Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-1 Vpr degrades the HLTF DNA translocase in T cells and macrophages

Significance Human immunodeficiency viruses (HIV) have developed strategies to interfere with DNA repair in host cells. Some DNA repair pathways represent restriction mechanisms that counteract the virus as soon as it penetrates into the host cell, before the establishment of an interferon response. Here we identify helicase-like transcription factor (HLTF) as a new protein degraded by the viral protein R (Vpr) from HIV-1. HLTF mediates the repair of stalled replication forks to bypass DNA lesions and ensure genome integrity. HLTF is degraded early after Vpr delivery to T lymphocytes or macrophages that represent relevant target cells for HIV. The discovery of HLTF as a DNA repair protein degraded by Vpr in infected cells paves the way for novel unexpected restriction mechanisms. Viruses often interfere with the DNA damage response to better replicate in their hosts. The human immunodeficiency virus 1 (HIV-1) viral protein R (Vpr) protein has been reported to modulate the activity of the DNA repair structure-specific endonuclease subunit (SLX4) complex and to promote cell cycle arrest. Vpr also interferes with the base-excision repair pathway by antagonizing the uracil DNA glycosylase (Ung2) enzyme. Using an unbiased quantitative proteomic screen, we report that Vpr down-regulates helicase-like transcription factor (HLTF), a DNA translocase involved in the repair of damaged replication forks. Vpr subverts the DDB1–cullin4-associated-factor 1 (DCAF1) adaptor of the Cul4A ubiquitin ligase to trigger proteasomal degradation of HLTF. This event takes place rapidly after Vpr delivery to cells, before and independently of Vpr-mediated G2 arrest. HLTF is degraded in lymphocytic cells and macrophages infected with Vpr-expressing HIV-1. Our results reveal a previously unidentified strategy for HIV-1 to antagonize DNA repair in host cells.
An Efficient Soft Error Detection in Multicore Processors Running Server Applications

In this paper, a throughput-aware transient fault detection method is presented with respect to the features of server processors. The proposed method takes the advantages of combination of reconfigurable redundant execution-based fault detection and speculative fault detection. The reconfigurable redundant execution-based fault detection method by using configuration manager module couples two free adjacent cores on which a thread will be executed, and decouples them when resources are limited for normal execution. This method exploits unused resources in the multi-core processors to ensure high throughput reliable execution. The speculative fault detection method uses a history of block addresses requested form L1 cache to L2 cache during thread execution to find abnormal execution behavior. In order to evaluate the proposed method, the alpha processor model is utilized in the context of Gem5 simulator. The experimental results showed that 70% of injected faults can be detected with negligible hardware overhead.
Study of Synchronization Technique in OFDM System

We present an OFDM frequency synchronization scheme. This paper presents an extended solution for the carrier frequency synchronization problem of OFDM. The scheme uses number of bits, modulation level, cyclic prefix, FFT size similarly to the algorithm proposed by Tilde Fusco (21). The proposed scheme attains considerably higher accuracy than the scheme by (21) requiring convolutional encoding data and viterbi decoding technique. Pilot Insertion and Cyclic Extension also included in the synchronization scheme. Our proposed method gives better results for different values of signal to noise ratio.
Expression, Purification, and Monitoring of Conformational Changes of hCB2 TMH67H8 in Different Membrane-Mimetic Lipid Mixtures Using Circular Dichroism and NMR Techniques

This work was intended to develop self-assembly lipids for incorporating G-protein coupled receptors (GPCRs) in order to improve the success rate for nuclear magnetic resonance spectroscopy (NMR) structural elucidation. We hereby report the expression and purification of uniformly 15N-labeled human cannabinoid receptor-2 domain in insect cell media. The domain was refolded by screening several membrane mimetic environments. Different q ratios of isotropic bicelles were screened for solubilizing transmembrane helix 6, 7 and 8 (TMH67H8). As the concentration of dimyristoylphosphocholine (DMPC) was increased such that the q ratio was between 0.16 and 0.42, there was less crowding in the cross peaks with increasing q ratio. In bicelles of q = 0.42, the maximum number of cross peaks were obtained and the cross peaks were uniformly dispersed. The receptor domain in bicelles beyond q = 0.42 resulted in peak crowding. These studies demonstrate that GPCRs folding especially in bicelles is protein-specific and requires the right mix of the longer chain and shorter chain lipids to provide the right environment for proper folding. These findings will allow further development of novel membrane mimetics to provide greater diversity of lipid mixtures than those currently being employed for GPCR stability and folding, which are critical for both X-ray and NMR studies of GPCRs.
The role of C4-binding protein and {beta }1H in proteolysis of C4b and C3b

Two forms of C4-binding protein (C4-bp) (C4-bp low, C4-bp high), which differ slightly in net charge and apparent molecular weight, as determined by SDS- PAGE, were separated by ion-exchange chromatography and contaminants removed with specific antisera. Both forms of C4-bp served as cofactors for the cleavage of C4b in solution by C3b inactivator, and the resulting fragments of the a’-chain of C4b had identical molecular weights. In addition, similarly to β1H, C4-bp low or high served as cofactors for the cleavage of fluid phase C3b by C3bINA. However, important quantitative differences between the activities of C4-bp and β1H were observed. With regard to C3b in solution, the cofactor activity of β1H was {approximately equal to}20 times greater than that of C4-bp on a weight basis. In relation to cell-bound C3b, the differences in activity were even more marked. Whereas β1H enhanced the effects of C3bINA on the erythrocyte intermediate EC3b, inhibiting the assembly of EC3bBb, C4-bp was without effect even at concentrations {approximately equal to}300 times greater than β1H. Therefore, under physiological conditions, it is likely that β1H is the key protein which controls the function of C3b, and that C4-bp activity is directed mainly toward the cleavage of C4b. We also examined the relation between C4-bp and the C3b-C4bINA cofactor described by Stroud and collaborators (3, 4). By functional, physico-chemical and immunological criteria, they are the same protein.
BUPTTeam at the NTCIR-13 STC-2 Task

This paper provides an overview of BUPTTeam’s system participated in the Short Text Conversation (STC) task of Chinese at NTICR-13. STC is a new NTCIR challenging task which is defined as an information retrieval (IR) or natural language generation problem. In this paper, we propose a novel method to generate appropriate comments based on the following four steps: 1) preprocessing, 2) model building, 3) candidate comments generation, 4) candidate comments ranking. The evaluation results show that our methods finish the task successfully and have positive effect on improving the evaluation measurement.
The use of electric fields in tissue engineering

The use of electric fields for measuring cell and tissue properties has a long history. However, the exploration of the use of electric fields in tissue engineering is only very recent. A review is given of the various methods by which electric fields may be used in tissue engineering, concentrating on the assembly of artificial tissues from its component cells using electrokinetics. A comparison is made of electrokinetic techniques with other physical cell manipulation techniques which can be used in the construction of artificial tissues.
LTE Measurements With CRS Interference Cancellation

Measurements of neighboring cells received power are one of the critical tasks of the user equipment in cellular networks. These measurements are used by the network to make decisions on user handover between cells and, therefore, have a significant impact on the network overall capacity. Recently, new requirements were added to the Long Term Evolution (LTE) specifications in order to improve the measurements accuracy in dense cellular environments by taking into account interference from neighboring base stations. In this letter, we propose a novel, low complexity and robust measurement algorithm for LTE that is capable of canceling interference from neighboring base stations and demonstrate its excellent performance through extensive simulations.
Clustering di-graphs for continuously verifying users according to their typing patterns

Traditionally users are authenticated based on a username and password. However, a logged station is still vulnerable to imposters when the user leaves her computer without logging off. Keystroke dynamics methods can be useful to continuously verify a user, after the authentication process has successfully ended. Within the last decade several studies proposed the use of keystroke dynamics as a behavioral biometric tool to verify users. We propose a new method, for compactly representing the keystroke patterns by joining similar pairs of consecutive keystrokes. The proposed method considers clustering di-graphs based on their temporal features. The proposed method was evaluated on 10 legitimate users and 15 imposters. Encouraging results suggest that the proposed method detection performance is better than that of existing methods. Specifically we reach a False Acceptance Rate (FAR) of 0.41% and a False Rejection Rate (FRR) of 0.63%.
MglA/SspA Complex Interactions Are Modulated by Inorganic Polyphosphate

The transcription factors MglA and SspA of Francisella tularensis form a heterodimer complex and interact with the RNA polymerase to regulate the expression of the Francisella pathogenicity island (FPI) genes. These genes are essential for this pathogen’s virulence and survival within host cells. Our goal was to determine if an intracellular metabolite modulate these protein/protein interactions. In this study, we identified inorganic polyphosphate (polyP) as a signal molecule that promotes the interaction of MglA and SspA from F. tularensis SCHU S4. Analysis of the Mgla/SspA interaction was carried out using a two-hybrid system. The Escherichia coli reporter strain contained a deletion on the ppK-ppX operon, inhibiting polyP synthesis. The interaction between MglA and SspA was significantly impaired, as was the interaction between the MglA/SspA complex and the regulatory protein, FevR, indicating the stabilizing effect of polyP. In F. tularensis, chromatin immune precipitation studies revealed that in the absence of polyP, binding of the MglA/SspA complex to the promoter region of the pdpD, iglA, fevR and ppK genes is decreased. Isothermal titration calorimetry (ITC) indicated that polyP binds directly to the MglA/SspA complex with high affinity (KD = 0.3 µM). These observations directly correlated with results obtained from calorimetric scans (DSC), where a strong shift in the mid-transition temperature (Tm) of the MglA/SspA complex was observed in the presence of polyP.
Decomposing bytecode verification by abstract interpretation

Bytecode verification is a key point in the security chain of the Java platform. This feature is only optional in many embedded devices since the memory requirements of the verification process are too high. In this article we propose an approach that significantly reduces the use of memory by a serial/parallel decomposition of the verification into multiple specialized passes. The algorithm reduces the type encoding space by operating on different abstractions of the domain of types. The results of our evaluation show that this bytecode verification can be performed directly on small memory systems. The method is formalized in the framework of abstract interpretation.
Design of scalable dense linear algebra libraries for multithreaded architectures: the LU factorization

The scalable parallel implementation, targeting SMP and/or multicore architectures, of dense linear algebra libraries is analyzed. Using the LU factorization as a case study, it is shown that an algorithm-by-blocks exposes a higher degree of parallelism than traditional implementations based on multithreaded BIAS. The implementation of this algorithm using the SuperMatrix runtime system is discussed and the scalability of the solution is demonstrated on two different platforms with 16 processors.
A Comprehensive Test Strategy for Network Protocols in Diverse Environment

In order to analyze important properties of network protocols, such as robustness and applicability, we may need exhaustive tests to observe effects of various factors under different settings. For recent protocols on dynamic, large-scale and environment-aware networks such as wireless sensor networks and mobile ad-hoc networks, we should consider many factors due to diversity of hardware profiles, upper/lower layer protocols and physical environments. In this paper, we propose a comprehensive test method to analyze the effect of (usually 10 or more) factors on such network systems. Our method takes a set of factors to be considered and their (representative) domain values as inputs, analyzes their effects on the systems, and determines dominant factors that have impact on the performance and their interactions. Instead of applying exhaustive tests that require all the combinations of domain values, we take a step-wise approach that examines step-by-step suspected sets of factors, which requires fewer combinations. We also justify this approach based on a reasonable fault model. The approach also contains an analytical method to identify the performance characteristics. Through realistic case studies, we show that we could find sets of dominant factors in wireless networks systematically.
Two independent mechanisms for escaping epidermal growth factor- mediated growth inhibition in epidermal growth factor receptor- hyperproducing human tumor cells

Human squamous cell carcinoma cell lines often possess increased levels of epidermal growth factor (EGF) receptor. The growth of these EGF receptor-hyperproducing cells is usually inhibited by EGF. To investigate the mechanism of EGF-mediated inhibition of cell growth, variants displaying alternate responses to EGF were isolated from two squamous cell carcinoma lines, NA and Ca9-22; these cell lines possess high numbers of the EGF receptor and an amplified EGF receptor (EGFR) gene. The variants were isolated from NA cells after several cycles of EGF treatment and they have acquired EGF-dependent growth. Scatchard plot analysis revealed a decreased level of EGF receptor in these ER variants as compared with parental NA cells. Southern blot analysis and RNA dot blot analysis demonstrated that the ER variants had lost the amplified EGFR gene. One variant isolated from Ca9-22 cells, CER-1, grew without being affected by EGF. CER-1 cells had higher numbers of EGF receptor than parental Ca9-22 but similar EGFR gene copy number. Flow cytometric analysis indicated an increase in ploidy and cell volume which may give rise to the increase in receptor number per cell. The EGF receptors on both Ca9-22 and CER-1 cells were autophosphorylated upon EGF exposure in a similar manner suggesting no obvious alteration in receptor tyrosine kinase. However, very efficient down-regulation of the EGF receptor occurred in CER-1 cells. These data suggest two independent mechanisms by which EGF receptor-hyperproducing cells escape EGF-mediated growth inhibition: one mechanism is common and involves the loss of the amplified EGFR genes, and another is novel and involves the efficient down-regulation of the cell-surface receptor.
Fabrication of 3D nanoimprint stamps with continuous reliefs using dose-modulated electron beam lithography and thermal reflow

3D electron beam lithography and thermal reflow were combined to fabricate structures with multilevel and continuous profiles. New shapes, smooth surfaces and sharp corners were achieved. By using exposure with variable doses, up to 20 steps were fabricated in a 500 nm thick resist with a lateral resolution of 200 nm. Steps were reflowed into continuous slopes by thermal post-processing, and were transferred into silicon substrates by proportional plasma etching. The method can be used for the fabrication of 3D nanoimprint stamps with both sharp features and continuous profiles.
Twentieth century turnover of Mexican endemic avifaunas: Landscape change versus climate drivers

Evaluation of various climate change factors on Mexican bird populations shows temperature has the strongest influence. Numerous climate change effects on biodiversity have been anticipated and documented, including extinctions, range shifts, phenological shifts, and breakdown of interactions in ecological communities, yet the relative balance of different climate drivers and their relationships to other agents of global change (for example, land use and land-use change) remains relatively poorly understood. This study integrated historical and current biodiversity data on distributions of 115 Mexican endemic bird species to document areas of concentrated gains and losses of species in local communities, and then related those changes to climate and land-use drivers. Of all drivers examined, at this relatively coarse spatial resolution, only temperature change had significant impacts on avifaunal turnover; neither precipitation change nor human impact on landscapes had detectable effects. This study, conducted across species’ geographic distributions, and covering all of Mexico, thanks to two large-scale biodiversity data sets, could discern relative importance of specific climatic drivers of biodiversity change.
Modelling of Cyclic Plasticity and Crack Propagation

An experimental and numerical study of the cyclic deformation and low-cycle fatigue behaviour of the aluminium alloy AlCu5BiPb–T8 is presented. The experimental program included monotonic tensile tests, symmetric and unsymmetric strain-controlled fatigue tests, fracture toughness tests, as well as fatigue crack initiation and propagation tests. Within the framework of numerical investigations an efficient algorithm for modelling of cyclic plasticity is proposed. This algorithm is implemented into the finite element program ABAQUS and applied to the analysis of a crack growth near the notch. The accuracy of the computational procedure is tested by comparing the computed results with the real experimental data.
Reply & Supply: Efficient crowdsourcing when workers do more than answer questions

Crowdsourcing works by distributing many small tasks to large numbers of workers, yet the true potential of crowdsourcing lies in workers doing more than performing simple tasks—they can apply their experience and creativity to provide new and unexpected information to the crowdsourcer. One such case is when workers not only answer a crowdsourcer’s questions but also contribute new questions for subsequent crowd analysis, leading to a growing set of questions. This growth creates an inherent bias for early questions since a question introduced earlier by a worker can be answered by more subsequent workers than a question introduced later. Here we study how to perform efficient crowdsourcing with such growing question sets. By modeling question sets as networks of interrelated questions, we introduce algorithms to help curtail the growth bias by efficiently distributing workers between exploring new questions and addressing current questions. Experiments and simulations demonstrate that these algorithms can efficiently explore an unbounded set of questions without losing confidence in crowd answers.
Vesicular systems for delivering conventional small organic molecules and larger macromolecules to and through human skin

The history of using vesicular systems for drug delivery to and through skin started nearly three decades ago with a study utilising phospholipid liposomes to improve skin deposition and reduce systemic effects of triamcinolone acetonide. Subsequently, many researchers evaluated liposomes with respect to skin delivery, with the majority of them recording localised effects and relatively few studies showing transdermal delivery effects. Shortly after this, transfersomes were developed with claims about their ability to deliver their payload into and through the skin with efficiencies similar to subcutaneous administration. Since these vesicles are ultradeformable, they were thought to penetrate intact skin deep enough to reach the systemic circulation. Their mechanisms of action remain controversial, with diverse processes being reported. Parallel to this development, other classes of vesicles were produced, with ethanol being included into the vesicles to provide flexibility (as in ethosomes); vesicles were constructed from surfactants and cholesterol (as in niosomes). The ultradeformable vesicles showed variable efficiency in delivering low-molecular-weight and macromolecular drugs. This article will critically evaluate vesicular systems for dermal and transdermal delivery of drugs, considering both their efficacy and their potential mechanisms of action.
Meshing Streaming Updates with Persistent Data in an Active Data Warehouse

Active data warehousing has emerged as an alternative to conventional warehousing practices in order to meet the high demand of applications for up-to-date information. In a nutshell, an active warehouse is refreshed online and thus achieves a higher consistency between the stored information and the latest data updates. The need for online warehouse refreshment introduces several challenges in the implementation of data warehouse transformations, with respect to their execution time and their overhead to the warehouse processes. In this paper, we focus on a frequently encountered operation in this context, namely, the join of a fast stream 5" of source updates with a disk-based relation R, under the constraint of limited memory. This operation lies at the core of several common transformations such as surrogate key assignment, duplicate detection, or identification of newly inserted tuples. We propose a specialized join algorithm, termed mesh join (MESHJOIN), which compensates for the difference in the access cost of the two join inputs by 1) relying entirely on fast sequential scans of R and 2) sharing the I/O cost of accessing R across multiple tuples of 5". We detail the MESHJOIN algorithm and develop a systematic cost model that enables the tuning of MESHJOIN for two objectives: maximizing throughput under a specific memory budget or minimizing memory consumption for a specific throughput. We present an experimental study that validates the performance of MESHJOIN on synthetic and real-life data. Our results verify the scalability of MESHJOIN to fast streams and large relations and demonstrate its numerous advantages over existing join algorithms.