Miracle-dz/UniFAR-FTUs huggingface dataset:
The Human Immunodeficiency Virus Type 1 TAR RNA Upper Stem-Loop Plays Distinct Roles in Reverse Transcription and RNA Packaging

ABSTRACT The human immunodeficiency virus type 1 (HIV-1) RNA genome is flanked by a repeated sequence (R) that is required for HIV-1 replication. The first 57 nucleotides of R form a stable stem-loop structure called the transactivation response element (TAR) that can interact with the virally encoded transcription activator protein, Tat, to promote high levels of gene expression. Recently, we demonstrated that TAR is also important for efficient HIV-1 reverse transcription, since HIV-1 mutated in the upper stem-loop of TAR showed a reduced ability both to initiate and to complete reverse transcription. We have analyzed a series of HIV-1 mutant viruses to better defined the structural or sequence elements required for natural endogenous reverse transcription and packaging of virion RNA. Our results indicate that the requirement for TAR in reverse transcription is conformation dependent, since mutants with mutations that alter the upper stem-loop orientation are defective for reverse transcription initiation and have minor defects in RNA packaging. In contrast, TAR mutations that allowed the formation of alternative upper stem-loop structure greatly reduced RNA packaging but did not affect reverse transcription efficiency. These results are consistent with direct involvement of the upper stem-loop structure in packaging of genomic RNA and suggest that the TAR RNA stem-loop from nucleotide +18 to +42 interacts with other components of the reverse transcription initiation complex to promote efficient reverse transcription.
Computing Mod Without Mod

Encryption algorithms are designed to be difficult to break without knowledge of the secrets or keys. To achieve this, the algorithms require the keys to be large, with some algorithms having a recommend size of 2048-bits or more. However most modern processors only support computation on 64-bits at a time. Therefore standard operations with large numbers are more complicated to implement. One operation that is particularly challenging to implement efficiently is modular reduction. In this paper we propose a highly-efficient algorithm for solving large modulo operations; it has several advantages over current approaches as it supports the use of a variable sized lookup table, has good spatial and temporal locality allowing data to be streamed, and only requires basic processor instructions. Our proposed algorithm is theoretically compared to widely used modular algorithms, before practically compared against the state-of-the-art GNU Multiple Precision (GMP) large number library.
KSHV Genome Replication and Maintenance

Kaposi's sarcoma associated herpesvirus (KSHV) or human herpesvirus 8 (HHV8) is a major etiological agent for multiple severe malignancies in immune-compromised patients. KSHV establishes lifetime persistence in the infected individuals and displays two distinct life cycles, generally a prolonged passive latent, and a short productive or lytic cycle. During latent phase, the viral episome is tethered to the host chromosome and replicates once during every cell division. Latency-associated nuclear antigen (LANA) is a predominant multifunctional nuclear protein expressed during latency, which plays a central role in episome tethering, replication and perpetual segregation of the episomes during cell division. LANA binds cooperatively to LANA binding sites (LBS) within the terminal repeat (TR) region of the viral episome as well as to the cellular nucleosomal proteins to tether viral episome to the host chromosome. LANA has been shown to modulate multiple cellular signaling pathways and recruits various cellular proteins such as chromatin modifying enzymes, replication factors, transcription factors, and cellular mitotic framework to maintain a successful latent infection. Although, many other regions within the KSHV genome can initiate replication, KSHV TR is important for latent DNA replication and possible segregation of the replicated episomes. Binding of LANA to LBS favors the recruitment of various replication factors to initiate LANA dependent DNA replication. In this review, we discuss the molecular mechanisms relevant to KSHV genome replication, segregation, and maintenance of latency.
The role of topological constraints in the kinetics of collapse of macromolecules

It is shown that the kinetics of collapse of a polymer coil consisting of N segments after an abrupt decrease of temperature is a two-stage process if N >> Ne. The first stage takes a time ∼ N2 and leads to the peculiar state — crumpled, or fractal, globule. Any part of a chain of any scale is itself a globule in this state ; these parts are segregated from each other in space due to the non-phantomness of a chain. The chain fold in the crumpled globule is a fractal line with fractal dimension 3, equal to the space dimension. The second stage is a chain knotting ; it is realized by means of reptation-like mechanism of motion, takes a time ∼ N3 and is accompanied by an increase of globule density.
Neurostimulation périphérique et entraînement moteur en lombalgie chronique : influence sur les mécanismes corticaux et le contrôle postural

Chronic low back pain (CLBP) is associated to a faulty volitional activation of the transversus abdominis muscle (TrA). An underlying mechanism could be a maladaptive reorganization of TrA motor cortical representation (M1 ) and a correlated delay of TrA activation during anticipatory postural adjustment (APA). Training at TrA hollowing seems to improve this dysfunction. Also, new evidences suggest that repetitive peripheral magnetic stimulation (RPMS) over muscle/nerve would provide a therapeutic window to improve motor control. Our study thus combined peripheral neurostimulation over TrA and TrA hollowing training for further improving TrA activation and normalizing Ml excitability. Neurostimulation alone over TrA/IO restored intracortical inhibition whereas sham stimulation did not affect it. Combining neurostimulation and motor training improve postural control. Therefore, bilateral activation of TrA was enhanced in experimental group. Neurostimulation and motor training could be used as an adjuvant for improving APA in one session. Peripheral neurostimulation could contribute to enhance conventional motor training efficacy.
Blueprints for a Large-Scale Early Warning System

Modern aggressive types of malcode demonstrate that existing security applications are not able to neutralise them efficiently. We present a Large-Scale Early Warning System named PROTOS, which is able to gather intelligence from a large number of personal computers, acting as sensors, utilising their default security mechanisms and applications, to collect and analyse locally intercepted malicious network traffic and generate an estimation of the global malware activity.
CTSHIV: a knowledge-based system for the management of HIV-infected patients

A rule based expert system, CTSHIV (Customized Treatment Strategies for HIV) that recommends an individualized treatment strategy for HIV patients is described. Since the HIV virus mutates rapidly, a patient can develop a resistance to particular antiretroviral agents. CTSHIV addresses this problem by recommending a treatment strategy that avoids antiretroviral agents for which a resistance has developed. By monitoring the HIV virus of the patient, the treatment strategy can be switched in response to mutations of the virus. CTSHIV contains a knowledge base that encodes information from the medical literature on drug resistant mutations. It also contains additional rules that rank and weight combinations of antiretroviral agents based upon antiviral activities, redundant mechanisms of action, and overlapping toxicities. To recommend a treatment for an HIV infected patient, plasma is obtained from the patient and the RNA extracted. Segments of the HIV pol gene encoding the entire protease, reverse transcriptase and integrase proteins are amplified by RT-PCR (using a total of 3 primer pairs) and cloned. The patient's HIV sequencing data is entered into the expert program and the information is downloaded directly into the CTSHIV program. The program produces the five most effective 2, 3, and 4 drug regimens coupled with an explanation for their choice. Thus, the CTSHIV system couples efficient genetic sequencing with an expert program that recommends regimens based upon information in the current medical literature. Clinical trials are underway to evaluate the effectiveness of this approach to the management of HIV infected patients.
An Evaluation Study of Machine Learning Techniques for Identifying Spam

In this work, we investigate the use of two kinds of machine learning techniques Decision Trees and Naive Bayes applied to the problem of spam classification. We first consider building a decision tree for this purpose and then, investigate building an ensemble of decision trees using boosting. Decision trees are seen to give fairly good classification accuracy of around 92% and with the use of an ensemble, this accuracy further increases to around 95%. However, overfitting with respect to the training data is also observed in both cases. Our explorations with the Naive Bayes classifier show that it yields extremely high classification accuracy of the order of 99%. Its performance was however found to further improve by using a simpler binomial model assumption and incorporating one of the modifications to Naive Bayes suggested in (Rennieet al. 2003).
An Efficient Approach to VLSI Circuit Partitioning Using Evolutionary Algorithms

Circuit Partitioning generally formulated as graph partitioning problem is an important step in physical design of circuits. The use of Evolutionary techniques is increasingly used to solve NP complete problems i.e. Applications for logic minimization and simulation heuristics. This paper explores the evolutionary approach of genetic algorithm and propose a hybrid technique involving the strengths of the existing techniques resulting in a better partitioning and placement of circuits. It can further be extended to the Hardware/Software boundary of algorithms and can be applied to real world physical design problems.
Effect of mode-stirrer configurations on dielectric heating performance in multimode microwave applicators

In this paper, several mode-stirrer configurations are compared in order to establish their influence on the electric-field uniformity within an irradiated dielectric sample inserted in a microwave-heating applicator. Two different scenarios are evaluated with metallic sheets moving inside the multimode applicator. The different stirrer configurations are tested and compared for low-, medium-, and high-loss dielectric sample materials. Additionally, a straightforward procedure based on a generalized plane-wave approach is proposed and evaluated as a computationally efficient alternative for calculating the electric-field distribution inside materials processed in these microwave applicators with mode stirrers. Although very different electric patterns are achieved depending on stirrer geometry and sample permittivity, the plane-wave approach has been shown to provide a very good approximation for medium and high lossy dielectric materials.
Un modèle cognitif de l'interaction pour agents logiciels

Cet article presente un modele d’interaction humaine fonde sur une experimentation psychologique, ainsi qu’une architecture appelee BDI GGY reliant de facon homogene interaction et planification grâce au concept BDI. BDI GGY comprend un modele d’interaction humaine concu sur deux niveaux : 1) un modele de l’enonce s’appuyant sur la theorie des actes de langage ; 2) un modele du discours, sous la forme d’automates temporises, qui permet de tenir compte de la dynamique des conversations humaines. Les niveaux du discours et des enonces sont lies par une semantique des performatives.
The Emotional Underpinnings of Social Status Which Emotions Influence Status Attainment and Hierarchy Negotiation ?

J. T. Cheng et al. (eds.), The Psychology of Social Status, DOI 10.1007/978-1-4939-0867-7_10, © Springer Science+Business Media New York 2014 C. M. Steckler () · J. L. Tracy Department of Psychology, University of British Columbia, Vancouver, Canada e-mail: conor.steckler@psych.ubc. ca Emotions are critically important for navigating the social hierarchy. Emotions motivate people to seek and retain high status, and the nonverbal expressions that are typically displayed as part of an emotional experience communicate important status-related information to others. In this chapter, we examine the ways in which a number of distinct emotions influence status-related behaviors and outcomes. Throughout this chapter, we use the terms status and rank interchangeably, to describe one’s relative position on the social ladder (i.e., the social hierarchy), regardless of how he or she got there. In all human societies examined thus far, there are individual differences in social rank, such that some individuals have greater opportunities for resource and mate acquisition than others, or receive greater deference than others (Brown 1991; c.f. Ellis 1995). This hierarchical social structure results in clear benefits for those at the top of the hierarchy, but those at the bottom also benefit from the hierarchical system, more so than they would from abandoning social living all together (see Alexander 1974; Williams 1966). As a result, differences in social rank are a reliably occurring part of human social life.
Accessing the mind: relating metacognition to attention, memory, and cognitive function

The ability to reflect on one’s own thinking, [i]metacognition[/i], is a popular topic in consciousness research. However, our understanding of metacognition is still in its infancy and requires an examination of how metacognition relates to consciousness but also important brain functions including attention and memory. This thesis includes several empirical studies that investigate these processes in healthy and clinical populations. The overall view that emerges is metacognition and conscious awareness are closely related but distinct phenomena. Nuanced treatment of this distinction can advance basic and applied research on each process and how they relate to overall brain function.
Geographical Embeddedness Of The Firm. A Case Study Based On The Knowledge-Based View

Recently, collaborative advantage and geographical embeddedness of the firm has received growing attention in a dynamic vision of the attainment and sustainability of the firm competitive advantage. Concepts such as Industrial District and Regional Cluster have been used in these studies. However and in spite of this interest few efforts have been devoted to establish links between these competitive dimensions and theories of firm performance differences. This work has consisted on a multisource case study on the Spanish Ceramic Tile Industry. This empirical study has been focus on three major aspects: interfirm relationships, innovation process and social control. Findings have guided final discussion, linking these findings with dominant theories of the firm. The paper suggests that relational and geographical embedded strategies are related to both low transaction costs and strategic knowledge based resources.
The Polyhedral Escape Problem is Decidable

The Polyhedral Escape Problem for continuous linear dynamical systems consists of deciding, given an affine function $f: \mathbb{R}^{d} \rightarrow \mathbb{R}^{d}$ and a convex polyhedron $\mathcal{P} \subseteq \mathbb{R}^{d}$, whether, for some initial point $\boldsymbol{x}_{0}$ in $\mathcal{P}$, the trajectory of the unique solution to the differential equation $\dot{\boldsymbol{x}}(t)=f(\boldsymbol{x}(t))$, $\boldsymbol{x}(0)=\boldsymbol{x}_{0}$, is entirely contained in $\mathcal{P}$. We show that this problem is decidable, by reducing it in polynomial time to the decision version of linear programming with real algebraic coefficients, thus placing it in $\exists \mathbb{R}$, which lies between NP and PSPACE. Our algorithm makes use of spectral techniques and relies among others on tools from Diophantine approximation.
Capsule Type of Streptococcus pneumoniae Determines Growth Phenotype

The polysaccharide capsule of Streptococcus pneumoniae defines over ninety serotypes, which differ in their carriage prevalence and invasiveness for poorly understood reasons. Recently, an inverse correlation between carriage prevalence and oligosaccharide structure of a given capsule has been described. Our previous work suggested a link between serotype and growth in vitro. Here we investigate whether capsule production interferes with growth in vitro and whether this predicts carriage prevalence in vivo. Eighty-one capsule switch mutants were constructed representing nine different serotypes, five of low (4, 7F, 14, 15, 18C) and four of high carriage prevalence (6B, 9V, 19F, 23F). Growth (length of lag phase, maximum optical density) of wildtype strains, nontypeable mutants and capsule switch mutants was studied in nutrient-restricted Lacks medium (MLM) and in rich undefined brain heart infusion broth supplemented with 5% foetal calf serum (BHI+FCS). In MLM growth phenotype depended on, and was transferred with, capsule operon type. Colonization efficiency of mouse nasopharynx also depended on, and was transferred with, capsule operon type. Capsule production interfered with growth, which correlated inversely with serotype-specific carriage prevalence. Serotypes with better growth and higher carriage prevalence produced thicker capsules (by electron microscopy, FITC-dextran exclusion assays and HPLC) than serotypes with delayed growth and low carriage prevalence. However, expression of cpsA, the first capsule gene, (by quantitative RT-PCR) correlated inversely with capsule thickness. Energy spent for capsule production (incorporation of H3-glucose) relative to amount of capsule produced was higher for serotypes with low carriage prevalence. Experiments in BHI+FCS showed overall better bacterial growth and more capsule production than growth in MLM and differences between serotypes were no longer apparent. Production of polysaccharide capsule in S. pneumoniae interferes with growth in nutrient-limiting conditions probably by competition for energy against the central metabolism. Serotype-specific nasopharyngeal carriage prevalence in vivo is predicted by the growth phenotype.
Paradoxical Regulation of Human FGF21 by Both Fasting and Feeding Signals: Is FGF21 a Nutritional Adaptation Factor?

Fibroblast growth factor 21 (FGF21) has recently emerged as a metabolic hormone involved in regulating glucose and lipid metabolism in mouse, but the regulatory mechanisms and actions of FGF21 in humans remain unclear. Here we have investigated the regulatory mechanisms of the human FGF21 gene at the transcriptional level. A deletion study of the human FGF21 promoter (−1672 to +230 bp) revealed two fasting signals, including peroxisome proliferator-activated receptor α (PPARα) and glucagon signals, that independently induced human FGF21 gene transcription in mouse primary hepatocytes. In addition, two feeding signals, glucose and xylitol, also dose-dependently induced human FGF21 gene transcription and mRNA expression in both human HepG2 cells and mouse primary hepatocytes. FGF21 protein expression and secretion were also induced by high glucose stimulation. The human FGF21 promoter (−1672 to +230 bp) was found to have a carbohydrate-responsive element at −380 to −366 bp, which is distinct from the PPAR response element (PPRE). Knock-down of the carbohydrate response element binding protein by RNAi diminished glucose-induced human FGF21 transcription. Moreover, we found that a region from −555 to −443 bp of the human FGF21 promoter region exerts an important role in the activation of basic transcription. In conclusion, human FGF21 gene expression is paradoxically and independently regulated by both fasting and feeding signals. These regulatory mechanisms suggest that human FGF21 is increased with nutritional crisis, including starvation and overfeeding.
Intensive cognitive-communication rehabilitation for college-bound young adults with brain injury

Background: Young individuals with acquired brain injury (ABI) would typically be involved in higher education, yet their post-injury cognitive deficits often preclude their academic advancement. Cognitive rehabilitation (CR; Cicerone et al., 2011), the gold standard ABI treatment, consists of both impairmentand functionally-based approaches through a variety of service delivery mechanisms. Principles of experiencedependent neural plasticity suggest that the brain reorganization responsible for recovery occurs as a function of behavioral, sensory, and cognitive experiences that promote intensive, repetitive, and specific skill use in salient contexts (Kleim & Jones, 2008). Current cognitive rehabilitation approaches do not incorporate all of these tenets into one program, nor were they specifically designed as a ramp to academic success for college-age individuals with ABI who are not yet enrolled in higher education due to the severity of their cognitive deficits. Intensive Cognitive-Communication Rehabilitation (ICCR) was explicitly developed to support the young college-bound ABI population Aims: Do experimental participants
Modeling and Analysis of Workflow Based on TLA

We proposed an approach in modeling and analysis of workflow based on temporal logic of action. A workflow model is divided in to two parts: the description of scheduler as well as database updating and the description of properties, each part is expressed in a TLA formula. The analysis of properties is composed by scheduling analysis and database properties analysis and their proof process is equivalence to the verification of the implementation relationship between the model formula and the formula of its properties. Thus, established an unified framework for modeling and property analysis of workflow in deferent levels.
A Simulation Tool Chain for Investigating Future V2X-based Automotive E/E Architectures

Due to the evermore rising number of functions, current E/E architectures are more and more a vulnerable source for faults and a barrier to innovation. This situation is aggravated by the integration of new technologies like Vehicle-to-X Communication (V2XC) which form the basis for a large number of future services and applications. At the same time, this “opening” of the E/E architecture to the outside world increases potential for non-deterministic disturbances. In order to overcome the limitations of current E/E architectures, application of new design principles and methodologies is necessary. Platform-based design (PBD) is a promising solution for the development of safety-critical functions, to increase reliability and to reduce development cost. Within this context, we propose a novel extensible tool chain that targets the facilitation of exploration, validation and verification of future V2X-based automotive E/E architectures. The tool chain supports composition of heterogeneous domain-specific models by integrating a heterogeneous modeling tool with a simulation middleware and serves as starting point for the investigation of PBD concepts in the V2X context. We believe that the tool chain can support modeling and validation of future V2X-based E/E architectures. In the final paper, we will evaluate the proposed approach by means of a case study regarding validation capabilities as well as execution performance.