gebhart/patrepeval huggingface dataset:
Triple-error-correcting BCH-like codes (2009)

The binary primitive triple-error-correcting BCH code is a cyclic code of minimum distance d = 7 with generator polynomial having zeros alpha, alpha <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> and alpha <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> where alpha is a primitive (2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> - 1)-root of unity. The zero set of the code is said to be {1, 3, 5}. In the 1970's Kasami showed that one can construct similar triple-error-correcting codes using zero sets consisting of different triples than the BCH codes. Furthermore, in 2000 Chang et. al. found new triples leading to triple-error-correcting codes. In this paper a new such triple is presented. In addition a new method is presented that may be of interest in finding further such triples. The method is illustrated by giving a new and simpler proof of one of the known Kasami triples {1, 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</sup> + 1, 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3k</sup> + 1} where n is odd and gcd(k, n) = 1 as well as to find the new triple given by {1, 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</sup> + 1, 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2k</sup> + 1} for any n where gcd(k, n) = 1.
Probing structural elements in RNA using engineered disulfide cross- links (1998)

Three analogs of unmodified yeast tRNAPhe, each possessing a single disulfide cross-link, have been designed and synthesized. One cross-link is between G1 and C72 in the amino acid acceptor stem, a second cross-link is in the central D region of yeast tRNAPhe between C11 and C25 and the third cross-link bridges U16 and C60 at the D loop/T loop interface. Air oxidation to form the cross-links is quantitative and analysis of the cross-linked products by native and denaturing PAGE, RNase T1 mapping, Pb(II) cleavage, UV cross-linking and thermal denaturation demonstrates that the disulfide bridges do not alter folding of the modified tRNAs relative to the parent sequence. The finding that cross-link formation between thiol-derivatized residues correlates with the position of these groups in the crystal structure of native yeast tRNAPhe and that the modifications do not significantly perturb native structure suggests that this methodology should be applicable to the study of RNA structure, conformational dynamics and folding pathways.
Two glycerol uptake systems contribute to the high osmotolerance of <scp><i>Z</i></scp><i>ygosaccharomyces rouxii</i> (2015)

The accumulation of glycerol is essential for yeast viability upon hyperosmotic stress. Here we show that the osmotolerant yeast Zygosaccharomyces rouxii has two genes, ZrSTL1 and ZrSTL2, encoding transporters mediating the active uptake of glycerol in symport with protons, contributing to cell osmotolerance and intracellular pH homeostasis. The growth of mutants lacking one or both transporters is affected depending on the growth medium, carbon source, strain auxotrophies, osmotic conditions and the presence of external glycerol. These transporters are localised in the plasma membrane, they transport glycerol with similar kinetic parameters and besides their expected involvement in the cell survival of hyperosmotic stress, they surprisingly both contribute to an efficient survival of hypoosmotic shock and to the maintenance of intracellular pH homeostasis under non-stressed conditions. Unlike STL1 in Sa. cerevisiae, the two Z. rouxii STL genes are not repressed by glucose, but their expression and activity are downregulated by fructose and upregulated by non-fermentable carbon sources, with ZrSTL1 being more influenced than ZrSTL2. In summary, both transporters are highly important, though Z. rouxii CBS 732(T) cells do not use external glycerol as a source of carbon.
Genetic algorithm based simulated annealing method for solving unit commitment problem in utility system (2010)

The objective of this paper is to find the generation scheduling such that the total operating cost can be minimized, when subjected to a variety of constraints. This also means that it is desirable to find the optimal generating unit commitment in the power system for the next H hours. Genetic Algorithms (GA's) are general-purpose optimization techniques based on principles inspired from the biological evolution using metaphors of mechanisms such as neural section, genetic recombination and survival of the fittest. In this, the unit commitment schedule is coded as a string of symbols. An initial population of parent solutions is generated at random. Here, each schedule is formed by committing all the units according to their initial status (“flat start”). Here the parents are obtained from a pre-defined set of solution's i.e. each and every solution is adjusted to meet the requirements. Then, a random recommitment is carried out with respect to the unit's minimum down times. And SA improves the status. A 66-bus utility power system with twelve generating units in India demonstrates the effectiveness of the proposed approach. Numerical results are shown comparing the cost solutions and computation time obtained by using the Genetic Algorithm method and other conventional methods.
Imaging of the three-dimensional alveolar structure and the alveolar mechanics of a ventilated and perfused isolated rabbit lung with Fourier domain optical coherence tomography (2006)

In this feasibility study, Fourier domain optical coherence tomography (FDOCT) is used for visualizing the 3-D structure of fixated lung parenchyma and to capture real-time cross sectional images of the subpleural alveolar mechanics in a ventilated and perfused isolated rabbit lung. The compact and modular setup of the FDOCT system allows us to image the first 500 microm of subpleural lung parenchyma with a 3-D resolution of 16 x 16 x 8 microm (in air). During mechanical ventilation, real-time cross sectional FDOCT images visualize the inflation and deflation of alveoli and alveolar sacks (acini) in successive images of end-inspiratory and end-expiratory phase. The FDOCT imaging shows the relation of local alveolar mechanics to the setting of tidal volume (VT), peak airway pressure, and positive end-expiratory pressure (PEEP). Application of PEEP leads to persistent recruitment of alveoli and acini in the end-expiratory phase, compared to ventilation without PEEP where alveolar collapse and reinflation are observed. The imaging of alveolar mechanics by FDOCT will help to determine the amount of mechanical stress put on the alveolar walls during tidal ventilation, which is a key factor in understanding the development of ventilator induced lung injury (VILI).
Modulation of protein–protein interactions by synthetic receptors: Design of molecules that disrupt serine protease–proteinaceous inhibitor interaction (2002)

In the present article we describe the design and evaluation of a synthetic receptor that binds to the exterior surface of chymotrypsin and disrupts its interaction with proteinaceous inhibitors, such as soybean trypsin inhibitor, basic pancreatic trypsin inhibitor, ovomucoid turkey inhibitor, and Bowman-Birk inhibitor. Using enzyme kinetics, nondenaturing gel electrophoresis, and gel filtration chromatography we show that the receptor is particularly effective at blocking the chymotrypsin-soybean trypsin inhibitor complex and that the mechanism involves formation of an initial ternary complex followed by a time-dependent displacement of the proteinaceous inhibitor.
Mechanisms associated with tumor vascular shut-down induced by combretastatin A-4 phosphate: intravital microscopy and measurement of vascular permeability. (2001)

The tumor vascular effects of the tubulin destabilizing agent disodium combretastatinA-4 3-O-phosphate (CA-4-P) were investigated in the rat P22 tumor growing in a dorsal skin flap window chamber implanted into BD9 rats. CA-4-P is in clinical trial as a tumor vascular targeting agent. In animal tumors, it can cause the shut-down of blood flow, leading to extensive tumor cell necrosis. However, the mechanisms leading to vascular shut-down are still unknown. Tumor vascular effects were visualized and monitored on-line before and after the administration of two doses of CA-4-P (30 and 100 mg/kg) using intravital microscopy. The combined effect of CA-4-P and systemic nitric oxide synthase (NOS) inhibition using N(omega)-nitro-L-arginine (L-NNA) was also assessed, because this combination has been shown previously to have a potentiating effect. The early effect of CA-4-P on tumor vascular permeability to albumin was determined to assess whether this could be involved in the mechanism of action of the drug. Tumor blood flow reduction was extremely rapid after CA-4-P treatment, with red cell velocity decreasing throughout the observation period and dropping to <5% of the starting value by 1 h. NOS inhibition alone caused a 50% decrease in red cell velocity, and the combined treatment of CA-4-P and NOS inhibition was approximately additive. The mechanism of blood flow reduction was very different for NOS inhibition and CA-4-P. That of NOS inhibition could be explained by a decrease in vessel diameter, which was most profound on the arteriolar side of the tumor circulation. In contrast, the effects of CA-4-P resembled an acute inflammatory reaction resulting in a visible loss of a large proportion of the smallest blood vessels. There was some return of visible vasculature at 1 h after treatment, but the blood in these vessels was static or nearly so, and many of the vessels were distended. The hematocrit within larger draining tumor venules tended to increase at early times after CA-4-P, suggesting fluid loss from the blood. The stacking of red cells to form rouleaux was also a common feature, coincident with slowing of blood flow; and these two factors would lead to an increase in viscous resistance to blood flow. Tumor vascular permeability to albumin was increased to approximately 160% of control values at 1 and 10 min after treatment. This could lead to an early decrease in tumor blood flow via an imbalance between intravascular and tissue pressures and/or an increase in blood viscosity as a result of increased hematocrit. These results suggest a mechanism of action of CA-4-P in vivo. Combination of CA-4-P with a NOS inhibitor has an additive effect, which it may be possible to exploit therapeutically.
A processing system for programming specifications in a natural language (2003)

An English-language fragment L/sub NS/, which is used for writing program specifications, is defined using the algebraic language ASL/*. In order to define the semantics of L/sub NS/, the translation from each sentence in L/sub NS/ into a formula in a formal system is defined. If a sentence s in L/sub NS/ is translated into a formula t, then the semantics of s is defined to be the semantics of t in the system. The definition of nonlogical words such as nouns and verbs are given as axioms. A processing system for natural-language specifications that is based on this method has been implemented. Since the number of nonlogical words is very large and their semantics depend on problem domains, it seems to be difficult to define the semantics of all the words from the beginning. The system not only translates specifications into formulas but also supports dictionary expansion. Several specifications have been analyzed using the system, and the nonlogical words have been defined and stored in the dictionary.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
StuffNet: Using ‘Stuff’ to Improve Object Detection (2017)

We propose a Convolutional Neural Network (CNN) based algorithm - StuffNet - for object detection. In addition to the standard convolutional features trained for region proposal and object detection [33], StuffNet uses convolutional features trained for segmentation of objects and 'stuff' (amorphous categories such as ground and water). Through experiments on Pascal VOC 2010, we show the importance of features learnt from stuff segmentation for improving object detection performance. StuffNet improves performance from 18.8% mAP to 23.9% mAP for small objects. We also devise a method to train StuffNet on datasets that do not have stuff segmentation labels. Through experiments on Pascal VOC 2007 and 2012, we demonstrate the effectiveness of this method and show that StuffNet also significantly improves object detection performance on such datasets.
Ultrathin Strained-Ge Channel P-MOSFETs With High-$K$ /Metal Gate and Sub-1-nm Equivalent Oxide Thickness (2012)

Surface-channel strained-Ge (s-Ge) p-MOSFETs with high- <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> /metal gate stack and ozone surface passivation are fabricated, for the first time. The channel is ultrathin (approximately 3-6 nm thick) s-Ge (approximately 2.2%, biaxial compression) epitaxially grown on a relaxed Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.56</sub> Ge <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.44</sub> virtual substrate. Split capacitance-voltage measurements along with quantum-mechanical simulations demonstrate a capacitance-equivalent thickness of 1.3 nm and sub-1-nm equivalent oxide thickness. The effective hole mobility of these devices was extracted and exhibits 3× and 2.2× mobility enhancement over universal Si hole mobility, for s-Ge channel thicknesses of ~6 and ~3 nm, respectively.
2D broadband beamsteering with large-scale MEMS optical phased array (2019)

Optical-phased arrays (OPAs) enable complex beamforming, random-access beam pointing, and simultaneous scan and tracking of multiple targets by controlling the phases of two-dimensional (2D) coherent emitters. So far, no OPA can achieve all desirable features including large 2D arrays, high optical efficiency, wideband operation in wavelengths, fast response time, and large steering angles at the same time. Here, we report on a large-scale 2D OPA with novel microelectro-mechanical-system (MEMS)-actuated phase shifters. Wavelength-independent phase shifts are realized by physically moving a grating element in the lateral direction. The OPA has 160 x 160 independent phase shifters across an aperture of 3.1 mm x 3.2 mm. It has a measured beam divergence of 0.042 degrees x 0.031 degrees, a field of view (FOV) of 6.6 degrees x 4.4 degrees, and a response time of 5.7 mu s. It is capable of providing about 25,600 rapidly steerable spots within its FOV. The grating phase shifters are optimized for the near-infrared telecom wavelength bands from 1200 to 1700 nm with 85% optical efficiency. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
Numerical analysis of the transportation characteristics of a self-running sliding stage based on near-field acoustic levitation (2015)

Owing to its distinct non-contact and oil-free characteristics, a self-running sliding stage based on near-field acoustic levitation can be used in an environment, which demands clean rooms and zero noise. This paper presents a numerical analysis on the lifting and transportation capacity of a non-contact transportation system. Two simplified structure models, namely, free vibration and force vibration models, are proposed for the study of the displacement amplitude distribution of two cases using the finite element method. After coupling the stage displacement into the film thickness, the Reynolds equation is solved by the finite difference method to obtain the lifting and thrusting forces. Parametric analyses of the effects of amplitude, frequency, and standing wave ratio (SWR) on the sliding stage dynamic performance are investigated. Numerical results show good agreement with published experimental values. The predictions also reveal that greater transportation capacity of the self-running sliding stage is generally achieved at less SWR and at higher amplitude.
A Large Retinal Capillary Hemangioma in the Anterior Retina Treated with Photodynamic Therapy (2012)

PDT can be delivered effectively to a lesion in the anterior retina and should be included as an option for treating anteriorly located RCH when conventional cryotherapy and laser photocoagulation fail.
Structure and Biological Activities of Beta Toxin from<i>Staphylococcus aureus</i> (2007)

Beta toxin is a neutral sphingomyelinase secreted by certain strains of Staphylococcus aureus. This virulence factor lyses erythrocytes in order to evade the host immune system as well as scavenge nutrients. The structure of beta toxin was determined at 2.4-A resolution using crystals that were merohedrally twinned. This structure is similar to that of the sphingomyelinases of Listeria ivanovii and Bacillus cereus. Beta toxin belongs to the DNase I folding superfamily; in addition to sphingomyelinases, the proteins most structurally related to beta toxin include human endonuclease HAP1, Escherichia coli endonuclease III, bovine pancreatic DNase I, and the endonuclease domain of TRAS1 from Bombyx mori. Our biological assays demonstrated for the first time that beta toxin kills proliferating human lymphocytes. Structure-directed active site mutations show that biological activities, including hemolysis and lymphotoxicity, are due to the sphingomyelinase activity of the enzyme.
The Synthesis and Natural Distribution of the Major Ketone Constituents in Echinacea pallida (2007)

The first synthesis of a series of ketones naturally occurring in E. pallida is described. The natural distribution of these ketones among different Echinacea species is also reported.
[Effect of androgen on penile erection induced by L-arginine in paraventricular nucleus]. (2002)

Nitric oxide (NO) is one of the neurotransmitters in PVN particularly relevant for the control of penile erection. Penile erection induced by L-arginine in PVN depends on androgen.
Black Carbon Increases Cation Exchange Capacity in Soils (2006)

Black Carbon (BC) may significantly affect nutrient retention and play a key role in a wide range of biogeochemical processes in soils, especially for nutrient cycling. Anthrosols from the Brazilian Amazon (ages between 600 and 8700 yr BP) with high contents of biomass‐derived BC had greater potential cation exchange capacity (CEC measured at pH 7) per unit organic C than adjacent soils with low BC contents. Synchrotron‐based near edge X‐ray absorption fine structure (NEXAFS) spectroscopy coupled with scanning transmission X‐ray microscopy (STXM) techniques explained the source of the higher surface charge of BC compared with non‐BC by mapping cross‐sectional areas of BC particles with diameters of 10 to 50 μm for C forms. The largest cross‐sectional areas consisted of highly aromatic or only slightly oxidized organic C most likely originating from the BC itself with a characteristic peak at 286.1 eV, which could not be found in humic substance extracts, bacteria or fungi. Oxidation significantly increased from the core of BC particles to their surfaces as shown by the ratio of carboxyl‐C/aromatic‐C. Spotted and non‐continuous distribution patterns of highly oxidized C functional groups with distinctly different chemical signatures on BC particle surfaces (peak shift at 286.1 eV to a higher energy of 286.7 eV) indicated that non‐BC may be adsorbed on the surfaces of BC particles creating highly oxidized surface. As a consequence of both oxidation of the BC particles themselves and adsorption of organic matter to BC surfaces, the charge density (potential CEC per unit surface area) was greater in BC‐rich Anthrosols than adjacent soils. Additionally, a high specific surface area was attributable to the presence of BC, which may contribute to the high CEC found in soils that are rich in BC.
A Transient Harmonic Current Protection Scheme for HVDC Transmission Line (2012)

Based on the boundary characteristic of a dc transmission line, the response of transient harmonic current in the line-commutated converter HVDC transmission system is analyzed under various fault conditions in this paper. A new transient harmonic current protection scheme is proposed. The discrete Fourier transform is used to extract transient harmonic currents at both terminals of the dc transmission line and the type of fault can be identified by the transient harmonic currents. Two main factors including fault resistance and fault location that affect performance of the protection are also discussed in this study. The test system is modeled based on the CIGRE benchmark including distributed parameters of the dc transmission line. Comprehensive test studies show that the performance of the transient harmonic current protection scheme is encouraging. It can not only identify internal faults and external faults correctly and quickly, but also can respond to high ground resistance faults.
Immunohistochemistry (1995)

Abstract This unit surveys immunohistochemical techniques for protein localization. The first four protocols focus on indirect immunofluorescence which is the easiest and most widely used method of optical detection. Additional protocols present methods suitable for bright‐field microscopy, such as immunoperoxidase and immunogold labeling. The commentary contains an extensive troubleshooting guide with a list of suitable routine controls. The chosen method of tissue or cellular preparation must be suitable to answer the fundamental objective of the protocol (i.e., where the protein is localized within the system). Furthermore, the choice of fluorochrome and the method of labeling are also important to optimize the sensitivity of antigen localization. The basic protocol is therefore divided into two sections: (1) cellular preparations (monolayers of adherent cells and cells grown in suspension) and (2) tissue section labeling.
Electrochemistry and Optical Absorbance and Luminescence of Molecule-like Au<sub>38</sub> Nanoparticles (2004)

This paper describes electrochemical and spectroscopic properties of a well-characterized, synthetically accessible, 1.1 nm diam Au nanoparticle, Au(38)(PhC(2)S)(24), where PhC(2)S is phenylethylthiolate. Properties of other Au(38) nanoparticles made by exchanging the monolayer ligands with different thiolate ligands are also described. Voltammetry of the Au(38) nanoparticles in CH(2)Cl(2) reveals a 1.62 V energy gap between the first one-electron oxidation and the first reduction. Based on a charging energy correction of ca. 0.29 V, the indicated HOMO-LUMO gap energy is ca. 1.33 eV. At low energies, the optical absorbance spectrum includes peaks at 675 nm (1.84 eV) and 770 nm (1.61 eV) and an absorbance edge at ca. 1.33 eV that gives an optical HOMO-LUMO gap energy that is consistent with the electrochemical estimate. The absorbance at lowest energy is bleached upon electrochemical depletion of the HOMO level. The complete voltammetry contains two separated doublets of oxidation waves, indicating two distinct molecular orbitals, and two reduction steps. The ligand-exchanged nanoparticle Au(38)(PEG(135)S)(13)(PhC(2)S)(11), where PEG(135)S is -SCH(2)CH(2)OCH(2)CH(2)OCH(3), exhibits a broad (1.77-0.89 eV) near-IR photoluminescence band resolvable into maxima at 902 nm (1.38 eV) and 1025 nm (1.2 eV). Much of the photoluminescence occurs at energies less than the HOMO-LUMO gap energy. A working model of the energy level structure of the Au(38) nanoparticle is presented.