gebhart/patrepeval huggingface dataset:
Conversion of nicotine to nornicotine in <i>Nicotiana tabacum</i> is mediated by CYP82E4, a cytochrome P450 monooxygenase (2005)

Nornicotine is a secondary tobacco alkaloid that is produced by the N-demethylation of nicotine. Nornicotine production and accumulation in tobacco are undesirable because nornicotine serves as the precursor in the synthesis of the well characterized carcinogen N'-nitrosonornicotine during the curing and processing of tobacco. Although nornicotine is typically a minor alkaloid in tobacco plants, in many tobacco populations a high percentage of individuals can be found that convert a substantial proportion of the nicotine to nornicotine during leaf senescence and curing. We used a microarray-based strategy to identify genes that are differentially regulated between closely related tobacco lines that accumulate either nicotine (nonconverters) or nornicotine (converters) as the predominant alkaloid in the cured leaf. These experiments led to the identification of a small number of closely related cytochrome P450 genes, designated the CYP82E2 family, whose collective transcript levels were consistently higher in converter versus nonconverter tobacco lines. RNA interference-induced silencing of the CYP82E2 gene family suppressed the synthesis of nornicotine in strong converter plants to levels similar to that observed in nonconverter individuals. Although each of the six identified members of the P450 family share >90% nucleotide sequence identity, sense expression of three selected isoforms revealed that only one (CYP82E4v1) was involved in the conversion of nicotine to nornicotine. Yeast expression analysis revealed that CYP82E4v1 functions as a nicotine demethylase. Identification of the gene(s) responsible for nicotine demethylation provides a potentially powerful tool toward efforts to minimize nornicotine levels, and thereby N'-nitrosonornicotine formation, in tobacco products.
A Solver for Estimating Range-Resolved Beam Attenuation Coefficient from In-Water LiDAR Waveforms (2018)

The beam attenuation coefficient (c) is a critical optical property for ecosystem models and military operations. Time-resolved waveforms produced by remotely located LiDAR (Light detection and ranging) backscattering systems carry high spatial resolution information relating to c. Due to multiple scattering, beam spreading and energy decay with range, the LiDAR attenuation coefficient (K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sy</sub> s) tends to under-estimate the true c value at greater optical thicknesses. An inversion technique to estimate c as a function of range was developed based on empirical relationships between the arithmetic average of range-resolved backscattering values (βm) and changes on c - K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sys</sub> using backscattering measurements at a wavelength of 532 nm and derived from a scanning FSUIL LiDAR instrument (Fine Structure Underwater Imaging LiDAR). Lab models differed from parameterizations derived from field measurements obtained in coastal waters of the Gulf of Mexico as tank experiments were performed using a constant single scattering albedo (ω <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> ). Our approach can be potentially applied to other regions previous adjustment of empirical model coefficients due to variations of ω <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> . The use of lab-derived models is feasible as a long as βm, c and K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sys</sub> are related for different ω <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> values.
Preclinical studies on immunogenicity of the HIV‐1 p17‐based synthetic peptide AT20‐KLH (2004)

Several studies have suggested that HIV-1 p17 matrix protein may play an important role in AIDS pathogenesis, since anti-p17 antibodies represent a serological marker of disease progression during HIV-1 infection both in adults and children. Moreover, it has been recently reported that the viral protein is capable of significantly increasing the proliferation of preactivated T lymphocytes and the release of proinflammatory cytokines. Recombinant HIV-1 p17 also has induced an increased rate of HIV-1 replication in vitro. All p17 biological activities are exerted after its binding to a specific cellular receptor expressed on activated T lymphocytes. The functional p17 epitope involved in receptor binding was found to be located at the NH(2)-terminal region of the viral protein. Immunization of C57BL/6 mice with a 20 amino acid synthetic peptide representative of the HIV-1 p17 functional region (AT20) coupled to the carrier protein keyhole limpet hemocyanin (KLH) and given in Freund's incomplete adjuvant, resulted in the development of p17-neutralizing antibodies capable of blocking p17/p17 receptor interaction, and consequently, all biological activities of the viral protein. Moreover, it was possible to skew the humoral response induced by priming mice with AT20-KLH toward cell-mediated immune responses, boosting animals with p17. Our findings may provide a new strategy to develop a synthetic AIDS vaccine based on a potentially effective and safe subunit vaccine against the HIV-1 cytokine-like matrix protein p17. Preclinical immunogenicity data for AT20-KLH provide the basis for evaluation of the peptide-based vaccine, alone and in combination with p17 or p17 DNA vaccines, in Phase I clinical trials.
The Zyggregator method for predicting protein aggregation propensities (2008)

Protein aggregation causes many devastating neurological and systemic diseases and represents a major problem in the preparation of recombinant proteins in biotechnology. Major advances in understanding the causes of this phenomenon have been made through the realisation that the analysis of the physico-chemical characteristics of the amino acids can provide accurate predictions about the rates of growth of the misfolded assemblies and the specific regions of the sequences that promote aggregation. More recently it has also been shown that the toxicity in vivo of protein aggregates can be predicted by estimating the propensity of polypeptide chains to form protofibrillar assemblies. In this tutorial review we describe the development of these predictions made through the Zyggregator method and the applications that have been explored so far.
Abstract 17836: High Throughput Functional Screening Identifies microRNAs Inducing Cardiac Regeneration (2013)

Whereas enlargement of the heart during mammalian development relies on cardiomyocyte proliferation, at birth cardiomyocytes stop dividing and further growth occurs through hypertrophy. As a conseq...
Verification of Embedded Memory Systems using Efficient Memory Modeling (2005)

We describe verification techniques for embedded memory systems using efficient memory modeling (EMM), without explicitly modeling each memory bit. We extend our previously proposed approach of EMM in bounded model checking (BMC) for a single read/write port single memory system, to more commonly occurring systems with multiple memories, having multiple read and write ports. More importantly, we augment such EMM to providing correctness proofs, in addition to finding real bugs as before. The novelties of our verification approach are in (a) combining EMM with a proof-based abstraction that preserves the correctness of a property up to a certain analysis depth of SAT-based BMC, and (b) modeling arbitrary initial memory state precisely and thereby providing inductive proofs using SAT-based BMC for embedded memory systems. Similar to the previous approach, we construct a verification model by eliminating memory arrays, but retaining the memory interface signals with their control logic and adding constraints on those signals at every analysis depth to preserve the data forwarding semantics. The size of these EMM constraints depends quadratically on the number of memory accesses and the number of read and write ports; and linearly on the address and data widths and the number of memories. We show the effectiveness of our approach on several industry designs and software programs.
Antitumor activity of new anthracycline antibiotics, aclacinomycin-A and its analogs, and their toxicity. (1977)

New anthracycline antibiotics have been isolated from the culture of Streptomyces galilaeus MA144-M1. Among 14 anthracycline compounds, aclacinomycin-A showed the strongest activity in inhibiting leukemia L-1210 and had lower toxicity than others. Antitumor activity of aclacinomycin-A against leukemia L-1210 and P-388, solid sarcoma-180, and lymphosarcoma 6C3HED was examined in comparison with adriamycin and daunomycin. Aclacinomycin-A showed the same degree of activity against leukemia L-1210 and P-388, when administered intraperitoneally, as daunomycin and somewhat less than adriamycin. In oral administration, aclacinomycin-A also exhibited a significant activity on leukemia L-1210. The degree of inhibition of the growth of sarcoma-180 and 6C3HED lymphosarcoma transplanted subcutaneously by aclacinomycin-A was almost the same as that of adriamycin and daunomycin, although the optimal dose was about twice more than adriamycin. Acute cardiotoxicity of aclacinomycin-A by a test using hamsters was more than 10 times lower than that of adriamycin.
A framework for defining FLASH dose rate for pencil beam scanning (2020)

We have developed a method of calculating the dose rate distribution of a PBS proton field and have recommended nomenclature for reporting PBS treatment dose rate. We believe that standardizing the method for calculating and reporting PBS treatment dose rates, in a manner that corresponds with other treatment modalities, will advance the research and potential application of PBS FLASH radiotherapy.
An integrated serum proteomic approach capable of monitoring the low molecular weight proteome with sequencing of intermediate to large peptides (2009)

The low-abundance, low molecular weight serum proteome has high potential for the discovery of new biomarkers using mass spectrometry (MS). Because the serum proteome is large and complex, defining relative quantitative differences for a molecular species between comparison groups requires an approach with robust separation capability, high sensitivity, as well as high mass resolution. Capillary liquid chromatography (cLC)/MS provides both the necessary separation technique and the sensitivity to observe many low-abundance peptides. Subsequent identification of potential serum peptide biomarkers observed in the cLC/MS step can in principle be accomplished by in series cLC/MS/MS without further sample preparation or additional instrumentation. In this report a novel cLC/MS/MS method for peptide sequencing is described that surpasses previously reported size limits for amino acid sequencing accomplished by collisional fragmentation using a tandem time-of-flight MS instrument. As a demonstration of the approach, two low-abundance peptides with masses of approximately 4000-5000 Da were selected for MS/MS sequencing. The multi-channel analyzer (MCA) was used in a novel way that allowed for summation of 120 fragmentation spectra for each of several customized collision energies, providing more thorough fragmentation coverage of each peptide with improved signal to noise. The peak list from this composite analysis was submitted to Mascot for identification. The two index peptides, 4279 Da and 5061 Da, were successfully identified. The peptides were a 39 amino acid immunoglobulin G heavy chain variable region fragment and a 47 amino acid fibrin alpha isoform C-terminal fragment. The method described here provides the ability both to survey thousands of serum molecules and to couple that with markedly enhanced cLC/MS/MS peptide sequencing capabilities, providing a promising technique for serum biomarker discovery.
FissureNet: A Deep Learning Approach For Pulmonary Fissure Detection in CT Images (2018)

Pulmonary fissure detection in computed tomography (CT) is a critical component for automatic lobar segmentation. The majority of fissure detection methods use feature descriptors that are hand-crafted, low-level, and have local spatial extent. The design of such feature detectors is typically targeted toward normal fissure anatomy, yielding low sensitivity to weak, and abnormal fissures that are common in clinical data sets. Furthermore, local features commonly suffer from low specificity, as the complex textures in the lung can be indistinguishable from the fissure when the global context is not considered. We propose a supervised discriminative learning framework for simultaneous feature extraction and classification. The proposed framework, called FissureNet, is a coarse-to-fine cascade of two convolutional neural networks. The coarse-to-fine strategy alleviates the challenges associated with training a network to segment a thin structure that represents a small fraction of the image voxels. FissureNet was evaluated on a cohort of 3706 subjects with inspiration and expiration 3DCT scans from the COPDGene clinical trial and a cohort of 20 subjects with 4DCT scans from a lung cancer clinical trial. On both data sets, FissureNet showed superior performance compared with a deep learning approach using the U-Net architecture and a Hessian-based fissure detection method in terms of area under the precision-recall curve (PR-AUC). The overall PR-AUC for FissureNet, U-Net, and Hessian on the COPDGene (lung cancer) data set was 0.980 (0.966), 0.963 (0.937), and 0.158 (0.182), respectively. On a subset of 30 COPDGene scans, FissureNet was compared with a recently proposed advanced fissure detection method called derivative of sticks (DoS) and showed superior performance with a PR-AUC of 0.991 compared with 0.668 for DoS.
Eight-inch f5 deformable magnetic-membrane mirror (2006)

We demonstrate a method for producing a large, inexpensive, highly curved deformable mirror by stretching a thin polymer membrane coated with a reflective, magnetic material over a rigid frame. The membrane tension, thickness profile, and the transmembrane pressure differential determine the curvature of the mirror, while a computer-controlled electromagnet array deforms the membrane, both to correct the figure and to compensate for an aberrated wavefront. A telescope with an eight-inch f5 magnetic-membrane primary mirror and an adaptive-optics wavefront-measurement-andcontrol system was built and tested. The versatility, high surface quality, large actuator stroke, and low cost-to-aperture ratio of this design suggest that magnetic-membrane mirrors can be used to overcome many of the limitations of both deformable and static mirrors made from solid materials.
12‐crown‐4–ether and tri(ethylene glycol) dimethyl–ether plasma‐coated stainless steel surfaces and their ability to reduce bacterial biofilm deposition (2001)

Abstract It has been demonstrated that surfaces coated with poly(ethylene glycol) (PEG) are capable of reducing protein adsorption, bacterial attachment, and biofilm formation. In this communication cold‐plasma–enhanced processes were employed for the deposition of PEG‐like structures onto stainless steel surfaces. Stainless steel samples were coated under 1,4,7,10‐tetraoxacyclododecane (12‐crown‐4)–ether and tri(ethylene glycol) dimethyl ether (triglyme)–radio frequency (RF)–plasma conditions. The chemistry and characteristics of plasma‐coated samples and biofilms were investigated using electron spectroscopy for chemical analysis (ESCA), atomic force microscopy (AFM), and water contact angle analysis. ESCA analysis indicated that the plasma modification resulted in the deposition of PEG‐like structures, built up mainly of –CH 2 CH 2 O– linkages. Plasma‐coated stainless steel surfaces were more hydrophilic and had lower surface roughness values compared to those of unmodified substrates. Compared to the unmodified surfaces, they not only significantly reduced bacterial attachment and biofilm formation in the presence of a mixed culture of S almonella typhimurium, Staphylococcus epidermidis, and Pseudomonas fluorescens but also influenced the chemical characteristics of the biofilm. Thus, plasma deposition of PEG‐like structures will be of use to the food‐processing and medical industries searching for new technologies to reduce bacterial contamination. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 81: 3425–3438, 2001
Thermal Contact Conductance Enhancement With Carbon Nanotube Arrays (2004)

The present work reports on an experimental study of carbon nanotube (CNT) arrays used for thermal contact conductance enhancement. Multiwall carbon nanotubes were synthesized directly on silicon wafers using plasma-enhanced chemical vapor deposition. Thermal contact conductance was experimentally measured with a steady-state contact conductance technique. To reduce heat losses and experimental uncertainty, testing occurred in a high-vacuum environment with radiation shielding, and temperature measurements were made with an infrared camera. In addition, results from other thermal interface materials (phase change material and metal foil) are presented, and the performance of combinations of these materials with CNT arrays are also reported.
Single-Crystal Metal Halide Perovskites Electronics (2020)

Metal halide perovskites have demonstrated tremendous promising electronic and optoelectronic properties that make them appealing in various device applications. Even though surprising improvement has been achieved during the past few years in polycrystalline perovskite-based devices, problems of their intrinsic high defects level, existence of grain boundaries, strong ion migration rates, and poor stabilities can heavily hinder the further development of polycrystalline perovskite electronics and their realistic applications. In contrast, their single-crystal counterpart is well-studied to have much better crystalline qualities, enhanced electrical properties, and excellent material stabilities, making them intriguing for reaching advanced device performance and realistic applications. However, the development of single-crystal perovskite electronic devices is still in its infancy; even the controlling over dimensions, scalabilities, morphologies, and compositions on single-crystal perovskites, are still challenging.Based on those motivations, this research aims to develop a general platform for realizing single-crystal metal halide perovskites electronics from the material growth to the thin-film device fabrication. The solution-based chemical epitaxy method, the lithography and etching approaches, and the transfer printing processes will be combined together to form this fabrication protocol, which is also compatible with the conventional semiconductor processes.In Chapter One, the basic properties of metal halide perovskites and the current problems presented in this field will be introduced and discussed. In Chapter Two, an epitaxial growth method of metal halide perovskite will be introduced. Our work presents the first controllable growth of single-crystal perovskites with different dimensions, morphologies, crystalline orientations, and compositions. In Chapter Three, a general fabrication process for metal halide single-crystal perovskite electronic integrations will be introduced. Our work presents a reliable approach to integrate metal halide single-crystal perovskite into electronics/microelectronics. In Chapter Four, a general strategy for fabricating flexible metal halide single-crystal perovskite electronics will be introduced. Our work presents the first realization of flexible single-crystal perovskite electronics/micro-electronics, which paves the way for realizing high-performance single-crystal metal halide perovskites wearable electronics.
<title>Fast-lapped transform for image coding</title> (2000)

This paper introduces a class of linear phase lapped biorthogonal transforms with basis functions of variable length. A lattice is used to enforce both linear phase and perfect reconstruction properties as well as to provide a fast and efficient transform implementation for image coding applications. In the proposed formulation which we call fast lapped transform (FLT), the higher frequency filters (basis functions) are those of the DCT, which are compact to limit ringing. The lower frequency filters (basis functions) are overlapped for representing smooth signals while avoiding blocking artifacts. A great part of the FLT computation is spent at the DCT stage, which can be implemented through fast algorithms, while just a few more operations are needed to implement the extra stages. For example, compared to the DCT, an FLT with good performance can be implemented with only 8 extra additions and 6 extra multiplications for an 8-sample block. Yet, image coding examples show that the FLT is far superior to the DCT and is close to the 9/7-tap biorthogonal wavelet in subjective coding performance.
An architecture for rapid retrieval of structured information using speech with application to spoken address recognition (2004)

We describe an iterative recognition strategy that can be used to improve vastly the performance of a speech recognition system when the speech pertains to structured information that can be looked up in a database. The framework that we present is designed to extract specific fields of interest from the speech signal during each iteration, query a database using these fields, and thereby construct the hypothesis space for searching during the next iteration. The architecture has been found to be significantly useful in applications such as spoken address recognition where a proof of concept and a demonstration system had been developed. We also present results on a small test set to compare the performance of the described system with the more common baseline approach.
Velocity estimation using synthetic aperture imaging (2001)

In a previous paper we have demonstrated that the velocity can be estimated for a plug flow using recursive ultrasound imaging [1]. The approach involved the estimation of the velocity at every emission and using the estimates for motion compensation. An error in the estimates, however, would lead to an error in the compensation further increasing the error in the estimates. In this paper the approach is further developed such that no motion compensation is necessary. In recursive ultrasound imaging a new high resolution image is created after every emission. The velocity was estimated by cross correlating RF lines from two successive emissions n and n+ 1, and then average over a number of lines. In the new approach images n and n+N, n+1 and n+N+1 are cross correlated, where N is the number of emissions for one image. These images experience the same phase distortion due to motion and therefore have a high correlation without motion compensation. The advantage of the approach is that a color flow map can be created for all directions in the image simultaneously at every emission, which makes it possible to average over a large number of lines. This makes stationary echo canceling easier and significantly improves the velocity estimates. The approach is verified using simulations with the program Field II and measurements on a blood-mimicking phantom. The estimates from the simulations have a bias of -3.5 % and a mean standard deviation less than 2.0 % for a parabolic velocity profile. The estimates from the measurements for the same setup exhibit a larger bias - 11 %, but the standard deviation is comparable to the simulations (σ ∼ 2.5 %).