gebhart/patrepeval huggingface dataset:
Probabilistic nodule filtering in thoracic CT scans (2006)

Automated detection of lung nodules in thoracic CT scans is an important clinical challenge. Blood vessels form a major source of false positives in automated nodule detection systems. Hence, the performance of such systems may be improved by enhancing nodules while suppressing blood vessels. Ideally, nodule enhancement filters should enhance nodules while suppressing vessels and lung tissue. A distinction between vessels and nodules is normally obtained through eigenvalue analysis of the Hessian matrix. The Hessian matrix is a second order differential quantity and so is sensitive to noise. Furthermore, by relying on principal curvatures alone, existing filters are incapable of distinguishing between nodules and vessel junctions, and are incapable of handling cases in which nodules touch vessels. In this paper we develop novel nodule enhancement filters that are capable of suppressing junctions and are capable of handling cases in which nodules appear to touch or even overlap with vessels. The proposed filters are based on optimized probabilistic models derived from eigenvalue analysis of the gradient correlation matrix which is a first order differential quantity and so are less sensitive to noise compared with known vessel enhancement filters. The proposed filters are evaluated and compared to known techniques both qualitatively, quantitatively. The evaluation includes both synthetic and actual clinical data.
Subfeature speckle interferometry (1995)

A novel speckle technique, subfeature speckle interferometry, is introduced that relies on the amplitude interference of two independent speckle patterns, originating from coherent illumination, by use of an optical system that produces interferometric quality interference fringes on a scale comparable with the speckle correlation length. Examples are given for in-plane translation, sample tilt, and temperature measurement (strain). A temperature measurement accuracy sigma = 0.92 degrees C is realized. In contrast to traditional full-field speckle crosscorrelation techniques, this technique requires only a small number of detector elements with minimal signal processing and is compatible with many real-time sensor applications.
Tunable thin film filters based on thermo-optic semiconductor films (2003)

Thermo-optic layers of thin film semiconductors are deposited by PEVCD to create thermally tunable bandpass filters for WDM optical networks. Amorphous semiconductor films, adapted from the solar cell and display industries, are the primary ingredient. Single-cavity tunable filters with FWHM=0.085 nm, >40 nm tuning range, and insertion losses 0.2-4 dB are demonstrated. Key enablers for this new family of index-tunable thin film devices are PECVD deposition, large internal temperature changes >400C, high conductivity polysilicon heater films, and extremely robust film adhesion. Possible applications include optical monitoring, add/drop multiplexing, dynamic gain equalization, and dispersion compensation.
Synthesis and muscarinic activity of quinuclidinyl- and (1-azanorbornyl)pyrazine derivatives (1992)

The synthesis and cortical muscarinic activity of a novel series of pyrazine-based agonists is described. Quinuclidine and azanorbornane derivatives were prepared either by reaction of lithiated pyrazines with azabicyclic ketones, followed by chlorination and reduction, or by reaction of the lithium enolate of the azabicyclic ester with 2-chloropyrazines followed by ester hydrolysis and decarboxylation. Substitution at all three positions of the heteroaromatic ring has been explored. Optimal muscarinic agonist activity was observed for unsubstituted pyrazines in the azanorbornane series. The exo-1-azanorbornane 18a is one of the most efficacious and potent centrally active muscarinic agonists known. Studies on the 3-substituted derivatives have provided evidence of the preferred conformation of these ligands for optimal muscarinic activity. Substitution at C6 gave ligands with increased affinity and reduced efficacy. Moving the position of the diazine ring nitrogens to give pyrimidine and pyridazine derivatives resulted in a significant loss of muscarinic activity.
A Second Antigenic Heat Shock Protein of <i>Plasmodium falciparum</i> (1988)

We describe here an antigen of Plasmodium falciparum, defined by a cDNA clone designated Ag361. The antigen is a soluble cytoplasmic 70-kD polypeptide present in all isolates analyzed and in all stages of asexual development in the blood. The antigen is a natural immunogen, although it lacks repeating epitopes of many P. falciparum antigens. Ag361 shares extensive sequence homology with the hsp70 proteins of Xenopus laevis, Drosophila melanogaster, Escherichia coli, and man, as well as a previously isolated P. falciparum hsp70 protein. The genome of P. falciparum contains at least five hsp70-like genes, located on at lest four different chromosomes.
Increased Virus Production in Suspension Culture by a Trichoplusia ni Cell Line in Serum-Free Media (1997)

Trichoplusia ni-derived BTI-Tn5B1–4 (Tn-5B1–4) cells were grown in 50 mL spinner flasks in four different formulations of serum-free medium (SFM) . The objectives of this work were to determine the capacity of this cell line to grow and support virus replication in suspension culture in different SFM. Maximum cell densities exceeding 3.0 × 106 cells/mL were attained for all cell/medium combinations. Likewise, cell doubling times were all within 20–22 h. Infection studies with a wild-type isolate of Autographa californicanuclear polyhedrosis virus (AcMNPV) yielded between 156 and 187 occlusion bodies (OBs) /cell. The lethal effect of AcMNPV-OBs produced in this cell line in the various types of media was demonstrated in vivousing T. ni neonate larvae. The percent mortality at a single dose (1.0 × 106 OBs/mL) ranged from 40 to 60% at 4 days post-inoculation (p.i.) . These results compared favorably with mortality rates found for AcMNPV-OBs produced in vivo.DNA quantification analysis, comparing polyhedra-derived viral DNA concentrations from an equal number of cell culture- and larval-derived OBs, was also determined. The larval-derived OB DNA concentration averaged 0.514 μg/108 OBs, whereas the cell culture-derived viral DNA concentrations ranged from 0.347 to 0.710 μg/108 OBs. These results suggest that no significant differences exist in DNA content between larvae- and cell culture-derived samples. Expression of the recombinant protein, secreted alkaline phosphatase (SEAP), ranged from 2.7 to 5.5 IU/mL for each cell/medium combination, which was consistent with previous static culture results for this same cell line in serum-containing TNM-FH medium. Electron microscopic analysis of OBs produced in vivo or in vitro revealed no obvious differences in packaging or number of enveloped nucleocapsids per OB between samples. However, AcMNPV-OBs from infected larvae appeared physically smaller (1.28 ± 0.164 μm) than those produced in cell culture (1.72 ± 0.120) . The Tn-5B1–4 cell line is adaptable to suspension culture in serum-free medium and is suitable for further development in the production of viruses and recombinant proteins on an industrial scale.
Structure-Induced Enhancement in Electrooxidation of Trimetallic FePtAu Nanoparticles (2012)

Using FePtAu nanoparticles (NPs) as an example, this Communication demonstrates a new structure-control strategy to tune and optimize NP catalysis. The presence of Au in FePtAu facilitates FePt structure transformation from chemically disordered face-centered cubic (fcc) structure to chemically ordered face-centered tetragonal (fct) structure, and further promotes formic acid oxidation reaction (FAOR). The fct-FePtAu NPs have mass activity as high as 2809.9 mA/mg Pt and retain 92.5% of this activity after a 13 h stability test. They become the most efficient NP catalyst ever reported for FAOR. This structure-control strategy can be extended to other multimetallic NP systems, providing a general approach to advanced NP catalysts with desired activity and durability control for practical applications.
Sputtered carbon as a corrosion barrier for x-ray detector windows (2016)

Sputtered amorphous carbon thin films were explored as corrosion resistant coatings on aluminum thin films to be incorporated into x-ray detector windows. The requirements for this application include high corrosion resistance, low intrinsic stress, high strains at failure, and high x-ray transmission. Low temperature sputtering was used because of its compatibility with the rest of the window fabrication process. Corrosion resistance was tested by exposure of carbon coated and uncoated Al thin films to humidity. Substrate curvature and bulge testing measurements were used to determine intrinsic stress and ultimate strain at failure. The composition and bonding of the carbon films were further characterized by electron energy loss spectroscopy, Raman spectroscopy, and carbon, hydrogen, and nitrogen elemental analyses. Samples had low compressive stress (down to.08 GPa), a high strain at failure (3%), and a low fraction of sp3 carbon–carbon bonds (less than 5%). The high breaking strain and excellent x-ray transmission of these sputtered carbon films indicate that they will work well as corrosion barriers in this application.
Characterization of surface enhanced Raman scattering (SERS) substrates fabricated from colloidal printing inks (2010)

Surface enhanced Raman scattering (SERS) is now a well-established technique to greatly amplify the normally weak Raman scattering signals. The amplification is achieved by using SERS substrates - specially structured metallic substrates with nano-scale morphological features. One of the most widely used methods for SERS amplification employs nanoparticles of silver or gold either in colloidal suspension or in dry-drop form. In such substrates SERS amplification factors (AF) exceeding 10<sup>12</sup> have been reported. The reproducibility of the colloid-based substrates, however, is a problem. The lack of reproducibility can be caused by a variety of factors that can change the interparticle distances. In this paper we show that thermal annealing of SERS substrates fabricated using commercially available nano-particle inks can be used to create thermally stable substrates with high reproducibility. It appears that thermal annealing destroys the unstable hot-spots with very high AF's but still leaves the sample with high AF sites yielding spatially averaged substrate AF's exceeding 10<sup>8</sup>.
High speed laser Doppler perfusion imaging system e.g. blood flow imaging system, detects laser Doppler signal and/or laser speckle signal from light reflected from selected blood vessel area, to obtain flow data (2006)

An instrument for high-speed laser perfusion imaging comprises a laser source, a detector, a signal-processing unit, data memory, and a screen to display the results. A section of the sample surface is illuminated with laser light; the reemitted light from the irradiated surface is collected by the focusing optics on a 2D array of integrating photo detectors. The elements of the 2D array can be accessed individually or in a pre-defined selection of pixels at high speed. This 2D array of random-pixel-access integrating photo detectors (for example an integrating CMOS image senor) is utilized to measure the intensity variations at each individual pixel. The average amplitude and the mean frequency of the measured signal contain information about concentration and speed of moving blood cells. For real-time imaging, the exposure time is used as a parameter to measure relative perfusion changes. These data are stored in a memory and processed with a signal-processing unit. The instrument delivers 2D flow maps of the illuminated sample section. In parallel a conventional image of the sample can be obtained with the same 2D array of photo detectors allowing a simple overlay between a conventional image and processed flow maps. The instrument enables objective high-speed tissue perfusion imaging and real-time perfusion monitoring.
SLIME: robust, high-speed 3D microvascular mapping (2019)

Abstract Three dimensional (3D) microvascular imaging of cubic millimeter to centimeter size volumes often requires much time and expensive instruments. By combining optical clearing with a novel scatter-based optical coherence tomography (OCT) contrast agent, we have greatly extended OCT imaging depth in excised tissues while maintaining a simple and low cost approach that does not require in-depth OCT knowledge. The new method enables fast 3D microvascular mapping in large tissue volumes, providing a promising tool for investigating organ level microvascular abnormalities in large cohorts.
High data rate relay transmissions with multiple antennas (2009)

Herein, we present a novel approach for decode-forward relay transmissions using multiple antennas. In this approach, multiple independent spatial data streams are sent to the destination directly and/or through different relays simultaneously, where the relays are selected in an opportunistic way. We show the efficiency of the proposed approach through simulations.
Visually-Aware Fashion Recommendation and Design with Generative Image Models (2017)

Building effective recommender systems for domains like fashion is challenging due to the high level of subjectivity and the semantic complexity of the features involved (i.e., fashion styles). Recent work has shown that approaches to `visual' recommendation (e.g.~clothing, art, etc.) can be made more accurate by incorporating visual signals directly into the recommendation objective, using `off-the-shelf' feature representations derived from deep networks. Here, we seek to extend this contribution by showing that recommendation performance can be significantly improved by learning `fashion aware' image representations directly, i.e., by training the image representation (from the pixel level) and the recommender system jointly; this contribution is related to recent work using Siamese CNNs, though we are able to show improvements over state-of-the-art recommendation techniques such as BPR and variants that make use of pre-trained visual features. Furthermore, we show that our model can be used \emph{generatively}, i.e., given a user and a product category, we can generate new images (i.e., clothing items) that are most consistent with their personal taste. This represents a first step towards building systems that go beyond recommending existing items from a product corpus, but which can be used to suggest styles and aid the design of new products.
The safety and effectiveness of a long‐acting transdermal fentanyl solution compared with oxymorphone for the control of postoperative pain in dogs: a randomized, multicentered clinical study (2013)

A prospective, double-blinded, positive-controlled, multicenter, noninferiority study was conducted to evaluate the safety and effectiveness of transdermal fentanyl solution (TFS) compared with oxymorphone for the control of postoperative pain in dogs. Five hundred and two (502) client-owned dogs were assigned to a single dose of TFS (2.7 mg/kg) applied 2-4 h prior to surgery or oxymorphone hydrochloride (0.22 mg/kg) administered subcutaneously 2-4 h prior to surgery and q6h through 90 h. Pain was evaluated over 4 days by blinded observers using a modified Glasgow composite pain scale, and the a priori criteria for treatment failure was a pain score ≥ 8 or adverse event necessitating withdrawal. Four TFS- and eight oxymorphone-treated dogs were withdrawn due to lack of pain control. Eighteen oxymorphone-treated, but no TFS-treated dogs were withdrawn due to severe adverse events. The one-sided upper 95% confidence interval of the difference between TFS and oxymorphone treatment failure rates was -5.3%. Adverse events associated with oxymorphone were greater in number and severity compared with TFS. It was concluded that a single administration of TFS was safe and noninferior to repeated injections of oxymorphone for the control of postoperative pain over 4 days at the dose rates of both formulations used in this study.
Joint adaptive pulse compression to enable multistatic radar (2004)

The fundamental limitation on the concurrent use of the same spectrum by two or more radars is the cross-correlation between the waveforms employed by the respective radars. The waveform transmitted by each individual radar is reflected by an illuminated range profile and is then received by all of the radars (accounting for aspect angle diversity). The received signal at a given radar is therefore the superposition of the return signals from all radars. Hence the use of standard matched filtering can result in masking that arises from the inherent waveform cross-correlations (in addition to the masking that results from autocorrelation range sidelobes). This paper presents a method for adaptively pulse compressing two or more concurrently received radar return signals that occupy the same portion of the frequency spectrum. The proposed method extends the recently developed concept of Reiterative Minimum Mean-Square Error (RMMSE) estimation to estimate adaptively the appropriate pulse compression filter for each particular range cell of each received radar return signal. The resulting algorithm, denoted as Multistatic Adaptive Pulse Compression (MAPC), effectively mitigates the interference caused by autocorrelation range sidelobes and waveform cross-correlations.
Identification of Murine Poxvirus-Specific CD8+ CTL Epitopes with Distinct Functional Profiles (2005)

Murine T cell epitopes against vaccinia virus (VV) have not been characterized to date in part due to the large and complex genome of VV. We have identified and characterized two CD8+ T cell epitopes on the A47L (modified VV Ankara strain (MVA)-029) and J6R (MVA-043) proteins of VV that are Db and Kb restricted, respectively. Following i.p. immunization with VV New York City Board of Health (NYCBH) strain, MVA-029 peptide-stimulated splenocytes secreted IFN-gamma from 7 days to 7 mo postimmunization, and virus-stimulated effectors were also able to lyse MVA-029-pulsed target cells at the same time points. In contrast, MVA-043 peptide-stimulated splenocytes secreted very low levels of IFN-gamma only at day 7 but maintained the ability to lyse target cells up to 2 mo postimmunization. Both MVA-029 and MVA-043 peptide-stimulated lymph node cells degranulated similarly as assessed by Ag-induced CD107 expression. T cell responses to whole-virus stimulation remained robust and steady during the acute and memory T cell response to VV. Identification of T cell epitopes on VV will enable further studies to increase our understanding of the role of CD8+ T cells in VV infection and assist in the design of new protective strategies.
"Liquid armor": Protective fabrics utilizing shear thickening fluids (2004)

Significant research and development effort has led to the development of fabric-based armors which protect against ballistic threats (Bogetti and Cheeseman, 2003). However, new materials are required to address the emerging need for stab protection. In the civilian sector, stab resistant armors are primarily utilized in correctional facilities, where the most likely threats to officers are improvised, sharp objects. Strict gun ownership restrictions in some countries, especially in Europe, have also led to an increase in the proportion of assaults which are committed with knives. Correspondingly, police forces in these countries are increasingly requesting stab-resistant armors. For military applications, a demand exists for protection in close-quarters, urban conflict. In addition to direct stab assaults, these environments often require operating near sharp objects such as broken glass, debris, and razor wire.
Design and synthesis of highly potent and selective cyclic dynorphin A analogs. 2. New analogs (1993)

We have designed and synthesized several cyclic disulfide-containing peptide analogs of dynorphin A (Dyn A) which are conformationally constrained in the putative "address" segment of the opioid ligand. Several of these Dyn A analogs exhibit unexpected apparent selectivities for the kappa and mu opioid receptors(s) of the central vs peripheral nervous systems. Thus, incorporation of conformational constraint in the putative "address" segment of Dyn A analogs has resulted in the kappa/mu opioid receptor ligands [L-Pen5,Cys11]Dyn A1-11-NH2 (4), [Cys5,Cys10]Dyn A1-11-NH2 (5), [Cys5,Cys9]DynA1-11-NH2 (6), and [Cys4,Cys9,Arg10]DynA1-11-NH2(7). All of these analogs possess high kappa and mu opioid receptor affinities for the central receptor (guinea pig brain), but effect only weak potency at peripheral kappa and mu opioid receptors (GPI). In fact cyclic dynorphin A analog 4 shows > 19,000-fold differences between central kappa opioid affinity and potency in the guinea pig ileum (GPI). Additionally analog 4 is not an antagonist in the GPI, suggesting possible receptor differences between these sites. Substitution of Tyr1 by Phe1 in the cyclic 1-11 series gave the analog [Phe1,Cys5,Cys11]Dyn A1-11-NH2 (1) that was surprisingly potent in the guinea pig brain binding assay (IC50 = 15.1 nM) at the kappa receptor, but was inactive in the GPI and mouse vas deferens bioassays. D-Ala2 and Tic4 analogs of 1 had lower affinity at brain kappa receptors and had very weak potencies in the GPI and MVD bioassays. On the other hand, [Cys6,Cys10]DynA1-11-NH2 (8), [Cys8,D-Cys13]DynA1-13-NH2 (9), [D-Cys8,D-Cys12]DynA1-13-NH2 (10), and [D-Pro10,Cys5,Cys13]-Dyn A1-13-NH2 (11) were surprisingly potent in the GPI bioassay, though considerable apparent selectivity for central receptors is still retained. The apparent lack of correlation between the pharmacological profiles observed in smooth muscle and in the brain binding assays, particularly with 1 and 4, may suggest the existence of different subtypes of the kappa and mu opioid receptors in the brain and peripheral systems.
Cloning of the cDNA of the heme-regulated eukaryotic initiation factor 2 alpha (eIF-2 alpha) kinase of rabbit reticulocytes: homology to yeast GCN2 protein kinase and human double-stranded-RNA-dependent eIF-2 alpha kinase. (1991)

We have cloned the cDNA of the heme-regulated eIF-2 alpha kinase (HRI) of rabbit reticulocytes. In vitro translation of mRNA transcribed from the HRI cDNA yields a 90-kDa polypeptide that exhibits eIF-2 alpha kinase activity and is recognized by a monoclonal antibody directed against authentic HRI. The open reading frame sequence of the HRI cDNA contains all 11 catalytic domains of protein kinases with consensus sequences of protein-serine/threonine kinases in conserved catalytic domains VI and VIII. The HRI cDNA also contains an insert of approximately 140 amino acids between catalytic domains V and VI. The HRI cDNA coding sequence has extensive homology to GCN2 protein kinase of Saccharomyces cerevisiae and to human double-stranded-RNA-dependent eIF-2 alpha kinase. This observation suggests that GCN2 protein kinase may be an eIF-2 alpha kinase in yeast. In addition, HRI has an unusually high degree of homology to three protein kinases (NimA, Wee1, and CDC2) that are involved in the regulation of the cell cycle.
Neutron response result of hybrid scintillator; Ce:LiCaAlF<sub>6</sub> covered with plastic scintillator coupled to APD (2011)

We report first read out result of inorganic-organic hybrid scintillator; Ce:LiCaAlF6 single crystal covered with plastic scintillator for neutron detection. The Ce:LiCaAlF <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> sample coated with POPOP containing PPO showed great light output and energy resolution than the Ce:LiCaAlF <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> itself when it was coupled to PMT. Light output was increased up to 203% and energy resolution was improved to 9%, which originally it was 16%. Moreover, we succeed in clear neutron peak this new hybrid scintillator APD (Hamamats S8664-1010).