gebhart/patrepeval huggingface dataset:
Prise en charge de la personne âgée en consultation douleur (2009)

La problematique de la douleur prend toute sa dimension en raison des projections demographiques, des chiffres de prevalence de la douleur dans cette population fragile, en raison de la frequence chez le sujet âge des pathologies susceptibles d’entrainer des douleurs. La prevalence de la douleur a ete etudiee au domicile ou en institution (tableau 1). A domicile (interrogation telephonique des personnes âgees), les resultats des etudes suedoise (1996) et espagnole (2007) sont comparables a plus de 10 ans d'intervalle. De meme, en institution, en 1990,71 % des patients etaient douloureux et 69 % en 2008. En ce qui concerne la typologie de la douleur, si la majeure partie des douleurs est d’origine traumatique (37 %),les douleurs neurogenes arrivent en 2e position (25 %) bien avant les douleurs cardiovasculaires (18 %), traumatologiques (14 %),celles accompagnant les escarres (13 %) ou le cancer (6 %). Les douleurs neurogenes sont certainement sous-estimees. On pense en particulier qu’apres un acte de chirurgie,90 % des douleurs sont d'origine neurogene. Il faut donc ameliorer le depistage de ce type de douleurs. La chronicisation des douleurs chez le sujet âge, peut entrainer un etat de regression qui peut etre aggrave par l'instauration d'un traitement antalgique inadapte (effet indesirable).
A High-Throughput Method for Illumina RNA-Seq Library Preparation (2012)

With the introduction of cost effective, rapid, and superior quality next generation sequencing techniques, gene expression analysis has become viable for labs conducting small projects as well as large-scale gene expression analysis experiments. However, the available protocols for construction of RNA-sequencing (RNA-Seq) libraries are expensive and/or difficult to scale for high-throughput applications. Also, most protocols require isolated total RNA as a starting point. We provide a cost-effective RNA-Seq library synthesis protocol that is fast, starts with tissue, and is high-throughput from tissue to synthesized library. We have also designed and report a set of 96 unique barcodes for library adapters that are amenable to high-throughput sequencing by a large combination of multiplexing strategies. Our developed protocol has more power to detect differentially expressed genes when compared to the standard Illumina protocol, probably owing to less technical variation amongst replicates. We also address the problem of gene-length biases affecting differential gene expression calls and demonstrate that such biases can be efficiently minimized during mRNA isolation for library preparation.
Single-channel signal separation using time-domain basis functions (2003)

We present a new technique for achieving blind source separation when given only a single-channel recording. The main idea is based on exploiting the inherent time structure of sound sources by learning a priori sets of time-domain basis functions that encode the sources in a statistically efficient manner. We derive a learning algorithm using a maximum likelihood approach given the observed single-channel data and sets of basis functions. For each time point, we infer the source parameters and their contribution factors using a flexible but simple density model. We show the separation results of two music signals as well as the separation of two voice signals.
A Genetically Encoded Norbornene Amino Acid for the Mild and Selective Modification of Proteins in a Copper‐Free Click Reaction (2012)

Built in for clicks: A specially evolved pyrrolysyl-tRNA synthetase from Methanosarcina mazei was used to incorporate a norbornene amino acid into proteins in E. coli. This unit can be site-selectively modified under mild physiological conditions using a [3+2] cycloaddition reaction with nitrile imines (see scheme).
Use of the DNA polymerase chain reaction for homology probing: isolation of partial cDNA or genomic clones encoding the iron-sulfur protein of succinate dehydrogenase from several species. (1989)

The DNA polymerase chain reaction was developed for in vitro amplification of specific DNA sequences, and it has been used for a wide variety of purposes in several fields. We have developed an application of the polymerase chain reaction that is useful for the isolation of partial cDNA or genomic clones of conserved genes. We used this technique to clone the gene encoding the iron protein subunit (27 kDa) of succinate dehydrogenase (EC 1.3.5.1) from several species, including human, rat, Drosophila melanogaster, Arabidopsis thaliana, Schizosaccharomyces pombe, and Saccharomyces cerevisiae. Mixed oligonucleotide primers corresponding to two conserved regions of the protein were used in conjunction with genomic and cDNA templates in the reaction. The primers contained all possible nucleotide combinations that could encode the corresponding peptide sequences. These oligonucleotide mixtures contained 262,144 (2(18] and 8192 (2(13] unique sequences, respectively. Use of the polymerase chain reaction for homology probing allows one to utilize more complex mixtures of oligonucleotides as probes than is possible with filter hybridization screening techniques. In addition, the polymerase chain reaction offers the advantage of synthesizing the DNA product directly, in some cases obviating the need to construct cDNA or genomic libraries. This application of the polymerase chain reaction should be useful not only for the identification of conserved genes in a variety of species but also for the isolation of previously unknown members of gene families.
Dendroflorin retards the senescence of MRC-5 cells. (2008)

The influence of dendroflorin, a potentially active compound extracted from Dendrobium nobile, on cell growth and cell cycles was assessed in a human embryo lung fibroblastic MRC-5 cell line. An MTT assay indicated that dendroflorin benefits cell proliferation. Additionally, we used flow cytometry to examine the cell cycles in senescent MRC-5 cells after treatment with dendroflorin, discovering that dendroflorin could trigger cells in the G1 phase to enter the S phase. Further examination of intracellular ROS contents using DCFH-DA suggested that dendroflorin helps ROS degradation, partly elucidating the mechanism of its effects. All of the above results suggest that dendroflorin is a potential candidate with anti-senescence activity.
Translation-dependent and independent mRNA decay occur through mutually exclusive pathways that are defined by ribosome density during T Cell activation (2020)

Abstract mRNA translation and degradation are strongly interconnected processes that participate in the fine tuning of gene expression. Particularly, targeting mRNAs to translation-dependent degradation (TDD) could attenuate protein expression by making any increase in mRNA translation self-limiting. However, the extent to which TDD is a general mechanism for limiting protein expression is currently unknown. Here we describe a comprehensive analysis of basal and signal-induced TDD in mouse primary CD4 T cells. Our data indicate that most cellular transcripts are decayed to some extent in a translation-dependent manner, both in resting and activated cells. Our analysis further identifies the length of untranslated regions, the density of ribosomes and the GC content of the coding region as major determinants of TDD magnitude. Consistent with this, all transcripts that undergo changes in ribosome density upon T cell activation display a corresponding change in their TDD level. Surprisingly, the amplitude of translation-independent mRNA decay (TID) appears as a mirror image of TDD. Moreover, TID also responds to changes in ribosome density upon T cell activation but in the opposite direction from the one observed for TDD. Our data demonstrate a strong interconnection between mRNA translation and decay in mammalian cells. Furthermore, they indicate that ribosome density is a major determinant of the pathway by which transcripts are degraded within cells.
Effects of propofol on bronchoconstriction and bradycardia induced by vagal nerve stimulation (2003)

Propofol has vagolytic effects on the airway but does not worsen bradycardia produced by parasympathetic stimulation.
Regulation of pro‐inflammatory and pro‐fibrotic factors by CCN2/CTGF in H9c2 cardiomyocytes (2010)

Connective tissue growth factor (CTGF), also known as CCN2, is implicated in fibrosis through both extracellular matrix (ECM) induction and inhibition of ECM degradation. The role of CTGF in inflammation in cardiomyocytes is unknown. In some mesenchymal cell systems, CTGF mediates effects through TGF-beta or tyrosine kinase cell surface receptor, TrkA, signalling. In this study, cellular mechanisms by which CTGF regulates pathways involved in fibrosis and inflammation were explored. Murine H9c2 cardiomyocytes were treated with recombinant human (rh)CTGF and ECM formation gene expression: fibronectin, collagen type -I and -III and ECM degradation genes: TIMP-1, TIMP-2 and PAI-1 were found to be induced. CTGF treatment also increased pro-inflammatory cytokines TNF-alpha, IL-6, MCP-1 and IL-8. CTGF upregulated TGF-beta1 mRNA and rapidly induced phosphorylation of TrkA. The CTGF-induced pro-fibrotic and pro-inflammatory effects were blocked by anti-TGF-beta neutralizing antibody and Alk 5 inhibitor (SB431542). A specific blocker of TrkA activation, k252a, also abrogated CTGF-induced effects on fibrosis and gene expresison of MCP-1 and IL-8, but not TNF-alpha or IL-6. Collectively, this data implicates CTGF in effects on pro-fibrotic genes and pro-inflammatory genes via TGF-beta pathway signalling and partly through TrkA.
Tactile Imaging of Breast Masses (2001)

Tactile imaging can provide accurate and reproducible estimates of the size of breast masses. This capability can enhance cancer surveillance for patients with benign masses (eg, due to scarring or fibrocystic changes) because previous work suggests that reliable detection of a difference in mass size by physical examination requires a 40% change in diameter. In contrast, this study suggests tactile imaging requires only a 15% change (95% confidence interval).
Molecular characterization of a novel metabotropic glutamate receptor mGluR5 coupled to inositol phosphate/Ca2+ signal transduction. (1992)

A cDNA clone for a new metabotropic glutamate receptor, mGluR5, was isolated through polymerase chain reaction-mediated DNA amplification by using primer sequences conserved among the metabotropic glutamate receptor (mGluR) family and by the subsequent screening of a rat brain cDNA library. The cloned receptor consists of 1171 amino acid residues and exhibits a structural architecture common to the mGluR family, possessing a large extracellular domain preceding the seven putative membrane-spanning segments. mGluR5 shows the highest sequence similarity to mGluR1 among the mGluR members and is coupled to the stimulation of phosphatidylinositol hydrolysis/Ca2+ signal transduction in Chinese hamster ovary cells transfected with the cloned cDNA. This receptor also resembles mGluR1 in its agonist selectivity and antagonist responses; the potency rank order of agonists for mGluR5 was determined to be quisqualate greater than L-glutamate greater than or equal to ibotenate greater than trans-1-aminocyclopentane-1,3-dicarboxylate. Blot and in situ hybridization analyses indicated that mGluR5 mRNA is widely distributed in neuronal cells of the central nervous system and is expressed differently from mGluR1 mRNA in many brain regions. This investigation thus demonstrates that there is an additional mGluR subtype which closely resembles mGluR1 in its signal transduction and pharmacological properties and is expressed in specialized neuronal cells in the central nervous system.
Comparative toxicity of Rosmarinus officinalis L. essential oil and blends of its major constituents against Tetranychus urticae Koch (Acari: Tetranychidae) on two different host plants (2006)

Abstract Bioassays of Rosmarinus officinalis L. essential oil and blends of its major constituents were conducted using host‐specific strains of the two‐spotted spider mite, Tetranychus urticae Koch, on bean and tomato plants. Two constituents tested individually against a bean host strain and five constituents tested individually against a tomato host strain accounted for most of the toxicity of the natural oil. Other constituents were relatively inactive when tested individually. Toxicity of blends of selected constituents indicated a synergistic effect among the active and inactive constituents, with the presence of all constituents necessary to equal the toxicity of the natural oil. Copyright © 2006 Society of Chemical Industry
Characterization of cDNA Clones in Size-Fractionated cDNA Libraries from Human Brain (1997)

To evaluate the size-fractionated cDNA libraries of human brain previously constructed (O. O'hara et al. DNA Research, 4, 53-59, 1997), the occurrence of chimeric clones and the content of clones with coding potentiality were analyzed using the randomly sampled clones with insert sizes of 5 to 7 kb. When the chromosomal location of 30 clones was determined by the radiation-hybrid mapping method, the map positions assigned from the 3'- and 5'-end sequences separately were coincident for 29 clones, suggesting that the occurrence of chimeric clones is at most 1/30. Using 91 clones mapped to chromosome 1, the content of clones that have the potentiality coding for proteins larger than 100 amino acid residues was estimated to be approximately 50% (46 out of 91 clones) on the basis of nucleotide sequence analysis and coding potentiality assay in vitro. No significant open reading frames were detected in the remaining clones. Although the clones coding for short peptides may not have been included in the above estimation, the libraries constructed from the whole brain mRNA fraction appear to contain a considerable amount of clones corresponding to the 5'-truncated transcripts in an unprocessed form and/or those with long 3'-untranslated regions.
The Aspergillus nidulans F‐box protein GrrA links SCF activity to meiosis (2006)

Cellular differentiation relies on precise and controlled means of gene expression that act on several levels to ensure a flexible and defined spatio-temporal expression of a given gene product. In our aim to identify transcripts enriched during fruiting body formation of the homothallic ascomycete Aspergillus (Emericella) nidulans, the grrA gene could be identified in a negative subtraction hybridization screening procedure. It encodes a protein similar to fungal F-box proteins, which function as substrate receptors for ubiquitin ligases, and that is highly related to the Saccharomyces cerevisiae regulatory protein Grr1p. Expression studies confirmed induction of grrA transcription and expression of its gene product during cleistothecial development of A. nidulans. Functional complementation of a yeast grr1Delta mutant was achieved by overexpression of the grrA coding sequence. A grrADelta deletion mutant resembles the wild-type in hyphal growth, asexual sporulation, Hülle cell formation or development of asci-containing cleistothecia, but is unable to produce mature ascospores due to a block in meiosis as demonstrated by cytological staining of cleistothecial contents. Our results specify a particular involvement of the E3 ubiquitin ligase SCFGrrA in meiosis and sexual spore formation of an ascomyceteous fungus and shed light on the diverse functions of ubiquitin-proteasome-mediated protein degradation in eukaryotic development.
Intracellular Signaling by 14-hydroxy-4,14- Retro -Retinol (1991)

In mammals, retinol is the precursor for retinoids, which affect various aspects of morphogenesis and development. However, B lymphocytes, although retinol-dependent, do not use retinoic acid as mediator. Retinol is metabolized by B lymphocytes and other cell lines to optically active 14-hydroxy-4,14-retro-retinol; it is this compound that mediates the growth control. Thus another second messenger molecule, in addition to retinoic acid and retinal, is derived from retinol.
Comparisons between oriented film and solution tertiary structure of various nucleic acids (1979)

Abstract We have considered whether or not the tertiary structure of a biomolecule is the same in a crystal (or an oriented film) as it is in solution. A methodology has been developed for comparing polarized absorption spectra obtained from a solid‐state sample with those obtained from an oriented solute to further resolve this question. An electric dichroism instrument built in our laboratory was used to measure the solution dichroism signal which, along with the ordinary solution uv absorption spectra, yields polarized absorption spectra in the directions parallel and perpendicular to the applied electric field. These were then compared to polarized absorption data from oriented films of nucleic acids to determine whether the two sets of data could be rotated into coincidence. This rotation was accomplished using a computer program based on a nonlinear programming method. Four nucleic acids were studied and the film and solution data for three of these were found to be equivalent, requiring rotation through an angle of 3°−20°, depending on film humidity, to bring them into coincidence. For the fourth sample we were unable, perhaps because of signal‐to‐noise ratio limitations, to find a correlation. Flow dichroism and electric dichroism data were also found to be quite similar. Thus it is clear that the induced dipole moment is along the helical axis and that the physical, hydrodynamical, and electrical axes of the nucleic acid molecules are equivalent.
Effects of Bursectomy, Irradiation, and Cyclophosphamide on Turkeys Vaccinated with CU Cholera Strain (1987)

Turkeys surgically bursectomized, irradiated, and/or injected with cyclophosphamide at 1 day were vaccinated with the live Clemson University (CU) strain of Pasteurella multocida. Bursectomized turkeys vaccinated via drinking water or wing-web puncture at 7 weeks and challenged at 11 weeks had a significantly (P less than 0.05) lower survival rate after challenge than unbursectomized controls. Bursectomized and unbursectomized turkeys vaccinated via drinking water at 7 weeks, revaccinated via the auditory tube at 11 weeks, and challenged at 15 weeks had similar survival rates. The vaccinated bursectomized turkeys had significantly (P less than 0.05) lower levels of serum anti-P. multocida antibody than vaccinated unbursectomized controls. Radiation had no immunosuppressive effect. The immunosuppressive effect of cyclophosphamide was dosage-dependent. Bursectomy and injection of cyclophosphamide in the same turkey were complementary. It was concluded that in young turkeys, the development of immunity to the avirulent CU vaccine is highly dependent upon the bursa of Fabricius, but that as they grow older the bursa is of less importance, particularly if they were vaccinated via a parenteral route, such as in the air spaces of the head.
Tau protein becomes long and stiff upon phosphorylation: correlation between paracrystalline structure and degree of phosphorylation. (1989)

In a previous report we have shown that microtubule-associated protein tau can be induced to form paracrystals (Lichtenberg, B., E.-M. Mandelkow, T. Hagestedt, and E. Mandelkow. 1988. Nature [Lond.]. 334:359-362). A striking feature was the high degree of elasticity of the molecules. We now report that this property is related to the state of phosphorylation. When tau is dephosphorylated by alkaline phosphatase, it becomes shorter and more elastic; when it is phosphorylated by Ca++/calmodulin-dependent kinase, it becomes longer and stiffer. This may provide a model for the control of structural properties of tau-like molecules by phosphorylation.
Isopeptide Ligation Catalyzed by Quintessential Sortase A (2011)

The housekeeping transpeptidase sortase A (SrtA) from Staphyloccocus aureus catalyzes the covalent anchoring of surface proteins to the cell wall by linking the threonyl carboxylate of the LPXTG recognition motif to the amino group of the pentaglycine cross-bridge of the peptidoglycan. SrtA-catalyzed ligation of an LPXTG containing polypeptide with an aminoglycine-terminated moiety occurs efficiently in vitro and has inspired the use of this enzyme as a synthetic tool in biological chemistry. Here we demonstrate the propensity of SrtA to catalyze "isopeptide" ligation. Using model peptide sequences, we show that SrtA can transfer LPXTG peptide substrates to the ε-amine of specific Lys residues and form cyclized and/or a gamut of branched oligomers. Our results provide insights about principles governing isopeptide ligation reactions catalyzed by SrtA and suggest that although cyclization is guided by distance relationship between Lys (ε-amine) and Thr (α-carboxyl) residues, facile branched oligomerization requires the presence of a stable and long-lived acyl-enzyme intermediate.
Sequence analysis of the 22K, SH and G genes of turkey rhinotracheitis virus and their intergenic regions reveals a gene order different from that of other pneumoviruses (1992)

The nucleotide and deduced amino acid sequences of three genes of turkey rhinotracheitis virus (TRTV) together with the nucleotide sequences of the relevant intergenic regions were determined. The deduced amino acid sequence of one of the genes shows significant identity (42%) to that of the 22K protein of human respiratory syncytial virus (RSV). The TRTV 22K gene, like that of RSV, has a second open reading frame, although the amino acid sequence deduced from this reading frame does not show any similarity to the equivalent predicted RSV protein. The other two genes and their deduced amino acid sequences do not show any sequence similarity to the genes of other pneumoviruses. However, the hydrophobicity profiles of the predicted proteins do show similarities to those of the small hydrophobic (SH) and attachment protein (G) genes of RSV. The TRTV G gene is 1193 nucleotides in length and encodes a protein of 391 amino acids (M(r) 42984), which is rather larger than the RSV G protein (predicted M(r) 36000). The TRTV SH gene is 589 nucleotides in length, encoding a protein of 174 amino acids (M(r) 18797), which is considerably larger than the size of the RSV SH protein (M(r) 7500). The sequences of the intergenic regions derived from clones of polycistronic mRNAs and polymerase chain reaction products obtained with primers from different genes reveal the order on the virus genome to be 3' F-22K-SH-G 5'. This differs from the gene order of paramyxoviruses and morbilliviruses, which lack a 22K gene (and in some cases a SH gene), and the pneumoviruses RSV and pneumonia virus of mice, which have the F and 22K genes located after the G gene.