gebhart/patrepeval huggingface dataset:
Rapid Molecular Characterization of Acinetobacter baumannii Clones with rep-PCR and Evaluation of Carbapenemase Genes by New Multiplex PCR in Hospital District of Helsinki and Uusimaa (2014)

Multidrug-resistant Acinetobacter baumannii (MDRAB) is an increasing problem worldwide. Prevalence of carbapenem resistance in Acinetobacter spp. due to acquired carbapenemase genes is not known in Finland. The purpose of this study was to examine prevalence and clonal spread of multiresistant A. baumannii group species, and their carbapenemase genes. A total of 55 Acinetobacter isolates were evaluated with repetitive PCR (DiversiLab) to analyse clonality of isolates, in conjunction with antimicrobial susceptibility profile for ampicillin/sulbactam, colistin, imipenem, meropenem, rifampicin and tigecycline. In addition, a new real-time PCR assay, detecting most clinically important carbapenemase genes just in two multiplex reactions, was developed. The assay detects genes for KPC, VIM, IMP, GES-1/-10, OXA-48, NDM, GIM-1, SPM-1, IMI/NMC-A, SME, CMY-10, SFC-1, SIM-1, OXA-23-like, OXA-24/40-like, OXA-58 and ISAbaI-OXA-51-like junction, and allows confident detection of isolates harbouring acquired carbapenemase genes. There was a time-dependent, clonal spread of multiresistant A. baumannii strongly correlating with carbapenamase gene profile, at least in this geographically restricted study material. The new carbapenemase screening assay was able to detect all the genes correctly suggesting it might be suitable for epidemiologic screening purposes in clinical laboratories.
Image editing using level set trees (2014)

An efficient method for precise computation of image-aware geodesic distances for image editing algorithms is proposed. It exploits the connection between image representation as a mapping from a Cartesian grid and as a collection of its level sets, organized into a tree structure. The distance computation is reformulated in the domain of the image level sets, where it can be calculated without introducing approximation errors, which are unavoidable when working the image domain. Advantages of the proposed approach are demonstrated for image segmentation application.
Synthesis, characterization, and solution properties of a surface‐active hydrophobically associating polymer (2018)

ABSTRACT A nonionic surfmer (MAA‐EO 23 C 12 ) was prepared and reacted with acrylamide, acrylic acid, and a double tailed hydrophobic monomer (BTMAM) to synthesize a surface‐active hydrophobically associating copolymer (SHAP) through photoinitiated free radical copolymerization in aqueous solution. Fourier transform infrared and 1 H‐nuclear magnetic resonance spectroscopy were used to characterize the functional monomer and the SHAP. Several performance evaluations, such as viscosification property, temperature resistance, salt tolerance, and shear resistance, were also conducted. Experiment results demonstrated that the introduced nonionic surfmer and hydrophobic monomer could endow the copolymer with excellent temperature resistance, salt tolerance, and shear resistance capability at low concentration. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2018 , 135 , 46569.
Determining Data Distribution for Large Disk Enclosures with 3-D Data Templates (2019)

Conventional RAID solutions with fixed layouts partition large disk enclosures so that each RAID group uses its own disks exclusively. This achieves good performance isolation across underlying disk groups, at the cost of disk under-utilization and slow RAID reconstruction from disk failures. We propose RAID+, a new RAID construction mechanism that spreads both normal I/O and reconstruction workloads to a larger disk pool in a balanced manner. Unlike systems conducting randomized placement, RAID+ employs deterministic addressing enabled by the mathematical properties of mutually orthogonal Latin squares, based on which it constructs 3-D data templates mapping a logical data volume to uniformly distributed disk blocks across all disks. While the total read/write volume remains unchanged, with or without disk failures, many more disk drives participate in data service and disk reconstruction. Our evaluation with a 60-drive disk enclosure using both synthetic and real-world workloads shows that RAID+ significantly speeds up data recovery while delivering better normal I/O performance and higher multi-tenant system throughput.
Quantitative Analysis of mRNA as a Marker for Viability of <i>Mycobacterium tuberculosis</i> (1999)

Numerous assays which use conserved DNA or rRNA sequences as targets for amplification have been described for the diagnosis of tuberculosis. However, these techniques have not been applied successfully to the monitoring of therapeutic efficacy owing to the persistence of amplifiable nucleic acid beyond the point at which smears and cultures become negative. Semiquantitative analysis of rRNA has been used to reduce the time required for antimicrobial susceptibility testing of Mycobacterium tuberculosis, although growth for up to 5 days in the presence of some drugs is still required to discriminate resistant strains. The purpose of the present study was to determine whether quantitative analysis of M. tuberculosis mRNA could be used to assess bacterial viability and to illustrate the application of this technique to rapid determination of drug susceptibility. Levels of mRNA encoding the 85B protein (alpha-antigen), IS6110 DNA, and 16S rRNA were compared in parallel cultures of M. tuberculosis that were treated with either no drug, 0. 2 microg of isoniazid per ml, or 1 microg of rifampin per ml. Exposure of sensitive strains to isoniazid or rifampin for 24 h reduced the levels of 85B mRNA to <4 and <0.01%, respectively, of those present in control cultures without drug. In contrast, the levels of IS6110 DNA and 16S rRNA did not diminish over the same period. Strains which were resistant to either isoniazid or rifampin demonstrated no reduction in 85B mRNA in the presence of the drug to which they were nonresponsive. Quantitative analysis of 85B mRNA offers a potentially useful tool for the rapid determination of M. tuberculosis drug susceptibility and for the monitoring of therapeutic efficacy.
Dynamic Nuclear Polarization with a Rigid Biradical (2009)

Abstract Eine starre Spirobrücke verknüpft zwei 2,2,6,6‐Tetramethylpiperidin‐1‐oxyl(TEMPO)‐Einheiten in einem neuen diradikalischen Polarisierungsmittel für DNP‐Experimente. Die beobachteten NMR‐Signalintensitäten sind 1.4mal größer als für TOTAPOL, ein zuvor beschriebenes Diradikal aus zwei TEMPO‐Einheiten und einer flexiblen Brücke. magnified image
Image-based 3D photography using opacity hulls (2002)

We have built a system for acquiring and displaying high quality graphical models of objects that are impossible to scan with traditional scanners. Our system can acquire highly specular and fuzzy materials, such as fur and feathers. The hardware set-up consists of a turntable, two plasma displays, an array of cameras, and a rotating array of directional lights. We use multi-background matting techniques to acquire alpha mattes of the object from multiple viewpoints. The alpha mattes are used to construct an opacity hull. The opacity hull is a new shape representation, defined as the visual hull of the object with view-dependent opacity. It enables visualization of complex object silhouettes and seamless blending of objects into new environments. Our system also supports relighting of objects with arbitrary appearance using surface reflectance fields, a purely image-based appearance representation. Our system is the first to acquire and render surface reflectance fields under varying illumination from arbitrary viewpoints. We have built three generations of digitizers with increasing sophistication. In this paper, we present our results from digitizing hundreds of models.
ChemInform Abstract: The Rhodium Complex of Bis(diphenylphosphinomethyl)dopamine‐coated Magnetic Nanoparticles as an Efficient and Reusable Catalyst for Hydroformylation of Olefins. (2015)

Abstract A new bis(diphenylphosphinomethyl)dopamine (bpd) ligand is prepared and anchored on the surface of magnetic nanoparticles (MNP).
A 7-μm praseodymium-based solid-state laser (1996)

We report the first demonstration of laser emission from the /sup 3/F/sub 3/ to /sup 3/F/sub 2/ transition in the rare earth praseodymium. This new 7-/spl mu/m solid-state laser operates with an optical efficiency of 2.3% at 293 K and 10% at 150 K using an upconversion pumping mechanism. A discussion of the dynamics in this new laser material is included.
Localized two‐dimensional shift correlated MR spectroscopy of human brain (2001)

A two-dimensional (2D) chemical shift correlated MR spectroscopic (COSY) sequence integrated into a new volume localization technique (90 degrees -180 degrees -90 degrees ) is proposed for whole-body MR spectroscopy (MRS). Using the product operator formalism, a theoretical calculation of the volume localization as well as the coherence transfer efficiencies in 2D MRS is presented. Phantom model solutions were used to test and optimize the efficiency of the proposed sequence. A combination of different MRI transmit/receive RF coils was used: a head MRI coil and a 3" surface coil receive combined with a body coil transmit. The J cross-peaks due to N-acetyl aspartate (NAA), glutamate/glutamine (Glx), myo-inositol (mI), creatine (Cr), choline (Ch), aspartate (Asp), gamma-aminobutyrate (GABA), taurine (Tau), glutathione (GSH), threonine (Thr), and macromolecules (MM) were identified. The cross-peak intensities excited by the proposed 2D sequence were asymmetric with respect to the diagonal peaks. Localized COSY (L-COSY) spectra of cerebral prefrontal and occipital gray/white matter regions in 15 healthy controls are presented. Magn Reson Med 46:58-67, 2001.
Data from Preclinical Development of U3-1784, a Novel FGFR4 Antibody Against Cancer, and Avoidance of Its On-target Toxicity (2023)

<div>Abstract<p>The FGFR4/FGF19 signaling axis is overactivated in 20% of liver tumors and currently represents a promising targetable signaling mechanism in this cancer type. However, blocking FGFR4 or FGF19 has proven challenging due to its physiological role in suppressing bile acid synthesis which leads to increased toxic bile acid plasma levels upon FGFR4 inhibition. An FGFR4-targeting antibody, U3-1784, was generated in order to investigate its suitability as a cancer treatment without major side effects.</p><p>U3-1784 is a high-affinity fully human antibody that was obtained by phage display technology and specifically binds to FGFR4. The antibody inhibits cell signaling by competing with various FGFs for their FGFR4 binding site thereby inhibiting receptor activation and downstream signaling via FRS2 and Erk. The inhibitory effect on tumor growth was investigated in 10 different liver cancer models <i>in vivo</i>. The antibody specifically slowed tumor growth of models overexpressing FGF19 by up to 90% whereas tumor growth of models not expressing FGF19 was unaffected. In cynomolgus monkeys, intravenous injection of U3-1784 caused elevated serum bile acid and liver enzyme levels indicating potential liver damage. These effects could be completely prevented by the concomitant oral treatment with the bile acid sequestrant colestyramine, which binds and eliminates bile acids in the gut. These results offer a new biomarker-driven treatment modality in liver cancer without toxicity and they suggest a general strategy for avoiding adverse events with FGFR4 inhibitors.</p></div>
Components for optical qubits in the radio frequency basis (2004)

We describe a scheme for the encoding and manipulation of single photon qubits in radio frequency sideband modes using standard optical elements. I.
Improving Business Process Quality through Exception Understanding, Prediction, and Prevention (2001)

Business process automation technologies are being increasingly used by many companies to improve the efficiency of both internal processes as well as of e-services offered to customers. In order to satisfy customers and employees, business processes need to be executed with a high and predictable quality. In particular, it is crucial for organizations to meet the Service Level Agreements (SLAs) stipulated with the customers and to foresee as early as possible the risk of missing SLAs, in order to set the right expectations and to allow for corrective actions. In this paper we focus on a critical issue in business process quality: that of analyzing, predicting and preventing the occurrence of exceptions, i.e., of deviations from the desired or acceptable behavior. We characterize the problem and propose a solution, based on data warehousing and mining techniques. We then describe the architecture and implementation of a tool suite that enables exception analysis, prediction, and prevention. Finally, we show experimental results obtained by using the tool suite to analyze internal HP processes. 1. Introduction and
Oral Toxicity of <i>Photorhabdus</i> <i>luminescens</i> W14 Toxin Complexes in <i>Escherichia</i> <i>coli</i> (2001)

Previous attempts to express the toxin complex genes of Photorhabdus luminescens W14 in Escherichia coli have failed to reconstitute their oral toxicity to the model insect Manduca sexta. Here we show that the combination of three genes, tcdA, tcdB, and tccC, is essential for oral toxicity to M. sexta when expression in E. coli is used. Further, when transcription from native toxin complex gene promoters is used, maximal toxicity in E. coli cultures is associated with the addition of mitomycin C to the growth medium. In contrast, the expression of tcdAB (or the homologous tcaABC operon) with no recombinant tccC homolog in a different P. luminescens strain, K122, is sufficient to confer oral toxicity on this strain, which is otherwise not orally toxic. We therefore infer that P. luminescens K122 carries a functional tccC-like homolog within its own genome, a hypothesis supported by Southern analysis. Recombinant toxins from both P. luminescens K122 and E. coli were purified as high-molecular-weight particulate preparations. Transmission electron micrograph (TEM) images of these particulate preparations showed that the expression of tcdAB (either with or without tccC) in E. coli produces visible approximately 25-nm-long complexes with a head and tail-like substructure. These data are consistent with a model whereby TcdAB constitutes the majority of the complex visible under TEM and TccC either is a toxin itself or is an activator of the complex. The implications for the potential mode of action of the toxin complex genes are discussed.
Disparity-to-depth calibration in light field imaging (2016)

We developed two calibration methods for disparity-to-depth mapping in plenoptic imaging. Both approaches can correct for a variety of optical aberrations (e.g., field curvature) in depth estimation from plenoptic data.
Cellular Interactions on Epitaxial Graphene on SiC (0001) Substrates (2011)

An ever-increasing demand for biocompatible materials provides motivation for the development of advanced materials for challenging applications ranging from disease detection to organ function restoration. Carbon-based materials are considered promising candidates because they combine good biocompatibility with high chemical resistance. In this work we present an initial assessment of the biocompatibility of epitaxial graphene on 6H-SiC(0001). We have analyzed the interaction of HaCaT (human keratinocyte) cells on epitaxial graphene and compared it with that on bare 6H-SiC(0001). We have found that for both graphene and 6H-SiC there is evidence of cell-cell and cell substrate interaction which is normally an indication of the biocompatibility of the material.
Efficient Activation and High Mobility of Ion-Implanted Silicon for Next-Generation GaN Devices (2023)

Selective area doping via ion implantation is crucial to the implementation of most modern devices and the provision of reasonable device design latitude for optimization. Herein, we report highly effective silicon ion implant activation in GaN via Symmetrical Multicycle Rapid Thermal Annealing (SMRTA) at peak temperatures of 1450 to 1530 °C, producing a mobility of up to 137 cm2/Vs at 300K with a 57% activation efficiency for a 300 nm thick 1 × 1019 cm−3 box implant profile. Doping activation efficiency and mobility improved alongside peak annealing temperature, while the deleterious degradation of the as-grown material electrical properties was only evident at the highest temperatures. This demonstrates efficient dopant activation while simultaneously maintaining low levels of unintentional doping and thus a high blocking voltage potential of the drift layers for high-voltage, high-power devices. Furthermore, efficient activation with high mobility has been achieved with GaN on sapphire, which is known for having relatively high defect densities but also for offering significant commercial potential due to the availability of cheap, large-area, and robust substrates for devices.
Mixing two monoclonal antibodies yields enhanced affinity for antigen. (1982)

We observed that mixing monoclonal antibodies directed against various epitopes of human chorionic gonadotropin (hCG) can increase the sensitivity of antigen-binding assays. Depending on the antibody pair chosen, the affinity of the mixture was as much as 10-fold higher than either of the monoclonal antibodies assayed separately. Because hCG does not have any repeating sequences, these results do not reflect a change in avidity of an individual antibody. The increased avidity of the mixture can be detected in both solid-phase assays and liquid-phase double antibody radioimmunoassays. This was not a general property of all monoclonal antibodies raised against hCG. Certain antibodies, apparently reacting with the same region of the antigen molecule, do not bind simultaneously and do not result in enhanced affinity when mixed. In addition, certain other pairs of antibodies do not bind cooperatively even though they can bind simultaneously. The mechanism for the increase in affinity depends on the formation of a multicomponent complex. If one of the antibodies of a pair that results in enhanced affinity upon mixing is replaced by its F(ab) fragment, the enhancement is no longer detectable, indicating it is unlikely the enhancement is due to an allosteric effect. Although the F(ab')2 fragment shows some enhancement when mixed with another antibody, it is not as effective as the intact antibody.
Ultrahigh Strength and High Electrical Conductivity Characteristics of Cu-Zr Alloy Wires with Nanoscale Duplex Fibrous Structure (2006)

The cold drawing of cast Cu100−xZrx (x=3, 4 and 5 at%) alloys to the reduction ratio of 99.7% was found to cause simultaneous achievement of ultrahigh tensile strength of 1350 to 1800 MPa and high electrical conductivity of 30 to 45%IACS (International Annealed Copper Standard). The cold-drawn Cu95Zr5 alloy wire has a well-developed fibrous structure of fcc-Cu and tetragonal Cu9Zr2 phases. The volume ratio of the fcc-Cu phase was evaluated to be about 76%. A very high density of internal defects was observed inside the Cu9Zr2 phase in the cold-drawn Cu95Zr5 alloy. The microstructure data suggest that the Cu fibrous phase with high aspect ratios is the origin for the achievement of high electrical conductivity and the well-developed fibrous structure contributes to the high tensile strength. The success of synthesizing the Cu-Zr alloy wire with simultaneously high tensile strength and high electrical conductivity exceeding the best combination of all Cu-based alloys reported up to data is expected to be used as a new type of high-strength and high conductivity material because of some advantages of energy saving, low materials cost and simple production process.
<i>tert</i>-Butylsulfonamide. A New Nitrogen Source for Catalytic Aminohydroxylation and Aziridination of Olefins (1999)

[reaction: see text] The N-chloramine salt of tert-butylsulfonamide has been shown to be an efficient nitrogen source and the terminal oxidant for catalytic aminohydroxylation and aziridination of olefins, resembling closely Chloramine-T by its behavior in these catalytic reactions. The sulfonyl-nitrogen bond in the product or its derivatives is easily cleaved under mild acidic conditions, allowing for facile liberation of the amino group.
<title>Surface-enhanced Raman sensor for trace chemical detection in water</title> (1999)

Surface-enhanced Raman spectroscopy (SERS) promises to be one of the most sensitive methods for chemical detection and in recent years SERS has been used for chemical, biochemical, environmental, and physiological applications. A variety of methods using various media (electrodes, colloids, and substrates) have been successfully developed to enhance Raman signals by six orders of magnitude and more. However, SERS has not become a routine analytical technique because these methods are unable to provide quantitative measurements. This is largely due to the inability to fabricate a sampling medium that provides reversible chemical adsorption, analysis-to-analysis reproducibility, unrestricted solution requirements (reagent concentration and pH) or sample phase (liquid or solid). In an effort to overcome these restrictions, we have developed metal-doped sol-gels to provide surface-enhancement of Raman scattering.
A Chemically Patterned Microfluidic Paper-based Analytical Device (C-µPAD) for Point-of-Care Diagnostics (2017)

A chemically patterned microfluidic paper-based analytical device (C-µPAD) is developed to create fluidic networks by forming hydrophobic barriers using chemical vapor deposition (CVD) of trichlorosilane (TCS) on a chromatography paper. By controlling temperature, pattern size, and CVD duration, optimal conditions were determined by characterizing hydrophobicity, spreading patterns, and flow behavior on various sized fluidic patterns. With these optimal conditions, we demonstrated glucose assay, immunoassay, and heavy metal detection on well-spot C-µPAD and lateral flow C-µPAD. For these assays, standard curves showing correlation between target concentration and gray intensity were obtained to determine a limit of detection (LOD) of each assay. For the glucose assays on both well-spot C-µPAD and lateral flow C-µPAD, we achieved LOD of 13 mg/dL, which is equivalent to that of a commercial glucose sensor. Similar results were obtained from tumor necrosis factor alpha (TNFα) detection with 3 ng/mL of LOD. For Ni detection, a colorimetric agent was immobilized to obtain a stationary and uniform reaction by using thermal condensation coupling method. During the immobilization, we successfully functionalized amine for coupling the colorimetric agent on the C-µPAD and detected as low as 150 μg/L of Ni. These C-µPADs enable simple, rapid, and cost-effective bioassays and environmental monitoring, which provide practically relevant LODs with high expandability and adaptability.
Real-time multi-constellation Precise Point Positioning with integer ambiguity resolution (2015)

The Precise Point Positioning (PPP) technique has been intensively developed in the GNSS community for the last decade. The technique makes use of precise orbit and clock corrections to perform precise positioning for a single receiver. However, the traditional PPP technique does not fix carrier-phase ambiguities to their integers because satellite hardware biases are not eliminated when using data from a single receiver. Additional corrections are needed to form and fix integer ambiguities, and consequently improve the accuracy of positioning. In March 2015 Fugro introduced the G2+ (or G2 Plus) service that provides hardware-bias-like corrections together with orbit and clock corrections for GPS and GLONASS systems. All these corrections are computed in real-time and broadcasted globally to our clients in the field via L-band communication satellites. This paper describes the technology that Fugro has developed and presents some results obtained using the service.