gebhart/patrepeval huggingface dataset:
Prognostic significance of differential expression of angiogenic genes in women with invasive high-grade serous ovarian carcinoma. (2013)

5509 Background: High-grade serous ovarian carcinoma (HGSC) is an aggressive type of epithelial ovarian cancer associated with numerous genetic alterations and poor survival. Our objective was to identify novel angiogenic biomarkers that are associated with tumor angiogenesis and clinical outcome in women with HGSC. Methods: Between 1988 and 2001, 51 snap frozen samples from women with advanced HGSC were obtained. RNA was extracted and analyzed by the Affymetrix GeneChip U133A array. A panel of 285 probe sets (features) linked to 145 genes involved in angiogenesis were screened. Microvessel density (MVD) counts, surrogates of angiogenesis, were determined using CD31 and CD105, markers of proliferating endothelial cells. The association between mRNA expression levels and overall survival (OS) were assessed using a rank score statistic. The effect size was estimated parametrically as a hazard ratio (HR) under a proportional hazards model. We accounted for multiple testing within the false-discovery rate (FDR) framework using the Storey q-value method. The associations between expression level and OS for the implicated genes were further assessed in a published HGSC cohort from the “The Cancer Genome Atlas” (TCGA) database. Results: A panel of 43 features linked to 31 angiogenic genes were significantly associated with long term OS (FDR q-value (q) < 0.05). In the TCGA cohort, four genes exhibited some level of significance and concordant direction of effect as assessed by HRs: AKT1 (q = 0.018, HR = 0.44; TCGA unadjusted p-value (p) <0.011, HR = 0.81), and CD44 (q < 0.003, HR = 0.48; TCGA p < 0.054, HR = 0.89) were associated with better survival; while EPHB2 (q < 0.009, HR = 8.12; TCGA p < 0.051, HR = 1.23) and ERBB2(q < 0.019, HR = 2.86, TCGA p < 0.055, HR = 1.19) were associated with worse survival. After adjusting for multiple comparisons, CD105-MVD and CD31-MVD were not significantly associated with angiogenic gene expression. Conclusions: Our data demonstrated that mRNA levels of 31 angiogenic genes were associated with OS in advanced HGSC. Among these 4 were externally confirmed using TCGA data. Further evaluation is warranted to verify our preliminary findings.
A zero voltage and zero current switching three level DC/DC converter (2002)

This paper presents a novel zero voltage and zero current switching (ZVZCS) three-Level (TL) DC/DC power converter. This converter overcomes the drawbacks presented by the conventional zero voltage switching (ZVS) three-level converter, such as high circulating energy, severe parasitic ringing on the rectifier diodes, and limited ZVS load range for the inner switches. The converter presented in this paper uses a phase shift control with a flying capacitor in the primary side to achieve ZVS for the outer switches. Additionally, the converter uses an auxiliary circuit to reset the primary current during the freewheeling stage to achieve ZCS for the inner switches. The principle of operation and the DC characteristics of the new converter are analyzed and verified on a 6kW, 100 kHz experimental prototype.
A Fully Automated Adaptive Unsharp Masking Technique in Digital Chest Radiograph (1992)

The authors are developing a fully automated adaptive unsharp masking technique with parameters that depend on regional image features of a digital chest radiograph. A chest radiograph includes various regions such as lung fields, retrocardiac area, and spine. These areas have very different texture patterns and optical densities. Therefore, for best evaluation, it is necessary to enhance the image contrast of each region by an optimal parameter. In the current study, a chest radiograph was automatically divided into three segments (lung field, retrocardiac area, and spine) by using a histogram analysis of pixel values. The lung fields and retrocardiac area were selectively enhanced with a small mask size and mild weighting factors that had been previously determined to be optimal. The spine was enhanced with a large mask size and adequate weighting factors. An observer performance test indicated that this technique provides excellent diagnostic accuracy for simulated nodules in chest radiographs.
Physician-Controlled System For Image-Guided Bronchoscopy (2012)

We first tested the system using two MDCT-based human airway-tree phantoms with lesions as summarized below. Using the IGI system, we successfully guided the bronchoscope to all sites, with no assistance from a technician, using the precomputed bronchoscope maneuvers associated with the planned routes. Figure 4 shows final sampling sites for two of the lesions in the two phantoms. 3. Results and Discussion 1. Background
Spin-transfer switching in full-Heusler Co2FeAl-based magnetic tunnel junctions (2012)

We demonstrated spin-transfer magnetization switching using magnetic tunnel junctions (MTJs) with a full-Heusler alloy Co2FeAl (CFA). We prepared CFA (1.5 nm)/MgO/CoFe (4 nm) (“CFA-free”) and CFA (30 nm)/MgO/CoFeB (2 nm) (“CFA-reference”) MTJs on a Cr(001) layer. The intrinsic critical current density (Jc0) of the CFA-free (CFA-reference) MTJ was 29 MA/cm2 (7.1 MA/cm2). The larger Jc0 of the CFA-free MTJ is attributed to the significant enhancement of the Gilbert damping factor (∼0.04) of the CFA due to the Cr layer. The Jc0 of the CFA-reference is as small as that reported for typical CoFeB/MgO/CoFeB MTJs.
<title>Monitoring glucose in vivo by measuring laser-induced acoustic profiles</title> (2000)

The optoacoustic method of monitoring absorbed optical energy distribution in tissues was employed to measure changes in glucose concentration in vivo. Glucose osmotic and hydrophilic properties cause reduction of tissue scattering as a result of glucose concentration increase around scattering particles and fibers. The opto-acoustic (OA) method utilizes time-resolved measurements of laser- induced ultrasonic profile in tissue resembling the distribution of absorbed optical energy. This opto-acoustic profile yields effective optical attenuation coefficient, which decreases with decrease of scattering. Glucose effect has been investigated initially in phantoms resembling optical properties of sclera and polystyrene microspheres water solution colored with potassium chromate and then in sclera in vitro and in sclera of live rabbits. The forward mode of opto-acoustic detection was used in the experiments in vitro. Experiments were performed in UV spectral range at the wavelength of (lambda) equals 355-nm. Experimental results demonstrated that an increase in glucose concentration from 5 mM to 60 mM was expressed in the 3 percent reduction of (mu) <SUB>eff</SUB> in aqueous solution of polystyrene microspheres. The effect of glucose on sclera in vitro was more prominent and measured as 10 percent reduction of (mu) <SUB>eff</SUB> with increase of glucose concentration from 1 mM to 50 mM. It was found that both the amplitude and the profile of OA signal were influenced by mechanical pressure applied to sclera specimen toward the surface of OA transducer. In experiments in live tissue, the backward detection mode was employed, as the only one side access to the tissue surface was available. In experiments in vivo the opto-acoustic profiles were measured in rabbit's sclera before and after intravenous glucose administering. The glucose concentration in rabbit blood was simultaneously measured using commercial device employing chemical analysis of blood. Experimental results demonstrated that a 1 mM increase in glucose concentration resulted in a 3 percent decrease of optical attenuation in rabbit sclera in vivo. Such a pronounced change of optical scattering in sclera in response to physiologic change in blood glucose concentration encourages us to continue measurements in vivo and modeling glucose effect on tissue optics.
Efficient linear equalization for high data rate downlink CDMA signaling (2004)

In this paper, we propose an FFT-based linear equalization algorithm for the CDMA downlink. By approximating the correlation matrix with a circulant matrix, which is diagonalized by the DFT matrix, we are able to incorporate the efficient FFT operations and avoid the direct matrix inversion. Furthermore, we show that with the help of Kronecker algebra and the notion of dimension-wise and element-wise FFT, we are able to extend the FFT-based method to cases where multi-channel diversity, such as over-sampling or receive antenna array diversity, is present. Numerical simulations show that the FFT-based algorithm overlaps with the direct matrix inversion method for most of the low to medium SNR range and have a small loss at high SNR.
Folding of Conotoxins: Formation of the Native Disulfide Bridges During Chemical Synthesis and Biosynthesis of <i>Conus</i> Peptides (2007)

Conopeptides from >700 species of predatory marine Conus snails provide an impressive molecular diversity of cysteine-rich peptides. Most of the estimated 50,000-100,000 distinct conopeptides range in size from 10 to 50 amino acid residues, often with multiple posttranslational modifications. The great majority contain from two to four disulfide bridges. As the biosynthetic and chemical production of this impressive repertoire of disulfide-rich peptides has been investigated, particularly the formation of native disulfide bridges, differences between in vivo and in vitro oxidative folding have become increasingly evident. In this article, we provide an overview of the molecular diversity of conotoxins with an emphasis on the cysteine patterns and disulfide frameworks. The conotoxin folding studies reviewed include regioselective and direct oxidation strategies, recombinant expression, optimization of folding methods, mechanisms of in vitro folding, and preliminary data on the biosynthesis of conotoxins in venom ducts. Despite these studies, how the cone snails efficiently produce properly folded conotoxins remains unanswered. As chemists continue to master oxidative folding techniques, insights gleaned from how conotoxins are folded in vivo will likely lead to the development of the new folding methods, as well as shed some light on fundamental mechanisms relevant to the protein folding problem.
The basis and architecture for the reduction of tones in a sigma-delta DAC (1993)

A basis and architecture for a digital-to-analog conversion (DAC) technique that allows a significant, if not complete, reduction of the in-band tones found in single-bit sigma-delta modulators, while easing the component matching requirements compared to conventional multibit architectures, is presented. The architecture uses a combination of coarse and fine quantization levels, which resolves the input data at a rate that is sufficient to keep tones, caused by DC inputs, from occurring in the signal bandwidth. Although a DAC is discussed, it is noted that an analog-to-digital converter (ADC) has similar characteristics. Observations and additional comments relating to the time domain point of view of a sigma-delta converter are offered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Thymol and related phenols are potent activators of the transient receptor potential channel, TRPA1 (2007)

Thymol is a major component of the spice thyme. It has a distinctive pungent flavor mediated by receptor mechanisms in the nose and tongue in addition to having aversive properties. Using a voltage‐sensitive fluorescent dye, we show that thymol specifically activates the human transient receptor potential channel A1 (TRPA1), EC 50 12 μM, but not other taste sensory TRP channels (TRPV1 and TRPM5). Electrophysiology measurements further demonstrated that thymol activation was concentration‐dependent, reversible, and rapidly desensitized TRPA1. A number of related phenols including 3‐tert‐butyl‐4‐hydroxyanisol (BHA), a food preservative, and propofol, an intravenous anesthetic, also selectively activated TRPA1 (EC 50 3 and 13 μM, respectively). Phenols with less bulky carbon substitutions adjacent to the phenolic group, such as 2, 6‐dimethlyphenol and 2‐methlyphenol (o‐cresol), were less potent. TRPA1‐specific siRNA inhibited thymol activation, confirming the specificity of the response. In addition, thymol activation was blocked by camphor (IC 50 200–500 μM) whereas other camphor analogs, e.g. camphorquinone, camphoric acid and limonene were TRPA1 agonists (EC 50 0.3, 2, 3 mM, respectively). Our results suggest a role of TRPA1 activation in the reported pungent and aversive properties of some of the pharmaceutically important phenols.
Gas Cell based on Segmented Hollow-Core Photonic Crystal Fiber and its Application in an Intracavity Absorption Spectroscopy System (2021)

A gas cell was developed by segmenting Hollo-Core Photonic Crystal Fiber, which increased the rate at which gas could be exchanged and allowed the cell to be used in an Intra Cavity Absorption Spectroscopic system.
Forward model of Cerenkov luminescence tomography with the third-order simplified spherical harmonics approximation (2011)

Applying Cerenkov luminescence tomography (CLT) to localizing Cerenkov light sources in situ is still in its nascent stage. One of the obstacles hindering the development of the CLT is the lack of dedicated imaging mode. In this contribution, the paper presented a Cerenkov optical imaging mode, in which the propagation of optical photons inside tissues generated by the Vavilov-Cerenkov effect is modeled based on simplified spherical harmonics approximation. As a significantly more transport-like and computational-efficient approximation theory, the performance of the third-order simplified spherical harmonics approximation (<i>SP</i><sub>3</sub>) in the CLT forward is investigated in stages. Finally, the performance of the proposed forward model is validated using numerical phantoms and compared with the simulation data based on the Monte Carlo method.
Code Division Switching (2001)

Chapter 4 introduces the method of code division switching for routing calls and packets at the exchange node of the network. The Code Division Switch (CDS) can route the user data if they are in CDMA or TDMA form at a network node. Code division switch (CDS) architectures for satellite and terrestrial applications are presented, and their complexity is evaluated and compared with traditional switching techniques.
Tunable Multicolor Electroluminescent Polymer Devices for Full Color Displays (1999)

Abstract : Efficient light emitting diodes (LEDs) of various colors and suitable methods of their pixelation are essential to incorporating polymer LEDs into full color display systems. We have developed polymer/polymer heterojunction LEDs that exhibit multicolor emission which is tunable by the bias voltage. These LEDs are based on poly(p-phenylenevinylene) (PPV)/n-type polymer structures. ITO/PPV/polyquinoiine/Al diodes fabricated under ambient air environment had a turn-on voltage of 3.5 V, luminance levels of over 800 cd/sq m, and efficiencies of up to 1%. Such devices, for example, reversibly switch colors (red -- yellow --green) in the 5-12 V range, facilitating easy pixelation. Origin of the color tunability will be discussed.
Cavity-ringdown molecular spectroscopy based on an optical frequency comb at 145-165 μm (2007)

Optical frequency comb-based cavity-ringdown spectroscopy has recently enabled high-sensitivity absorption detection of molecules over a broad spectral range. We demonstrate an improved system based on a mode-locked erbium-doped fiber laser source centered at 1.5 microm, resulting in a spectrometer that is inexpensive, simple, and robust. It provides a very large spectral bandwidth (1.45-1.65 microm) for investigation of a wide variety of molecular absorptions. Strong molecular absorptions at 1.5 mum allow for detection at sensitivities approaching the 1 part in 10(9) volume level. We provide a detailed description of our spectrometer and present measurements of the rovibrational spectra for CO, NH3, and C2H2 with an absorption sensitivity of 2 x 10(-8) cm(-1)Hz(-1/2) per detection channel.
Novel distributed-feedback resonant-periodic-gain structure for vertical-cavity surface-emitting semiconductor lasers (1990)

A novel distributed feedback structure for wavelength-resonant surface-emitting semiconductor lasers is proposed. The total thickness of the new structure can be considerably reduced compared with earlier resonant-periodic-gain devices. The characteristic features of the resonant-periodicgain active medium are retained.
Protein structure-based design of potent orally bioavailable, nonpeptide inhibitors of human immunodeficiency virus protease. (1995)

A class of potent nonpeptidic inhibitors of human immunodeficiency virus protease has been designed by using the three-dimensional structure of the enzyme as a guide. By employing iterative protein cocrystal structure analysis, design, and synthesis the binding affinity of the lead compound was incrementally improved by over four orders of magnitude. An inversion in inhibitor binding mode was observed crystallographically, providing information critical for subsequent design and highlighting the utility of structural feedback in inhibitor optimization. These inhibitors are selective for the viral protease enzyme, possess good antiviral activity, and are orally available in three species.
Isolation of the Causative Agent of Hantavirus Pulmonary Syndrome (1994)

Investigation of a recent outbreak of acute respiratory illness in the southwestern United States resulted in the recognition of a new disease, hantavirus pulmonary syndrome (HPS) with high mortality. Different animals and cell lines were used in attempts to isolate the causative agent. A previously unknown hantavirus was passaged in laboratory-bred deer mice, recovered from lung tissues of a deer mouse, Peromyscus maniculatus, and propagated in the E6 clone of Vero cells. Virus antigen was readily detected in the infected cells by an indirect immunofluorescence assay, using convalescent-phase sera from HPS patients. By electron microscopy, the virus was shown to have the typical morphologic features of members of the genus Hantavirus, family Bunyaviridae. Virus sequences corresponded to those previously detected by a nested reverse transcriptase-polymerase chain reaction assay of hantavirus-infected specimens from rodents and humans. This newly recognized virus, the etiologic agent of HPS, has been tentatively named Muerto Canyon virus.
Advantage of Medium Earth Orbit for a GPS Augmentation System (1998)

Satellite orbits for augmentation of the Global Positioning
System (GPS) have been almost exclusively confined to
geostationary earth orbits (GEO) or inclined GEO
(IGEO). The objective of this research was to conduct
trades of alternative orbits that potentially offer
augmentation of the GPS for aviation navigation. The
methodology consisted of examining orbits ranging from
low earth orbit to GEO as well as elliptical orbits. These
orbits were studied using accuracy as the primary measure
of effectiveness as well as availability of host satellites,
orbit slot locations, and user receiver performance as
factors in the evaluation. A service volume model was
used to express accuracy availability for the U.S. National
Airspace System (NAS) as well as availability on a global
basis. The study results show a clear performance
improvement in the availability of system accuracy for
equivalent numbers of medium earth orbit (MEO)
satellites vs. GEO satellites. Because MEO orbits are
non-geostationary they also offer global coverage and, as
a result, provide the same performance advantage to any
sovereign area of the world that establishes the associated
ground support infrastructure.
BinRank: Scaling Dynamic Authority-Based Search Using Materialized SubGraphs (2009)

Dynamic authority-based keyword search algorithms, such as ObjectRank and personalized PageRank, leverage semantic link information to provide high quality, high recall search in databases and the Web. Conceptually, these algorithms require a query-time PageRank-style iterative computation over the full graph. This computation is too expensive for large graphs, and not feasible at query time. Alternatively, building an index of pre-computed results for some or all keywords involves very expensive preprocessing. We introduce BinRank, a system that approximates ObjectRank results by utilizing a hybrid approach inspired by materialized views in traditional query processing. We materialize a number of relatively small subsets of the data graph in such a way that any keyword query can be answered by running ObjectRank on only one of the sub-graphs. BinRank generates the sub-graphs by partitioning all the terms in the corpus based on their co-occurrence, executing ObjectRank for each partition using the terms to generate a set of random walk starting points, and keeping only those objects that receive non-negligible scores. The intuition is that a sub-graph that contains all objects and links relevant to a set of related terms should have all the information needed to rank objects with respect to one of these terms. We demonstrate that BinRank can achieve sub-second query execution time on the English Wikipedia dataset, while producing high quality search results that closely approximate the results of ObjectRank on the original graph. The Wikipedia link graph contains about 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> edges, which is at least two orders of magnitude larger than what prior state of the art dynamic authority-based search systems have been able to demonstrate. Our experimental evaluation investigates the trade-off between query execution time, quality of the results, and storage requirements of BinRank.
Surface patches from unorganized space curves (2012)

Recent 3D sketch tools produce networks of three-space curves that suggest the contours of shapes. The shapes may be non-manifold, closed three-dimensional, open two-dimensional, or mixed. Our video demonstrates a system that automatically generates intuitively appealing, piecewise-smooth surface patches from such a curve network, and an intelligent user interface for modifying the automatically chosen surface patches. Both parts of the system use a linear algebra representation of the set of surface patches to track the topology.
Patterned Paper Sensors Printed with Long‐Chain DNA Aptamers (2015)

There is growing interest in developing printable paper sensors to enable rapid testing of analytes for environmental, food safety, and clinical applications. A major challenge is to find suitable bioinks that are amenable to high-speed printing and remain functional after printing. We report on a simple and effective approach wherein an aqueous ink composed of megadalton-sized tandem repeating structure-switching DNA aptamers (concatemeric aptamers) is used to rapidly create patterned paper sensors on filter paper by inkjet printing. These concatemeric aptamer reporters remain immobilized at the point of printing through strong adsorption but retain sufficient segmental mobility to undergo structure switching and fluorescence signaling to provide both qualitative and quantitative detection of small molecules and protein targets. The convenience of inkjet printing allows for the patterning of internally referenced sensors with multiplexed detection, and provides a generic platform for on-demand printing of sensors even in remote locations.