Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleation and Cross-Slip of Partial Dislocations in FCC Metals

Nucleation of partial dislocations at a crack and cross-slip of partial dislocations under general loading in FCC metals are analyzed based on a multiscale model which incorporates atomic information into continuum-mechanics approach. In both analyses, the crack and the slip planes are modeled as surfaces of displacement discontinuities embedded in elastic media. The atomic potentials between the adjacent atomic layers along the slip planes are assumed to be the generalized stacking fault energies, which are obtained based on atomic calculations. The relative displacements along the slip planes, corresponding to the configurations of partial dislocations and stacking faults, are solved through the variational boundary integral method. The energetics of partial dislocation nucleation at the crack and cross-slip in FCC metals Al and Cu are comparatively studied for their distinctive difference in the intrinsic stacking fault energy. For the analysis of nucleation of partial dislocations at a crack, several new features have emerged compared with nucleation of perfect dislocations in previous studies. Among them, the critical stress and activation energy for nucleation of partial dislocations are markedly lowered. Depending on the value of stacking fault energy and crack configuration, the saddle-point configurations of partial dislocations can be vastly different in terms of the nucleation sequence and the size of the stacking fault. The implications of these new findings on mechanical behavior of nanostructured crystalline materials are elaborated.For the analysis of cross-slip of partial dislocations, the conclusion from previous studies that cross-slip in FCC metals can be influenced by intrinsic stacking fault energy is confirmed. Furthermore, it is found that in Al, the preference of the gliding plane depends on the competition between the two resolved shear stresses on the slip planes. In Cu, the most preferred loading condition for cross-slip is that a lager compressing Escaig shear stress on the primary slip plane is accompanied with stretching Escaig shear stress on the cross-slip plane. The analysis of activation energy indicates that thermal motion plays an important role in cross-slip in FCC metals.
Medial Prefrontal Theta Bursts Precede Rapid Motor Responses during Visual Selective Attention

After visual target stimuli presented infrequently at a covertly attended location, quicker speeded button presses immediately followed a larger positive (P3f) ramp in averaged electroencephalographic (EEG) recordings from the forehead. We show this peak in the mean response time locked to the button press to be principally composed of triphasic, primarily low-theta band (4.5 Hz) complexes preceding but only partially phase-locked to the button press, with larger complexes preceding quicker motor responses. For 10 of 15 subjects, independent component analysis of the unaveraged 31-channel data identified a temporally independent medial frontal EEG process contributing to these phenomena. Low-resolution tomographic modeling localized related components of two 253-channel data sets to medial frontal polar cortex (BA32/10). The far-frontal low-theta complexes and concomitant mean P3f positivity may index cortical activity induced by paralimbic processes involved in disinhibiting impulsive motor responses to rewarding or goal-fulfilling stimuli or events.
A Cost-Effective Certification-Based Service Composition for the Cloud

The cloud computing paradigm provides an environment where services can be composed and reused at high rates. Existing composition techniques focus on providing the desired functionality and at a given deployment cost. In this paper, we focus on the definition of cloud service compositions driven by certified non-functional properties. We define a cost evaluation methodology aimed to provide the composition that minimizes the total costs of the cloud provider taking into account deployment, certification, and mismatch costs, and evaluate it using three different cost profiles.
The NP Search Problems of Frege and Extended Frege Proofs

We study consistency search problems for Frege and extended Frege proofs—namely the NP search problems of finding syntactic errors in Frege and extended Frege proofs of contradictions. The input is a polynomial time function, or an oracle, describing a proof of a contradiction; the output is the location of a syntactic error in the proof. The consistency search problems for Frege and extended Frege systems are shown to be many-one complete for the provably total NP search problems of the second-order bounded arithmetic theories U12 and V12, respectively.
DIRECT DETECTION OF INSTABILITY POINTSUSING AN AUGMENTED FORMULATIONFernando

This paper introduces an augmented formulation to directly compute instability points in power systems. The formulation is an extension of the direct \Point of Collapse" formulation for the computation of static system instabilities. The paper demonstrates the differences between purely static limits (based on power ow Jacobians) and steady-state dynamic instability points (based on eigenvalue determination). Steady-state dynamic instabilities often dominate system behavior. The paper discusses both kinds of dynamic instabilities: Hopf bifurcations and voltage collapse. When controlled devices such as AVR (Automatic Voltage Regulators) and SVC (Static VAR Compensators) components are added, Hopf bifurcations rather than voltage collapse often dominates system behavior. A technique to set controller gains in SVC devices in order to improve dynamic stability limits is described.
Using Red List Indices to measure progress towards the 2010 target and beyond

The World Conservation Union (IUCN) Red List is widely recognized as the most authoritative and objective system for classifying species by their risk of extinction. Red List Indices (RLIs) illustrate the relative rate at which a particular set of species change in overall threat status (i.e. projected relative extinction-risk), based on population and range size and trends as quantified by Red List categories. RLIs can be calculated for any representative set of species that has been fully assessed at least twice. They are based on the number of species in each Red List category, and the number changing categories between assessments as a result of genuine improvement or deterioration in status. RLIs show a fairly coarse level of resolution, but for fully assessed taxonomic groups they are highly representative, being based on information from a high proportion of species worldwide. The RLI for the world's birds shows that that their overall threat status has deteriorated steadily during the years 1988–2004 in all biogeographic realms and ecosystems. A preliminary RLI for amphibians for 1980–2004 shows similar rates of decline. RLIs are in development for other groups. In addition, a sampled index is being developed, based on a stratified sample of species from all major taxonomic groups, realms and ecosystems. This will provide extinction-risk trends that are more representative of all biodiversity.
Defects of Intergenomic Communication: Where Do We Stand?

An expanding number of autosomal diseases has been associated with mitochondrial DNA (mtDNA) depletion and multiple deletions. These disorders have been classified as defects of intergenomic communication because mutations of the nuclear DNA are thought to disrupt the normal cross‐talk that regulates the integrity and quantity of mtDNA. In 1989, autosomal dominant progressive external ophthalmoplegia with multiple deletions of mitochondrial DNA was the first of these disorders to be identified.Two years later, mtDNA depletion syndrome was initially reported in infants with severe hepatopathy or myopathy. The causes of these diseases are still unclear, but genetic linkage studies have identified three chromosomal loci for AD‐PEO. Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE), an autosomal recessive disorder associated with both mtDNA depletion and multiple deletions, is now known to be due to loss‐of‐function mutations in the gene encoding thymidine phosphorylase. Increased plasma thymidine levels in MNGIE patients suggest that imbalanced nucleoside and nucleotide pools in mitochondria may lead to impaired replication of mtDNA. Future research will certainly lead to the identification of additional genetic causes of intergenomic communication defects and will likely provide insight into the normal “dialogue” between the two genomes.
Identifying the impact of G-Quadruplexes on Affymetrix 3' Arrays using Cloud Computing

A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays.
Evaluation of 2,3,5-triphenyltetrazolium chloride as a stain for detection and quantification of experimental cerebral infarction in rats.

We have evaluated the use of 2,3,5-triphenyltetrazolium chloride (TTC) as an histopathologic stain for identification of infarcted rat brain tissue. The middle cerebral artery (MCA) of 35 normal adult rats was occluded surgically. At various times after surgical occlusion, rats were sacrificed and brain slices were obtained and stained with TTC or hematoxolin and eosin (H & E); the size of the area of infarcted tissue stained by each method was quantified. In rats sacrificed 24 hr after occlusion of the MCA, the size of the area of infarction was 21 +/- 2% of the coronal section for TTC, and 21 +/- 2% for H & E (mean +/- S.D., N = 13). The size of areas of infarction determined by either staining method was not significantly different in area by the paired test, and a significant correlation between sizes determined by each method was found by linear regression analysis (r = 0.91, slope = 0.89, and the y intercept = 4.4%). Staining with TTC is a rapid, convenient, inexpensive, and reliable method for the detection and quantification of cerebral infarction in rats 24 hr after the onset of ischemia.
Semantic similarity analysis of protein data: assessment with biological features and issues

The integration of proteomics data with biological knowledge is a recent trend in bioinformatics. A lot of biological information is available and is spread on different sources and encoded in different ontologies (e.g. Gene Ontology). Annotating existing protein data with biological information may enable the use (and the development) of algorithms that use biological ontologies as framework to mine annotated data. Recently many methodologies and algorithms that use ontologies to extract knowledge from data, as well as to analyse ontologies themselves have been proposed and applied to other fields. Conversely, the use of such annotations for the analysis of protein data is a relatively novel research area that is currently becoming more and more central in research. Existing approaches span from the definition of the similarity among genes and proteins on the basis of the annotating terms, to the definition of novel algorithms that use such similarities for mining protein data on a proteome-wide scale. This work, after the definition of main concept of such analysis, presents a systematic discussion and comparison of main approaches. Finally, remaining challenges, as well as possible future directions of research are presented.
Efficient Subquadratic Space Complexity Binary Polynomial Multipliers Based on Block Recombination

Some applications like cryptography involve a large number of multiplications of binary polynomial. In this paper, we consider two-, three-, and four-way methods for parallel implementation of binary polynomial multiplication. We propose optimized three- and four-way split formulas which reduce the space and time complexity of the best known methods. Moreover, we present a block recombination method which provides some further reduction in the space complexity of the considered two-, three-, and four-way split multipliers.
Distribution-based similarity measures for multi-dimensional point set retrieval applications

Effective and efficient method of similarity assessment continues to be one of the most fundamental problems in multimedia data analysis. In case of retrieving relevant items from a collection of objects based on series of multivariate observations (e.g., searching the similar video clips in a repository to a query example), satisfactory performance cannot be expected using many conventional similarity measures based on the aggregation of element pairwise comparisons. Some correlation information among the individual elements has also been investigated to characterize each set of multi-dimensional points for ranked retrieval, by making use of an unwarranted assumption that the underlying data distribution has a particular parametric form. Motivated by this observation, this paper introduces a novel collective gauge of relevance ranking by evaluating the probabilities that point sets are consistent with the same distribution of the query. Two non-parametric hypothesis tests in statistics are justified to exploit the distributional discrepancy of samples for assessing the similarity between two ensembles of points. While our methodology is mainly presented in the context of video similarity search, it enjoys great flexibility and can be easily adapted to other applications involving generic multi-dimensional point set representation for each object such as human gesture recognition.
Collaborative Group Key Extraction Leveraging Received Signal Strength in Real Mobile Environments

Secret key generation among wireless devices using physical layer information of radio channel has been an attractive alternative for ensuring security in mobile environments. Received Signal Strength (RSS) based secret key extraction gains much attention due to its readily availability in wireless infrastructure. However, the problem of using RSS to generate keys among multiple devices to ensure secure group communication in practice remains open. In this work, we propose a framework for collaborative key generation among multiple wireless devices leveraging RSS. To deal with mobile devices not within each other’s communication range, we employ relay nodes to achieve reliable key extraction. To enable secure group communication, two protocols are developed to perform collaborative group key generation via star and chain topologies respectively. We further provide the theoretic analysis on the achievable secrecy rate for both star and chain topologies in the presence of an eavesdropper. Our prototype development using MICAz motes and extensive experiments using fading trend based key extraction demonstrate the feasibility of using RSS for group key generation in both indoor and outdoor environments, and concurrently achieving a lower bit mismatch rate compared to
A Comparison of Modulations for Energy Optimization in Wireless Sensor Network Links

We study the energy consumption of individual links in wireless sensor networks (WSN). Three widely used digital modulation schemes, i.e. MQAM, MPSK, and MFSK, are analyzed and compared. Both transmitted signal power and circuit power consumptions are considered. For modeling the signal power, we use the relation between channel capacity or cutoff rate and signal to noise ratio (SNR). By numerical calculation, we find the optimized parameters for minimizing the energy consumption per information bit in a point-to-point wireless link.
Improving text classification with vectors of reduced precision

This paper presents the analysis of the impact of a floating-point number precision reduction on the quality of text classification. The precision reduction of the vectors representing the data (e.g. TF-IDF representation in our case) allows for a decrease of computing time and memory footprint on dedicated hardware platforms. The impact of precision reduction on the classification quality was performed on 5 corpora, using 4 different classifiers. Also, dimensionality reduction was taken into account. Results indicate that the precision reduction improves classification accuracy for most cases (up to 25% of error reduction). In general, the reduction from 64 to 4 bits gives the best scores and ensures that the results will not be worse than with the full floating-point representation.
Tooling for Micro-and Nano-Imprinting and its Consequences for Manufacturing ISNM 2006 Paper No . : 09

Imprinting processes show remarkable potential for manufacturing devices with microto nanometer-scale features and planar 2-D geometry for a variety of applications. This work specifically considers tooling for thermoplastic imprinting processes such as hot microembossing (HME), and applications where the imprint process produces the actual functional features, such as microfluidic channels or optical elements (rather than, for example, imprinting an etch barrier). Tooling is critical for manufacturing by HME, since the tool is in intimate contact with the part and defines its geometry. Tool-to-tool variation also has a direct impact on the overall quality of imprinted parts. Tool life contributes to overall cost, as well as reducing quality if a large number of tools must be used and tool-to-tool variation is large. Various materials and techniques for producing tools are reviewed, and the unique characteristics of each process are considered with regard to their consequences for mass-manufacturing of polymer devices by HME.
The membrane remodeling protein Pex11p activates the GTPase Dnm1p during peroxisomal fission

Significance Peroxisomal fission is crucial for cell viability because peroxisome fission defects cause severe disease. The initial step in peroxisomal fission, membrane elongation, requires the membrane remodeling protein Peroxin 11 (Pex11p). Here, we identify an additional function for Pex11p, demonstrating that Pex11p also plays a crucial role in the final step of peroxisomal fission: membrane separation. We show that Pex11p functions as a GTPase activating protein (GAP) for Dynamin-related 1 (Dnm1p) and that this GAP activity is conserved from yeast to mammalians. This work identifies a previously unknown requirement for a GAP in dynamin-like protein function. The initial phase of peroxisomal fission requires the peroxisomal membrane protein Peroxin 11 (Pex11p), which remodels the membrane, resulting in organelle elongation. Here, we identify an additional function for Pex11p, demonstrating that Pex11p also plays a crucial role in the final step of peroxisomal fission: dynamin-like protein (DLP)-mediated membrane scission. First, we demonstrate that yeast Pex11p is necessary for the function of the GTPase Dynamin-related 1 (Dnm1p) in vivo. In addition, our data indicate that Pex11p physically interacts with Dnm1p and that inhibiting this interaction compromises peroxisomal fission. Finally, we demonstrate that Pex11p functions as a GTPase activating protein (GAP) for Dnm1p in vitro. Similar observations were made for mammalian Pex11β and the corresponding DLP Drp1, indicating that DLP activation by Pex11p is conserved. Our work identifies a previously unknown requirement for a GAP in DLP function.
Graphical representation of statistics hidden in unstructured data: A software application

The unstructured data, which volume grows exponentially, often hide important and even vital information for society and companies. It takes a lot of work to extract information such as the nature of consumption in a category of individuals, trends, etc. When it comes to statistical data, it is often very useful to synthesize this kind of information in the form of graphical representations. In this paper, we present an approach for processing unstructured data containing statistics in order to represent them graphically. An application that implements this process is also presented.
Host Factors That Interact with the Pestivirus N-Terminal Protease, Npro, Are Components of the Ribonucleoprotein Complex

ABSTRACT The viral N-terminal protease Npro of pestiviruses counteracts cellular antiviral defenses through inhibition of IRF3. Here we used mass spectrometry to identify a new role for Npro through its interaction with over 55 associated proteins, mainly ribosomal proteins and ribonucleoproteins, including RNA helicase A (DHX9), Y-box binding protein (YBX1), DDX3, DDX5, eIF3, IGF2BP1, multiple myeloma tumor protein 2, interleukin enhancer binding factor 3 (IEBP3), guanine nucleotide binding protein 3, and polyadenylate-binding protein 1 (PABP-1). These are components of the translation machinery, ribonucleoprotein particles (RNPs), and stress granules. Significantly, we found that stress granule formation was inhibited in MDBK cells infected with a noncytopathic bovine viral diarrhea virus (BVDV) strain, Kyle. However, ribonucleoproteins binding to Npro did not inhibit these proteins from aggregating into stress granules. Npro interacted with YBX1 though its TRASH domain, since the mutant C112R protein with an inactive TRASH domain no longer redistributed to stress granules. Interestingly, RNA helicase A and La autoantigen relocated from a nuclear location to form cytoplasmic granules with Npro. To address a proviral role for Npro in RNP granules, we investigated whether Npro affected RNA interference (RNAi), since interacting proteins are involved in RISC function during RNA silencing. Using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) silencing with small interfering RNAs (siRNAs) followed by Northern blotting of GAPDH, expression of Npro had no effect on RNAi silencing activity, contrasting with other viral suppressors of interferon. We propose that Npro is involved with virus RNA translation in the cytoplasm for virus particle production, and when translation is inhibited following stress, it redistributes to the replication complex. IMPORTANCE Although the pestivirus N-terminal protease, Npro, has been shown to have an important role in degrading IRF3 to prevent apoptosis and interferon production during infection, the function of this unique viral protease in the pestivirus life cycle remains to be elucidated. We used proteomic mass spectrometry to identify novel interacting proteins and have shown that Npro is present in ribosomal and ribonucleoprotein particles (RNPs), indicating a translational role in virus particle production. The virus itself can prevent stress granule assembly from these complexes, but this inhibition is not due to Npro. A proviral role to subvert RNA silencing through binding of these host RNP proteins was not identified for this viral suppressor of interferon.