gebhart/patrepeval huggingface dataset:
The origin and evolution of Archaea: a state of the art (2006)

Environmental surveys indicate that the Archaea are diverse and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the planet. Archaea display unique capacities, such as methanogenesis and survival at temperatures higher than 90 degrees C, that make them crucial for understanding the nature of the biota of early Earth. Molecular, genomics and phylogenetics data strengthen Woese's definition of Archaea as a third domain of life in addition to Bacteria and Eukarya. Phylogenomics analyses of the components of different molecular systems are highlighting a core of mainly vertically inherited genes in Archaea. This allows recovering a globally well-resolved picture of archaeal evolution, as opposed to what is observed for Bacteria and Eukarya. This may be due to the fact that no rapid divergence occurred at the emergence of present-day archaeal lineages. This phylogeny supports a hyperthermophilic and non-methanogenic ancestor to present-day archaeal lineages, and a profound divergence between two major phyla, the Crenarchaeota and the Euryarchaeota, that may not have an equivalent in the other two domains of life. Nanoarchaea may not represent a third and ancestral archaeal phylum, but a fast-evolving euryarchaeal lineage. Methanogenesis seems to have appeared only once and early in the evolution of Euryarchaeota. Filling up this picture of archaeal evolution by adding presently uncultivated species, and placing it back in geological time remain two essential goals for the future.
Novel Psychrophilic and Thermolabile <scp>l</scp> -Threonine Dehydrogenase from Psychrophilic <i>Cytophaga</i> sp. Strain KUC-1 (2003)

A psychrophilic bacterium, Cytophaga sp. strain KUC-1, that abundantly produces a NAD(+)-dependent L-threonine dehydrogenase was isolated from Antarctic seawater, and the enzyme was purified. The molecular weight of the enzyme was estimated to be 139,000, and that of the subunit was determined to be 35,000. The enzyme is a homotetramer. Atomic absorption analysis showed that the enzyme contains no metals. In these respects, the Cytophaga enzyme is distinct from other L-threonine dehydrogenases that have thus far been studied. L-Threonine and DL-threo-3-hydroxynorvaline were the substrates, and NAD(+) and some of its analogs served as coenzymes. The enzyme showed maximum activity at pH 9.5 and at 45 degrees C. The kinetic parameters of the enzyme are highly influenced by temperatures. The K(m) for L-threonine was lowest at 20 degrees C. Dead-end inhibition studies with pyruvate and adenosine-5'-diphosphoribose showed that the enzyme reaction proceeds via the ordered Bi Bi mechanism in which NAD(+) binds to an enzyme prior to L-threonine and 2-amino-3-oxobutyrate is released from the enzyme prior to NADH. The enzyme gene was cloned into Escherichia coli, and its nucleotides were sequenced. The enzyme gene contains an open reading frame of 939 bp encoding a protein of 312 amino acid residues. The amino acid sequence of the enzyme showed a significant similarity to that of UDP-glucose 4-epimerase from Staphylococcus aureus and belongs to the short-chain dehydrogenase-reductase superfamily. In contrast, L-threonine dehydrogenase from E. coli belongs to the medium-chain alcohol dehydrogenase family, and its amino acid sequence is not at all similar to that of the Cytophaga enzyme. L-Threonine dehydrogenase is significantly similar to an epimerase, which was shown for the first time. The amino acid residues playing an important role in the catalysis of the E. coli and human UDP-glucose 4-epimerases are highly conserved in the Cytophaga enzyme, except for the residues participating in the substrate binding.
1,5-Diazabicyclo[3.3.0]octadienediones (9,10-dioxabimanes). Strongly fluorescent syn isomers (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1,5-Diazabicyclo[3.3.0]octadienediones (9,10-dioxabimanes). Strongly fluorescent syn isomersEdward M. Kosower, Barak Pazhenchevsky, and Eli HershkowitzCite this: J. Am. Chem. Soc. 1978, 100, 20, 6516–6518Publication Date (Print):September 1, 1978Publication History Published online1 May 2002Published inissue 1 September 1978https://doi.org/10.1021/ja00488a050RIGHTS & PERMISSIONSArticle Views455Altmetric-Citations81LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (442 KB) Get e-Alerts Get e-Alerts
Programmed Self-Sorting of Coiled Coils with Leucine and Hexafluoroleucine Cores (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTProgrammed Self-Sorting of Coiled Coils with Leucine and Hexafluoroleucine CoresBasar Bilgiçer, Xuechao Xing, and Krishna KumarView Author Information Department of Chemistry, Tufts University Medford, Massachusetts 02155-5813 Cite this: J. Am. Chem. Soc. 2001, 123, 47, 11815–11816Publication Date (Web):November 3, 2001Publication History Received6 August 2001Published online3 November 2001Published inissue 1 November 2001https://pubs.acs.org/doi/10.1021/ja016767ohttps://doi.org/10.1021/ja016767orapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1382Altmetric-Citations149LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Disulfides,Equilibrium,Oligomers,Peptides and proteins,Redox reactions Get e-Alerts
Acquisition of conceptual data models from natural language descriptions (1987)

Acquiring information systems specifications from natural language description is presented as a problem class that requires a different treatment of semantics when compared with other applied NL systems such as database and operating system interfaces. Within this problem class, the specific task of obtaining explicit conceptual data models from natural language text or dialogue is being investigated. The knowledge brought to bear on this task is classified into syntactic, semantic and systems analysis knowledge. Investigations with a simple syntactic parse and with a semantic analysis using McCorcl's Slot Grammar are reported, and the structure of the systems analysis knowledge is considered.
Decomposition of Trace Phenol in Solution Using Gas–Liquid Interface Discharge (2006)

Many researchers have investigated the decomposition of trace phenol in solution using liquid-phase discharge. However, liquid-phase discharge has a problem of consuming an extremely high energy. We have investigated phenol decomposition using a gas–liquid interface discharge induced by an ultra-short width (∼600 ns) pulse of high voltage. Gas bubbling was employed to enhance both convection and the gas–liquid interface area, because chemical reactions take place mainly at the surface of a solution. A significant improvement in energy efficiency of phenol decomposition was achieved. In addition, phenol decomposition using air mixed with argon (Ar) and hydrogen peroxide (H2O2) as a bubbling gas was investigated. Phenol removal using air together with H2O2 bubbling was approximately twice as efficient as air bubbling alone, which was attributed to the increase in the amount of hydroxyl (OH) radicals.
Metal finishing with ionic liquids: scale-up and pilot plants from IONMET consortium (2010)

(2010). Metal finishing with ionic liquids: scale-up and pilot plants from IONMET consortium. Transactions of the IMF: Vol. 88, No. 6, pp. 285-293.
Sbi00515, a Protein of Unknown Function from <i>Streptomyces bingchenggensis</i>, Highlights the Functional Versatility of the Acetoacetate Decarboxylase Scaffold (2015)

The acetoacetate decarboxylase-like superfamily (ADCSF) is a group of ~4000 enzymes that, until recently, was thought to be homogeneous in terms of the reaction catalyzed. Bioinformatic analysis shows that the ADCSF consists of up to seven families that differ primarily in their active site architectures. The soil-dwelling bacterium Streptomyces bingchenggensis BCW-1 produces an ADCSF enzyme of unknown function that shares a low level of sequence identity (~20%) with known acetoacetate decarboxylases (ADCs). This enzyme, Sbi00515, belongs to the MppR-like family of the ADCSF because of its similarity to the mannopeptimycin biosynthetic protein MppR from Streptomyces hygroscopicus. Herein, we present steady state kinetic data that show Sbi00515 does not catalyze the decarboxylation of any α- or β-keto acid tested. Rather, we show that Sbi00515 catalyzes the condensation of pyruvate with a number of aldehydes, followed by dehydration of the presumed aldol intermediate. Thus, Sbi00515 is a pyruvate aldolase-dehydratase and not an acetoacetate decarboxylase. We have also determined the X-ray crystal structures of Sbi00515 in complexes with formate and pyruvate. The structures show that the overall fold of Sbi00515 is nearly identical to those of both ADC and MppR. The pyruvate complex is trapped as the Schiff base, providing evidence that the Schiff base chemistry that drives the acetoacetate decarboxylases has been co-opted to perform a new function, and that this core chemistry may be conserved across the superfamily. The structures also suggest possible catalytic roles for several active site residues.
Asymmetry During Load-Loss Measurement of Three-Phase Three-Limb Transformers (2007)

When the load-loss measurement test is conducted on three-phase transformers, an appreciable asymmetry is observed among the power readings of the three phases. This asymmetry is the result of two causes, viz. asymmetrical disposition of phases in space with respect to each other and unequal stray losses produced by phases. The disposition of phases leads to asymmetrical mutual impedances between phases and this is the principal contributor to the phenomenon. Another factor that may have an important contribution to the phenomenon is the deviation of the phase angle difference between the voltages of the three phase source (used during the test) from 120deg. The causes are analyzed using a detailed three-dimensional (3-D) finite-element (FE) simulation of a 31.5MVA, 132/33 kV transformer. In addition, a six-port network impedance model is deduced from open-circuit 3-D FE simulations. The impedance model is able to reproduce any condition of the transformer (e.g., open-circuit, short-circuit or on-load conditions) since it captures all the transformer electromagnetic phenomena. The six-port network results are discussed in order to elaborately clarify the intriguing problem of asymmetrical load-loss distribution, which is important for both transformer manufacturers and users. The results are further explained through sequence components of currents.
Improved Face Recognition Using 2D-LDA with Weighted Covariance Scatter (2014)

In this paper, we propose a newly developed 2D-LDA method based on weighted covariance scatter for face recognition. Existing LDA uses the transform matrix that maximizes distances between classes. In LDA, we have to convert from an image to one-dimensional vector as training vector. In 2D-LDA, on the other hand, we can directly use two-dimensional image itself as training matrix, so that the classification performance can be enhanced about 20% comparing LDA, since the training matrix preserves the spatial information of two-dimensional image. However 2D-LDA uses same calculation schema for transformation matrix and therefore both LDA and 2D-LDA has the heteroscedastic problem which means that the class classification cannot obtain beneficial information of spatial distances of class clusters since LDA uses only data correlation-based covariance matrix of the training data without any reference to distances between classes. In this paper, we propose a new method to apply training matrix of 2D-LDA by using WPS-LDA idea that calculates the reciprocal of distance between classes and apply this weight to between class scatter matrix. To evaluate the performance of proposed algorithm, we use the ORL face database that includes 40 people and 10 images individually. The experimental result shows that the discriminating power of proposed 2D-LDA with weighted between class scatter has been improved up to 2% than original 2D-LDA. This method has good performance especially when the distance between two classes is very close and the dimension of projection axis is low.
Preparation of Spherical Si<sub>3</sub>N<sub>4</sub> Particles from Polysilazane by Ultrasonic Spray Pyrolysis Technique (1989)

Fine, spherical Si3N4 particles were prepared by spray pyrolysis of a polysilazane solution. Amorphous spherical particles were prepared in N2 at 700°C. Calcination of the amorphous particles at 1400°C in N2 resulted in spherical particles of α-Si3N4 without agglomeration. The contents of carbon and oxygen in the spherical crystalline particles determined by chemical analysis were 1.63 and 2.33wt%, respectively. The as-prepared spherical and agglomeration-free particles had an average diameter of 0.38μm and a geometric standard deviation σg of 1.50.
Crystal structure, microstructure, and electrical properties in nonstoichiometric SBT thin films (1998)

Abstract The relation between the electrical properties and the microstructure of the layered-perovskite SBT thin films were studied. The crystal structure of the powder SBT samples were also analyzed by the Rietveld refinement method for clarifying the relationship between the two. The Rietveld refinement results for the Sr1Bi2Ta2O9, Sr0.7Bi2.2Ta2O9, Sr0.7Bi2Ta2O9 and (Sr0.87Bi0.13)Bi2(Ta1.93Bi0.07)O9 samples showed that excess-Bi occupies the Sr site forming (Sr1−3/2xBix)Bi2Ta2O9 solid solution. The Sr0.7Bi2Ta2O9 and (Sr0.87Bi0.13)Bi2(Ta1.93Bi0.07)O9 samples produced minor impurity phases in addition the major SBT phase. The SBT thin films with molar ratio (Sr:Bi:Ta) of 1:2:2, 0.7:2.2:2, 1.87:2.2:1.93, 1:2.2:2 and 0.7:2:2 were prepared by MOD method. The spin-coated films were crystallized at 750°C for 1 hour under O2. Remanent polarization of the thin films critically depended on the crystallinity and grain size, while the leakage current density depended on the minor impurity phase contained in the thin films. The 0.7:2.2:2 thin films showed the best electrical properties: 2Pr = 8.2 μC/cm2, Ec = 43.6KV/cm, Jleakage current = 6.4x10−8 A/cm2 at 3V.
Fast reaching in clutter while regulating forces using model predictive control (2013)

Moving a robot arm quickly in cluttered and unmodeled workspaces can be difficult because of the inherent risk of high impact forces. Additionally, compliance by itself is not enough to limit contact forces due to multi-contact phenomena (jamming, etc.). The work in this paper extends our previous research on manipulation in cluttered environments by explicitly modeling robot arm dynamics and using model predictive control (MPC) with whole-arm tactile sensing to improve the speed and force control. We first derive discrete-time dynamic equations of motion that we use for MPC. Then we formulate a multi-time step model predictive controller that uses this dynamic model. These changes allow us to control contact forces while increasing overall end effector speed. We also describe a constraint that regulates joint velocities in order to mitigate unexpected impact forces while reaching to a goal. We present results using tests from a simulated three link planar arm that is representative of the kinematics and mass of an average male's torso, shoulder and elbow joints reaching in high and low clutter scenarios. These results show that our controller allows the arm to reach a goal up to twice as fast as our previous work, while still controlling the contact forces to be near a user-defined threshold.
Hydrophobic Recovery of Plasma-Treated Polydimethylsiloxane (1995)

Abstract Plasma treatment of silicone surfaces is a useful, environmentally-sound method of increasing wettability to improve adhesion. A thin, wettable silica-like layer is produced with various plasma gases such as argon, helium, oxygen and nitrogen. However, in each case the surfaces gradually recover their hydrophobicity. The silica-like layer is brittle and microcracking is evident at more severe levels of plasma treatment. The onset of cracking is a function of plasma gas, RF power, pressure and treatment time. Scanning electron microscopy has been used to characterize the cracks. The hydrophobic recovery has been monitored by water contact angle changes. It occurs with both cracked and uncracked treated surfaces. There is an initial jump in hydrophobicity at the onset of cracking. Thereafter, the recovery of both cracked and uncracked surfaces broadly parallels each other with virtually complete recovery of original hydrophobicity within one week. These effects can be accounted for by rapid surface diffusion of low molecular weight material out of fresh cracks followed by slower bulk diffusion through the polymer matrix. Significant differences in recovery rates are also evident between different plasma gases.
Design of wireless transcutaneous energy transmission system for totally artificial hearts (2002)

A wireless transcutaneous energy transmission system has been developed for totally artificial hearts. The complete system includes a dc-to-dc converter, dc-to-high-frequency transfer circuit, a coil-coupling structure, and a high-frequency-to-dc rectifying circuit. The power transfer is stabilized by feedback control of the phase of the input impedance of the resonant circuit. Experimental results showed that the output voltage variation was kept within /spl plusmn/0.4 volts when the coil spacing varied from 6 to 18 mm. The optimized conversion efficiency of this system was about 68% when the output power was 36 watts.
Development of a Basement Membrane Substitute Incorporated Into an Electrospun Scaffold for 3D Skin Tissue Engineering (2014)

Yes
ID-Based Authenticated Multi-party Key Agreement Protocol to Multimedia Applications Systems (2008)

An ID-based authenticated multi-party key agreement scheme without trusted PKG is proposed in this paper. The proposed scheme is ID-based, but without any assumption of prefixed trust relationship between members, which effectively solves the problem that exists in some existing ID-based key agreement protocols in which a trusted PKG and key escrow is needed. The proposed scheme employs shared password evolvement authentication mechanism, which generates a one-time password for every session key agreement. Our scheme can be applied to multimedia application environment more efficiently because of the low computation and communication cost.
Alchemi: A .NET-based Enterprise Grid Computing System. (2005)

Computational grids that couple geographically distributed resources are becoming the de-facto computing platform for solving large-scale problems in science, engineering, and commerce. Software to enable grid computing has been primarily written for Unix-class operating systems, thus severely limiting the ability to effectively utilize the computing resources of the vast majority of Windows-based desktop computers. Addressing Windows-based grid computing is particularly important from the software industry&apos;s viewpoint where interest in grids is emerging rapidly. Microsoft&apos;s .NET Framework has become near-ubiquitous for implementing commercial distributed systems for Windows-based platforms, positioning it as the ideal platform for grid computing in this context. In this paper we present Alchemi , a .NETbased framework that provides the runtime machinery and programming environment required to construct enterprise/desktop grids and develop grid applications. It allows flexible application composition by supporting an object-oriented application programming model in addition to a file-based job model. Cross-platform support is provided via a web services interface and a flexible execution model supports dedicated and non-dedicated (voluntary) execution by grid nodes.
Human Induced Pluripotent Stem Cell (hiPSC)-Derived Cells to Assess Drug Cardiotoxicity: Opportunities and Problems (2017)

Billions of US dollars are invested every year by the pharmaceutical industry in drug development, with the aim of introducing new drugs that are effective and have minimal side effects. Thirty percent of in-pipeline drugs are excluded in an early phase of preclinical and clinical screening owing to cardiovascular safety concerns, and several lead molecules that pass the early safety screening make it to market but are later withdrawn owing to severe cardiac side effects. Although the current drug safety screening methodologies can identify some cardiotoxic drug candidates, they cannot accurately represent the human heart in many aspects, including genomics, transcriptomics, and patient- or population-specific cardiotoxicity. Despite some limitations, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are a powerful and evolving technology that has been shown to recapitulate many attributes of human cardiomyocytes and their drug responses. In this review, we discuss the potential impact of the inclusion of the hiPSC-CM platform in premarket candidate drug screening.
Novel mutations in MERTK associated with childhood onset rod-cone dystrophy. (2010)

Mutations in MERTK are a rare cause of retinal dystrophy. Non homologous recombination between Alu Y repeats near or within disease genes may be an important cause of retinal dystrophies.
Asexual Embryogenesis and Plantlet Development in Anther Culture of Cucumis sativus L.1 (1982)

Abstract Callus developed from anther explants of Cucumis sativus L. cultured an modified Nitsch and Nitsch and on Murashige and Skoog basal media. Meristemoids and embryoids were induced when callus was recultured on solidified Nitsch medium containing 20 g/liter rafflnose. Embryoids developed into seedlings.