gebhart/patrepeval huggingface dataset:
The <i>sbcDC</i> Locus Mediates Repression of Type 5 Capsule Production as Part of the SOS Response in <i>Staphylococcus aureus</i> (2007)

Most strains of Staphylococcus aureus produce one type of capsular polysaccharide that belongs to either type 5 or type 8. The production of these capsules has been shown to be regulated by various regulators. Here we report that the sbcD and sbcC genes are involved in the repression of type 5 capsule production. Chromosomal deletions in the sbcDC genes resulted in increased capsule promoter activity, capsule gene transcripts, and capsule production. The survival rates of the sbcDC deletion mutant were reduced upon UV irradiation compared to those for the wild-type strain Newman, suggesting that the genes are involved in DNA repair in S. aureus. The two genes were organized as an operon and were expressed very early in the exponential growth phase. A subinhibitory concentration of ciprofloxacin or mitomycin C induced sbcDC transcription but repressed the capsule promoter activity, suggesting that the sbcDC genes and the capsule genes are part of the SOS regulon. By reporter gene fusion and Northern blotting, we found that sbcDC regulated capsule by downregulating arl and mgr. Further genetic studies indicate that sbcDC functions upstream of arl and mgr in capsule regulation. Collectively, our results indicate that sbcDC, upon the SOS response, represses type 5 capsule production through an arl-mgr pathway. To our knowledge, this is the first demonstration that an SbcDC homolog was involved in transcriptional regulation.
Tat Acetylation: A Regulatory Switch between Early and Late Phases in HIV Transcription Elongation (2004)

The HIV transcriptional activator Tat enhances the processivity of RNA polymerase II by recruiting the CyclinT1/CDK9 complex to the TAR RNA element. In addition, Tat synergizes with the histone acetyltransferase p300 and is acetylated by p300 at a single lysine residue (K50) in the TAR RNA binding domain. We have recently reported that this post-translational modification is necessary for the interaction and transcriptional synergy of Tat with the transcriptional coactivator PCAF. We have further studied the relevance of Tat acetylation during HIV transcription and generated antibodies specific for acetylated Tat (AcTat). Microinjection of anti-AcTat antibodies inhibited Tat-mediated transactivation in cells. Similarly, the specific p300 inhibitor Lys-CoA and short inhibitory RNAs specific for p300 suppressed Tat transcriptional activity. Full-length synthetic AcTat bound to TAR RNA and CyclinT1 with high affinity, but formation of the Tat-TAR-CyclinT1 ternary complex was inhibited when K50 was acetylated. Our data collectively show that Tat acetylation by p300 defines a critical step in Tat transactivation that serves to disrupt the Tat/TAR/CyclinT1 complex and helps in recruiting PCAF to the elongating RNA polymerase II.
Measure of Spin Period in Randomly Birefringent Low-PMD Fibers (2004)

We present a polarization-sensitive optical time-domain reflectometer-based method for measuring the spin period in randomly birefringent long single-mode spun fibers. Several samples of ad hoc drawn fibers have been tested to measure the spin period and to control the quality of spin process. Experimental results are in excellent agreement with the nominal values.
The role of alloy composition in the heat treatment of aluminium high pressure die castings (2013)

High pressure die-cast (HPDC) aluminium components that respond to age hardening cannot normally be solution treated at high temperatures because the presence of internal porosity and entrapped gases leads to the formation of surface blisters.Parts may also become dimensionally unstable due to swelling.These factors that prevent heat treatment present significant limitations to the utilisation of HPDC components.Now it has been found that blistering and dimensional change can be avoided by using modified shorter solution treatment procedures which still allow strong responses to age hardening to be achieved with a wide range of Al-Si-(Cu/Mg) alloys.In the present paper, the roles of critical alloying elements are considered in both current commercial and experimental alloy compositions in this series.It is shown that values of 0.2% proof stress exceeding 400 MPa may be readily achieved by heat treating conventionally produced HPDC components.RIASSUNTO I componenti in lega di alluminio ottenuti per pressocolata da rafforzare tramite invecchiamento non possono subire normalmente un trattamento di solubilizzazione ad alta temperatura in quanto la presenza di porosit interne o di gas intrappolati conduce alla formazione di rigonfiamenti superficiali.Alcune parti possono inoltre diventare dimensionalmente instabili a causa di dilatazioni.Questi fattori che contrastano il trattamento termico comportano una limitazione importante nell'utilizzo di componenti pressocolati.Si ora riscontrato che rigonfiamenti e variazioni dimensionali possono essere evitati riducendo la durata del trattamento di solubilizzazione e consentendo cos a numerose leghe Al-Si(Cu/Mg) di essere notevolmente rafforzate per invecchiamento.
Least‐Square Deconvolution: A Framework for Interpreting Short Tandem Repeat Mixtures<sup>*</sup> (2006)

Interpreting mixture short tandem repeat DNA data is often a laborious process, involving trying different genotype combinations mixed at assumed DNA mass proportions, and assessing whether the resultant is supported well by the relative peak-height information of the mixture sample. If a clear pattern of major-minor alleles is apparent, it is feasible to identify the major alleles of each locus and form a composite genotype profile for the major contributor. When alleles are shared between the two contributors, and/or heterozygous peak imbalance is present, it becomes complex and difficult to deduce the profile of the minor contributor. The manual trial and error procedures performed by an analyst in the attempt to resolve mixture samples have been formalized in the least-square deconvolution (LSD) framework reported here for two-person mixtures, with the allele peak height (or area) information as its only input. LSD operates on the peak-data information of each locus separately, independent of all other loci, and finds the best-fit DNA mass proportions and calculates error residual for each possible genotype combination. The LSD mathematical result for all loci is then to be reviewed by a DNA analyst, who will apply a set of heuristic interpretation guidelines in an attempt to form a composite DNA profile for each of the two contributors. Both simulated and forensic peak-height data were used to support this approach. A set of heuristic guidelines is to be used in forming a composite profile for each of the mixture contributors in analyzing the mathematical results of LSD. The heuristic rules involve the checking of consistency of the best-fit mass proportion ratios for the top-ranked genotype combination case among all four- and three-allele loci, and involve assessing the degree of fit of the top-ranked case relative to the fit of the second-ranked case. A different set of guidelines is used in reviewing and analyzing the LSD mathematical results for two-allele loci. Resolution of two-allele loci is performed with less confidence than for four- and three-allele loci. This paper gives a detailed description of the theory of the LSD methodology, discusses its limitations, and the heuristic guidelines in analyzing the LSD mathematical results. A 13-loci sample case study is included. The use of the interpretation guidelines in forming composite profiles for each of the two contributors is illustrated. Application of LSD in this case produced correct resolutions at all loci. Information on obtaining access to the LSD software is also given in the paper.
Influence of Predicted and Measured Fingerprint on the Accuracy of RSSI-based Indoor Location Systems (2007)

WLAN indoor location that is based on received signal strength indication (RSSI) technique needs extensive calibration to build a signal fingerprint. Re-calibration is also needed if there is a major change in the propagation environment. The use of propagation models to predict signal fingerprint becomes an interesting preposition. This paper will investigate the influence of predicted fingerprint on the accuracy of indoor location. They include empirical propagation models (i.e. one-slope model and multi-wall model) and a semi-deterministic model. A framework for indoor location with the nearest-neighbour and particle filter are developed to evaluate predicted and measured fingerprints. In order to take advantage of environment description, a map-filtering technique is also elaborated.
Fundamental Distortion Limits of Analog-to-Digital Compression (2018)

Representing a continuous-time signal by a set of samples is a classical problem in signal processing. We study this problem under the additional constraint that the samples are quantized or compressed in a lossy manner under a limited bitrate budget. To this end, we consider a combined sampling and source coding problem in which an analog stationary Gaussian signal is reconstructed from its encoded samples. These samples are obtained by a set of bounded linear functionals of the continuous-time path, with a limitation on the average number of samples per unit time given in this setting. We provide a full characterization of the minimal distortion in terms of the sampling frequency, the bitrate, and the signal's spectrum. Assuming that the signal's energy is not uniformly distributed over its spectral support, we show that for each compression bitrate there exists a critical sampling frequency smaller than the Nyquist rate, such that the distortion in signal reconstruction when sampling at this frequency is minimal. Our results can be seen as an extension of the classical sampling theorem for bandlimited random processes in the sense that they describe the minimal amount of excess distortion in the reconstruction due to lossy compression of the samples and provide the minimal sampling frequency required in order to achieve this distortion. Finally, we compare the fundamental limits in the combined source coding and sampling problem to the performance of pulse code modulation, where each sample is quantized by a scalar quantizer using a fixed number of bits.
Reusable methyltrimethoxysilane-based mesoporous water-repellent silica aerogel membranes for CO<sub>2</sub>capture (2013)

For the first time, highly mesoporous and water-repellent SiO2 aerogels were successfully coated onto a macroporous Al2O3 membrane using methyltrimethoxysilane (MTMS) precursors. The MTMS-derived hydrophobic SiO2 aerogel membranes exhibited at least 500% higher CO2 absorption flux than the uncoated MTMS-based aerogel membranes and could be reused and continuously operated for CO2 absorption for extended periods of time. As a result, MTMS-derived water-repellent silica aerogel membrane contactors are a potential candidate for large-scale CO2 absorption in industrial power plants.
A phrase-driven grammar system for interactive data visualization (2007)

A Phrase-Driven Grammar System (PDGS) is a novel GUI for facilitating the visualization of data. The PDGS integrates data source applications and external visualization tools into its framework and functions as a middle-layer application to coordinate their operations. It allows users to formulate data query and visualization descriptions by selecting graphical icons in a menu or on a map. To specify data query and visualization intuitively and efficiently, we designed Graphical User Interface and a natural-language-like grammar, Phrase-Driven Grammar (PDG). The formulation of PDG data query and visualization descriptions is a constrained natural-language phrase building process. PDG phrases produce graphical visualizations of the data query, allowing users to interactively explore meaningful data relationships, trends, and exceptions.
Ten-channel coherent optical fibre transmission (1986)

A laboratory ten-channel coherent fibre-optic broadband transmission system is reported. The frequency-division-multiplexed optical carriers are separated by 6 GHz and are demultiplexed by a tunable heterodyne receiver having a sensitivity of -46 dBm at a bit error rate of 10-9. In this system a maximum number of 64 channels can be installed.
Theory and Algorithm of Estimating Energy Consumption Breakdowns using ON/OFF State Sensing (2014)

This article considers a problem of periodically estimating energy consumption breakdowns for main appliances inside building using a single power meter and the knowledge of the ON/OFF states of individual appliances. In the first part of this article, we formulate the problem as a constrained convex optimization problem with tunable parameters. Then we propose an online algorithm that adaptively determines the optimization parameters to robustly estimate the breakdown information. The proposed solution is evaluated by experiment using a scaled-down proof-of-concept prototype with real measurements. In the second part, we provide detailed analysis to understand the performance of our proposed algorithm. We first develop a stochastic model to describe evolution of appliances’ ON/OFF states using continuous-time Markov chain. Then we derive analytical bounds of estimation error and the probability of a rank-deficient binary matrix. Those analytical bounds are verified by extensive simulations. Finally, we study the effect of collinearity of binary data matrix on estimation performance. Simulation results suggest that our algorithm is robust against the collinearity of binary dataset.
Simulation of the cardiovascular mechanics during rate adaptive pacing (2005)

A numerical model of the human cardiovascular system will be presented that was developed for simulating the short-term regulatory processes that adapt the cardiac output of the heart to changing circulatory demands. Both normal and pathological states, e.g. sick sinus or AV block, are considered. The purpose of the simulations is to investigate the control aspects of rate responsive pacing and to develop and test algorithms for rate adaptation based on cardiac control signals.
42.1: A Real‐time 3D Multi‐view Rendering From a Real‐time 3D Capture (2013)

Abstract As often declared by customers, wearing glasses is a clear limiting factor for 3D adoption in the home. Auto‐stereoscopic systems bring an interesting answer to this issue. These systems are evolving very fast providing improved picture quality. Nevertheless, they require adapted content which are today highly demanding in term of computation power. The system we describe here is able to generate in real‐time adapted content to these displays: from a real‐time stereo capture up to a real‐time multi‐view rendering. A GPU‐based solution is proposed that ensures a real‐time processing of both disparity estimation and multi‐view rendering on the same platform.
Noise normalization and windowing functions for VALIDAR in wind parameter estimation (2006)

The wind parameter estimates from a state-of-the-art 2-μm coherent lidar system located at NASA Langley, Virginia, named VALIDAR (validation lidar), were compared after normalizing the noise by its estimated power spectra via the periodogram and the linear predictive coding (LPC) scheme. The power spectra and the Doppler shift estimates were the main parameter estimates for comparison. Different types of windowing functions were implemented in VALIDAR data processing algorithm and their impact on the wind parameter estimates was observed. Time and frequency independent windowing functions such as Rectangular, Hanning, and Kaiser-Bessel and time and frequency dependent apodized windowing function were compared. The briefing of current nonlinear algorithm development for Doppler shift correction subsequently follows.
Identification of <i>Chlamydia trachomatis</i> proteins recognized by T cells from high-risk women resistant to reinfection and/or protected from ascending infection. (VAC7P.961) (2014)

Abstract Murine and human data indicate IFNγ-producing Chlamydia-responsive CD4 T cells are key to protection from genital tract disease, and chlamydial proteins have been identified that induce protection in mice. A preventative vaccine against C. trachomatis requires the identification of T cell antigens that induce protection in humans. We analyzed peripheral blood CD4 and CD8 T cell responses from high-risk women defined as “resistant” or “susceptible” based on negative evidence for reinfection or detection of repeated reinfection during a 12-month follow-up period. Autologous APCs preincubated with E. coli clones expressing individual chlamydial ORFs were coincubated with CD4 or CD8 T cells and IFN-γ measured by ELISA. CD4 T cells from resistant women recognized 16 proteins significantly more frequently when compared to susceptible women, and only 2 of 16 were among a subset of immunodominant CD4 proteins suggesting restricted MHC recognition. No proteins recognized by CD8 T cells met immunoprotective criteria. Five CD4 and 5 CD8 antigens were more frequently recognized by women who had cervical infection but no evidence of endometrial infection by PCR. Thus, although protection from reinfection appears dependent on CD4 T cells, both CD4 and CD8 T cells may contribute to disease prevention. The use of samples from persons with evidence of natural immune protection for antigen discovery should advance development of a vaccine against C. trachomatis.
A Lightweight Deep Learning Model for Vehicle Viewpoint Estimation from Dashcam Images (2020)

Vehicle viewpoint estimation from vehicle cameras is a crucial component of road scene understanding. In this paper, we propose a deep lightweight method to predict vehicle viewpoint from a single RGB dashcam image. To this aim, we customize and adapt state-of-the-art deep learning techniques for general object viewpoint estimation to the vehicle viewpoint estimation task. Furthermore, we define a novel objective function that takes into account errors at different granularity to improve neural network training. To keep the model lightweight and fast, we rely upon MobileNetV2 as backbone. Tested both on benchmark viewpoint estimation data (Pascal3D+) and on actual vehicle camera data (nuScenes), our method is shown to outperform the state of the art in vehicle viewpoint estimation, in terms of both accuracy and memory footprint.
Predictive Blacklisting as an Implicit Recommendation System (2009)

A widely used defense practice against malicious traffic on the Internet is through blacklists: lists of prolific attack sources are compiled and shared. The goal of blacklists is to predict and block future attack sources. Existing blacklisting techniques have focused on the most prolific attack sources and, more recently, on collaborative blacklisting. In this paper, we formulate the problem of forecasting attack sources (also referred to as predictive blacklisting) based on shared attack logs as an implicit recommendation system. We compare the performance of existing approaches against the upper bound for prediction, and we demonstrate that there is much room for improvement. Inspired by the recent Netflix competition, we propose a multi-level prediction model that is adjusted and tuned specifically for the attack forecasting problem. Our model captures and combines various factors, namely: attacker-victim history (using time-series) and attackers and/or victims interactions (using neighborhood models). We evaluate our combined method on one month of logs from Dshield.org and demonstrate that it improves significantly the state-of-the-art.
Low Energy Magnetic Domain Wall Logic in Short, Narrow, Ferromagnetic Wires (2012)

We present circuit simulation results of an implementation of universal logic that operates at low switching energy. Information is stored in the position of a single domain wall in a thin, short ferromagnetic wire. The gate is switched by current-driven domain wall motion, and information is read out using a magnetic tunnel junction. The inputs and outputs of the device are currents controlled by voltage clocks, making it compatible with CMOS. Using devices that operate at 100-1 mV, we simulate a shift register circuit and a full-adder circuit. The simulations show that the magnetic logic gates can operate at lower switching energy than CMOS electronics.
Polarization-independent optical directional coupler switch using weighted coupling (1979)

We report the first demonstration of a guided-wave polarization-independent electro-optic switch. Using a specially designed weighted Ti-diffused directional coupler with stepped electrodes, we have achieved crosstalk levels below −23 dB for both switch states for arbitrary incident optical polarization.
Abstract 3231: Identifying high quality, potent and selective pyrimidinylthienopyrrolone inhibitors of ERK1/2 kinase: LY3214996 (2017)

Abstract The ERK/MAPK pathway plays a central role in the regulation of critical cellular processes and is activated in more than 30% of human cancers. While targeting upstream nodes with RAF and MEK inhibitors has proven effective clinically, resistance frequently develops through reactivation of the pathway. ERK inhibitors have the potential to address resistance caused by ERK reactivation. Herein, a potent, selective small molecule ERK1/2 inhibitor is described. LY3214996 possesses an optimal balance of potency (hERK1 IC50 5 nM, hERK2 IC50 5nM, pRSK IC50 0.43 µM), solubility (FaSSIF solubility at pH 6.5 0.133 µM), PK properties (dog, AUCoral 23800 nM*hr, CL 12.1 mL/min/kg, bioavailability 75.4%), IVTI (TED50 =16 mg/kg pRSK1) and demonstrated significant in vivo efficacy in several human cancer xenograft models. LY3214996 is currently undergoing early clinical evaluation. Citation Format: Gaiying Zhao, William T. McMillen, Shufen Cai, Baohui Zhao, Matthew Whitesell, Wenjuan Wu, Karen Huss, Bryan Anderson, Xiu-Juan Yuan, Susan Jaken, Lisa Kindler, Robert S. Flack, Denis McCann, Brian Mathes, Andrew J. Dropsey, Jennie Walgren, Eunice Yuen, Jason Manro, Xueqian Gong, Guillermo Cortez, Johnathan McLean, Michael J. Rodriguez, Ramon V. Tiu, Shripad V. Bhagwat, Sajan Joseph. Identifying high quality, potent and selective pyrimidinylthienopyrrolone inhibitors of ERK1/2 kinase: LY3214996 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3231. doi:10.1158/1538-7445.AM2017-3231
Channel decoding using residualintra-frame correlation in GSM system (1997)

The authors present a new channel decoding algorithm that can be usefully employed for exploiting the residual intra-frame correlation in the GSM system. For transmissions over a fully interleaved Rayleigh fading channel it is possible to achieve a gain of 1.7 dB in terms of bit error probabillty for the most significant bits, with respect to the standard GSM system.