gebhart/patrepeval huggingface dataset:
<i>In vivo</i>evaluation of EGFRvIII mutation in primary glioblastoma patients via complex multiparametric MRI signature (2018)

An imaging signature of EGFRvIII was found, revealing a complex, yet distinct macroscopic glioblastoma phenotype. By non-invasively capturing the tumor in its entirety, the proposed methodology can assist in evaluating the tumor's spatial heterogeneity, hence overcoming common spatial sampling limitations of tissue-based analyses. This signature can preoperatively stratify patients for EGFRvIII-targeted therapies, and potentially monitor dynamic mutational changes during treatment.
Exploiting the JPEG compression scheme for image retrieval (1996)

We address the problem of retrieving images from a large database using an image as a query. The method is specifically aimed at databases that store images in JPEG format, and works in the compressed domain to create index keys. A key is generated for each image in the database and is matched with the key generated for the query image. The keys are independent of the size of the image. Images that have similar keys are assumed to be similar, but there is no semantic meaning to the similarity.
Light field projection for lighting reproduction (2015)

We propose a novel approach to generate 4D light field in the physical world for lighting reproduction. The light field is generated by projecting lighting images on a lens array. The lens array turns the projected images into a controlled anisotropic point light source array which can simulate the light field of a real scene. In terms of acquisition, we capture an array of light probe images from a real scene, based on which an incident light field is generated. The lens array and the projectors are geometric and photometrically calibrated, and an efficient resampling algorithm is developed to turn the incident light field into the images projected onto the lens array. The reproduced illumination, which allows per-ray lighting control, can produce realistic lighting result on real objects, avoiding the complex process of geometric and material modeling. We demonstrate the effectiveness of our approach with a prototype setup.
Arc-Light Reflector For Television Weld Monitoring (1989)

Conical, stainless-steel mirror attached to end of welding torch improves distribution of light on work-piece as welding monitored through torch by television. Television monitoring protects operators from intense arc light and facilitates automated welding. Simple, small, and easy to install and remove, mirror relatively nonintrusive.
Use of Conjugated Linoleic Acid (CLA) Enrichments to Examine the Effects of trans-8, cis-10 CLA, and cis-11, trans-13 CLA on Milk-Fat Synthesis (2004)

Conjugated linoleic acid (CLA) supplements have typically been comprised of 4 isomers (trans-8, cis-10; cis-9, trans-11; trans-10, cis-12; and cis-11, trans-13 CLA). Abomasal infusion of pure isomers has shown that trans-10, cis-12 CLA is a potent inhibitor of milk-fat synthesis, whereas cis-9, trans-11 CLA has no effect. However, there appear to be additional fatty acids that inhibit milk-fat synthesis, and the objective of this study was to investigate the effects of additional CLA isomers present in CLA supplements. Four rumen fistulated Holstein cows (141+/-8 DIM, mean+/-SE) were randomly assigned in a 4 x 4 Latin square experiment. Treatments were abomasal infusion of (1) skim milk (negative control), (2) trans-10, cis-12 CLA supplement (positive control), (3) trans-8, cis-10 CLA supplement, and (4) cis-11, trans-13 CLA supplement. Treatments 2 through 4 were targeted to provide 4 g/d of the CLA isomer of interest. The trans-8, cis-10 CLA supplement had no effect on milk-fat yield, whereas the trans-10, cis-12 CLA supplement reduced milk-fat yield by 35%. The cis-11, trans-13 CLA supplement contained some trans-10, cis-12 CLA, and when data were compared to the positive control treatment group, it was obvious that cis-11, trans-13 CLA also had no effect on milk-fat synthesis. Milk-fat content of specific CLA isomers was significantly elevated within respective treatment groups. Milk yield, DMI, and milk protein yield were unaffected by treatment. Overall, trans-10, cis-12 CLA reduced milk-fat synthesis, whereas the other major isomers present in CLA supplements (trans-8, cis-10 CLA and cis-11, trans-13 CLA) had no effect.
Inverse Precision Velocity Update for Monopulse Calibration (2007)

A critical function of a radar system is to precisely locate moving targets for identification and targeting. The moving target location is determined with respect to the actual boresight of the radar antenna performing the angle measurements. The accuracy of these angle measurements is often limited by bias errors (e.g., radome errors, sum and difference channel isolation and imbalances, and harmonization errors) which are not related to the signal-to-noise ratio of the received radar return. In effect, the bias errors preclude accurate monopulse angle measurement to a target, even if the target is clearly visible by the radar. A new technique is proposed which avoids these limitations, deriving a correction for the electrical boresight of a monopulse antenna mounted on a moving platform. It exploits highly accurate velocity measurements from currently available low-cost INS/GPS systems with carrier phase measurements. The measured velocity coupled with advanced multichannel processing of a monopulse SAR mode provide independent pointing error estimates from many pixels. This patented technique has been named Inverse Precision Velocity Update (or Inverse PVTJ) for monopulse calibration. The angle estimates from a selected set of pixels are weighted and averaged to obtain a precise estimate of the monopulse beam pointing for accurate moving target geolocation.
Parallel Soft Spherical Detection for Coded MIMO Systems (2010)

This Chapter briefly evaluates different multiple-input multiple-output (MIMO) detection techniques in the literature as the candidates for the next generation wireless systems. The authors evaluate the associated problems and solutions with these methods. The focus of the chapter is on two categories of MIMO decoding: i) hard detection and ii) soft detection. These techniques significantly increase the capacity of wireless communications systems. Theoretically, a-posteriori probability (APP) MIMO decoder with soft information can achieve the capacity of a MIMO system. A sub-optimum APP detector is proposed for iterative joint detection/decoding in a MIMO wireless communication system employing an outer code. The proposed detector searches inside a given sphere in a parallel manner to simultaneously find a list of m-best points based on an additive metric. The metric is formed by combining the channel output and the a-priori information. The parallel structure of the proposed method is suitable for hardware parallelization. The radius of the sphere and the value of m are selected according to the channel condition to reduce the complexity. Numerical results are provided showing a significant reduction in the average complexity (for a similar performance and peak complexity) as compared to the best earlier known method. This positions the proposed algorithm as a candidate for the next generation wireless systems. The proposed scheme is applied for the decoding of the rate 2, 4 × 2 MIMO code employed in the IEEE 802.16e standard.
Dimensioning of a multibeam coherent photonic beamformer fed by a phased array antenna (2018)

The design and dimensioning of a photonic-aided payload for a multi-beam high-throughput communications satellite is a complex problem in which the antenna, RF and photonic subsystems must be considered as a whole for achieving best performance with lowest mass and power consumption. In this paper, we propose and dimension the receiving stage of a communications satellite comprising a phased array antenna (PAA) feeding a multibeam photonic beamforming system (PBS). The PBS uses a single wavelength and resorts to heterodyne detection such that the retrieved beams are frequency downconverted. End-to-end system modeling shows that the complexity of the PAA and PBS can be traded-off for signal-to-noise ratio (SNR) or power consumption without compromising the beam width. The dimensioning of a realistic scenario is presented, showing that an SNR and beam crosstalk on the order of 20 dB are achievable with a total power consumption below 1 kW for a typical number of 100 antenna elements (AEs).
Non-manifold implicit surfaces based on discontinuous implicitization and polygonization (2003)

Implicit surfaces in 3D geometric modeling are limited to two manifolds because the corresponding implicit fields are usually defined by real-valued functions which bisect space into interior and exterior. We present a novel method of modeling non-manifold surfaces by implicit representation. Our method allows discontinuity of the field function and assesses the special meaning of the locus where the function is not differentiable. The enhancement can yield a non-manifold surface with such features as holes and boundaries. The discontinuous field function also enables multiple classification of the field, which makes it possible to represent branches and intersections of the implicit surfaces. The implicit field is polygonized by the algorithm based on the marching cubes algorithm, which is extended to treat discontinuous fields correctly. We also describe an efficient implementation of converting a surface model into a set of discrete samples of field function, and finally present the result of the non-manifold surfaces reproduced by our method.
Memristors Empower Spiking Neurons With Stochasticity (2015)

Recent theoretical studies have shown that probabilistic spiking can be interpreted as learning and inference in cortical microcircuits. This interpretation creates new opportunities for building neuromorphic systems driven by probabilistic learning algorithms. However, such systems must have two crucial features: 1) the neurons should follow a specific behavioral model, and 2) stochastic spiking should be implemented efficiently for it to be scalable. This paper proposes a memristor-based stochastically spiking neuron that fulfills these requirements. First, the analytical model of the memristor is enhanced so it can capture the behavioral stochasticity consistent with experimentally observed phenomena. The switching behavior of the memristor model is demonstrated to be akin to the firing of the stochastic spike response neuron model, the primary building block for probabilistic algorithms in spiking neural networks. Furthermore, the paper proposes a neural soma circuit that utilizes the intrinsic nondeterminism of memristive switching for efficient spike generation. The simulations and analysis of the behavior of a single stochastic neuron and a winner-take-all network built of such neurons and trained on handwritten digits confirm that the circuit can be used for building probabilistic sampling and pattern adaptation machinery in spiking networks. The findings constitute an important step towards scalable and efficient probabilistic neuromorphic platforms.
Correlated effects of exotic pollen‐fertility restorer genes on agronomic and quality traits of hybrid rye (2017)

Abstract In CMS (cytoplasmic male sterility)‐based hybrid rye ( Secale cereale L.) breeding, effective pollen‐fertility restoration is an essential prerequisite for achieving maximum grain yield on the one hand and for minimizing ergot ( Claviceps purpurea ) infestation on the other. Restorer genes for the CMS ‐inducing ‘Pampa’ cytoplasm derived from landraces collected in Iran and Argentina are used by breeders for achieving this goal. Here, restorer genes from four germplasm sources (‘Altevogt 14160’, ‘ IRAN III ’, ‘Trenelense’ and ‘Pico Gentario’) were analysed by producing three‐way cross hybrids between an elite CMS single cross and pollinators with and without a given restorer gene. Materials were evaluated on large drilled plots for restorer index ( RI ), grain yield, plant height and other traits in six environments. In experiment 1, a restorer gene from ‘Altevogt 14160’ was used. Seven pairs of marker‐selected carrier and non‐carrier backcross lines served as pollinators. In experiment 2, the pollinators were 17 backcross line pairs from the other three germplasm sources. These lines were grouped as high ( RI > 67%) and low restorers ( RI < 30%), respectively, using testcrosses with a highly diagnostic CMS tester. Hybrids carrying an exotic restorer gene suffered from a significant grain yield reduction by 4.4% and 9.4% and were 9.3 and 4.8 cm taller in experiments 1 and 2, respectively. Thousand‐kernel weight was reduced, whereas quality traits were only slightly affected. For all traits, significant genetic variance existed among the testcrosses to the presence vs. absence of a given exotic restorer gene. This offers a chance for the breeder to reduce or ultimately overcome the presently observed performance reductions brought about by exotic restorer genes.
Mechanism of platelet-derived growth factor (PDGF) AA, AB, and BB binding to alpha and beta PDGF receptor. (1993)

The biological effects of platelet-derived growth factor (PDGF) are mediated by cell surface alpha and beta PDGF receptors, which, as a result of ligand binding, undergo dimerization in a manner consistent with PDGF being bivalent. In order to directly demonstrate PDGF bivalency and to define the binding of PDGF AB to isolated beta receptor, we developed solid-phase binding assays using purified recombinant extracellular domain of human PDGF receptors. PDGF AA, AB, and BB were prepared from the monomeric chains expressed in Escherichia coli, and each was purified to homogeneity; PDGF AB contained < 0.5% of either homodimer. The interactions of these isoforms with immobilized PDGF receptors were examined by several approaches. Scatchard analysis revealed high affinity binding (Kd = 0.5-1.0 nM) of radiolabeled PDGF AA and AB to alpha receptor and of PDGF BB to both receptor subtypes. Contrary to previous reports, PDGF AB also bound beta receptor with high affinity (Kd = 0.9 nM). When a B-chain-specific monoclonal antibody that recognizes the putative binding domain of PDGF BB was used for ligand detection, we found that PDGF AB binding to beta receptor occurred exclusively through the B-chain subunit, whereas binding to alpha receptor occurred through either subunit. In addition, site-directed mutagenesis was used to specifically inactivate the B chain of PDGF AB, which eliminated binding to the beta receptor without affecting alpha receptor binding. These results establish that PDGF is bivalent and that monovalent ligand retains high affinity receptor binding.
Character string detection algorithm using horizontal boundaries and its application to a part number entry system (1991)

This paper proposes a new algorithm for detecting character strings in an image containing illustrations and characters. It also describes a part number entry system that utilizes this algorithm. The algorithm detects character strings by investigating the horizontal boundaries of rectangles representing characters strings. It can be performed a high speed, and can detect characters touching an illustration. Using this algorithm, the part number entry system extracts areas of part numbers scattered among illustrations and then recognizes the. This is a software program implemented on a personal computer, and is composed of four subprograms: detection of character strings, character recognition, post-processing, and flexible user-interface for error correction.© (1991) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Tumor Necrosis Factor Receptors 1 and 2 Differentially Regulate Survival, Cardiac Dysfunction, and Remodeling in Transgenic Mice With Tumor Necrosis Factor-α–Induced Cardiomyopathy (2004)

Ablation of the TNFR2 gene exacerbates heart failure and reduces survival, whereas ablation of TNFR1 blunts heart failure and improves survival. Signaling via TNFR2 may play a cardioprotective role in the pathogenesis of cytokine-mediated heart failure.
Multi-source Multi-modal Activity Recognition in Aerial Video Surveillance (2014)

Recognizing activities in wide aerial/overhead imagery remains a challenging problem due in part to low-resolution video and cluttered scenes with a large number of moving objects. In the context of this research, we deal with two un-synchronized data sources collected in real-world operating scenarios: full-motion videos (FMV) and analyst call-outs (ACO) in the form of chat messages (voice-to-text) made by a human watching the streamed FMV from an aerial platform. We present a multi-source multi-modal activity/event recognition system for surveillance applications, consisting of: (1) detecting and tracking multiple dynamic targets from a moving platform, (2) representing FMV target tracks and chat messages as graphs of attributes, (3) associating FMV tracks and chat messages using a probabilistic graph-based matching approach, and (4) detecting spatial-temporal activity boundaries. We also present an activity pattern learning framework which uses the multi-source associated data as training to index a large archive of FMV videos. Finally, we describe a multi-intelligence user interface for querying an index of activities of interest (AOIs) by movement type and geo-location, and for playing-back a summary of associated text (ACO) and activity video segments of targets-of-interest (TOIs) (in both pixel and geo-coordinates). Such tools help the end-user to quickly search, browse, and prepare mission reports from multi-source data.
Base doping limits in heterostructure bipolar transistors (1990)

Heterostructure bipolar transistors are used to experimentally determine band offsets in lattice-matched In0.53Ga0.47As devices. Valence-band offsets of ΔEV=0.24 eV for Al0.48In0.52As/In0.53Ga0.47As and ΔEV=0.34 eV for InP/In0.53Ga0.47As are measured. Because of band filling in the base, these values place important constraints on p-type doping levels and emitter injection efficiency in practical devices.
Abstract 1384: Promoter methylation of tumor suppressor genes in convalescent saliva samples from patients with head and neck squamous cell carcinoma (2014)

Abstract Purpose: Silencing of tumor suppressor genes (TSGs) plays an important role in head and neck carcinogenesis. Methylation of CpG islands in the promoter regions of genes acts as a significant mechanism of epigenetic gene silencing. In this study, we assessed the feasibility of epigenetic alterations in TSGs in post-treatment DNA shed from the oral mucosa as a prognostic marker for persistent/recurrent head and neck cancer. A panel of four genes (KIF1A, EDNRB, p16, DCC) was evaluated in this study. Experimental Design: Hypermethylation of the promoter regions was investigated by bisulfite modification and quantitative methylation-specific PCR (Q-MSP) which provides more objective and rapid estimation of gene methylation status. Fresh tumor samples and pre- and post-treatment salivary rinses were collected from 83 patients with HNSCC. Post-treatment saliva samples were collected once in every 3 months. In addition, 46 normal saliva and 16 normal mucosal samples from healthy individuals were obtained. Then we evaluated the correlation of the results with the clinical parameters. Results: KIF1A, EDNRB, p16 and DCC genes were methylated in 94%, 95%, 37% and 84% of primary HNSCC tissues, respectively and were only methylated in 2%, 6.8%, 5% and 10% of the salivary rinses from normal subjects. In addition, KIF1A, EDNRB, p16 and DCC were methylated in 35%, 69%, 8.4% and 38.6% of pre-treatment salivary rinses from HNSCC patients, respectively. We evaluated whether methylation levels of these genes in the post treatment saliva may predict the recurrence/prognosis or the chance of cure after treatment. Our data indicate that these genes may be potential biomarkers for HNSCC detection and follow up. Sixteen of 83 patients had recurrent tumors and KIF1A+EDNRB+p16+DCC methylation was observed in 37.5% of the patients in this group. The three gene panel (KIF1A, EDNRB and DCC) was also observed in 37.5% of the recurrent group and 46% of the overall patients, respectively. Conclusion: Methylation of the KIF1A, EDNRB and DCC gene promoters is a frequent event in HNSCC and these genes are not methylated in normal salivary rinses, demonstrating potential that they may act as biomarkers in detection strategies. Patients with presence of methylation in surveillance salivary rinses are at significant risk for recurrence. Quantitative measurement of salivary methylated DNA may have promise for surveillance and early detection of recurrence. Citation Format: Semra Demokan, Jatinder Kaur, Alice Y. Chuang, Wojciech K. Mydlarz, Kavita M. Pattani, Wayne M. Koch, David Sidransky, Nejat Dalay, Joseph A. Califano. Promoter methylation of tumor suppressor genes in convalescent saliva samples from patients with head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1384. doi:10.1158/1538-7445.AM2014-1384
Immunoconjugates that neutralize HIV virions kill T cells infected with diverse strains of HIV-1. (1990)

Two murine monoclonal antibodies, G3.519, recognizing the CD4-binding region, and BAT123, a variable region of gp120 of human immunodeficiency virus, were chemically coupled to pokeweed antiviral protein isolated from seeds (PAP-S). The immunoconjugates were purified by Sephacryl S-200 gel filtration and Mono S ion exchange chromatography. Immunoconjugate G3.519-PAP-S specifically killed human T cells, H9, infected with three diverse HIV-1 strains, HTLV-IIIB, -IIIMN, and -IIIRF. Inhibition of thymidine incorporation by the immunoconjugate was concentration-dependent, with the ID50 ranging from 1.4 x 10(-10) M to 1.7 x 10(-9) M. Immunoconjugate BAT123-PAP-S was effective in killing H9 cells infected with HTLV-IIIB (ID50 = 4.3 x 10(-11) M) and -IIIMN (ID50 = 4.7 x 10(-10) M), but not -IIIRF. Both immunoconjugates did not inhibit thymidine incorporation in uninfected H9 cells up to a concentration of 5.3 x 10(-8) M, and their cytotoxic activities could be competitively blocked by the respective unconjugated antibodies. The immunoconjugates retained the ability to neutralize HIV virions to infect T cells and to prevent the syncytium formation. These in vitro studies suggest that the use of immunoconjugates capable of killing HIV-infected T cells and neutralizing virus may provide an alternative treatment for HIV-infected persons.
Simplified AIP‐II Peptidomimetics Are Potent Inhibitors of <i>Staphylococcus aureus</i> AgrC Quorum Sensing Receptors (2016)

The bacterial pathogen Staphylococcus aureus controls many aspects of virulence by using the accessory gene regulator (agr) quorum sensing (QS) system. The agr system is activated by a macrocyclic peptide signal known as an autoinducing peptide (AIP). We sought to develop structurally simplified mimetics of AIPs for use as chemical tools to study QS in S. aureus. Herein, we report new peptidomimetic AgrC receptor inhibitors based on a tail-truncated AIP-II peptide that have almost analogous inhibitory activities to the parent peptide. Structural comparison of one of these peptidomimetics to the parent peptide and a highly potent, all-peptide-derived, S. aureus agr inhibitor (AIP-III D4A) revealed a conserved hydrophobic motif and overall amphipathic nature. Our results suggest that the AIP scaffold is amenable to structural mimicry and minimization for the development of synthetic agr inhibitors.