gebhart/patrepeval huggingface dataset:
NOONAN SYNDROME AND RELATED DISORDERS: Genetics and Pathogenesis (2005)

Noonan syndrome is a pleiomorphic autosomal dominant disorder with short stature, facial dysmorphia, webbed neck, and heart defects. In the past decade, progress has been made in elucidating the pathogenesis of this disorder using a positional cloning approach. Noonan syndrome is now known to be a genetically heterogeneous disorder with nearly one half of cases caused by gain-of-function mutations in PTPN11, the gene encoding the protein tyrosine phosphatase SHP-2. Similar germ line mutations cause two related genetic disorders, Noonan-like disorder with multiple giant cell lesion syndrome and LEOPARD syndrome, and somatic PTPN11 mutations can underlie certain pediatric hematopoietic malignancies, including juvenile myelomonocytic, acute lymphoblastic, and acute myelogenous leukemias. A mouse model of PTPN11-related Noonan syndrome was recently generated, providing a reagent for studying disease pathogenesis in greater depth as well as experimenting with novel therapeutic strategies.
Expression of cutaneous lymphocyte-associated antigen by CD8+ T cells specific for a skin-tropic virus (2002)

Virus-specific CD8+ T cells traffic to infected tissues to promote clearance of infection. We used herpes simplex virus type 2 (HSV-2) as a model system to investigate CD8+ T cell trafficking to the skin in humans. Using human leukocyte antigen (HLA) class I tetramers, we observed that HSV-specific CD8+ T cells in the peripheral blood expressed high levels of cutaneous lymphocyte-associated antigen (CLA). In contrast, CD8+ T cells specific for non–skin-tropic herpesviruses lacked CLA expression. CLA-positive HSV-2–specific CD8+ T cells had the characteristics of central memory cells, expressing CCR7, CD62L, and CD28, and they proliferated briskly in response to antigen. CLA is related to a functional E-selectin ligand, and both E-selectin and CLA-positive cells were detected in HSV-2–infected skin. HSV-2–specific T cells adhered to cells transfected with E-selectin. A higher proportion of HSV-specific CD8+ T cells recovered from herpes lesions express CLA compared with blood, consistent with a role for CLA in skin homing. To our knowledge, this is the first report of expression of tissue-specific adhesion-associated molecules by virus-specific CD8+ T cells. The evaluation of vaccines for skin and mucosal pathogens should include study of the induction of appropriate tissue-specific homing molecules.
Applications of the liquid core optical ring resonator platform (2007)

The liquid core optical ring resonator (LCORR) integrates an array of optical ring resonators into a microfluidics channel. The LCORR is made of a micro-sized glass capillary; the circular cross-section of the capillary acts as an optical ring resonator while the resonating light interacts with the fluid sample passing through the core. Q-factors larger than 10<sup>7</sup> have been achieved in LCORRs on the order of 100 micrometers in diameter. This implies an effective interaction length between the evanescent field of the resonator and the fluidic core of over 10 cm. The novel integrated architecture and excellent photonic performance lead to a number of applications in sensing, analytical chemistry, and photonics. For the last decade, optical ring resonators have been explored for label-free bio/chemical detection. The LCORR architecture possesses the same capabilities as other optical ring resonator bio/chemical sensors while also integrating micro-capillary-based fluidics with the sensor head. The integrated fluidics design in combination with the micro-sized sensor head and pico-liter sample volume lead to a lab-on-a-chip sensor for biomolecules, such as biomarkers and specific DNA sequences. Also, because the ring resonator creates a high-intensity field inside the microfluidic channel, the LCORR is an excellent microfluidic platform for surface-enhanced Raman scattering (SERS) detection in silver colloids. Finally, the high quality factor of the capillary-based resonator enables novel opto-fluidic devices, such as dye lasers. We will discuss the details of these concepts and present our research results in each of these applications.
Autofluorescence Removal by Non-Negative Matrix Factorization (2010)

This paper describes a new, physically interpretable, fully automatic algorithm for removal of tissue autofluorescence (AF) from fluorescence microscopy images, by non-negative matrix factorization. Measurement of signal intensities from the concentration of certain fluorescent reporter molecules at each location within a sample of biological tissue is confounded by fluorescence produced by the tissue itself (autofluorescence). Spectral mixing models use mixing coefficients to specify how much fluorescence from each source is present and unmixing algorithms separate the two fluorescent sources. Current spectral unmixing methods for AF removal often require a priori knowledge of mixing coefficients. Those which do not, such as principal component analysis, generate negative mixing coefficients that are not physically meaningful. Non-negative matrix factorization constrains mixing coefficients to be non-negative, and has been used for spectral unmixing, but not AF removal. This paper describes a novel non-negative matrix factorization algorithm which separates fluorescent images into true signal and AF components utilizing an estimate of the dark current. We also present a test-bed, based on fluorescent beads, to compare the performance of different AF removal algorithms. Our algorithm out-performed previous state of the art on validation images.
Sensory eye dominance is retinal location specific and affects stereopsis (2010)

Sensory eye dominance (SED) refers to one eye having a competitive advantage over the fellow eye when viewing a pair of binocular rivalry stimuli with equal strength (Ooi & He, 2001). SED is largely related to the interocular inhibitory mechanism underlying various binocular percepts. To date, we have only measured the global SED using a binocular rivalry display that stimulates large visual field coverage. We now measured the local SED at various retinal locations (SED Perimetry) using a binocular rivalry method similar to that used in the global SED and a QUEST procedure. We selected 17 different retinal locations that included one at the fovea, eight at 2deg and eight at 4deg eccentricity. At each test location, we measured the SED by presenting a binocular rivalry display (vertical vs. horizontal grating) on an 11×11deg gray background (35 cd/m2) for 0.5 sec. At the fovea the spatial frequency and size of the rivalry grating discs were 5cpd and 0.75deg, respectively; and at the peripheral locations the discs were scaled according to the retinal eccentricity. Furthermore, at each test location we measured: (i) The right and left eye's contrast sensitivity using monocular gratings having the same parameters as the binocular rivalry display; (ii) Stereo threshold of a front disc defined by random-dots; (iii) Choice reaction time to the onset of the random-dots defined disc with either 6 min front or back binocular disparity. We found that: (1) both the sign (right or left eye) and magnitude of the local SED vary with test location, indicating that the local SED is retinal location specific; (2) the local SED cannot be attributed to the difference in monocular contrast sensitivity; (3) both the stereo threshold and reaction time tend to increase with the magnitude of the local SED, suggesting that SED can impede stereo processing.
Distance measurement using a subcarrier frequency-modulated continuous-wave radar based on a resonant-tunneling-diode oscillator (2020)

We have previously introduced a new principle for distance measurement using terahertz waves, similar to the frequency-modulated continuous-wave (FMCW) radar, but where the sawtooth frequency modulation is applied to an amplitude modulation subcarrier of the terahertz wave instead of the carrier itself. The method is particularly useful when the terahertz-wave source is a resonant-tunneling-diode (RTD) oscillator, which can be more reliably modulated in amplitude than in frequency. This report describes using the new principle in a typical radar configuration as well as ways of achieving a better accuracy.
18-26 GHz finline resonance isolators using hexagonal ferrites (1985)

A finline resonance isolator is an attractive solution to the construction of millimetre wave isolators, except for the fact that a large direct magnetic field is normally required for its operation. One way to overcome this drawback is to employ an hexagonal ferrite material with a large internal uniaxial anisotropy energy. Such devices are simple to fabricate and provide perhaps the most practical solution to the design of millimetre band isolators. The paper describes some experimental finline devices in WR 42 waveguide.
Femtosecond ytterbium fiber laser with photonic crystal fiber for dispersion control (2002)

We demonstrate the use of photonic-crystal fiber for dispersion compensation in a soliton fiber laser. The anomalous dispersion provided by the photonic-crystal fiber enables us to construct a femtosecond .ber laser at 1 microm wavelength without prisms or diffraction gratings. The laser produces ~100-fs pulses with 1 nJ energy, and is a major step toward environmentally-stable all-fiber devices at 1 microm.
Segregation gettering by implantation-formed cavities and B-Si precipitates in silicon (1998)

The authors show that Fe, Co, Cu, and Au in Si undergo strong segregation gettering to cavities and B-Si precipitates formed by He or B ion implantation and annealing. The respective mechanisms are argued to be chemisorption on the cavity walls and occupation of solution sites within the disordered, B-rich, B-Si phase. The strengths of the reactions are evaluated, enabling prediction of gettering performance.
Q-learning with Language Model for Edit-based Unsupervised Summarization (2020)

Unsupervised methods are promising for abstractive text summarization in that the parallel corpora is not required. However, their performance is still far from being satisfied, therefore research on promising solutions is on-going. In this paper, we propose a new approach based on Q-learning with an edit-based summarization. The method combines two key modules to form an Editorial Agent and Language Model converter (EALM). The agent predicts edit actions (e.t., delete, keep, and replace), and then the LM converter deterministically generates a summary on the basis of the action signals. Q-learning is leveraged to train the agent to produce proper edit actions. Experimental results show that EALM delivered competitive performance compared with the previous encoder-decoder-based methods, even with truly zero paired data (i.e., no validation set). Defining the task as Q-learning enables us not only to develop a competitive method but also to make the latest techniques in reinforcement learning available for unsupervised summarization. We also conduct qualitative analysis, providing insights into future study on unsupervised summarizers.
Isolation of new minor benanomicins. (1991)

Four minor benanomicins, dexylosylbenanomicins A and B, 2'-demethylbenanomicin A and 7-methoxybenanomicinone have been isolated from the culture filtrate of Actinomadura sp. MH193-16F4. Their structures were confirmed by spectral analyses. Dexylosylbenanomicins A and B were derived chemically from benanomicins A and B, respectively.
High-throughput identification of FLT3 wild-type and mutant kinase substrate preferences and application to design of sensitive <i>in vitro</i> kinase assay substrates (2018)

Summary Acute myeloid leukemia (AML) is an aggressive disease that is characterized by abnormal increase of immature myeloblasts in blood and bone marrow. The FLT3 receptor tyrosine kinase plays an integral role in haematopoiesis, and one third of AML diagnoses exhibit gain-of-function mutations in FLT3, with the juxtamembrane domain internal tandem duplication (ITD) and the kinase domain D835Y variants observed most frequently. Few FLT3 substrates or phosphorylation sites are known, which limits insight into FLT3’s substrate preferences and makes assay design particularly challenging. We applied in vitro phosphorylation of a cell lysate digest (adaptation of the Kinase Assay Linked with Phosphoproteomics (KALIP) technique and similar methods) for high-throughput identification of substrates for three FLT3 variants (wild-type, ITD mutant, and D835Y mutant). Incorporation of identified substrate sequences as input into the KINATEST-ID substrate preference analysis and assay development pipeline facilitated the design of several peptide substrates that are phosphorylated efficiently by all three FLT3 kinase variants. These substrates could be used in assays to identify new FLT3 inhibitors that overcome resistant mutations to improve FLT3-positive AML treatment.
Direct P(Y)-Code Acquisition Algorithm forSoftware GPS Receivers (1999)

The general approach for GPS P-code reception starts
with C/A code acquisition which is then handed over for
precise timing to the P-code tracking loop. However, if P-code
tracking is interrupted in a jamming environment and
C/A code acquisition is also denied, a long period of P-code
signal is needed for correlation in order to increase
the integration gain and achieve the required signal-to-jam
ratio for re-aquisition. Several papers related to P-code
direct acquisition for GPS hardware receivers have been
published in previous ION conferences (1) . This paper will
discuss an efficient coherent acquisition algorithm in the
frequency domain. This algorithm was developed for
digital signal processing in software GPS receivers to
acquire long and weak P-code or C/A code sampled data.
The algorithm breaks down a set of long data into M
subsets and performs local correlation in the frequency
domain. The local results are then coherently integrated
by an M-point DFT (Discrete Fourier Transform) for
global detection. M is the number of the Doppler bins
which are derived from the total integration time and the
total Doppler range to be covered. The calculation time
can be significantly reduced by performing correlation in
the frequency domain and by dealing with multiple
smaller DFTs in block level instead of a single large DFT
. Several sampled data sets which were generated by the
hardware GPS signal simulator of Advanced Concept
Exploitation Facility (ACEF) (2) at Sensors Directorate,
Air Force Research Laboratory were used for technique
development and the result demonstration. The reason for
use of simulated data instead of measured real data was to
avoid any security issues. The sample data are RF (Radio
Frequency) modulated P-code plus C/A code, and the
thermal noise which is 21 dB higher than signal was
added in software.
An Electron Beam Initiated Fusion Neutron Generator (1974)

An experimental scheme is proposed which seems to satisfy all the requirements for use of a high energy electron beam to initiate a thermonuclear plasma. One-dimensional expansion is utilized to obtain confinement times longer than the pulse length of the electron beams. A magnetic field is used to limit the radial heat conductivity, and this magnetic field also serves as a guiding field for the electron beams when they are in the vicinity of the target. Two opposing electron beams are employed and the forces produced by these counterstreaming current in the overlap region of the beams are sufficient to stop the beams within the target. Estimates made of all the critical factors indicate that beams achievable with current technology can be focused and stopped in T-D target 6 cm long with densities as low as 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">21</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> . With a containing magnetic field of 750 kilogauss the containment time of the plasma is sufficiently long so that beam pulse lengths up to 8×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> sec can be used. Furthermore a positive fusion energy yield relative to the energy delivered to the target is predicted.
Ethyl (3<i>S</i>,4a<i>R</i>,6<i>S</i>,8a<i>R</i>)-6-(4-Ethoxycar- bonylimidazol-1-ylmethyl)decahydroiso- quinoline-3-carboxylic Ester:  A Prodrug of a GluR5 Kainate Receptor Antagonist Active in Two Animal Models of Acute Migraine (2002)

Amino diacid 3, a highly selective competitive GluR5 kainate receptor antagonist, exhibited high GluR5 receptor affinity and selectivity over other glutamate receptors. Its diethyl ester prodrug 4 was orally active in two models of migraine: the neurogenic dural plasma protein extravasation model and the nucleus caudalis c-fos expression model. These data suggest that a GluR5 kainate receptor antagonist might be an efficacious antimigraine therapy with a novel mechanism of action.
Advancements in the selective inhibition sintering process development (2005)

Selective inhibition sintering (SIS) is a new layer-based rapid prototyping process that fabricates parts by joining polymer powder particles in the part's body to form a coherent solid and by preventing particles from joining at the part's boundary to form edges. This paper presents the fundamentals of the SIS process, its dedicated path generator, material selection research and the application of response surface methodology which has led to optimum performance, given various factors affecting part strength, surface quality and dimensional accuracy.
Needle shear wave driver for magnetic resonance elastography (2006)

Magnetic resonance elastography (MRE) is capable of quantitatively depicting the mechanical properties of tissues in vivo. In contrast to mechanical excitation at the surface of the tissue, the method proposed in this study describes shear waves produced by an inserted needle. The results demonstrate that MRE performed with the needle driver provides shear stiffness estimates that correlate well with those obtained using mechanical testing. Comparisons between MRE acquisitions obtained with surface and needle drivers yielded similar results in general. However, the well-defined wave propagation pattern provided by the needle driver in a target region can reduce section orientation-related error in wavelength estimation that occurs with surface drivers in 2D MRE acquisitions. Preliminary testing of the device was performed on animals. This study demonstrates that the needle driver is an effective option that offers advantages over surface drivers for obtaining accurate stiffness estimates in targeted regions that are accessible by the needle.
Improved eye-fixation detection using polarization-modulated retinal birefringence scanning, immune to corneal birefringence (2014)

We present an improved method for remote eye-fixation detection, using a polarization-modulated approach to retinal birefringence scanning (RBS), without the need for individual calibration or separate background measurements and essentially independent of corneal birefringence. Polarization-modulated RBS detects polarization changes generated in modulated polarized light passing through a unique pattern of nerve fibers identifying and defining the retinal region where fixation occurs (the fovea). A proof-of-concept demonstration in human eyes suggests that polarization-modulated RBS has the potential to reliably detect true foveal fixation on a specified point with an accuracy of at least ± 0.75°, and that it can be applied to the general population, including individuals with sub-optimal eyes and young children, where early diagnosis of visual problems can be critical. As could be employed in an eye-controlled display or in other devices, polarization-modulated RBS also enables and paves the way for new and reliable eye-fixation-evoked human-machine interfaces.
Self-Assembled Monolayers and Multilayered Stacks of Lyotropic Chromonic Liquid Crystalline Dyes with In-Plane Orientational Order (2000)

A simple method to create large areas of in-plane oriented molecular mono- and multilayers is presented. The method is based on layer-by-layer adsorption of polyions and a lyotropic chromonic (nonamphiphilic) liquid crystal, which allows one to orient the molecules uniformly in the plane of deposition. The long-range in-plane orientation of the chromonic molecules determines the unique structural and optical properties of the films. Control of the orientational order allows one to use the films as polarizers, alignment layers, optical compensators, retarders, filters, etc.
Mechanically Strong, Flexible Polyimide Aerogels Cross-Linked with Aromatic Triamine (2012)

Polyimide gels are produced by cross-linking anhydride capped polyamic acid oligomers with aromatic triamine in solution and chemically imidizing. The gels are then supercritically dried to form nanoporous polyimide aerogels with densities as low as 0.14 g/cm3 and surface areas as high as 512 m2/g. To understand the effect of the polyimide backbone on properties, aerogels from several combinations of diamine and dianhydride, and formulated oligomer chain length are examined. Formulations made from 2,2′-dimethylbenzidine as the diamine shrink the least but have among the highest compressive modulus. Formulations made using 4,4′-oxydianiline or 2,2′dimethylbenzidine can be fabricated into continuous thin films using a roll to roll casting process. The films are flexible enough to be rolled or folded back on themselves and recover completely without cracking or flaking, and have tensile strengths of 4–9 MPa. Finally, the highest onset of decomposition (above 600 °C) of the polyimide aerogels was obtained usi...
A Review and Comparison of Measures for Automatic Video Surveillance Systems (2008)

Abstract Today's video surveillance systems are increasingly equipped with video content analysis for a great variety of applications. However, reliability and robustness of video content analysis algorithms remain an issue. They have to be measured against ground truth data in order to quantify the performance and advancements of new algorithms. Therefore, a variety of measures have been proposed in the literature, but there has neither been a systematic overview nor an evaluation of measures for specific video analysis tasks yet. This paper provides a systematic review of measures and compares their effectiveness for specific aspects, such as segmentation, tracking, and event detection. Focus is drawn on details like normalization issues, robustness, and representativeness. A software framework is introduced for continuously evaluating and documenting the performance of video surveillance systems. Based on many years of experience, a new set of representative measures is proposed as a fundamental part of an evaluation framework.