Miracle-dz/UniFAR-FTUs huggingface dataset:
The type three secreted effector SipC regulates the trafficking of PERP during Salmonella infection

abstract Salmonella enterica Typhimurium employs type III secreted effectors to induce cellular invasion and pathogenesis. We previously reported the secreted effector SipA is in part responsible for inducing the apical accumulation of the host membrane protein PERP, a host factor we have shown is key to the inflammatory response induced by Salmonella. We now report that the S. Typhimurium type III secreted effector SipC significantly contributes to PERP redistribution to the apical membrane surface. To our knowledge, this is the first report demonstrating a role for SipC in directing the trafficking of a host membrane protein to the cell surface. In sum, facilitation of PERP trafficking appears to be a result of type III secreted effector-mediated recruitment of vesicles to the apical surface. Our study therefore reveals a new role for SipC, and builds upon previous reports suggesting recruitment of vesicles to the cell surface is important for Salmonella invasion.
A group signature scheme with unbounded message-dependent opening

Group signature with message-dependent opening (GS-MDO) is a kind of group signature in which only the signers who have created group signatures on problematic messages will be identified. In the previous GS-MDO scheme, however, the number of problematic messages is bounded owing to a limitation of the Groth-Sahai proofs. In this paper, we propose the first GS-MDO scheme with the unbounded-MDO functionality in the random oracle model. Our unbounded GS-MDO scheme is based on the short group signature scheme proposed by Boneh, Boyen, and Shacham and the Boneh-Franklin identity-based encryption scheme. To combine these building blocks and to achieve CCA-anonymity, we also construct a special type of multiple encryption. This technique yields an efficient construction compared with the previous bounded GS-MDO scheme: the signature of our scheme contains about 16 group elements (3630 bits), whereas that of the previous scheme has about 450 group elements (75820 bits).
Stability on multi-robot formation with dynamic interaction topologies

The formation task achieved by multiple robots is a tough issue because of the limitations of the sensing abilities and communicating functions among them. Due to an individual robot can only handle local information, an adjacency graph is applied to describe the relationship among multiple robots. Since the relative positions among robots change from time to time, the topology graph describing information exchange is variant. A local control strategy is proposed for an individual robot based on NN control with robust terms. It has been proved that under an assumption of adjacency matrices associated with interaction graph being always connected, the system will converge based on the individual control strategy and multiple robots can construct an unique formation even if interaction topology is variant.
Learning semantic categories for 3D model retrieval

A shape similarity judgment among a pair of 3D models is often influenced by their semantics, in addition to their shapes. If we could somehow incorporate semantic knowledge into a "shape similarity" comparison method, retrieval performance of a shape-based 3D model retrieval system could be improved. This paper presents a 3D model retrieval method that successfully incorporates semantic information from human-made categories (labels) in a training database. Our off-line, 2-stage semi-supervised approach learns efficiently from a small set of labeled models. The method first performs unsupervised learning from a large set of unlabeled 3D models to find a non-linear subspace on which the shape features are distributed. It then performs a supervised learning from a much smaller set of labeled 3D models to learn multiple semantic categories at once. Our experimental evaluation showed that the retrieval performance using proposed method is significantly higher than those of both supervised-only and unsupervised-only learning methods.
PW-MMAC: Predictive-Wakeup Multi-channel MAC Protocol for Wireless Sensor Networks

Challenges faced by Medium access control (MAC) protocols for Wireless Sensor Networks (WSNs) include energy efficient operation and bandwidth limitations. Low duty cycle MAC conserves energy but at the same time it affects delivery ratio and latency. Use of multiple channels can improve the throughput and latency by alleviating the bandwidth limitations. This paper presents the design and performance evaluation of PW-MMAC (Predictive Wake up Multi-Channel MAC) protocol which addresses these challenges by coupling the benefits of multiple channels with adaptive duty cycling and predictive wake-up mechanism. PW-MMAC significantly improves energy efficiency and channel utilization by adapting dynamically to varying network conditions without the need of a dedicated control channel. Implemented in ns-2, PWMMAC shows significant improvement over other duty cycle MAC protocols. PW-MMAC achieves lowest duty cycle, 100% delivery ratio, and lowest packet delivery latency in different network scenarios in both multi-hop and single-hop clique, grid, and random networks.
Participación juvenil y activismo digital. Una introducción a una nueva agenda de estudio

espanolSin caer en un discurso apocaliptico ni tampoco apologetico, las TIC estan cambiando la manera en que los individuos se comunican y se relacionan. La infraestructura tecnologica de los medios sociales permite nuevas y variadas formas de interaccion social y de participacion. Este intercambio dinamico entre individuos, grupos e instituciones es lo que genera una red social. La red no la hace la plataforma o el medio, sino los agentes sociales en el dia a dia, al participar de este intercambio de bienes y expresiones simbolicos y/o materiales. Sucesos como la Primavera Arabe, el movimiento de los Indignados en Espana, el movimiento Ocuppy Wall Street o en el caso de Mexico, el movimiento #Yosoy132, son ejemplos de como plataformas digitales como facebook y twitter, pueden representar nuevas maneras para la organizacion y la accion politica. Todos estos escenarios representan una oportunidad para replantear el papel de los jovenes como agentes de cambio. EnglishWithout being apologetic nor apocalyptic, ICT are changing the way individuals communicate and relate to each other. The technological infrastructure of social media allows new and varied forms of social interaction and participation. This dynamic exchange between individuals, groups and institutions is what creates a social network. The Network is noti build by the platform or the media, is constructed by their stakeholders every day, as they participate in the exchange of goods and symbolic expressions and/or materials. Events such as the Arab spring, the movement of the “Indignados” at Spain, Ocuppy Wall Street or in the case of Mexico, the #Yosoy132 movement, are examples of how social media platforms such as facebook and twitter, can represent new ways for the organization and political action. All these scenarios represent an opportunity to rethink the role of young people as agents of change.
Structural basis of DNA recognition by PCG2 reveals a novel DNA binding mode for winged helix-turn-helix domains

The MBP1 family proteins are the DNA binding subunits of MBF cell-cycle transcription factor complexes and contain an N terminal winged helix-turn-helix (wHTH) DNA binding domain (DBD). Although the DNA binding mechanism of MBP1 from Saccharomyces cerevisiae has been extensively studied, the structural framework and the DNA binding mode of other MBP1 family proteins remains to be disclosed. Here, we determined the crystal structure of the DBD of PCG2, the Magnaporthe oryzae orthologue of MBP1, bound to MCB–DNA. The structure revealed that the wing, the 20-loop, helix A and helix B in PCG2–DBD are important elements for DNA binding. Unlike previously characterized wHTH proteins, PCG2–DBD utilizes the wing and helix-B to bind the minor groove and the major groove of the MCB–DNA whilst the 20-loop and helix A interact non-specifically with DNA. Notably, two glutamines Q89 and Q82 within the wing were found to recognize the MCB core CGCG sequence through making hydrogen bond interactions. Further in vitro assays confirmed essential roles of Q89 and Q82 in the DNA binding. These data together indicate that the MBP1 homologue PCG2 employs an unusual mode of binding to target DNA and demonstrate the versatility of wHTH domains.
Design of energy-efficient, adaptable throughput systems at near/sub-threshold voltage

Voltage scaling has been a prevalent method of saving energy for energy-constrained applications. However, current technology trends which shrink transistors sizes exacerbate process variation effects in voltage-scaled systems. Large variations in transistor parameters result in high variation in performance and power across the chip. These effects, if ignored at the design, stage, will result in unpredictable behavior when deployed in the field. In this article, we leverage the benefits of voltage scaling methodology for obtaining energy efficiency and compensate for the loss in throughput by exploiting parallelism present in the various DSP designs. We show that such a hybrid method consumes 8%--77% less power, compared to simple dynamic voltage scaling over different throughputs. We study this system architecture in two different workload environments: static and dynamic. We show that to achieve the highest level of energy efficiency, the number of cores and the operating voltages vary widely between a BASE design versus a process variation-aware (PVA) design. We further demonstrate that the PVA design enjoys an average of 26.9% and 51.1% reduction in energy consumption for the static and dynamic designs, respectively. Since different cores will have a wide range of speeds at operating voltages close to near/sub-thresholds due to process variation, we gather characteristic behavior of each core. With knowledge of the core speeds, we can further increase the energy efficiency. Furthermore, in this article, we show that of this methodology will be 49.3% more energy efficient, compared to that building the system with no knowledge about the characteristics of each core.
Relative and absolute term selection criteria: a comparative study for English and Japanese IR

Pseudo-relevance feedback (PRF) is an unreliable method, as it does not use any true relevance information. Typically, it extracts candidate expansion terms from the top R documents initially retrieved, sorts them using a term selection criterion, and adds the top T terms to the initial query. In [9], we explored exbile PRF for selecting appropriate R and/or T for each request to enhance the reliability of PRF. Although this did not show any substantial gain over traditional PRF, the results suggested that the top 10 average document scores in the initial ranked output and the number of initial search terms may be useful clues for predicting R and/or T . Since then, we tackled a simpler problem, of deciding whether PRF should be applied or not: using the above two statistics as predictors, we applied quadratic discriminant analysis to separate requests that PRF cannot improve from others. However, as the requests could not be discriminated accurately, we realised that even this \binary decision" version of the exible PRF problem is challenging. Thus this paper explores an alternative way of improving the reliability of PRF, namely, to enhance the term selection criterion itself. We re ne an existing criterion based on regression analysis, and compare various criteria using English and Japanese test collections of respectable size.
Aberrant pulvinar effective connectivity in generalized social anxiety disorder

AbstractRecent neuroimaging findings in general social anxiety disorder (gSAD) have extended our understanding of the neural mechanisms of gSAD beyond an amygdala-centric fear-based hyperactivity model to include other brain regions and networks relevant to salient cues. In particular, higher order areas compromising visual networks that process emotional and social information have been implicated. The pulvinar anchors this network and is a key regulatory node that mediates complex sensory inputs and the integration between limbic and frontal brain systems. However, the role of the pulvinar and specifically alteration of its effective connectivity with the rest of the brain has not been examined in the pathophysiology of gSAD, a disorder characterized by aberrant socio-emotional processing. The main aim of this study was to examine the pulvinar network effective connectivity in gSAD. In this study, we recruited 21 individuals with gSAD and 19 demographically matched healthy controls (HC), who performed an emotional face processing task while brain activity was recorded using functional magnetic resonance imaging (fMRI). To examine pulvinar-based network dynamics, Granger causality (GC) based effective connectivity (EC) analysis was applied on fMRI data to compare gSAD and HC. The EC analysis revealed heightened casual influential dynamics between pulvinar in higher order visual and frontal regions in gSAD. In conclusion, these preliminary data suggest a novel network-based cortico-pulvino-cortical neural mechanism in the pathophysiology of gSAD.
A multiresolution framework for volume rendering

In dieser Arbeit wurde ein genereller hierarchischer Ansatz zur Visualisierung skalarer Volumendaten entwickelt. Dieser ermoglicht die direkte Visualisierung komprimierter Daten, die Beschleunigung des Darstellungsvorgangs und die Extraktion und Hervorhebung der wesentlichen Strukturen. Grundlegende Konzepte der Multiskalenanalyse mittels hierarchischer Basisfunktionen wurden hierzu verwendet und entsprechend den Anforderungen erweitert. Insbesondere resultierte die Arbeit in speziellen Verfahren zur Vorverarbeitung und Darstellung zeitvarianter Datensequenzen. Sowohl fur die Datenanalyse als auch fur die Bildsynthese wurden Parallelisierungskonzepte entworfen und implementiert. Die integrierte Analyse und Darstellung komplexer skalarer Volumendaten wurde durch diese Entwicklungen ermoglicht.
Regulatory Analysis for Exploring Human Disease Progression

A crucial goal in post-genomic research is unravelling the regulatory network of transcription factors and their target genes. This is especially important in the human genome where many TFs are involved in disease progression. Similarly to our previous work in the yeast genome, machine learning methods can be applied to known examples of target genes to create decision rules that aid in the identification of new targets. Using targets in publicly available databases as training examples, classifiers have been built and tested for 153 human TFs. These classifiers base their decisions upon the integration of three types of sequence information: composition, conservation, and overrepresentation. Overall, 33 TF classifiers achieve a precision greater than 60%. Many high confidence predictions are made for all TFs, and all targets are made available for download on our web server and as supplementary information. To highlight the power of this method we briefly discuss the regulator Oct4, a known marker for stem cells. Results for the TF Wt1 are then discussed in detail, showing that many of the predictions share functions with the known targets. Since Wt1 and its targets are intimately involved in development of Wilms’ tumor, new models for its action in cancer are proposed. We show that our predictions for Wt1 are statistically enriched for genes which fall into specific chromosomal loci known to be associated with Wilms’ tumor. This finding suggests new models for Wilms’ tumor progression where dysregulation in these regions is important for disease progression, either through loss of Wt1 or loss of the associated region. Genes in significant loci include several oncogenes and tumor suppressors which are candidates for involvement in cancer progression and may partially explain the observed clinical and biochemical data on this cancer. The anti-apoptotic effects of Wt1 are also discussed along with several new target genes, including bax and pde4b, which may help mediate this effect. Finally, motif discovery is used to propose a new binding motif for Wt1 which will be useful in later site identification. SVM-based classifiers provide a comprehensive platform for analysis of regulatory networks, and the results can be used to make new hypothesis for disease progression in humans. Obvious extensions of this work include incorporating new kinds of data, and expanding the analysis to more TFs when binding data becomes available.
Quantum Deformed Canonical Transformations, W_{\infty}-algebras and Unitary Transformations

We investigate the algebraic properties of the quantum counterpart of the classical canonical transformations using the symbol-calculus approach to quantum mechanics. In this framework we construct a set of pseudo-differential operators which act on the symbols of operators, i.e., on functions defined over phase-space. They act as operatorial left- and right- multiplication and form a $W_{\infty}\times W_{\infty}$- algebra which contracts to its diagonal subalgebra in the classical limit. We also describe the Gel'fand-Naimark-Segal (GNS) construction in this language and show that the GNS representation-space (a doubled Hilbert space) is closely related to the algebra of functions over phase-space equipped with the star-product of the symbol-calculus.
A simple and rapid method to assay triacylglycerol in cells and tissues Published, JLR Papers in Press, August 23, 2007.

We have developed a reliable, rapid, and economical assay for the quantification of triacylglycerol (TG) in cells and animal tissues. In a few hours, this assay quantifies microgram amounts of TG from tens or even hundreds of samples. The protocol includes an organic extraction to partition TG away from proteins and other hydrophilic molecules found in cells and tissues that may interfere with the colorimetric enzyme-linked TG detection method. In addition, this assay is economical, as no expensive reagents, supplies, or equipment are needed. Another benefit of this assay is that it does not require environmentally unfriendly halogenated solvents.
Implicit Self-Esteem as a Potential Link between Gender Identity Threat in Males and Attitudes towards Women in Managerial Positions

This experiment investigated the effects of male gender threat on implicit self-esteem, and how that in turn may influence prejudices towards women in managerial positions. The Self-Esteem Implicit Association Test (IAT) was administered to 82 male undergraduate students prior to and after a gender threat intervention using false results on a measure of gender roles. After the gender threat intervention and IAT, respondents answered the Women as Managers Scale. Results showed that participants who received the gender threat intervention did not show significant differences in attitudes toward women in managerial positions compared to participants who were randomly assigned to the group that did not receive the gender threat. However, there was a significant positive relationship within the overall sample between implicit self-esteem and positive attitudes towards women in managerial positions.
Centralspindlin regulates ECT2 and RhoA accumulation at the equatorial cortex during cytokinesis

During determination of the cell division plane, an actomyosin contractile ring is induced at the equatorial cell cortex by signals from the mitotic apparatus and contracts to cause cleavage furrow progression. Although the small GTPase RhoA is known to regulate the progression, probably by controlling actin filament assembly and enhancing actomyosin interaction, any involvement of RhoA in division plane determination is unknown. In this study, using a trichloroacetic acid (TCA) fixation protocol we recently developed, we show that RhoA accumulates at the equatorial cortex before furrow initiation and continues to concentrate at the cleavage furrow during cytokinesis. We also demonstrate that both Rho activity and microtubule organization are required for RhoA localization and proper furrowing. Selective disruption of microtubule organization revealed that both astral and central spindle microtubules can recruit RhoA at the equatorial cortex. We find that centralspindlin and ECT2 are required for RhoA localization and furrowing. Centralspindlin is localized both to central spindle microtubules and at the tips of astral microtubules near the equatorial cortex and recruits ECT2. Positional information for division plane determination from microtubules is transmitted to the cell cortex to organize actin cytoskeleton through a mechanism involving these proteins.
Real-time system development: The programming model of MARS

The systematic development of fault-tolerant real-time systems with guaranteed timeliness requires an appropriate system architecture and a rigorous design methodology. Those services of the architecture that help to simplify the work of the real-time programmer are described, taking the MARS architecture as an example. Programming in the large activities, i.e., the systematic derivation of task timing parameters from the requirements specification, are then addressed. Programming to meet a time budget is discussed, and the programming interface, the programming environment, and the testing and support tools are presented. The architecture and most of the tools have been implemented and can be demonstrated on a fault-tolerant prototype application. <<ETX>>
Resistance Training Improves Hemodynamic Function, Collagen Deposition and Inflammatory Profiles: Experimental Model of Heart Failure

The role of resistance training on collagen deposition, the inflammatory profile and muscle weakness in heart failure remains unclear. Therefore, this study evaluated the influence of a resistance training program on hemodynamic function, maximum strength gain, collagen deposition and inflammatory profile in chronic heart failure rats. Thirty-two male Wistar rats submitted to myocardial infarction by coronary artery ligation or sham surgery were assigned into four groups: sedentary sham (S-Sham, n = 8); trained sham (T-Sham, n = 8); sedentary chronic heart failure (S-CHF, n = 8) and trained chronic heart failure (T-CHF, n = 8). The maximum strength capacity was evaluated by the one maximum repetition test. Trained groups were submitted to an 8-week resistance training program (4 days/week, 4 sets of 10–12 repetitions/session, at 65% to 75% of one maximum repetition). After 8 weeks of the resistance training program, the T-CHF group showed lower left ventricular end diastolic pressure (P<0.001), higher left ventricular systolic pressure (P<0.05), higher systolic blood pressure (P<0.05), an improvement in the maximal positive derivative of ventricular pressure (P<0.05) and maximal negative derivative of ventricular pressure (P<0.05) when compared to the S-CHF group; no differences were observed when compared to Sham groups. In addition, resistance training was able to reduce myocardial hypertrophy (P<0.05), left ventricular total collagen volume fraction (P<0.01), IL-6 (P<0.05), and TNF-α/IL-10 ratio (P<0.05), as well as increasing IL-10 (P<0.05) in chronic heart failure rats when compared to the S-CHF group. Eight weeks of resistance training promotes an improvement of cardiac function, strength gain, collagen deposition and inflammatory profile in chronic heart failure rats.