gebhart/patrepeval huggingface dataset:
High‐Specificity Affinity Reagents for the Detection of Glycan Sialylation (2018)

Glycans have distinct properties that make them appealing as disease biomarker targets, and novel highly specific reagents are essential to overcome current limitations in the discovery and exploitation of disease‐related glycans. Lectenz ® Bio is engineering glycan‐processing enzymes into catalytically inactive, high affinity glycan binding reagents with tunable specificities. These novel lectin‐like, enzyme‐derived reagents called Lectenz ® are being developed for a variety of glycan detection and enrichment applications including affinity chromatography, Western blot, and immunohistochemistry. The conversion of such enzymes into affinity reagents is facilitated by computationally‐guided directed evolution. Using site‐directed mutagenesis and yeast display selection of a site‐saturation mutagenesis library, multiple Lectenz ® candidates can be identified. Here we present two novel sialic acid recognizing Lectenz ® engineered from a sialidase enzyme: 1) the pan‐specific sialic acid reagent, Sia‐PS1 Lectenz ® , which recognizes sialic acid in a linkage independent manner; and 2) the Sia‐3S1 Lectenz ® , which is specific for α2,3‐linked sialoglycans. The data demonstrate that the Sia‐PS1 Lectenz ® reagent recognizes glycans terminating in α2,3‐, α2,6‐, and α2,8‐linked sialic acid sequences, but not Gal‐terminating sequences. With the Sia‐3S1 Lectenz ® , we demonstrate binding to Neu5Acα2,3Galβ1,4Glc, but not Neu5Acα2,6 Galβ1,4Glc or Galβ1,4Glc. Support or Funding Information National Institutes of Health (R41GM113351) This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Multicusp ion source with external rf antenna for production of protons (2004)

Proton beams are needed in neutral-beam injection for diagnostic development of an internal magnetic field measurement. High proton fraction, low axial energy spread, current density in excess of 30 mA/cm2, and a parallel ion beam with cw operation are the requirements for the ion source/extraction system. A multicusp-type ion source with an external rf antenna was constructed at Lawrence Berkeley National Laboratory. A proton fraction of 85% and proton current density of 32 mA/cm2 were achieved at 1.8 kW of rf power. Plasma parameters were measured with a rf compensated Langmuir probe.
Peptides of a Novel<i>Mycobacterium tuberculosis</i>–Specific Cell Wall Protein for Immunodiagnosis of Tuberculosis (2009)

The sequencing of the Mycobacterium tuberculosis genome revealed the existence of several genes encoding novel proteins with unknown functions, one of which is the proline-threonine repetitive protein (PTRP; Rv0538). Genomic studies of various mycobacterial species and M. tuberculosis clinical isolates demonstrate that ptrp is specific to the M. tuberculosis complex and ubiquitous in clinical isolates. Enzyme-linked immunosorbent assay, Western blot analysis, and electron microscopic evaluation of M. tuberculosis subcellular fractions and intact bacteria confirm that PTRP is a cell wall protein. Antibodies to PTRP are present in serum specimens from human immunodeficiency virus (HIV)-negative, tuberculosis (TB)-positive and HIV-positive, TB-positive patients but not purified protein derivative (PPD)-negative or PPD-positive healthy control subjects, demonstrating its diagnostic potential. Epitope mapping of PTRP delineated 4 peptides that can identify >80% of sputum smear-positive and >50% of smear-negative, HIV-negative, TB-positive patients and >80% of HIV-positive, TB-positive patients. These results demonstrate that immunodominant epitopes of carefully selected M. tuberculosis-specific proteins can be used to devise a simple peptide-based serodiagnostic test for TB.
Friction Increase due to Roughness of Ship Hull Paint (2013)

IMO adopted a revision of MARPOL Annex VI to establish the Energy Efficiency Design Index (EEDI) for new build ships in July 2011. The target EEDI will be tightened incrementally until 2025. The ship hull roughness is one of the most important factors that affect ship resistance and efficiency. In this study, friction measurements of cylinders painted with antifouling paint were conducted using double rotating cylinder equipment. Some antifouling paints showed lower Rz and higher RSm values, thus resulting in lower Friction Increasing Ratios (FIR) of currently available antifouling paints. Actual ship hull surface roughness is measured using a roughness analyzer that can measure only Rz at a standard length of 50mm. However, the Rz value alone does not provide enough information to predict friction. Therefore, the replicate method was developed in order to analyze the hull roughness parameters. Roughness analysis using both roughness amplitude and wave length parameters is shown to be very useful for predicting more accurately the ships’ friction resistance.
High photo-electrochemical activity of thylakoid–carbon nanotube composites for photosynthetic energy conversion (2013)

Spinach thylakoids were immobilized onto multiwalled carbon nanotubes using a molecular tethering chemistry. The resulting thylakoid–carbon nanotube composites showed high photo-electrochemical activity under illumination. Multiple membrane proteins have been observed to participate in direct electron transfer with the electrode, resulting in the generation of photocurrents, the first of its kind reported for natural photosynthetic systems. Upon inclusion of a mediator, the photo-activity was enhanced. The major contributor to the photocurrent was the light-induced water oxidation reaction at the photosystem II complex. The thylakoid–MWNT composite electrode yielded a maximum current density of 68 μA cm−2 and a steady state current density of 38 μA cm−2, which are two orders of magnitude larger than previously reported for similar systems. The high electrochemical activity of the thylakoid–MWNT composites has significant implications for both photosynthetic energy conversion and photofuel production applications. A fuel cell type photosynthetic electrochemical cell developed using a thylakoid–MWNT composite anode and laccase cathode produced a maximum power density of 5.3 μW cm−2, comparable to that of enzymatic fuel cells. The carbon based nanostructured electrode has the potential to serve as an excellent immobilization support for photosynthetic electrochemistry based on the molecular tethering approach as demonstrated in this work.
Distribution of an antigenically related iron-regulated protein among the Neisseria spp (1986)

Several iron-regulated proteins of Neisseria gonorrhoeae have been reported. One of these, a 37,000-molecular-weight protein (37K protein), appears to be common to all gonococcal isolates. Recently, the occurrence of a similar protein has also been noted in N. meningitidis. The gonococcal 37K protein has been purified and used to produce both rabbit monospecific antiserum and murine monoclonal antibodies. Using these antibody reagents, we analyzed 57 strains from nine species of Neisseria and the closely related organism Branhamella catarrhalis for the presence of proteins antigenically related to the gonococcal 37K protein. Strains grown on medium with low iron content were probed for antigenic reactivity by Western blot techniques and an enzyme-linked immunosorbent assay. Proteins which cross-reacted with the rabbit monospecific antiserum were designated as AgR-37K proteins. The data indicated that the AgR-37K proteins were conserved among the 40 strains of N. gonorrhoeae, N. meningitidis, N. lactamica, and N. cinerea tested. Seventeen strains from other species of Neisseria and Branhamella did not express AgR-37K proteins with the exception of one N. subflava isolate. All AgR-37K proteins appeared to be regulated by the amount of available iron in the growth medium. Murine monoclonal antibodies were used to probe the antigenic heterogeneity of the AgR-37K proteins from different Neisseria spp. Two of seven monoclonal antibodies were broadly cross-reactive, recognizing the AgR-37K proteins from all species examined. The remaining five monoclonal antibodies were more discriminating, recognizing the AgR-37K proteins from certain species. The antigenic conservation of these AgR-37K proteins, particularly among the pathogenic members of the genus Neisseria, may imply that these proteins serve a common function in pathogenicity.
Magnesium alterations and pharmacokinetic data in gallium-treated lung cancer patients. (1989)

The dose of gallium chloride required to inhibit tumor growth after oral and chronic administration depends on the stage of the cancer disease and of the type of metastases. A dose regimen of 800 mg/24 h of gallium chloride will provide serum gallium concentrations greater than or equal to 600 micrograms/l in lung cancer patients with a small and limited disease. A dose of 1,400 mg/24 h is well tolerated in metastatic patients but may not be high enough to reach the desired serum gallium concentrations especially in patients with bone metastases. Radiotherapy and/or a chemotherapy will permit one to increase the serum gallium concentrations and the tumor gallium uptake by reducing the volume of the tumor. After chronic, oral administration of gallium a decrease in RBC Mg is noted. To avoid the Mg deficiency, the treatment must not be interrupted and may perhaps be decreased with care and slowly without resulting in a decrease of the serum gallium concentrations provided the treatment has been prolonged over a sufficient time to enable one to induce intratumor biological modifications and a decrease in the number of the malignant cells. Acute pharmacokinetic data are related to the histologic type of the tumor and may not be used to predict the serum gallium concentrations after chronic administration. The serum gallium concentrations required to inhibit the tumor growth may be higher in small cell lung carcinomas than in nonsmall cell lung carcinomas. Frequent Mg and Ga blood determinations are necessary to manage effective gallium treatment.
Quantum cascade lasers (2019)

In this chapter, we present a brief overview of the QCL technology with an emphasis on the commercially important 3 μm to 12 μm spectral region covering the infrared fingerprint spectral region and the two infrared atmospheric windows (3 to 5 μm and 8 to 12 μm). Specifically, laser core design, waveguide design, and various aspects of mode control for QCLs are discussed below.
ChemInform Abstract: Novel Inhibitors of Nucleoside Triphosphate Diphosphohydrolases: Chemical Synthesis and Biochemical and Pharmacological Characterizations. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Patient Characteristics, Outcomes, and Effects of Dapagliflozin According to the Duration of Heart Failure: A Prespecified Analysis of the DELIVER Trial (2023)

gov; Unique identifier: NCT03619213.
Uniaxial strain relaxation on ultra-thin strained-Si directly on insulator (SSDOI) substrates (2006)

Uniaxial strain relaxation of ultra-thin biaxial-tensile SSDOI is realized by ion-implant amorphization and solid phase epitaxy (II/SPE). The selective full amorphization in the thin SSDOI region, between raised source/drain (RSD) and channel, induces uniaxial strain relaxation in the channel. The SSDOI uniaxial strain relaxation enhances PFETs drive current by more than 20%
Supercritical Fluid Cleaning of Banknotes (2013)

With nearly 150 billion new banknotes being manufactured and printed every year around the world, the replacing of unfit currency is approaching $10 billion annually. In addition, central banks must also deal with the environmental challenge of annually disposing of nearly 150,000 tons worth of notes unfit for recirculation. Seminal work by the De Nederlandsche Bank (DNB) has identified that soiling is primarily a yellowing of the notes due to the accumulation of oxidized sebum. We show that supercritical CO2 (SCCO2) can be effectively utilized to remove sebum and other oils and contaminants, including common bacterial colonies, from both paper and polymer banknotes without destroying the costly and sophisticated security features employed by central banks to prevent counterfeiting. SCCO2 cleaning at 60°C and 5000 psi was shown to be effective in cleaning conventional straps of 100 banknotes, extracting nearly 4% of the initial strap weight. Measurements of note soiling distributions on a banknote sorting machine running at 10 banknotes per second showed a significant shift in soiling levels after cleaning, supporting the claim that processing of SCCO2-cleaned notes would result in significantly fewer notes being classified as unfit due to soiling and shredded.
Thermal-defocusing/scattering optical limiter (1994)

We recently described1,2 a passive broadband optical limiter that exhibited exceptional limiting performance, yet relied only on a refractive thermal nonlinearity for its operation. That optical limiter employed f/5 defocusing optics and a broadband absorbing dye, nigrosin, dissolved in a solvent, carbon disulfide (CS2), having a large thermal figure of merit. Following the absorption of an intense light pulse by the nigrosin dye, rapid nonradiative relaxation results in strong, localized heating of the CS2 solution, leading to thermal defocusing and aberration of the beam. As a result, light is deflected outside of the light collection cone defined by the f/5 optics, thereby limiting the energy transmitted to the detector. The figure of merit3 of that limiter, defined as the product of the linear transmission and the ratio of the incident energy at damage to the transmitted energy at damage, was 25.
Spatial-phase locking with shaped-beam lithography (2003)

Spatial-phase-locked electron-beam lithography is a method of precisely locating pattern elements on a substrate by providing real-time feedback of the beam’s location by means of a fiducial grid located on the substrate surface. Previously, this technique has been demonstrated in Gaussian-beam systems, in one and two dimensions. In this note we propose a method of extending the spatial-phase-locking concept to a vector shaped-beam architecture. In the proposed method, an image of a screen grid is superimposed on the projected shape, and this grid image is dithered in X and Y to provide a periodic signal whose phase can be interpreted to determine the position of the projected shape relative to the fiducial grid.
iX-BSP: Incremental Belief Space Planning (2021)

Deciding what's next? is a fundamental problem in robotics and Artificial Intelligence. Under belief space planning (BSP), in a partially observable setting, it involves calculating the expected accumulated belief-dependent reward, where the expectation is with respect to all future measurements. Since solving this general un-approximated problem quickly becomes intractable, state of the art approaches turn to approximations while still calculating planning sessions from scratch. In this work we propose a novel paradigm, Incremental BSP (iX-BSP), based on the key insight that calculations across planning sessions are similar in nature and can be appropriately re-used. We calculate the expectation incrementally by utilizing Multiple Importance Sampling techniques for selective re-sampling and re-use of measurement from previous planning sessions. The formulation of our approach considers general distributions and accounts for data association aspects. We demonstrate how iX-BSP could benefit existing approximations of the general problem, introducing iML-BSP, which re-uses calculations across planning sessions under the common Maximum Likelihood assumption. We evaluate both methods and demonstrate a substantial reduction in computation time while statistically preserving accuracy. The evaluation includes both simulation and real-world experiments considering autonomous vision-based navigation and SLAM. As a further contribution, we introduce to iX-BSP the non-integral wildfire approximation, allowing one to trade accuracy for computational performance by averting from updating re-used beliefs when they are "close enough". We evaluate iX-BSP under wildfire demonstrating a substantial reduction in computation time while controlling the accuracy sacrifice. We also provide analytical and empirical bounds of the effect wildfire holds over the objective value.
Dilated FCN for Multi-Agent 2D/3D Medical Image Registration (2018)

2D/3D image registration to align a 3D volume and 2D X-ray images is a challenging problem due to its ill-posed nature and various artifacts presented in 2D X-ray images. In this paper, we propose a multi-agent system with an auto attention mechanism for robust and efficient 2D/3D image registration. Specifically, an individual agent is trained with dilated Fully Convolutional Network (FCN) to perform registration in a Markov Decision Process (MDP) by observing a local region, and the final action is then taken based on the proposals from multiple agents and weighted by their corresponding confidence levels. The contributions of this paper are threefold. First, we formulate 2D/3D registration as a MDP with observations, actions, and rewards properly defined with respect to X-ray imaging systems. Second, to handle various artifacts in 2D X-ray images, multiple local agents are employed efficiently via FCN-based structures, and an auto attention mechanism is proposed to favor the proposals from regions with more reliable visual cues. Third, a dilated FCN-based training mechanism is proposed to significantly reduce the Degree of Freedom in the simulation of registration environment, and drastically improve training efficiency by an order of magnitude compared to standard CNN-based training method. We demonstrate that the proposed method achieves high robustness on both spine cone beam Computed Tomography data with a low signal-to-noise ratio and data from minimally invasive spine surgery where severe image artifacts and occlusions are presented due to metal screws and guide wires, outperforming other state-of-the-art methods (single agent-based and optimization-based) by a large margin.
Constant frequency pulsed phase-locked-loop instrument for measurement of ultrasonic velocity (1991)

A new instrument based on a constant frequency pulsed phase-locked-loop (CFPPLL) concept has been developed to accurately measure the ultrasonic wave velocity in liquids and changes in ultrasonic wave velocity in solids and liquids. An analysis of the system shows that it is immune to many of the frequency-dependent effects that plague other techniques including the constant phase shifts of reflectors placed in the path of the ultrasonic wave. Measurements of the sound velocity in ultrapure water are used to confirm the analysis. The results are in excellent agreement with values from the literature, and establish that the CFPPLL provides a reliable, accurate way to measure velocities, as well as for monitoring small changes in velocity without the sensitivity to frequency-dependent phase shifts common to other measurement systems. The estimated sensitivity to phase changes is better than a few parts in 107.
Ovarian failure in ataxia with oculomotor apraxia type 2 (2007)

Ataxia with oculomotor apraxia type 2 (AOA2) is an autosomal recessive disorder associated with mutations in the Senataxin (SETX) gene. Clinical manifestations (ataxia, peripheral neuropathy, oculomotor apraxia) of this disease have previously been limited to the nervous system. We describe a patient homozygous for a novel mutation of SETX who manifested not only ataxia but also ovarian failure.
Multidimensional Flash Codes (2009)

Flash memory is a non-volatile computer memory comprised of blocks of cells, wherein each cell can take on q different levels corresponding to the number of electrons it contains. Increasing the cell level is easy; however, reducing a cell level forces all the other cells in the same block to be erased. This erasing operation is undesirable and therefore has to be used as infrequently as possible. We consider the problem of designing codes for this purpose, where k bits are stored using a block of n cells with q levels each. The goal is to maximize the number of bit writes before an erase operation is required. We present an efficient construction of codes that can store an arbitrary number of bits. Our construction can be viewed as an extension to multiple dimensions of the earlier work of Jiang and Bruck, where single-dimensional codes that can store only 2 bits were proposed.
A review of dielectric optical metasurfaces for wavefront control (2018)

Abstract During the past few years, metasurfaces have been used to demonstrate optical elements and systems with capabilities that surpass those of conventional diffractive optics. Here, we review some of these recent developments, with a focus on dielectric structures for shaping optical wavefronts. We discuss the mechanisms for achieving steep phase gradients with high efficiency, simultaneous polarization and phase control, controlling the chromatic dispersion, and controlling the angular response. Then, we review applications in imaging, conformal optics, tunable devices, and optical systems. We conclude with an outlook on future potentials and challenges that need to be overcome.
Geometric studies on variable radius spiral cone‐beam scanning (2004)

The goal is to perform geometric studies on cone-beam CT scanning along a three-dimensional (3D) spiral of variable radius. First, the background for variable radius spiral cone-beam scanning is given in the context of electron-beam CT/micro-CT. Then, necessary and sufficient conditions are proved for existence and uniqueness of PI lines inside the variable radius 3D spiral. These results are necessary steps toward exact cone-beam reconstruction from a 3D spiral scan of variable radius, adapting Katsevich's formula for the standard helical cone-beam scanning. It is shown in the paper that when the longitudinally projected planar spiral is not always convex toward the origin, the PI line may not be unique in the envelope defined by the tangents of the spiral. This situation can be avoided by using planar spirals whose curvatures are always positive. Using such a spiral, a longitudinally homogeneous region inside the corresponding 3D spiral is constructed in which any point is passed by one and only one PI line, provided the angle omega between planar spiral's tangent and radius is bounded by [omega - 90 degrees] < or = < epsilon for some positive epsilon < or = 32.48 degrees. If the radius varies monotonically, this region is larger and one may allow epsilon < or = 51.85 degrees. Examples for 3D spirals based on logarithmic and Archimedean spirals are given. The corresponding generalized Tam-Danielsson detection windows are also formulated.
Method for stimulating well production. [aqueous acid solution containing sulfonated ethoxylated aliphatic hydrocarbon] (1974)

A method is given of increasing the production of fluids from a subterranean fluid-bearing formation having present therein acid-soluble components comprising injecting down the well bore into formation under a pressure greater than the formation pressure, an aqueous acidic solution containing from about 0.5 to about 28 percent by weight of a mineral acid having a compound therein in an amount of from about 0.005 percent to about 2 percent by weight, said compound being a water soluble sulfonated, ethoxylated compound, maintaining said solution in contact with the formation and production equipment for a time sufficient for the acid component to chemically react with the acid-soluble components of the formation to etch passageways therethrough thereby increasing substantially the flow capacity of the said subterranean formation and whereby said sulfonated, ethoxylated compound component is effective to prevent the formation of insoluble calcium compounds or the precipitation of calcium carbonate from the acid-spent solution.