Miracle-dz/UniFAR-FTUs huggingface dataset:
Usage of Integrin and Heparan Sulfate as Receptors for Mouse Adenovirus Type 1

ABSTRACT Adenovirus fiber knobs are the capsid components that interact with binding receptors on cells, while an Arg-Gly-Asp (RGD) sequence usually found in the penton base protein is important for the interaction of most adenoviruses with integrin entry receptors. Mouse adenovirus type 1 (MAV-1) lacks an RGD sequence in the virion penton base protein. We tested whether an RGD sequence found in the MAV-1 fiber knob plays a role in infection. Treatment of cells with a competitor RGD peptide or a purified recombinant RGD-containing fiber knob prior to infection resulted in reduced virus yields compared to those of controls, indicating the importance of the RGD sequence for infection. An investigation of the role of integrins as possible receptors showed that MAV-1 yields were reduced in the presence of EDTA, an inhibitor of integrin binding, and in the presence of anti-αv integrin antibody. Moreover, mouse embryo fibroblasts that were genetically deficient in αv integrin yielded less virus, supporting the hypothesis that αv integrin is a likely receptor for MAV-1. We also investigated whether glycosaminoglycans play a role in MAV-1 infection. Preincubation of MAV-1 with heparin, a heparan sulfate glycosaminoglycan analog, resulted in a decrease in MAV-1 virus yields. Reduced MAV-1 infectivity was also found with cells that genetically lack heparan sulfate or cells that were treated with heparinase I. Cumulatively, our data demonstrate that the RGD sequence in the MAV-1 fiber knob plays a role in infection by MAV-1, αv integrin acts as a receptor for the virus, and cell surface heparin sulfate glycosaminoglycans are important in MAV-1 infection.
Resource Classification Based Negotiation in Web Services

Trust establishment is necessary in every negotiation between entities from different security domains. It is seen as a first step before gaining access to protected resources. In this paper, we introduce a new classification methodology for protected resources. We use this classification to define the behavior of entities within a state based negotiation process. This process is enforced by two modules, the negotiation module and the exception treatment module. The first one intercepts all the requests for access. It collects credentials and exchanges policies according to the available negotiation policies. The second one is called by the first one whenever an exception is raised. An exception is a non negotiated denied access or locked negotiation.
Hard Tick Factors Implicated in Pathogen Transmission

Ticks are the most common arthropod vector, after mosquitoes, and are capable of transmitting the greatest variety of pathogens. For both humans and animals, the worldwide emergence or re-emergence of tick-borne disease is becoming increasingly problematic. Despite being such an important issue, our knowledge of pathogen transmission by ticks is incomplete. Several recent studies, reviewed here, have reported that the expression of some tick factors can be modulated in response to pathogen infection, and that some of these factors can impact on the pathogenic life cycle. Delineating the specific tick factors required for tick-borne pathogen transmission should lead to new strategies in the disruption of pathogen life cycles to combat emerging tick-borne disease.
Proteins encoded by a complex chloroplast transcription unit are each translated from both monocistronic and polycistronic mRNAs.

Chloroplast genes are typically organized into polycistronic transcription units that give rise to complex sets of overlapping RNAs through a series of processing steps. The functional significance of this complicated mode of expression is unknown. To determine whether processing of the primary transcript is required to create translatable mRNAs, the translational properties of the RNAs derived from the maize psbB gene cluster (containing the psbB, psbH, petB and petD genes) were examined. Almost all of the approximately 20 RNAs derived from this region co‐sediment with polysomes in sucrose gradients, suggesting that at least one coding region on most transcripts is translated. To determine which sequences are translated on each polycistronic RNA, antibodies to psbB, petB or petD proteins were used to immunoselect polysomes engaged in the synthesis of each protein. Northern and S1 nuclease analyses of the immunoselected RNAs revealed that (i) potential start codons within the petB and petD introns are not functional in translation; (ii) all transcripts containing spliced petB or petD sequences are translated to give these proteins, regardless of upstream or downstream sequences; (iii) psbB is translated from all transcripts encoding it. It is concluded that intercistronic processing is not required for translation of these RNAs, although certain processing steps may enhance translational efficiency.
Motion feature detection using steerable flow fields

The estimation and detection of occlusion boundaries and moving bars are important and challenging problems in image sequence analysis. Here, we model such motion features as linear combinations of steerable basis flow fields. These models constrain the interpretation of image motion, and are used in the same way as translational or affine motion models. We estimate the subspace coefficients of the motion feature models directly from spatiotemporal image derivatives using a robust regression method. From the subspace coefficients we detect the presence of a motion feature and solve for the orientation of the feature and the relative velocities of the surfaces. Our method does not require the prior computation of optical flow and recovers accurate estimates of orientation and velocity.
Accelerated Reliability Testing of InGaP/GaAs HBTs

Although InGaP/GaAs HBTs are usually reliable devices, their reliability can be compromised by processing or epitaxial material issues. Here we describe a number of techniques for determining the reliability of HBTs at accelerated rates compared with the normal threetemperature method. Some of these techniques show great promise for the rapid assessment of lifetime, which is especially useful for routine qualification of devices and for the rapid assessment of the suitability of processing or epitaxial material changes. Examples are chosen from epitaxial materials with both good and bad reliability.
Devonian deposits of the Baruunhuurai Terrane, Western Mongolia (IGCP 596 Field Workshop)

IGCP 596 (2011-2015) has a primary focus on climate change and biodiversity patterns in the Mid-Paleozoic (Early Devonian to Late Carboniferous). As a part of this project, we conducted a field workshop in western Mongolia in the summer of 2012. The goal was to locate fossiliferous sections that expose the stage boundaries from the Eifelian/Givetian boundary (Middle Devonian) to the Devonian/Carboniferous boundary to expand our knowledge of the key Devonian biotic and geochemical events such as the Frasnian/Famennian extinction event and the Kacak, Kellwasser and Hangenberg oceanographic events. During the field workshop, we examined sections in the Nariinhar Formation, Baruunhuurai Formation and Samnuuruul Formation from the Baruunhuurai Terrane.
Eurographics/siggraph Symposium on Computer Animation (2003) Unsupervised Learning for Speech Motion Editing

We present a new method for editing speech related facial motions. Our method uses an unsupervised learning technique, Independent Component Analysis (ICA), to extract a set of meaningful parameters without any annotation of the data. With ICA, we are able to solve a blind source separation problem and describe the original data as a linear combination of two sources. One source captures content (speech) and the other captures style (emotion). By manipulating the independent components we can edit the motions in intuitive ways.
Kv7.2 regulates the function of peripheral sensory neurons

The Kv7 (KCNQ) family of voltage‐gated K+ channels regulates cellular excitability. The functional role of Kv7.2 has been hampered by the lack of a viable Kcnq2‐null animal model. In this study, we generated homozygous Kcnq2‐null sensory neurons using the Cre‐Lox system; in these mice, Kv7.2 expression is absent in the peripheral sensory neurons, whereas the expression of other molecular components of nodes (including Kv7.3), paranodes, and juxtaparanodes is not altered. The conditional Kcnq2‐null animals exhibit normal motor performance but have increased thermal hyperalgesia and mechanical allodynia. Whole‐cell patch recording technique demonstrates that Kcnq2‐null sensory neurons have increased excitability and reduced spike frequency adaptation. Taken together, our results suggest that the loss of Kv7.2 activity increases the excitability of primary sensory neurons. J. Comp. Neurol. 522:3262–3280, 2014. © 2014 Wiley Periodicals, Inc.
A Framework for Ontology Creation and Management for Semantic Web

An ontology is a model of reality of the world and the concepts in the ontology must reflect this reality. Ontologies are building blocks of Semantic Web based systems. Creating ontologies is not an easy task and obviously there is no unique correct ontology for any domain. There are many other important issues related to the ontology domain engineering some of which are ontology integration, ontology mapping, ontology translation, ontology reuse and ontology consistency check. Due to unavailability of any standard for ontology building, ontologies on the same subject are different. There are different ontology tools that use different ontology languages. Due to these reasons, interoperability between the ontologies is very low. Current ontology tools concentrate mostly on the functions: create, edit, and inference. Most of the tools do not support the merging of heterogeneous domain ontologies. Moreover, the issues of duplicate information across documents and redundant annotations are major challenges of automatic ontology creation as the automatically populating ontology from diverse and distributed web resources poses significant challenges.
Land subsidence in southwest Cyprus revealed from C-band radar interferometry

Land subsidence is a major worldwide hazard, and causes many problems including: damage to public facilities such as bridges, roads, railways, electric power lines, underground pipes; damage to private and public buildings; and in some cases of low-lying land, can increase the risk of coastal flooding from storm surges and rising sea-levels. The island of Cyprus is famous for its complex geology, particularly in the southwest part of the island. Deposits of massive breccias (melange) are widely exposed in the Paphos District situated between the Troodos Mountains and the sea. These deposits are rich in clay minerals that are prone to landslide phenomena. With its global coverage and all-weather imaging capability, Interferometric SAR (InSAR) is revolutionizing our ability to image the Earth’s surface and the evolution of its shape over time. In this paper, an advanced InSAR time series technique, InSAR TS + AEM, has been employed to analysed C-band ERS and Envisat data collected over southwest Cyprus during the period from 1992 to 2010. Our InSAR time series results suggest that: (1) a total number of 274,619 coherent pixels with a density of 46 points per squared km were detected in the area of interest; and (2) clear surface displacements can be observed in several areas. The combination of archived ESA SAR datasets allows a long record (~18 years) of historic deformation to be measured over a large region. Ultimately this should help inform land managers in assessing land subsidence and planning appropriate remedial measures.
Learning to Re-Rank Questions in Community Question Answering Using Advanced Features

We study the impact of different types of features for question ranking in community Question Answering: bag-of-words models (BoW), syntactic tree kernels (TKs) and rank features. It should be noted that structural kernels have never been applied to the question reranking task, i.e., question to question similarity, where they have to model paraphrase relations. Additionally, the informal text, typically present in forums, poses new challenges to the use of TKs. We compare our learning to rank (L2R) algorithms against a strong baseline given by the Google rank (GR). The results show that (i) our shallow structures used in TKs are robust enough to noisy data and (ii) improving GR requires effective BoW features and TKs along with an accurate model of GR features in the used L2R algorithm.
A unified framework for simultaneous layout decomposition and mask optimization

In advanced technology nodes, layout decomposition and mask optimization are two key stages in integrated circuit design. Due to the inconsistency of the objectives of these two stages, the performance of conventional layout and mask optimization may be suboptimal. To tackle this problem, in this paper we propose a unified framework, which seamlessly integrates layout decomposition and mask optimization. We propose a gradient based approach to solve the unified mathematical formulation, as well as a set of discrete optimization techniques to avoid being stuck in local optimum. The conventional optimization process can be accelerated as some inferior decompositions can be smartly pruned in early stages. The experimental results show that the proposed unified framework can achieve more than 17 x speed-up compared with the conventional two-stage flow, meanwhile it can reduce EPE violations by 18%, and thus maintain better design quality.
Hierarchical classification of web content using Naïve Bayes approach

— This paper explores the use of hierarchical structure to classify a heterogeneous collection of web pages. In the hierarchical classification, a model learns to distinguish a second level category from all other categories that are within the same top level. In the flat non hierarchical classification, a model distinguishes a second level category from all existing second level categories. We use Naïve Bayes classifier which has been proved to be effective for web content classification, but has not been previously explored in the case of hierarchical classification. This paper analyses the feasibility of a web page classifier which exploits the hierarchical structure of categories and studies their recall, precision and F-measure scores.
Effect of a signal decorrelation on adaptive filtering algorithms for acoustic echo cancellation

Acoustic echo cancellation (AEC) is a well-known issue in voice communication systems; it is used to reduce undesired echoes. Adaptive filtering is generally employed for AEC. However, the performances of adaptive filtering algorithms are limited for a correlated input signal. This paper presents the effect of an input signal decorrelation on the performances of adaptive filtering algorithms for AEC application. Therefore, normalized least mean squares (NLMS) algorithm is used, performed by: USASI noise and speech signals. Simulation results show an improvement in term of convergence speed of NLMS algorithm for the decorrelated signal compared to the original signal.
Exploring Pair Programming in Distributed Object-Oriented Team Projects

Previous research [1, 4] has indicated that pair programming is better than individual programming when the pairs are physically collocated. However, important questions arise: How effective is pair programming if the pairs are not physically next to each other? What if the programmers are geographically distributed? An experiment was conducted at North Carolina State University to compare the different working arrangements of student teams developing objectoriented software. The teams were both collocated and in distributed environments; some teams practiced pair programming while others did not. The results of the experiment indicate that it is feasible to develop software using distributed pair programming, and that the resulting software is comparable to software developed in collocated or virtual teams. Our findings will be of significant help to educators dealing with team projects for distance-learning students, as well as organizations that are involved in distributed development of software.
Single Ion Occupancy and Steady-state Gating of Na Channels in Squid Giant Axon

The properties of the small fraction of tetrodotoxin (TTX)-sensitive Na channels that remain open in the steady state were studied in internally dialyzed voltage clamped squid giant axons. The observed Ussing flux ratio exponent (n′) of 0.97 ± 0.03 (calculated from simultaneous measurements of TTX-sensitive current and 22Na efflux) and nonindependent behavior of Na current at high internal [Na] are explained by a one-site (“1s”) permeation model characterized by a single effective binding site within the channel pore in equilibrium with internal Na ions (apparent equilibrium dissociation constant K Nai(0) = 0.61 ± 0.08 M). Steady-state open probability of the TTX-sensitive channels can be modeled by the product p a p ∞, where p a represents voltage-dependent activation described by a Boltzmann distribution with midpoint V a = −7 mV and effective valence z a = 3.2 (Vandenberg, C.A., and F. Bezanilla. 1991. Biophys. J. 60:1499–1510) coupled to voltage-independent inactivation by an equilibrium constant (Bezanilla, F., and C.M. Armstrong. 1977. J. Gen. Physiol. 70:549–566) K eq = 770. The factor p ∞ represents voltage-dependent inactivation with empirical midpoint V ∞= −83 ± 5 mV and effective valence z ∞ = 0.55 ± 0.03. The composite p a p ∞ 1s model describes the steady-state voltage dependence of the persistent TTX-sensitive current well.
A TRANSPLANTABLE RABBIT CARCINOMA ORIGINATING IN A VIRUS-INDUCED PAPILLOMA AND CONTAINING THE VIRUS IN MASKED OR ALTERED FORM

A squamous cell carcinoma derived from a virus-induced rabbit papilloma has been propagated in fourteen successive groups of animals. It grows rapidly now in most individuals to which it is transplanted, killing early and metastasizing frequently. The original cancer was the outcome of alterations in epidermal cells already rendered neoplastic by the virus, and the latter, or an agent nearly related to it, has persisted and increased in the malignant tissue, as a study of the blood of the first ten groups of cancerous animals has shown. An antibody capable of specifically neutralizing the virus in vitro appeared in the blood of every new host in which the tumor enlarged progressively, and reached a titer comparable with that obtaining in animals which had long carried large papillomas. The antibody was absent from normal rabbits and those in which the cancer failed to grow. The implications of these facts are considered.
A Systematic Review and Meta-Analysis of Perforator-Pedicled Propeller Flaps in Lower Extremity Defects: Identification of Risk Factors for Complications

Background: Currently, increased interest in the perforator-pedicled propeller flap should not obscure the fact that it is, in reality, a complex procedure requiring experience and monitoring similar to free flaps. Through a meta-analysis, the authors aimed to identify the risk factors of perforator-pedicled propeller flap failure in lower extremity defects. Methods: The MEDLINE, PubMed Central, Embase, and Cochrane databases were searched from 1991 to May of 2014 for articles describing perforator-pedicled propeller flaps in the lower extremity. The study selection met the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Fixed-effects models were used. Results: Forty articles complied with the inclusion criteria, representing 428 perforator-pedicled propeller flaps. The most common cause was posttraumatic (55.2 percent). Most of the defects were at the distal third of the lower leg (45.6 percent). The arc of rotation was 180 degrees for 34.3 percent. Complications were found in 25.2 percent, including partial necrosis (10.2 percent) and complete necrosis (3.5 percent). Complete flap survival was found in 84.3 percent. The authors identified three significant risk factors: age older than 60 years (relative risk, 1.61; p = 0.03), diabetes (relative risk, 2.00; p = 0.02), and arteriopathy (relative risk, 3.12; p = 0.01). No significant results were found regarding smoking status other than a tendency (p = 0.06), acute cause (p = 0.59), posttraumatic cause (p = 0.97), distal third of the lower leg (p = 0.66), fascia inclusion (p = 0.70), and pedicle rotation greater than 120 degrees (p = 0.41). Conclusion: Age older than 60 years, diabetes, and arteriopathy are significant risk factors of perforator-pedicled propeller flap complications in the lower extremity. CLINICAL QUESTION/LEVEL OF EVIDENCE: Risk, IV.
A COMPARISON OF DELTA CHANGE AND DOWNSCALED GCM SCENARIOS FOR THREE MOUNTAINOUS BASINS IN THE UNITED STATES 1

ABSTRACT: Simulated daily precipitation, temperature, and runoff time series were compared in three mountainous basins in the United States: (1) the Animas River basin in Colorado, (2) the East Fork of the Carson River basin in Nevada and California, and (3) the Cle Elum River basin in Washington State. Two methods of climate scenario generation were compared: delta change and statistical downscaling. The delta change method uses differences between simulated current and future climate conditions from the Hadley Centre for Climate Prediction and Research (HadCM2) General Circulation Model (GCM) added to observed time series of climate variables. A statistical downscaling (SDS) model was developed for each basin using station data and output from the National Center for Environmental Prediction/National Center for Atmospheric Research (NCEPINCAR) reanalysis regridded to the scale of HadCM2. The SDS model was then used to simulate local climate variables using HadCM2 output for current and future conditions. Surface climate variables from each scenario were used in a precipitation‐runoff model. Results from this study show that, in the basins tested, a precipitation‐runoff model can simulate realistic runoff series for current conditions using statistically down‐scaled NCEP output. But, use of downscaled HadCM2 output for current or future climate assessments are questionable because the GCM does not produce accurate estimates of the surface variables needed for runoff in these regions. Given the uncertainties in the GCMs ability to simulate current conditions based on either the delta change or downscaling approaches, future climate assessments based on either of these approaches must be treated with caution.
Findings of the 2012 Workshop on Statistical Machine Translation

This paper presents the results of the WMT12 shared tasks, which included a translation task, a task for machine translation evaluation metrics, and a task for run-time estimation of machine translation quality. We conducted a large-scale manual evaluation of 103 machine translation systems submitted by 34 teams. We used the ranking of these systems to measure how strongly automatic metrics correlate with human judgments of translation quality for 12 evaluation metrics. We introduced a new quality estimation task this year, and evaluated submissions from 11 teams.