gebhart/patrepeval huggingface dataset:
Rational design of substituted tripyrrole peptides that complex with DNA by both selective minor-groove binding and electrostatic interaction with the phosphate backbone. (1992)

The structures of the compounds we call 3a, 3b, and 3c-compounds that incorporate (i) the tripyrrole peptide of the minor-groove-binding distamycin class of compounds and (ii) polyamine ligands that extend from the minor groove and can interact with phosphodiester bonds--were arrived at by computer-graphics designing by using the x-ray structure of distamycin A complexed in the minor groove of d(CGCAAATTTGCG)2. Compounds 3a, 3b, and 3c are elaborations of distamycin analog 2, designed for improved stability in solution and easier synthesis and purification, which itself binds weakly to DNA. Compounds 3a, 3b, and 3c have been synthesized, and the interaction of distamycin A, 2, 3a, 3b, and 3c with calf thymus DNA, poly(dA-dT), poly(dG-dC), poly(dI-dC), pBR322 superhelical plasmid DNA, and, in the case of 3b, T4 coliphage DNA have been studied. The following pertinent conclusions can be drawn. Binding of 3a, 3b, and 3c occurs in the minor groove of DNA and, because of favorable electrostatic interaction of diprotonated polyamine side chains and DNA phosphodiester linkages, the tenacity of DNA binding and site specificity of 3a, 3b, and 3c are comparable to that of native distamycin A. 3b has been found to induce changes in the superhelical density of pBR322 plasmid DNA. The study establishes that the central pyrrole N-CH3 substituent of 2 can be replaced by bulky polyamine metal ligands to create any number of compounds that bind into the minor groove at A + T-rich sites and are putative catalysts for the hydrolysis of DNA.
Electrophoretically Deposited Porous Ceramics and their Characterisation by X-Ray Computer Tomography (2009)

Planar zirconia green bodies with unidirectionally aligned pore channels were prepared by an electrophoretic deposition method using an effect which is usually disadvantageous for the EPD from aqueous suspensions: the formation of gas bubbles by electrolysis. Aqueous ZrO2 suspensions containing acetic acid to enable a sufficient gas generation were used for the EPD experiments. The influence of selected parameters – electrolyte content, applied voltage, and kind of deposition electrode – on the pore structure has been investigated. The green bodies were sintered at 1450 °C in air. Optical microscopy and X-ray computer tomography (CT) were used for characterising the porous structures. CT-investigations have the advantage of a three-dimensional characterisation of the samples by a non-destructive method. The resulting pore structure depended to a high degree on the experimental conditions of the EPD. The kind of the deposition electrode – platinum foil or platinum gauze on foil – had a strong influence on the arrangement of the pores. The EPD on Pt-foil led to randomly arranged pores, whereas very regular pore structures were obtained by the use of Pt-gauze.
Improvements of HEVC SCC Palette Mode and Intra Block Copy (2016)

Palette mode and intra block copy are two new coding tools that have been adopted in the screen content coding extensions of high efficiency video Ccoding (HEVC SCC). Palette mode can represent color clusters for screen content efficiently. Intra block copy (IBC) facilitates block prediction within the same frame. Both tools have demonstrated promising benefits for screen content coding. In addition to HEVC SCC, this paper introduces five new coding techniques to enhance palette mode or IBC: transition copy, prediction across coding unit boundary, advanced motion vector coding, modified temporal merge candidate derivation, and new default IBC merge candidates. Experimental results show that the proposed techniques can achieve 5.4%, 5.2%, and 4.9% BD-rate savings compared with HEVC SCC for “YUV, text & graphics with motion, 1080p & 720p sequences” under all intra, random access, and low-delay B common test conditions, respectively.
Bioluminescence Resonance Energy Transfer Reveals Ligand-induced Conformational Changes in CXCR4 Homo- and Heterodimers (2005)

Homo- and heterodimerization have emerged as prominent features of G-protein-coupled receptors with possible impact on the regulation of their activity. Using a sensitive bioluminescence resonance energy transfer system, we investigated the formation of CXCR4 and CCR2 chemokine receptor dimers. We found that both receptors exist as constitutive homo- and heterodimers and that ligands induce conformational changes within the pre-formed dimers without promoting receptor dimer formation or disassembly. Ligands with different intrinsic efficacies yielded distinct bioluminescence resonance energy transfer modulations, indicating the stabilization of distinct receptor conformations. We also found that peptides derived from the transmembrane domains of CXCR4 inhibited activation of this receptor by blocking the ligand-induced conformational transitions of the dimer. Taken together, our data support a model in which chemokine receptor homo- and heterodimers form spontaneously and respond to ligand binding as units that undergo conformational changes involving both protomers even when only one of the two ligand binding sites is occupied.
Direction of Ring Opening in the Reduction of p-Substituted Styrene Oxides with Lithium Borohydride (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDirection of Ring Opening in the Reduction of p-Substituted Styrene Oxides with Lithium BorohydrideRichard Fuchs and Calvin A. VanderWerfCite this: J. Am. Chem. Soc. 1954, 76, 6, 1631–1634Publication Date (Print):March 1, 1954Publication History Published online1 May 2002Published inissue 1 March 1954https://pubs.acs.org/doi/10.1021/ja01635a049https://doi.org/10.1021/ja01635a049research-articleACS PublicationsRequest reuse permissionsArticle Views282Altmetric-Citations23LEARN 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
Le syndrome d’obstruction sinusoïdal du foie : une complication de la chimiothérapie du cancer colorectal ? (2005)

Auteur(s) :, Jean-Baptiste Trabut*, Benoit Terris Service d’Hepato-Gastroenterologie et d’Anatomopathologie, hopital Cochin, 27, rue du Fbg St-Jaques, 75014, Paris La chimiotherapie occupe une place fondamentale dans le traitement du cancer colorectal [1]. Son interet est bien demontre a la fois en situation adjuvante (en complement de la chirurgie) chez les patients ayant une maladie localement avancee et en situation palliative chez les patients ayant des metastases non resecables. La [...]
The properties and mec A gene of the methicillin-resistant Staphylococcus aureus isolated in Fukushima Medical College Hospital. (1993)

The 106 methicillin-resistant strains of Staphylococcus aureus (MRSA) isolated in Fukushima Medical College Hospital were examined for their properties and mecA gene. The strains produced four types of coagulase, of which type II was the most common, produced by 84 (79.2%). Beta-lactamase was produced by 58 (50%). Enterotoxins were produced by 45 (42.5%), most of which (39/106, 36.8%) were of type A. Thirty-four strains (32.1%) produced both enterotoxins and toxic shock syndrome toxin-1. All strains were susceptible to vancomycin and arbekacin, although they were mostly resistant to many other antibiotics. Using the polymerase chain reaction (PCR) technique, the mecA gene was detected in 57 (91.9%) of the 62 strains used. In addition, one of the 42 methicillin-susceptible strains isolated had the mecA gene. These results indicate that detection of the mecA gene by the PCR technique is a rapid and accurate way to identify methicillin resistance.
NMR Characterization of Native Liquid Spider Dragline Silk fromNephila edulis (2004)

Solid spider dragline silk is well-known for its mechanical properties. Nonetheless a detailed picture of the spinning process is lacking. Here we report NMR studies on the liquid silk within the wide sac of the major ampullate (m.a.) gland from the spider Nephila edulis. The resolution in the NMR spectra is shown to be significantly improved by the application of magic-angle spinning (MAS). From the narrow width of the resonance lines and the chemical shifts observed, it is concluded that the silk protein within the wide sac of the m.a. gland is dynamically disordered throughout the molecule in the sense that each amino acid of a given type senses an identical environment, on average. The NMR data obtained are consistent with an isotropic liquid phase.
The Psoas Compartment Block for Hip Surgery: The Past, Present, and Future (2011)

A posterior lumbar plexus block or psoas compartment block (PCB) is an effective locoregional anesthetic technique for analgesia and anesthesia of the entire lower extremity including the hip. Since the first description in the early seventies, this technique has been modified based on advanced knowledge of the anatomical localization of the lumbar plexus and the improvement of technical equipment. This paper provides an overview of the history, clinical efficacy, and risk profile of the PCB focused on hip surgery. Current status and future expectations are discussed.
Disruption of the ASXL1 gene is frequent in primary, post-essential thrombocytosis and post-polycythemia vera myelofibrosis, but not essential thrombocytosis or polycythemia vera: analysis of molecular genetics and clinical phenotypes (2011)

ASXL1 haploinsufficiency is associated with a myelofibrosis phenotype in the context of other known and unknown lesions, and disruption of ASXL1 function may contribute to the disease pathogenesis of myelofibrosis.
The Biological Frontier of Physics (2006)

Problems at the interface between biology and physics offer unique opportunities for physicists to make quantitative contributions to biology. Equally important, they enrich the discipline of physics by challenging its practitioners to think in new ways.
Superconducting Qubit with Purcell Protection and Tunable Coupling (2011)

We present a superconducting qubit for the circuit quantum electrodynamics architecture that has a tunable qubit-resonator coupling strength g. This coupling can be tuned from zero to values that are comparable with other superconducting qubits. At g = 0, the qubit is in a decoherence-free subspace with respect to spontaneous emission induced by the Purcell effect. Furthermore, we show that in this decoherence-free subspace, the state of the qubit can still be measured by either a dispersive shift on the resonance frequency of the resonator or by a cycling-type measurement.
Aeneas -- Colony I Meets Three-Axis Pointing (2011)

A dedicated satellite mission is currently under development at the USC Space Engineering Research Center. Named “Aeneas,” (after the Trojan warrior who personifies duty and courage) the cubesat will be used to track cargo containers worldwide. To accomplish this feat, the satellite must maintain a 2-degree-accuracy surface track – the first of its kind in cubesat technology. This paper describes the requirements, design, implementation and tests to date in the areas of: flight dynamics, flight software, deployable spacecraft antenna, store-and-forward software, custom flight processor including MEMS gyroscopes, Doppler-based orbit determination enhancement and mobile ground station dish with helical feedhorn. Details are provided about the attitude control system and communications.
Channel coding with multilevel/phase signals (1982)

A coding technique is described which improves error performance of synchronous data links without sacrificing data rate or requiring more bandwidth. This is achieved by channel coding with expanded sets of multilevel/phase signals in a manner which increases free Euclidean distance. Soft maximum--likelihood (ML) decoding using the Viterbi algorithm is assumed. Following a discussion of channel capacity, simple hand-designed trellis codes are presented for 8 phase-shift keying (PSK) and 16 quadrature amplitude-shift keying (QASK) modulation. These simple codes achieve coding gains in the order of 3-4 dB. It is then shown that the codes can be interpreted as binary convolutional codes with a mapping of coded bits into channel signals, which we call "mapping by set partitioning." Based on a new distance measure between binary code sequences which efficiently lower-bounds the Euclidean distance between the corresponding channel signal sequences, a search procedure for more powerful codes is developed. Codes with coding gains up to 6 dB are obtained for a variety of multilevel/phase modulation schemes. Simulation results are presented and an example of carrier-phase tracking is discussed.
Flexible Use of High-Density Oligonucleotide Arrays for Single-Nucleotide Polymorphism Discovery and Validation (2001)

A method for identifying and validating single nucleotide polymorphisms (SNPs) with high-density oligonucleotide arrays without the need for locus-specific polymerase chain reactions (PCR) is described in this report. Genomic DNAs were divided into subsets with complexity of ~10 Mb by restriction enzyme digestion and gel-based fragment size resolution, ligated to a common adaptor, and amplified with one primer in a single PCR reaction. As a demonstration of this approach, a total of 124 SNPs were located in 190 kb of genomic sequences distributed across the entire human genome by hybridizing to high-density variant detection arrays (VDA). A set of independent validation experiments was conducted for these SNPs employing bead-based affinity selection followed by hybridization of the affinity-selected SNP-containing fragments to the same VDA that was used to identify the SNPs. A total of 98.7% (74/75) of these SNPs were confirmed using both DNA dideoxynucleotide sequencing and the VDA methodologies. With flexible sample preparation, high-density oligonucleotide arrays can be tailored for even larger scale genome-wide SNP discovery as well as validation.
Intracellular replication is essential for the virulence of Salmonella typhimurium. (1991)

Salmonella typhimurium is a facultative intracellular parasite, capable of penetrating, surviving, and multiplying within diverse eukaryotic cell types, including epithelial and phagocytic cells. We have been studying intracellular replication of S. typhimurium and found that it is essential in the pathogenesis of this bacterium. A total of 45,000 independent mini-Mu MudJ transposon mutants in S. typhimurium SL1344 were screened in Madin-Darby canine kidney (MDCK) epithelial cells with a beta-lactam, cefotaxime, to enrich for mutants defective for intracellular replication. Ten different auxotrophic (purine, pyrimidine, purine/methionine, and valine/isoleucine) and three prototrophic replication-defective mutants (Rep-) were identified. All Rep- mutants showed no differences in aerobic and anaerobic growth patterns, motility, serum sensitivity, mouse macrophage survival, iron uptake, and phosphate requirements. All Rep- mutants were unable to multiply inside MDCK, HeLa, and Caco-2 epithelial cells. When required nutrients for various auxotrophs were supplemented, auxotrophs then replicated inside MDCK cells. Although the parental strain multiplies in large vacuoles inside MDCK cells that distort the host cells, MDCK cells infected with the Rep- mutants appeared relatively normal and few bacteria were seen inside vacuoles. The purine auxotrophs and the three prototrophic Rep- mutants were highly attenuated in mice, and oral and intraperitoneal LD50 levels were 3 to 4 orders of magnitude higher than the wild type level. The three prototrophs were invasive and persisted in the murine organs such as livers and spleens for at least 3 weeks. Therefore, these prototrophic genes are needed for intracellular replication and are essential to the virulence of S. typhimurium.
Active immunogene therapy of cancer with vaccine on the basis of chicken homologous matrix metalloproteinase-2. (2003)

Matrix metalloproteinase (MMP) family, in particular MMP-2, may play a key role in angiogenesis and tumor growth. It is conceivable that the breaking of immune tolerance of MMP-2 should be a useful approach to cancer therapy by active immunity. To test this concept, we constructed a plasmid DNA encoding chicken homologous MMP-2 (c-MMP-2) and control vectors. We found that the vaccine based on chicken homologous MMP-2 as a model antigen could induce both protective and therapeutic antitumor immunity. Autoantibodies against MMP-2 in sera of mice immunized with c-MMP-2 could be found by Western blotting analysis and ELISA assay. There was the deposition of autoantibodies within the tumor. IgG1 and IgG2b were substantially increased in response to c-MMP-2 immunization. The elevation of MMP-2 in the sera of tumor-bearing mice was abrogated with the vaccination of c-MMP-2. Transmigration of human endothelial cells and tumor cells through gelatin-coated filters was inhibited with immunoglobulins isolated from mice immunized with c-MMP-2. The gelatinase activity of MMP-2, including both latent MMP-2 (M(r) 72,000) and active MMP-2 (M(r) 66,000) derived from tumor tissues, was apparently inhibited by the vaccination with c-MMP-2. The antitumor activity and the inhibition of angiogenesis were acquired by the adoptive transfer of the purified immunoglobulins. The antitumor activity and production of autoantibodies against MMP-2 could be abrogated by the depletion of CD4(+) T lymphocytes. Angiogenesis was apparently inhibited within tumor, and chick CAMs angiogenesis was also inhibited. Thus, our findings may provide a vaccine strategy for cancer therapy through the induction of an autoimmune response against MMP-2 in a cross-reaction by the immunization with the single xenogeneic homologous MMP-2 gene and may be of importance in the additional exploration of the application of other xenogeneic homologous genes identified in human and other animal genome projects in cancer therapy.
Phase separation of integral membrane proteins in Triton X-114 solution. (1981)

A solution of the nonionic detergent Triton X-114 is homogeneous at 0 degrees C but separates in an aqueous phase and a detergent phase above 20 degrees C. The extent of this detergent phase separation increases with the temperature and is sensitive to the presence of other surfactants. The partition of proteins during phase separation in solutions of Triton X-114 is investigated. Hydrophilic proteins are found exclusively in the aqueous phase, and integral membrane proteins with an amphiphilic nature are recovered in the detergent phase. Triton X-114 is used to solubilize membranes and whole cells, and the soluble material is submitted to phase separation. Integral membrane proteins can thus be separated from hydrophilic proteins and identified as such in crude membrane or cellular detergent extracts.
Role of Vector in Activation of T Cell Subsets in Immune Responses against the Secreted Transgene Product Factor IX (2000)

Defining immune responses against the secreted transgene product in a gene therapy setting is critical for treatment of genetic diseases such as hemophilia B (coagulation factor IX deficiency). We have previously shown that intramuscular administration of an adeno-associated viral (AAV) vector results in stable expression of therapeutic levels of factor IX (F.IX) and may be associated with humoral immune responses against F.IX. This study demonstrates that intramuscular injection of an AAV vector expressing F.IX fails to activate F.IX-specific cytotoxic T lymphocytes (CTLs) in hemostatically normal or in hemophilia B mice, so that there is an absence of cellular immune responses against F.IX. However, transgene-derived F.IX can cause B cell responses characterized by production of T helper cell-dependent antibodies (predominantly IgG1, but also IgG2 subclasses) resulting from activation of CD4+ T helper cells primarily of the Th2 subset. In contrast, administration of an adenoviral vector efficiently activated F.IX-specific CTLs and T helper cells of both Th1 and Th2 subsets, leading to inflammation and destruction of transduced muscle tissue and activation of B cells as well. Therefore, vector sequences fundamentally influence T cell responses against transgene-encoded F.IX. In conclusion, activation of the immune system in AAV-mediated gene transfer is restricted to pathways mediated by F.IX antigen presentation through MHC class II determinants resulting in T and B cell responses that are more comparable to responses in the setting of protein infusion rather than of viral infection/gene transfer.
Cycloadditions of keteneimmonium cations to olefins and dienes. New synthesis of four-membered rings (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCycloadditions of keteneimmonium cations to olefins and dienes. New synthesis of four-membered ringsJacqueline Marchand-Brynaert and Leon GhosezCite this: J. Am. Chem. Soc. 1972, 94, 8, 2870–2872Publication Date (Print):April 1, 1972Publication History Published online1 May 2002Published inissue 1 April 1972https://pubs.acs.org/doi/10.1021/ja00763a062https://doi.org/10.1021/ja00763a062research-articleACS PublicationsRequest reuse permissionsArticle Views680Altmetric-Citations83LEARN 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
A topological measurement for weighted protein interaction network (2005)

High-throughput methods for detecting protein-protein interactions (PPI) have given researchers an initial global picture of protein interactions on a genomic scale. The usefulness of this understanding is, however, typically compromised by noisy data. The effective way of integrating and using these non-congruent data sets has received little attention to date. This paper proposes a model to integrate different data sets. We construct this model using our prior knowledge of data set reliability. Based on this model, we propose a topological measurement to select reliable interactions and to quantify the similarity between two proteins' interaction profiles. Our measurement exploits the small-world network topological properties of protein interaction network. Meanwhile, we discovered some additional properties of the network. We show that our measurement can be used to find reliable interactions with improved performance and to find protein pairs with higher function homogeneity.