Miracle-dz/UniFAR-FTUs huggingface dataset:
Differences in Processing Determinants of Nonstructural Polyprotein and in the Sequence of Nonstructural Protein 3 Affect Neurovirulence of Semliki Forest Virus

ABSTRACT The A7(74) strain of Semliki Forest virus (SFV; genus Alphavirus) is avirulent in adult mice, while the L10 strain is virulent in mice of all ages. It has been previously demonstrated that this phenotypic difference is associated with nonstructural protein 3 (nsP3). Consensus clones of L10 (designated SFV6) and A7(74) (designated A774wt) were used to construct a panel of recombinant viruses. The insertion of nsP3 from A774wt into the SFV6 backbone had a minor effect on the virulence of the resulting recombinant virus. Conversely, insertion of nsP3 from SFV6 into the A774wt backbone or replacement of A774wt nsP3 with two copies of nsP3 from SFV6 resulted in virulent viruses. Unexpectedly, duplication of nsP3-encoding sequences also resulted in elevated levels of nsP4, revealing that nsP3 is involved in the stabilization of nsP4. Interestingly, replacement of nsP3 of SFV6 with that of A774wt resulted in a virulent virus; the virulence of this recombinant was strongly reduced by functionally coupled substitutions for amino acid residues 534 (P4 position of the cleavage site between nsP1 and nsP2) and 1052 (S4 subsite residue of nsP2 protease) in the nonstructural polyprotein. Pulse-chase experiments revealed that A774wt and avirulent recombinant virus were characterized by increased processing speed of the cleavage site between nsP1 and nsP2. A His534-to-Arg substitution specifically activated this cleavage, while a Val1052-to-Glu substitution compensated for this effect by reducing the basal protease activity of nsP2. These findings provide a link between nonstructural polyprotein processing and the virulence of SFV. IMPORTANCE SFV infection of mice provides a well-characterized model to study viral encephalitis. SFV also serves as a model for studies of alphavirus molecular biology and host-pathogen interactions. Thus far, the genetic basis of different properties of SFV strains has been studied using molecular clones, which often contain mistakes originating from standard cDNA synthesis and cloning procedures. Here, for the first time, consensus clones of SFV strains were used to map virulence determinants. Existing data on the importance of nsP3 for virulent phenotypes were confirmed, another determinant of neurovirulence and its molecular basis was characterized, and a novel function of nsP3 was identified. These findings provide links between the molecular biology of SFV and its biological properties and significantly increase our understanding of the basis of alphavirus-induced pathology. In addition, the usefulness of consensus clones as tools for studies of alphaviruses was demonstrated.
Structure and electronic properties of single–walled zigzag BN and B3C2N3 nanotubes using first-principles methods

The structure and the electronic properties of single-walled zigzag BN and B3C2N3 nanotubes (n, 0; n=4–10) were investigated using first-principles calculations based on a density functional theory. A plane–wave basis set with periodic boundary conditions in conjunction with Vanderbilt ultrasoft pseudo-potential was employed. The energy gap of ZB3C2N3NTs was calculated and compared with the corresponding value for BNNTs. It was found that in both types of nanotube (BNNTs and B3C2N3NTs), the band gap energy is increased as the diameter of the tubes becomes larger and also these nanotubes are semiconductors with direct band gap. Although the band gap energy of the BN tubes are much larger than that of B3C2N3 ones, they have similar dependence on the diameter of the tubes and a semiconducting characteristic is maintained. There is a peak near the conduction band in B3C2N3NT nanotubes. Thus, energy gaps are reduced. These kind of ternary BCN nanotubes are of n–
Fusing points and lines for high performance tracking

This paper addresses the problem of real-time 3D model-based tracking by combining point-based and edge-based tracking systems. We present a careful analysis of the properties of these two sensor systems and show that this leads to some non -trivial design choices that collectively yield extremely high performance. In particular, we present a method for integrating the two systems and robustly combining the pose estimates they produce. Further we show how on-line learning can be used to improve the performance of feature tracking. Finally, to aid real-time performance, we introduce the FAST feature detector which can perform full-frame feature detection at 400Hz. The combination of these techniques results in a system which is capable of tracking average prediction errors of 200 pixels. This level of robustness allows us to track very rapid motions, such as 50deg camera shake at 6Hz
Plasma Deposition of Amine‐Embedded Nanoporous Ultrathin Films on Polyester Enables Substrate Independent Surface Dyeing

The paper describes the work of developing an original process of plasma deposition of nanoporous functionalized coatings, which was applied to polyester (PES) textiles enabling substrate independent surface dyeing. This novel approach is essentially based on a fine control of rivaling deposition/etching processes during plasma co-polymerization of ammonia with hydrocarbons at low pressure and at low temperature. A nanoporous structure with a large surface area was achieved that contained functional groups inside the coating volume, which were accessible to dye molecules, thus facilitating substrate independent surface dyeing. Depending on the gas ratio, a crosslinked and branched hydrocarbon network yielded excellent mechanical properties and a durable coating as indicated by the high color fastness to washing of the dyed textiles. The dyeing time can be reduced remarkably due to the porous nanoscaled coatings. Since amine-embedded functionalized films were deposited, it was possible for acid dyeing to be applied to the PES at low temperatures.
FRR for latency reduction and QoS provisioning in OBS networks

We propose a forward resource reservation (FRR) scheme to reduce the data burst delay at edge nodes in optical burst switching (OBS) systems. We also explore algorithms to implement the various intrinsic features of the FRR scheme. Linear predictive filter (LPF)-based methods are investigated and demonstrated to be effective for dynamic burst-length prediction. An aggressive resource reservation algorithm is proposed to deliver a significant performance improvement with controllable bandwidth cost. By reserving resources in an aggressive manner, an FRR system can reduce both the signaling retransmission probability and the bandwidth wastage as compared with a system without the aggressive reservation. An FRR-based QoS strategy is also proposed to achieve burst delay differentiation for different classes of traffic. Theoretical analysis and simulation results verify the feasibility of the proposed algorithms and show that our FRR scheme yields a significant delay reduction for time-critical traffic without incurring a deleterious bandwidth overhead.
Myth and Reality Application of Magnetite Nanoparticles as Selective Contrasting Means of the Malignant Tumors in MRI Investigation

In an experiment it is shown on rats that biocompatible standardized nanoparticles of ICNB can be effectively used at MRI. It is well-proven that nanoparticles of ICNB for certain (р<0.001) strengthen a contrasting effect at MRI. Methodology of safe intravenous application of ICNB is excluding the use of magnetite of nanoparticles in the variant of independent contrasting means at MRI. It is set that in 24 hours after intravenous inject of ICNB the magnetite of nanoparticles for certain (p<0.001) selectively accumulate in tissue of malignant tumour and rise brightness of image.
Development of facial expressions generator for emotion expressive humanoid robot

Human-robot communication is a very important aspect in the field of Humanoid Robotics. Non-verbal communication is one of the components that make interaction natural. However, despite the most recent efforts, robots still can show only limited expression capabilities. The purpose of this work is to create a facial expression generator that can be applied to the new 24 DoF head of the humanoid robot KOBIAN-R. In this paper, we present a system based on relevant studies of human communication and facial anatomy, adapted to the specific robotic face. It makes use of polynomial classifiers and is able to produce over 600 thousands of facial cues combinations, together with appropriate neck movement. Results showed that the recognition rate of expressions produced by this system is comparable to the rate of recognition of the most common facial expressions. We conclude that our system can successfully improve the communication capabilities of the robot KOBIAN-R, and that there is potential for using it to implement more complex interaction.
Role Of Information In Pricing Default-Sensitive Contingent Claims

We consider a financial market with a savings account and a stock S that follows a general diffusion. The default of the company, which issues the stock S, is modeled as a stopping time with respect to the filtration generated by the value of the firm that is not observable by regular investors. We assume that the stock price and the value of the firm are correlated. We study three investors with different information levels trading in the market who aim to price a general default-sensitive contingent claim. We use the density approach and Yor's method to solve the pricing problem. Specifically, we find the sets of equivalent martingale measures in three cases and, when needed, we choose one of them using f-divergence approach.
How Minds Will Be Built

Artificial intelligence started with the goal of understanding minds by attempting to build them. This essay discussed how our field’s research has become unbalanced, and what might be done to change this situation. Specifically, I argue that more of our efforts should be focused on creating integrated cognitive systems. The founding of this journal will hopefully help by promoting such research.
GPS-measured distance to clinic, but not self-reported transportation factors, are associated with missed HIV clinic visits in rural Uganda

Objective:Studies of the association between transportation barriers and HIV-related health outcomes have shown both positive and negative effects, possibly because a reliable, validated measure of transportation barriers has not been identified. Design:Prospective cohort study of HIV-infected patients in rural Uganda. Methods:Participants were enrolled from the HIV clinic at the regional referral hospital in Mbarara, Uganda as part of the Uganda AIDS Rural Treatment Outcomes (UARTO) Study. We collected the following measures of transportation barriers to HIV clinic: global positioning systems (GPS)-tracked distance measured by driving participants to their homes along their typical route; straight-line GPS distance from clinic to home, calculated with the Great Circle Formula; self-reported travel time; and self-reported travel cost. We assessed inter-measure agreement using linear regression, correlation coefficients and &kgr; statistics (by measure quartile) and validated measures by fitting linear regression models to estimate associations with days late for clinic visits. Results:One hundred and eighty-eight participants were tracked with GPS. Seventy-six percent were women, with a median age of 40 years and median CD4 cell count of 193 cells/&mgr;l. We found a high correlation between GPS-based distance measures (&bgr; = 0.74, P < 0.001, R2 = 0.92, &kgr; = 0.73), but little correlation between GPS-based and self-reported measures (all R2 ⩽ 0.4). GPS-based measures were associated with days late to clinic (P < 0.001); but neither self-reported measure was associated (P > 0.85). Conclusion:GPS-measured distance to clinic is associated with HIV clinic absenteeism and should be prioritized over self-reported measures to optimally risk-stratify patients accessing care in rural, resource-limited settings.
A daily Azores–Iceland North Atlantic Oscillation index back to 1850

We present the construction of a continuous, daily (09:00 UTC), station‐based (Azores–Iceland) North Atlantic Oscillation (NAO) Index back to 1871 which is extended back to 1850 with additional daily mean data. The constructed index more than doubles the length of previously existing, widely available, daily NAO time series. The index is created using entirely observational sea‐level pressure (SLP) data from Iceland and 73.5% of observational SLP data from the Azores – the remainder being filled in via reanalysis (Twentieth Century Reanalysis Project and European Mean Sea Level Pressure) SLP data. Icelandic data are taken from the Southwest Iceland pressure series. We construct and document a new Ponta Delgada SLP time series based on recently digitized and newly available data that extend back to 1872. The Ponta Delgada time series is created by splicing together several fractured records (from Ponta Delgada, Lajes, and Santa Maria) and filling in the major gaps (pre‐1872, 1888–1905, and 1940–1941) and occasional days (145) with reanalysis data. Further homogeneity corrections are applied to the Azores record, and the daily (09:00 UTC) NAO index is then calculated. The resulting index, with its extended temporal length and daily resolution, is the first reconstruction of daily NAO back into the 19th Century and therefore is useful for researchers across multiple disciplines.
Two-photon spectroscopy of trapped HD+ ions in the Lamb-Dicke regime

We study the feasibility of nearly-degenerate two-photon rovibrational spectroscopy in ensembles of trapped, sympathetically cooled hydrogen molecular ions using a resonance-enhanced multiphoton dissociation (REMPD) scheme. Taking advantage of quasi-coincidences in the rovibrational spectrum, the excitation lasers are tuned close to an intermediate level to resonantly enhance two-photon absorption. Realistic simulations of the REMPD signal are obtained using a four-level model that takes into account saturation effects, ion trajectories, laser frequency noise and redistribution of population by blackbody radiation. We show that the use of counterpropagating laser beams enables optical excitation in an effective Lamb-Dicke regime. Sub-Doppler lines having widths in the 100 Hz range can be observed with good signal-to-noise ratio for an optimal choice of laser detunings. Our results indicate the feasibility of molecular spectroscopy at the $10^{-14}$ accuracy level for improved tests of molecular QED, a new determination of the proton-to-electron mass ratio, and studies of the time (in)dependence of the latter.
Physics and modeling of tera-and nano-devices

Semiconductor Device Scaling: Physics, Transport, and the Role of Nanowires Polaronic Effects at the Field Effect Junctions for Unconventional Semiconductors Cellular Monte Carlo Simulation of High Field Transport in Semiconductor Devices Nanoelectronic Device Simulation Based on the Wigner Function Formalism Quantum Simulations of Dual Gate MOSFET Devices: Building and Deploying Community Nanotechnology Software Tools on Nanohub.org Positive Magneto-Resistance in a Point Contact: Possible Manifestation of Interactions Impact of Intrinsic Parameter Fluctuations in Nano-CMOS Devices on Circuits and Systems HEMT-Based Nanometer Devices Toward Terahertz Era Plasma Waves in Two-Dimensional Electron Systems and Their Applications Resonant Terahertz Detection Antenna Utilizing Plasma Oscillations in Lateral Schottky Diode Terahertz Polarization Controller Based on Electronic Dispersion Control of 2D Plasmons Higher-Order Plasmon Resonances in GaN-Based Field-Effect Transistor Arrays with Connected and Isolated Channels Ultra-Highly Sensitive Terahertz Detection Using Carbon-Nanotube Quantum Dots Generation of Ultrashort Electron Bunches in Nanostructures by Femtosecond Laser Pulses Characterization of Voltage-Controlled Oscillator Using RTD Transmission Line Infrared Quantum-Dot Detectors with Diffusion-Limited Capture Magneto-Resistance in Fe/MgO/Fe Magentic Tunnel Junctions Modeling and Implementation of Spin-Based Quantum Computation Quantum Engineering for Threat Reduction and Homeland Security Strong Phase Shift Mask Manufacturing Error Impact on the 65nm Poly Line Printability.
p53 and Sp1 Interact and Cooperate in the Tumor Necrosis Factor-induced Transcriptional Activation of the HIV-1 Long Terminal Repeat (*)

Tumor necrosis factor α (TNF) is a potent activator of transcription directed by the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR). We have recently reported that the p53 tumor suppressor gene product binds to a site within the Sp1 binding region of the HIV-1 LTR and contributes to the TNF induction of this promoter. In this study we show that the transcription factor Sp1 cooperates with p53 in the transcriptional activation directed by the HIV-1 LTR. The presence of Sp1 increased p53 binding to its recognition sequence in the HIV-1 LTR, and experiments in Drosophila cells show that Sp1 is necessary for full transactivation by mutant p53. Importantly, TNF induced the association between p53 and Sp1 in Jurkat T cells. These data demonstrate a synergistic role for these proteins in the mechanism of TNF induction of HIV-1 LTR-mediated transcription and suggest that Sp1 may play an important role in modulating certain functions of p53.
Open architecture of virtual machine tool for cloud computing

For complex multi-axis or compound machine tools, checking machining processes by simulation software is needed. This paper aims to develop open virtual machine tool (VMT) for cloud computing. According to users' needs, they can extend virtual machine's functions by themselves, so virtual machine tool can be used widely with machining systems and reduces costs. Due to cloud computing, it can save large memory space in computer, and virtual machine tool can also be used to simulate machining of multi-axis machines in large scales production line.
Gender-Based Vocation Identification in Swedish 19th Century Prose Fiction using Linguistic Patterns, NER and CRF Learning

This paper investigates how literature could be used as a means to expand our understanding of history. By applying macroanalytic techniques we are aiming to investigate how women enter literature and particularly which functions do they assume, their working patterns and if we can spot differences in how often male and female characters are mentioned with various types of occupational titles (vocation) in Swedish literary texts. Modern historiography, and especially feminist and women’s history has emphasized a relative invisibility of women’s work and women workers. The reasons to this are manifold, and the extent, the margin of error in terms of women’s work activities is of course hard to assess. Therefore, vocation identification can be used as an indicator for such exploration and we present a hybrid system for automatic annotation of vocational signals in 19th century Swedish prose fiction. Beside vocations, the system also assigns gender (male, female or unknown) to the vocation words, a prerequisite for the goals of the study and future in-depth explorations of the corpora.
Advisor-advisee relationship mining from dynamic collaboration network

In academic world, people are interested in how researchers are connected to each other and how the research community is formed by each individual researcher. As a first step, identifying advisor-advisee relationship can help us answer these questions. Given a collaboration network of researchers, this relationship is hidden in the collaboration records and characterized by the development of each researcher and the change of their social role. To discover this potential information from the collaboration data, we need develop a technique to analyze the network evolving with time. This project aims to model the dynamic collaboration network in order to discover the advisor-advisee relationship between coauthors. A time-constrained probabilistic factor graph model (TPFG) is proposed. It takes the DBLP collaboration network as input and models jointly the likelihood of one researcher advising another for each potential pair of coauthors in this relationship. An efficient algorithm is designed to estimate the optimal joint probability by message propagation on the whole graph. Based on the estimation we can rank the most probable advisors for every author. Experimental results show that the proposed approach can efficiently infer the advisor-advisee relationship and achieve a high accuracy over 80%. The discovered relations can be further used to analyze the research community evolution. And the methodology can be generalized to mine the roles or relations in a evolving network.
Pocket gophers and chewing lice: a test of the maternal transmission hypothesis

The life‐history traits of pocket gophers and their chewing lice suggest that there is little opportunity for transmission of parasites among pocket gophers, with the exception of transmission from mother to offspring. Herein, we test the hypothesis that lice are transmitted maternally by using an indirect approach that compares the distribution of louse populations to the distribution of mitochondrial DNA haplotypes in the pocket gophers. Comparison of the chewing louse distributions to the distribution of mtDNA haplotypes for the gophers revealed no significant concordance, and thus falsifies the maternal transmission hypothesis.
The Brown University Robocup 2006 Four-Legged League Team Report

This paper describes the design and implementation of the first four-legged RoboCup team at Brown University and lessons learned from our first year of RoboCup competition. The paper provides background about our team, outlines the overall structure to our implementation architecture, and describes each component of this architecture in more detail. The strengths and weaknesses of each module are discussed. Based on these observations, specific improvements are proposed for improvements to realize in future years of the Brown University RoboCup Team
Impaired Recognition of Social Emotions following Amygdala Damage

Lesion, functional imaging, and single-unit studies in human and nonhuman animals have demonstrated a role for the amygdala in processing stimuli with emotional and social significance. We investigated the recognition of a wide variety of facial expressions, including basic emotions (e.g., happiness, anger) and social emotions (e.g., guilt, admiration, flirtatiousness). Prior findings with a standardized set of stimuli indicated that recognition of social emotions can be signaled by the eye region of the face and is disproportionately impaired in autism (Baron-Cohen, Wheelwright, & Jolliffe, 1997). To test the hypothesis that the recognition of social emotions depends on the amygdala, we administered the same stimuli to 30 subjects with unilateral amygdala damage (16 left, 14 right), 2 with bilateral amygdala damage, 47 brain-damaged controls, and 19 normal controls. Compared with controls, subjects with unilateral or bilateral amygdala damage were impaired when recognizing social emotions; moreover, they were more impaired in recognition of social emotions than in recognition of basic emotions, and, like previously described patients with autism, they were impaired also when asked to recognize social emotions from the eye region of the face alone. The findings suggest that the human amygdala is relatively specialized to process stimuli with complex social significance. The results also provide further support for the idea that some of the impairments in social cognition seen in patients with autism may result from dysfunction of the amygdala.