Miracle-dz/UniFAR-FTUs huggingface dataset:
Toll-like receptor ligands synergize through distinct dendritic cell pathways to induce T cell responses: Implications for vaccines

Toll-like receptors (TLRs) may need to cooperate with each other to be effective in detecting imminent infection and trigger immune responses. Understanding is still limited about the intracellular mechanism of this cooperation. We found that when certain TLRs are involved, dendritic cells (DCs) establish unidirectional intracellular cross-talk, in which the MyD88-independent TRIF-dependent pathway amplifies the MyD88-dependent DC function through a JNK-dependent mechanism. The amplified MyD88-dependent DC function determines the induction of the T cell response to a given vaccine in vivo. Therefore, our study revealed an underlying TLR mechanism governing the functional, nonrandom interplay among TLRs for recognition of combinatorial ligands that may be dangerous to the host, providing important guidance for design of novel synergistic molecular vaccine adjuvants.
Microarchitectural Design Space Exploration Using an Architecture-Centric Approach

The microarchitectural design space of a new processor is too large for an architect to evaluate in its entirety. Even with the use of statistical simulation, evaluation of a single configuration can take excessive time due to the need to run a set of benchmarks with realistic workloads. This paper proposes a novel machine learning model that can quickly and accurately predict the performance and energy consumption of any set of programs on any microarchitectural configuration. This architecture-centric approach uses prior knowledge from off-line training and applies it across benchmarks. This allows our model to predict the performance of any new program across the entire microarchitecture configuration space with just 32 further simulations. We compare our approach to a state-of-the-art program-specific predictor and show that we significantly reduce prediction error. We reduce the average error when predicting performance from 24% to just 7% and increase the correlation coefficient from 0.55 to 0.95. We then show that this predictor can be used to guide the search of the design space, selecting the best configuration for energy-delay in just 3 further simulations, reducing it to 0.85. We also evaluate the cost of off-line learning and show that we can still achieve a high level of accuracy when using just 5 benchmarks to train. Finally, we analyse our design space and show how different microarchitectural parameters can affect the cycles, energy and energy-delay of the architectural configurations.
Lateral transmission of force is impaired in skeletal muscles of dystrophic mice and very old rats

Non‐technical summary The force developed by a single fibre in frog muscles is transmitted laterally to the muscle surface with little or no loss. To demonstrate this phenomenon in mammals, a ‘yoke’ apparatus was developed that attached to the surface of whole, parallel‐fibred muscles and permitted measurements of the lateral transmission of forces. We then demonstrated that for wild‐type mice and rats longitudinal and lateral transmission of forces in muscles were not different. In contrast, for skeletal muscles of dystrophic mice and very old rats, in which the dystrophin‐associated glycoprotein complex (DGC) of fibres was disrupted, the forces transmitted laterally were impaired severely. We conclude that during contractions of skeletal muscles, an intact DGC is essential for the lateral transmission of force and disruptions of the DGC lead to sarcomere instability and contraction‐induced injury.
A Study on Personalization and Customization Mechanisms of Vehicular Cloud Platform

This study discusses the concept of personalization and customization mechanism performed specifically for a cloud based vehicular platform. The proof-of-concept prototype allows the user to create a personalized environment on the Vehicular On-Board Unit (OBU) from hand-held devices of vehicular users. The paper discusses an extensive analysis on different type of vehicular users using different type of services, methodologies to use intermediary component between the vehicle and service providers in-order to personalize OBU. For this purpose, we have defined methodologies both for the service providers and vehicular users. For users, we have enabled peer-to-peer application layer personalization including the module of object storage on cloud. For service providers we have illustrated the idea of an engine allowing them to orchestrate services with respective to the user-types. Although it was implemented as a proof-of-concept system but it can be easily applicable for various users, service providers and hence can be extended further.
Direct Democratic Choice: The Swiss Experience

Chapter 1 Introduction: Toward a Realistic Theory of Direct Democracy Chapter 2 The Structuration of the Choice Chapter 3 The Campaign: The Role of the Political Elite Chapter 4 Political Awareness Chapter 5 Participation Chapter 6 Heuristic Strategies Chapter 7 Argument-Based Strategies Chapter 8 The Relative Importance of the Two Strategies Chapter 9 Conclusion
Learning, forgetting and remembering: statistical support for rule-based MT

The paper describes the incorporation of statistical knowledge into two different Rule-Based MT (RBMT) systems. In earlier experiments, these systems were linked with Memory-Base MT components, so that by now the translation process is supported by three MT paradigms. The paper concentrates on the acquisition of rich, informative, balanced, and up-to-date statistical data from monolingual and parallel corpora and on ways of using these data in RBMT systems. The authors keep their pledge of a systematic investigation of the linkage of different MT paradigms aimed at improving the quality of translation.
A Procedure for Identification of Principal Variables by Least Generalized Dependence

Principal components are often used for reducing dimensions in multivariate data, but they frequently fail to provide useful results and their interpretation is rather difficult. In this article, the use of entropy optimization principles for dimensional reduction in multivariate data is proposed. Under the assumptions of multivariate normality, a four-step procedure is developed for selecting principal variables and hence discarding redundant variables. For comparative performance of the information theoretic procedure, we use simulated data with known dimensionality. Principal variables of cluster bean (Guar) are identified by applying this procedure to a real data set generated in a plant breeding experiment.
Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate (between ∼5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-times greater than an Illumina-only assembly (678kb versus 59.9kbp), and has greater than 99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly. Reviewer link to data http://schatzlab.cshl. edu/data/nanocorr/
PHENOMENOLOGICAL STUDY OF PARADOXICAL PHASE AND REVERSE PARADOXICAL PHASE OF SLEEP.

1. A peculiar phase other than p. p can be seen in human natural sleep, . which might be called reverse paradoxical phase (r. p. p), for the relation between EEG pattern and the activity level of many other physiological. functions is the reverse of that in p. p.2. P. p and r. p. p are two different manifestations of the dissociation between EEG and many other physiological activities, especially vegetative functions.3. The fact that p. p is apt to appear at the end of each single sleep cycleand r. p. p comes at the beginning or in the middle of each single sleep cycle could account for the phasic shift of changes in EEG and other physiological functions.4. The prominent occurrence of p. p in the latter half and r. p. p in the first half of the natural night sleep could be attributed to the difference in distribution pattern of activity level of each physiological function. For instance, more occurence of EEG III can be seen in the earlier period of the night sleep, while the depressed or minor activity of GSR, blood pressure is distributed more in the latter half of the night sleep.
A case report of tongue metastasis from lung squamous cell carcinoma and literature review

Rationale: Tongue metastasis from lung cancer is extremely rare, and the prognosis of these patients is rather poor. Patient concers: A 56-year-old man was found a 4-cm cavity lesion in the left upper lobe, which was initially misdiagnosed as tuberculosis. Diagnoses: A case of lung squamous cell carcinoma that metastasized to the base of a patient's tongue. Intervations: We send the biopsy of the lung and the tongue lesions for gene sequencing. Outcomes: He received systemic chemotherapy, but continued to have pain at the base of his tongue and died 7 months later. Lessons: From sequencing data, mutations in KRAS proto-oncogene, GTPase (KRAS), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), and tumor protein p53 (TP53) were found in the tumor biopsy of the patient. All of these were indicators of poor prognosis.
High pressure effects on proteins and other biomolecules.

In a discussion about pressure effects on deep-sea animals, Regnard (100) showed that pressures below 1 kbar do not irreversibly affect enzyme processes in bacteria. In contrast, pressures up to 8 kbar coagulate ovalbumin irreversibly (7). These observations have dominated the field of pressure research on biological molecules for some time: pressure effects were assumed to be reversible below I kbar and irreversible at higher pressures. More recently it was found that low pressures affect protein-ligand binding (58) and protein-protein interactions (45); the reversibility at higher pressures depends on the nature of the protein and the solvent conditions (121). On the other hand, it has been shown that DNA is pressure resistant (Il l ) and the melting temperature of lipids is strongly pressure dependent (23, 119). Since then two lines of research are discernable: the biological ap­ proach, which seeks to understand deep-sea phenomena (63, 78), and the physicochemical approach in which pressure is used as a tool to study the behavior of biological molecules. In this review we concentrate on the physicochemical approach. Activation and reaction volumes provide information on reaction mechanisms that is not available from other studies. This is illustrated in reviews on pressure effects in organic (2) and inorganic chemistry (95). Generally, the response of a system to the application of pressure is governed by the principle of Le Chatelier, which states that if a system can shrink, it will reduce its volume upon squeezing (44). This reduction in volume can be the consequence of a chemical reaction or a closer packing of the molecules. It is obvious that
IL‐4 induces a wide‐spectrum intracellular signaling cascade in CD8+ T cells

IL‐4 has distinct effects on the differentiation and functional properties of CD8+ T cells. In vivo studies have shown that it is critical for the development of protective memory responses against tumors and infections by Leishmania and Plasmodium parasites. The intracellular signaling events mediated by IL‐4/IL‐4 receptor (IL‐4R) interactions on CD4+ T cells have been studied extensively; however, the nature of IL‐4‐induced signaling on CD8+ T cells has not been characterized. Using naïve, activated, as well as differentiated CD8+ T cells, we show that IL‐4 has a strong in vivo and in vitro antiapoptotic effect on activated and resting CD8+ T cells. We demonstrate that IL‐4 induces the phosphorylation of the IL‐4R, which is followed by the activation of at least two distinct intracellular signaling cascades: the Jak1/STAT6 and the insulin receptor substrate/PI‐3K/protein kinase B pathways. We also found that IL‐4 induces the Jak3‐mediated phosphorylation and nuclear migration of STAT1, STAT3, and STAT5 in naïve, activated, as well as differentiated, IFN‐γ‐producing CD8+ T cells. The induction of this broad signaling activity in CD8+ T cells coincides with a transcriptional activity of suppressors of cytokine signaling genes, which are decreased significantly in comparison with CD4+ T cells. To our knowledge, this report constitutes the first comprehensive analysis of the signaling events that shape CD8+ T cell responses to IL‐4.
Analytical placement for heterogeneous FPGAs

We present HeAP, an analytical placement algorithm for heterogeneous FPGAs comprised of LUT-based logic blocks, multiplier/DSP blocks and block RAMs. Specifically, we adapt a state-of-the-art ASIC-based analytical placer to target FPGAs with heterogeneous blocks located at discrete locations throughout the fabric. Our placer also handles macros of LUT-based blocks with specific layout requirements, such as carry chains. Results show that our placer delivers a 4× speedup, on average, compared to Altera's non-timing driven flow, at the cost of a 5% increase in postrouted wirelength, and an 11× speedup compared to Altera's timing-driven flow, at the cost of a 4% increase in post-routed wirelength and a 9% reduction in maximum operating frequency. We also compare with an academic simulated annealing-based placer and demonstrate a 7.4× runtime advantage with 6% better placement quality.
Consequences of the functional interpretations of psychological terms

The Behavior Analysis (BA) has benefited in the past and continues to benefit from a specific kind of operational interpretations of terms/expressions developed in other systems of Psychology and similar areas. The Skinnerian model of the operational interpretation of terms of other theories consists of the analysis of the context where theoreticians and researchers emit the analyzed terms/expressions. Therefore, these interpretations are analysis of the verbal behavior of psychologists. Innumerable examples of this practice can be found in the workmanship of Skinner and are recurrent in diverse periodics of the BA. In this article we argue the implications of these analyses for the survival of the BA as a cultural practice, for the conceptual, theoretical, and technological perfectioning of the BA and for teaching BA. Based on these analyses, it can be argued that the interpretation of terms of other theories should be considered an important program of research and should receive greater attention from the behavior analysts.
New medium for improved recovery of coliform bacteria from drinking water

A new membrane filter medium was developed for the improved recovery of injured coliforms from drinking water. The new medium, termed m-T7, consists of 5.0 g of Difco Proteose Peptone no. 3, 20 g of lactose, 3.0 g of yeast extract, 0.4 ml of Tergitol 7 (25% solution), 5.0 g of polyoxyethylene ether W-1, 0.1 g of bromthymol blue, 0.1 g of bromcresol purple, and 15 g of agar per liter of distilled water. Additional selectivity may be obtained by aseptically adding 0.1 microgram of penicillin G per ml to the medium after autoclaving. In laboratory studies, m-T7 agar recovered 86 to 99% more laboratory-injured coliforms than did m-Endo agar. m-T7 agar also recovered an average of 43% more verified coliforms from 67 surface and drinking water samples than did the standard m-Endo membrane filter technique. From drinking water, m-T7 agar recovered nearly three times more coliforms than did m-Endo agar. Less than 0.5% of the colonies on m-T7 agar gave false-negative reactions, whereas greater than 70% of the typical yellow colonies from m-T7 agar produced gas in lauryl tryptose broth. Most of the verified coliforms isolated on m-T7 agar belonged to one of the four common coliform genera: Escherichia, 17.6%; Klebsiella, 21.7%; Citrobacter, 17.3%; Enterobacter, 32.2%. The results demonstrate that m-T7 agar is superior to m-Endo agar, especially for the isolation of injured coliforms from drinking water.
Mathematical model of MCCA-based streaming process in mesh networks in the presence of noise

One of the today challenges for the mesh networks researches is reliable transmission of multimedia traffic. This traffic demands high quality of service (QoS), to provide which it is suitable to use Mesh Coordinated Channel Access (MCCA) - the novel medium access method described in IEEE 802.11s. According to MCCA, mesh stations (STAs) set up periodic reservations; if all STAs in the network support MCCA, every STA gets access to the medium with no contention during the reservations it has scheduled. Most papers devoted to MCCA are written under the assumption of ideal channel conditions. However, in order to satisfy QoS demands, it is necessary to take random noise into account. In this paper we propose an analytical model of the multihop MCCA-based streaming process in the presence of noise. The model predicts the Packet Loss Ratio (PLR) over the transmission route and can be efficiently utilized to analyze and optimize the process of traffic transmission.
An improved body action recognition method based on manifold learning

The body action recognition is one of the key technologies of the computer vision. As the fact that the features of body action usually reside on low dimensional manifolds embedded in a high dimensional ambient space, a new method of body action recognition based on manifold learning is proposed in this paper. In the proposed method, a Linear Local Embedding of Difference (DLLE) algorithm is applied to get the low dimensional manifolds of the images and achieve human action recognition. The result shows that the DLLE method has more advantage in time-consuming and recognition accuracy rate than the other dimensionality reduction methods. Furthermore, the experimental results demonstrated the feasibility and effectiveness of the proposed algorithm in body action recognition.
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data

MOTIVATION Metabolomics is a rapidly evolving field that holds promise to provide insights into genotype-phenotype relationships in cancers, diabetes and other complex diseases. One of the major informatics challenges is providing tools that link metabolite data with other types of high-throughput molecular data (e.g. transcriptomics, proteomics), and incorporate prior knowledge of pathways and molecular interactions. RESULTS We describe a new, substantially redesigned version of our tool Metscape that allows users to enter experimental data for metabolites, genes and pathways and display them in the context of relevant metabolic networks. Metscape 2 uses an internal relational database that integrates data from KEGG and EHMN databases. The new version of the tool allows users to identify enriched pathways from expression profiling data, build and analyze the networks of genes and metabolites, and visualize changes in the gene/metabolite data. We demonstrate the applications of Metscape to annotate molecular pathways for human and mouse metabolites implicated in the pathogenesis of sepsis-induced acute lung injury, for the analysis of gene expression and metabolite data from pancreatic ductal adenocarcinoma, and for identification of the candidate metabolites involved in cancer and inflammation. AVAILABILITY Metscape is part of the National Institutes of Health-supported National Center for Integrative Biomedical Informatics (NCIBI) suite of tools, freely available at http://metscape.ncibi. org. It can be downloaded from http://cytoscape.org or installed via Cytoscape plugin manager. CONTACT metscape-help@umich.edu; akarnovs@umich.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Visible spectroscopy of the new ESO large programme on trans-Neptunian objects and Centaurs: final results

Context. A second large programme (LP) for the physical studies of TNOs and Centaurs, started at ESO Cerro Paranal on October 2006 to obtain high-quality data, has recently been concluded. In this paper we present the spectra of these pristine bodies obtained in the visible range during the last two semesters (November 2007−November 2008) of the LP. Aims. We investigate the spectral behaviour of the TNOs and Centaurs observed, and we analyse the spectral slopes distribution of the full data set coming from this LP and from the literature. Methods. Spectroscopic observations in the visible range were carried out at the UT1 (Antu) telescope using the instrument FORS2. We computed the spectral slope for each observed object, and searched for possible weak absorption features. A statistical analysis was performed on a total sample of 73 TNOs and Centaurs to look for possible correlations between dynamical classes, orbital parameters, and spectral gradient. Results. We obtained new spectra for 28 bodies (10 Centaurs, 6 classical, 5 resonant, 5 scattered disk, and 2 detached objects), 15 of which were observed for the first time. All the new presented spectra are featureless, including 2003 AZ84, for which a faint and broad absorption band possibly attributed to hydrated silicates on its surface has been reported. The data confirm a wide variety of spectral behaviours, with neutral-grey to very red gradients. An analysis of the spectral slopes available from this LP and in the literature for a total sample of 73 Centaurs and TNOs shows that there is a lack of very red objects in the classical population. We present the results of the statistical analysis of the spectral slope distribution versus orbital parameters. In particular, we confirm a strong anticorrelation between spectral slope and orbital inclination for the classical population. Nevertheless, we do not observe a change in the slope distribution at i ∼ 5 ◦ , the boundary between the dynamically hot and cold populations, but we find that objects with i < 12 ◦ show no correlation between spectral slope and inclination, as has already been noticed on the colour-inclination relation for classical TNOs. A strong correlation is also found between the spectral slope and orbital eccentricity for resonant TNOs, with objects having higher spectral slope values with increasing eccentricity.