gebhart/patrepeval huggingface dataset:
TGF-β-induced EMT: mechanisms and implications for fibrotic lung disease (2007)

Epithelial-mesenchymal transition (EMT), a process whereby fully differentiated epithelial cells undergo transition to a mesenchymal phenotype giving rise to fibroblasts and myofibroblasts, is increasingly recognized as playing an important role in repair and scar formation following epithelial injury. The extent to which this process contributes to fibrosis following injury in the lung is a subject of active investigation. Recently, it was demonstrated that transforming growth factor (TGF)-beta induces EMT in alveolar epithelial cells (AEC) in vitro and in vivo, and epithelial and mesenchymal markers have been colocalized to hyperplastic type II (AT2) cells in lung tissue from patients with idiopathic pulmonary fibrosis (IPF), suggesting that AEC may exhibit extreme plasticity and serve as a source of fibroblasts and/or myofibroblasts in lung fibrosis. In this review, we describe the characteristic features of EMT and its mechanistic underpinnings. We further describe the contribution of EMT to fibrosis in adult tissues following injury, focusing especially on the critical role of TGF-beta and its downstream mediators in this process. Finally, we highlight recent descriptions of EMT in the lung and the potential implications of this process for the treatment of fibrotic lung disease. Treatment for fibrosis of the lung in diseases such as IPF has heretofore focused largely on amelioration of potential inciting processes such as inflammation. It is hoped that this review will stimulate further consideration of the cellular mechanisms of fibrogenesis in the lung and especially the role of the epithelium in this process, potentially leading to innovative avenues of investigation and treatment.
VSL#3 can prevent ulcerative colitis-associated carcinogenesis in mice (2018)

VSL#3 can prevent UC-associated carcinogenesis in mice, reduce the colonic mucosal inflammation levels, and rebalance the fecal and mucosal intestinal microbiota.
Overlapping cytotoxic T-lymphocyte and B-cell antigenic sites on the influenza virus H5 hemagglutinin (1990)

To define the recognition site of cytotoxic T lymphocytes (CTLs) on influenza virus H5 hemagglutinin (HA), an H5 HA-specific CTL clone was examined for the ability to recognize monoclonal antibody-selected HA variants of influenza virus A/Turkey/Ontario/7732/66 (H5N9). On the basis of 51Cr release assays with the variants, a CTL epitope was located near residue 168 of H5 HA. To define the epitope more precisely, a series of overlapping peptides corresponding to this region was synthesized and tested for CTL recognition. The minimum peptide recognized by the CTL clone encompassed residues 158 to 169 of H5 HA. Relative to the H3 HA three-dimensional structure, this CTL epitope is located near the distal tip of the HA molecule, also known as a major B-cell epitope on H3 HA. A single mutation at residue 168 (Lys to Glu) in the H5 HA variants abolished CTL recognition; this same amino acid was shown previously to be critical for B-cell recognition (M. Philpott, C. Hioe, M. Sheerar, and V. S. Hinshaw, J. Virol. 64:2941-2947, 1990). Additionally, mutations within this region of the HA molecule were associated with attenuation of the highly virulent A/Turkey/Ontario/7732/66 (H5N9) (M. Philpott, B. C. Easterday, and V.S. Hinshaw, J. Virol. 63:3453-3458, 1989). When tested for recognition of other H5 viruses, the CTL clone recognized the HA of A/Turkey/Ireland/1378/83 (H5N8) but not that of A/Chicken/Pennsylvania/1370/83 (H5N2), even though these viruses contain identical HA amino acid 158-to-169 sequences. These results suggest that differences outside the CTL epitope affected CTL recognition of the intact HA molecule. The H5 HA site defined in these studies is, therefore, important in both CTL and B-cell recognition, as well as the pathogenesis of the virus.
Composition of the Essential Oil from Roots and Rhizomes ofValeriana wallichii DC. (1997)

The volatile constituents isolated from roots and rhizomes of Valeriana wallichii DC. ( = V. jatamansi Jones) were investigated by GC and GC–MS (EI and NICI) analysis. The plant material was obtained from different sources, namely from a local market in Kathmandu (Nepal), from plants grown in The Netherlands and in Germany, and from commercially available material from several German importers. The various roots and rhizomes yielded between 0.09 and 1.30% (v/w) essential oil on a dry weight basis. The main constituents of the oils from the plants grown in Europe were an unidentified sesquiterpene hydrocarbon, α-santalene, ar-curcumene and xanthorrhizol. In the oils from the Nepalese material and from the commercially available roots, except in one sample, patchouli alcohol was the main component. © 1997 John Wiley & Sons, Ltd.
Enhancement of Sleeping Beauty Transposition by CpG Methylation: Possible Role of Heterochromatin Formation (2004)

The Sleeping Beauty (SB) transposase is the most active transposase in vertebrate cells, and the SB transposon system has been used as a tool for insertional mutagenesis and gene delivery. Previous studies have indicated that the frequency of chromosomal transposition is considerably higher in mouse germ cells than in mouse embryonic stem cells, suggesting the existence of unknown mechanisms that regulate SB transposition. Here, we demonstrated that CpG methylation of the transposon region enhances SB transposition. The transposition efficiencies of a methylated transposon and an unmethylated transposon which had been targeted in the same genomic loci by recombination-mediated cassette exchange in mouse erythroleukemia cells were compared, and at least a 100-fold increase was observed in the methylated transposon. CpG methylation also enhanced transposition from plasmids into the genome. Chromatin immunoprecipitation assays revealed that histone H3 methylated at lysine-9, a hallmark of condensed heterochromatin, was enriched at the methylated transposon, whereas the unmethylated transposon formed a relaxed euchromatin structure, as evidenced by enrichment of acetylated histone H3 and reporter gene expression. Possible roles of heterochromatin formation in the transposition reaction are discussed. Our findings indicate a novel relationship between CpG methylation and transposon mobilization.
Simplified coupled-wave equations for cylindrical waves in circular grating planar waveguides (1992)

A simplified form of the coupled-wave equations for cylindrical waves in circular grating distributed feedback (DFB) planar waveguides is presented. The coupling coefficients can be expressed as the product of a cylindrical-wave factor and the corresponding coupling coefficient between planar waveguide modes. Under the large radius approximation ( beta r>>1), which covers most practical cases, the interpolarization coupling between TE and TM cylindrical waves approaches zero. The coupled-wave equations can then be reduced to two independent families, one for TE- and the other for TM-cylindrical waves. >
Hyperinsulinism induced by targeted suppression of beta cell K ATP channels (2002)

ATP-sensitive K+ (K(ATP)) channels couple cell metabolism to electrical activity. To probe the role of K(ATP) in glucose-induced insulin secretion, we have generated transgenic mice expressing a dominant-negative, GFP-tagged K(ATP) channel subunit in which residues 132-134 (Gly-Tyr-Gly) in the selectivity filter were replaced by Ala-Ala-Ala, under control of the insulin promoter. Transgene expression was confirmed by both beta cell-specific green fluorescence and complete suppression of channel activity in those cells ( approximately 70%) that did fluoresce. Transgenic mice developed normally with no increased mortality and displayed normal body weight, blood glucose levels, and islet architecture. However, hyperinsulinism was evident in adult mice as (i) a disproportionately high level of circulating serum insulin for a given glucose concentration ( approximately 2-fold increase in blood insulin), (ii) enhanced glucose-induced insulin release from isolated islets, and (iii) mild yet significant enhancement in glucose tolerance. Enhanced glucose-induced insulin secretion results from both increased glucose sensitivity and increased release at saturating glucose concentration. The results suggest that incomplete suppression of K(ATP) channel activity can give rise to a maintained hyperinsulinism.
Direct Exposure of Mouse Spermatozoa to Very High Concentrations of a Serotype-2 Adeno-Associated Virus Gene Therapy Vector Fails to Lead to Germ Cell Transduction (2004)

In a clinical safety trial involving an adeno-associated virus (AAV) gene therapy vector encoding human factor IX, intrahepatic administration of the vector was associated with the finding of vector DNA in semen that persisted for several weeks. Uncertainty remains as to the route by which the vector reached semen, but the finding raised the prospect that mature sperm could be exposed to the vector and sustain integration of vector DNA. To provocatively test for the ability of AAV vectors to transduce mature sperm, we exposed mouse sperm to concentrations of the same vector used in clinical studies at concentrations ranging from 840 to 3400 particles per sperm cell, performed in vitro fertilization and embryo transfer, and evaluated newborn pups by Southern analysis for the presence of vector sequences. Of 102 pups analyzed, none showed evidence of vector DNA integration. We conclude from these studies that exposure of mature sperm to AAV gene therapy vectors is highly unlikely to lead to germline transduction.
Layered Dendritic Block Copolymers (1998)

A star-shaped molecule and a layered structure are displayed by the title compound, where the layers consist of high molecular weight polymers. A core molecule that is functionalized by six hydroxyl groups acts as the initiator for the ring-opening polymerization of ε-caprolactone, leading to a six-arm star polymer. The second layer of the dendritic block copolymer with 12, 24, or 48 hydroxyl groups (depending on the dendron generation in use) is obtained by the linkage of chain ends with functionalized dendrons. These macromoleculse act as "macroinitiators" for the construction of a further layer of poly(ε-caprolatone), the third generation of dendritic block copolymers.
Improved obstacle detection by sensor fusion (1992)

The authors describe recent work at Lucas in developing sensors and signal processing for collision avoidance. Results are presented that show the success of vehicle detection and lane marking detection using a video camera and a 94GHz microwave radar. Also discussed is research that is currently in progress that aims to combine the measurements from these sensors to give improved results.
Introduction: Interpreting the Transformation of Gender Inequalities in Southern Europe (1999)

(1999). Introduction: Interpreting the Transformation of Gender Inequalities in Southern Europe. South European Society and Politics: Vol. 4, Gender Inequalities in Southern Europe (Guest Editors: María José González, Teresa Jurado and Manuela Naldini), pp. 4-34.
Duplication of 10 nucleotides in the erythroid band 3 (AE1) gene in a kindred with hereditary spherocytosis and band 3 protein deficiency (band 3PRAGUE). (1994)

We describe a duplication of 10 nucleotides (2,455-2,464) in the band 3 gene in a kindred with autosomal dominant hereditary spherocytosis and a partial deficiency of the band 3 protein that is reflected by decreased rate of transmembrane sulfate flux and decreased density of intramembrane particles. The mutant allele potentially encodes an abnormal band 3 protein with a 3.5-kD COOH-terminal truncation; however, we did not detect the mutant protein in the membrane of mature red blood cells. Since the mRNA levels for the mutant and normal alleles are similar and since the band 3 content is the same in the light and dense red cell fractions, we conclude that the mutant band 3 is either not inserted into the plasma membrane or lost from the membrane prior to the release of red blood cells into circulation. We further show that the decrease in band 3 content principally involves the dimeric laterally and rotationally mobile fraction of the band 3 protein, while the laterally immobile and rotationally restricted band 3 fraction is left essentially intact. We propose that the decreased density of intramembrane particles decreases the stability of the membrane lipid bilayer and causes release of lipid microvesicles that leads to surface area deficiency and spherocytosis.
Autophosphorylation of cGMP‐dependent protein kinase is stimulated only by occupancy of one the two cGMP binding sites (1983)

cGMP-Dependent protein kinase contains, per subunit, 2 binding sites for cGMP. The apparent KD values for site 1 and 2 were 12 and 55 nM. The analogues 8-benzyl-amino-cAMP and N2-monobutyryl-cGMP bind preferentially to site 1 and 2, respectively. Both analogues stimulate autophosphorylation of the enzyme at concentrations at which only half of the phosphotransferase activity of the enzyme is expressed. Complete expression of the phosphotransferase activity requires a high concentration of each analogue and is accompanied by inhibition of the autophosphorylation reactions. It is concluded that occupancy of site 1 or 2 stimulates autophosphorylation while occupancy of both sites prevents autophosphorylation.
Kinetic Mechanism of the GCN5-Related Chromosomal Aminoglycoside Acetyltransferase AAC(6‘)-Ii from Enterococcus faecium:  Evidence of Dimer Subunit Cooperativity (2003)

The aminoglycoside 6'-N-acetyltransferase AAC(6')-Ii from Enterococcus faecium is an important microbial resistance determinant and a member of the GCN5-related N-acetyltransferase (GNAT) superfamily. We report here the further characterization of this enzyme in terms of the kinetic mechanism of acetyl transfer and identification of rate-contributing step(s) in catalysis, as well as investigations into the binding of both acetyl-CoA and aminoglycoside substrates to the AAC(6')-Ii dimer. Product and dead-end inhibition studies revealed that AAC(6')-Ii follows an ordered bi-bi ternary complex mechanism with acetyl-CoA binding first followed by antibiotic. Solvent viscosity studies demonstrated that aminoglycoside binding and product release govern the rate of acetyl transfer, as evidenced by changes in both the k(cat)/K(b) for aminoglycoside and k(cat), respectively, with increasing solvent viscosity. Solvent isotope effects were consistent with our viscosity studies that diffusion-controlled processes and not the chemical step were rate-limiting in drug modification. The patterns of partial and mixed inhibition observed during our mechanistic studies were followed up by investigating the possibility of subunit cooperativity in the AAC(6')-Ii dimer. Through the use of AAC-Trp(164) --> Ala, an active mutant which exists as a monomer in solution, the partial nature of the competitive inhibition observed in wild-type dead-end inhibition studies was alleviated. Isothermal titration calorimetry studies also indicated two nonequivalent antibiotic binding sites for the AAC(6')-Ii dimer but only one binding site for the Trp(164) --> Ala mutant. Taken together, these results demonstrate subunit cooperativity in the AAC(6')-Ii dimer, with possible relevance to other oligomeric members of the GNAT superfamily.
Dynamic membrane-cytoskeletal interactions: specific association of integrin and talin arises in vivo after phorbol ester treatment of peripheral blood lymphocytes. (1988)

Members of the family of transmembrane integral membrane proteins called integrins have been implicated in forming attachments to actin microfilaments of the cytoskeleton. These attachments are thought to involve one or more intervening peripheral membrane proteins linked to integrin. To detect such possible linkages in vivo, the integrin molecules on the surfaces of intact chicken peripheral blood lymphocytes were collected into caps by cross-linking with specific antibodies, and the capped cells were examined by double immunofluorescence to determine whether particular cytoskeletal proteins were co-collected with the integrin. With resting lymphocytes, the capping of integrin did not result in any detectable redistribution of either talin, vinculin, or alpha-actinin inside the cells. However, if the capping was carried out upon the addition of phorbol 12-myristate 13-acetate (PMA) to the cells, then talin, but not vinculin or alpha-actinin, was found associated with the integrin caps. PMA is known to activate protein kinase C. These results suggest that after, but not before, PMA stimulation of intact cells, talin becomes linked either directly or indirectly with integrin, reflecting the formation of a membrane-cytoskeletal association that is metabolically regulated.
Sliding Mode with Time Delay Control for MIMO nonlinear Systems With unknown dynamics (2015)

In this paper, the control problem of Multi-Input Multi-Output (MIMO) nonlinear Systems with unknown dynamics is proposed. A novel method based on the Sliding Mode with Time Delay Control (SMTDC) is proposed by combining a Sliding Mode Control (SMC) with saturation (sat) function and Time Delay Control (TDC). This method (SMTDC), allows chattering reduction on control inputs and estimates the amounts of unknown or unmodeled nonlinear dynamics and unexpected uncertainties and cancels them. This algorithm was simulated on the model of the ANAT robot arm system to demonstrate the effectiveness of the proposed design method.
Cyclophilin A is required for an early step in the life cycle of human immunodeficiency virus type 1 before the initiation of reverse transcription (1996)

Cyclophilin A (CyPA) is incorporated into human immunodeficiency virus type 1 (HIV-1) virions via contact with the Gag polyprotein. Genetic or pharmacologic disruption of CyPA incorporation causes a quantitative reduction in virion infectivity with no discernible effects on virion assembly or on endogenous reverse transcriptase activity. Instead, the reduction of virion-associated CyPA is accompanied by a parallel, quantitative decrease in the initiation of viral DNA synthesis after infection of T cells. The infectivity of CyPA-deficient virions is not restored by pseudotyping with Env of amphotropic murine leukemia virus, demonstrating that CyPA is not required for the HIV-1-Env-CD4 interaction. These results indicate that CyPA is required for an early step in the HIV-1 life cycle following receptor binding and membrane fusion but preceding reverse transcription. CyPA is the first cellular protein other than the cell surface receptor shown to be required for an early event in the life cycle of a retrovirus.
Inhibition of Neurotensin Receptor 1 Selectively Sensitizes Prostate Cancer to Ionizing Radiation (2011)

Radiotherapy combined with androgen depletion is generally successful for treating locally advanced prostate cancer. However, radioresistance that contributes to recurrence remains a major therapeutic problem in many patients. In this study, we define the high-affinity neurotensin receptor 1 (NTR1) as a tractable new molecular target to radiosensitize prostate cancers. The selective NTR1 antagonist SR48692 sensitized prostate cancer cells in a dose- and time-dependent manner, increasing apoptotic cell death and decreasing clonogenic survival. The observed cancer selectivity for combinations of SR48692 and radiation reflected differential expression of NTR1, which is highly expressed in prostate cancer cells but not in normal prostate epithelial cells. Radiosensitization was not affected by androgen dependence or androgen receptor expression status. NTR1 inhibition in cancer cell-attenuated epidermal growth factor receptor activation and downstream signaling, whether induced by neurotensin or ionizing radiation, establish a molecular mechanism for sensitization. Most notably, SR48692 efficiently radiosensitized PC-3M orthotopic human tumor xenografts in mice, and significantly reduced tumor burden. Taken together, our findings offer preclinical proof of concept for targeting the NTR1 receptor as a strategy to improve efficacy and outcomes of prostate cancer treatments using radiotherapy.
Codon usage and tRNA content in unicellular and multicellular organisms. (1985)

Choices of synonymous codons in unicellular organisms are here reviewed, and differences in synonymous codon usages between Escherichia coli and the yeast Saccharomyces cerevisiae are attributed to differences in the actual populations of isoaccepting tRNAs. There exists a strong positive correlation between codon usage and tRNA content in both organisms, and the extent of this correlation relates to the protein production levels of individual genes. Codon-choice patterns are believed to have been well conserved during the course of evolution. Examination of silent substitutions and tRNA populations in Enterobacteriaceae revealed that the evolutionary constraint imposed by tRNA content on codon usage decelerated rather than accelerated the silent-substitution rate, at least insofar as pairs of taxonomically related organisms were examined. Codon-choice patterns of multicellular organisms are briefly reviewed, and diversity in G+C percentage at the third position of codons in vertebrate genes--as well as a possible causative factor in the production of this diversity--is discussed.
Magneto-optical properties of one-dimensional photonic crystals composed of magnetic and dielectric layers (1998)

The magneto-optical (MO) Faraday effect of one-dimensional photonic crystals (1D-PCs) composed of Bi-substituted yttrium–iron–garnet films and dielectric films such as SiO2 and TiO2 films were studied theoretically. Because of considerable localization of light, these media exhibit a very large MO effect. For instance, when the film structure is chosen to be appropriate for supporting the localization of light, the 1D-PC films can possess a huge Faraday rotation angle reaching to −28 deg/μm at λ=1.15 μm. The analysis reveals that the MO characteristics of the 1D-PC films are almost governed by the degree of localization of light, which can be controlled by varying the number of reflection layers in the films.