gebhart/patrepeval huggingface dataset:
The Androgen Receptor: Structure, Mutations, and Antiandrogens (2003)

Androgens play a critical role not only in the physiological development of the prostate but also in the genesis of prostate cancer. The effects of androgen on the prostate gland and on the other tissues of the body are mediated by activation of the androgen receptor. The androgen receptor is a member of the superfamily of hormone receptors with a DNA-binding site, two zinc finger domains, and a hormone-binding site. Mutations in this receptor can be associated with loss of function or chronic endogeneous activation, depending upon the site of change. Androgens effect a conformal change in the structure of the androgen receptor associated with a change in protein phosphorylation. The androgen receptor can be activated by additional ligands affecting the hormone-binding site besides androgens. Activators and repressors of the androgen receptor modify this protein's function and are very delicately balanced such that disruptions of either function are associated with a disease state. Antiandrogens, which bind to the receptor and thus down-regulate the effects of endogeneous circulating androgens, remain the first line treatment for palliation of advanced prostate cancer. Mutations in the receptor are associated with a change in function of such compounds from antagonist to agonist in vitro. Newer evidence suggests there may be a role of intermittent androgen suppression rather than continuous suppression, perhaps by preventing overgrowth of hormone independent tumor cells. Future research focuses on the development of drugs directed at suppressing the androgen drive of the androgen sensitive clone of the tumor and making the nonsensitive subset more susceptible to cytotoxics.
Hb Long Island: a hemoglobin variant with a methionyl extension at the NH2 terminus and a prolyl substitution for the normal histidyl residue 2 of the beta chain. (1985)

Hb Long Island was found in a diabetic man and his nondiabetic mother as the result of a routine clinical measurement of Hb AIc. It is present in amounts approximately equal to Hb A. Its alpha chains are normal but its beta chains have two alterations compared to the normal. A methionyl residue is attached to the usual NH2-terminal valyl residue. This valyl residue is followed by prolyl residue in place of the usual histidyl residue 2. The remaining sequence of the beta chain is normal. No hemoglobin or abnormal beta chain containing only the prolyl substitution could be detected by several different electrophoretic and HPLC procedures. We postulate that Hb Long Island is the result of a mutation in which a single nucleotide change causes the substitution of a prolyl residue for the normal histidyl residue at position 2 of the beta chain. We further postulate that this abnormal prolyl residue inhibits enzymatic cleavage of the initiator methionyl residue from the abnormal beta chain during posttranslational processing. Although the oxygen affinities of the whole blood, suspended cells, and hemolysate are normal, the affinity of the isolated Hb Long Island is slightly decreased and the effects of organic phosphates are reduced compared to normal. These changes are consistent with the loss of the normal histidyl residue 2 and the extension of the NH2-terminal end of the beta-chain molecule.
Componentwise energy amplification in channel flows (2005)

We study the linearized Navier–Stokes (LNS) equations in channel flows from an input–output point of view by analysing their spatio-temporal frequency responses. Spatially distributed and temporally varying body force fields are considered as inputs, and components of the resulting velocity fields are considered as outputs into these equations. We show how the roles of Tollmien–Schlichting (TS) waves, oblique waves, and streamwise vortices and streaks in subcritical transition can be explained as input–output resonances of the spatio-temporal frequency responses. On the one hand, we demonstrate the effectiveness of input field components, and on the other, the energy content of velocity perturbation components. We establish that wall-normal and spanwise forces have much stronger influence on the velocity field than streamwise force, and that the impact of these forces is most powerful on the streamwise velocity component. We show this using the relative scaling of the different input–output system components with the Reynolds number. We further demonstrate that for the streamwise constant perturbations, the spanwise force localized near the lower wall has, by far, the strongest effect on the evolution of the velocity field.
Steam-quality relationships for direct-contact steam generators. [Down the hole] (1982)

The information required for computation of steam quality is: mass flows of fuel, oxidizer and water, effluent total pressure, and temperature. Evaluation of steam quality and temperature as a function of total pressure and water injection rate impacts reservoir response modeling, delivery line sizing, packer elastomeric seal selection, etc. This paper is thus timely in providing such information as direct contact downhole generators approach commercialization. We discuss how the state of the effluent of a direct contact steam generator can be determined thermodynamically and present charts useful to the designers of these systems. The analysis utilizes the following assumptions: a stoichiometric ratio of fuel/oxidizer is maintained; the reaction is complete and the discharge is in thermal equilibrium; all processes are adiabatic; the pressure throughout the steam generator is uniform; entering streams of fuel, oxidizer and water are near reference state of 25/sup 0/C (77/sup 0/F); and Dalton's law applies to the gaseous mixture and the noncondensible gases obey the ideal gas equation of state.
Strong interferon-inducing capacity of a highly virulent variant of influenza A virus strain PR8 with deletions in the NS1 gene (2009)

Influenza viruses lacking the interferon (IFN)-antagonistic non-structural NS1 protein are strongly attenuated. Here, we show that mutants of a highly virulent variant of A/PR/8/34 (H1N1) carrying either a complete deletion or C-terminal truncations of NS1 were far more potent inducers of IFN in infected mice than NS1 mutants derived from standard A/PR/8/34. Efficient induction of IFN correlated with successful initial virus replication in mouse lungs, indicating that the IFN response is boosted by enhanced viral activity. As the new NS1 mutants can be handled in standard biosafety laboratories, they represent convenient novel tools for studying virus-induced IFN expression in vivo.
tmRNA Is Essential in Shigella flexneri (2013)

Nonstop mRNAs pose a challenge for bacteria, because translation cannot terminate efficiently without a stop codon. The trans-translation pathway resolves nonstop translation complexes by removing the nonstop mRNA, the incomplete protein, and the stalled ribosome. P1 co-transduction experiments demonstrated that tmRNA, a key component of the trans-translation pathway, is essential for viability in Shigella flexneri. tmRNA was previously shown to be dispensable in the closely related species Escherichia coli, because E. coli contains a backup system for trans-translation mediated by the alternative release factor ArfA. Genome sequence analysis showed that S. flexneri does not have a gene encoding ArfA. E. coli ArfA could suppress the requirement for tmRNA in S. flexneri, indicating that tmRNA is essential in S. flexneri because there is no functional backup system. These data suggest that resolution of nonstop translation complexes is required for most bacteria.
Two-pot Oxidative Preparation of Dicarboxylic Acid Containing Cellulosefor the Removal of Beryllium (Be2+) from Aqueous Solution (2020)

Background: Cellulose is one of the most abundant, non-toxic, and renewable natural biopolymers. The presence of hydroxyl groups in cellulose leads to further modification of it. Preparation and modification of cellulose-based sorbents and their applications on water treatment gained traction in recent years. Objective: A low-cost and eco-friendly biosorbent was designed and fabricated by introducing the acetate functional groups into cellulose for removing Beryllium (Be2+) from an aqueous solution. The so rption of Be2+ on acetate containing cellulose was evaluated for varying sorbent doses and initial solution pH values. Method: The sorbent was prepared by a two-step oxidation process. In the initial step, cellulose reacted with NaIO4 and aldehyde groups were introduced to cellulose. In the second step, newly obtained aldehyde groups were oxidized to create acetate groups. Results: The kinetics of the sorption process showed that Be2+ uptake reached equilibrium in 3 minutes. The sorption isotherm was well fitted in the Langmuir model, and maximum sorption capacity was 4.54 mg/g. Moreover, the thermodynamic studies demonstrated that Be2+ sorption is spontaneous and exothermic. Furthermore, the prepared sorbent can be regenerated by using 0.1 M HCl or H2SO4 solutions. Conclusion: Removal of Be2+ is pH dependent and it is favorable at high solution pH. The kinetics of the prepared sorbent is rapid and equilibrium attained in 3 minutes. The prepared sorbent can be regenerated with 0.1 M acid solution with > 99% efficiency.
Stable and unstable chromosome aberrations measured after occupational exposure to ionizing radiation and ultrasound. (2007)

Fluorescence in situ hybridization-based translocation detection was a reliable method for monitoring chronic occupational clastogen exposure. Chromosome aberration assay correlated with translocation frequency. Stable chromosomal aberrations reflected cumulative genome damage during job exposure.
Platinum-Catalyzed Ethylene Hydroamination with Aniline: Synthesis, Characterization, and Studies of Intermediates (2009)

Starting from either K2PtCl4 or K[PtCl3(C2H4)]·H2O (Zeise’s salt), complexes (nBu4P)2[PtBr4] (1), nBu4P[PtBr3(C2H4)] (2), nBu4P[PtBr3(PhNH2)] (3), trans-[PtBr2(C2H4)(PhNH2)] (4), cis-[PtBr2(C2H4)(PhNH2)] (5), and cis-[PtBr2(PhNH2)2] (6) have been obtained by efficient one-pot procedures. All have been fully characterized by microanalysis (C, H, N), multinuclear NMR spectrometry (1H, 13C, 195Pt), UV−visible spectroscopy, and single-crystal X-ray diffraction. Compound 1 slowly loses Br− in solution to yield (nBu4P)2[Pt2Br6] (1′), which has also been characterized crystallographically. The relative stability of the various compounds has been probed experimentally by NMR studies in several solvents and computationally by gas-phase geometry optimizations followed by C-PCM calculations of the solvation effects in dichloromethane and aniline. The calculations also included the bis(ethylene) complexes [PtBr2(C2H4)2] in the trans (two different conformations 7 and 7′) and cis (8) configurations. The solution experiments gave no evidence for a nucleophilic attack of aniline onto coordinated ethylene under mild conditions (T up to 68 °C), setting a lower limit of 29 kcal mol−1 for the activation barrier of this process. Therefore, the relative energies computed for the other compounds suggest that all ethylene-containing complexes (2, 4, 5, 7, and 8) are viable candidates for the nucleophilic addition step of the PtBr2-catalyzed ethylene hydroamination by aniline. Use of the isolated complex 2, 4, or 5 in combination with nBu4Br as precatalysts for the ethylene hydroamination by aniline yields similar catalytic activities.
Photon-stimulated desorption from<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">CaF</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">BaF</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>thin films grown epitaxially on GaAs(100) surfaces (1992)

Photon-stimulated desorption from thin films of ${\mathrm{CaF}}_{2}$ exhibit distinctly different desorption channels for ions depending on the site where the initial core hole was created. In addition to ${\mathrm{H}}^{+}$, the most prominent desorbed ionic species observed in ${\mathrm{CaF}}_{2}$ is ${\mathrm{F}}^{+}$. Upon the creation of a F 1s core exciton, there is enhanced ${\mathrm{F}}^{+}$ desorption compared with the ion yield for complete ionization of a F 1s electron. A similar enhancement is not observed at the fluorine edge in ${\mathrm{BaF}}_{2}$. In ${\mathrm{BaF}}_{2}$, the ${\mathrm{H}}^{+}$ ion yield is, to within an order of magnitude, the same as in ${\mathrm{CaF}}_{2}$, but ${\mathrm{HF}}^{+}$ ions are also observed. Excitation of Ca 2p and Ba 3d core excitons does not result in an additional desorption channel that directly leads to the production of ions, but rather the desorption is caused nonspecifically by enhancing the secondary electron current through the surface.
Phylogenetic analysis of the rompB genes of Rickettsia felis and Rickettsia prowazekii European-human and North American flying-squirrel strains. (2000)

The rickettsial outer membrane protein B (rompB) gene encodes the major surface antigens of Rickettsia species. We undertook sequencing and molecular analysis of the rompB gene of Rickettsia felis and a comparison with its homologs in spotted fever group (SFG) and typhus group (TG) rickettsiae, including the complete sequences of two North American flying squirrel strains and two European human strains of Rickettsia prowazekii. We sequenced 5,226 base pairs (bp) of the R. felis rompB, encoding a protein of 1,654 amino acids. We also sequenced 5,015 bp of rompB of the flying squirrel strains, encoding a protein of 1,643 amino acids. Analysis of the R. felis rompB gene sequence showed 10-13% divergence from SFG rickettsiae and 18% divergence from the TG rickettsiae. The rompB of all sequenced strains of R. prowazekii showed an overall similarity of 99.7-99.9%.
Model reference adaptive control using only input and output measurements (1981)

A new method of designing model reference adaptive controllers using only input and output measurements is presented. The adjustable parameters are all contained in the control input signal to the process. State variable filters are used to avoid taking pure derivatives of the process output while the hyperstability theorem ensures global stability of the parameter adaptations. The control input can also contain a term to diminish the effect of external load disturbance. The natural extensions to multivariable and certain non-linear systems are then presented. The performance of the adaptive controller in the presence of noise can be further improved by the use of the instrumental variable approach together with an adjustable series compensator. The theoretical development is substantiated by extensive simulation results.
Expression of Epstein-Barr virus in cutaneous T-cell lymphoma including mycosis fungoides (2001)

Cutaneous T-Cell lymphoma (CTCL) is a non-Hodgkin's lymphoma of unknown pathogenesis. Mycosis fungoides (MF) is a clinically determined subset of CTCL with intensive infiltration of lymphoma cells into the epidermis. To determine whether Epstein-Barr virus (EBV) is associated with these lymphoma cells, we performed mRNA in situ hybridization in 5 cases of CTCL and 7 cases of MF using an RNA probe transcribed from BamHI W fragment of EBV genome. These transcripts were detected in the majority of lymphoma cells in all cases examined. We also detected intensive hybridization signals on epidermal squamous cells contiguous to strong infiltration with lymphoma cells into the subcutaneous connective tissue. Similarly, positive signals were detected using the probes transcribed from the sequences of EBV-encoded small nonpolyadenylated RNAs-1 (EBER1) and EBV-determined nuclear antigen-2 (EBNA2). The EBNA2 latent membrane protein-1 (LMP1) and BZLF1 product (ZEBRA) were also detected by immunofluorescence staining using monoclonal antibodies. Further in the same experiment, we detected immunofluorescence of epidermal cells. EBV DNA was detected in all cases tested by DNA in situ hybridization. Moreover, we also identified the signals on epidermal cells via this technique. Polymerase chain reaction revealed amplified EBV DNA for most cases tested. Double staining with immunohistochemistry and RNA in situ hybridization showed that T-cell marker-positive cells, but not EBV-carrying B-cells, exhibited signals for the EB viral RNA. These findings suggest that EBV is involved in the neoplastic transformation of CTCL and MF.
Low loss Kagome hollow-core photonic crystal fiber for high power fast laser beam transportation and pulse compression (2012)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Y. Y. Wang, X. Peng, M. Alharbi, C. F. Dutin, T. D. Bradley, M. Mielke, T. Booth, and F. Benabid, "Low loss Kagome hollow-core photonic crystal fiber for high power fast laser beam transportation and pulse compression," in Conference on Lasers and Electro-Optics 2012, OSA Technical Digest (online) (Optica Publishing Group, 2012), paper JTh3I.6. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
A comme Anthologie (2012)

Anthologie : ce modeste usuel qui entend donner à connaître le meilleur ou le plus significatif d’une littérature, d’un mouvement artistique ou d’une culture est dans sa démarche et dans son esprit proche d’une exposition. Outil de connaissance, elle donne à voir, et en même temps elle interprète et reconstruit la réalité qu’elle expose : en montrant elle démontre. L’anthologie s’offre donc dans un même mouvement comme reflet d’une réalité et fabrique de cette dernière. Parce qu’elle est issu...
Disulfide-Bridged Heterotrimeric Collagen Peptides Containing the Collagenase Cleavage Site of Collagen Type I. Synthesis and Conformational Properties (1999)

Collagenous peptides containing the collagenase cleavage site α1(772−784) and α2(772−784) of collagen type I were synthesized and assembled into heterotrimers via regioselective C-terminal interchain-disulfide bridging in a defined α1α2α1' staggered register of the three peptide strands. Various approaches were attempted to induce and stabilize the collagen-characteristic triple-helical fold even in the sequence portion of the collagenase cleavage site with its weak triple-helix propensity. By N-terminal chain elongation with (Gly-Pro-Hyp)n tripeptide repeats, particularly with n = 5, and in an even more pronounced manner, by incorporation of an additional tripeptide repeat adjacent to the cystine knot, a collagenous heterotrimer was obtained which was found to exhibit dichroic properties fully consistent with the triple-helical fold. Thermal denaturation revealed a remarkable stability with a melting temperature of 41 °C. Although the complex cystine knot of natural collagen was reduced in these synthetic heterotrimers to two interchain-disulfide bridges, it showed not only the expected entropic contribution to the refolding process by keeping the three chains assembled, but more importantly a triple-helix nucleation was induced. In fact, temperature jump experiments clearly revealed two-phase refolding kinetics very similar to those of the disulfide-bridged natural collagen fragment of Col 1−3, where refolding without nucleation difficulty was obtained followed by a slower process dominated by the cis → trans isomerization for triple-helix propagation. These results would indicate that even the simplified artificial cystine knot is capable of aligning the three peptide chains in the defined α1α2α1' one-residue shift register. Moreover, the synthetic heterotrimers were cleaved by interstitial collagenases in a single cut through all three chains without release of intermediates during the relatively slow enzymatic digestion process. This observation confirms that, with the de novo designed heterotrimers, functional collagen epitopes were mimicked in highly efficient manner; it also strongly suggests that the preselected α1α2α1' register may indeed represent the correct staggered alignment of the α subunits at least in collagen type I.
A New Approach to Comparing Several Equating Methods in the Context of the NEAT Design (2010)

The nonequivalent groups with anchor test (NEAT) design involves missing data that are missing by design. Three equating methods that can be used with a NEAT design are the frequency estimation equipercentile equating method, the chain equipercentile equating method, and the item‐response‐theory observed‐score‐equating method. We suggest an approach to perform a fair comparison of the three methods. The approach is then applied to compare the three equating methods using three data sets from operational tests. For each data set, we examine how the three equating methods perform when the missing data satisfy the assumptions made by only one of these equating methods. The chain equipercentile equating method is somewhat more satisfactory overall than the other methods.
Activation of the fibrinogen binding site on platelets isolated from a patient with the Strasbourg I variant of Glanzmann's thrombasthenia (1994)

One proposed ligand binding site on platelet integrin alpha IIb beta 3 is the region of the beta 3 subunit encompassing amino acids 211-221. However, we recently showed that synthetic peptides corresponding to amino acids 211-221 inhibit fibrinogen binding to alpha IIb beta 3 by binding to alpha IIb beta 3 and not to fibrinogen. In this study, we show that AP6, a monoclonal antibody (MoAb) directed against amino acids 214-221 of beta 3, bound to immobilized active alpha IIb beta 3 but did not inhibit fibrinogen binding to the complex. We then determined whether nonfunctional alpha IIb beta 3 on platelets with a beta 3 Arg-214-->Trp mutation (Strasbourg I variant of Glanzmann's thrombasthenia or GTV) could be induced to aggregate after treatment with dithiothreitol (DTT). DTT has been shown to expose the fibrinogen receptor on normal platelets. DTT treatment of GTV platelets did result in the formation of the fibrinogen binding site as indicated by the binding of pI-55, an MoAb that only binds to the activated form of alpha IIb beta 3. Furthermore, DTT-treated GTV platelets aggregated in the presence of fibrinogen and divalent cations. This aggregation was inhibited by EDTA, RGDS, and the selective alpha IIb beta 3 antagonist, Ro 43-5054. These data show that Arg-214 of beta 3 is not required for fibrinogen binding or for platelet aggregation. However, this amino acid appears to be critical for the formation and for the maintenance of the correct tertiary structure of the fibrinogen binding site on alpha IIb beta 3.
Workload Reduction for Multi-input Feedback-Directed Optimization (2009)

Feedback-directed optimization is an effective technique to improve program performance, but it may result in program performance and compiler behavior that is sensitive to both the selection of inputs used for training and the actual input in each run of the program. Cross-validation over a workload of inputs can address the input-sensitivity problem, but introduces the need to select a representative workload of minimal size from the population of available inputs. We present a compiler-centric clustering methodology to group similar inputs so that redundant inputs can be eliminated from the training workload. Input similarity is determined based on the compile-time code transformations made by the compiler after training separately on each input. Differences between inputs are weighted by a performance metric based on cross-validation in order to account for code transformation differences that have little impact on performance. We introduce the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CrossError</i> metric that allows the exploration of correlations between transformations based on the results of clustering. The methodology is applied to several SPEC benchmark programs, and illustrated using selected case studies.