gebhart/patrepeval huggingface dataset:
Design, Setup and First Results of a Miniaturized Time-of-Flight Mass Spectrometer with a Simple Reflector of a New Design (2004)

A new kind of reflector with only one element has been constructed and used in a miniaturized time-of- flight mass spectrometer. Details from the simulation of the instrument with SIMION and its design are presented and discussed. The instrumental setup is displayed and some first results from measurements are presented. Laser- generated electron ionization (LEI) and resonance-enhanced multi-photon ionization (REMPI) are used for ion production. While both methods yield good mass spectra, the mass resolving power of the instrument is different for both methods. The results of the measurements are compared and discussed with respect to the design. It is found that the resolution of the new instrument is satisfactory for mass spectrometric measurements of small molecules and not limited by the reflector.
Terahertz Metamaterials for Linear Polarization Conversion and Anomalous Refraction (2013)

Polarization is one of the basic properties of electromagnetic waves conveying valuable information in signal transmission and sensitive measurements. Conventional methods for advanced polarization control impose demanding requirements on material properties and attain only limited performance. We demonstrated ultrathin, broadband, and highly efficient metamaterial-based terahertz polarization converters that are capable of rotating a linear polarization state into its orthogonal one. On the basis of these results, we created metamaterial structures capable of realizing near-perfect anomalous refraction. Our work opens new opportunities for creating high-performance photonic devices and enables emergent metamaterial functionalities for applications in the technologically difficult terahertz-frequency regime.
Automated MALDI-TOF Mass Spectrometry based SNP Genotyping (2001)

____________________________________________________________ With the advancement of the human genome project the determination of the general structure of the human genome approaches its completion. A working draft covering 90% of the genomic sequence has already been published [a, 1]. Pharmacogenomic research now has to elucidate the molecular polymorphisms underlying individual phenotypic differences. This knowledge will significantly increase the understanding of individual predispositions to certain diseases, as well as the efficacy and potential adverse effects of certain drugs [2]. The most common genetic variations are single nucleotide polymorphisms (SNPs). A SNP is the occurence of a different nucleotide in different individuals at a given chromosomal position [3]. It is estimated that SNPs account for approximately 90% of the individual genotypic variations [3]. Accordingly, in order to fully exploit the available genomic information, there is a growing demand for reliable, fast, cost effective and highly automated analysis methods for SNP genotyping. SNP genotyping can be addressed by several different methods and technologies. However, many of them do not allow the required sample throughput, or they rely on indirect detection reactions, involving specific nucleic acid labelling or hybridization steps. In contrast, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) measures directly a physical property of the analyte - its molecular mass. Accordingly, MALDI-TOF MS SNP genotyping is not susceptible to background problems resulting from hybridization based detection reactions. Here we present our MALDI-TOF MS SNP genotyping system that allows fully automated data acquisition and SNP genotyping (Bruker Daltonik, Bremen, Germany). The sample preparation starts with a PCR amplification of a genomic DNA fragment containing the polymorphic site of interest. After a purification step with the genopure magnetic bead system (Bruker Saxonia, Leipzig, Germany), the PCR products are used as templates to generate allele-specific
Reactive Adsorption of NO<sub>2</sub> at Dry Conditions on Sewage Sludge-Derived Materials (2007)

Composite inorganic-carbonaceous adsorbents were obtained by pyrolysis of sewage sludge at 500, 650, and 950 degrees C for various periods of time. They were used as media for reactive adsorption of NO2. The surface structure and chemistry of the initial and exhausted materials were analyzed using adsorption of nitrogen, XRD, FTIR, and thermal analysis. The results indicate the high level of conversion of NO2 to NO with the retention of both species on the surface depending on its chemistry. At 650 degrees C as the pyrolysis temperature, the most efficient adsorbents were obtained owing to a high reactivity of their oxides toward the formation of nitrites and nitrates. When the pyrolysis temperature is low, NO2 is reduced to NO on surface sulfides and reacts with surface oxides, forming nitrites and nitrates. When adsorbents are obtained at 950 degrees C, the chemically stable surface prevents the formation of nitrites and nitrates, and the majority of NO2 is reduced to NO in the highly carbonized carbonaceous phase.
Tailored Intensity Distributions with Vertical-Cavity Surface-Emitting Laser Systems (2011)

Robust top-hat laser beams with a large degree of freedom of the outer shape and scalable in optical power are realised by laser modules consisting of surface-emitting laser diodes (VCSELs) and a simple optic.
Robust detection of audio watermarks after acoustic path transmission (2010)

This paper presents an algorithm to improve the robustness of audio watermarks after acoustic path transmission. This includes a brief presentation of the variety of signal alterations a watermarked audio track undergo in such a scenario. After presenting the underlying audio watermarking algorithm, the involved effects with respect to the correlation based detection will be discussed. Based on this observations a new detection metric is introduced exploiting the multipath reception of the watermarked signal after acoustic path transmission. The new detection metric is based on determining the false positive probability, which is effectively computed via a recursive calculation algorithm during detection. The effectiveness of the presented detection method will be underlined by an exhaustive experimental evaluation.
A peptide uncoupling CRMP-2 from the presynaptic Ca2+ channel complex demonstrates efficacy in animal models of migraine and AIDS therapy-induced neuropathy (2012)

Biological, genetic, and clinical data provide compelling proof for N-type voltage-gated calcium channels (CaV2.2) as therapeutic targets for chronic pain. While decreasing channel function is ultimately anti-nociceptive, directly targeting the channel can lead to multiple adverse effects. Targeting regulators of channel activity may facilitate improved analgesic properties associated with channel block and afford a broader therapeutic window. Towards this end, we recently identified a short peptide, designated CBD3, derived from collapsin response mediator protein 2 (CRMP-2) that suppressed inflammatory and neuropathic hypersensitivity by inhibiting CRMP-2 binding to CaV2.2 [Brittain et al., Nature Medicine 17:822-829 (2011)]. Rodents administered CBD3 intraperitoneally, fused to the HIV TAT protein cell penetrating domain, exhibited antinociception lasting ~4 hours highlighting potential instability, limited oral bioavailability, and/or rapid elimination of peptide. This report focuses on improving upon the parental CBD3 peptide. Using SPOTScan analysis of synthetic versions of the parental CBD3 peptide, we identified peptides harboring single amino acid mutations that bound with greater affinity to CaV2.2. One such peptide, harboring a phenylalanine instead of glycine (G14F), was tested in rodent models of migraine and neuropathic pain. In vivo laser Doppler blood flowmetry measure of capsaicin-induced meningeal vascular responses related to headache pain was almost completely suppressed by dural application of the G14F peptide. The G14F mutant peptide, administered intraperitoneally, also exhibited greater antinociception in Stavudine (2'-3'-didehydro-2'-3'-dideoxythymidine (d4T)/Zerit®) model of AIDS therapy-induced peripheral neuropathy compared to the parent CBD3 peptide. These results demonstrate the patent translational value of small biologic drugs targeting CaV2.2 for management of clinical pain.
Electrical Spin Driving by <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi>g</mml:mi></mml:mrow></mml:math>-Matrix Modulation in Spin-Orbit Qubits (2018)

In a semiconductor spin qubit with sizable spin-orbit coupling, coherent spin rotations can be driven by a resonant gate-voltage modulation. Recently, we have exploited this opportunity in the experimental demonstration of a hole spin qubit in a silicon device. Here we investigate the underlying physical mechanisms by measuring the full angular dependence of the Rabi frequency, as well as the gate-voltage dependence and anisotropy of the hole g factor. We show that a g-matrix formalism can simultaneously capture and discriminate the contributions of two mechanisms so far independently discussed in the literature: one associated with the modulation of the g factor, and measurable by Zeeman energy spectroscopy, the other not. Our approach has a general validity and can be applied to the analysis of other types of spin-orbit qubits.
Preparation of Barium Titanate–Potassium Niobate Solid Solution System Ceramics and Their Piezoelectric Properties (2008)

Barium titanate (BaTiO3, BT)–potassium niobate (KNbO3, KN) solid solution system ceramics were prepared by normal sintering, and their piezoelectric properties were measured. The phase diagram of the BT–KN system was investigated by dielectric measurement and X-ray diffraction (XRD). The Curie temperature (TC) was almost constant at approximately 130 and 430 °C for ceramics with KN contents below and above 50 mol %, respectively. At room temperature, two phases, ferroelectric tetragonal and ferroelectric orthorhombic, coexisted in the composition range from 0.7BT–0.3KN to 0.1BT–0.9KN. This system was found to be a limited solid solution system that involves BT- and KN-rich phases. Their piezoelectric properties were investigated on the basis of the electric-field dependence of strain measurements. For ceramics with KN contents below 30 mol %, the apparent piezoelectric constant (d33) decreased approximately with increasing KN content, whereas above 30 mol %, the apparent d33 increased as a function of KN content.
Analogies Between Digital Radio and Chemical Orthogonality as a Method for Enhanced Analysis of Molecular Recognition Events (2008)

Acoustic wave biosensors are a real-time, label-free biosensor technology, which have been exploited for the detection of proteins and cells. One of the conventional biosensor approaches involves the immobilization of a monolayer of antibodies onto the surface of the acoustic wave device for the detection of a specific analyte. The method described within includes at least two immobilizations of two different antibodies onto the surfaces of two separate acoustic wave devices for the detection of several analogous analytes. The chemical specificity of the molecular recognition event is achieved by virtue of the extremely high (nM to pM) binding affinity between the antibody and its antigen. In a standard ELISA (Enzyme-Linked ImmunoSorbent Assay) test, there are multiple steps and the end result is a measure of what is bound so tightly that it does not wash away easily. The fact that this "gold standard" is very much not real time, masks the dance that is the molecular recognition event. X-Ray Crystallographer, Ian Wilson, demonstrated more than a decade ago that antibodies undergo conformational change during a binding event[1, 2]. Further, it is known in the arena of immunochemistry that some antibodies exhibit significant cross-reactivity and this is widely termed antibody promiscuity. A third piece of the puzzle that we will exploit in our system of acoustic wave biosensors is the notion of chemical orthogonality. These three biochemical constructs, the dance, antibody promiscuity and chemical orthogonality will be combined in this paper with the notions of in-phase (I) and quadrature (Q) signals from digital radio to manifest an approach to molecular recognition that allows a level of discrimination and analysis unobtainable without the aggregate. As an example we present experimental data on the detection of TNT, RDX, C4, ammonium nitrate and musk oil from a system of antibody-coated acoustic wave sensors.
Low NO.sub.x combustor (1994)

A combustor includes a dome assembly having radially outer and inner liners joined thereto and defining therebetween a combustion zone. The dome assembly includes at least one annular dome having a pair of axially extending first flanges between which are disposed a plurality of circumferentially spaced apart carburetors for discharging a fuel/air mixture into the combustion zone for generating combustion gases. An annular heat shield includes a pair of axially extending legs integrally joined to a radially extending face in a generally U-shaped configuration, with the face including a plurality of circumferentially spaced apart ports disposed concentrically with perspective ones of the carburetors for allowing the fuel/air mixture to be discharged therefrom through the heat shield. At least one of the heat shield legs includes a plurality of circumferentially spaced apart mounting holes disposed adjacent to a respective one of the dome flanges, and a plurality of mounting pins are fixedly joined to the dome flange and extend radially through respective ones of the mounting holes without interference therewith for allowing unrestrained thermal movement between the heat shield and the dome while supporting the heat shield against axial pressure loads thereon. In a preferred embodiment, the dome assembly includes three domes having respective ones of the heat shield, and respective baffles are spaced from the heat shields for providing impingement cooling thereof.
Chargrid-OCR: End-to-end trainable Optical Character Recognition through Semantic Segmentation and Object Detection (2019)

We present an end-to-end trainable approach for Optical Character Recognition (OCR) on printed documents. Specifically, we propose a model that predicts a) a two-dimensional character grid (\emph{chargrid}) representation of a document image as a semantic segmentation task and b) character boxes for delineating character instances as an object detection task. For training the model, we build two large-scale datasets without resorting to any manual annotation - synthetic documents with clean labels and real documents with noisy labels. We demonstrate experimentally that our method, trained on the combination of these datasets, (i) outperforms previous state-of-the-art approaches in accuracy (ii) is easily parallelizable on GPU and is, therefore, significantly faster and (iii) is easy to train and adapt to a new domain.
Molecular Triage of Premalignant Lesions in Liquid-Based Cervical Cytology and Circulating Cell-Free DNA from Urine, Using a Panel of Methylated Human Papilloma Virus and Host Genes (2016)

Clinically useful molecular tools to triage women for a biopsy upon referral to colposcopy are not available. We aimed to develop a molecular panel to detect cervical intraepithelial neoplasia (CIN) grade 2 or higher lesions (CIN2<sup>+</sup>) in women with abnormal cervical cytology and high-risk HPV (HPV<sup>+</sup>). We tested a biomarker panel in cervical epithelium DNA obtained from 211 women evaluated in a cervical cancer clinic in Chile from 2006 to 2008. Results were verified in a prospective cohort of 107 women evaluated in a high-risk clinic in Puerto Rico from 2013 to 2015. Promoter methylation of ZNF516, FKBP6, and INTS1 discriminated cervical brush samples with CIN2<sup>+</sup> lesions from samples with no intraepithelial lesions or malignancy (NILM) with 90% sensitivity, 88.9% specificity, 0.94 area under the curve (AUC), 93.1% positive predictive value (PPV), and 84.2% negative predictive value (NPV). The panel results were verified in liquid-based cervical cytology samples from an independent cohort with 90.9% sensitivity, 60.9% specificity, 0.90 AUC, 52.6% PPV, and 93.3% NPV, after adding HPV16-L1 methylation to the panel. Next-generation sequencing results in HPV<sup>+</sup> cultured cells, and urine circulating cell-free DNA (ccfDNA) were used to design assays that show clinical feasibility in a subset (n = 40) of paired plasma (AUC = 0.81) and urine (AUC = 0.86) ccfDNA samples obtained from the prospective cohort. Viral and host DNA methylation panels can be tested in liquid cytology and urine ccfDNA from women referred to colposcopy, to triage CIN2<sup>+</sup> lesions for biopsy and inform personalized screening algorithms. Cancer Prev Res; 9(12); 915-24. ©2016 AACR.
A Novel Class of Potent Nonglycosidic and Nonpeptidic Pan-Selectin Inhibitors (2006)

An early step of the inflammatory response, the rolling of leukocytes on activated endothelial cells, is mediated by selectin/carbohydrate interactions. The tetrasaccharide sialy Lewisx is a ligand for E-, P-, and L-selectin and therefore serves as a lead structure for the development of analogues. A combination of synthesis and structure-based design allowed rapid optimization. The current lead 2a was evaluated in our E-selectin cell flow chamber assay where it proved to inhibit rolling and adhesion with an IC50 of 28+/-7 microM. The assays used are predictive for the in vivo efficacy of test compounds as shown for 2a in a proteose peptone induced peritonitis model of acute inflammation in mice.
Ontological content‐based filtering for personalised newspapers (2010)

Purpose The purpose of this paper is to describe a new ontological content‐based filtering method for ranking the relevance of items for readers of news items, and its evaluation. The method has been implemented in ePaper, a personalised electronic newspaper prototype system. The method utilises a hierarchical ontology of news; it considers common and related concepts appearing in a user's profile on the one hand, and in a news item's profile on the other hand, and measures the “hierarchical distances” between these concepts. On that basis it computes the similarity between item and user profiles and rank‐orders the news items according to their relevance to each user. Design/methodology/approach The paper evaluates the performance of the filtering method in an experimental setting. Each participant read news items obtained from an electronic newspaper and rated their relevance. Independently, the filtering method is applied to the same items and generated, for each participant, a list of news items ranked according to relevance. Findings The results of the evaluations revealed that the filtering algorithm, which takes into consideration hierarchically related concepts, yielded significantly better results than a filtering method that takes only common concepts into consideration. The paper determined a best set of values (weights) of the hierarchical similarity parameters. It also found out that the quality of filtering improves as the number of items used for implicit updates of the profile increases, and that even with implicitly updated profiles, it is better to start with user‐defined profiles. Originality/value The proposed content‐based filtering method can be used for filtering not only news items but items from any domain, and not only with a three‐level hierarchical ontology but any‐level ontology, in any language.
Automatic generation of endocardial surface meshes with 1-to-1 correspondence from cine-MR images (2015)

In this work, we develop an automatic method to generate a set of 4D 1-to-1 corresponding surface meshes of the left ventricle (LV) endocardial surface which are motion registered over the whole cardiac cycle. These 4D meshes have 1- to-1 point correspondence over the entire set, and is suitable for advanced computational processing, such as shape analysis, motion analysis and finite element modelling. The inputs to the method are the set of 3D LV endocardial surface meshes of the different frames/phases of the cardiac cycle. Each of these meshes is reconstructed independently from border-delineated MR images and they have no correspondence in terms of number of vertices/points and mesh connectivity. To generate point correspondence, the first frame of the LV mesh model is used as a template to be matched to the shape of the meshes in the subsequent phases. There are two stages in the mesh correspondence process: (1) a coarse matching phase, and (2) a fine matching phase. In the coarse matching phase, an initial rough matching between the template and the target is achieved using a radial basis function (RBF) morphing process. The feature points on the template and target meshes are automatically identified using a 16-segment nomenclature of the LV. In the fine matching phase, a progressive mesh projection process is used to conform the rough estimate to fit the exact shape of the target. In addition, an optimization-based smoothing process is used to achieve superior mesh quality and continuous point motion.
Large-volume data delivery from low-Earth orbit to ground using efficient single-mode optical receivers (2016)

Space systems operating in low-Earth orbit are often constrained by how much data can be delivered from space to ground. Traditional data delivery approaches are often limited by either large link losses associated with transmission via a geosynchronous relay satellite or short contact times and spectrum-constrained data rates associated with direct-to-Earth radio-frequency links. Direct-to-Earth optical communication links from low-Earth orbit based on fiber telecommunications technologies that can operate at high data rates (> 100 Gb/s per wavelength channel) can enable the delivery of extremely large volumes of data from space to ground. We analyze the performance of such systems and discuss the performance gains that are enabled by coupling the received signal to an efficient single-mode-fiber-based receiver, even in the presence of turbulence-induced losses.
In Vivo Adaptation of the Wayne Model of Latent Tuberculosis (2007)

Cultures of Mycobacterium tuberculosis grown under oxygen depletion conditions enter into a state of nonreplicating persistence that may reflect a physiologically latent state. When these cultures were harvested and injected intranasally into mice, no bacteria could be recovered from the lungs for about 3 weeks, but after that evidence of regrowth was observed. Preimmunization of mice with a panel of selected vaccine candidates slowed or prevented this event. This simple model has potential for identifying vaccines targeting latent tuberculosis.
Design of 2-D multiplierless IIR filters using the genetic algorithm (2002)

When digital filters are designed with power-of-two coefficients, the multiplications can be implemented by simple shifting operations. For VLSI implementations, multiplierless filters are faster and more compact than filters with multipliers. In this paper, the genetic algorithm (GA) is used to design two-dimensional (2-D) IIR multiplierless filters. The 2-D filter is designed to have periodically shift variant (PSV) coefficients. This increases the degrees of freedom for the multiplierless coefficients so that a better approximation can be achieved. The design involves finding the impulse response of the 2-D PSV filter in closed form and then using the GA to find the filter coefficients. Two different types of GA are used, namely, the Binary-GA and the Integer-GA. Some design examples are presented to illustrate the results.