gebhart/patrepeval huggingface dataset:
Alternatively Spliced Transcripts of the Aromatase Cytochrome P450 (<i>CYP19</i>) Gene in Adipose Tissue of Women<sup>1</sup> (1997)

Estrogen biosynthesis in adipose tissue has assumed great significance in terms of a number of estrogen-related diseases. The biosynthesis of estrogens from C19 steroids is catalyzed by a specific form of cytochrome P450, namely aromatase cytochrome P450 (P450arom; the product of the CYP19 gene). The human CYP19 gene comprises nine coding exons, II-X, and its transcripts are expressed in the ovary, placenta, testes, adipose tissue, and brain. Tissue-specific expression of the CYP19 gene is determined at least in part by the use of tissue-specific promoters, which give rise to transcripts with unique 5'-noncoding termini. Thus, the distal promoter I.1 is responsible for expression uniquely in placenta. On the other hand, the proximal promoter II, which regulates expression via a cAMP-dependent signaling pathway, is responsible for expression in the gonads. Transcripts in breast adipose tissue contain 5'-termini corresponding to expression derived from promoters I.4, II, and I.3, with I.4-specific termini predominating. The latter are derived from promoter I.4, which contains a glucocorticoid response element and an interferon-gamma activation site element and is responsible for expression in the presence of glucocorticoids and members of the class I cytokine family. The object of the present study was to determine the distribution of these various transcripts in adipose tissue from abdomen, buttocks, and thighs of women, as this would provide important clues to the factors regulating aromatase expression in these sites. To achieve this, we employed competitive reverse transcription-PCR to amplify unique 5'-ends of each of the transcripts of the CYP19 gene that are expressed in adipose tissue as well as for the coding region to evaluate total CYP19 gene (P450arom) transcript levels. We observed that exon I.4-specific transcripts were predominantly present in adipose tissue samples obtained from women regardless of the tissue site or the age of the individual. In these tissues, promoter II- and exon I.3-specific transcripts were present in lower copy numbers. We also demonstrated that in these sites total or exon-specific P450arom transcripts levels increased in direct proportion to advancing age and that transcript levels were the highest in buttocks, followed by thighs, and lowest in the abdomen. These results suggest that in normal human adipose tissue, aromatase expression is mainly under local control by a number of cytokines via paracrine and autocrine mechanisms in the presence of systemic glucocorticoids.
Integrated lithography to produce complex structures for spectral engineering (2011)

An integrated interference and colloid sphere lithography (IICL) is presented to produce complex plasmonic structures consisting of wavelength-scaled periodic arrays of nano-objects with arbitrary array symmetry and controllable nano-scaled sub-structure. The IICL method is based on illumination of colloid sphere monolayers by interference patterns synchronized with sphere arrays along arbitrary crystallographic directions. This nano-kaleidoscope method enables to tune four structure parameters independently: the symmetry and characteristic periodicity of the interference pattern might be varied by the wavelength, number and angle of incidence of the interfering beams; the colloid-spheres' diameter-scaled distance between the nano-objects is controllable by the relative orientation of the interference pattern with respect to the hexagonal lattice of colloid spheres; the size of individual nano-objects is determined by the colloid-spheres diameter and by the light wavelength and is influenced by power density; the sub-structure size-parameter sensitively depends on the polarization state and can be tuned with the nano-object size simultaneously. Finite element method is applied to demonstrate the capabilities of IICL, and the impact of the resulted complex plasmonic patterns on spectral properties of thin gold films. The possibility to realize spectral engineering with predesigned rectangular arrays of hole-doublets that may be produced uniquely by IICL is shown.
Amino acid derived latent isocyanates: irreversible inactivation of porcine pancreatic elastase and human leukocyte elastase (1985)

Several amino acid derived azolides (I) have been synthesized and investigated for their inhibitory activity toward human leukocyte elastase and porcine pancreatic elastase. The inhibitory activity was found to be dependent on the nature of the precursor amino acid ester. Thus, compounds derived from L-valine methyl ester 3, L-norvaline methyl ester 5, DL-norleucine methyl ester 9, and L-methionine methyl ester 10 were found to inhibit irreversibly both enzymes. Compound 10 was found to be a specific and selective inhibitor of human leukocyte elastase. In contrast to these, inhibitors derived from glycine methyl ester 1, D-valine methyl ester 4, and D-norvaline methyl ester 6 were found to be inactive. The results of the present study show that latent isocyanates derived from appropriate amino acids can serve as selective inhibitors of serine proteases and are of potential pharmacological value.
Name=Struct:  A Practical Approach to the Sorry State of Real-Life Chemical Nomenclature (1999)

The interpretation (automatic or otherwise) of chemical names is complicated by the poor quality of such names in common usage. A practical interpretation system for chemical names must consider not only the published rules for chemical nomenclature but also their misinterpretations, corruptions, and popular extensions. This paper describes the design of Name=Struct, an automated system for the conversion of chemical names to their corresponding structures, and discusses the nomenclature interpretation problems addressed in its development. The comprehensiveness and accuracy of Name=Struct are analyzed in several contexts.
Decapeptide agonists of human C5a: the relationship between conformation and neutrophil response (1995)

A series of decapeptide analogues corresponding to the C-terminal region of the human C5a anaphylatoxin (C5a65-74) was synthesized with residue substitutions to restrict conformational flexibility in the C-terminal region (residues 71-74). These analogues behaved as full agonists of natural C5a in their ability to induce shape change (polarization) and the release of enzyme (beta-glucuronidase) from human neutrophils (PMNs). There was a significant pharmacological correlation between the polarization and enzyme-release assays, suggesting similarities in PMN responsiveness toward these constrained peptides. Good correlations were also observed between these two PMN responses and spasmogenic activity (smooth muscle contraction of human fetal artery). A structure-function analysis for PMN polarization and enzyme release led to the identification of the following preferred backbone conformations: a twisted, helix-like conformation for residues 65-69, an extended conformation for residues 70-71, and a beta-turn of type V for residues (71)72-74. The existence of a C-terminal, type V beta-turn is supported by the NOE (nuclear Overhauser effect) results of two peptides from this series. These conformational features are reminiscent of those that were shown to correlate with the expression of spasmogenic and platelet aggregatory activities in an earlier investigation (Sanderson, S.D.; et al. J. Med. Chem. 1994, 37, 3171). These results suggest that PMNs and the cells responsible for smooth muscle contraction possess C5a receptors that respond to similar topochemical features presented by the agonist peptide ligand.
Distribution of prothymosin alpha in rat tissues. (1984)

A radioimmunoassay, using a rabbit antiserum directed against thymosin alpha 1, was employed to detect the presence of crossreacting peptides in rat tissues. Highest concentrations were present in thymus, but thymosin alpha 1 cross-reacting material was also detected in brain, liver, kidney, lung, and spleen, in amounts ranging from 15% to 65% of the quantities found in thymus. In each case, the major immunoreactive peptide, after extraction and purification by a procedure that avoids proteolytic modification, was identified as prothymosin alpha, a peptide containing approximately equal to 112 amino acid residues. Prothymosin alpha is believed to be the endogenous peptide from which thymosin alpha 1 and other fragments are formed by proteolytic modification during the preparation of thymosin fraction 5. No peptides corresponding in size and chromatographic behavior to thymosin alpha 1 were detected with the extraction procedure employed.
A block-coded modulation method for one-way multimode data transmission (2002)

This paper presents a multimode block-coded modulation method that enables both multimode transmission and coding gain. In multimode transmission, the property of data is changed for each mode, and the data are adaptively transmitted. In our method, all modes are constructed by separate multilevel block codes, wherein the number of levels, set partition, rate, and distance properties of each mode may differ from those of the other modes. Different modes may also have different signal constellations, that is, different modulation methods. The code length is the same for all modes, and the mode can be switched at each block boundary, if desired. This method uses one-way transmission where the transmitter has no feedback information from the receiver. In decoding, the maximum-likelihood decoding is carried out using the Viterbi (1967) algorithm. The decoding of all modes, including decoding of the mode index, can be accomplished using one trellis diagram. This paper describes the multimode encoding and decoding method, and analyzes the distance properties and upper bounds for inter- and intramodes. It is clarified at which distance the code should be increased to reduce the decoding mode error. Three design examples are presented for unequal error protection/equal error protection, variable rate, and hybrid additive white Gaussian noise/flat-fading codes.
Fabrication of vapor-deposited micro heat pipe arrays as an integral part of semiconductor devices (1995)

Vapor-deposited micro heat pipe arrays (VDMHP) were fabricated as an integral part of semiconductor devices to act as efficient heat spreaders by reducing the thermal path between the heat sources and heat sink. Fabrication of the VDMHP was accomplished by first establishing a series of grooves in a silicon wafer. Orientation dependent etching (ODE) using a KOH-1-propanol-H/sub 2/O solution on a (100) wafer with a (111) flat covered with an oxide mask, resulted in grooves 25 /spl mu/m wide and 25 /spl mu/m deep with sharp, perpendicular edges. The wafers were predeposited with a layer of chromium followed by a layer of gold to improve the adhesion characteristics. Dual electron beam vapor deposition, followed by planetary process using molybdenum crucibles, were used to deposit copper 31.5-33.0 /spl mu/m thick, and provide complete closure of the grooves. A glass cover slip was bonded on the top of the deposited layer. The grooves were finally charged and sealed. A computer model Simulation and Modeling of Evaporated Deposition Profiles (SAMPLE) was used to optimize the metal step coverage and successfully predict the cross-sectional profile of the VDMHP.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An Enzymatic System for Removing Heparin in Extracorporeal Therapy (1982)

The need to fully heparinize patients undergoing extracorporeal therapy often leads to hemorrhagic complications. To enable heparinization of only the extracorporeal circuit, a blood filter containing immobilized heparinase was developed. This filter degraded 99 percent of heparin's anticoagulant activity within minutes in both canine and human blood.
Recursive bilateral filter for encoder-integrated video denoising (2012)

Video denoising based on temporal or spatiotemporal filtering is highly effective but computationally expensive due to the requirement of motion estimation. Encoder-integrated denoising is an efficient framework that embeds the filtering process into the encoding pipeline so that motion estimation for denoising can be avoided. State-of-the-arts encoder-integrated methods use Least Minimum Mean Square Error (LMMSE) optimal filters to reduce noise based on additive noise models. However, in practice, the LMMSE filters could result in blurred edges and visual artifacts due to inaccurate image signal estimation caused by outlier input samples and non-adaptivity within macroblocks. This paper presents new recursive bilateral filters that can be easily integrated into video encoders to tackle the limitations of the LMMSE filters. The robustness of the bilateral filters results in substantially better objective and subjective quality with marginal computation cost increase.
A CMOS Array Sensor for Sub-800-ps Time-Resolved Fluorescence Detection (2007)

This paper describes the design of an active CMOS sensor array for fluorescence applications which enables time-gated, time-resolved fluorescence spectroscopy. The 64 times 64 array is sensitive to photon densities as low as 8 times 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> photons/cm with 64-point averaging and, through a differential pixel design, has a measured impulse response of better than 800 ps. Applications include both active microarrays and high-frame-rate imagers for fluorescence lifetime imaging microscopy.
Wind Turbine Blade Deflection Sensing Using Blade-Mounted Ultrawideband Antennas (2020)

Wind turbine blade deflection sensing system using ultrawideband radio links propagating along the blade is presented. Special focus is given to the challenges related to the multipath propagation along the blade. Results of electromagnetic modeling of the wireless link budget for deflected blades are presented. Some aspects of the sensing system that are different from a typical wireless communication link are discussed.
Is it congestion or a DDoS attack? (2009)

We propose a new stealthy DDoS attack model referred to as the "quiet" attack. The attack traffic consists of TCP traffic only. Widely used botnets in today's various attacks and newly introduced network feedback control are integral part of the quiet attack model. We show that shortlived TCP flows can be intentionally misused. The quiet attack is detrimental to the Internet traffic and at the same time difficult to be detected by using current defense systems. We demonstrate the inability of representative defense schemes such as adaptive queue management and aggregate congestion control to detect the quiet attack.
Iodonium Ylide–Mediated Radiofluorination of <sup>18</sup>F-FPEB and Validation for Human Use (2015)

Radiofluorination of iodonium (III) ylides proved to be an efficient radiosynthetic strategy for synthesis of (18)F-labeled radiopharmaceuticals.
Preparation and properties of 1,2,2,2‐tetrachloroethyl esters of β‐vinylacrylic, fumaric, and muconic acids and their homopolymers or copolymers (1974)

Abstract 1,2,2,2‐Tetrachloroethyl esters of β‐vinylacrylic, muconic, and fumaric acids were prepared by the addition reaction of chloral with pentadienoyl chloride, hexadienedioyl chloride, and fumaroyl chloride in the presence of FeCl 3 . The homopolymer of the first and copolymers of the other esters with styrene were obtained by radical polymerization. The basic chemical and physical characteristics of the compounds prepared were determined, and the assumed structure was confirmed by the infrared, NMR, and mass spectra.
Electrical resistance tomography using steel cased boreholes as long electrodes (1999)

Electrical resistance tomography (ERT) using multiple electrodes installed in boreholes has been shown to be useful for both site characterization and process monitoring. In some cases, however, installing multiple downhole electrodes is too costly (e.g., deep targets) or risky (e.g., contaminated sites). For these cases we have examined the possibility of using the steel casings of existing boreholes as electrodes. Several possibilities can be considered. The first case we investigated uses an array of steel casings as electrodes. This results in very few data and thus requires additional constraints to limit the domain of possible inverse solutions. Simulations indicate that the spatial resolution and sensitivity are understandably low but it is possible to coarsely map the lateral extent of subsurface processes such as steam floods. The second case uses an array of traditional point borehole electrodes combined with long-conductor electrodes (steel casings). Although this arrangement provides more data, in many cases it results in poor reconstructions of test targets. Results indicate that this method may hold promise for low resolution imaging where steel casings can be used as electrodes but the merits depend strongly on details of each application. Field tests using these configurations are currently being conducted.
Modeling multidimensional data and control flow (1993)

Multidimensional (M-D) signal processing is a key component of most real-time signal and data processing VLSI systems in industry. Handling the M-D nature of data in an efficient way is crucial to arrive at acceptable system implementations. This aspect of design has often been ignored up to now in high-level synthesis. In this paper, a polyhedral based model is presented for the linear, piecewise linear and data dependent signal indexing as occurring in practical M-D signal processing applications. The model features a mathematical description of dependencies between individual operations and signal instances of M-D signals for all algorithms that contain signal indexing specified by a mixture of indexing by iterators and M-D signals embedded in the data flow. The exact modeling of M-D signal indexing is especially essential for deriving alternative control flow structures for a given data flow specification. Exploration of various control flow structures allows one to arrive at an efficient large-scale memory organization during high level synthesis of architectures, both in terms of storage locations and access order.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Application of dynamic metabolic flux analysis for process modeling: Robust flux estimation with regularization, confidence bounds, and selection of elementary modes (2020)

In macroscopic dynamic models of fermentation processes, elementary modes (EM) derived from metabolic networks are often used to describe the reaction stoichiometry in a simplified manner and to build predictive models by parameterizing kinetic rate equations for the EM. In this procedure, the selection of a set of EM is a key step which is followed by an estimation of their reaction rates and of the associated confidence bounds. In this paper, we present a method for the computation of reaction rates of cellular reactions and EM as well as an algorithm for the selection of EM for process modeling. The method is based on the dynamic metabolic flux analysis (DMFA) proposed by Leighty and Antoniewicz (2011, Metab Eng, 13(6), 745-755) with additional constraints, regularization and analysis of uncertainty. Instead of using estimated uptake or secretion rates, concentration measurements are used directly to avoid an amplification of measurement errors by numerical differentiation. It is shown that the regularized DMFA for EM method is significantly more robust against measurement noise than methods using estimated rates. The confidence intervals for the estimated reaction rates are obtained by bootstrapping. For the selection of a set of EM for a given st oichiometric model, the DMFA for EM method is combined with a multiobjective genetic algorithm. The method is applied to real data from a CHO fed-batch process. From measurements of six fed-batch experiments, 10 EM were identified as the smallest subset of EM based upon which the data can be described sufficiently accurately by a dynamic model. The estimated EM reaction rates and their confidence intervals at different process conditions provide useful information for the kinetic modeling and subsequent process optimization.
SEU-Tolerant QDI Circuits (2005)

This paper addresses the issue of single-event upset (SEU) in quasi delay-insensitive (QDI) asynchronous circuits. We show that an SEU can cause abnormal computations in QDI circuits beside deadlock, and we propose a general method to make QDI circuits SEU-tolerant. We present simplified SEU-tolerant buffer implementations for CMOS technology. Finally, we present a case study of a one-bit comparator and show SPICE-simulation results.
A Polarimetric Thermal Database for Face Recognition Research (2016)

We present a polarimetric thermal face database, the first of its kind, for face recognition research. This database was acquired using a polarimetric longwave infrared imager, specifically a division-of-time spinning achromatic retarder system. A corresponding set of visible spectrum imagery was also collected, to facilitate crossspectrum (also referred to as heterogeneous) face recognition research. The database consists of imagery acquired at three distances under two experimental conditions: neutral/baseline condition, and expressions condition. Annotations (spatial coordinates of key fiducial points) are provided for all images. Cross-spectrum face recognition performance on the database is benchmarked using three techniques: partial least squares, deep perceptual mapping, and coupled neural networks.
In Defense of the Triplet Loss for Visual Recognition. (2019)

We employ triplet loss as a space embedding regularizer to boost classification performance. Standard architectures, like ResNet and DesneNet, are extended to support both losses with minimal hyper-parameter tuning. This promotes generality while fine-tuning pretrained networks. Triplet loss is a powerful surrogate for recently proposed embedding regularizers. Yet, it is avoided for large batch-size requirement and high computational cost. Through our experiments, we re-assess these assumptions. 
During inference, our network supports both classification and embedding tasks without any computational overhead. Quantitative evaluation highlights how our approach compares favorably to the existing state of the art on multiple fine-grained recognition datasets. Further evaluation on an imbalanced video dataset achieves significant improvement (>7%). Beyond boosting efficiency, triplet loss brings retrieval and interpretability to classification models.
HiFi-GAN: High-Fidelity Denoising and Dereverberation Based on Speech Deep Features in Adversarial Networks (2020)

Real-world audio recordings are often degraded by factors such as noise, reverberation, and equalization distortion.This paper introduces HiFi-GAN, a deep learning method to transform recorded speech to sound as though it had been recorded in a studio.We use an end-to-end feed-forward WaveNet architecture, trained with multi-scale adversarial discriminators in both the time domain and the time-frequency domain.It relies on the deep feature matching losses of the discriminators to improve the perceptual quality of enhanced speech.The proposed model generalizes well to new speakers, new speech content, and new environments.It significantly outperforms state-of-the-art baseline methods in both objective and subjective experiments.