gebhart/patrepeval huggingface dataset:
GraXSR Proteins Interact with the VraFG ABC Transporter To Form a Five-Component System Required for Cationic Antimicrobial Peptide Sensing and Resistance in Staphylococcus aureus (2011)

The GraSR two-component system (TCS) controls cationic antimicrobial peptide (CAMP) resistance in Staphylococcus aureus through the synthesis of enzymes that increase bacterial cell surface positive charges, by d-alanylation of teichoic acids and lysylination of phosphatidylglycerol, leading to electrostatic repulsion of CAMPs. The GraS histidine kinase belongs to the "intramembrane-sensing kinases" subfamily, with a structure featuring a short amino-terminal sensing domain, and two transmembrane helices separated only by a short loop, thought to be buried in the cytoplasmic membrane. The GraSR TCS is in fact a multicomponent system, requiring at least one accessory protein, GraX, in order to function, which, as we show here, acts by signaling through the GraS kinase. The graXRS genes are located immediately upstream from genes encoding an ABC transporter, vraFG, whose expression is controlled by GraSR. We demonstrated that the VraFG transporter does not act as a detoxification module, as it cannot confer resistance when produced on its own, but instead plays an essential role by sensing the presence of CAMPs and signaling through GraS to activate GraR-dependent transcription. A bacterial two-hybrid approach, designed to identify interactions between the GraXSR and VraFG proteins, was carried out in order to understand how they act in detecting and signaling the presence of CAMPs. We identified many interactions between these protein pairs, notably between the GraS kinase and both GraX and the VraG permease, indicating the existence of an original five-component system involved in CAMP sensing and signal transduction to promote S. aureus resistance.
Heterodyne Interferometric Measurement of the Thermo-Optic Coefficient of Single Mode Fiber (2000)

The thermo-optic coefficient of a single mode fiber is determined by a heterodyne interferometric technique. The heterodyne beat signal, resulting from the beating of the carrier and two side-band frequencies, is related to the phase shift difference between the carrier and the side-band waves in a fiber Fabry-Perot interferometer. This phase shift difference is determined with a phase sensitive detection technique and is found to be temperature dependent. From the temperature dependence, the thermo-optic coefficient of the single mode fiber is determined to be 9.2 x 10^-6 C^-1. The experimental result agrees well with a theoretical simulation using the temperature dependent Sellmeier equation for fused silica.
Algebraic Signal Processing Theory: Cooley–Tukey Type Algorithms for Real DFTs (2008)

In this paper, we systematically derive a large class of fast general-radix algorithms for various types of real discrete Fourier transforms (real DFTs) including the discrete Hartley transform (DHT) based on the algebraic signal processing theory. This means that instead of manipulating the transform definition, we derive algorithms by manipulating the polynomial algebras underlying the transforms using one general method. The same method yields the well-known Cooley-Tukey fast Fourier transform (FFT) as well as general radix discrete cosine and sine transform algorithms. The algebraic approach makes the derivation concise, unifies and classifies many existing algorithms, yields new variants, enables structural optimization, and naturally produces a human-readable structural algorithm representation based on the Kronecker product formalism. We show, for the first time, that the general-radix Cooley-Tukey and the lesser known Bruun algorithms are instances of the same generic algorithm. Further, we show that this generic algorithm can be instantiated for all four types of the real DFT and the DHT.
A Hybrid Approach for Event Extraction (2012)

Event extraction is a popular and interesting research field in the area of Natural Language Processing (NLP). In this paper, we propose a hybrid approach for event extraction within the TimeML framework. Initially, we develop a machine learning based system based on Conditional Random Field (CRF). But most of the deverbal event nouns are not correctly identified by this machine learning approach. From this observation, we came up with a hybrid approach where we introduce several strategies in conjunction with machine learning. These strategies are based on semantic role-labeling, WordNet and handcrafted rules. Evaluation results on the TempEval-2010 datasets yield the precision, recall and F-measure values of approximately 93.00%, 96.00% and 94.47%, respectively. This is approximately 12% higher F-measure in comparison with the best performing system of SemEval-2010.
Pathologists’ diagnosis of invasive melanoma and melanocytic proliferations: observer accuracy and reproducibility study (2017)

<b>Objective</b> To quantify the accuracy and reproducibility of pathologists' diagnoses of melanocytic skin lesions.<b>Design</b> Observer accuracy and reproducibility study.<b>Setting</b> 10 US states.<b>Participants</b> Skin biopsy cases (n=240), grouped into sets of 36 or 48. Pathologists from 10 US states were randomized to independently interpret the same set on two occasions (phases 1 and 2), at least eight months apart.<b>Main outcome measures</b> Pathologists' interpretations were condensed into five classes: I (eg, nevus or mild atypia); II (eg, moderate atypia); III (eg, severe atypia or melanoma in situ); IV (eg, pathologic stage T1a (pT1a) early invasive melanoma); and V (eg, ≥pT1b invasive melanoma). Reproducibility was assessed by intraobserver and interobserver concordance rates, and accuracy by concordance with three reference diagnoses.<b>Results</b> In phase 1, 187 pathologists completed 8976 independent case interpretations resulting in an average of 10 (SD 4) different diagnostic terms applied to each case. Among pathologists interpreting the same cases in both phases, when pathologists diagnosed a case as class I or class V during phase 1, they gave the same diagnosis in phase 2 for the majority of cases (class I 76.7%; class V 82.6%). However, the intraobserver reproducibility was lower for cases interpreted as class II (35.2%), class III (59.5%), and class IV (63.2%). Average interobserver concordance rates were lower, but with similar trends. Accuracy using a consensus diagnosis of experienced pathologists as reference varied by class: I, 92% (95% confidence interval 90% to 94%); II, 25% (22% to 28%); III, 40% (37% to 44%); IV, 43% (39% to 46%); and V, 72% (69% to 75%). It is estimated that at a population level, 82.8% (81.0% to 84.5%) of melanocytic skin biopsy diagnoses would have their diagnosis verified if reviewed by a consensus reference panel of experienced pathologists, with 8.0% (6.2% to 9.9%) of cases overinterpreted by the initial pathologist and 9.2% (8.8% to 9.6%) underinterpreted.<b>Conclusion</b> Diagnoses spanning moderately dysplastic nevi to early stage invasive melanoma were neither reproducible nor accurate in this large study of pathologists in the USA. Efforts to improve clinical practice should include using a standardized classification system, acknowledging uncertainty in pathology reports, and developing tools such as molecular markers to support pathologists' visual assessments.
Strategic directions in computer architecture (1996)

article Free Access Share on Strategic directions in computer architecture Author: Trevor Mudge Univ. of Michigan, Ann Arbor Univ. of Michigan, Ann ArborSearch about this author Authors Info & Claims ACM Computing SurveysVolume 28Issue 4pp 671–678https://doi.org/10.1145/242223.242271Published:01 December 1996Publication History 5citation1,611DownloadsMetricsTotal Citations5Total Downloads1,611Last 12 Months64Last 6 weeks10 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Pd<sub>2</sub>dba<sub>3</sub>/Bippyphos: A Robust Catalyst System for the Hydroxylation of Aryl Halides with Broad Substrate Scope (2013)

Abstract A mixture of tris(dibenzylideneacetone)dipalladium(0) (Pd 2 dba 3 ) and 5‐(di‐ tert ‐butylphosphino)‐1′,3′,5′‐triphenyl‐1′ H ‐[1,4′]bipyrazole (Bippyphos) is shown to be a robust and efficient catalyst system for the hydroxylation of structurally diverse (hetero)aryl halides under mild conditions and with broad substrate scope. Included in this reactivity survey is the successful synthesis of substituted benzofurans and related heteroatomic derivatives, which are formed via the hydroxylation of 2‐haloalkynylarenes. Notably, a significant number of the reactions reported herein proceed at room temperature, and we have demonstrated that it is possible to conduct reactions on the benchtop under air using unpurified solvents with negligible loss in reactivity versus related transformations conducted under inert atmosphere conditions. We also report herein the first crystallographically characterized (Bippyphos)Pd(II) complex, which confirms the ability of this synthetically useful ligand to adopt a bidentate binding motif in a manner similar to Buchwald’s biarylphosphine ligand class.
Optical and Structural Properties of Titanium Dioxide Films from and Starting Materials Annealed at Various Temperatures (2013)

We investigated the optical and structural properties of titanium dioxide films deposited from and starting materials by electron beam evaporation at annealing temperatures from to . We find that the refractive index of as-deposited films from starting material is higher than that of as-deposited films from starting material. In addition, during thermal annealing, the refractive index fluctuates slightly as compared with films from starting material. This should be attributed to the fact that the deposited molecules had a higher packing density, such that the film was denser. The transmittance spectra of films from starting material indicate that transmittance edge slightly shifts to longer wavelength with the annealing temperature increasing when compared with starting material, in which the transmittance spectra indicate that the transmittance edge strongly shifts to longer wavelength with the same annealing temperature increasing. These findings should be attributed to the absence of oxygen and scattering of rough surface.
Energy considerations in hot-gas defrosting of industrial refrigeration coils (1983)

Le procede de degivrage par du gaz haute pression provenant du refoulement du compresseur est une des cibles d'economie d'energie dans les installations de refrigeration. Des essais de laboratoire sur un systeme au R-22 et des essais reels sur un systeme a l'ammoniac ont identifie quelques caracteristiques pouvant reduire les besoins en energie associes au degivrage par gaz chaud. Il s'agit essentiellement de la pression minimale de gaz chaud pouvant donner un degivrage efficace, et de la methode de drainage du liquide condense a partir du serpentin
Short-Sequence DNA Repeats in Prokaryotic Genomes (1998)

Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10(-4) per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant.
<title>Application of polyfluorenes and related polymers in light-emitting diodes</title> (1999)

We report our progress to date in the materials and processing aspects of developing organic light emitting diode technology based on high molecular weight polymers. A portfolio of fluorene-related polymers are prepared through the coupling of 9,9-disubstituted 2,7-bis-1,3,2- dioxaborolanyl-fluorene with a variety of aromatic dibromides. In the case of fluorene homopolymers, the polyphenylene main chain provides the mechanical, electrical and electronic properties and the C-9 maintains coplanarity of the biphenylene unit and a site for property modification without altering effective conjugation. In the case of alternating polymers, the optical and electronic properties of the polymers are tailored through selective incorporation of different aromatic unit into the system. These polymers are soluble in common organic solvents and are readily processed into uniformed films of high quality by spin casting. Unlike PPV and related materials, LED devices with fluorene polymers in a conventional configuration appear to have electrons as the majority carrier and their performance is markedly improved when modified with an appropriate polymeric hole transporting layer. Bright green light with a luminance of 10000 Cd/m<SUP>2</SUP> is achieved at a very low drive voltage of < 6 V attributable in part to the high hole mobility of fluorene-based polymers.
Human Gaze-Driven Spatial Tasking of an Autonomous MAV (2019)

In this letter, we address the problem of providing human-assisted quadrotor navigation using a set of eye tracking glasses. The advent of these devices (i.e., eye tracking glasses, virtual reality tools, etc.) provides the opportunity to create new, noninvasive forms of interaction between humans and robots. We show how a set of glasses equipped with gaze tracker, a camera, and an inertial measurement unit (IMU) can be used to estimate the relative position of the human with respect to a quadrotor, and decouple the gaze direction from the head orientation, which allows the human to spatially task (i.e., send new 3-D navigation waypoints to) the robot in an uninstrumented environment. We decouple the gaze direction from head motion by tracking the human's head orientation using a combination of camera and IMU data. In order to detect the flying robot, we train and use a deep neural network. We experimentally evaluate the proposed approach, and show that our pipeline has the potential to enable gaze-driven autonomy for spatial tasking. The proposed approach can be employed in multiple scenarios including inspection and first response, as well as by people with disabilities that affect their mobility.
Design and fabrication of high efficiency diffuser film based on laser speckle (2012)

Diffuser film is one of the main components in liquid crystal display backlight unit. It can cause strong scattering for the light out from the light guide plate, and it have the ability to make diffuse reflection and uniform diffusion of the out light occur. How to improve the brightness, the uniformity of backlight unit, and make it more and more slimmer are not only what manufacturers pursuit to, but also an hotspot recently. In this paper, we make use of the statistical analysis law of laser speckle to achieve the fabrication of diffuser film. According to the requirements for the technical parameters of diffuser film, the structure characteristics of laser speckle and manufacturing methods are analyzed and discussed in detail. They consist of producing the original edition of the laser speckle figure (Photoresist board was used as recording medium to produce embossment laser speckle images, and this is one of the most important process in moulding technology ), using electricity molding system to manufacture metal formwork (It is also called as electrotyping, which is transfer the embossment speckle image from the photoresist board to a metal plate), and moulding replication (In a certain temperature and pressure, template stripes were transferred to the film). The diffusion light uniformity and brightness can be controlled via adjusting intensity distribution and average diameter of the speckles. Then the preliminary experiment results are given under laboratory conditions (argon ion laser, λ=457.9nm), and meanwhile the effects of several common diffuser films are compared in this paper.
Unbalanced Growth and the U.S. Productivity Slowdown (1992)

An explanation of the slower trend rate of U.S. productivity growth in the past two decades as a natural response to unbalanced growth, whereby resources are shifted from sectors with high productivity growth rates to those with lower rates, such as the rapidly expanding service sector.
The high mobility group protein HMG1 can reversibly inhibit class II gene transcription by interaction with the TATA-binding protein. (1994)

Regulation of transcription by RNA polymerase II in eukaryotic cells requires both basal and accessory factors, which interact through specific protein-DNA or protein-protein interactions. The high mobility group 1 protein (HMG1) was previously demonstrated to be a nonhistone chromatin-associated protein, which selectively recognizes cruciform DNA rather than a specific primary sequence element. During our investigations of proteins that interact with TFIID, we found that purified mammalian HMG1, as well as recombinant human HMG1, can interact with TATA-binding protein (TBP) in the presence of a TATA box-containing oligonucleotide to form a specific HMG1.TBP.promoter complex. This complex prevents TFIIB binding to TBP and consequently blocks formation of the preinitiation complex. In contrast, TFIIA can compete with HMG1 for binding to TBP. In an in vitro transcription assay reconstituted with highly purified or recombinant general factors, HMG1 is able to inhibit transcription by RNA polymerase II over 30-fold. As expected, addition of TFIIA can partially reverse this repression in a concentration-dependent manner. These results demonstrate that HMG1, a chromatin-associated protein, has the potential to act as a TBP-dependent negative transcription factor and may provide an important link between chromatin structure and the modulation of class II gene transcription.
Quantitative Analysis of Cadmium Selenide Nanocrystal Concentration by Comparative Techniques (2007)

In this paper, we compared atomic absorption spectroscopy (AAS), anodic stripping voltammetry (ASV), and UV-vis spectroscopy for the determination of the concentration of CdSe nanocrystal (NC) solutions. The experimental results were combined with crystallographic calculations of the NC size, which led to a very accurate determination of the nanocrystal concentration--a crucial parameter for bioanalytical applications. Furthermore, such a combined approach can be extended to the determination of shell thickness of core/shell materials (e.g., CdSe/ZnS).
Characterization of Carbon Deposits from Jet Fuel on Inconel 600 and Inconel X Surfaces (2000)

Flow reactor experiments were conducted to study carbon deposit formation from decomposition of a jet fuel (JP-8) at 500 °C and 500 psig for 5 h on the surface of two superalloys, Inconel 600 and Inconel X. The deposits collected on superalloy surfaces were characterized by temperature-programmed oxidation, size exclusion microscopy, and energy-dispersive X-ray spectroscopy. Significantly lower deposition on Inconel X compared to that on Inconel 600 was attributed to the presence of minor elemental components, such as Al, Ti, Nb, and Ta in the Inconel X alloy.
Dual Role of α6β4 Integrin in Epidermal Tumor Growth: Tumor-suppressive Versus Tumor-promoting Function (2007)

An increased expression of the integrin alpha6beta4 is correlated with a poor prognosis in patients with squamous cell carcinomas. However, little is known about the role of alpha6beta4 in the early stages of tumor development. We have isolated cells from mouse skin (mouse tumor-initiating cells [mTICs]) that are deficient in both p53 and Smad4 and carry conditional alleles of the beta4 gene (Itgb4). The mTICs display many features of multipotent epidermal stem cells and produce well-differentiated tumors after subcutaneous injection into nude mice. Deletion of Itgb4 led to enhanced tumor growth, indicating that alpha6beta4 mediates a tumor-suppressive effect. Reconstitution experiments with beta4-chimeras showed that this effect is not dependent on ligation of alpha6beta4 to laminin-5, but on the recruitment by this integrin of the cytoskeletal linker protein plectin to the plasma membrane. Depletion of plectin, like that of beta4, led to increased tumor growth. In contrast, when mTICs had been further transformed with oncogenic Ras, alpha6beta4 stimulated tumor growth, as previously observed in human squamous neoplasms. Expression of different effector-loop mutants of Ras(V12) suggests that this effect depends on a strong activation of the Erk pathway. Together, these data show that depending on the mutations involved, alpha6beta4 can either mediate an adhesion-independent tumor-suppressive effect or act as a tumor promotor.
A New Video Image Analysis System to Study Red Blood Cell Dynamics and Oxygenation in Capillary Networks (2005)

MASCOT is a robust and flexible system that requires simple hardware, including a SGI workstation fitted with an audio-visual module, a VCR, and an oscilloscope. Since the new system provides information on an individual cell basis from entire capillary segments, the authors believe that results obtained using MASCOT will be more accurate than those obtained from previous systems. Due to its flexibility and ease of extension to other applications, MASCOT has the potential to be applied widely as an analysis tool for capillary oxygen transport measurements.
Application of a Time Reversal Process to Baseline-free Structural Monitoring (2005)

A new nondestructive testing (NDT) methodology is developed based on the premise that “certain types of damage can be instantaneously detected without using prior baseline data.” The key idea of this reference-free damage diagnosis is the concept of a time reversal process. According to the time reversal acoustics, an input signal can be reconstructed at an excitation point if an output signal recorded at another point is reversed in a time domain and emitted back to the original source point. This concept of time reversal is extended to Lamb wave propagation in order to detect crack damage in plate-like structures such as bridge steel girders.