gebhart/patrepeval huggingface dataset:
Active site mutants of pyruvate decarboxylase from <i>Zymomonas mobilis</i> (1998)

The homotetrameric pyruvate decarboxylase (PDC) from Zymomonas mobilis requires the cofactors thiamin diphosphate and Mg2+ for catalytic activity. We have investigated the role of various amino acid residues in the direct environment of the active site. The role of residue E473 in the catalytic activity and stability of the enzyme was probed by several mutations. All mutant enzymes were either inactive or failed to give any recombinant protein. The close interaction of E473 and N482, which can be deduced from the X-ray structure, has been probed by mutagenesis of N482 to D. This mutation has a significant influence especially on the carboligation reaction of PDC, whereas the binding of the cofactors and the thermostability were not affected. These data suggest a specific interaction of N482 and EA73 which is essential for coordinating the second aldehyde molecule during carboligation. Three hydrophobic residues (L112, I472 and I476) in the vicinity of the active centre have been investigated with respect to their potential influence on the transition states during catalysis. In contrast to L112, I472 and I476 influence the decarboxylation and carboligation reactions. The enlarged substrate-binding site of PDCI472A allows the decarboxylation of longer aliphatic 2-keto acids (C4-C6) as well as aromatic 2-keto acids besides pyruvate. Carboligations using PDCI472A as a catalyst yielded 2-hydroxypropiophenone, benzoin and phenylacetylcarbinol. The enantioselectivity of PAC formation is impaired by mutations of both I472 and I476. The stereochemistry is most significantly affected with the mutant enzyme PDCI476E, which catalyses predominantly the synthesis of (S)-phenylacetylcarbinol.
Optimizing the Planarity of Sound Zones (2013)

Reproduction of personal sound zones can be attempted by sound field synthesis, energy control, or a combination of both. Energy control methods can create an unpredictable pressure distribution in the listening zone. Sound field synthesis methods may be used to overcome this problem, but tend to produce a lower acoustic contrast between the zones. Here, we present a cost function to optimize the cancellation and the plane wave energy over a range of incoming azimuths, producing a planar sound field without explicitly specifying the propagation direction. Simulation results demonstrate the performance of the methods in comparison with the current state of the art. The method produces consistent high contrast and a consistently planar target sound zone across the frequency range 80-7000Hz. Copyright © (2013) by the Audio Engineering Society.
SubIslands: the probabilistic match assignment algorithm for subcircuit recognition (2003)

The recognition of subcircuit instances in a larger circuit is widely used in the simulation, verification, and testing of integrated circuit computer-aided designs. Subcircuit recognition (SR) can be stated as a problem of finding images of a small model bipartite graph (BG) corresponding to a subcircuit in a large object BG corresponding to a circuit. The best-known SR algorithms are based on the search-oriented subgraph isomorphism methods. Unfortunately, these methods may require a long runtime for large and highly symmetrical circuits. The authors develop a new high-performance probabilistic recognition method for solving the SR problem. This method combines: 1) the graduated assignment matching technique; 2) two well-known concepts from pattern recognition theory, namely, the error propagation and the delayed decision making; and 3) an efficient probabilistic BG labeling algorithm. In contrast to the search-based algorithms, the new recognition method solves the SR problem as an optimization task and, as a consequence, allows extremely fast simultaneous finding of subcircuit images. The experimental results show that this approach recognizes all the subcircuit instances orders of magnitude faster than the search-oriented algorithms.
Prevention of C3 deposition by capsular polysaccharide is a virulence mechanism of type III group B streptococci (1992)

Strains of type III group B streptococci isolated from patients with neonatal sepsis are generally resistant to complement-mediated phagocytic killing in the absence of specific antibody. It has been suggested that the resistance of type III group B streptococci to phagocytosis results from inhibition of alternative-complement-pathway activation by sialic acid residues of the type III polysaccharide. To better define the relationship between structural features of the type III capsule and resistance of type III group B streptococci to complement-mediated phagocytic killing, we measured deposition of human C3 on group B streptococcal strains with altered capsule phenotypes. C3 binding was quantified by incubating bacteria with purified human 125I-C3 in 10% serum. Wild-type group B Streptococcus sp. strain COH1 bound eightfold fewer C3 molecules than did either of two isogenic mutant strains, one expressing a sialic acid-deficient capsule and the other lacking capsule completely. Similar results were obtained when the incubation with 125I-C3 was performed in serum chelated with Mg-ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'- tetraacetic acid (MgEGTA), suggesting that the majority of C3 deposition occurred via the alternative pathway. In contrast to the wild-type strain, which was relatively resistant, both mutant strains were killed by human leukocytes in 10% serum with or without MgEGTA. We also measured C3 binding to 14 wild-type strains of type III group B streptococci expressing various amounts of capsule. Comparison of degree of encapsulation with C3 binding revealed a significant inverse correlation (r = -0.72; P less than 0.01). C3 fragments released by methylamine treatment of wild-type strain COH1 were predominantly in the form of C3bi, while those released from the acapsular mutant were predominantly C3b and those from the asialo mutant represented approximately equal amounts of C3b and C3bi. We conclude from these studies that the sialylated type III capsular polysaccharide inhibits alternative-pathway activation, prevents C3 deposition on group B streptococci, and protects the organisms from phagocytic killing.
Transgenic potato plants resistant to the phytopathogenic bacterium <i>Erwinia carotovora</i> (1993)

The phytopathogenic bacterium Erwina carotovora spp. which infects potato plants causes severe losses in agriculture. No protective means or resistance traits usable for plant breeding are known. Introduction of a new resistance gene into potato by gene technology leads to a reduced susceptibility of the transgenic plants towards Erwinia carotovora atroseptica infection. Bacteriophage T4 lysozyme is the most active member of a class of bacteriolytic enzymes also detected in several plant species. Secretion of the foreign T4 lysozyme into the intercellular spaces of transgenic potato plants effects a resistance against the phytopathogenic bacterium already at low expression levels.
Inhibition of hepatic fibrogenesis by matrix metalloproteinase‐9 mutants in mice (2006)

Tissue inhibitor of metalloproteinases-1 (TIMP-1) plays a crucial role in the pathogenesis of hepatic fibrosis and thus may represent an important therapeutic target in the design of anti-fibrotic strategies for chronic liver disease. We present an innovative therapy based on the assignment of inactivated enzymes acting as scavengers for TIMP-1. Hepatic fibrosis was induced in BALB/c mice by repetitive intraperitoneal CCl4 injection. The animals were treated with proteolytic inactive matrix metalloproteinase-9 mutants (E402Q, H401A, E402H/H411E) using adenovirus-mediated gene transfer. Application of these MMP-9 mutants inhibited fibrogenesis, which was indicated by decreasing portal and periportal accumulation of collagen. Total hydroxyproline of liver tissue, the morphometric stage of fibrosis as well as mRNA expression of marker proteins for hepatic fibrosis in livers of E402Q- and H401A-treated mice were significantly reduced. MMP-9 mutants suppressed transdifferentiation of hepatic stellate cells to the myofibroblast like phenotype in vitro and in vivo. Moreover, adenoviral application of the mutants MMP-9-H401A and -E402Q led to increased apoptosis of activated hepatic stellate cells, thought to be the main promoters of hepatic fibrosis. Application of MMP-9 mutants as TIMP-1 scavengers may provide a new therapeutic strategy for hepatic fibrosis.
Endometrial stem/progenitor cells and proliferative disorders of the endometrium. (2006)

The human endometrium undergoes cyclical processes of regeneration, differentiation and shedding as part of the menstrual cycle. In non-menstruating species, there are cycles of endometrial growth and apoptosis rather than physical shedding. It was hypothesized many years ago that endometrial stem cells are responsible for the remarkable regenerative capacity of endometrium. In this review, we summarize the first data providing evidence for the presence of adult stem/progenitor cells in human and mouse endometrium using functional assays. This is because adult stem cells are defined by their functional properties rather than by marker expression, and there are no known markers of endometrial stem/progenitor cells. Evidence will be presented which demonstrates that the endometrium contains rare populations of both and epithelial and stromal stem/progenitor cells. These fundamental studies on endometrial stem/progenitor cells will provide new insights into the pathophysiology of various gynecological disorders associated with abnormal endometrial proliferation, including endometriosis, endometrial cancer, endometrial hyperplasia, and adenomyosis. The possible use of endometrial stem/progenitor cells in tissue engineering applications relevant to urogynecology will also be mentioned.
Operating Characteristics of Loop Heat Pipes (1999)

<div class="section abstract"><div class="htmlview paragraph">The loop heat pipe (LHP) was invented in Russia in the early 1980’s. It is a two-phase heat transfer device that utilizes the evaporation and condensation of a working fluid to transfer heat, and the capillary forces developed in fine porous wicks to circulate the fluid. The LHP is known for its high pumping capability and robust operation because it uses fine-pored metal wicks and the integral evaporator/hydro-accumulator design. It has gained rapid acceptance in recent years as a thermal control device in space applications. This paper presents an overview of the LHP operation. The physical processes and the thermal-hydraulic behaviors of the LHP are first described. Operating characteristics as functions of various parameters including the heat load, sink temperature, ambient temperature, and elevation are presented. Peculiar behaviors in LHP operation such as temperature hysteresis and temperature overshoot during start-up are explained. Issues related to multiple-evaporator LHP’s are also addressed.</div></div>
Laser-Induced Breakdown Spectrometry of Titanium Dioxide Antireflection Coatings in Photovoltaic Cells (1996)

Silicon photovoltaic cells have design and material requirements different from those of most other silicon electronic devices. Not only are nearly ideal silicon surfaces required, but also the bulk properties must be of uniform high quality for high-energy conversion efficiency. In this paper, emission spectra of laser-generated plasmas from titanium dioxide antireflection coatings in solar cells are reported. A pulsed nitrogen laser at 337.1 nm was used with a pulse width of 10 ns and a laser fluence of 8.6 J/cm(2) onto the sample. The plasmas were detected using a charge-coupled device. Depth profilings from several samples with different thicknesses of titanium dioxide have been studied. A method for measuring thin TiO(2) films based on the observation of such profiles was developed. The effect of the laser fluence on the sensitivity of the present method has been examined. Depth resolutions are fluence-dependent but are on the order of 40 nm. The dependence between titanium dioxide plasma intensity and material reflectivity at the laser wavelength is discussed. Another valuable aspect of the technique is the ability to perform measurements in a contactless manner at room temperature and atmospheric pressure on wafer-sized samples.
Reaction of Reduced PQQ (PQQH2) and Molecular Oxygen (1986)

Abstract Reduced PQQ (PQQH2) is prepared by the reaction of PQQ with thiophenol, 1-benzyl-1,4-dihydronicotinamide (BNAH), sodium dithionite, or sodium borohydride. Oxidation of PQQH2 to PQQ by molecular oxygen in aqueous solutions is investigated kinetically. The oxidation is accelerated gradually with proceeding of the reaction, which may be attributed to the side reaction of PQQH2 and H2O2 produced by the reaction of PQQH2 and O2. As in fact, the yield of H2O2 is found to be 50% based on PQQH2. Initial rate is first-order in oxygen concentration. The pH-rate profile suggests that an active species in the reaction is PQQH−. Autocatalysis of O2\ewdot and PQQ itself is scarcely detected in this reaction. The mechanism of the oxidation is also discussed.
Exploring EEG-based biometrics for user identification and authentication (2014)

As human brain activities, represented by EEG brainwave signals, are more confidential, sensitive, and hard to steal and replicate, they hold great promise to provide a far more secure biometric approach for user identification and authentication. In this study, we present an EEG-based biometric security framework. Specifically, we propose to reduce the noise level through ensemble averaging and low-pass filter, extract frequency features using wavelet packet decomposition, and perform classification based on an artificial neural network. We explicitly discuss four different scenarios to emulate different application cases in authentication. Experimental results show that: the classification rates of distinguishing one subject or a small group of individuals (e.g., authorized personnel) from others (e.g., unauthorized personnel) can reach around 90%. However, it is also shown that recognizing each individual subject from a large pool has the worst performance with a classification rate of less than 11%. The side-by-side method shows an improvement on identifying all the subjects with classification rates of around 40%. Our study lays a solid foundation for future investigation of innovative, brainwave-based biometric approaches.
Fog Computing: Issues, Challenges and Future Directions (2017)

In Cloud Computing, all the processing of the data collected by the node is done in the central server. This involves a lot of time as data has to be transferred from the node to central server before the processing of data can be done in the server. Also it is not practical to stream terabytes of data from the node to the cloud and back. To overcome these disadvantages, an extension of cloud computing, known as fog computing, is introduced. In this, the processing of data is done completely in the node if the data does not require higher computing power and is done partially if the data requires high computing power, after which the data is transferred to the central server for the remaining computations. This greatly reduces the time involved in the process and is more efficient as the central server is not overloaded. Fog is quite useful in geographically dispersed areas where connectivity can be irregular. The ideal use case requires intelligence near the edge where ultra-low latency is critical, and is promised by fog computing. The concepts of cloud computing and fog computing will be explored and their features will be contrasted to understand which is more efficient and better suited for real-time application.
High frequency-low loss SAW resonators built on NanoCrystalline Diamond-based substrate (2014)

The interest of surface acoustic wave devices (SAW) operating in radio-frequency range is their very high compactness, low losses and high quality factor. Thus, they are very interesting components for the stabilization of ultra-low noise on-board oscillators operating in direct bands. The need for working frequency beyond 3 GHz has lead SAW manufacturers to develop multilayer diamond-based waveguides providing higher phase velocity than conventional single-crystal materials, typically ranging from 7 to 12 km.s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> for elliptically polarized waves. The very problem in this approach is the excitation and detection of acoustic waves requiring a high quality piezoelectric layer of less than one micrometer thick with physical properties as close as possible to the tabulated ones. An ultimate control of the film thickness and roughness is required to control dispersion and diffusion losses. In this work, we investigated a structure based on Nano-Crystalline Diamond (NCD). The waves are launched and detected using a Zinc Oxide film deposited atop the diamond layer, yielding notable dispersive properties of the device. In this way, technological developments have been achieved (NCD growth, piezoelectric layer deposition, e-beam and optical lithography) to build SAW devices taking advantage of NCD films to try and benefit from their suspected low acoustic damping. Results show the possibility of developing devices operating between 2 and 3 GHz at minimum, having losses lower than 10 dB. At last, devices whose dimensions are compatible with conventional lithography processes, show resonances at more than 4 GHz with less than 8 dB of insertion loss, what is, at the knowledge of the authors, the best experimental result for such devices. To compare with previous results, a device operating near 3 GHz has been used to stabilize an oscillator. Short term stability has been measured at 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-8</sup> s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> and a phase noise floor was observed at -170 dB at 3 MHz from the carrier. Although not yet meeting the expected requirements, these results show the impact of loss reduction and general device improvement and allow for preparing future work near 5 GHz.
Using iPodLinux in an introductory OS course (2008)

This paper describes a proof of concept for introducing iPods and iPodLinux into a one-semester introductory undergraduate operating systems course. iPodLinux is a version of the Linux operating system modified to run on iPods. We added a project to our course in which the students modified the iPodLinux kernel, and we supplemented lectures by discussing specifics of the Linux implementation as they relate to general operating systems concepts. We feel the course was much improved by these additions, with no substantive omission of regular material. Student response was very enthusiastic, and we feel the new material enhanced their course experience by providing a component that was empowering and helped to further improve their knowledge and skills.
Fos-related Antigen (Fra-1), junB, and junD Activate Human Involucrin Promoter Transcription by Binding to Proximal and Distal AP1 Sites to Mediate Phorbol Ester Effects on Promoter Activity (1995)

Human involucrin (hINV) is a cornified envelope precursor that is specifically expressed in the suprabasal epidermal layers. We previously demonstrated that 2500 base pairs of the hINV gene upstream regulatory region confers differentiation appropriate regulation in transgenic mice. An analysis of the hINV gene sequence upstream of the transcription start site reveals five potential AP1 binding sites (AP1-1 to 5). Using reporter gene constructs in human keratinocytes, we show that the most distal (AP1-5) and most proximal (AP1-1) AP1 sites are essential for high level transcriptional activity. Simultaneous mutation of these sites reduces transcription by 80%. Gel supershift experiments indicate the interaction of these sites with Fra-1, junB, and junD. Involucrin mRNA levels increase 10-fold and promoter activity 5-11-fold when differentiation is induced by phorbol ester. Functional studies implicate AP1-1 and AP1-5 in mediating the phorbol ester-dependent increase in promoter activity. No involucrin promoter activity or involucrin mRNA was detected in 3T3 fibroblasts. We conclude that (i) two AP1 sites in the hINV promoter are important elements required for keratinocyte-specific expression, (ii) these AP1-1 sites mediate the phorbol ester-dependent increase in promoter activity, and (iii) Fra-1, junB, and junD may be important regulators of hINV expression in epidermis.
Organic and Organometallic Molecular Magnetic Materials—Designer Magnets (1994)

Abstract Magnets composed of molecular species or polymers and prepared by relatively low‐temperature organic synthetic methodologies are a focus of contemporary materials science research. The anticipated properties of such molecular‐species‐based magnetic materials, particularly in combination with other properties associated with molecules and polymers, may enable their use in future generations of electronic, magnetic, and/or photonic/photronic devices ranging from information storage and magnetic imaging to static and low‐frequency magnetic shielding. A tutorial of typical magnetic behavior of molecular materials is presented. The three distinct models (intramolecular spin coupling through orthogonal orbitals in the same spatial region within a molecule/ion, intermolecular spin coupling through pairwise “configuration interaction” between spin‐containing moieties, and dipole—dipole, through‐space interactions) which enable the design of new molecular‐based magnetic materials are discussed. To achieve the required spin couplings for bulk ferro‐ or ferrimagnetic behavior it is crucial to prepare materials with the necessary primary, secondary, and tertiary structures akin to proteins. Selected results from the worldwide effort aimed at preparing molecular‐based magnetic materials by these mechanisms are described. Some organometallic solids comprised of linear chains of alternating metallocenium donors (D) and cyanocarbon acceptors (A) that is, …︁D •+ A •− D •+ A •− …︁, exhibit cooperative magnetic phenomena. Bulk ferromagnetic behavior was first observed below the critical (Curie) temperature T c of 4.8 K for [Fe III (C 5 Me 5 ) 2 ] •+ [TCNE] •− (Me = methyl; TCNE = tetracyanoethylene). Replacement of Fe III with Mn III leads to a ferromagnet with a T c of 8.8 K in agreement with mean‐field models developed for this class of materials. Replacement with Cr III , however, leads to a ferromagnet with a T c lowered to 3.65 K which is at variance with this model. Extension to the reaction of a vanadium(o) complex with TCNE leads to the isolation of a magnet with a T c ≈ 400 K, which exceeds the thermal decomposition temperature of the material. This demonstrates that a magnetic material with a T c substantially above room temperature is achievable in a molecule/organic/polymeric material. Finally, a new class of one‐dimensional ferrimagnetic materials based on metalloporphins is discussed.