gebhart/patrepeval huggingface dataset:
Antifreeze Proteins of Teleost Fishes (2001)

Marine teleosts at high latitudes can encounter ice-laden seawater that is approximately 1 degrees C colder than the colligative freezing point of their body fluids. They avoid freezing by producing small antifreeze proteins (AFPs) that adsorb to ice and halt its growth, thereby producing an additional non-colligative lowering of the freezing point. AFPs are typically secreted by the liver into the blood. Recently, however, it has become clear that AFP isoforms are produced in the epidermis (skin, scales, fin, and gills) and may serve as a first line of defense against ice propagation into the fish. The basis for the adsorption of AFPs to ice is something of a mystery and is complicated by the extreme structural diversity of the five antifreeze types. Despite the recent acquisition of several AFP three-dimensional structures and the definition of their ice-binding sites by mutagenesis, no common ice-binding motif or even theme is apparent except that surface-surface complementarity is important for binding. The remarkable diversity of antifreeze types and their seemingly haphazard phylogenetic distribution suggest that these proteins might have evolved recently in response to sea level glaciation occurring just 1-2 million years ago in the northern hemisphere and 10-30 million years ago around Antarctica. Not surprisingly, the expression of AFP genes from different origins can also be quite dissimilar. The most intensively studied system is that of the winter flounder, which has a built-in annual cycle of antifreeze expression controlled by growth hormone (GH) release from the pituitary in tune with seasonal cues. The signal transduction pathway, transcription factors, and promoter elements involved in this process are just beginning to be characterized.
CCK-B agonist or antagonist activities of structurally hindered and peptidase-resistant Boc-CCK4 derivatives (1993)

Replacement of Met31 by (N-Me)Nle in CCK8 or CCK4 has been shown to improve the affinity and selectivity for CCK-B receptors. In order to obtain molecules with enhanced bioavailability, two novel series of protected tetrapeptides of the general formula Boc-Trp30-X-Asp-Y33 have been developed. Introduction of (N-Me)Nle and the bulky, aromatic naphthylalaninamide (Nal-NH2) in positions X and Y, respectively, does not greatly modify the affinity for guinea pig brain CCK-B receptors. In contrast, incorporation of hindering N-methyl amino acids such as (N-Me)Phe, (N-Me)Phg, or (N-Me)Chg, but not their non-methylated counterparts, in position X induced a large decrease in affinity for the CCK-B binding sites. Among the various peptides synthesized, Boc-[(N-Me)Nle31,1Nal-NH2(33)]CCK4 (2) (KI = 2.8 nM), Boc-[Phg31,1Nal-NH2(33)]CCK4 (15) (KI = 14 nM), and Boc-[Phg31,1Nal-N(CH3)2(33)]CCK4 (17) (KI = 39 nM) displayed good affinities for brain CCK-B receptors and had good selectivity ratios. These pseudopeptides, in which the presence of unnatural and hydrophobic residues is expected to improve their penetration of the central nervous system, were shown to be very resistant to brain peptidases. Interestingly, whereas compounds 2 and 15 proved to be full agonists for rat hippocampal CCK-B receptors when measured in an electrophysiological assay, compound 17 behaved as a potent antagonist in the same test and displayed a good affinity in rat brain KI(CCK-B) = 51 nM as compared to the Merck antagonist L365,260,KI(CCK-B) = 12 nM. This illustrates a simple means to obtain CCK-B antagonists and suggests that the free, CONH2 group plays a critical role in the recognition of the agonist state of brain CCK-B receptors.
Human tumour-associated cell adhesion protein MN/CA IX: identification of M75 epitope and of the region mediating cell adhesion (2000)

MN/CA IX is a cell surface protein, strongly associated with several types of human carcinomas. It exerts activity of carbonic anhydrase and capacity of binding to cell surface receptors. In the present work, we used affinity purified MN/CA IX protein to demonstrate that the cells adhere to immobilized MN/CA IX and that the monoclonal antibody M75 abrogates cell attachment to MN/CA IX. Using synthetic oligopeptides, we identified M75 epitope and located it in the proteoglycan domain, which contains a sixfold tandem repeat of six amino acids GEEDLP. From phage display library of random heptapeptides we identified and chemically synthesized those which compete for the epitope with M75 and inhibit adhesion of cells to MN/CA IX. These heptapeptides might serve as lead compounds for drug design. © 2000 Cancer Research Campaign
A Human Early Response Gene Homologous to Murine nur77 and Rat NGFI-B, and Related to the Nuclear Receptor Superfamily (1990)

When a human fetal muscle cDNA library was screened with the human thyroid hormone receptor alpha 2 cDNA at low stringency, we found a weakly hybridizing cDNA. The sequence of the insert was 2498 basepairs, with an open reading frame of 1794 basepairs encoding a protein of 598 amino acids and a predicted molecular mass of 64 kDa. The DNA-binding domain and the ligand-binding domain are similar to those of steroid and thyroid hormone receptors. Moreover, this cDNA is highly homologous to mouse nur77 and rat NGFI-B, which are early response genes induced by nerve growth factor and other serum growth factors. We designated this gene NAK1. The modulation of expression of NAK1 during stimulation of cell growth was studied. The mRNA of NAK1 was induced rapidly and transiently by growth-stimulating agents, such as adenosine diphosphate, in monkey kidney cells (BSC-1), by phytohemagglutinin in human lymphocytes, and by serum stimulation of arrested fibroblasts. It is expressed in human fetal muscle and adult liver, brain, and thyroid. NAK1 could be a nuclear receptor. It will be of great interest to determine the ligand for NAK1 and the genes that are regulated by it.
Road Surface Status Classification Using Spectral Analysis of NIR Camera Images (2014)

There is a need for an automated road status classification system considering the vast number of weather-related accidents that occur every winter. Previous research has shown that it is possible to detect hazardous road conditions, including, for example, icy pavements, using single point infrared illumination and infrared detectors. In this paper, we extend this research into camera surveillance of a road section allowing for classification of area segments of weather-related road surface conditions such as wet, snow covered, or icy. Infrared images have been obtained using an infrared camera equipped with a set of optical wavelength filters. The images have primarily been used to develop multivariate data models and also for the classification of road conditions in each pixel. This system is a vast improvement on existing single spot road status classification systems. The resulting imaging system can reliably distinguish between dry, wet, icy, or snow covered sections on road surfaces.
A histopathologic study on the effects of radiofrequency thermotherapy on malignant tumors of the lung (1979)

Malignant cells are thermosensitive but this does not fully explain the wide-spread pathologic changes observed in solid cancers following local therapy with radiofrequency heating. The histopathology of human malignant tumors after radiofrequency thermotherapy reveals not only the expected degeneration of tumor cells, but significant changes in the tumor's stroma as well. Stromal blood capillary walls are massively infiltrated with round cells and undergo degenerative changes leading to necrosis and obliteration of the tumor's vascular supply. Extensive infiltration of the stroma with the host's round cells occurs. Following focal necrosis and rupture of the stroma, pools of lymphocytes establish direct contact with heat damaged malignant cells leading to further destruction of persisting tumor. The histologic signs of the generalized breakdown of lung tumors consequent to radiofrequency heat-therapy bear close resemblance to lesions in acutely rejecting organ allografts.
Étude, modélisation et réalisation de composants diffractants : contribution à l'étude de matériaux accordables et application à l'enregistrement holographique de filtres résonants (2006)

This thesis is in keeping with the research activities of the optics department of the ENST Bretagne concerning<br />optical information processing functions. This work is based on the study of 1D or 2D diffraction<br />gratings realized holographically in order to obtain functions such as Bragg gratings or resonant optical<br />filters. Suitable simulation tools are developed to determine the theoretical response of these structures:<br />the rigorous coupled-wave theory and the differential method, which take the vector nature of light into<br />account. Two holographic materials used for recording volume holograms are studied: Dupont photopolymers<br />for which a diffusion model is established and H-PDLCs (Holographic Polymer Dispersed Liquid<br />Crystals) which can be used to realize electrically switchable Bragg gratings. These studies concerning<br />modelling and recording materials allow us to validate the principle of two resonant optical filters. The<br />first filter is a 2D photonic crystal made of two orthogonal periodic structures. The filtering operation<br />is due to the enhancement of the diffraction by the structure when the incident light is at the photonic<br />band-edge. The second resonant filter is tunable and uses surface plasmon resonance phenomena occurring<br />for metallic surface relief gratings, the tunability being provided by the PDLC material.
De novogeneration of antigen-specific CD4+CD25+regulatory T cells from human CD4+CD25–cells (2005)

Antigen-specificity is a hallmark of adaptive T cell-mediated immune responses. CD4+CD25+FOXP3+ regulatory T cells (T(R)) also require activation through the T cell receptor for function. Although these cells require antigen-specific activation, they are generally able to suppress bystander T cell responses once activated. This raises the possibility that antigen-specific T(R) may be useful therapeutically by localizing generalized suppressive activity to tissues expressing select target antigens. Here, we demonstrate that T(R) specific for particular peptide-MHC complexes can be generated from human CD4+CD25- T cells in vitro and isolated by using HLA class II tetramers. Influenza hemagglutinin epitopes were used to generate hemagglutinin-specific T(R), which required cognate antigen for activation but which subsequently suppressed noncognate bystander T cell responses as well. These findings have implications for the generation of therapeutic regulatory T cells in disease, and also suggest an important mechanism by which T cells may be regulated at the site of inflammation.
Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations (2003)

Genomic aberrations in a series of paired biopsy samples from patients who presented initially with follicle center lymphoma (FCL) and subsequently transformed to diffuse large B-cell lymphoma (DLBCL) were measured by array comparative genomic hybridization (CGH). The consequences of these aberrations on gene expression were determined by comparison with expression analysis on these specimens using cDNA microarrays. A heterogeneous pattern of acquired genomic abnormalities was observed upon transformation, some of which were recurrent in small subsets of patients. Some of the genomic aberration acquired upon transformation, such as gain/amplification of 1q21-q24, 2p16 (REL/BCL11A gene loci), 3q27-q29 (including the BCL6 locus), 7q11.2-q22.1, 12pter-q12, 18q21 (including the BCL2 locus) and Xq, and deletion of 6q22-q24, 13q14-q21 and 17p13 (P53 locus) have been previously implicated in the FCL/DLBCL pathogenesis. In addition, novel genomic imbalances not previously reported in association with FCL transformation, such as overrepresentation of 4p12-pter, 5p12-p15, 6p12.3-p21, 9p23, 9q13-q31, 16q, 17q21, and loss of 1p36.3, 4q21-q23, 5q21-q23, 9q31-qter, 11q24-q25, and 15q23, were identified. We observed a differential expression profile of many genes within regions of gain and deletion upon transformation, including novel target genes associated with FCL transformation. However, other genes did not show deregulated expression despite their location within these areas. In summary, the combination of array CGH and expression analysis provides a more comprehensive picture of the transformation of FCL to DLBCL. This process is associated with the acquisition of a variable spectrum of genomic imbalances affecting recurrent chromosomal areas that harbor overexpressed or underexpressed genes targeted upon transformation.
ansa-Vanadocene Complexes - Syntheses, Structures and Ligand Exchange Reactions (1997)

Tetramethylethano-bridged vanadocene dichlorides (CH 3 ) 4 C 2 (3-R-C 5 H 3 ) 2 VCl 2 with R = H, Me, t -Bu are obtained by reacting the corresponding ligand MgCl salts with vanadium(III) acetylacetonato compounds, followed by oxidation with PCl 3 or AgCl. Smooth ligand exchange reactions of these ansa -vanadocene dichlorides afford acetylacetonato cations and binaphtholate complexes; from these, the dichlorides are regenerated by exposure to MgCl 2 in THF solution. Separation of meso and rac isomers (as well as enantiomer separation) is achieved via corresponding binaphtholate complexes; conversion to the vanadium(III) diisonitrile cations (CH 3 ) 4 C 2 (3-R-C 5 H 3 ) 2 V(CN t -Bu) 2 + allows an assessment of diastereoisomer ratios by 1 H NMR. Lewis-acidic bistriflate derivatives of these ansa -vanadocene complexes are obtained from the dichlorides by reaction with silver triflate.
The Impact of Methicillin Resistance in Staphylococcus aureus Bacteremia on Patient Outcomes: Mortality, Length of Stay, and Hospital Charges (2005)

Abstract Objective: To evaluate the impact of methicillin resistance in Staphylococcus aureus on mortality, length of hospitalization, and hospital charges. Design: A cohort study of patients admitted to the hospital between July 1, 1997, and June 1, 2000, who had clinically significant S. aureus bloodstream infections. Setting: A 630-bed, urban, tertiary-care teaching hospital in Boston, Massachusetts. Patients: Three hundred forty-eight patients with S. aureus bacteremia were studied; 96 patients had methicillin-resistant S. aureus (MRSA). Patients with methicillin-susceptible S. aureus (MSSA) and MRSA were similar regarding gender, percentage of nosocomial acquisition, length of hospitalization, ICU admission, and surgery before S. aureus bacteremia. They differed regarding age, comorbidities, and illness severity score. Results: Similar numbers of MRSA and MSSA patients died (22.9% vs 19.8%; P = .53). Both the median length of hospitalization after S. aureus bacteremia for patients who survived and the median hospital charges after S. aureus bacteremia were significantly increased in MRSA patients (7 vs 9 days, P = .045; $19,212 vs $26,424, P = .008). After multivariable analysis, compared with MSSA bacteremia, MRSA bacteremia remained associated with increased length of hospitalization (1.29 fold; P = .016) and hospital charges (1.36 fold; P = .017). MRSA bacteremia had a median attributable length of stay of 2 days and a median attributable hospital charge of $6,916. Conclusion: Methicillin resistance in S. aureus bacteremia is associated with significant increases in length of hospitalization and hospital charges.
Mechanisms of protein localization (1983)

Revue des donnees biochimiques sur la localisation des proteines chez les cellules eucaryotes et chez Escherichia coli. Revue des techniques genetiques utilisees pour l'etude de la localisation des proteines chez les bacteries
Correction: Spatial Genetic Structure Patterns of Phenotype-Limited and Boundary-Limited Expanding Populations: A Simulation Study (2014)

Range expansions may create a unique spatial genetic pattern characterized by alternate genetically homogeneous domains and allele frequency clines. Previous attempts to model range expansions have mainly focused on the loss of genetic diversity during expansions. Using individual-based models, we examined spatial genetic patterns under two expansion scenarios, boundary-limited range expansions (BLRE) and phenotype-limited range expansions (PhLRE). Our simulation revealed that the genetic diversity within populations lost quickly during the range expansion, while the genetic difference accumulated between populations. Consequently, accompanying the expansions, the overall diversity featured a slow decrease. Specifically, during BLREs, high speed of boundary motion facilitated the maintenance of total genetic diversity and sharpened genetic clines. Very slight constraints on boundary motion of BLREs drastically narrowed the homogeneous domains and increased the allele frequency fluctuations from those levels exhibited by PhLREs. Even stronger constraints, however, surprisingly brought the width of homogeneous domains and the allele frequency fluctuations back to the normal levels of PhLREs. Furthermore, high migration rates maintained a higher total genetic diversity than low ones did during PhLREs. Whereas, the total genetic diversities during BLREs showed a contrary pattern: higher when migration was low than those when migration was high. Besides, the increase of migration rates helped maintain a greater number of homogeneous domains during PhLREs, but their effects on the number of homogeneous domains during BLREs were not monotonous. Previous studies have showed that the homogenous domains can merge to form a few broad domains as the expansion went on, leading to fewer homogeneous domains. Our simulations, meanwhile, revealed that the range expansions could also rebuild homogeneous domains from the clines during the range expansion. It is possible that that the number of homogeneous domains was determined by the interaction of merging and newly emerging homogeneous domains.
Enantioselective Total Synthesis of the Potent Anti-inflammatory (+)-Myrrhanol A (2009)

The first total synthesis of potent anti-inflammatory polypodanes (+)-myrrhanol A (1), (+)-myrrhanone A (2), (+)-myrrhanone B (3), and (+)-myrrhanol B (4) has been achieved. Key steps in our convergent, highly stereocontrolled route are a Ti(III)-mediated radical cyclization of a chiral monoepoxide to furnish a bicyclic synthon that combines stereospecifically with an acyclic vinyl iodide via an intermolecular B-alkyl Suzuki-Miyaura cross-coupling.
CD28 is not directly involved in the response of human CD3−CD56+ natural killer cells to lipopolysaccharide: a role for T cells (2004)

We have previously shown that human CD3- CD56+ and CD3+ CD56+ cells from some individuals mount vigorous proliferative responses to lipopolysaccharide. Such responses have been blocked by the presence of cytotoxic T-lymphocyte antigen-4 immunoglobulin fusion protein in the cultures, implicating a role for B7-mediated costimulation. Here we confirm this inhibition of natural killer (NK) expansion using antibodies against B7-1 and B7-2. We were unable to specifically detect CD28 on the surface of resting or stimulated human peripheral blood NK cells, however, in either lipopolysaccharide-responsive or non-responsive individuals, using a panel of four different anti-CD28 monoclonal antibodies. T-cell depletion from peripheral blood mononuclear cell cultures resulted in a reduction in the induction of CD25 on activated CD3- CD56hi cells and in the expansion and proliferation of CD3- CD56+ NK cells. Furthermore, reconstitution experiments using peripheral blood dendritic cells and purified NK cells demonstrated that NK expansion could only be achieved in the presence of purified T cells.
Cell Cycle-dependent Expression of Thyroid Hormone Receptor-β Is a Mechanism for Variable Hormone Sensitivity (2004)

Thyroid hormone receptors (TRs) are ligand-regulatable transcription factors. Currently, little is known about the expression of TRs or other nuclear hormone receptors during the cell cycle. We thus developed a stable expression system to express green fluorescent protein-TRbeta in HeLa cells under tetracycline regulation, and studied TR expression during the cell cycle by laser scanning cytometry. Only approximately 9-15% of the nonsynchronized cell population expressed TR because the majority of cells were in G(1) phase and did not express detectable amounts of TR. However, when cells were synchronized in early S phase with hydroxyurea and then released, TR expression levels increased in a cell cycle-dependent manner and peaked to 30-40% cells expressing TR at late G(2)/M phase before declining to nonsynchronized levels. Moreover, we observed a direct correlation between transcriptional activity and TR expression during the cell cycle. Similar cell cycle-dependent findings also were observed for endogenous TR in rat pituitary GH(3) cells. Last, cycloheximide studies demonstrated that the increase in TR expression was primarily due to increased translation. These novel observations of cell cycle-dependent expression of TR suggest that differential hormone sensitivity can occur during the cell cycle and may contribute to cell cycle progression during normal development and oncogenesis.
Mutation in the primer binding site of the type 1 human immunodeficiency virus genome affects virus production and infectivity. (1992)

In an effort to understand the contribution of the primer-binding site (PBS) region to human immunodeficiency virus (HIV) replication, we have constructed a mutant HIV proviral DNA with an alteration in the 5' end of the PBS. The PBS mutant proviral DNA was characterized by transfection of the viral DNA into CD4+ and non-CD4+ target cells. The results indicate that mutation in the PBS reduced the level of viral particles released into the medium of transfected cells in comparison to wild-type proviral DNA. The viral particles were noninfectious upon transmission to established CD4+ cell lines and phytohemagglutinin-stimulated peripheral blood lymphocytes. Electron microscopic analysis of the transfected cells revealed no abnormalities in the structure of the virion directed by the mutant proviral DNA. Also, the protein and RNA contents of the mutant virions were similar to the wild type. The quantitation of intracellular viral structural protein in the transfected cells, however, indicated that the PBS mutation may have an effect on the assembly of viral particles in addition to completely abolishing reverse transcription of viral RNA into DNA. These results provide evidence that the PBS region of the viral genome has multiple functions in HIV-1 replication.