gebhart/patrepeval huggingface dataset:
Autoimmunity against Fibrinogen Mediates Inflammatory Arthritis in Mice (2009)

Abstract Rheumatoid arthritis (RA) is an autoimmune synovitis characterized by the presence of anticitrullinated protein Abs, although the exact targets and role of anticitrullinated protein autoimmunity in the pathogenesis of RA remain to be defined. Fibrinogen, which can be citrullinated, has recently emerged as a candidate autoantigen. To determine whether autoimmunity against fibrinogen can mediate inflammatory arthritis, we immunized a variety of common mouse strains with fibrinogen and found that DBA/1 and SJL mice developed an inflammatory and erosive arthritis. Mice with fibrinogen-induced arthritis (FIA) possess fibrinogen-reactive T cells that produce the proinflammatory cytokines IL-6, IL-17, TNF-α, and IFN-γ. FIA can be adoptively transferred with either plasma or fibrinogen-specific T cells from diseased mice. Mice with FIA possess rheumatoid factor, circulating immune complexes, and anticyclic citrullinated peptide Abs, all of which are characteristic of human RA. These observations demonstrate that fibrinogen is arthritogenic in mice and that the pathogenesis of FIA is mediated by both autoantibodies and fibrinogen-reactive T cells.
Characterization of gaseous mixtures of organic compounds with dual-secondary column comprehensive two-dimensional gas chromatography (GC×2 GC) (2002)

A comprehensive two-dimensional gas chromatograph with dual secondary columns (GC×2 GC) was used to characterize gaseous mixtures of volatile organic compounds (VOCs). Samples were collected on multi-layer sorbent tubes and introduced into the gas chromatograph using a thermal desorption apparatus. Differential flow modulation was used to couple the primary column to the secondary columns. Each GC×2 GC analysis produced a pair of two-dimensional gas chromatograms. The chromatograms provided complementary information due to the unique selectivities of the secondary columns. The additional information was especially useful in separating and identifying oxygenated and aromatic compounds. Samples of outdoor air, indoor air, and exhaled breath were analyzed with the GC×2 GC system. More than 100 volatile organic compounds could be separated in less than 10 minutes. The identities of approximately 50 peaks were determined for each sample.
Bridge-Enhanced Nanoscale Impedance Microscopy on Organic Light-Emitting Diodes, (2006)

The use of a variable resistor-capacitor (RC) bridge circuit was previously reported to be a viable solution to the spurious contribution of fringe capacitance during nanoscale impedance microscopy (NIM). In this paper, a refinement of this technique combined with standard NIM is presented as an impedance characterization tool for organic light-emitting diodes (OLEDs). In this technique, a sinusoidal bias is split into two equal branches, which are subsequently sent to the tunable RC circuit and the sample. By balancing the phase and magnitude of the two branches, the contribution to the current through the sample/tip junction can be directly monitored. To demonstrate the improved detection limit offered by this technique over more conventional NIM, conductive AFM measurements were performed on 8 µm by 8 µm OLED devices, demonstrating significant improvement in resolution in the current and phase maps. This paper also suggests possible future research that is necessary to fully enable impedance spectroscopy at the nanoscale.
Abstract P248: Oxidized Phospholipids and Risk of Peripheral Arterial Disease in Men (2012)

Background: Peripheral arterial disease (PAD) is highly prevalent, found in 25% of adults ≥70 years, but its risk factors are less well studied than coronary and carotid atherosclerosis. Proinflammatory oxidized phospholipids (OxPL) are a novel cardiovascular risk factor produced by oxidative stress and are preferentially bound and transported by lipoprotein (a) [Lp(a)] in plasma. Previous studies have shown an association between OxPL on apolipoprotein B-100 (OxPL/apoB) and carotid and femoral atherosclerosis. However, no previous studies have specifically examined the prospective association between OxPL/apoB and risk of PAD in a population-based cohort. Methods: We conducted a nested case-control study among men free of cardiovascular disease within the Health Professionals Follow-up Study (1994–2008) including 143 men with PAD and 429 controls matched on age, month of blood draw, and smoking. OxPL/apoB and Lp(a) were measured in stored baseline plasma. We identified cases of clinically significant PAD based on at least one of the following: (1) amputation, bypass, or other revascularization procedure for occlusive arterial disease, (2) angiogram/ultrasound confirming at least 50% stenosis of at least one artery with congruent symptoms in the ipsilateral limb, (3) ankle-brachial index < 0.9, or (4) physician's diagnosis. We used conditional logistic regression to estimate odds ratios (OR) for PAD according to level of OxPL/apoB. Results: The OR for PAD was 1.24 (95% CI 1.05–1.46) for each 1-standard deviation (SD) increase in OxPL/apoB after adjusting for matching factors. Additional adjustment for family history of MI, triglycerides, HDL-C, LDL-C, C-reactive protein, hemoglobin A1c, pack-years of smoking, physical activity, hypertension, diabetes, hypercholesterolemia, body-mass index, and aspirin use did not change this estimate: 1.24 (95% CI 1.00–1.54). OxPL/apoB was not correlated with any conventional risk factors: Spearman correlation coefficients ranged from 0.0 to 0.13. We observed no interaction with age or LDL-C. Similarly, the OR for PAD was 1.25 (95% CI 0.95–1.63) for each 1- SD increase in ln[Lp(a)] after adjusting for all of the above covariates. Conclusion: OxPL/apoB is positively associated with risk of PAD in men with no appreciable attenuation after adjustment for conventional risk factors.
Chlamydia trachomatis species-specific epitope detected on mouse biovar outer membrane protein (1984)

A common antigenic determinant on the chlamydial major outer membrane protein was detected on each of the three Chlamydia trachomatis biovars (trachoma, lymphogranuloma venereum, and mouse). This determinant was prominently displayed on the surface of chlamydial strains from both the trachoma and lymphogranuloma venereum biovars. However, detection of this determinant on a mouse biovar strain required denaturation by sodium dodecyl sulfate or periodate oxidation. This determinant provides a definable taxonomic link between the three biovars of C. trachomatis.
Automatic semantic image annotation and retrieval (2010)

As the number of Web images is increasing at a rapid rate, searching them semantically presents a significant challenge. Many raw images are constantly uploaded with few meaningful direct annotations of semantic content, limiting their search and discovery. As definite relationships exist between the type of scenes and image acquisition parameters, image metadata and parametric dimensions, it is possible to determine from these the semantic content of images. By exploiting the judgment and expertise that has gone into the image-capture process, and through the use of decision trees and rule induction, we have established a set of rules which allows the semantic contents of images to be identified. When jointly applied with ontology-based and contextual-based expansion approaches, they are able to produce a new level of meaningful automatic image annotation, from which meaningful high-level semantic image searches are performed. The system is evaluated quantitatively using more than 100,000 Web images with 1,000,000 associated human tags outside the training database. Experimental results indicate that this approach is able to deliver highly competent performance, attaining good recall and precision rates of sometimes over 80%. This approach enables an advanced degree of semantic richness to be automatically associated with images which could previously only be performed manually.
Edge adaptive graph-based transforms: Comparison of step/ramp edge models for video compression (2016)

In this paper, we propose a new edge model for edge adaptive graph-based transforms (EA-GBTs) in video compression. In particular, we consider step and ramp edge models to design graphs used for defining transforms, and compare their performance on coding intra and inter predicted residual blocks. In order to reduce the signaling overhead of block-adaptive coding, a new edge coding method is introduced for the ramp model. Our experimental results show that the proposed methods outperform classical DCT-based encoding and that ramp edge models provide better performance than step edge models for intra predicted residuals.
Thermoplastic amphiphilic conetworks (2008)

Abstract Our main objective was the design, synthesis, characterization, and testing of a novel class of materials, thermoplastic amphiphilic conetworks (TP‐APCNs). A further objective was the evaluation of TP‐APCNs as biomaterials, for example, as immunoisolatory membranes in a bioartificial pancreas, or as extended‐wear soft contact lenses. The synthesis of the first TP‐APCNs was accomplished by blending an amphiphilic graft polymer, poly(dimethyl acryl amide)‐ g ‐polydimethylsiloxane (PDMAAm‐ g ‐PDMS), with a commercial PDMS‐containing polyurethane (PU). The common PDMS segments coalesce and form a single phase, whereas the hard/crystalline segments of the PU physically crosslink the blend. The properties of TP‐APCNs can be controlled by the graft/PU ratio and segment molecular weights. TP‐APCNs with cocontinuous hydrophilic and hydrophobic phases were prepared as demonstrated by swelling in water and n ‐heptane. Depending on the blend ratio and molecular weights, optically clear water‐swollen TP‐APCNs with 0.5–4 MPa tensile strength, 70–280% elongation, together with 2–11 × 10 −7 cm 2 /s glucose permeability, and 1.2–8 × 10 −8 cm 2 /s insulin permeability were prepared. TP‐APCNs are processible by casting and molding. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 682–691, 2009
[Production of L-citrulline by a recombinant Corynebacterium crenatum SYPA 5-5 whole-cell biocatalyst]. (2017)

Arginine deiminase (ADI) was first high-efficient expressed in Corynebacterium crenatum SYPA 5-5. The ADI was purified by Ni-NTA affinity chromatography and SDS-PAGE analysis showed the molecular weight (MW) was 46.8 kDa. The optimal temperature and pH of ADI were 37 ℃ and 6.5 respectively. The Michaelis constant was 12.18 mmol/L and the maximum velocity was 0.36 μmol/(min·mL). Under optimal conditions, 300 g/L of arginine was transformed and the productivity reach 8 g/(L·h). The recombinant strain was cultivated in a 5-L fermentor and used for whole-cell transformation of 300 g/L arginine, under repeated-batch bioconversion, the cumulative production reached 1 900 g/L.
On-Chip Octave-Spanning Supercontinuum in Nanostructured Silicon Waveguides Using Ultralow Pulse Energy (2012)

We present an approach for generating an octave-spanning supercontinuum on a silicon chip using input pulse energy as low as 6.8 pJ. This is enabled by advanced dispersion engineering with a nanoscale slot structure. We analyze the performance of the supercontinuum generation in terms of bandwidth, spectral coherence, and flatness, under different operating conditions. We show that, accompanying with the spectral broadening, the input pulse is compressed to 12 fs, which opens an opportunity for on-chip few-cycle pulse generation.
New applications of the infrared emission microscopy to wafer-level backside and flip-chip package analyses (2003)

The Infrared Emission Microscopy (IREM) has been used in the semiconductor industry to locate hot carrier emission and thermal emission sites in CMOS ICs. In this paper, new applications to wafer-level backside Photon Emission Microscopy (PEM) and Flip-chip package analysis will be presented. At the die level, Photon Emission Microscopy (PEM) is a straightforward procedure of biasing the device and collecting photons. At wafer-level, this task becomes complicated because there are the various dice on the reticle field and the numerous reticle fields on the wafer, and it is difficult to tell which die is the DUT from the backside. A new method for die location is developed before wafer-level Backside PEM can be performed. In this method, the wafer is powered by reversed biased voltage to clamp the current appropriate to the device technology, and then PEM acquisition is started. The die with emission is the target. Real-time X-ray (RTX) inspection is a conventional way to locate anomalies in solder bumps in Flip-chip packages. This procedure has become routine. The drawback of RTX is its high capital costs and its limit. For a company where the real-time X-ray system is not available, IREM could be an alternative for failure analysis in Flip-chip packages. This application had been reserved for RTX.
A novel variable-gravity simulation method: potential for astronaut training. (1995)

Zero gravity conditions for astronaut training have traditionally used neutral buoyancy tanks, and with such tanks hypogravity conditions are produced by the use of supplemental weights. This technique does not allow for the influence of water viscosity on any reduced gravity exercise regime. With a water-foam fluid produced by using a microbubble air flow together with surface active agents to prevent bubble agglomeration, it has been found possible to simulate a range of gravity conditions without the need for supplemental weights and additionally with a substantial reduction in the resulting fluid viscosity. This new technique appears to have application in improving the simulation environment for astronaut training under the reduced gravity conditions to be found on the moon or on Mars, and may have terrestrial applications in patient rehabilitation and exercise as well.
Structural basis for broad neutralization of ebolaviruses by an antibody targeting the glycoprotein fusion loop (2018)

The severity of the 2014-2016 ebolavirus outbreak in West Africa expedited clinical development of therapeutics and vaccines though the countermeasures on hand were largely monospecific and lacked efficacy against other ebolavirus species that previously emerged. Recent studies indicate that ebolavirus glycoprotein (GP) fusion loops are targets for cross-protective antibodies. Here we report the 3.72 Å resolution crystal structure of one such cross-protective antibody, CA45, bound to the ectodomain of Ebola virus (EBOV) GP. The CA45 epitope spans multiple faces of the fusion loop stem, across both GP1 and GP2 subunits, with ~68% of residues identical across > 99.5% of known ebolavirus isolates. Extensive antibody interactions within a pan-ebolavirus small-molecule inhibitor binding cavity on GP define this cavity as a novel site of immune vulnerability. The structure elucidates broad ebolavirus neutralization through a highly conserved epitope on GP and further enables rational design and development of broadly protective vaccines and therapeutics.
Temporal noise reduction of Bayer matrixed video data (2003)

This paper describes a new approach for noise reduction of video sequences that directly processes raw data frames acquired by an image sensor. The proposed noise reduction filter operates on Bayer matrixed video sequences instead of the canonical YUV format allowing saving of resources in terms of time and space; this is particularly relevant for real time processing. Noise level is constantly monitored in order to change the filter strength adaptively. Experiments show the effectiveness of the proposed approach.
A Safe Foot-and-Mouth Disease Vaccine Platform with Two Negative Markers for Differentiating Infected from Vaccinated Animals (2012)

Vaccination of domestic animals with chemically inactivated foot-and-mouth disease virus (FMDV) is widely practiced to control FMD. Currently, FMD vaccine manufacturing requires the growth of large volumes of virulent FMDV in biocontainment-level facilities. Here, two marker FMDV vaccine candidates (A(24)LL3D(YR) and A(24)LL3B(PVKV)3D(YR)) featuring the deletion of the leader coding region (L(pro)) and one of the 3B proteins were constructed and evaluated. These vaccine candidates also contain either one or two sets of mutations to create negative antigenic markers in the 3D polymerase (3D(pol)) and 3B nonstructural proteins. Two mutations in 3D(pol), H(27)Y and N(31)R, as well as RQKP(9-12)→PVKV substitutions, in 3B(2) abolish reactivity with monoclonal antibodies targeting the respective sequences in 3D(pol) and 3B. Infectious cDNA clones encoding the marker viruses also contain unique restriction endonuclease sites flanking the capsid-coding region that allow for easy derivation of custom designed vaccine candidates. In contrast to the parental A(24)WT virus, single A(24)LL3D(YR) and double A(24)LL3B(PVKV)3D(YR) mutant viruses were markedly attenuated upon inoculation of cattle using the natural aerosol or direct tongue inoculation. Likewise, pigs inoculated with live A(24)LL3D(YR) virus in the heel bulbs showed no clinical signs of disease, no fever, and no FMD transmission to in-contact animals. Immunization of cattle with chemically inactivated A(24)LL3D(YR) and A(24)LL3B(PVKV)3D(YR) vaccines provided 100% protection from challenge with parental wild-type virus. These attenuated, antigenically marked viruses provide a safe alternative to virulent strains for FMD vaccine manufacturing. In addition, a competitive enzyme-linked immunosorbent assay targeted to the negative markers provides a suitable companion test for differentiating infected from vaccinated animals.
Deep Gaussian Conditional Random Field Network: A Model-Based Deep Network for Discriminative Denoising (2016)

We propose a novel end-to-end trainable deep network architecture for image denoising based on a Gaussian Conditional Random Field (GCRF) model. In contrast to the existing discriminative denoising methods that train a separate model for each individual noise level, the proposed deep network explicitly models the input noise variance and hence is capable of handling a range of noise levels. Our deep network, which we refer to as deep GCRF network, consists of two sub-networks: (i) a parameter generation network that generates the pairwise potential parameters based on the noisy input image, and (ii) an inference network whose layers perform the computations involved in an iterative GCRF inference procedure. We train two deep GCRF networks (each network operates over a range of noise levels: one for low input noise levels and one for high input noise levels) discriminatively by maximizing the peak signal-to-noise ratio measure. Experiments on Berkeley segmentation and PASCALVOC datasets show that the proposed approach produces results on par with the state of-the-art without training a separate network for each individual noise level.
Free‐breathing combined three‐dimensional phase sensitive late gadolinium enhancement and T<sub>1</sub> mapping for myocardial tissue characterization (2014)

The proposed sequence enables simultaneous acquisition of 3D PS-LGE images and spatially registered 3D T1 maps in a single scan.
Experimental study of an advanced three‐component borehole seismic receiver (1991)

An advanced three-component borehole seismic receiver has been designed, developed, and tested. This receiver was designed with the aid of finite element vibration modeling to be free of significant clamp resonances below 2000 Hz. This broad frequency range makes this sonde well suited for cross-well seismic imaging applications. State-of-the art piezoelectric accelerometers are used as the three-component sensors and provide signal enhancement relative to conventional geophones. The use of these accelerometers offer a signal-to-noise enhancement of approximately 20 dB at 1000 Hz over moving-coil seismic geophones. Additional features of the sonde include high temperature/pressure operation, small size, lightweight, field-durable construction, and multi-station expansion capability. A prototype accelerometer-based sonde was field tested at the Texaco Humble Field to determine its performance characteristics. A borehole explosive source was used to test the sonde in a cross-well configuration (815 ft well-to-well separation). For comparison purposes, similar cross-well tests were performed using a commercial VSP-type tool and buried/cemented geophones. The advanced sonde exhibited significantly improved coupling relative to the VSP tool as evidenced by increased bandwidth and signal-to-noise ratio. Accordingly, the advanced sonde produced signals which rival those produced by the buried/cemented geophones.
Hot-press fabrication and joining of boron carbide (1979)

A method has been developed for fabricating long, cylindrical rubber-mill rolls of boron carbide for use with abrasive materials. The technique consisted of initially hot pressing the boron carbide (to 90% of the theoretical density) to short, hollow cylinders having a length-to-diameter ratio of about one. This initial hot-press operation was followed by a second hot press to join or bond, and further densify, the short sections into a final compact having a length-to-diameter ratio of three. Flexural-strength data show that the integrity of the bond is comparable to that of the base material.
Laser pulse-stretching with multiple optical ring cavities (2002)

We describe a simple and passive nanosecond-long laser-pulse stretcher using multiple optical ring cavities. We present a model of the pulse-stretching process for an arbitrary number of optical ring cavities. This new model explicitly includes the effects of cavity delay time, beam-splitter reflectivity, total number of optical cavities, and describes the effects of spatial profile sensitivity. Using the model, we optimize the design of a pulse stretcher for use in a spontaneous Raman-scattering excitation system that avoids laser-induced plasma spark problems. From the optimized design, we then experimentally demonstrate and verify the model with a three-cavity pulse-stretcher system that converts a 1000-mJ, 8.4-ns-long input laser pulse into an approximately 75-ns-long (FWHM) output laser pulse with a peak power reduction of 0.10x and an 83% efficiency.
Hardware acceleration of lucky-region fusion (LRF) algorithm for image acquisition and processing (2013)

“Lucky-region fusion” (LRF) is an image processing technique that has proven successful in enhancing the quality of images distorted by atmospheric turbulence. The LRF algorithm extracts sharp regions of an image obtained from a series of short exposure frames, and “fuses” them into a final image with improved quality. In previous research, the LRF algorithm had been implemented on a PC using a compiled programming language. However, the PC usually does not have sufficient processing power to handle real-time extraction, processing and reduction required when the LRF algorithm is applied not to single picture images but rather to real-time video from fast, high-resolution image sensors. This paper describes a hardware implementation of the LRF algorithm on a Virtex 6 field programmable gate array (FPGA) to achieve real-time video processing. The novelty in our approach is the creation of a “black box” LRF video processing system with a standard camera link input, a user controller interface, and a standard camera link output.