gebhart/patrepeval huggingface dataset:
Chromium oxide as a hard mask material better than metallic chromium (2017)

In nanofabrication, use of thin resist is required to achieve very high resolution features. But thin resist makes pattern transferring by dry etching difficult because typical resist has poor resistance to plasma etching. One widely employed strategy is to use an intermediate hard mask layer, with the pattern first transferred into this layer, then into the substrate or sublayer. Cr is one of the most popular hard etching mask materials because of its high resistance to plasma etching. Cr etching is carried out in O2 and Cl2 or CCl4 environment to form the volatile etching product CrO2Cl2, but addition of O2 gas leads to fast resist etching. In this work, the authors show that Cr2O3 can be etched readily in a Cl2/O2 gas mixture with less oxygen than needed for Cr etching, because Cr2O3 contains oxygen by itself. Thus it is easier to transfer the resist pattern into Cr2O3 than into Cr. For the subsequent pattern transferring into the substrate here silicon using nonswitching pseudo-Bosch inductively coupled plasma-reactive ion etching with SF6/C4F8 gas and Cr or Cr2O3 as mask, it was found that the two materials have the same etching resistance and selectivity of 100:1 over silicon. Therefore, Cr2O3 is a more suitable hard mask material than Cr for pattern transferring using dry plasma etching.
Likelihood-Ratio-Based Biometric Verification (2004)

The paper presents results on optimal similarity measures for biometric verification based on fixed-length feature vectors. First, we show that the verification of a single user is equivalent to the detection problem, which implies that, for single-user verification, the likelihood ratio is optimal. Second, we show that, under some general conditions, decisions based on posterior probabilities and likelihood ratios are equivalent and result in the same receiver operating curve. However, in a multi-user situation, these two methods lead to different average error rates. As a third result, we prove theoretically that, for multi-user verification, the use of the likelihood ratio is optimal in terms of average error rates. The superiority of this method is illustrated by experiments in fingerprint verification. It is shown that error rates below 10/sup -3/ can be achieved when using multiple fingerprints for template construction.
Design optimization of gate-all-around (GAA) MOSFETs (2006)

The design of gate-all-around (GAA) MOSFETs was optimized and compared with that of double-gate MOSFETs. We discussed the optimal ratio of the fin width to the gate length and investigated short-channel effects of GAA MOSFETs. Using three-dimensional simulations, we confirmed that short-channel effects were properly suppressed although the fin width was the same as the gate length in GAA MOSFETs. Finally, we compared cubical channel GAA MOSFETs with cylindrical-channel ones. As a result, it was observed that the latter showed the maximized ratio of the fin width to the gate length up to 1.2.
The receptors for ATP and fMetLeuPhe are independently coupled to phospholipases C and A2 via G-protein(s). Relationship between phospholipase C and A2 activation and exocytosis in HL60 cells and human neutrophils (1989)

The relationship between phospholipase A2 and C activation and secretion was investigated in intact human neutrophils and differentiated HL60 cells. Activation by either ATP or fMetLeuPhe leads to [3H]arachidonic acid release into the external medium from prelabelled cells. This response was inhibited when the cells were pretreated with pertussis toxin. When the [3H]arachidonic acid-labelled cells were stimulated with fMetLeuPhe, ATP or Ca2+ ionophore A23187, and the lipids analysed by t.l.c., the increase in free fatty acid was accompanied by decreases in label from phosphatidylinositol and phosphatidylcholine. Moreover, incorporation of label into triacylglycerol and to a lesser extent phosphatidylethanolamine was evident. Activation of secretion was evident with ATP and fMetLeuPhe but not with A23187. The pharmacological specificity of the ATP receptor in HL60 cells was investigated by measuring secretion of beta-glucuronidase, formation of inositol phosphatases and release of [3H]arachidonic acid. External addition of ATP, UTP, ITP, adenosine 5'-[gamma-thio]triphosphate (ATP[S]), adenosine 5'-[beta gamma-imido]triphosphate (App[NH]p), XTP, CTP, GTP, 8-bromo-ATP and guanosine 5'-[gamma-thio]triphosphate (GTP[S]) to intact HL60 cells stimulated inositol phosphate production, but only the first five nucleotides were effective at stimulating secretion or [3H]arachidonic acid release. In human neutrophils, addition of ATP, ITP, UTP and ATP[S] also stimulated secretion from specific and azurophilic granules, and this was accompanied by increases in cytosolic Ca2+ and in [3H]arachidonic acid release. The addition of phorbol 12-myristate 13-acetate (PMA; 1 nM) prior to the addition of either fMetLeuPhe or ATP led to inhibition of phospholipase C activity. In contrast, this had no effect on phospholipase A2 activation, whilst secretion was potentiated. Phospholipase A2 activation by either agonist was dependent on an intact cell metabolism, as was secretion. It is concluded that (1) activation of phospholipase C does not always lead to activation of phospholipase A2, (2) phospholipase A2 is coupled to the receptor independently of phospholipase C via a pertussis-toxin-sensitive G-protein and (3) for secretion to take place, the receptor has to activate both phospholipases C and A2.
A COMPARISON BETWEEN THE GENETIC ALGORITHM AND THE FUNCTION SPECIFICATION METHODS FOR AN INVERSE THERMAL FIELD PROBLEM (1993)

In principle, it is possible to apply genetic algorithms (GAs) to the solution of inverse problems in the simulation of manufacturing processes. In this context, an inverse problem can be stated as ‘knowing the desired output of a process, what combination of process parameters are required for its achievement?’. Since the simulation of many processes requires the simulation of thermal, solids and/or fluids problems, the application of GAs to inverse process modelling depends on their ability to solve a wide range of inverse field problems. This paper has two major objectives: (a) to demonstrate the application of a GA to a simple inverse thermal field problem, and (b) to compare its performance against a relatively mature technique for the solution of such problems. The results of this study indicate that, despite the relatively large computational cost of GAs, their accuracy and robustness warrants further investigation of their performance in more demanding applications.
High-resolution HDX-MS reveals distinct mechanisms of RNA recognition and activation by RIG-I and MDA5 (2014)

RIG-I and MDA5 are the major intracellular immune receptors that recognize viral RNA species and undergo a series of conformational transitions leading to the activation of the interferon-mediated antiviral response. However, to date, full-length RLRs have resisted crystallographic efforts and a molecular description of their activation pathways remains hypothetical. Here we employ hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) to probe the apo states of RIG-I and MDA5 and to dissect the molecular details with respect to distinct RNA species recognition, ATP binding and hydrolysis and CARDs activation. We show that human RIG-I maintains an auto-inhibited resting state owing to the intra-molecular HEL2i-CARD2 interactions while apo MDA5 lacks the analogous intra-molecular interactions and therefore adopts an extended conformation. Our work demonstrates that RIG-I binds and responds differently to short triphosphorylated RNA and long duplex RNA and that sequential addition of RNA and ATP triggers specific allosteric effects leading to RIG-I CARDs activation. We also present a high-resolution protein surface mapping technique that refines the cooperative oligomerization model of neighboring MDA5 molecules on long duplex RNA. Taken together, our data provide a high-resolution view of RLR activation in solution and offer new evidence for the molecular mechanism of RLR activation.
A Miniaturized <i>Escherichia coli</i> Green Light Sensor with High Dynamic Range (2018)

Genetically engineered photoreceptors enable unrivaled control over gene expression. Previously, we ported the Synechocystis PCC 6803 CcaSR two-component system, which is activated by green light and deactivated by red, into Escherichia coli, resulting in a sensor with a sixfold dynamic range. Later, we optimized pathway protein expression levels and the output promoter sequence to decrease transcriptional leakiness and to increase the dynamic range to approximately 120-fold. These CcaSR v 1.0 and v 2.0 systems have been used for precise quantitative, temporal, and spatial control of gene expression for a variety of applications. Recently, other workers deleted two PAS domains of unknown function from the CcaS sensor histidine kinase in a system similar to CcaSR v 1.0. Here we apply these deletions to CcaSR v 2.0, resulting in a v 3.0 light sensor with an output four times less leaky and a dynamic range of nearly 600-fold. We demonstrate that the PAS domain deletions have no deleterious effect on CcaSR green light sensitivity or response dynamics. CcaSR v 3.0 is the best-performing engineered bacterial green light sensor available, and should have broad applications in fundamental and synthetic biology studies.
Towards Sketched-based Garment Design and Animation (2015)

Abstract—One of the most tedious tasks in the virtual clothing process is the garment creation phase with its direct pre-visualization, and animation on the body. In this paper, we propose a new approach for garment design from the outlines drawn directly on a 3D mannequin. These outlines represent the boundaries of closed regions that are quad meshed to generate the garment pieces. The garments can then be animated in a simulation system based on Finite Elements and using a rediscretization of the generated mesh into triangular elements containing a reconstructed metric of the cloth surface. This allows previewing the garment on bodies with various poses and animations. I.
Adaptive Sliding-Mode Guidance of a Homing Missile (1999)

Sliding-mode control is applied to design robust homing missile guidance law. The sufe cient and necessary condition for the sliding-mode motion of a linear time-varying system not to be affected by disturbances and the sufe cient condition for that motion not to be affected by parameter perturbations are given. An adaptive reaching law of sliding mode for a linear time-varying system is then presented and used to derive an adaptive sliding-mode guidance law. Theoretical analysis and simulation results show that the adaptive sliding-mode guidance law is robust against disturbances and parameter perturbations. Furthermore, the presented guidance law is simple to implement in practice.
<i>Pseudomonas syringae</i>Phytotoxins: Mode of Action, Regulation, and Biosynthesis by Peptide and Polyketide Synthetases (1999)

SUMMARY Coronatine, syringomycin, syringopeptin, tabtoxin, and phaseolotoxin are the most intensively studied phytotoxins of Pseudomonas syringae, and each contributes significantly to bacterial virulence in plants. Coronatine functions partly as a mimic of methyl jasmonate, a hormone synthesized by plants undergoing biological stress. Syringomycin and syringopeptin form pores in plasma membranes, a process that leads to electrolyte leakage. Tabtoxin and phaseolotoxin are strongly antimicrobial and function by inhibiting glutamine synthetase and ornithine carbamoyltransferase, respectively. Genetic analysis has revealed the mechanisms responsible for toxin biosynthesis. Coronatine biosynthesis requires the cooperation of polyketide and peptide synthetases for the assembly of the coronafacic and coronamic acid moieties, respectively. Tabtoxin is derived from the lysine biosynthetic pathway, whereas syringomycin, syringopeptin, and phaseolotoxin biosynthesis requires peptide synthetases. Activation of phytotoxin synthesis is controlled by diverse environmental factors including plant signal molecules and temperature. Genes involved in the regulation of phytotoxin synthesis have been located within the coronatine and syringomycin gene clusters; however, additional regulatory genes are required for the synthesis of these and other phytotoxins. Global regulatory genes such as gacS modulate phytotoxin production in certain pathovars, indicating the complexity of the regulatory circuits controlling phytotoxin synthesis. The coronatine and syringomycin gene clusters have been intensively characterized and show potential for constructing modified polyketides and peptides. Genetic reprogramming of peptide and polyketide synthetases has been successful, and portions of the coronatine and syringomycin gene clusters could be valuable resources in developing new antimicrobial agents.
Molecular mechanisms of nitrovasodilator bioactivation (1991)

All nitrovasodilators act intracellularly by a common molecular mechanism. This is characterized by the release of nitric oxide (NO). They are, thus, prodrugs or carriers of the active principle NO, responsible for endothelial controlled vasodilation. The rate of NO-formation strongly correlates with the activation of the soluble guanylate cyclase in vitro, resulting in a stimulation of cGMP synthesis. Nitrovasodilators thus are therapeutic substitutes for endogenous EDRF/NO. The pathways of bioactivation, nevertheless, differ substantially, depending on the individual chemistry of the nitrovasodilator. Besides NO, numerous other reaction products such as nitrite and nitrate anions are formed. The guanylate cyclase is only activated if NO is liberated. In the case of organic nitrates such as GTN, NO is only formed if certain thiol compounds are present as an essential cofactor. The rate of NO-formation correlates with the number of nitrate ester groups and proceeds with a simultaneous nitrite formation (with a ratio of 1:14 in the presence of cysteine). Nitrosamines such as molsidomine do not need thiol compounds for bioactivation. They directly liberate NO from the ring-open A-forms. This process basically depends on the presence of oxygen as electron acceptor from the sydnonimine molecule. Therefore, besides NO also superoxide radicals are formed, which may react with the generated NO under formation of nitrate ions. Organic nitrites (such as amyl nitrite) require the preceding interaction with a mercapto group to form a S-nitrosothiol intermediate, from which finally NO radicals are liberated. Nitrosothiols (like S-nitroso-acetyl-penicillamine) and sodium nitroprusside spontaneously release NO. The molecules themselves do not possess a direct enzyme activating potency. In the presence of thiol compounds organic nitrites (e.g., amyl nitrite) and nitrosothiols may act as intermediary products of NO generation.
Study of lipid rich compositions in the intimal wall of aorta by Raman spectroscopy (2008)

We report an ex-vivo study on Raman spectra of adipose tissue covered by layers of aortic intimal wall tissue with different thicknesses. The Raman vibration modes of 1435cm<sup>-1</sup>, 2850cm<sup>-1</sup> and 2892cm<sup>-1</sup> were investigated for the first time on fresh porcine aortic adipose tissue with 633 nm laser excitation. The adipose tissue was taken from adventitial fat grown on aorta walls. The frozen sections of porcine aorta wall tissue with a thickness of 25μ - 50μ were cut from intimal surface. The samples were prepared by placing the variable numbers of the aorta intimal wall tissue layers on the top of adipose tissue. The Raman spectra of adipose tissue were investigated. The changes of intensities of the Raman modes versus thickness of the aorta intimal wall tissue layers were measured. The total thickness of the aorta intimal wall tissue layers was varied in the range of 50μ - 1800μ. The main characteristic Raman vibration modes of adipose tissue were found at 1435cm<sup>-1</sup>, 2850cm<sup>-1</sup> and 2892cm<sup>-1</sup>. Among them, the intensities of the modes of 2850 cm<sup>-1</sup> and 2892 cm<sup>-1</sup> are about four-times stronger than that of the 1435cm<sup>-1</sup> mode. The study on Raman vibration modes of 1435cm<sup>-1</sup>, 2800 cm<sup>-1</sup> and 2950 cm<sup>-1</sup> may be useful for developing a simple, inexpensive and accurate optical technique for monitoring the degree of vulnerability of the aorta intimal surface due to atherogenesis. These three Raman modes can be used as new molecular spectroscopic indicators to monitor <i>in situ </i>the development of fatty-streaks and lipid core in aorta walls, and determine the thickness change of aorta intimal wall at different stages of atherogenesis.
An improved Q-tuning scheme and a fully symmetric OTA (2003)

An improved tuning scheme for continuous-time high-Q biquad filters is proposed. An improvement over the existing implementation of the modified-LMS Q-tuning scheme is combined with frequency tuning using PLL. The scheme has less area overhead, consumes less power and is more robust to offsets in the building blocks without compromising the accuracy achieved previously. A new architecture for a pseudo-differential fully-symmetric high frequency transconductor is also proposed. It combines CMFF and CMFB to achieve a faster common mode response. A bandpass filter with center frequency 100 MHz and Q of 20 is built using the proposed OTA. The proposed tuning scheme is used to tune the filter. The circuit is fabricated in standard CMOS 0.5/spl mu/m technology and the experimental results show that the Q tuning error is around 1%.
Optimization of toroidal field coil conductor properties for BPX (2002)

Mechanical, thermal, and electrical properties, as well as its commercial availability in large plate form, made CDA C17510 copper alloy the primary candidate for use as the TF (toroidal field) coil conductor. Research was performed in order to improve the material properties. A set of small plates having different production processes was produced with enhanced strength, ductility, and electrical conductivity. Results of the program led to the production of a C17510 plate with properties optimized for the BPX (Burning Plasma Experiment).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Modifying the surface charge of single track-etched conical nanopores in polyimide (2008)

Chemical modification of nanopore surfaces is of great interest as it means that the surface composition is no longer fixed by the choice of substrate material, even to the point where large biomolecules can be attached to the pore walls. Controlling nanopore transport characteristics is one important application of surface modification which is very relevant given the significant interest in sensors based on the transport of ions and molecules through nanopores. Reported here is a method to change the surface charge polarity of single track-etched conical nanopores in polyimide, which also has the potential to attach more complex molecules to the carboxyl groups on the nanopore walls. These carboxyl groups were converted into terminal amino groups, first by activation with N-(3-dimethylaminopropyl)-N-ethylcarbodiimide (EDC) and N-hydroxysuccinimide (NHS) followed by the covalent coupling of ethylenediamine. This results in a changed surface charge polarity. Regeneration of a carboxyl-terminated surface was also possible, by reaction of the amino groups with succinic anhydride. The success of these reactions was confirmed by measurements of the pore's pH sensitive current-voltage (I-V) characteristics before and after the chemical modification, which depend on surface charge. The permselectivity of the pores also changed accordingly with the modification.
Outcomes in Adults With Bicuspid Aortic Valves (2008)

In this study population of young adults with bicuspid aortic valve, age, severity of aortic stenosis, and severity of aortic regurgitation were independently associated with primary cardiac events. Over the mean follow-up duration of 9 years, survival rates were not lower than for the general population.
Design of high-performance photodiode receivers for optical tomography (2005)

The design of instrumentation hardware for tomographic systems must take careful account of measurement noise. This is especially true in near-infrared absorption tomography, where the signal of interest is typically only a few percent of the total signal at the detector, and the available optical power may have to be shared among many measurement channels. In this paper, the monitoring of photodiodes in near-IR absorption tomography is examined in detail, but much of the material is applicable at wavelengths ranging from the UV to beyond 2.5 /spl mu/m. The authors' application involves the frequency region 50 kHz to 2 MHz, which lies above that utilized in the majority of radiometric sensing systems, yet substantially below telecoms bit rates. The problem is further distinguished by the use of phase-sensitive detection schemes, which make local noise density more relevant than wideband noise performance and relax the requirement for dc precision. Alternative transimpedance circuit configurations, including both single-ended and differential topologies, are analyzed with a view to optimization of the signal-to-noise ratio. Typical values of photodiode capacitance and shunt resistance are shown to result in significant noise gain, greatly increasing the importance of amplifier voltage noise relative to other intrinsic noise sources. It is shown that for applications of this type, viable alternatives to the traditionally dominant FET amplifier do exist. The relative susceptibility to coupled interference is also considered. The results of practical tests, involving class-leading operational amplifiers, are presented to support the analyses. These results also underline the need for careful circuit layout and shielding if the capabilities of these devices are to be fully exploited.
Conversion of vestitone to medicarpin in alfalfa (Medicago sativa L.) is catalyzed by two independent enzymes. Identification, purification, and characterization of vestitone reductase and 7,2‘-dihydroxy-4‘-methoxyisoflavanol dehydratase. (1994)

Pterocarpan phytoalexins are antimicrobial compounds in leguminous plants. The final step of pterocarpan biosynthesis, conversion of vestitone to medicarpin, was thought to be catalyzed by a single enzyme "pterocarpan synthase." We have shown that the pterocarpan synthase activity observed in crude extracts of alfalfa suspension cell cultures is the sum of two independent enzymatic activities: vestitone reductase, which catalyzes the NADPH-dependent reduction of vestitone to 7,2'-dihydroxy-4'-methoxyisoflavanol (DMI), and DMI dehydratase, which catalyzes loss of water and closure of an ether ring to form medicarpin. The first enzyme, vestitone reductase, was purified 1,840-fold to homogeneity by a 5-step procedure. Purified vestitone reductase showed a single band on SDS-polyacrylamide gel electrophoresis with an estimated molecular mass of 38 kDa. The native molecular mass measured by gel filtration was shown to be 34 kDa, indicating that vestitone reductase is a monomer. Vestitone reductase has strict substrate stereo specificity for (3R)-vestitone with a Km value of 45 microM. The second enzyme, DMI dehydratase, was partially purified 962-fold. DMI dehydratase had a native molecular mass of 38 kDa as estimated by gel filtration and a Km value of 5 microM for DMI. Both enzymes have a temperature optimum of 30 degrees C and a pH optimum of 6.0. The discovery of vestitone reductase and DMI dehydratase will facilitate future genetic manipulation of pterocarpan biosynthesis.
Importance of Vacuum for Breastmilk Expression (2008)

Use of the mother's maximum comfortable vacuum enhances milk flow rate and milk yield. The cream content of the milk at the end of the expression period was an indicator of how effectively the breast had been drained.