Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of a New World Monopartite Begomovirus Causing Leaf Curl Disease of Tomato in Ecuador and Peru Reveals a New Direction in Geminivirus Evolution

ABSTRACT All characterized whitefly-transmitted geminiviruses (begomoviruses) with origins in the New World (NW) have bipartite genomes composed of a DNA-A and DNA-B component. Recently, an NW begomovirus lacking a DNA-B component was associated with tomato leaf curl disease (ToLCD) in Peru, and it was named Tomato leaf deformation virus (ToLDeV). Here, we show that isolates of ToLDeV associated with ToLCD in Ecuador and Peru have a single, genetically diverse genomic DNA that is most closely related to DNA-A components of NW bipartite begomoviruses. Agroinoculation of multimeric clones of the genomic DNA of three ToLDeV genotypes (two variants and a strain) resulted in the development of tomato leaf curl symptoms indistinguishable from those of ToLCD in Ecuador and Peru. Biological properties of these ToLDeV genotypes were similar to those of Old World (OW) monopartite tomato-infecting begomoviruses, including lack of sap transmissibility, phloem limitation, a resistance phenotype in tomato germplasm with the Ty-1 gene, and functional properties of the V1 (capsid protein) and C4 genes. Differences in symptom phenotypes induced by the ToLDeV genotypes in tomato and Nicotiana benthamiana plants were associated with a highly divergent left intergenic region and C4 gene. Together, these results establish that ToLDeV is an emergent NW monopartite begomovirus that is causing ToLCD in Ecuador and Peru. This is the first report of an indigenous NW monopartite begomovirus, and evidence is presented that it emerged from the DNA-A component of a NW bipartite progenitor via convergent evolution and recombination.
Cascade Subspace Clustering

In this paper, we recast the subspace clustering as a verification problem. Our idea comes from an assumption that the distribution between a given sample x and cluster centers Omega is invariant to different distance metrics on the manifold, where each distribution is defined as a probability map (i.e. soft-assignment) between x and Omega. To verify this so-called invariance of distribution, we propose a deep learning based subspace clustering method which simultaneously learns a compact representation using a neural network and a clustering assignment by minimizing the discrepancy between pair-wise sample-centers distributions. To the best of our knowledge, this is the first work to reformulate clustering as a verification problem. Moreover, the proposed method is also one of the first several cascade clustering models which jointly learn representation and clustering in end-to-end manner. Extensive experimental results show the effectiveness of our algorithm comparing with 11 state-of-the-art clustering approaches on four data sets regarding to four evaluation metrics.
New fast depth image-based rendering method for 3DTV

Virtual view rendering is one of the key technologies to realize Three-Dimensional Television (3DTV) system. This paper presents a novel fast method of virtual view rendering that the holes are divided into large and small hole regions, which can be processed according to their size, also we propose using a new way of rendering that some pixels refer to the warping relation of previous frame and the other pixels update the warping relation by re-computing in the current rendering frame, in the process of selecting threshold to determine the two parts of pixel regions, we propose a mathematical model to adaptive select the threshold after a large number of experiments. Experimental results show that the proposed method is effective, and it effectively reduces the rendering time within a certain range of the quality of virtual image declining.
Simultaneous identification of species and molecular forms of the Anopheles gambiae complex by PCR‐RFLP

Abstract For differential identification of sibling species in the Anopheles gambiae Giles complex (Diptera: Culicidae), including simultaneous separation of M and S molecular forms within An. gambiae Giles sensu stricto, we describe a PCR‐RFLP method. This procedure is more efficient, faster and cheaper than those used before, so is recommended for large‐scale processing of field‐collected larval and adult specimens to be identified in malaria vector studies.
A Comparative Study of Intrusion Detection Algorithms

Intrusion detection system (IDS) is a kind of security management model that can be installed in computers and networks. IDS gather information from the network and computer and analyses it to find the possible security breaches into the system, which contain both intrusions and misuse. If we see modern IDS they also have few vulnerabilities, these systems also have drawbacks of false detection. So we aim to make a new model which can decrease the possibilities of false detection. In this paper we have done a survey of different algorithm used in intrusion detection system and then designed a new model that will use correlation based feature selection algorithm and SVM. This model will be tested on KDDCup99 dataset.
Building a learning community among faculty, librarians and students using computer-supported collaborative learning: An activity theory approach

Activity Theory has a specific use as a tool that shows the structure of the activities between people and mediation under particular context. In this paper, the researchers use it as a framework for the design of the collaborative learning activities under creative problem solving process using Computer-Supported Collaborative Learning as mediated tools. It is also used as a unit of analysis framework to examine and to get a better understanding of the interactions among the students, instructors and librarians through Computer-Supported Collaborative Learning environment. Indepth interview and participants' observation are used as main qualitative approach to collect data in order to explain the way the participants use the tools, and how the tools support and affect them in their collaborative learning to achieve the goals.
Variants of soybean cells which can grow in suspension with maltose as a carbon-energy source.

Suspension cultures of soybean line SB-1 have been grown using maltose as an carbon-energy source. The very slow growth in medium containing maltose has been used to select rapidly growing variants. These appear to arise as a series of sequential genetic changes (mutations? ). These variant strains are stable when grown in sucrose medium for 100 generations and appear to be able to transport maltose actively into the cell.
Simultaneous acquisition of phase‐contrast angiograms and stationary‐tissue images with Hadamard encoding of flow‐induced phase shifts

A technique for the simultaneous acquisition of three‐dimensional phase‐contrast angiograms and stationary‐tissue images is described. Hadamard multiplexed encoding of flow information permits image acquisition times that are a third shorter than those of previous phase‐contrast methods. The encoding scheme described also enables differentiation of flow‐induced phase shifts from phase shifts due to resonance offset conditions such as field inhomogeneities and chemical shift. Display strategies that combine this phase information with the flow image are described.
Analyzing cell fate control by cytokines through continuous single cell biochemistry

Cytokines are important regulators of cell fates with high clinical and commercial relevance. However, despite decades of intense academic and industrial research, it proved surprisingly difficult to describe the biological functions of cytokines in a precise and comprehensive manner. The exact analysis of cytokine biology is complicated by the fact that individual cytokines control many different cell fates and activate a multitude of intracellular signaling pathways. Moreover, although activating different molecular programs, different cytokines can be redundant in their biological effects. In addition, cytokines with different biological effects can activate overlapping signaling pathways. This prospect article will outline the necessity of continuous single cell biochemistry to unravel the biological functions of molecular cytokine signaling. It focuses on potentials and limitations of recent technical developments in fluorescent time‐lapse imaging and single cell tracking allowing constant long‐term observation of molecules and behavior of single cells. J. Cell. Biochem. 108: 343–352, 2009. © 2009 Wiley‐Liss, Inc.
Transient heat transfer analysis of housing and PMM using 3-D FE code

This paper proposes finite element (FE) numerical methodologies for the transient heat transfer analysis of highly integrated actuators for demanding aerospace applications. A FE surface heat source is developed which permits to independently simulate the thermal performance of the housing of the actuator. As a result, the complexity of the FE model is reduced significantly and the computational cost is minimized. The proposed technique is integrated into a three dimensional (3-D) FE package that employs preprocessors capable of producing highly parameterized cooling housings of arbitrary configurations. The specific 3-D FE code was used for the transient heat transfer analysis of a surface mounted permanent magnet motor (PMM) and its non-standardized and unsymmetrical cooling housing.
SEALANT: A detection and visualization tool for inter-app security vulnerabilities in androic

Android's flexible communication model allows interactions among third-party apps, but it also leads to inter-app security vulnerabilities. Specifically, malicious apps can eavesdrop on interactions between other apps or exploit the functionality of those apps, which can expose a user's sensitive information to attackers. While the state-of-the-art tools have focused on detecting inter-app vulnerabilities in Android, they neither accurately analyze realistically large numbers of apps nor effectively deliver the identified issues to users. This paper presents SEALANT, a novel tool that combines static analysis and visualization techniques that, together, enable accurate identification of inter-app vulnerabilities as well as their systematic visualization. SEALANT statically analyzes architectural information of a given set of apps, infers vulnerable communication channels where inter-app attacks can be launched, and visualizes the identified information in a compositional representation. SEALANT has been demonstrated to accurately identify inter-app vulnerabilities from hundreds of real-world Android apps and to effectively deliver the identified information to users. (Demo Video: https://youtu.be/E4lLQonOdUw)
Prediction Error of Small Area Predictors Shrinking Both Means and Variances

The article considers a new approach for small area estimation based on a joint modelling of mean and variances. Model parameters are estimated via expectation–maximization algorithm. The conditional mean squared error is used to evaluate the prediction error. Analytical expressions are obtained for the conditional mean squared error and its estimator. Our approximations are second‐order correct, an unwritten standardization in the small area literature. Simulation studies indicate that the proposed method outperforms the existing methods in terms of prediction errors and their estimated values.
The Use of Remifentanil to Facilitate the Insertion of the Cobra Perilaryngeal Airway

BACKGROUND: The use of remifentanil before propofol administration facilitates the insertion of the Laryngeal Mask Airway. We designed the present study to determine whether remifentanil would also create more suitable conditions for providing Cobra Perilaryngeal airway (CobraPLA) insertion when administered with propofol. METHODS: Both remifentanil and propofol were given as effect-site target-controlled infusions. There were four groups of 25 patients each. The propofol effect-site concentration was set at 6 &mgr;g/mL in all groups. Group R1 received a target effect-site remifentanil concentration of 1 ng/mL, Group R2 received remifentanil at 2 ng/mL, Group R3 received remifentanil at 3 ng/mL, and Group R4 received remifentanil at 4 ng/mL before the induction of anesthesia with propofol. The ease of insertion of CobraPLA was graded by the following 3-point scale: Grade 1, excellent, no response to CobraPLA insertion; Grade 2, acceptable, gagging or swallowing with insertion of CobraPLA; Grade 3, poor, unable to open mouth or biting upon insertion of CobraPLA. RESULTS: The most patients ranked as excellent for the first CobraPLA insertion (Grade 1) were found in Group R4, which was significantly higher than Groups R1 and R2 (P < 0.01), whereas no significant difference was found when compared with Group R3. The duration of apnea showed a significant dose-related increase (P < 0.01), especially between Group R2 (median 2.95 min) and R3 (median 7.9 min), but there was no significant difference between Groups R3 and R4. The incidence of hypotension in Group R4 within 1 min after insertion of CobraPLA was significantly more than for Groups R1 and R2 (P < 0.01). No significant differences could be found between the incidence of hypotension between Group R3 and the other groups. The incidence of hypertension at 1 min postinsertion was significantly more common in Groups R1 and R2 than Groups R3 and R4 (P < 0.01). CONCLUSION: An effect-site concentration of remifentanil of 2 ng/mL provides excellent conditions for insertion of the CobraPLA on the first attempt with minimal hemodynamic perturbations and a shorter duration of apnea.
Phenotypic characterization of the archaebacterial genus Sulfolobus: comparison of five wild-type strains

Though amenable to routine manipulation and a popular subject of molecular genetic and biochemical studies on archaebacteria, the genus Sulfolobus has remained poorly described in phenotypic terms. To delineate their physiological capabilities and diversity, five laboratory strains, including type strains of the described species Sulfolobus acidocaldarius and S. solfataricus, were compared with respect to a variety of growth and biochemical parameters, including component profile of the surface-layer cell wall, inhibitors of growth, growth rate as a function of temperature and pH, and compounds used as sole sources of carbon or nitrogen. Motility and photoregulated production of an orange pigment were detected in all five strains tested. The results provide new criteria for distinguishing Sulfolobus strains as well as potential tools for the physiological and genetic manipulation of these extreme thermophiles.
Chemokines in islet allograft rejection

Chemokines have emerged as important regulators in the development, differentiation, and anatomic distribution of leukocytes. Studies of renal and cardiac allograft biopsies have revealed that the expression of many chemokine receptors and their ligands was associated with acute allograft rejection. However, the importance of these chemokine receptor systems varies in the host response to a particular allograft. In this regard, CXCR3 appears to play a more important role in cardiac allograft rejection than CCR2 and CCR5. We have found that CCR2, CCR5, and CXCR3 and their ligands, as well as Th1 cytokines are induced to high levels in rejecting islet allografts. Interestingly, targeting CCR5 resulted in a significant prolongation of islet allograft survival. This prolongation was associated with a Th2 response. Our data indicate that in the process of acute rejection, the temporal expression and the ultimate function of a given chemokine vary among different organs or tissues. Hence, each organ or tissue may require a unique set of chemokines to generate acute rejection. Targeting the appropriate chemokine receptors may provide a clinically useful strategy to prevent islet allograft rejection. Copyright © 2003 John Wiley & Sons, Ltd.
Shamans of the Siberian Eskimos

Description des institutions et des pratiques chamanistiques chez les Eskimos de Siberie (village de Naukan) par un ethnographe autochtone de 50 ans : les types de chamans (homme, femme, comment devenir un chaman), leurs roles sociaux (attribution du nom, guerison), leur relation avec la mort et la divination (interrogation du corps, chance, prophetie), avec les esprits, et la sorcellerie sont expliques. Si les jeunes chamans ne s'opposent pas a l'autorite sovietique, les plus anciens ne la reconnaissent pas
High-performance signal processing on emerging many-core architectures using cuda

This paper provides a short introduction to CUDA programming paradigm and recent standardization efforts. We also present a new 2D Fast Wavelet Transform implementation on GPUs using CUDA. Our novel implementation achieves almost two orders of magnitude improvements versus a typical quad-core CPU, and demonstrates that emerging manycore architectures are ideal platforms for achieving highperformance signal processing.
Crystal Structure of Tritrichomonas foetus Inosine Monophosphate Dehydrogenase in Complex with the Inhibitor Ribavirin Monophosphate Reveals a Catalysis-dependent Ion-binding Site*

Inosine monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in GMP biosynthesis. The resulting intracellular pool of guanine nucleotides is of great importance to all cells for use in DNA and RNA synthesis, metabolism, and signal transduction. The enzyme binds IMP and the cofactor NAD+ in random order, IMP is converted to XMP, NAD+ is reduced to NADH, and finally, NADH and then XMP are released sequentially. XMP is subsequently converted into GMP by GMP synthetase. Drugs that decrease GMP synthesis by inhibiting IMPDH have been shown to have antiproliferative as well as antiviral activity. Several drugs are in use that target the substrate- or cofactor-binding site; however, due to differences between the mammalian and microbial isoforms, most drugs are far less effective against the microbial form of the enzyme than the mammalian form. The high resolution crystal structures of the protozoan parasiteTritrichomonas foetus IMPDH complexed with the inhibitor ribavirin monophosphate as well as monophosphate together with a second inhibitor, mycophenolic acid, are presented here. These structures reveal an active site cation identified previously only in the Chinese hamster IMPDH structure with covalently bound IMP. This cation was not found previously in apo IMPDH, IMPDH in complex with XMP, or covalently bound inhibitor, indicating that the cation-binding site may be catalysis-dependent. A comparison of T. foetus IMPDH with the Chinese hamster andStreptococcus pyogenes structures reveals differences in the active site loop architecture, which contributes to differences in cation binding during the catalytic sequence and the kinetic rates between bacterial, protozoan, and mammalian enzymes. Exploitation of these differences may lead to novel inhibitors, which favor the microbial form of the enzyme.
Metastasis Suppressor Tetraspanin CD82/KAI1 Regulates Ubiquitylation of Epidermal Growth Factor Receptor*

Background: Tetraspanin CD82/KAI1 is associated with EGF receptor and regulates its signaling. Results: CD82 controls ubiquitylation of EGF receptor after stimulation with heparin-binding ligands and alters receptor trafficking. Conclusion: CD82 regulates communication between heparan sulfate proteoglycans and ligand-bound EGFR, thus affecting the activity of c-Cbl. Significance: Lateral cross-talk initiated by CD82-dependent interactions is critical for modulation of EGFR function. Ligand-induced ubiquitylation of EGF receptor (EGFR) is an important regulatory mechanism that controls endocytic trafficking of the receptor and its signaling potential. Here we report that tetraspanin CD82/KAI1 specifically suppresses ubiquitylation of EGFR after stimulation with heparin-binding EGF or amphiregulin and alters the rate of recruitment of the activated receptor to EEA1-positive endosomes. The suppressive effect of CD82 is dependent on the heparin-binding domain of the ligand. Deletion of the C-terminal cytoplasmic domain of CD82 (CD82ΔC mutant) inhibits endocytic trafficking of the tetraspanin and compromises its activity toward heparin-binding EGF-activated EGFR. Reduced ubiquitylation of EGFR is accompanied by PKC-dependent increase in serine phosphorylation of c-Cbl in cells expressing elevated levels of CD82. Furthermore, phosphorylation of threonine 654 (PKC phosphorylation site) in the juxtamembrane domain of the receptor is considerably increased in CD82-expressing cells. These results describe previously unsuspected links between tetraspanin proteins and ubiquitylation of their molecular partners (e.g., EGFR). Our data identify CD82 as a new regulator of c-Cbl, which discriminatively controls the activity of this E3 ubiquitin ligase toward heparin-binding ligand-EGFR pairs. Taken together, these observations provide an important new insight into the modulatory role of CD82 in endocytic trafficking of EGF receptor.
Singing Voice Enhancement for Monaural Music Signals Based on Multiple Time-Frequency Analysis

We propose a novel technique to enhance singing voice in monaural music audio signals by capturing fluctuation of singing voice on spectrogram. Based on multiple spectrogram representation, the method separates an input signal into three components: stationary, fluctuated, and transient components, and singing voice is mainly included in the fluctuated component. The proposed algorithm consists of two stage processing of the sinusoidal/non-sinusoidal separation algorithm which we have recently developed. It is called harmonic/percussive sound separation (HPSS). In first stage, we filter out the stationary component based on HPSS analysis with long frame, and in second stage, we filter out the transient component based on HPSS analysis with short frame. We show that the proposed method effectively enhances the singing voice in music by experiments and show its application to melody extraction, which also supports the effectiveness of the method.