gebhart/patrepeval huggingface dataset:
BXR, an embryonic orphan nuclear receptor activated by a novel class of endogenous benzoate metabolites (1998)

Nuclear receptors are ligand-modulated transcription factors that respond to steroids, retinoids, and thyroid hormones to control development and body physiology. Orphan nuclear receptors, which lack identified ligands, provide a unique, and largely untapped, resource to discover new principles of physiologic homeostasis. We describe the isolation and characterization of the vertebrate orphan receptor, BXR, which heterodimerizes with RXR and binds high-affinity DNA sites composed of a variant thyroid hormone response element. A bioactivity-guided screen of embryonic extracts revealed that BXR is activatable by low-molecular-weight molecules with spectral patterns distinct from known nuclear receptor ligands. Mass spectrometry and 1H NMR analysis identified alkyl esters of amino and hydroxy benzoic acids as potent, stereoselective activators. In vitro cofactor association studies, along with competable binding of radiolabeled compounds, establish these molecules as bona fide ligands. Benzoates comprise a new molecular class of nuclear receptor ligand and their activity suggests that BXR may control a previously unsuspected vertebrate signaling pathway.
Multiple ROI Support in the Scalable Video Coding (2006)

In this paper, we propose a new functionality to Scalable Video Coding (SVC), which is the support of multiple ROIs for heterogeneous display resolution. Scalable video coding is targeted at giving temporal, spatial, and quality scalability for the encoded bit stream. Region of interest (ROI) is an area that is semantically important to a particular user, especially users with heterogeneous display resolutions. The bitstream containing the ROIs could to be extracted without any transcoding operations, which may be one of way to satisfy QoS. To define multiple ROI in SVC, we adapted FMO, a tool defined in H.264, and based on it, we propose a way to encode and decode ROIs. The proposed method is implemented on the JSVM1.0 and the functionality is verified using it.
ST-MRAM fundamentals, challenges, and applications (2013)

Magnetoresistive Random Access Memory (MRAM) technology emerged from research and development into volume production within the last decade in the form of Toggle MRAM. The latest Magnetic Tunnel Junction (MTJ) based memory technology, Spin-Torque MRAM, has reached the level of customer sampling, offering higher density and bandwidth. Spin-Torque MRAM enables new applications, offers a wide range of features for use in embedded memory, and has the potential to extend to technology nodes beyond the capability of DRAM. This paper describes the devices, fundamental circuit challenges, and applications of this evolving MTJ based memory.
Phase contrast x-ray imaging at high energies (Conference Presentation) (2019)

Gratings-based x-ray imaging can provide additional materials signatures, including refraction which is proportional to variations in electron density, and scatter which is sensitive to sub-resolution texture. Phase contrast measurements have been conducted using a variety of approaches, including Talbot-Lau interferometry, coded aperture systems, and single absorption grid systems. Because of the simultaneous requirements for fine spatial patterns to detect small angular changes, and the thickness of material required to modulate a penetrating beam, many phase contrast measurements are conducted at relatively low energy, below 100 kV. Many applications in security screening require higher energies in order to penetrate larger objects. Here, we use a single absorption grid with direct imaging of the projected pattern to perform phase contrast measurements. A second grid is used for a beam hardening correction. We present measurements of pattern visibility as a function of energy up to 450 kV, demonstrating that the necessary beam patterning can be extended to higher energies. We also present measurements of a textured and homogeneous material as a function of energy, demonstrating that a texture signature is still present as energy is increased, and that the beam-hardening correction correctly accounts for and removes spectral effects on pattern visibility. To the best of our knowledge, this represents the highest energy demonstration of this technique to date, and enables new application areas.
Nanoscale approaches to define biologic signatures and measure proteomic response to targeted therapies in hematologic and solid tumors (2010)

Abstract The ability to quantify changes in protein activation in a clinical setting is important for the development of therapeutics that target cancer signaling pathways. A barrier to analyzing proteomic response in patients is the large amount of specimen required to make measurements at each time point. To overcome this barrier, we have developed the use of a highly sensitive microfluidic nano-immunoassay system (NIA) to quantify unphosphorylated, single- and multiple phosphorylated isoforms of proteins in patient specimens collected by minimally invasive blood draws or fine needle aspirates. We first developed tissue collection, handling and processing protocols to produce reliable NIA results using as little as 4 nanoliters of lysate. We next developed assays to measure over 40 proteomic parameters, including changes in proteins that mediate RAS and MAP Kinase signaling, cell cycle and apoptosis. To investigate the diagnostic potential of NIA, we have collected over 300 specimens from normal controls and patients with hematopoietic and solid tumors. We found that phosphoprotein profiles in tumor cells could distinguish tumor from normal cells. Further, patient tumors could be grouped based upon different patterns of percent ERK and MEK phosphorylation. In a clinical trial setting, we have now used NIA in conjunction with multicolor intracellular flow cytometry (FACS) to monitor changes in phospho-profiles in patients with receiving novel agents for hematopoietic cancers. In a prospective study of a novel cell cycle inhibitor in myelodysplastic syndrome (MDS), we have used NIA to measure changes in MAPK and cell cycle proteins in patient leukocytes sampled throughout serial time points during the study. In a prospective study of atorvastatin in patients with non-Hodgkin's lymphoma, we have used NIA and FACS to distinguish three patterns of signaling changes in patient tumor cells, monocytes, and T cells. First, pathways that were initially activated in tumor cells decreased upon treatment with atorvastatin, with up to a 70% decrease in phospho-STAT3 and phospho-STAT5. Second, pathways that were initially suppressed in tumor cells (including phospho-PLC), normalized upon treatment. Third, expression levels of proteins in apoptotic pathways, including p38, increased upon atorvastatin treatment. Finally, changes in signaling associated with atorvastatin were found to be cell specific: effects on tumor cells were distinct from effects on non-tumor T cells and monocytes. Our studies demonstrate that NIA and FACS are complementary proteomic methods that can be used to quantify changes in cell signaling and distinguish responses in different cellular populations from very small clinical specimens sampled during therapeutic interventions. Nanoscale analysis of patient specimens is a feasible and promising approach for the development of new diagnostic markers and biomarkers of therapeutic activity. This talk is also presented as Poster A21.
A Phase I Vaccine Trial with Peptides Reflecting ras Oncogene Mutations of Solid Tumors (1999)

Mutations in the ras genes occur in 20% of all human cancers. These genes, in turn, produce mutated proteins that are unique to cancer cells, rendering them distinguishable from normal cells by the immune system. Thus, mutated Ras proteins may form potential targets for immune therapy. We conducted a phase I/pilot clinical trial in patients with advanced cancers to test the toxicity and the ability to induce an immune response by vaccination with 13-mer mutated Ras peptides reflecting codon 12 mutations. These peptides corresponded to each of the patient's own tumor Ras mutation. Patients were vaccinated monthly x3 subcutaneously with the specific Ras peptide along with Detox adjuvant (RiBi ImmunoChem Research, Inc., Hamilton, MT, U.S.A.) at one of five different peptide dose levels (100, 500, 1,000, 1,500, and 5,000 micrograms). Three out of 10 evaluable patients generated a mutant Ras specific CD4+ and/or CD8+ T-cell immune response. The CD8+ cytotoxic cells specific for Gly to Val mutation at codon 12 were capable of lysing an HLA-A2-matched tumor cell line carrying the corresponding mutant but not the wild-type ras gene. The treatment has been well tolerated with no evidence of serious acute or delayed systemic side effects on any of the five dose levels. We demonstrated that we can generate in cancer patients specific T-lymphocyte responses that detect single amino acid differences in Ras oncoproteins. Neither the immune responses nor the minor side effects seen were found to be dose dependent. This approach may provide a unique opportunity for generating a tumor-directed therapy. Also, in vitro stimulation of these cells with the corresponding peptide generated specific T-cell lines that could be used for adoptive immune therapy.
A Simple Method of Handling Thermomechanical Coupling for Temperature Computation in a Rolling Tire (2004)

Abstract The thermomechanical analysis of a pneumatic tire is a highly complex process due to the effects of temperature on both the mechanical state and the viscoelastic energy dissipation in the tire. This coupled thermomechanical behavior typically requires that rolling tire temperatures be determined iteratively. As a result, a steady‐state analysis involves updating the temperature dependent elastic and viscoelastic properties as the solution proceeds. The process is further complicated in a non‐steady‐state analysis where material properties need to be updated at multiple intervals in time. A simplified method is proposed. First, the sensitivity of the tire elastic response of the tire to changes in material stiffness is characterized using the “deformation index”. Then, using a commercial finite element program and an appropriate user subroutine, heat generation is expressed as a function of the local temperature using a simple algebraic expression involving the temperature dependent material properties and the deformation indices. Temperatures are computed using the finite element program with the coupling information contained in the user subroutine. The result is a simplified method for a fully coupled thermomechanical analysis of a tire for steady‐state and transient thermal analysis. The accuracy and the simplicity of the method are demonstrated using a small “tire‐like” model. The simplified method is compared to the fully coupled iterative method for a steady‐state thermal solution.
Material characterization for III-nitride-based light emitters (1998)

A review is presented of the electrical and optical properties of nitride based optoelectronic devices, in particular AlGaInN light emitting diodes and laser diode structures. The III-nitride films and devices were grown by organometallic vapor-phase epitaxy on c- and a-face sapphire substrates. We will discuss the structural properties of GaN. InGaN and AlGaN films, heterostructures and InGaN/GaN quantum wells using x-ray diffraction and cross-sectional transmission electron microscope and describe their electrical and optical properties characterized by Hall effect, photoluminescence, and electroluminescence measurements.
Aspirin-Resistant Thromboxane Biosynthesis and the Risk of Myocardial Infarction, Stroke, or Cardiovascular Death in Patients at High Risk for Cardiovascular Events (2002)

In aspirin-treated patients, urinary concentrations of 11-dehydro thromboxane B2 predict the future risk of myocardial infarction or cardiovascular death. These findings raise the possibility that elevated urinary 11-dehydro thromboxane B2 levels identify patients who are relatively resistant to aspirin and who may benefit from additional antiplatelet therapies or treatments that more effectively block in vivo thromboxane production or activity.
Clock extraction using saturable absorption in a semiconductor nonlinear optical amplifier (1991)

A novel approach to clock extraction for non-return-to-zero (NRZ) formatted data is demonstrated using two contact semiconductor nonlinear optical amplifiers (NLOAs). The NLOA amplifies the transmitted data (fiber-fiber approximately 5 dB) and due to the absorptive nonlinearity, induced by bleaching a region of saturable absorption within the NLOA, an electrical clock component is generated at the absorber electrical contact. Narrow bandpass electrical filtering of the absorber contact electrical RF spectrum is all that is required in order to extract a stable clock signal. Bit-error-rate measurements at 155.6 Mb/s showed no receiver sensitivity penalty when using the NLOA extracted clock compared to the transmitter clock. Using quantum well material strong clock component generation has been achieved at modulation rates from < 100 Mb/s up to 5 Gb/s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Dynamic phase-sensitive optical coherence elastography at a true kilohertz frame-rate (2016)

Dynamic optical coherence elastography (OCE) techniques have rapidly emerged as a noninvasive way to characterize the biomechanical properties of tissue. However, clinical applications of the majority of these techniques have been unfeasible due to the extended acquisition time because of multiple temporal OCT acquisitions (M-B mode). Moreover, multiple excitations, large datasets, and prolonged laser exposure prohibit their translation to the clinic, where patient discomfort and safety are critical criteria. Here, we demonstrate the feasibility of noncontact true kilohertz frame-rate dynamic optical coherence elastography by directly imaging a focused air-pulse induced elastic wave with a home-built phase-sensitive OCE system. The OCE system was based on a 4X buffered Fourier Domain Mode Locked swept source laser with an A-scan rate of ~1.5 MHz, and imaged the elastic wave propagation at a frame rate of ~7.3 kHz. Because the elastic wave directly imaged, only a single excitation was utilized for one line scan measurement. Rather than acquiring multiple temporal scans at successive spatial locations as with previous techniques, here, successive B-scans were acquired over the measurement region (B-M mode). Preliminary measurements were taken on tissue-mimicking agar phantoms of various concentrations, and the results showed good agreement with uniaxial mechanical compression testing. Then, the elasticity of an <i>in situ </i>porcine cornea in the whole eye-globe configuration at various intraocular pressures was measured. The results showed that this technique can acquire a depth-resolved elastogram in milliseconds. Furthermore, the ultra-fast acquisition ensured that the laser safety exposure limit for the cornea was not exceeded.
Coupled Bayesian Framework for Dual Energy Image Registration (2006)

Image registration for X-ray dual energy imaging is challenging due to the overlaid transparent layers (i.e., the bone and soft tissue) and the different appearances between the dual images acquired with X-rays at different energy spectra. Moreover, subpixel accuracy is necessary for good reconstruction of the bone and soft-tissue layers. This paper addresses these problems with a novel coupled Bayesian framework, in which the registration and reconstruction can effectively reinforce each other. With the reconstruction results, we can design accurate matching criteria for aligning the dual images, instead of treating them as multi-modality registration. Furthermore, prior knowledge of the bone and soft tissue can be exploited to detect poor reconstruction due to inaccurate registration; and hence correct registration errors in the coupled framework. A multiscale freeform registration algorithm is implemented to achieve subpixel registration accuracy. Promising results are obtained in the experiments.
Quantification of Pulmonary Emphysema from Lung Computed Tomography Images (1997)

A texture-based adaptive multiple feature method (AMFM) for evaluating pulmonary parenchyma from computed tomography (CT) images is described. This method incorporates multiple statistical and fractal texture features. The AMFM was compared to two previously published methods, namely, mean lung density (MLD) and the lowest fifth percentile of the histogram (HIST). First, the ability of these methods to detect subtle differences in ventral-dorsal lung density gradient in the prone normal lung was studied. Second, their abilities to differentiate between normal and emphysematous whole lung slices were compared. Finally, regional analyses comparing normal and emphysematous regions were performed by dividing the lungs. In the CT slices into six equal regions, ventral to dorsal, and analyzing each region separately. The results demonstrated that the AMFM could separate the ventral from the dorsal one-third of the normal prone lung with 89.8% accuracy, compared to an accuracy of 74.6% with the MLD and 64.4% with the HIST methods. The normal and emphysematous slices were separated on a global basis with 100.0% accuracy using the AMFM as compared to an accuracy of 94.7% and 97.4% using the MLD and HIST methods, respectively. The regional normal and emphysematous tissues were discriminated with an average accuracy of 97.9%, 89.9%, and 99.1% with the AMFM, MLD, and HIST methods, respectively. The three methods and the pulmonary function tests in the normal and emphysema groups were poorly correlated. Quantitative texture analysis using adaptive multiple features holds promise for the objective noninvasive evaluation of the pulmonary parenchyma.
Sewage Sludge-Derived Materials as Efficient Adsorbents for Removal of Hydrogen Sulfide (2001)

Sewage sludge-derived materials were used as adsorbents of hydrogen sulfide from moist air. The adsorbent obtained by carbonization at 950 degrees C has a capacity twice of that of coconut-shell-based activated carbon. The capacity of the sludge-derived materials increases with increasing carbonization temperature. It is likelythatduring carbonization at 950 degrees C a mineral-like phase is formed that consists of such catalytically active metals as iron, zinc, and copper. The results obtained demonstrate that the presence of iron oxide significantly increases the capacity of commercial carbon and activated alumina. The sludge-derived adsorbents are efficient for hydrogen sulfide removal until the pore entrances are blocked with sulfur as the product of oxidation reaction. For materials in which the catalytic effect is predominant, hydrogen sulfide is adsorbed until all pores are filled with sulfur. There is also indication that chemisorption plays a significant role in the removal of hydrogen sulfide from moist air.
Introducing the ESAT-6 free IGRA, a companion diagnostic for TB vaccines based on ESAT-6 (2017)

There is a need for an improved vaccine for tuberculosis. ESAT-6 is a cardinal vaccine antigen with unique properties and is included in several vaccine candidates in development. ESAT-6 is also the core antigen in the IFN-γ release assays (IGRA) used to diagnose latent infection, rendering IGRA tests unspecific after vaccination. This challenge has prompted the development of a companion diagnostic for ESAT-6 based vaccines, an ESAT-6 free IGRA. We screened a panel of seven potential new diagnostic antigens not recognized in BCG vaccinated individuals. Three highly recognized antigens EspC, EspF and Rv2348c were identified and combined with CFP10 in an ESAT-6 free antigen cocktail. The cocktail was prepared in a field-friendly format, lyophilized with heparin in ready-to-use vacutainer tubes. The diagnostic performance of the ESAT-6 free IGRA was determined in a cross-validation study. Compared IGRA, the ESAT-6 free IGRA induced a comparable magnitude of IFN-γ release, and the diagnostic performance was on par with Quantiferon (sensitivity 84% vs 79%; specificity 99% vs 97%). The comparable performance of the ESAT-6 free IGRA to IGRA suggests potential as companion diagnostic for ESAT-6 containing vaccines and as adjunct test for latent infection.
Strata (2017)

Next generation devices, such as virtual reality (VR), augmented reality (AR), and smart appliances, demand a simple and intuitive way for users to interact with them. To address such needs, we develop a novel acoustic based device-free tracking system, called Strata, to enable a user to interact with a nearby device by simply moving his finger. In Strata, a mobile (e.g., smartphone) transmits known audio signals at inaudible frequency, and analyzes the received signal reflected by the moving finger to track the finger location. To explicitly take into account multipath propagation, the mobile estimates the channel impulse response (CIR), which characterizes signal traversal paths with different delays. Each channel tap corresponds to the multipath effects within a certain delay range. The mobile selects the channel tap corresponding to the finger movement and extracts the phase change of the selected tap to accurately estimate the distance change of a finger. Moreover, it estimates the absolute distance of the finger based on the change in CIR using a novel optimization framework. We then combine the absolute and relative distance estimates to accurately track the moving target. We implement our tracking system on Samsung Galaxy S4 mobile phone. Through micro-benchmarks and user studies, we show that our system achieves high tracking accuracy and low latency without extra hardware.
Microchannel heatsinks for high-average-power laser diode arrays (1992)

Detailed performance results and fabrication techniques for an efficient and low thermal impedance laser diode array heatsink are presented. High duty factor or even CW operation of fully filled laser diode arrays is enabled at high average power. Low thermal impedance is achieved using a liquid coolant and laminar flow through microchannels. The microchannels are fabricated in silicon using a photolithographic pattern definition procedure followed by anisotropic chemical etching. A modular rack-and-stack architecture is adopted for the heatsink design allowing arbitrarily large two-dimensional arrays to be fabricated and easily maintained. The excellent thermal control of the microchannel cooled heatsinks is ideally suited to pump array requirements for high average power crystalline lasers because of the stringent temperature demands that result from coupling the diode light to several nanometers wide absorption features characteristic of lasing ions in crystals.
D102 Experimental Study on Clathrate Hydrate Slurry : Heat Transfer Characteristics of Air Conditioner (2001)

The development clathrate hydrate has latent heat over the temp. range of 5〜12℃ and a mixture of clathrate hydrate and aqueous solution ( referred to as CHS ) has greater cooling capacity compared to cold water. The air-conditioning system utilizing the CHS is expected to reduce the pumping power consumption dramatically. This paper reports the results of a measured heat transfer characteristics of air conditioner using the CHS. The result of experiments, proved that CHS is capable for cold latent heat medium for air conditioning system.