated approach to performance-evaluation, -modeling and -prediction for different platforms. Our approach relies on a combination of analytical modeling and systematic experimentation with full application runs, application kernels and some benchmarks. We outline our met hodology of performance assessment with Opal, an example code in molecular biology, developed at our institution to run in parallel on Cray J90 “Classic” Vector SMPs. Besides a detailed assessment of performance achieved on these J90s, the primary goal of our study was to find the more suitable and potentially more cost effective hardware platform for the application, in particular to check the suitability of this application for slow CoPs, SMP CoPs and fast CoPs, three flavors of Clusters of PCs built with off-the-shelf microprocessors at our computer systems laboratory. The performance assessment based on our model is much easier than porting and parallelizing the application for a new target machine and so we could also obtain and include performance estimates for a T3E-900, a high end MPP system. The predicted execution times and speedup figures indicate that a well designed cluster of PCs achieves similar if not better performance than the J90 vector processors currently used and that the computational efficiency compares favorably to the T3E-900 for that particular application code.
Location strategies for agglomeration economies

Geographically concentrated industry activity creates pools of skilled labor and specialized suppliers, and increases opportunities for knowledge spillovers. The strategic value of these agglomeration economies may vary by firm, depending upon the relative value of each economy, and upon firm and agglomeration economy traits. To better determine when a firm will be attracted to agglomeration economies, we develop a three-layer framework. The first layer assesses the relative importance of skilled labor, suppliers, and knowledge spillovers. The second layer considers whether firms can benefit from geographic concentration without co-locating. The final layer examines why some firms are more inclined to co-locate than others based upon firm and agglomeration economy traits. We test our framework on the U.S. location choices of new manufacturing entrants between 1985 and 1994 and find that firms are far more attracted to skilled labor and specialized suppliers than they are to potential knowledge spillovers, even in R&D intensive industries. We also find that leading firms will be more attracted to pools of labor, suppliers, and potential knowledge spillovers when their own contributions are less fungible, and cannot be easily leveraged for strategic advantage by proximate competitors.
Integrating Technical Advance in Mobile Devices to Enhance the Information Retrieval in Mobile Learning

It has been a long time since the wireless technologies are used in learning activities to promote the interaction between teacher and learners. The recent advance in the mobile technologies has created new chances improving the flexibility, efficiency, and functionality of the learning interaction systems. This investigation identifies the weakness of the existing systems, and integrates the emerging mobile technologies to establish an open interaction framework to effectively enhance the interaction using students faced mobile devices and public wireless infrastructure. The main work of this investigation contains: 1 a teacher-learner response model for mobile based interaction is proposed and described with state machine logic; 2 a presentation-content retrieval mechanism is designed to efficiently utilise the limited computation resource; 3 device independence and context-aware techniques are integrated to created cross-platform application with mobile device features; 4 an open media framework is built for flexible learning material distribution and question organization. A lightweight mobile oriented Web-based Wireless Response System mobile-WRS is implemented as a case study. In-house testing and classroom application of the mobile-WRS in universities demonstrate that the proposed system outperforms the peer works in usability, interface, operational efficiency, learning material distribution, results presentation, and performance assessment, etc.
Age-Related Differences in Reorganization of Functional Connectivity for a Dual Task with Increasing Postural Destabilization

The aged brain may not make good use of central resources, so dual task performance may be degraded. From the brain connectome perspective, this study investigated dual task deficits of older adults that lead to task failure of a suprapostural motor task with increasing postural destabilization. Twelve younger (mean age: 25.3 years) and 12 older (mean age: 65.8 years) adults executed a designated force-matching task from a level-surface or a stabilometer board. Force-matching error, stance sway, and event-related potential (ERP) in the preparatory period were measured. The force-matching accuracy and the size of postural sway of the older adults tended to be more vulnerable to stance configuration than that of the young adults, although both groups consistently showed greater attentional investment on the postural task as sway regularity increased in the stabilometer condition. In terms of the synchronization likelihood (SL) of the ERP, both younger and older adults had net increases in the strengths of the functional connectivity in the whole brain and in the fronto-sensorimotor network in the stabilometer condition. Also, the SL in the fronto-sensorimotor network of the older adults was greater than that of the young adults for both stance conditions. However, unlike the young adults, the older adults did not exhibit concurrent deactivation of the functional connectivity of the left temporal-parietal-occipital network for postural-suprapostural task with increasing postural load. In addition, the older adults potentiated functional connectivity of the right prefrontal area to cope with concurrent force-matching with increasing postural load. In conclusion, despite a universal negative effect on brain volume conduction, our preliminary results showed that the older adults were still capable of increasing allocation of neural sources, particularly via compensatory recruitment of the right prefrontal loop, for concurrent force-matching under the challenging postural condition. Nevertheless, dual-task performance of the older adults tended to be more vulnerable to postural load than that of the younger adults, in relation to inferior neural economy or a slow adaptation process to stance destabilization for scant dissociation of control hubs in the temporal-parietal-occipital cortex.
Ubiquitin-specific Protease 36 (USP36) Controls Neuronal Precursor Cell-expressed Developmentally Down-regulated 4-2 (Nedd4-2) Actions over the Neurotrophin Receptor TrkA and Potassium Voltage-gated Channels 7.2/3 (Kv7.2/3)*

Ubiquitination of the TrkA neurotrophin receptor in response to NGF is critical in the regulation of TrkA activation and functions. TrkA is ubiquitinated, among other E3 ubiquitin ligases, by Nedd4-2. To understand mechanistically how TrkA ubiquitination is regulated, we performed a siRNA screening to identify deubiquitinating enzymes and found that USP36 acts as an important regulator of TrkA activation kinetics and ubiquitination. However, USP36 action on TrkA was indirect because it does not deubiquitinate TrkA. Instead, USP36 binds to Nedd4-2 and regulates the association of TrkA and Nedd4-2. In addition, depletion of USP36 increases TrkA·Nedd4-2 complex formation, whereas USP36 expression disrupts the complex, resulting in an enhancement or impairment of Nedd4-2-dependent TrkA ubiquitination, respectively. Moreover, USP36 depletion leads to enhanced total and surface TrkA expression that results in increased NGF-mediated TrkA activation and signaling that augments PC12 cell differentiation. USP36 actions extend beyond TrkA because the presence of USP36 interferes with Nedd4-2-dependent Kv7.2/3 channel regulation. Our results demonstrate that USP36 binds to and regulates the actions of Nedd4-2 over different substrates affecting their expression and functions.
Learning sparse metrics via linear programming

Calculation of object similarity, for example through a distance function, is a common part of data mining and machine learning algorithms. This calculation is crucial for efficiency since distances are usually evaluated a large number of times, the classical example being query-by-example (find objects that are similar to a given query object). Moreover, the performance of these algorithms depends critically on choosing a good distance function. However, it is often the case that (1) the correct distance is unknown or chosen by hand, and (2) its calculation is computationally expensive (e.g., such as for large dimensional objects). In this paper, we propose a method for constructing relative-distance preserving low-dimensional mapping (sparse mappings). This method allows learning unknown distance functions (or approximating known functions) with the additional property of reducing distance computation time. We present an algorithm that given examples of proximity comparisons among triples of objects (object i is more like object j than object k), learns a distance function, in as few dimensions as possible, that preserves these distance relationships. The formulation is based on solving a linear programming optimization problem that finds an optimal mapping for the given dataset and distance relationships. Unlike other popular embedding algorithms, this method can easily generalize to new points, does not have local minima, and explicitly models computational efficiency by finding a mapping that is sparse, i.e. one that depends on a small subset of features or dimensions. Experimental evaluation shows that the proposed formulation compares favorably with a state-of-the art method in several publicly available datasets.
Mitochondrial Defects in cw-Diamminedichloroplatinum(II)-resistant Human Ovarian Carcinoma Cells1

We have been studying the membranes of cisplatin (DDP)-resistant 2008 human ovarian carcinoma cells (C13* cells) for alterations that may account for their decreased DDP accumulation. We now report that C13* cells have significant changes in their mitochondrial and plasma mem brane potentials and in their mitochondrial morphology. C13* cells accumulated 2.0 Â±0.1-fold more of the membrane potential marker |'l I] tetraphenylphosphonium cation (TPP*) than sensitive cells. In high K+ medium, which depolarizes the plasma membrane but not the mitochon drial membrane, |'lI] I l'I" accumulation was still 2.3 Â±0.1fold greater in resistant cells, indicating that the mitochondrial membrane potential was higher. In the presence of car bonyIcyanide /Mrifluoromethoxyphenyl hydrazone, which depolarizes the mitochondrial membrane but not the plasma membrane, | '11]1PI>+accumulation demonstrated that the plasma membrane potential in C13* cells was elevated as well. These elevations were also present in C8 cells with low-level DDP resistance. After ouabain treatment, exposure to nigericin stimulated | 'I l|TIT+ accumulation 3fold in sensitive cells but had no effect in C13* cells, indicating either that: (a) the mitochondrial pH gradient was minimal; or (b) the mito chondrial electric potential was already at a maximal level in C13* cells. Fluorescence microscopy of living cells stained with the mitochondriaspecific dye rhodamine 123 revealed that resistant cells had significant changes in their mitochondrial morphology. Electron microscopy also revealed major alterations in the cristae structure. The C13* cells, which were approximately 15-fold resistant to DDP, were S-fold hypersensitive to the mitochondria! poison rhodamine 123. We conclude that these DDP-resistant 2008 cells have an elevated plasma membrane potential and alterations in their mitochondria as indicated by their membrane potential, morphology, and sensitivity to mitochondrial poisons. These results imply that mitochondria play an important role in the cellular pharmacology of DDP.
Impaired cognitive performance and responsiveness to reward in burnout patients: Two years later

Abstract Relatively little is known about the course of symptoms in patients suffering from burnout and even less about the status of their cognitive functioning. We followed 40 burnout patients and 40 healthy controls who had participated in a previous study on the effect of motivational interventions on cognitive performance in an experimental task and repeated these measurements two years later (T2). The burnout patients, who had received psychological treatment, showed substantial improvement regarding burnout symptoms and cognitive performance at T2. The pre-post-effect size for symptom reduction was large. Importantly, cognitive performance and responsiveness to motivational interventions improved to normal levels. The patients no longer fulfilled the criteria for burnout or any other psychiatric disorder. Despite these improvements, burnout patients still experienced more exhaustion, general fatigue, depressive symptoms and general distress in comparison to healthy controls and compared to normed groups. The same pattern was observed with regard to cognitive performance: performance improved but remained below normal levels. Perceived job competence, involvement in work and responsiveness to rewards had returned to normal levels. The results indicate that although recovery from burnout is possible, symptoms may persist over the long term (here, two years). This should be taken into consideration by employers.
Database cracking: fancy scan, not poor man's sort!

Database Cracking is an appealing approach to adaptive indexing: on every range-selection query, the data is partitioned using the supplied predicates as pivots. The core of database cracking is, thus, pivoted partitioning. While pivoted partitioning, like scanning, requires a single pass through the data it tends to have much higher costs due to lower CPU efficiency. In this paper, we conduct an in-depth study of the reasons for the low CPU efficiency of pivoted partitioning. Based on the findings, we develop an optimized version with significantly higher (single-threaded) CPU efficiency. We also develop a number of multi-threaded implementations that are effectively bound by memory bandwidth. Combining all of these optimizations we achieve an implementation that has costs close to or better than an ordinary scan on a variety of systems ranging from low-end (cheaper than $300) desktop machines to high-end (above $60,000) servers.
Evaluation and improvement of internet voting schemes based on legally-founded security requirements

In recent years, several nations and private associations have introduced Internet voting as additional means to conduct elections. To date, a variety of voting schemes to conduct Internet-based elections have been constructed, both from the scientific community and industry. Because of its fundamental importance to democratic societies, Internet voting – as any other voting method – is bound to high legal standards, particularly imposing security requirements on the voting method. However, these legal standards, and resultant derived security requirements, partially oppose each other. As a consequence, Internet voting schemes cannot enforce these legally-founded security requirements to their full extent, but rather build upon specific assumptions. The criticality of these assumptions depends on the target election setting, particularly the adversary expected within that setting. Given the lack of an election-specific evaluation framework for these assumptions, or more generally Internet voting schemes, the adequacy of Internet voting schemes for specific elections cannot readily be determined. Hence, selecting the Internet voting scheme that satisfies legally-founded security requirements within a specific election setting in the most appropriate manner, is a challenging task. To support election officials in the selection process, the first goal of this dissertation is the construction of a evaluation framework for Internet voting schemes based on legally-founded security requirements. Therefore, on the foundation of previous interdisciplinary research, legally-founded security requirements for Internet voting schemes are derived. To provide election officials with improved decision alternatives, the second goal of this dissertation is the improvement of two established Internet voting schemes with regard to legally-founded security requirements, namely the Polyas Internet voting scheme and the Estonian Internet voting scheme. Our research results in five (partially opposing) security requirements for Internet voting schemes. On the basis of these security requirements, we construct a capability-based risk assessment approach for the security evaluation of Internet voting schemes in specific election settings. The evaluation of the Polyas scheme reveals the fact that compromised voting devices can alter votes undetectably. Considering surrounding circumstances, we eliminate this shortcoming by incorporating out of band codes to acknowledge voters’ votes. It turns out that in the Estonian scheme, four out of five security requirements rely on the correct behaviour of voting devices. We improve the Estonian scheme in that regard by incorporating out of band voting and acknowledgment codes. Thereby, we maintain four out of five security requirements against adversaries capable of compromising voting devices.
A New Academic Word List

This article describes the development and evaluation of a new academic word list (Coxhead, 1998), which was compiled from a corpus of 3.5 million running words of written academic text by examining the range and frequency of words outside the first 2,000 most frequently occurring words of English, as described by West (1953). The AWL contains 570 word families that account for approximately 10.0% of the total words (tokens) in academic texts but only 1.4% of the total words in a fiction collection of the same size. This difference in coverage provides evidence that the list contains predominantly academic words. By highlighting the words that university students meet in a wide range of academic texts, the AWL shows learners with academic goals which words are most worth studying. The list also provides a useful basis for further research into the nature of academic vocabulary.
On long exact (π¯, ExtΛ)-sequences in module theory

In (2003), we proved the injective homotopy exact sequence of modules by a method that does not refer to any elements of the sets in the argument, so that the duality applies automatically in the projective homotopy theory (of modules) without further derivation. We inherit this fashion in this paper during our process of expanding the homotopy exact sequence. We name the resulting doubly infinite sequence the long exact ( π ¯ , Ext Λ ) -sequence in the second variableit links the (injective) homotopy exact sequence with the long exact Ext Λ -sequence in the second variable through a connecting term which has a structure containing traces of both a π ¯ -homotopy group and an Ext Λ -group. We then demonstrate the nontriviality of the injective/projective relative homotopy groups (of modules) based on the results ofs Su (2001). Finally, by inserting three ( π ¯ , Ext Λ ) -sequences into a one-of-a-kind diagram, we establish the long exact ( π ¯ , Ext Λ ) -sequence of a triple, which is an extension of the homotopy sequence of a triple in module theory.