Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid Typing of Human Adenoviruses by a General PCR Combined with Restriction Endonuclease Analysis

ABSTRACT We have developed a system for rapid typing of adenoviruses (Ads) based on a combination of PCR and restriction endonuclease (RE) digestion (PCR-RE digestion). Degenerated consensus primers were designed, allowing amplification of DNA from all 51 human Ad prototype strains and altogether 44 different genome variants of Ad serotypes 1, 3, 4, 5, 7, 11, 19, 40, and 41. The 301-bp amplimer of 22 prototype strains representing all six subgenera and the genome variant was selected as a target for sequencing to look for subgenus and genome type variabilities. The sequences obtained were used to facilitate the selection of specific REs for discrimination purposes in a diagnostic assay by following the concept of cleavage or noncleavage of the 301-bp amplimer. On the basis of these results, a flowchart was constructed, allowing identification of subgenus B:2 and D serotypes and almost complete distinction of subgenus A, B:1, C, E, and F serotypes. Application of the PCR-RE digestion system to clinical samples allowed typing of 34 of 40 clinical samples positive for Ad. The genome type determined by this method was identical to that obtained by traditional RE typing of full-length Ad DNA. The remaining six samples were positive only after a nested PCR. Therefore, to reduce the risk of false-negative results, samples scored negative by the PCR-RE digestion system should be evaluated by the described nested PCR. Used in combination, the PCR-RE digestion method and the nested PCR provide a reliable and sensitive system that can easily be applied to all kinds of clinical samples when rapid identification of adenoviruses is needed.
Ocin tsim-DVFS Aware Simulator for NoCs

Networks-on-Chip (NoCs) are a general purpose, scalable replacements for shared medium wired interconnec ts offering many practical applications in industry. Dynamic Voltage Frequency Scaling (DVFS) is a technique whereby a chip’s voltage-frequency levels are varied at run time, often usedto conserve dynamic power. Various DVFS-based optimization t echniques have been proposed; however, few have been implement d, in part due to the resources required to validate architectural decisions through prototyping. As a result, designers are f aced with a lack of insight into potential power savings or performance gains at early architecture stages. This paper proposes a DV FS aware NoC simulator with support for per node power-frequency modeling to allow the fine-tuning of such optimization techniques early on in the design cycle. The proposed simulator also pro vides a framework for benchmarking various candidate strategiesto allow selective prototyping.
JFFS : The Journalling Flash File System

Until recently, the common approach to using Flash memory technology in embedded devices has been to use a pseudo-filesystem on the flash chips to emulate a standard block device and provide wear levelling, and to use a normal file system on top of that emulated block device. JFFS is a log-structured file system designed by Axis Communications AB in Sweden specifically for use on flash devices in embedded systems, which is aware of the restrictions imposed by flash technology and which operates directly on the flash chips, thereby avoiding the inefficiency of having two journalling file systems on top of each other. This paper will give an overview of the restrictions imposed by flash technology and hence the design aims of JFFS, and the implementation of both JFFS and the improvements made in version 2, including compression and more efficient garbage collection.
Interpolation Algorithms of DFT for Parameters Estimation of Sinusoidal and Damped Sinusoidal Signals

Discrete Fourier Transform (DFT) is probably the most popular signal processing tool. Wide DFT use is partly dedicated to fast Fourier Transform (FFT) algorithms (Cooley & Tukey, 1965, Oppenheim et al., 1999, Lyons, 2004). DFT may also be efficiently computed by recursive algorithms in the window sliding by one sample (Jacobsen & Lyons, 2003, Duda, 2010). Unfortunately, DFT has two main drawbacks that deteriorate signal analysis which are (Harris, 1978, Oppenheim et al., 1999): 1) spectral leakage, and 2) sampling of the continuous spectrum of the discrete signal. Spectral leakage is reduced by proper time windows, and the frequency bins between DFT bins are computed by interpolated DFT (IpDFT) algorithms, thoroughly presented in this chapter.
Thrombin induces the release of the Y-box protein dbpB from mRNA: A mechanism of transcriptional activation

We have recently demonstrated that thrombin induces expression of the platelet-derived growth factor B-chain gene in endothelial cells (EC) through activation of the Y-box binding protein DNA-binding protein B (dbpB). We now present evidence that dbpB is activated by a novel mechanism: proteolytic cleavage leading to release from mRNA, nuclear translocation, and induction of thrombin-responsive genes. Cytosolic, full-length dbpB (50 kDa) was rapidly cleaved to a 30-kDa species upon thrombin stimulation of EC. This truncated, “active” dbpB exhibited nuclear localization and binding affinity for the thrombin response element sequence, which is distinct from the Y-box sequence. Oligo(dT) affinity chromatography revealed that cytosolic dbpB from control EC, but not active dbpB from thrombin-treated EC, was bound to mRNA. Latent dbpB immunoprecipitated from cytosolic extracts of control EC was activated by ribonuclease treatment. Furthermore, when EC cytosolic extracts were subjected to Nycodenz gradient centrifugation, latent dbpB fractionated with mRNA, whereas active dbpB fractionated with free proteins. The cytosolic retention domain of dbpB, which we localized to the region 247–267, was proteolytically cleaved during its activation. In contrast to full-length dbpB, truncated dbpB stimulated platelet-derived growth factor B-chain and tissue factor promoter activity by over 5-fold when transiently cotransfected with reporter constructs. These results suggest a novel mode of transcription factor activation in which an agonist causes release from mRNA of a latent transcription factor leading to its transport to the nucleus and its regulation of target gene expression.
Finding a large hidden clique in a random graph

We consider the following probabilistic model of a graph on n labeled vertices. First choose a random graph Gn ,1 r 2 ,and then choose randomly a subset Q of vertices of size k and force it to be a clique by joining every pair of vertices of Q by an edge. The problem is to give a polynomial time algorithm for finding this hidden clique almost surely for various values of k. This question was posed independently, in various variants, by Jerrum and by Kucera. In this paper we present an efficient algorithm for all k ) cn 0.5 , for ˇ 0.5 . 0.5 any fixed c ) 0, thus improving the trivial case k ) cn log n . The algorithm is based on the spectral properties of the graph. Q 1998 John Wiley & Sons, Inc. Random Struct. Alg. , 13, 457)466, 1998
Comparison of Various Template Matching Techniques for Face Recognition

This paper describes different methods for the pattern matching and face recognition using the template matching technique. Many different pattern matching techniques have been developed but more efficient and robust methods are needed [1]. The pattern matching algorithm is used to identify the patterns available in image. These algorithms shown in this paper generalize and extend the concept of convolution, normalized cross correlation (NCC), zero mean normalized cross correlation (ZNCC), sum of absolute difference (SAD), optimized sum of absolute difference (OSAD), zero mean sum of absolute difference (ZSAD), optimized sum of squared difference (OSSD), zero mean sum of square difference (ZSSD), locally scale sum of square difference (LSSD), sum of hamming distance (SHD). Pattern matching is a significant job of the prototype detection process in today's world for eradicating the structural and efficient activities in a given image. Even though the pattern matching techniques are normally utilized in information processing and computer vision, it can be established in daily tasks. Template matching is conceptually a simple process, this need to match a template to an image where the template pattern is a part of the source image that contains the shape inside it [1].
Adhesives and adhesive tapes

Adhesion theories raw materials for adhesives classification for adhesives individual adhesive systems (adhesives that set without a chemical reaction adhesives setting by chemical reaction) bonding techniques testing of adhesives applications of adhesives (bookbinding gluing of wood and wooden materials footwear adhesives bonding of plastics bonding of elastomers bonding of metals adhesives for wallcoverings floorcovering adhesives building construction adhesives adhesives for bonding textile fabrics flocking adhesives adhesives for bonding glass, in automobile manufacture, in aircraft construction and sealants in electronics medical adhesives household adhesives applications of anaerobic adhesives) economic aspects.
Efficacy of cytokine-induced killer cell infusion as an adjuvant immunotherapy for hepatocellular carcinoma: a systematic review and meta-analysis

This study was designed to evaluate the efficacy and safety of cytokine-induced killer (CIK) cell-based immunotherapy as an adjuvant therapy for hepatocellular carcinoma (HCC). Published studies were identified by searching Medline, Cochrane, EMBASE, and Google Scholar databases with the keywords: cytokine-induced killer cell, hepatocellular carcinoma, and immunotherapy. The outcomes of interest were overall survival, progression-free survival, and disease-free survival. Eight randomized controlled trials (RCTs), six prospective studies, and three retrospective studies were included. The overall analysis revealed that patients in the CIK cell-treatment group had a higher survival rate (pooled hazard ratio (HR) =0.594, 95% confidence interval [CI] =0.501–0.703, P<0.001). Patients treated with CIK cells in non-RCTs had a higher progression-free survival rate (pooled HR =0.613, 95% CI =0.510–0.738, P<0.001). However, CIK cell-treated patients in RCTs had progression-free survival rates similar to those of the control group (pooled HR =0.700, 95% CI =0.452–1.084, P=0.110). The comparison between pooled results of RCTs and non-RCTs regarding the progression-free survival rate did not reach statistical significance. Patients in the CIK cell-treatment group had lower rates of relapse in RCTs (pooled HR =0.635, 95% CI =0.514–0.784, P<0.001). Similar results were found when non-RCT and RCTs were pooled (pooled HR =0.623, 95% CI =0.516–0.752, P<0.001). Adjuvant CIK cell-based immunotherapy is a promising therapeutic approach that can improve overall survival and reduce recurrence in patients with HCC.
Genomic Information Retrieval

The in-silico revolution has changed how biologists characterise DNA and protein sequences. As a first step to exploring the structure and function of an unknown sequence, biologists search large genomic databases for similar sequences. This process of genomic information retrieval has allowed significant advances in biology and led to advancements in critical areas such as cancer research. In this paper, we present a background to genomic information retrieval by describing the problems, collections, and techniques used by biologists for searching large collections. In particular, we identify the problems inherent in the popular search techniques, and discuss how index-based approaches may be applied to solve these problems. We conclude by offering the challenge that information retrieval specialists must continue to make significant contributions to allow further advances in molecular biology research.
Nepheli : Scalable Decentralized Authorization in Federated File Services

We consider the problem of remote access control in federated file services across independent administrative domains. Existing approaches either establish complex trust relationships between distinct domains or require frequent update operations among different authentication and authorization services. In order to improve the manageability and scalability of current solutions, we propose to specify remote access rights on the basis of federation-wide user groups (virtual groups) instead of individual users. The members of a virtual group are users that originate from different domains and undertake a common role in the federation. The realization of a virtual group has a two-layer structure, where the upper layer consists of domains, and the lower layer consists of users contributed by the participating domains. We certify the domain membership of a virtual group at the authentication service of the domain that creates the group. User access requests carry an extended certificate that is issued by the local authentication service and encloses a list of the virtual groups whose members include the user. In order to authorize a remote access, the resource provider simply applies its local policy that pertains to the virtual groups of the requesting user. We achieve low maintenance cost because the remote update traffic only distributes the domain membership of virtual groups to the user authentication and the resource authorization services across the federation. We implement a prototype of our architecture and experimentally demonstrate reduced cost and improved scalability properties.
Analysis of Galactic Spectra using Noise-Aware Learning Algorithms

We introduce a novel learning algorithm for noise elimination. Our algorithm is based on the re-measurement idea for the correction of erroneous observations and is able to discriminate between noisy and noiseless observations by using kernel methods. We apply our noiseaware algorithms to the prediction of stellar population parameters, a challenging astronomical problem. Experimental results adding noise and useful anomalies to the data show that our algorithm provides a significant reduction in error, without having to eliminate any observation from the original dataset.
PKR and RNase L Contribute to Protection against Lethal West Nile Virus Infection by Controlling Early Viral Spread in the Periphery and Replication in Neurons

ABSTRACT West Nile virus (WNV) is a neurotropic, mosquito-borne flavivirus that can cause lethal meningoencephalitis. Type I interferon (IFN) plays a critical role in controlling WNV replication, spread, and tropism. In this study, we begin to examine the effector mechanisms by which type I IFN inhibits WNV infection. Mice lacking both the interferon-induced, double-stranded-RNA-activated protein kinase (PKR) and the endoribonuclease of the 2′,5′-oligoadenylate synthetase-RNase L system (PKR−/− × RL−/−) were highly susceptible to subcutaneous WNV infection, with a 90% mortality rate compared to the 30% mortality rate observed in congenic wild-type mice. PKR−/− × RL−/− mice had increased viral loads in their draining lymph nodes, sera, and spleens, which led to early viral entry into the central nervous system (CNS) and higher viral burden in neuronal tissues. Although mice lacking RNase L showed a higher CNS viral burden and an increased mortality, they were less susceptible than the PKR−/− × RL−/− mice; thus, we also infer an antiviral role for PKR in the control of WNV infection. Notably, a deficiency in both PKR and RNase L resulted in a decreased ability of type I IFN to inhibit WNV in primary macrophages and cortical neurons. In contrast, the peripheral neurons of the superior cervical ganglia of PKR−/− × RL−/− mice showed no deficiency in the IFN-mediated inhibition of WNV. Our data suggest that PKR and RNase L contribute to IFN-mediated protection in a cell-restricted manner and control WNV infection in peripheral tissues and some neuronal subtypes.
Cashing in on caching: on-demand contract design with linear pricing

There has been increasing interest in designing and developing highly scalable infrastructures to support the efficient distribution of content. This has led to the recent development of content-oriented network architectures that rely on on-demand caching. This paper addresses the question of how a cache provider can monetize its service. Standard cache management policies such as least recently used (LRU) treat different content in a strongly coupled manner that makes it difficult for a cache provider to design individualized contracts. We propose the use of timer-based caching for the purpose of designing contracts, which allow providers to monetize caching. We focus on on-demand request-based contracts that allow content providers (CPs) to negotiate contracts at the time that requests are made. We propose and analyze three variations, one where a contract is negotiated only at the time of a miss, and two where contracts are negotiated at the times of both misses and hits. The latter two differ from one another according to whether pricing is based on cache occupancy (time content spends in the cache) or on request rate. We conclude that the first one is least preferable and that the last one provides the provider greater opportunity for profit and greater flexibility to CPs.
Intact apoptosis signaling in myeloid leukemia cells determines treatment outcome in childhood AML.

Recently we reported that intact apoptosis signaling is indicative of favorable outcome in childhood acute lymphoblastic leukemia. Here we addressed this issue in 45 pediatric acute myeloid leukemia patients analyzing 2 core apoptogenic events: cytochrome c release and caspase-3 activation. In patients with good prognosis cytochrome c release was clearly found to be caspasedependent and correlated with activated caspase-3, indicating that activation of initiator or amplifier caspases such as caspase-8 together with an intact apoptosome function are elementary for favorable outcome. The functional integrity of this apoptogenic checkpoint is reflected by the parameter caspase-dependent cytochrome c-related activation of caspase-3 (CRAC(dep)). Patients with positive CRAC(dep) values (intact signaling) exhibited superior survival compared with CRAC(dep) negative patients (deficient signaling). Thus, the propensity to undergo apoptosis of leukemia cells is an important feature for favorable treatment outcome and may serve as an additional stratification tool for pediatric AML patients. This trial was registered at www.ClinicalTrials. gov as #NCT00111345.
Hecke C*-algebras and semi-direct products

Abstract We analyse Hecke pairs (G,H) and the associated Hecke algebra $\mathcal{H}$ when G is a semi-direct product N ⋊ Q and H = M ⋊ R for subgroups M ⊂ N and R ⊂ Q with M normal in N. Our main result shows that, when (G,H) coincides with its Schlichting completion and R is normal in Q, the closure of $\mathcal{H}$ in C*(G) is Morita–Rieffel equivalent to a crossed product I⋊βQ/R, where I is a certain ideal in the fixed-point algebra C*(N)R. Several concrete examples are given illustrating and applying our techniques, including some involving subgroups of GL(2,K) acting on K2, where K = ℚ or K = ℤ[p−1]. In particular we look at the ax + b group of a quadratic extension of K.
Effective Moduli of Random Short Fiber Composite: A Probabilistic Study

The behavior of short fiber composites are characterized by scatter in mechanical properties due to randomness in fiber orientation, spacing and packing arrangement etc. Thus probabilistic analysis is essential to study its behavior properly. A simulation method is proposed in the present work for computing statistical property of effective moduli of short fiber composite system in an isotropic matrix phase, appropriate to thin section in a state of plane stress. The effective isotropic properties of the composites derived are in terms of elastic properties of each phase and the volume concentration of the fiber phase. Changes in elastic moduli due to abovementioned parameters are taken into consideration in simulation algorithm. A case study is performed to elucidate the proposed algorithm and comparison is made with the available results.
A Text Similarity Meta-Search Engine Based on Document Fingerprints and Search Results Records

The retrieval of similar documents from the Web using documents as input instead of key-term queries is not currently supported by traditional Web search engines. One approach for solving the problem consists of fingerprint the document's content into a set of queries that are submitted to a list of Web search engines. Afterward, results are merged, their URLs are fetched and their content is compared with the given document using text comparison algorithms. However, the action of requesting results to multiple web servers could take a significant amount of time and effort. In this work, a similarity function between the given document and retrieved results is estimated. The function uses as variables features that come from information provided by search engine results records, like rankings, titles and snippets. Avoiding therefore, the bottleneck of requesting external Web Servers. We created a collection of around 10,000 search engine results by generating queries from 2,000 crawled Web documents. Then we fitted the similarity function using the cosine similarity between the input and results content as the target variable. The execution time between the exact and approximated solution was compared. Results obtained for our approximated solution showed a reduction of computational time of 86% at an acceptable level of precision with respect to the exact solution of the web document retrieval problem.
Regulation of the Subcellular Localization of Cyclic AMP-Dependent Protein Kinase in Response to Physiological Stresses and Sexual Differentiation in the Fission Yeast Schizosaccharomyces pombe

ABSTRACT We describe regulation of the subcellular localization of cyclic AMP (cAMP)-dependent protein kinase (PKA) regulatory (Cgs1p) and catalytic (Pka1p) subunits in the fission yeast Schizosaccharomyces pombe in response to physiological stresses and during sexual differentiation as determined by fluorescence microscopy of the Cgs1-green fluorescent protein (GFP) and Pka1-GFP fusion proteins, respectively. In wild-type S. pombe cells cultured to log phase under normal growth conditions, Cgs1p and Pka1p are concentrated in the nucleus and more diffusely present in the cytoplasm. Nuclear localization of both proteins is dependent on cAMP, since in cells lacking adenylate cyclase they are detectable only in the cytoplasm. In cells lacking Cgs1p or both Cgs1p and adenylate cyclase, Pka1p is concentrated in the nucleus, demonstrating a role for Cgs1p in the nuclear exclusion of Pka1p. Nuclear-cytoplasmic redistribution of Cgs1p and Pka1p is triggered by growth in glucose-limited or hyperosmotic media and in response to stationary-phase growth. In addition, both proteins are excluded from the nucleus in mating cells undergoing karyogamy and subsequently concentrated in postmeiotic spores. Cgs1p is required for subcellular redistribution of Pka1p induced by growth in glucose-limited and hyperosmotic media and during karyogamy but is not required for Pka1p redistribution triggered by stationary-phase growth or for the enrichment of Pka1p in spores. Our results demonstrate that PKA localization is regulated by cAMP and regulatory subunit-dependent and -independent mechanisms in S. pombe.
Automatically Building Training Examples for Entity Extraction

In this paper we present methods for automatically acquiring training examples for the task of entity extraction. Experimental evidence show that: (1) our methods compete with a current heavily supervised state-of-the-art system, within 0.04 absolute mean average precision; and (2) our model significantly outperforms other supervised and unsupervised baselines by between 0.15 and 0.30 in absolute mean average precision.