gebhart/patrepeval huggingface dataset:
<i>Medicago truncatula DMI1</i> Required for Bacterial and Fungal Symbioses in Legumes (2004)

Legumes form symbiotic associations with both mycorrhizal fungi and nitrogen-fixing soil bacteria called rhizobia. Several of the plant genes required for transduction of rhizobial signals, the Nod factors, are also necessary for mycorrhizal symbiosis. Here, we describe the cloning and characterization of one such gene from the legume Medicago truncatula. The DMI1 (does not make infections) gene encodes a novel protein with low global similarity to a ligand-gated cation channel domain of archaea. The protein is highly conserved in angiosperms and ancestral to land plants. We suggest that DMI1 represents an ancient plant-specific innovation, potentially enabling mycorrhizal associations.
Bardet-Biedl syndrome in Denmark-report of 13 novel sequence variations in six genes (2010)

Bardet-Biedl syndrome (BBS) is an autosomal recessive disease characterized by retinal dystrophy, polydactyly, obesity, learning disabilities, renal involvement, and male hypogenitalism. BBS is genetically heterogeneous with mutations of 14 genes, accounting for approximately 70% of cases. Triallelic inheritance has been suggested in about 5% of cases. Forty-nine unrelated BBS patients were screened for mutations by DHPLC analysis in BBS1, BBS2, BBS4, BBS6/MKKS, BBS10, and BBS12. The selected genes either account for more than 5% of the mutational load or are commonly reported in triallelic inheritance. Eight patients with only one or no BBS mutation were further investigated by single nucleotide polymorphism (SNP) analysis. In total, mutations were detected in 44 patients. Twenty percent had two mutations in BBS1, 18% in BBS2, 4% in BBS9, 43% in BBS10, and 2% in BBS12. Five patients were heterozygous for a sequence variation in BBS6/MKKS. We found eight patients with three sequence variations in two genes, which could be explained by triallelic inheritance, by the prevalence of heterozygous carriers or the third sequence variations representing rare polymorphisms. All changes found in a second BBS gene were amino acid substitutions. Genotype-phenotype correlations suggest a milder phenotype for BBS1 compared to BBS2 and BBS10, which we ascribe to the hypomorphic p.Met390Arg-mutation.
Physical simulation of long distance and directional wireless channels (2008)

In order to accurately test directional or multiplexed systems in a lab environment, a testbed should simulate both directional wireless channels and propagation delay. Using one or more RF lenses, one can test a radio system that uses switched or adaptively steerable antennas: one side is switched by an ldquoenvironmentrdquo controller, the other by the the discovery and tracking loop of the radio system. True path delay testing can be done by using analog RF-to-optical converters and miles of low-cost, low-loss fiber optics. Apart from verifying latency, this test can also determine if there are issues with ACK or other timeouts: information unavailable by simply attenuating a link to simulate distance.
Preliminary characterization of a novel peptide-Fc-fusion construct for targeting amyloid deposits (2017)

"Preliminary characterization of a novel peptide-Fc-fusion construct for targeting amyloid deposits." Amyloid, 24(sup1), pp. 26–27
Lithography overlay control improvement using patterned wafer geometry for sub-22nm technology nodes (2015)

The semiconductor industry continues to push the limits of immersion lithography through multiple patterning techniques for printing features with critical dimension 20 nm and below. As a result overlay has become one of the critical lithography control parameters impacting device performance and has a stringent budget for yielding at smaller half pitch nodes. Overlay has several sources of errors related to scanner, lens, mask, and wafer. Lithographers have developed both linear and higher order field and wafer models to successfully compensate for the static fingerprints from different sources of error. After the static modeled portion of the fingerprint is removed, the remaining overlay error can be characterized as unstable modeled error or un-modeled error, commonly called uncorrectable residual error. This paper explores the fundamental relationship of overlay to wafer geometry through mechanisms of process-induced contributions to the wafer overlay, categorized as plastic and elastic wafer deformation. Correlation of overlay to local features such as slip lines is proven experimentally. The paper describes methodologies and geometry-induced overlay metrics for the application of wafer geometry to perform overlay feedback and feed forward applications. Feedback applications allow for process development and controlling semiconductor processes through in-line monitoring of wafers. Feed forward applications could include geometrybased corrections to the scanner for compensating non-static wafer geometry related overlay errors, and grouping wafers based on higher-order geometry.
Characterization of a Major Outer-Membrane Antigen of<i>Edwardsiella ictaluri</i> (1991)

Edwardsiella ictaluri is the cause of enteric septicemia of catfish. A monoclonal antibody (MAb AA224) was used to identify a specific and predominant outer-membrane antigen of E. ictaluri. The MAb AA224 was produced by conventional cell fusion technology with spleen cells from mice immunized with an affinity-purified antigen. The affinity-purified antigen was obtained by immunoaffinity chromatography of an E. ictaluri extract with immunoaffinity purified immunoglobin from sera of channel catfish Ictalurus punctatus immune to E. ictaluri as a result of natural infection. The immunoaffinity-purified antigen was used for immunization and identification of the hybridoma producing MAb AA224 by enzyme-linked immunosorbent assay. The predominant antigen was purified by immunoaffinity chromatography with MAb AA224 as the immunoadsorbent. Immunoblotting and high-pressure liquid chromatography were used to determine that the relative sizes of the predominant antigens are 60 and 36 kilodaltons. Immunoelectron microscopy with MAb AA224 conjugated with colloidal gold localized the predominant antigen on the surface of the outer membrane of E. ictaluri
Advancements in automatic marking with range pattern matching (2013)

In previous work, an approach was detailed using CATS-MRCC-RPM, where new pattern matching functionality is used to find locations on a jobdeck that are suitable for mark placements and ultimately, metrology tool measurement locations. These locations are found by first creating pattern definitions. The defined patterns are passed to the CATS MRCC-RPM match algorithm which in turn outputs all found locations that match the description. In that previous work, the pattern definitions, also known as mark templates, had several limitations. For example, each template could hold only one mark placed at its center, and had to be symmetrical. This was considered to be severely limiting in nature and not production worthy for advanced mask manufacturing. This paper builds on top of the previous one in various ways, extends the possibilities, and provides mask makers unlimited options for extending metrology automation. Mark templates are expanded upon to hold multiple marks at different offsets from its center, and even of different types. Each template can be symmetrical or asymmetrical, and yet all the marks on it can still be correctly placed by taking advantage of match orientation information during the Classification step. Placement of other mark types beyond basic ones is also explored, such as Arbitrary Area. Lastly, the classification step is an enhancement process that thoroughly manages the use of chip/mark information. The result makes use of the output of JD MRC (jobdeck MRC) which executes RPM on jobdecks by chip in order to reduce redundant chips processing, rather than search all chip placements by extension.
Quinoxaline protects zebrafish lateral line hair cells from cisplatin and aminoglycosides damage (2018)

Hair cell (HC) death is the leading cause of hearing and balance disorders in humans. It can be triggered by multiple insults, including noise, aging, and treatment with certain therapeutic drugs. As society becomes more technologically advanced, the source of noise pollution and the use of drugs with ototoxic side effects are rapidly increasing, posing a threat to our hearing health. Although the underlying mechanism by which ototoxins affect auditory function varies, they share common intracellular byproducts, particularly generation of reactive oxygen species. Here, we described the therapeutic effect of the heterocyclic compound quinoxaline (Qx) against ototoxic insults in zebrafish HCs. Animals incubated with Qx were protected against the deleterious effects of cisplatin and gentamicin, and partially against neomycin. In the presence of Qx, there was a reduction in the number of TUNEL-positive HCs. Since Qx did not block the mechanotransduction channels, based on FM1-43 uptake and microphonic potentials, this implies that Qx's otoprotective effect is at the intracellular level. Together, these results unravel a novel therapeutic role for Qx as an otoprotective drug against the deleterious side effects of cisplatin and aminoglycosides, offering an alternative option for patients treated with these compounds.
Elucidation of a Carotenoid Biosynthesis Gene Cluster Encoding a Novel Enzyme, 2,2′-β-Hydroxylase, from <i>Brevundimonas</i> sp. Strain SD212 and Combinatorial Biosynthesis of New or Rare Xanthophylls (2005)

A carotenoid biosynthesis gene cluster mediating the production of 2-hydroxyastaxanthin was isolated from the marine bacterium Brevundimonas sp. strain SD212 by using a common crtI sequence as the probe DNA. A sequence analysis revealed this cluster to contain 12 open reading frames (ORFs), including the 7 known genes, crtW, crtY, crtI, crtB, crtE, idi, and crtZ. The individual ORFs were functionally analyzed by complementation studies using Escherichia coli that accumulated various carotenoid precursors due to the presence of other bacterial crt genes. In addition to functionally identifying the known crt genes, we found that one (ORF11, named crtG) coded for a novel enzyme, carotenoid 2,2'-beta-hydroxylase, which showed intriguingly partial homology with animal sterol-C5-desaturase. When this crtG gene was introduced into E. coli accumulating zeaxanthin and canthaxanthin, the resulting transformants produced their 2-hydroxylated and 2,2'-dihydroxylated products which were structurally novel or rare xanthophylls, as determined by their nuclear magnetic resonance and high-performance liquid chromatography/photodiode array detector/atmospheric pressure chemical ionization mass spectrometry spectral data. The new carotenoid produced was suggested to have a strong inhibitory effect on lipid peroxidation.
Reconstructable geometry shadow maps (2008)

Traditional shadow maps [Williams 1978] suffer from two main issues, aliasing errors and depth bias problems. We present a novel algorithm, the reconstructable geometry shadow maps (RGSM), as a solution to both problems. It is capable of producing sub-pixel depth accuracy in the camera view and thus reduces two categories of aliasing errors, the perspective aliasing errors and the projective aliasing errors. This goal is achieved by using the depth values faithfully reconstructed from the corresponding occluding triangles instead of taking point samples from the depth map. The experimental result also shows RGSM requires a much smaller depth bias value than other shadow mapping techniques.
Transverse motion of single particles in accelerators (1989)

Any accelerator must have focusing elements, usually magnetic quadrupoles, which hold individual particles close to an ideal central orbit. The purpose of this chapter is to analyse the transverse motion of particles and beams in such systems, with particular emphasis on circular machines. A particle not precisely on the central orbit is subject to a restoring force tending to reduce the deviation and, as a result, the particle oscillates around the central orbit. These oscillations are usually called betatron oscillations when they occur in a circular machine, and we will use the same terminology even for motion in any beam transport system. (AIP)
ChemInform Abstract: AROMATIC AMIDINES. COMPARISON OF THEIR ABILITY TO BLOCK RESPIRATORY SYNCYTIAL VIRUS INDUCED CELL FUSION AND TO INHIBIT PLASMIN, UROKINASE, THROMBIN, AND TRYPSIN (1983)

Abstract (V).
System for interstitial photodynamic therapy with online dosimetry: first clinical experiences of prostate cancer (2010)

The first results from a clinical study for Temoporfin-mediated photodynamic therapy (PDT) of low-grade (T1c) primary prostate cancer using online dosimetry are presented. Dosimetric feedback in real time was applied, for the first time to our knowledge, in interstitial photodynamic therapy. The dosimetry software IDOSE provided dose plans, including optical fiber positions and light doses based on 3-D tissue models generated from ultrasound images. Tissue optical property measurements were obtained using the same fibers used for light delivery. Measurements were taken before, during, and after the treatment session. On the basis of these real-time measured optical properties, the light-dose plan was recalculated. The aim of the treatment was to ablate the entire prostate while minimizing exposure to surrounding organs. The results indicate that online dosimetry based on real-time tissue optical property measurements enabled the light dose to be adapted and optimized. However, histopathological analysis of tissue biopsies taken six months post-PDT treatment showed there were still residual viable cancer cells present in the prostate tissue sections. The authors propose that the incomplete treatment of the prostate tissue could be due to a too low light threshold dose, which was set to 5 J∕cm2.
AUTOMATED INDUCTION THERMOGRAPHY OF GENERATOR COMPONENTS (2010)

Using Active Thermography defects such as cracks can be detected fast and reliably. Choosing from a wide range of excitation techniques the method can be adapted to a number of tasks in non‐destructive evaluation. Induction thermography is ideally suited for testing metallic components for cracks at or close to the surface. In power generation a number of components are subjected to high loads and stresses—therefore defect detection is crucial for a safe operation of the engines. Apart from combustion turbines this also applies to generators: At regular inspection intervals even small cracks have to be detected to avoid crack growth and consequently failure of the component. As an imaging technique thermography allows for a fast 100% testing of the complete surface of all relevant parts. An automated setup increases the cost effectiveness of induction thermography significantly. Time needed to test a single part is reduced, the number of tested parts per shift is increased, and cost for testing is reduced significantly. In addition, automation guarantees a reliable testing procedure which detects all critical defects. We present how non‐destructive testing can be automated using as an example an industrial application at the Siemens sector Energy, and a new induction thermography setup for generator components.
Fingerprint enhancement using a multispectral sensor (2005)

The level of performance of a biometric fingerprint sensor is critically dependent on the quality of the fingerprint images. One of the most common types of optical fingerprint sensors relies on the phenomenon of total internal reflectance (TIR) to generate an image. Under ideal conditions, a TIR fingerprint sensor can produce high-contrast fingerprint images with excellent feature definition. However, images produced by the same sensor under conditions that include dry skin, dirt on the skin, and marginal contact between the finger and the sensor, are likely to be severely degraded. This paper discusses the use of multispectral sensing as a means to collect additional images with new information about the fingerprint that can significantly augment the system performance under both normal and adverse sample conditions. In the context of this paper, "multispectral sensing" is used to broadly denote a collection of images taken under different illumination conditions: different polarizations, different illumination/detection configurations, as well as different wavelength illumination. Results from three small studies using an early-stage prototype of the multispectral-TIR (MTIR) sensor are presented along with results from the corresponding TIR data. The first experiment produced data from 9 people, 4 fingers from each person and 3 measurements per finger under "normal" conditions. The second experiment provided results from a study performed to test the relative performance of TIR and MTIR images when taken under extreme dry and dirty conditions. The third experiment examined the case where the area of contact between the finger and sensor is greatly reduced.
Enhanced identification technique for dynamic nonlinear power amplifiers modeling using twin-nonlinear two-box structures (2017)

This paper presents an enhanced identification technique for the behavioral modeling of radiofrequency power amplifiers using twin-nonlinear two-box structures. The proposed technique intentionally uses low nonlinearity order in the memoryless block and allows for performance degradation in the first box of the model. This helps reducing the coefficients dispersion of the second box, and therefore improves the numerical stability of the identification process. The model's accuracy is then recovered by adding the memory polynomial function of the twin-nonlinear two-box model. Experimental validation of the proposed technique shows a model size reduction of approximately 50% without any noticeable performance degradation.
Implementation and Experimental Verification of Flow Rate Control Based on Differential Flatness in a Tilting-Ladle-Type Automatic Pouring Machine (2019)

In this paper, we study an advanced pouring control system using a tilting-ladle-type automatic pouring machine. In such a machine, it is difficult to precisely pour the molten metal into the pouring basin of the mold, as the outflow from the ladle can be indirectly controlled by controlling its tilt. Therefore, model-based pouring control systems have been developed as a part of conventional studies to solve this problem. In the results of a recent study, the efficacy of a pouring flow rate control system based on differential flatness has been verified, by performing a simulation. In this study, we apply the flow rate control system based on differential flatness to a tilting-ladle-type automatic pouring machine, using experiments to verify the efficacy of the flow rate control system in suppressing any disturbances. In these experiments, the tracking performance using the developed flow rate control system was better than the performance obtained using a conventional feed-forward-type flow rate control system.
Piezoelectric and Ferroelectric Properties of the Modified SrBi 2 Nb 2 O 9 Ceramics (2002)

Piezoelectric properties of Bismuth layer compound ferroelectrics SrBi 2 Nb 2 O 9 (SBN) were investigated. Their piezoelectric properties were evaluated from m 150°C to 450°C. Good resonant characteristics were obtained throughout the whole temperature range. Temperature coefficients of the resonance frequency (TCf's) are small, around 20ppm/°C. These good resonant characteristics, especially the good TCf's, are strongly related to the elastic anomaly observed in the temperature range approximately between 250°C and 350°C. When Ba ion substitutes Sr in SBN, the elastic anomaly becomes smoother, and the TCf decreases. SBN also shows a relaxor characteristics with increasing the Ba substitution.
Interstitial Drug Therapy for Brain Tumors: A Case Study (1990)

A novel method of delivering cancer chemotherapeutic drugs to the brain in concentrations higher than those achievable by standard routes of administration has been developed. The drug was incorporated into wafers (trademarked BIODEL®) of a biodegradable, biocompatible polymer. The drug chosen for initial studies was BCNU (carmustine, 1,3-bis[2-chloroethyl]-1-nitrosourea), the most widely used chemotherapeutic agent for the disease to be treated, glioblastoma multiforme, a universally fatal form of brain cancer. Preclinical studies in a number of species demonstrated the safety of this material implanted either directly into the brain or subcutaneously. Efficacy studies in rats demonstrated that implanting BIODEL® wafers containing BCNU either at the time of tumor implantation or after 4 days of tumor growth could significantly prolong survival of the animals, while greatly diminishing side effects of the BCNU therapy.The safety of this material implanted into these patients during a Phase I/II study has been demonstrated. No systemic side effects of doses of BCNU which would produce marked effects on the hemopoeitic system when injected intravenously have been observed. Further studies, designed to measure the efficacy of this approach to the treatment of brain cancer in a multicentered Phase III clinical trial in the United States and Canada, are currently underway.
Mind the gaps (2009)

One-Class Collaborative Filtering (OCCF) is a task that naturally emerges in recommender system settings. Typical characteristics include: Only positive examples can be observed, classes are highly imbalanced, and the vast majority of data points are missing. The idea of introducing weights for missing parts of a matrix has recently been shown to help in OCCF. While existing weighting approaches mitigate the first two problems above, a sparsity preserving solution that would allow to efficiently utilize data sets with e.g., hundred thousands of users and items has not yet been reported. In this paper, we study three different collaborative filtering frameworks: Low-rank matrix approximation, probabilistic latent semantic analysis, and maximum-margin matrix factorization. We propose two novel algorithms for large-scale OCCF that allow to weight the unknowns. Our experimental results demonstrate their effectiveness and efficiency on different problems, including the Netflix Prize data.
Temporally and spectrally multiplexed single photon source using quantum feedback control for scalable photonic quantum technologies (2018)

Current proposals for scalable photonic quantum technologies require on-demand sources of indistinguishable single photons with very high efficiency. Even with recent progress in the field there is still a significant gap between the requirements and state of the art performance. Here, we propose an on-chip source of time-multiplexed, heralded photons. Using quantum feedback control on a photon storage cavity with an optimized driving protocol, we estimate an on-demand efficiency of 99% and unheralded loss of order 1%, assuming high efficiency detectors and intrinsic cavity quality factors of order 10 8 . We further explain how temporal-and spectral-multiplexing can be used in parallel to significantly reduce device requirements if single photon frequency conversion is possible with efficiency in the same range of 99%.