gebhart/patrepeval huggingface dataset:
Crystallization and preliminary crystallographic studies of 3-deoxy-D-manno-octulosonate-8-phosphate synthase fromEscherichia coli (1996)

3-Deoxy-D-manno-octulosonate-8-phosphate (KDOP) synthase catalyzes the production of KDOP from phosphoenolpyruvate (PEP) and arabinose-5-phosphate (A5P). In gram-negative bacteria KDOP is subsequently dephosphorylated, cytidylylated, and linked to lipid A and is required for lipid A incorporation into the outer membrane (Raetz, Annu. Rev. Biochem. 59:129-170, 1990). We have crystallized two forms of KDOP synthase belonging to space groups I23 or I2(1)3, one with a = b = c = 118.0 A and the other with a = b = c = 233 A.
Improved Trellis-Based Algorithm for Locating and Breaking Cycles in Bipartite Graphs with Applications to LDPC Codes (2018)

LDPC codes are typically decoded using belief propagation decoding algorithms applied to their Tanner graphs. Cycles of short lengths in these graphs, which are bipartite graphs representing parity-check equations of the codes, can negatively impact the performance of the decoder. In this paper, a trellis-based algorithm is presented to locate cycles in bipartite graphs. This algorithm is an improvement in complexity and run-time over the one developed by Lan et al. in 2004. When applied to Tanner graphs of quasi-cyclic LDPC codes, the newly proposed algorithm can exploit the structure of their parity-check matrices to cut the complexity further. Locating cycles in the Tanner graphs of codes allows for eliminating them to increase the girth and thus improve performance.
Seven Cysteine-Deficient Mutants Depict the Interplay between Thermal and Chemical Stabilities of Individual Cysteine Residues in Mitogen-Activated Protein Kinase c-Jun N-Terminal Kinase 1 (2012)

Intracellular proteins can have free cysteines that may contribute to their structure, function, and stability; however, free cysteines can lead to chemical instabilities in solution because of oxidation-driven aggregation. The MAP kinase, c-Jun N-terminal kinase 1 (JNK1), possesses seven free cysteines and is an important drug target for autoimmune diseases, cancers, and apoptosis-related diseases. To characterize the role of cysteine residues in the structure, function, and stability of JNK1, we prepared and evaluated wild-type JNK1 and seven cysteine-deficient JNK1 proteins. The nonreduced sodium dodecyl sulfate-polyacrylamide gel electrophoresis experiments showed that the chemical stability of JNK1 increased as the number of cysteines decreased. The contribution of each cysteine residue to biological function and thermal stability was highly susceptible to the environment surrounding the particular cysteine mutation. The mutations of solvent-exposed cysteine to serine did not influence biological function and increased the thermal stability. The mutation of the accessible cysteine involved in the hydrophobic pocket did not affect biological function, although a moderate thermal destabilization was observed. Cysteines in the loosely assembled hydrophobic environment moderately contributed to thermal stability, and the mutations of these cysteines had a negligible effect on enzyme activity. The other cysteines are involved in the tightly filled hydrophobic core, and mutation of these residues was found to correlate with thermal stability and enzyme activity. These findings about the role of cysteine residues should allow us to obtain a stable JNK1 and thus promote the discovery of potent JNK1 inhibitors.
On a Low Cost Fault Injection Framework for Security Assessment of Cyber-Physical Systems: Clock Glitch Attacks (2019)

Fault injection methods as a type of physical attack have gained significant importance in the security of MCU-based Internet-of-Things (IoTs) systems and they continue to become more and more important as the value of assets continues to increase. These attacks can pose severe security risks to the entire IoT system and their effects can quickly lead to security breaches. However, embedded software developers most often do not have the necessary expertise concerning existing vulnerabilities against such attacks. This makes it necessary to have a practical evaluation platform for measuring the degree of security, in a rapid and accurate way. These platforms are important not only from the performance and capability point of view, but also they need to be cost-effective, which is a critical factor to consider during their design. We present in this work a generic low cost and open platform, called HackMyMCU framework. While this platform offers both side channel and fault injection capabilities, this paper focuses on its clock glitch attacks. A first review of existing clock-based fault injectors is initially performed. Then we present two different clock glitchers and we use them to evaluate a modern MCU. The suggested methods consider the necessary parameters for the development of cost-effective and easy to use evaluation platforms which utilize easily accessible equipment. The findings show that a common and low-cost evaluation platform can be implemented with the goal to validate appropriate countermeasures against such attacks.
Content planner construction via evolutionary algorithms and a corpus-based fitness function (2002)

In this paper, we present a novel technique to learn a tree-like structure for a content planner from an aligned corpus of semantic inputs and corresponding, human-produced, outputs. We apply a stochastic search mechanism with a two-level fitness function. As a first stage, we use high level order constraints to quickly discard unpromising planners. As a second stage, alignments between regenerated text and human output are employed. We evaluate our approach by using the existing symbolic planner in our system as a gold standard, obtaining a 66 % improvement over a random baseline in just 20 generations of genetic search.
Vibrational spectroscopy of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mmultiscripts><mml:mtext>H</mml:mtext><mml:mn>2</mml:mn><mml:none/><mml:none/><mml:mo>+</mml:mo></mml:mmultiscripts></mml:mrow></mml:math>: Precise evaluation of the Zeeman effect (2008)

We present an accurate computation of the $g$ factors of the hyperfine states of the hydrogen molecular ion $\text{H}_{2}{}^{+}$. The results are in good agreement with previous experiments, and can be tested further by rf spectroscopy. Their implication for high-precision two-photon vibrational spectroscopy of $\text{H}_{2}{}^{+}$ is also discussed. It is found that the most intense hyperfine components of two-photon lines benefit from a very small Zeeman splitting.
Synthetic Peptides and Anti-Idiotypic Antibodies as Immunogens for the Induction of Antibody Response to Haemophilus influenzae Type b (1992)

Journal Article Synthetic Peptides and Anti-Idiotypic Antibodies as Immunogens for the Induction of Antibody Response to Haemophilus influenzae Type b Get access Bernard R. Brodeur, Bernard R. Brodeur National Laboratoryfor Immunology, LaboratoryCentre for Disease Control, Ottawa, and Connaught Centre for Biotechnology Research, Toronto, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Josée Hamel, Josée Hamel National Laboratoryfor Immunology, LaboratoryCentre for Disease Control, Ottawa, and Connaught Centre for Biotechnology Research, Toronto, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Denis Martin, Denis Martin National Laboratoryfor Immunology, LaboratoryCentre for Disease Control, Ottawa, and Connaught Centre for Biotechnology Research, Toronto, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Pele Chong Pele Chong National Laboratoryfor Immunology, LaboratoryCentre for Disease Control, Ottawa, and Connaught Centre for Biotechnology Research, Toronto, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 165, Issue Supplement_1, June 1992, Pages S162–S164, https://doi.org/10.1093/infdis/165-Supplement_1-S162 Published: 01 June 1992
Studies on marine microorganisms. V. A new antibiotic, aplasmomycin, produced by a streptomycete isolated from shallow sea mud. (1976)

A new antibiotic, aplasmomycin, which inhibits growth of Gram-positive bacteria including myobacteria in vitro, and plasmodia in vivo was obtained from a strain of Streptomyces griseus isolated from shallow sea sediment in Sagami Bay. The antibiotic forms colorless needle-like crystals and has a molecular formula of C41H60O14Na. Based on its physical and chemical properties, aplasmomycin was concluded to be a new antibiotic. The antibiotic was produced in selected media devised to relate to a marine environment.
Reinforcement Learning System Comprising Resistive Analog Neuromorphic Devices (2019)

Reinforcement learning algorithms are widely used in many practical artificial-intelligence (AI) applications. Herein, we propose a compact hardware-based learning system comprising analogue resistive memory devices called “resistive analogue neuromorphic devices (RAND).” We begin by showing that the resistance of a RAND linearly varies with the voltage pulses, meaning that a single RAND is sufficient to solve a reinforcement learning problem (i.e. the “2-armed bandit problem”) using “tug-of-war (TOW) dynamics.” Next, we show that 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</sup> -armed bandit problems are also solved by hierarchically combining 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k-1</sup> RANDs. Finally, we numerically demonstrate that the proposed methods are promising as compared with conventional methods.
Editorial Comment (1980)

No AccessJournal of Urology1 Nov 1980Editorial Comment Daniel C. Merrill Daniel C. MerrillDaniel C. Merrill More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)55607-4AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Editorial Comment." The Journal of Urology, 124(5), p. 682 © 1980 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 124Issue 5November 1980Page: 682 Advertisement Copyright & Permissions© 1980 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Daniel C. Merrill More articles by this author Expand All Advertisement Loading ...
Endoscopic Abscess Drainage for Colonic Diverticulitis: Report of Two Cases (2008)

結腸憩室炎に対する治療法は軽∼中等症の場合では絶食·抗生物質投与による治療が行われるが，穿孔ないし穿破をともなう場合，外科的治療が選択されることが多い．今回我々は穿破による膿瘍形成した憩室炎に対し，大腸内視鏡を用いて排膿術を施行，保存的治療にて軽快した2例を経験した．2症例は右側腹部痛，発熱を主訴に当院受診．CTにて上行結腸に広範な壁肥厚像，膿瘍形成を認め，穿破による憩室炎の診断となった．大腸内視鏡施行し上行結腸の広範な炎症を認め，表面に白苔をともなう排膿している憩室に対し，生理食塩水にて洗浄し，膿瘍ドレナージを施行した．術直後に腹痛，発熱が軽減し，保存的治療のみで退院した．結腸憩室炎に対する大腸内視鏡による膿瘍ドレナージは，外科的なサポート下において1つの治療オプションとして考慮できる手技と考えられた．
Microwave radar imaging of inhomogeneous breast phantoms using circular holography (2012)

Circular holography is a novel reconstruction technique for Breast Microwave Radar (BMR) imaging. Compared to current state of the art BMR image formation methods, this reconstruction approach yields spatially accurate images with higher signal to noise ratios and no artifacts. Nevertheless, a preclinical study is required to assess the feasibility of this technique in realistic breast imaging scenarios. In this paper, a series of preliminary results showing the performance of circular holography on preclinical datasets are presented. These datasets were recorded from inhomogeneous breast phantoms that mimic the dielectric properties and the anatomy of the different breast tissues. These phantoms were fabricated using Magnetic Resonance (MR) images a base model to emulate the shape and volumes of dense tissue regions. The reconstructed BMR images show that tumor and fibroglandular tissue responses can be effectively distinguished, suggesting that circular holography can be used as BMR reconstruction approach in clinical scenarios.
Fully Leakage-Resilient Signatures. (2010)

A signature scheme is fully leakage resilient (Katz and Vaikuntanathan, ASIACRYPT ’09) if it is existentially unforgeable under an adaptive chosen-message attack even in a setting where an adversary may obtain bounded (yet arbitrary) leakage information on all intermediate values that are used throughout the lifetime of the system. This is a strong and meaningful notion of security that captures a wide range of side-channel attacks. One of the main challenges in constructing fully leakage-resilient signature schemes is dealing with leakage that may depend on the random bits used by the signing algorithm, and constructions of such schemes are known only in the random-oracle model. Moreover, even in the random-oracle model, known schemes are only resilient to leakage of less than half the length of their signing key. In this paper we construct the first fully leakage-resilient signature schemes without random oracles. We present a scheme that is resilient to any leakage of length (1 − o(1))L bits, where L is the length of the signing key. Our approach relies on generic cryptographic primitives, and at the same time admits rather efficient instantiations based on specific number-theoretic
Maturation of endogenous glucose production in preterm and term calves (2011)

Glucose disposability is often impaired in neonatal calves and even more in preterm calves. The objective of this study was to investigate ontogenic maturation of endogenous glucose production (eGP) in calves and its effects on postnatal glucose homeostasis. Calves (n = 7 per group) were born preterm (PT; delivered by section 9 d before term) or at term (T; spontaneous vaginal delivery), or spontaneously born and fed colostrum for 4 d (TC). Blood samples were taken immediately after birth and before and 2h after feeding at 24h after birth (PT; T) or on d 4 of life (TC) to determine metabolic and endocrine changes. After birth (PT and T) or on d 3 of life (TC), fasted calves were gavaged with deuterium-labeled water to determine gluconeogenesis (GNG) and intravenously infused with [U(13)C]-glucose to measure eGP and glucose oxidation (GOx) in blood plasma. After slaughter at 26h after birth (PT, T) or on d 4 of life (TC), glycogen concentrations in liver and hepatic mRNA concentrations and enzyme activities of pyruvate carboxylase, phosphoenolpyruvate carboxykinase (PEPCK), and glucose-6-phosphatase were measured. Preterm calves had the lowest plasma concentrations of cortisol and 3,5,3'-triiodothyronine at birth. Plasma glucose concentrations from d 1 to 2 decreased more, but plasma concentrations of lactate and urea and glucagon:insulin ratio were higher in PT than in T and TC calves. The eGP, GNG, GOx, as well as hepatic glycogen concentrations and PEPCK activities, were lowest in PT calves. Results indicate impaired glucose homeostasis due to decreased eGP in PT calves and maturation of eGP with ontogenic development.
Langley Aircraft Landing Dynamics Facility (1987)

The Langley Research Center has recently upgraded the Landing Loads Track (LLT) to improve the capability of low-cost testing of conventional and advanced landing gear systems. The unique feature of the Langley Aircraft Landing Dynamics Facility (ALDF) is the ability to test aircraft landing gear systems on actual runway surfaces at operational ground speeds and loading conditions. A historical overview of the original LLT is given, followed by a detailed description of the new ALDF systems and operational capabilities.
Characterization of the first excited 1Π1 and the ground <i>X</i> 1Σ+ states of MgXe. I. Analysis of the 1Π1←<i>X</i> 1Σ+ bound–bound transitions (1993)

Laser induced fluorescence (LIF) excitation spectra recorded for the vibrational bands in the Mg(3s3p 1P1)⋅Xe(1Π1)←Mg(3s3s 1S0)⋅Xe (X 1Σ+) system have been analyzed, yielding absolute vibrational assignments and values of ωexe=1.585±0.02 and ωe=97.5±1.0 cm−1 for the 1Π1 state of 24Mg132Xe. From a Birge–Sponer extrapolation, the well depth of this state is estimated to be 1500 cm−1. Simulations of rotationally structured spectra of three of the most intense vibrational bands are consistent with R″e=4.56±0.12 Å for the X 1Σ+ state. From Morse function extrapolation of the excited state rotational constants from the simulations, and Franck–Condon intensity simulations of the 1Π1←X 1Σ+ vibrational progressions, R′e for the 1Π1 state is estimated to be 3.07±0.10 Å. The 1Π1 state of MgXe fluoresces strongly. The corresponding 1Π1 states of ZnXe and CdXe do not fluoresce, but ‘‘action’’ spectra from the production (via predissociation) of metal atom 3PJ states are observed. Possible reasons for these differences are discussed in terms of spin–orbit induced predissociation. It is concluded that predissociation of the MgXe(1Π1) state is not observed because the crossing between the repulsive 3∑+1 and the attractive 1Π1 potential curves does not occur until energies higher than those accessible experimentally. Possible reasons for the behavior of the diatomic MgXe(1Π1) state vs that of Mg(3s3p 1P1) isolated in solid Xe, where production of Mg(3s3p 3PJ) states competes with Mg(3s3p 1P1) fluorescence, are also discussed. Finally, the attractive ‘‘bonding’’ interactions in the MgXe(1Π1) state are analyzed in terms of electrostatic interactions and compared with those for other Π-type states of metal/rare-gas van der Waals diatomic molecules.
Gas Isotopes Tracing: an Important Tool for Hydrocarbons Exploration (2003)

Gas may be considered today both as a reliable tracer for the understanding of associated liquid hydrocarbons and as an economic target. Isotopic measurements of stables isotopes and noble gases give important clues to reconstruct the geological history of hydrocarbons from their generation to their accumulation. Recent analytical advances in carbon isotopes of natural gases (methane to butane and carbon dioxide) duemainly to the development of GC-C-IRMS (Gas Chromatograph-Combustion-Isotopic ratios mass spectrometer) have allowed to reconstruct some of the physico-chemical processes which affect naturalgas chemical signatures, instead of using these signatures as simple fingerprinting of origins as it was the case some time ago. These reconstructions provide important information on both the origins and the dynamic behavior of hydrocarbon fluids between the source rocks and the accumulations in reservoirs. Correlating this methodology with other natural tracers increases the understanding of hydrocarbon history in sedimentary basins. Among other new potential methodologies, noble gas coupled to stable isotopes are the new frontier tool, as their chemical inertia enables their use as precise tracers of sources and of associated physical processes (state of the phases, migration and leakage). Moreover, because some isotopes (4He, 40Ar for example) are produced by natural radioactivity, they may very well represent geological "clocks", giving potentially a quantification of the residence times of hydrocarbons in a reservoir. Several new applications of this association of stable isotopes and noble gases are presented in this paper: a new way for distinguishing bacterial and thermogenic gas origins, and the characterization of the parameters related to the genesis of thermogenic gas (primary versus secondary cracking, openness of the system, relations between gas isotope signatures and biodegradation). At last is presented a tentative quantification of the proportion of hydrocarbon gases leaked from a reservoir, and a quantitative relative residence times of hydrocarbons in heterogeneous reservoirs.
Density-functional theory modeling of bulk magnetism with spin-dependent pseudopotentials (2001)

The recently developed spin-dependent pseudopotentials markedly improve the description of the energetics of isolated transition metal atoms [S. C. Watson and E. A. Carter, Phys. Rev. B 58, R13 309 (1998)]. Spin-dependent pseudopotentials are obtained from a combination of spin-neutral and fully polarized atomic pseudopotentials, employing the self-consistent local spin polarization to adapt to different environments. Their use is extended to bulk materials in the current work, where we have implemented the spin-dependent pseudopotential formalism within a real-space density functional theory code. Calculations on bulk Fe, Co, and Ni yield lattice constants and bulk moduli within the accuracy expected of a method employing the local density approximation of density functional theory, except for an overestimated Fe bulk modulus. However, the magnetic moment is in dramatically better agreement with experiment and published all-electron calculations when the spin-dependent pseudopotentials are employed.
The Reaction of Phosphorus-containing Enzyme Inhibitors with Amines and Amino Acid Derivatives<sup>1</sup> (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Reaction of Phosphorus-containing Enzyme Inhibitors with Amines and Amino Acid Derivatives1T. Wagner-Jauregg, J. J. O'Neill, and W. H. SummersonCite this: J. Am. Chem. Soc. 1951, 73, 11, 5202–5206Publication Date (Print):November 1, 1951Publication History Published online1 May 2002Published inissue 1 November 1951https://pubs.acs.org/doi/10.1021/ja01155a059https://doi.org/10.1021/ja01155a059research-articleACS PublicationsRequest reuse permissionsArticle Views151Altmetric-Citations38LEARN 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-Alertsclose Get e-Alerts
Prophylactic Effect of Dietary Seaweed Fucoidan against Enteral Prion Infection (2007)

Dietary seaweed fucoidan delays the onset of disease of enterally infected mice with scrapie when given orally for 6 days after infection, but not when given before the infection. This effect was not modified at a tested fucoidan dose range and appeared to reach the maximum level at a concentration of 2.5% or less in feed. Daily uptake of fucoidan might be prophylactic against prion diseases caused by ingestion of prion-contaminated materials, although further evaluation of its pharmacology remains to be done.
Multi-port Multi-band Small Antenna Design (2007)

In this paper, a novel multi-port, multi-band small planar antenna is presented. It has three input ports; each of them has their own frequency bands, 2.4 GHz, 3.5 GHz and 5.5 GHz. These three antennas are printed on a small area, 250 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The proposed antenna is printed on a cheap organic material substrate with other RF components. It requires enough isolation among the antennas since each frequency band ought to operate at the same time. Polarizations of monopole antennas are all orthogonal as best as possible to minimize mutual couplings and open stubs are used at feed points to block the other frequency band signals. The antenna proposed in this paper is a solution to the onboard configuration of handset system needed multiple wireless services and they can be used simultaneously.
ChemInform Abstract: Current Technologies, Economics, and Perspectives for 2,5‐Dimethylfuran Production from Biomass‐Derived Intermediates (2015)

Abstract Review: [71 refs.