gebhart/patrepeval huggingface dataset:
Three-dimensional object construction using a self-mixing type scanning laser range finder (1998)

A self-mixing type scanning range finder has been designed for the acquisition of three-dimensional (3-D) image data and object construction. The optical beam backscattered by a rough target into the laser diode cavity causes strong variations of the optical output power, the pseudo period between two of these variations corresponding to a distance of a half wavelength. With such a device, images have been obtained with a resolution of 0.1% over ranges up to 3 m, for 3-D object construction.
A User-level Framework for Auditing and Monitoring (2006)

Logging and auditing is an important system facility for monitoring correct system operation and for detecting potential security problems. We present an architecture for implementing user-level auditing monitors which: (i) does not require superuser privileges; (ii) makes it simple to create user defined monitors which are transparent; and (iii) provides security guarantees such as mandatory and reliable monitoring while maintaining confidentiality of setuid processes. We avoid problems of self-referential monitoring. Monitor use policies can be specified to increase flexibility. We show that our framework can be tailored so that it is very efficient with low overhead on macro and micro benchmarks. This demonstrates that it is feasible to make use of arbitrary and programmable user-level monitors for system security and auditing applications.
Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations (2003)

Molecular dynamics (MD) is widely used in simulations of biomolecular systems such as DNA and proteins, systems which are multiscale in nature. However, current time stepping integrators are not able to address the time scale problems. Multiscale integrators, in which the presence of "fast" modes does not affect the time integration of "slow" modes, are pressingly needed in light of the fast growing biological data generated from the many genome sequencing projects. In this paper, we present a new multiple time stepping (MTS) multiscale integrator with stochasticity built in for constant temperature molecular dynamics simulations, called the targeted mollified impulse method (TM). TM combines the mollified impulse method, which is a stabler version of Verlet-I/r-RESPA ({\bf r}eversible {\bf RE}ference {\bf S}ystem {\bf P}ropagator {\bf A}lgorithm), and a self-consistent dissipative leapfrog integrator commonly used in dissipative particle dynamics. TM introduces the Langevin coupling in a targeted manner to stabilize the MTS integrator such that the total linear momentum is conserved and less randomness in slower modes is imposed. Numerical experiments of simple model problems provide evidence that TM samples from the canonical ensemble. Possible applications include kinetics calculations such as conformational transition rates, computation of structural quantities from a canonical ensemble, and approximation of dynamical quantities from a canonical ensemble. We present results for the last two by showing that both the radial distribution functions and the self-diffusion coefficient are correctly computed from the simulations of flexible TIP3P waters using TM with outermost time step of 16\,fs and innermost time step of 2\,fs. Compared to leapfrog with time step of 1\,fs, the implementation of TM achieves a six-fold computational speedup, whereas Verlet-I\slash r-RESPA with outer time step of 4\,fs and inner time step of 1\,fs achieves only a three-fold speedup. We also show how to generalize the method for the simulation of biological macromolecules.
Isolation and Characterization of cDNAs That Encode Homologs of a Pathogenesis-related Protein Allergen from<i>Cryptomeria japonica</i> (2002)

Many plant pathogenesis-related (PR) proteins are allergenic. We isolated three cDNAs, Cry j 3.1, Cry j 3.2, and Cry j 3.3, that encoded homologs of Jun a 3, a PR protein allergen in Juniperus ashei, from a cDNA library derived from the pollen of Cryptomeria japonica. The predicted amino acid sequences encoded by the three cDNAs were more than 85% identical to each other and about 57% identical to the sequence of Jun a 3. The Cry j 3 genes seemed to form a small multigene family in the genome of C. japonica. Expression of Cry j 3 was strong in roots and in female and male strobili; expression was weaker in cotyledons, leaves, stems, and pollen grains.
Notes- Preparation of Various Substituted Pyrimidines (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNotes- Preparation of Various Substituted PyrimidinesRaymond Mariella and James ZelkoCite this: J. Org. Chem. 1960, 25, 4, 647–648Publication Date (Print):April 1, 1960Publication History Published online13 March 2003Published inissue 1 April 1960https://pubs.acs.org/doi/10.1021/jo01074a611https://doi.org/10.1021/jo01074a611research-articleACS PublicationsRequest reuse permissionsArticle Views156Altmetric-Citations9LEARN 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
An Investigation of the Hydrogen-Bonding Structure in Bilirubin by <sup>1</sup>H Double-Quantum Magic-Angle Spinning Solid-State NMR Spectroscopy (2001)

The complex hydrogen-bonding arrangement in the biologically important molecule bilirubin IXalpha is probed by using 1H double-quantum (DQ) magic-angle spinning (MAS) NMR spectroscopy. Employing fast MAS (30 kHz) and a high magnetic field (16.4 T), three low-field resonances corresponding to the different hydrogen-bonding protons are resolved in a 1H MAS NMR spectrum of bilirubin. These resonances are assigned on the basis of the proton-proton proximities identified from a two-dimensional rotor-synchronized 1H DQ MAS NMR spectrum. An analysis of 1H DQ MAS spinning-sideband patterns for the NH protons in bilirubin allows the quantitative determination of proton-proton distances and the geometry. The validity of this procedure is proven by simulated spectra for a model three-spin system, which show that the shortest distance can be determined to a very high degree of accuracy. The distance between the lactam and pyrrole NH protons in bilirubin is determined to be 0.186 +/- 0.002 nm (corresponding to a dominant dipolar coupling constant of 18.5 +/- 0.5 kHz). The analysis also yields a distance between the lactam NH and carboxylic acid OH protons of 0.230 +/- 0.008 nm (corresponding to a perturbing dipolar coupling constant of 9.9 +/- 1.0 kHz) and an H-H-H angle of 122 +/- 4 degrees. Finally, a comparison of 1H DQ MAS spinning-sideband patterns for bilirubin and its dimethyl ester reveals a significantly longer distance between the two NH protons in the latter case.
Using Shibboleth for Authorization and Authentication to the Subversion Version Control Repository System (2007)

A version control repository structure has been created based on open source utility software. The structure consists of a subversion repository with an Apache Web interface that is protected by a Shibboleth authentication system. This structure can allow authorized and authenticated data sharing between institutions, yet retains simplicity and protects privacy for users. In addition, it also helps local administrators from having to perform extra account management for new users from other institutions
Using lesson study as an approach to developing teachers as researchers (2013)

Purpose – The purpose of this paper is to report on how an academy used lesson study to engage teachers in research, presenting the journey undertaken from its conception through to the implementation of the model. It suggests that lesson study is a suitable process to engage teachers in meaningful research. It shows that lesson study allows teachers to focus on their own practice and on the learning of their students and it is ideal in bridging the gap between research and practice. It will also show that research is enhanced through lesson study because it brings teachers together to work in a collaborative way. Design/methodology/approach – The paper reports the intended and actual journey an academy took in planning and implementing lesson study across the academy. Findings – The paper provides an explanation on how a school can set up a model which engages its teachers in relevant research. It explains how lesson study can be used as a powerful research tool which helps teachers develop collaboration and investigative minds around their own practice and their own students. It also puts forward recommendations for a school that would seek to introduce lesson study to its staff. Originality/value – The paper provides an account for school leadership teams and those with responsibility for developing the practice of other teachers. It will be helpful in assisting schools who desire to strengthen or develop the time devoted to teachers’ professional development.
α-Amino-β-carboxymuconate-ε-semialdehyde Decarboxylase (ACMSD) Inhibitors as Novel Modulators of De Novo Nicotinamide Adenine Dinucleotide (NAD<sup>+</sup>) Biosynthesis (2018)

NAD<sup>+</sup> has a central function in linking cellular metabolism to major cell-signaling and gene-regulation pathways. Defects in NAD<sup>+</sup> homeostasis underpin a wide range of diseases, including cancer, metabolic disorders, and aging. Although the beneficial effects of boosting NAD<sup>+</sup> on mitochondrial fitness, metabolism, and lifespan are well established, to date, no therapeutic enhancers of de novo NAD<sup>+</sup> biosynthesis have been reported. Herein we report the discovery of 3-[[[5-cyano-1,6-dihydro-6-oxo-4-(2-thienyl)-2-pyrimidinyl]thio]methyl]phenylacetic acid (TES-1025, 22), the first potent and selective inhibitor of human ACMSD (IC<sub>50</sub> = 0.013 μM) that increases NAD<sup>+</sup> levels in cellular systems. The results of physicochemical-property, ADME, and safety profiling, coupled with in vivo target-engagement studies, support the hypothesis that ACMSD inhibition increases de novo NAD<sup>+</sup> biosynthesis and position 22 as a first-class molecule for the evaluation of the therapeutic potential of ACMSD inhibition in treating disorders with perturbed NAD<sup>+</sup> supply or homeostasis.
Lactobacilli Reduce Cell Cytotoxicity Caused by <i>Streptococcus pyogenes</i> by Producing Lactic Acid That Degrades the Toxic Component Lipoteichoic Acid (2011)

Lactobacilli are known to prevent colonization by many pathogens; nevertheless, the mechanisms of their protective effect are largely unknown. In this work, we investigated the role of lactobacilli during infection of epithelial cells with group A streptococci (GAS). GAS cause a variety of illnesses ranging from noninvasive disease to more severe invasive infections, such as necrotizing fasciitis and toxic shock-like syndrome. Invasion of deeper tissues is facilitated by GAS-induced apoptosis and cell death. We found that lactobacilli inhibit GAS-induced host cell cytotoxicity and shedding of the complement regulator CD46. Further, survival assays demonstrated that lactic acid secreted by lactobacilli is highly bactericidal toward GAS. In addition, lactic acid treatment of GAS, but not heat killing, prior to infection abolishes the cytotoxic effects against human cells. Since lipoteichoic acid (LTA) of GAS is heat resistant and cytotoxic, we explored the effects of lactic acid on LTA. By applying such an approach, we demonstrate that lactic acid reduces epithelial cell damage caused by GAS by degrading both secreted and cell-bound LTA. Taken together, our experiments reveal a mechanism by which lactobacilli prevent pathogen-induced host cell damage.
Characterization of topoisomerase II‐DNA interaction and identification of a DNA‐binding domain by ultraviolet laser crosslinking (1996)

We have used ultraviolet laser crosslinking to characterize the DNA-binding properties of highly purified yeast topoisomerase II in the absence of ATP. A single 5 ns, 20 mJ pulse of 266 nm light produced optimal crosslinking to a short DNA duplex, with an efficiency of 0.25%. An equilibrium binding constant (Keq) of 1.2 +/- 0.5 x 10(8) M(-1) was determined from kinetic analysis. Topoisomerase II showed highest affinity for supercoiled DNA. Limited proteolysis of crosslinked topoisomerase II-DNA complexes showed a site of crosslinking to be within a 29-kDa fragment with Leu-681 at its amino-terminal end. This region contains the active Tyr-783 and is homologous to the amino-terminal region of the DNA-binding bacterial gyrase GyrA subunit, suggesting a conserved DNA-binding mechanism.
Retinoic Acid Signal Transduction Pathways<sup>a</sup> (1993)

Complexity in the retinoid signaling system arises from a combination of several forms of retinoic acid which possess differential activities, multiple cytoplasmic binding proteins and nuclear receptors that have distinct ligand specificities and functional properties, and the existence of polymorphic retinoic acid response elements. Additional diversity appears to be generated by heterodimeric interactions between the two classes of nuclear retinoic acid receptors and between retinoic acid receptors and some other members of the nuclear receptor superfamily. Thus, a complex array of combinatorial effects is beginning to emerge that may account for the pleiotropic effects of retinoids.
Polymerization of β-Lactones Initiated by Alkali Metal Naphthalenides. A Convenient Route to Telechelic Polymers (1992)

Abstract The polymerization of β-lactones initiated by potassium naphtha-lenide and its mechanism are discussed on the basis of 1H NMR 300 MHz measurement, GC-MS experiments, and model reactions. It was demonstrated that the initiator was not incorporated into the polymer chains, but unsaturated groups were formed as the dead endgroups of the polymer chains due to proton abstraction from the monomer. The salts of unsaturated acids, formed at the initiation step, are responsible for the growth of polymer chains at the propagation step.
Construction of a new anti-CD19 chimeric antigen receptor and the anti-leukemia function study of the transduced T cells (2016)

Chimeric antigen receptor (CAR) transduced T cells have been used to efficiently kill the target tumor cells depending on the single chain variable fragment (scFv) against the specific tumor associated antigen. Here we show the high specific cytotoxicity of the CAR-T cells with very low effector to target cell (E:T) ratio owing to the CD19-scFv, which was constructed in our laboratory and proved to be highly effective in our previous study. Four plasmids containing three generation of CAR were constructed by cloning the CD19-CAR fragment into the lentiviral vector pCDH. CD3 positive T cells were successfully transduced and the CAR protein expression was confirmed by flow cytometry and Western blot. When cocultured with CD19 positive leukemia cell line Nalm-6 cells, CAR-T cells showed specific cytotoxicity: the percentage of target cells decreased to 0 in 24 hours; IL-2, IFN-γ and TNF-α produced in cocultured supernatants increased obviously; and the cytotoxicity reached more than 80%, still remarkable even when the E:T ratio was as low as 1:4. Dynamic change of cell interaction between CAR-T and leukemia cells was visually tracked by using living cells workstation for the first time. A NOD/SCID B-ALL murine model was established using Nalm-6 cells inoculation with a morbidity rate of 100%, and the survival time was prolonged statistically with CAR-T cell treatment. These data demonstrate that the CAR-T cells we prepared could be a promising treatment strategy for CD19 positive tumor diseases.
Do salicylates and ascorbate increase the outer membrane permeability to hydrophobic antibiotics in Pseudomonas aeruginosa? (1990)

Acetylsalicylate and ascorbate have earlier been shown to increase the outer membrane (OM) permeability of Pseudomonas aeruginosa to a hydrophobic probe compound, nitrocefin. In order to elucidate whether these drugs increase the OM permeability to a wider set of hydrophobic compounds, the OM permeability to three other hydrophobic probes (rifampin, fusidic acid and sodium deoxycholate) was studied in the presence of salicylates or ascorbate. A high concentration (300 micrograms/ml, equal to 1.7 mM) of L-ascorbate decreased the minimum inhibitory concentration (MIC) of rifampin against P. aeruginosa by a factor of approximately 3. As a sharp contrast, the reference compound, polymyxin B nonapeptide (PMBN) which has a strong OM permeability-increasing action, decreased the MIC by a factor of approximately 100, at a concentration as low as 3 micrograms/ml (equal to 3 microM). If the assays were performed in a low ionic strength medium (L broth diluted 1/5 with water) instead of L broth, ascorbate was somewhat more effective. The MIC of fusidic acid was even less influenced by ascorbate. Additionally, ascorbate did not potentiate the bacteriolytic action of sodium deoxycholate, whereas the control compound hexametaphosphate had a marked effect. Furthermore, salicylate and acetylsalicylate sensitised, in all conditions tested, P. aeruginosa to none of the three probes. The results suggest that ascorbate and salicylates lack any significant OM permeability-increasing action.
Telecommunication-network dependability: a baseline on local-exchange network availability (2002)

A baseline objective on the availability of a local-exchange network due to failures (not including the effects of blocking due to traffic congestion) is provided. This end-to-end objective is derived from availability objectives which have been set for the segments of Bellcore's Client Company networks. A simple hypothetical reference connection for the local-exchange network is first given. Next, the baseline end-to-end network availability performance objective is derived. Application of the end-to-end and segment objectives to network architectures and equipment reference models that will provide existing and new services are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Conclusion (2016)

The book closes with a summary of the dynamics of neurodiversity in higher education. Philosophical approaches and practices with the potential to better support diversity in higher education and inclusionary campus climate are reviewed and highlighted.
Coaxial MnO<sub>2</sub>/Carbon Nanotube Array Electrodes for High-Performance Lithium Batteries (2009)

Coaxial manganese oxide/carbon nanotube (CNT) arrays deposited inside porous alumina templates were used as cathodes in a lithium battery. Excellent cyclic stability and capacity of MnO2/CNT coaxial nanotube electrodes resulted from the hybrid nature of the electrodes with improved electronic conductivity and dual mechanism of lithium storage. The reversible capacity of the battery was increased by an order compared to template grown MnO2 nanotubes, making them suitable electrodes for advanced Li ion batteries.
<i>Mycobacterium avium</i>subsp.<i>paratuberculosis</i>as one cause of Crohn’s disease (2001)

A number of theories regarding the aetiology of Crohn's disease have been proposed. Diet, infections, other unidentified environmental factors and immune disregulation, all working under the influence of a genetic predisposition, have been viewed with suspicion. Many now believe that Crohn's disease is a syndrome caused by several aetiologies. The two leading theories are the infectious and autoimmune theories. The leading infectious candidate is Mycobacterium avium subspecies paratuberculosis (Mycobacterium paratuberculosis), the causative agent of Johne's disease, an inflammatory bowel disease in a variety of mammals including cattle, sheep, deer, bison, monkeys and chimpanzees. The evidence to support M. paratuberculosis infection as a cause of Crohn's disease is mounting rapidly. Technical advances have allowed the identification and/or isolation of M. paratuberculosis from a significantly higher proportion of Crohn's disease tissues than from controls. These methodologies include: (i) improved culture techniques; (ii) development of M. paratuberculosis-specific polymerase chain reaction assays; (iii) development of a novel in situ hybridization method; (iv) efficacy of macrolide and anti-mycobacterial drug therapies; and (v) discovery of Crohn's disease-specific seroreactivity against two specific M. paratuberculosis recombinant antigens. The causal role for M. paratuberculosis in Crohn's disease and correlation of infection with specific stratification(s) of the disorder need to be investigated. The data implicating Crohn's as an autoimmune disorder may be viewed in a manner that supports the mycobacterial theory. The mycobacterial theory and the autoimmune theory are complementary; the first deals with the aetiology of the disorder, the second deals with its pathogenesis. Combined therapies directed against a mycobacterial aetiology and inflammation may be the optimal treatment of the disease.
Removal of Vaccinia Virus Genes That Block Interferon Type I and II Pathways Improves Adaptive and Memory Responses of the HIV/AIDS Vaccine Candidate NYVAC-C in Mice (2012)

Poxviruses encode multiple inhibitors of the interferon (IFN) system, acting at different levels and blocking the induction of host defense mechanisms. Two viral gene products, B19 and B8, have been shown to act as decoy receptors of type I and type II IFNs, blocking the binding of IFN to its receptor. Since IFN plays a major role in innate immune responses, in this investigation we asked to what extent the viral inhibitors of the IFN system impact the capacity of poxvirus vectors to activate immune responses. This was tested in a mouse model with single and double deletion mutants of the vaccine candidate NYVAC-C, which expresses the HIV-1 Env, Gag, Pol, and Nef antigens. When deleted individually or in double, the type I (B19) and type II (B8) IFN binding proteins were not required for virus replication in cultured cells. Studies of immune responses in mice after DNA prime/NYVAC boost revealed that deletion of B8R and/or B19R genes improved the magnitude and quality of HIV-1-specific CD8(+) T cell adaptive immune responses and impacted their memory phase, changing the contraction, the memory differentiation, the effect magnitude, and the functionality profile. For B cell responses, deletion of the viral gene B8R and/or B19R had no effect on antibody levels to HIV-1 Env. These findings revealed that single or double deletion of viral factors (B8 and B19) targeting the IFN pathway is a useful approach in the design of improved poxvirus-based vaccines.