gebhart/patrepeval huggingface dataset:
Desilylation‐Activated Propargylic Transformation: Enantioselective Copper‐Catalyzed [3+2] Cycloaddition of Propargylic Esters with β‐Naphthol or Phenol Derivatives (2016)

A copper-catalyzed asymmetric [3+2] cycloaddition of 3-trimethylsilylpropargylic esters with either β-naphthols or electron-rich phenols has been realized and proceeds by a desilylation-activated process. Under the catalysis of Cu(OAc)2⋅H2O in combination with a structurally optimized ketimine P,N,N-ligand, a wide range of optically active 1,2-dihydronaphtho[2,1-b]furans or 2,3-dihydrobenzofurans were obtained in good yields and with high enantioselectivities (up to 96 % ee). This represents the first desilylation-activated catalytic asymmetric propargylic transformation.
After Serrano Sacrifice and Church Politics (2000)

Casey, Fisher and Ramsay claim to speak in the name of "Christianity and the values of ordinary people". In order to claim to speak for Christianity, they must clearly demarcate who does and who does not have the right to call themselves Christian. Any ambiguity must be excluded. So called "liberals" must be cast out to the extent that they would compromise the integrity of the group. This attitude is much more akin to performing sacrifice than understanding it. But then, my respondents could make neither head nor tail of what I described as the logic of sacrifice. The logic of sacrifice as I understand it is founded in the binary logic of the "A" versus "not A" distinction. What is clear from the extensive anthropological and sociological literature on sacrifice is that it is sacrifice that forms identity and community through integration and separation. Both communion and expiation safeguard the unity of the community through a process of differentiation. Whether a particular sacrifice is concerned with communion or expiation, its underlying logic is grounded in opposition. The underlying unity of these two modes of sacrifice is perhaps best expressed by the English word "atonement" which "is also always at-one-ment", to make at one. Although Hubert and Mauss had recognised the irreducibility of these two modes, they were unable to establish their unity. Nancy Jay suggests that this was due primarily to their commitment to the idea, beloved of French sociology, that the unity of sacrifice lay in its function as a means of "establishing a means of communicating between the sacred and profane worlds" (Jay 1992: 165 n4). Although Durkheim would not accept this distinction, sacrifice is only about the sacred in as far as the sacred guarantees the identity of the community.
Intracerebroventricular infusion of monoclonal antibody or its derived Fab fragment against misfolded forms of SOD1 mutant delays mortality in a mouse model of ALS (2010)

The finding of a secretion pathway and toxicity for mutant superoxide dismutase 1 (SOD1) raised up the possibility of using immunization approaches to reduce or neutralize the burden of toxic SOD1 species in the nervous system. Here we tested a passive immunization approach based on intracerebroventricular infusion in G93A-SOD1 mice of monoclonal antibodies specific to misfolded forms of SOD1 (mSOD1). We tested two monoclonal antibodies that bind distinct epitopes in mSOD1 and that do not bind to intact wild-type (WT) SOD1. One antibody succeeded in reducing the level of mSOD1 by 23% in the spinal cord and in prolonging the lifespan of G93A-SOD1 mice in proportion to the duration of treatment. However, another monoclonal antibody binding to a different SOD1 epitope failed to confer protection indicating that not all anti-SOD1 antibodies might be suitable for immunotherapy. Interestingly, the variable Fab fragment of an anti-SOD1 antibody was sufficient to confer some protection in G93A-SOD1 mice. The partial dispensability of Fc region should offer some advantages for development of immunotherapy with antibodies of smaller molecular size and low immunogenicity. From these results, we propose that passive immunization strategies should be considered as potential avenues for treatment of familial amyotrophic lateral sclerosis caused by SOD1 mutations.
Industrial experience using rule-driven retargetable code generation for multimedia applications (2002)

The increasing usage of application-specific instruction set processors (ASIPs) in audio and video telecommunications has made strong demands on the rapid availability of dedicated compilers. A rule-driven approach to code generation may have benefits over model-based approaches as the user is not confined to the capabilities supported by the model. However, the sole use of transformation rules may or may not be sufficient in optimization abilities depending on the target architecture. This paper outlines experiences with a rule-driven code generation approach for two applications in audio and video processing. The first is a controller for the VideoPhone codec at SGS-Thomson Microelectronics. The second is a VLIW (very large instruction word) processor for high-fidelity and MPEG audio at Thomson Consumer Electronic Components. The experience has shown that a rule-driven approach to compilation is applicable to both the controller and VLIW architectures; however, is limited in optimization abilities for the latter.
Surflex:  Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine (2003)

Surflex is a fully automatic flexible molecular docking algorithm that combines the scoring function from the Hammerhead docking system with a search engine that relies on a surface-based molecular similarity method as a means to rapidly generate suitable putative poses for molecular fragments. Results are presented evaluating reliability and accuracy of dockings compared with crystallographic experimental results on 81 protein/ligand pairs of substantial structural diversity. In over 80% of the complexes, Surflex's highest scoring docked pose was within 2.5 A root-mean-square deviation (rmsd), with over 90% of the complexes having one of the top ranked poses within 2.5 A rmsd. Results are also presented assessing Surflex's utility as a screening tool on two protein targets (thymidine kinase and estrogen receptor) using data sets on which competing methods were run. Performance of Surflex was significantly better, with true positive rates of greater than 80% at false positive rates of less than 1%. Docking time was roughly linear in number of rotatable bonds, beginning with a few seconds for rigid molecules and adding approximately 10 s per rotatable bond.
IL-17E, a Novel Proinflammatory Ligand for the IL-17 Receptor Homolog IL-17Rh1 (2001)

We report identification of interleukin (IL)-17E, a novel member of the IL-17 family of cytokines. IL-17E is a ligand for the recently identified protein termed EVI27/IL-17BR, which we term IL-17 receptor homolog 1 (IL-17Rh1) in light of the multiple reported ligand-receptor relationships. Murine EVI27 was identified through its location at a common site of retroviral integration in BXH2 murine myeloid leukemias. IL-17Rh1 shows highest level expression in kidney with moderate expression in multiple other organs, whereas IL-17E mRNA was detected at very low levels in several peripheral tissues. IL-17E induces activation of NF-kappaB and stimulates production of the proinflammatory chemokine IL-8.
Formylation Is Not Essential for Initiation of Protein Synthesis in All Eubacteria (1999)

Formylation of the initiator methionyl-tRNA, catalyzed by methionyl-tRNA formyltransferase, has long been regarded as essential for initiation of protein synthesis in eubacteria. Here, we show that this process is, in fact, dispensable in Pseudomonas aeruginosa. Disruption of the chromosomal methionyl-tRNA formyltransferase gene in P. aeruginosa resulted only in a moderate decrease in the rate of cell growth, whereas in Escherichia coli cell growth was severely impaired. The ability of the P. aeruginosa mutant strain to grow was not due to an additional copy of the methionyl-tRNA formyltransferase gene or to N-acylation of the methionyl moiety by a group other than formyl. These results indicate that P. aeruginosa can carry out formylation-independent initiation of protein synthesis, using the nonformylated methionyl-tRNA. Therefore, the dogma that eubacteria require formylation of the initiator methionyl-tRNA for initiation of protein synthesis may have been an invalid generalization of results obtained with E. coli.
Efficient Inhibition of the Alzheimer's Disease β-Secretase by Membrane Targeting (2008)

beta-Secretase plays a critical role in beta-amyloid formation and thus provides a therapeutic target for Alzheimer's disease. Inhibitor design has usually focused on active-site binding, neglecting the subcellular localization of active enzyme. We have addressed this issue by synthesizing a membrane-anchored version of a beta-secretase transition-state inhibitor by linking it to a sterol moiety. Thus, we targeted the inhibitor to active beta-secretase found in endosomes and also reduced the dimensionality of the inhibitor, increasing its local membrane concentration. This inhibitor reduced enzyme activity much more efficiently than did the free inhibitor in cultured cells and in vivo. In addition to effectively targeting beta-secretase, this strategy could also be used in designing potent drugs against other membrane protein targets.
Efficacy of laser capture microdissection plus RT-PCR technique in analyzing gene expression levels in human gastric cancer and colon cancer (2008)

Abstract Background Thymidylate synthase, dihydropyrimidine dehydrogenase, thymidine phosphorylase, and orotate phosphoribosyltransferase gene expressions are reported to be valid predictive markers for 5-fluorouracil sensitivity to gastrointestinal cancer. For more reliable predictability, their expressions in cancer cells and stromal cells in the cancerous tissue (cancerous stroma) have been separately investigated using laser capture microdissection. Methods Thymidylate synthase, dihydropyrimidine dehydrogenase, thymidine phosphorylase, and orotate phosphoribosyltransferase mRNA in cancer cells and cancerous stroma from samples of 47 gastric and 43 colon cancers were separately quantified by reverse transcription polymerase chain reaction after laser capture microdissection. Results In both gastric and colon cancers, thymidylate synthase and orotate phosphoribosyltransferase mRNA expressions were higher (p &lt; 0.0001, p &lt;0.0001 respectively in gastric cancer and P = 0.0002, p &lt; 0.0001 respectively in colon cancer) and dihydropyrimidine dehydrogenase mRNA expressions were lower in cancer cells than in cancerous stroma (P = 0.0136 in gastric cancer and p &lt; 0.0001 in colon cancer). In contrast, thymidine phosphorylase mRNA was higher in cancer cells than in cancerous stroma in gastric cancer (p &lt; 0.0001) and lower in cancer cells than in cancerous stroma in colon cancer (P = 0.0055). Conclusion By using this method, we could estimate gene expressions separately in cancer cells and stromal cells from colon and gastric cancers, in spite of the amount of stromal tissue. Our method is thought to be useful for accurately evaluating intratumoral gene expressions.
T Cell Tolerance to Germline-Encoded Antibody Sequences in a Lupus-Prone Mouse (2005)

The BCR V region has been implicated as a potential avenue of T cell help for autoreactive B cells in systemic lupus erythematosus. In principle, either germline-encoded or somatically generated sequences could function as targets of such help. Preceding studies have indicated that class II MHC-restricted T cells in normal mice attain a state tolerance to germline-encoded Ab diversity. In this study, we tested whether this tolerance is intact in systemic lupus erythematosus-prone (New Zealand Black x SWR)F1 mice (SNF1). Using a hybridoma sampling approach, we found that SNF1 T cells were tolerant to germline-encoded Ab sequences. Specifically, they were tolerant to germline-encoded sequences derived from a lupus anti-chromatin Ab that arose spontaneously in this strain. This was true both for diseased and prediseased mice. Thus, there does not appear to be a global defect in T cell tolerance to Ab V regions in this autoimmune-prone strain either before or during autoimmune disease.
Hepatitis C new drugs (2010)

7‐11 November 2010, Tenth International Congress on Drug Therapy in HIV Infection, Glasgow, UK
Optical Properties and Ultrafast Dynamics of Metallic Nanocrystals (2003)

Noble metal particles have long fascinated scientists because of their intense color, which led to their application in stained glass windows as early as the Middle Ages. The recent resurrection of colloidal and cluster chemistry has brought about the strive for new materials that allow a bottoms-up approach of building improved and new devices with nanoparticles or artificial atoms. In this review, we discuss some of the properties of individual and some assembled metallic nanoparticles with a focus on their interaction with cw and pulsed laser light of different energies. The potential application of the plasmon resonance as sensors is discussed.
Responsiveness of Astrocytes in Serum-Free Aggregate Cultures to Epidermal Growth Factor: Dependence on the Cell Cycle and the Epidermal Growth Factor Concentration (1985)

Serum-free aggregating cell cultures of fetal rat telencephalon treated with low doses (0.5 nM) of epidermal growth factor (EGF) showed a small, transient increase in DNA synthesis but no significant changes in total DNA and protein content. By contrast, treatment with high doses (13 nM) of EGF caused a marked stimulation of DNA synthesis as well as a net increase in DNA and protein content. The expression of the astrocyte-specific enzyme, glutamine synthetase, was greatly enhanced both at low and at high EGF concentrations. These results suggest that at low concentration EGF stimulates exclusively the differentiation of astrocytes, whereas at high concentration, EGF has also a mitogenic effect. Nonproliferating astrocytes in cultures treated with 0.4 microM 1-beta-D-arabinofuranosyl-cytosine were refractory to EGF treatment, indicating that their responsiveness to EGF is cell cycle-dependent. Binding studies using a crude membrane fraction of 5-day cultures showed a homogeneous population of EGF binding sites (Kd approximately equal to 2.6 nM). Specific EGF binding sites were found also in non-proliferating (and nonresponsive) cultures, although they showed slightly reduced affinity and binding capacity. This finding suggests that the cell cycle-dependent control of astroglial responsiveness to EGF does not occur at the receptor level. However, it was found that the specific EGF binding sites disappear with progressive cellular differentiation.
Overview of the Stability of α-Chymotrypsin in Different Solvent Media (2012)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTOverview of the Stability of α-Chymotrypsin in Different Solvent MediaAwanish Kumar and Pannuru Venkatesu*View Author Information Department of Chemistry, University of Delhi, Delhi-110 007, India*E-mail: [email protected] (P.V.); tel: +91-11-27666646-142; fax: +91-11-2766 6605.Cite this: Chem. Rev. 2012, 112, 7, 4283–4307Publication Date (Web):April 16, 2012Publication History Received29 September 2011Published online16 April 2012Published inissue 11 July 2012https://pubs.acs.org/doi/10.1021/cr2003773https://doi.org/10.1021/cr2003773review-articleACS PublicationsCopyright © 2012 American Chemical SocietyRequest reuse permissionsArticle Views4709Altmetric-Citations204LEARN 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 SUBJECTS:Carbohydrates,Peptides and proteins,Protein structure,Solvents,Urea Get e-Alerts
Evaluation of susceptibility of gram-positive and -negative bacteria to human defensins by using radial diffusion assay (1996)

Defensins are small cationic bactericidal peptides present abundantly in the granules of polymorphonuclear neutrophils (PMNs). Human PMNs contain four defensins termed HNP-1 to HNP-4. We used a new assay system in agar plates, the radial diffusion assay, to evaluate the effects of human defensins against gram-positive and -negative bacteria. A crude mixture of HNP-1, -2, and -3 (crude HNPs) was purified from human PMN extracts by reversed-phase high-pressure liquid chromatography (RP-HPLC). The different components were later separated by RP-HPLC and gel permeation chromatography. We compared the antibacterial activities of purified HNP-1, -2, and -3 against Escherichia coli, Pseudomonas aeruginosa, methicillin-susceptible Staphylococcus aureus, and methicillin-resistant S. aureus strains using the radial diffusion assay. The antibacterial activities of HNP-1 and HNP-2 against all strains tested were similar to those of the crude HNPs, but the activity of HNP-3 was less than those of the other defensins. To quantitate the activities of HNPs against different bacteria, we defined the minimal dose of crude HNPs forming a detectable clear zone around the bacteria as the minimal inhibitory dose (MID) and determined the MIDs for 10 strains of E. coli, 12 strains of P. aeruginosa, 10 strains of methicillin-susceptible S. aureus, and 12 strains of methicillin-resistant S. aureus isolates, including clinical isolates. In general, the MIDs of the HNPs were similar against similar bacterial species. However, the MIDs for P. aeruginosa were higher than those for the other organisms tested. The radial diffusion assay is suitable as a screening test for measuring the susceptibilities of isolates to defensins, because it is sensitive and simple and has good reproducibility.
A tetrahedron beam computed tomography benchtop system with a multiple pixel field emission x-ray tube (2011)

A prototype system was developed, and preliminary phantom images were successfully acquired. MPFEX is a promising x-ray source for TBCT. Further improvement of tube output is needed in order for it to be used in clinical TBCT systems.
SENSOR BASED ROBOT LOCALISATION AND NAVIGATION: USING INTERVAL ANALYSIS AND NONLINEAR KALMAN FILTERS. (2005)

Multiple sensor fusion for robot localisation and navigation has attracted a lot of interest in recent years. This paper describes a sensor based navigation and localisation approach for an autonomous mobile robot using an interval analysis (IA) based adaptive mechanism for the non-linear Kalman filter namely the Extended Kalman filter (EKF). The map used for this study is two-dimensional and assumed to be known a priori. The robot is equipped with inertial sensors (INS), encoders and ultrasonic sensors. A non-linear Kalman filter is used to estimate the robots position using the inertial sensors and encoders. The ultrasonic sensors use an Interval Analysis (IA) algorithm for guaranteed robot localisation. Since the Kalman Filter estimates may be affected by bias, drift etc. we propose an adaptive mechanism using IA to correct these defects in estimates. In the presence of landmarks the complementary interval robot position information from the IA algorithm with uniform distribution using ultrasonic sensors is used to estimate and bound the errors in the non-linear Kalman filter robot position estimate with a Gaussian distribution.
A Unique Cogeneration Application in a Large Pulp Mill Electrical System (1997)

Canadian utilities have begun investigating the viability of independent power producers providing generation facilities to operate in parallel wit the utility systems. Cogeneration in industrial plants is often an excellent source of such generation. In the case described it was determined that two 48.7 MVA, 13.8.kV, 0.84 pf, 3600 RPM steam turbogenerator would be the most economical method of power supply for the 1500 Adt/d green field pulp mill. In this application, the local utility could not guarantee a 230 kV or 138 kV tie circuit to be in place at the projected start-up date of the mill, hence it was decided to use a 25 kV construction power line which was already in the vicinity of the mill and used for servicing rural customers. The maximum capacity of the 25 kV line was 7 MVA at 1.0 pf. Since this capacity could not fully support the mill during construction, black start or stand-by service when one generator is out of service, an additional process independent power source was required. A 14.2 MW (turbine limited), 22.0 MVA, 13.8 kV, 0.8 pf, 1200 RPM pre-owned gas turbine generator was selected to meet the mill construction schedule.
Optimal control data assimilation with an atmospheric model (1997)

The problem of time-continuous meteorological data assimilation is addressed. An optimal control method is proposed and studied for a simple well-posed 2D atmospheric model and continuous in time and space observations. An existence result for the optimal control problem is given. Then the first order necessary conditions of optimality are explicited using a forced version of the linearized adjoint model; allowing the use of a classical descent method to solve the problem. The reliability of the method is shown on some numerical tests. Finally, the existence and characterization results of an optimal control are extended to the case of observations distributed in time.
Multi-scale heterogeneity modelling in a giant carbonate field, northern Oman (2008)

A giant carbonate reservoir in northern Oman has been producing for some 40 years under primary depletion and secondary development schemes. Now the next brown field development phase is being prepared. Costs and potential rewards are substantial and require sound decision making. Geological, petrophysical and production data has revealed a multi-scale heterogeneity system. The driving forces for heterogeneity are sedimentary fabrics, depositional environments, large and small-scale depositional cyclicity, diagenesis, and fracturing/ faulting. Hydrocarbon storage and flow through the matrix is fundamentally influenced by variations in pore types on a scale much below that of normal static and dynamic reservoir models. With the goal of building reservoir-size dynamic models the extensive heterogeneity on a centimetre-decimetre scale provides a significant upscaling problem both for static and dynamic properties. In order to populate reservoir-size models with realistic properties reflecting small-scale heterogeneity,&lt;br&gt;both statically and dynamically, an approach has been chosen to define and model heterogeneities hierarchically. Small-scale heterogeneities were captured and simulated in mini-models (less than 1.0 cubic m in size), which provided pseudo-properties for volume cells in reservoir-size models. Principle rock types (PRT) are the fundamental building blocks of the matrix system. They cover and categorize the full range of pore types, sizes, pore-throat size distributions, capillary entry pressures, relative permeabilities, etc. PRTs were organised into Rock-type associations (RTA) based on sedimentary fabric (bioturbation, cross-bedding, layering, etc.). Mini-models were constructed using borehole image logs (BHI) data for all RTAs and their internal property variations. The distribution of RTAs in the reservoir is driven vertically by depositional cyclicity and laterally by facies dimensionalities. The key tools to distribute RTAs in the larger reservoir models are seismic data and the BHI logs, which provide control on both fabric and property heterogeneity.