gebhart/patrepeval huggingface dataset:
Improved second-harmonic generation from homomolecular Langmuir Blodgett films of a transparent dye (1998)

The optically nonlinear dye [E-N-dodecyl-4-(2-(4-docosyloxyphenyl)ethenyl)quinolinium]+-(octadecylsulfate-)x(bromide-)1-x forms noncentrosymmetric Langmuir–Blodgett films. The second-harmonic intensity increases quadratically with the number of layers in the range investigated, i.e., as I2ω(N)=I2ω(1)′N2 for 2≤N≤100, and shows long-term stability. Films of the dye are almost transparent, with an absorbance of 3×10-4 layer-1 at the second-harmonic wavelength, but, nonetheless, the equivalent monolayer intensity, I2ω(N)/N2, is ∼30% of the resonantly enhanced signal from monolayer films of the colored hemicyanine dye reported by Girling [J. Opt. Soc. Am. B4, 950 (1987)]. The second-order susceptibility, film thickness, and chromophore tilt angle relative to the normal to the substrate are χzzz(2)=26 pm V-1 at 1.064 μm, l=5.0 nm layer-1, and ϕ=30°, respectively, for x=0.5.
Brightness enhancement in a high-peak-power cladding-pumped Raman fiber amplifier (2009)

We demonstrate a cladding-pumped Raman fiber amplifier (CPRFA) whose brightness-enhancement factor depends on the cladding-to-core diameter ratio. The pump and the signal are coupled independently into different input arms of a pump-signal combiner, and the output is spliced to the Raman amplifier fiber. The CPRFA generates 20 microJ, 7 ns pulses at 1100 nm at a 2.2 kHz repetition rate with 300 microJ (25.1 kW peak power) of input pump energy. The amplified signal's peak power is 2.77 kW, and the brightness-enhancement factor is 192--the highest peak power and brightness enhancement achieved in a CPRFA at any wavelength, to our knowledge.
Spectral analysis of Doppler velocity patterns in normals and patients with carotid artery stenosis (1981)

A computerized pattern recognition program was utilized to assess the predictive ability of various parameters obtained from the spectra of ultrasonic pulsed Doppler signals from the carotid arteries. The most accurate features selected by linear regression analysis were the natural log (ln) of the ratio of the mean velocity in the internal carotid artery compared to that in the common carotid artery, and the ln of the maximum velocity, the ln of the maximum frequency, and the square of the fractional broadening term, all of which were measured at peak systole in the internal carotid artery. Using the combination of the velocity ratio and the fractional broadening term, the average difference in the estimated percentage stenosis, as compared to that obtained by arteriography, was 12.8%.
In Vitro Packaging of Adeno-Associated Virus DNA (1998)

We have developed an in vitro procedure for packaging of recombinant adeno-associated virus (AAV). By using AAV replicative-form DNA as the substrate, it is possible to synthesize an infectious AAV particle in vitro that can be used to transfer a marker gene to mammalian cells. The packaging procedure requires the presence of both the AAV Rep and capsid proteins. Two kinds of in vitro products can be formed which facilitate DNA transfer. Both are resistant to heat and have a density in cesium chloride gradients that is indistinguishable from that of the in vivo-synthesized wild-type virus. This indicates that the particles formed have the appropriate protein-to-DNA ratio and a structure that shares the heat resistance of mature AAV particles. The two types of particles can be distinguished by their sensitivity to chloroform and DNase I treatment. The chloroform-resistant product is, by several criteria, an authentic AAV particle. In addition to having the correct density and being resistant to treatment with chloroform, DNase I, and heat, this particle is efficiently synthesized only if the AAV genome contains intact terminal repeats, which are known to be required for AAV packaging. It is also precipitated by a monoclonal antibody that recognizes mature virus particles but not bound by an antibody that recognizes monomeric or denatured capsid proteins. The chloroform-resistant species is not made when aphidicolin is present in the reaction mixture, suggesting that active DNA replication is required for in vitro packaging. In contrast, the chloroform-sensitive product has several features that suggest it is an incompletely assembled virus particle. It is sensitive to DNase I, does not require the presence of AAV terminal repeats, and is capable of transferring DNA that is theoretically too large to package. Sucrose gradient centrifugation of the in vitro-synthesized products reveals that the particles have sedimentation values between 60S and 110S, which is consistent with partially assembled and mature AAV particles. The in vitro packaging procedure should be useful for studying the mechanism by which a human icosahedral DNA virus particle is assembled, and it may be useful for producing recombinant AAV for gene therapy. The chloroform-sensitive particle may also be useful for transferring DNA that is too large to be packaged in mature recombinant AAV.
Noise reduction of hyperspectral imagery using hybrid spatial-spectral derivative-domain wavelet shrinkage (2006)

In this paper, a new noise reduction algorithm is introduced and applied to the problem of denoising hyperspectral imagery. This algorithm resorts to the spectral derivative domain, where the noise level is elevated, and benefits from the dissimilarity of the signal regularity in the spatial and the spectral dimensions of hyperspectral images. The performance of the new algorithm is tested on two different hyperspectral datacubes: an Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) datacube that is acquired in a vegetation-dominated site and a simulated AVIRIS datacube that simulates a geological site. The new algorithm provides signal-to-noise-ratio improvement up to 84.44% and 98.35% in the first and the second datacubes, respectively.
Characterization of benzodiazepine receptors with a fluorescence-quenching ligand. (1990)

A conjugate of the high affinity benzodiazepine receptor ligand Ro 15-1788 and the fluorescent 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD) moiety was synthesized. This novel compound (BD 623) exhibited excitation and emission maxima at 486 and 542 nm, respectively, and possessed fluorescent properties that are dependent upon the polarity of its environment. BD 623 bound reversibly to benzodiazepine receptors in the central nervous system with an apparent affinity (K(i) 5.7 nM) comparable to the parent imidazobenzodiazepine (K(d) 2.8 nM). Addition of BD 623 to a suspension of brain membranes resulted in a time-dependent quenching of its fluorescence. Fluorescence quenching of this compound was readily reversed by specific benzodiazepine receptor ligands but not by a variety of other substances. Moreover, inactivation of benzodiazepine receptors by photoaffinity labeling with Ro 15-4513 resulted in a reduction in the fluorescence quenching of BD 623 consistent with the reduction in density of benzodiazepine receptors measured using a radioreceptor assay. Monitoring of fluorescence/dequenching of BD 623 in real time permitted a quantitative characterization of the ligand-receptor interaction, with both the K(d) of BD 623 (13.9 nM) and K(i) of Ro 15-1788 (5.7 nM) comparable with the estimates obtained using radioreceptor techniques. These results indicate that application of fluorescence quenching techniques with BD 623 could prove a useful adjunct for the study of benzodiazepine receptors. BD 623 may serve as a prototype for the development of other fluorescent ligands to study ligand-receptor interactions.
Thin rod heat flux transducer positioned in the earth having a uniform temperature gradient: a closed form solution (1977)

Signals from a thin rod heat flux transducer will be measured and translated into a geothermal heat flux. A mathematical temperature solution has been developed for an idealized thin rod positioned in an infinite solid with a uniform temperature gradient. This solution approximates the actual temperature to be encountered in the transducer when located in a drillhole. The solution is a closed form type for a thin rod wherein radial temperature differences are small compared to axial ones; the system can be classified as a fin with a variable environmental temperature gradient. The resulting temperature field is evaluated for a range of system parameters that are of interest in geothermal heat flux measurement. A description of how the mathematical results obtained will be used to extract the unknown geothermal heat flux and earth thermal conductivity from the experimental temperature information obtained by the heat flux transducer is also presented. In addition, the solution is extended to the case where there is a water or air annulus space between the transducer and the drillhole.
Wild-type EGFR Is Stabilized by Direct Interaction with HSP90 in Cancer Cells and Tumors (2012)

The epidermal growth factor receptor (EGFR) has been targeted for inhibition using tyrosine kinase inhibitors and monoclonal antibodies, with improvement in outcome in subsets of patients with head and neck, lung, and colorectal carcinomas. We have previously found that EGFR stability plays a key role in cell survival after chemotherapy and radiotherapy. Heat shock protein 90 (HSP90) is known to stabilize mutant EGFR and ErbB2, but its role in cancers with wild-type (WT) WT-EGFR is unclear. In this report, we demonstrate that fully mature, membrane-bound WT-EGFR interacts with HSP90 independent of ErbB2. Further, the HSP90 inhibitors geldanamycin (GA) and AT13387 cause a decrease in WT-EGFR in cultured head and neck cancer cells. This decrease results from a significantly reduced half-life of WT-EGFR. WT-EGFR was also lost in head and neck xenograft specimens after treatment with AT13387 under conditions that inhibited tumor growth and prolonged survival of the mice. Our findings demonstrate that WT-EGFR is a client protein of HSP90 and that their interaction is critical for maintaining both the stability of the receptor as well as the growth of EGFR-dependent cancers. Furthermore, these findings support the search for specific agents that disrupt HSP90's ability to act as an EGFR chaperone.
Droplet-based interfacial capacitive sensing (2011)

This paper presented a novel droplet-based pressure sensor using elastic and capacitive electrode-electrolyte interfaces to achieve ultrahigh mechanical-to-electrical sensitivity (1.58 μF kPa(-1)) and resolution (1.8 Pa) with a simple device architecture. The miniature transparent droplet sensors, fabricated by one-step laser micromachining, consisted of two flexible polymer membranes with conductive coating and a separation layer hosting a sensing chamber for an electrolyte droplet. The sensing principle primarily relied on high elasticity of the sensing droplet and large capacitance presented at the electrode-electrolyte interface. A simple surface modification scheme was introduced to the conductive coating, which reduced hysteresis of the droplet deformation without substantially compromising the interfacial capacitance. Moreover, the major concern of liquid evaporation was addressed by a mixture of glycerol and electrolyte with long-term stability in a laboratory environment. Theoretical analyses and experimental investigations on several design parameters (i.e., the dimensions of the sensing chamber and the droplet size) were thoroughly conducted to characterize and optimize the overall sensitivity of the device. Moreover, the environmental influences (e.g., temperature and humidity) on the capacitive measurement were further investigated. Finally, the simply constructed and mechanically flexible droplet sensor was successfully applied to detect minute blood pressure variations on the skin surface (with the maximum value less than 100 Pa) throughout cardiovascular cycles.
A new noninvasive blood-test for the early detection of colorectal cancer. (2013)

348 Background: Colorectal cancer (CRC) remains a major medical problem in the world. Its early detection impacts the prognosis and the cost of treatment. Fecal occult blood test is a current noninvasive screening method for CRC detection in asymptomatic average risk individuals. It detects less than 50% of cancers and yields a high number of “normal” colonoscopies. The dysregulation of DNA methylation has been recognized as playing a crucial role during CRC development. The aim of the study was to develop a CRC-specific methylated DNA test in serum. Methods: First, the GoldenGate Methylation microarray containing 1,505 CpG loci within 807 cancer-related genes was used to study methylation patterns in CRC patients. We performed such assays on 9 tissues (4 CRC, 4 normal autologous tissues, 1 polyp), 17 blood and urine pooled samples (7 CRC, 6 polyps, 4 normal) and 20 stool samples (7 CRC, 3 polyps, 10 normal). The clinical status of each sample was assessed by colonoscopy and/or pathology findings. Among methylated genes detected in tumour tissue, stools, and blood, NPY, PENK and WIF1 genes were selected taking into account their high degree of methylation. We then carried out a clinical validation by quantitative multiplex methylation-specific PCR (QM-MSP) in two phases: firstly on 30 tissues (15 CRC, 15 homologous normal tissues) and secondly on 193 serum samples (32 CRC, 161 normal). Results: For to obtain the best accuracy of QM-MSP test, we defined for both biological sources a cumulative methylation index (CMI) by adding of the methylation percentage of each gene. At the CMI of 20.0% on tissues, our QM-MSP test allows to diagnose the CRC with the highest accuracy (100% of specificity and 100% of sensitivity). From sera, the CMI has been standardized at 2.0% giving a sensitivity and specificity for detecting CRC of 94.4% and 59.4% respectively (NPV of 92.1% and PPV of 67.8%). Conclusions: We developed a QM-MSP-based analysis of NPY, PENK, and WIF1 methylated genes in serum. This test classified correctly and with a high accuracy the healthy individuals and colon cancer patients. We propose here new sensitive serum-based epigenetic biomarkers as an effective and simple new noninvasive test for CRC screening in the average and high risk populations.
Pneumatic Networks for Soft Robotics that Actuate Rapidly (2014)

Soft robots actuated by inflation of a pneumatic network (a “pneu‐net”) of small channels in elastomeric materials are appealing for producing sophisticated motions with simple controls. Although current designs of pneu‐nets achieve motion with large amplitudes, they do so relatively slowly (over seconds). This paper describes a new design for pneu‐nets that reduces the amount of gas needed for inflation of the pneu‐net, and thus increases its speed of actuation. A simple actuator can bend from a linear to a quasi‐circular shape in 50 ms when pressurized at ΔP = 345 kPa. At high rates of pressurization, the path along which the actuator bends depends on this rate. When inflated fully, the chambers of this new design experience only one‐tenth the change in volume of that required for the previous design. This small change in volume requires comparably low levels of strain in the material at maximum amplitudes of actuation, and commensurately low rates of fatigue and failure. This actuator can operate over a million cycles without significant degradation of performance. This design for soft robotic actuators combines high rates of actuation with high reliability of the actuator, and opens new areas of application for them.
Irregular Multidimensional Constellations for Orthogonal STBCs (2015)

Utilizing multiple antennas at the transmitter and receiver provides higher data rates and better reliability by exploiting spatial diversity. Space-time block codes (STBCs) is a simple approach for using multiple transmit and receive antennas that has been widely employed in standards. The STBCs introduced in the literature use independent two-dimensional constellations, while the performance of orthogonal STBCs may be improved with multidimensional constellations. These constellations are transmitted by combining multiple space-time resources to form a multidimensional signal space. In this paper, we propose a method for finding optimized multidimensional constellations for orthogonal STBCs. Optimization is performed by minimizing a novel bound on the block or symbol error rate. We show that a substantial improvement in the error probability can be achieved with these novel constellations.
Magnetic properties of extremely small Nd-Fe-B sintered magnet (2005)

Sintered magnets with various grain sizes and coercivities were prepared by the binary alloys method. Bulk magnets are cut into small pieces, some are etched by a nitric acid solution and heat treated and subjected to aging. Magnetic properties are measured by vibrating sample magnetometer. Grain size distributions are measured using optical images taken from the sintered magnets after lapping and etching by the Villela's reagent.
Palladium‐Catalyzed Amidation of Enol Triflates: A New Synthesis of Enamides. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Neuro-Retinal Optic Cup Detection in Glaucoma Diagnosis (2009)

Glaucoma is the one of the two major causes of blindness, which can be diagnosed through measurement of neuro-retinal optic cup-to-disc ratio (CDR). Automatic calculation of optic cup boundary is challenging due to the interweavement of blood vessels with the surrounding tissues around the cup. A multimodality fusion approach for neuroretinal cup detection improves the accuracy of the boundary estimation. The algorithm's effectiveness is demonstrated on 71 manually segmented retina fundus images collected from Singapore Eye Research Institute. By comparing our automatic cup height measurement to ground truth, we found that our method accurately detected neuro-retinal cup height for 69 images, achieved 97.2% accuracy. The evaluation was based on a criterion that is more stringent than the clinically acceptable interor intra-observer variability. This further leads to a large clinical evaluation of the algorithm involving 15 thousand patients from Australia and Singapore.
Microwave holography for analysis of conformal arrays (1975)

The report describes a new method for determining the field near a radiating antenna, which may be planar or conformal. The method uses phase and intensity values that are measured by scanning a probe antenna over a spherical surface. The surface may be in the Fresnel or Fraunhofer regions: in fact, it is chosen big enough to reduce antenna interactions but small enough to reduce reflections from the surroundings. The directive properties of the probe seem relatively unimportant because it is constantly pointed toward the antenna. The method computes the field at the antenna. The computations use the complex conjugate of the measured field so that the method is holographic. In physical terms the conjugation establishes sources that generated waves travelling inward from the measurement surface. Note that in this method the source antenna and the point at which the field is evaluated are inside the measurement surface. The authors deal with backward propagation. In contrast, other methods compute farfield patterns from data measured on a surface that separates the source from the field point.
Radio Resource Allocation in SC-FDMA Uplink with Resource Adjacency Constraints (2016)

Radio Resource Allocation (RRA) in cellular systems is a relevant and difficult task that shouldassign the system resources in the most efficient manner while fulfilling different constraints suchas Quality of Service (QoS). In wireless systems that employ Single Carrier - Frequency DivisionMultiple Access (SC-FDMA) as in Long Term Evolution (LTE) uplink, RRA is even more difficultsince the frequency resources should be assigned in contiguous blocks of subcarriers to eachterminal. In this work we study two important RRA problems in SC-FDMA: the total data ratemaximization and the total data rate maximization with minimum user satisfaction constraints. Weformulate them as optimization problems and show that the optimal solutions are not practical tobe employed in real systems due to the high computational complexity. Therefore, we propose twoefficient heuristic solutions for those problems. By simulation results, we show that both solutionsare near optimal and subject only to small performance degradation compared to the complex andimpractical optimal solutions.
Perfusion Angiography in Acute Ischemic Stroke (2016)

Visualization and quantification of blood flow are essential for the diagnosis and treatment evaluation of cerebrovascular diseases. For rapid imaging of the cerebrovasculature, digital subtraction angiography (DSA) remains the gold standard as it offers high spatial resolution. This paper lays out a methodological framework, named perfusion angiography, for the quantitative analysis and visualization of blood flow parameters from DSA images. The parameters, including cerebral blood flow (CBF) and cerebral blood volume (CBV), mean transit time (MTT), time-to-peak (TTP), and T max, are computed using a bolus tracking method based on the deconvolution of the time-density curve on a pixel-by-pixel basis. The method is tested on 66 acute ischemic stroke patients treated with thrombectomy and/or tissue plasminogen activator (tPA) and also evaluated on an estimation task with known ground truth. This novel imaging tool provides unique insights into flow mechanisms that cannot be observed directly in DSA sequences and might be used to evaluate the impact of endovascular interventions more precisely.
Molecular analysis and expression of a <i>Borrelia burgdorferi</i> gene encoding a 22kDa protein (pC) in <i>Escherichia coli</i> (1992)

Summary We describe the cloning and expression of the pc gene which encodes a major immunodominant protein of Borrelia burgdorferi , the causative agent of Lyme borreliosis. The pC protein was purified from lysates of B. burgdorferi strain PKo. After tryptic digestion of the pC protein the resulting oligopeptides were applied to a gas‐phase sequenator. Thus partial amino acid sequences were obtained. The deduced oligonucleotides were used as hybridization probes. After Southern blotting a reactive band in the 3 kb range of PstI ‐digested genomic DNA was detected. The insertion of these fragments into pUC vectors finally resulted in pc ‐positive Escherichia coli clones. The gene (encoding a protein with 212 amino acids) was expressed in E. coli with varying deletions at the 5′ end. A sequence comparison with other outer membrane proteins of B. burgdorferi indicates a processing of pC that is similar to that of lipoproteins.
Sequential Antigen Panning for Selection of Broadly Cross-Reactive HIV-1-Neutralizing Human Monoclonal Antibodies (2009)

Many phage display techniques drive selection toward the isolation of highly specific antibodies. However, the identification of monoclonal antibodies that are cross-reactive has implications for the development of diagnostics, therapeutics, and vaccines against pathogens or cancer cells that are able to rapidly generate variants and escape mutants. To identify human monoclonal antibodies with high activity against HIV and broad-spectrum activity, we developed a technique termed sequential antigen panning. This methodology could be used to isolated recombinant antibodies against any antigen that shares epitopes with other antigens.