gebhart/patrepeval huggingface dataset:
Role of NRF2 in Protection Against Hyperoxic Lung Injury in Mice (2002)

NRF2 is a transcription factor important in the protection against carcinogenesis and oxidative stress through antioxidant response element (ARE)-mediated transcriptional activation of several phase 2 detoxifying and antioxidant enzymes. This study was designed to determine the role of NRF2 in the pathogenesis of hyperoxic lung injury by comparing pulmonary responses to 95-98% oxygen between mice with site-directed mutation of the gene for NRF2 (Nrf2-/-) and wild-type mice (Nrf2+/+). Pulmonary hyperpermeability, macrophage inflammation, and epithelial injury in Nrf2-/- mice were 7.6-fold, 47%, and 43% greater, respectively, compared with Nrf2+/+ mice after 72 h hyperoxia exposure. Hyperoxia markedly elevated the expression of NRF2 mRNA and DNA-binding activity of NRF2 in the lungs of Nrf2+/+ mice. mRNA expression for ARE- responsive lung antioxidant and phase 2 enzymes was evaluated in both genotypes of mice to identify potential downstream molecular mechanisms of NRF2 in hyperoxic lung responses. Hyperoxia-induced mRNA levels of NAD(P)H:quinone oxidoreductase 1 (NQO1), glutathione-S-transferase (GST)-Ya and -Yc subunits, UDP glycosyl transferase (UGT), glutathione peroxidase-2 (GPx2), and heme oxygenase-1 (HO-1) were significantly lower in Nrf2-/- mice compared with Nrf2+/+ mice. Consistent with differential mRNA expression, NQO1 and total GST activities were significantly lower in Nrf2-/- mice compared with Nrf2+/+ mice after hyperoxia. Results demonstrated that NRF2 has a significant protective role against pulmonary hyperoxic injury in mice, possibly through transcriptional activation of lung antioxidant defense enzymes.
The identification of myogenic cells in skeletal muscle, with emphasis on the use of tritiated thymidine autoradiography and desmin antibodies (1998)

The identification of myogenic precursor cells (mpc) is a key factor in determining the early events in the myogenesis and regeneration of skeletal muscle. Although satellite cells have long been established as the providers of myoblastic cells, very little is really known (apart from their anatomical location in relation to muscle fibres and their ability to migrate) about the precise role of satellite cells in myogenesis. Numerous techniques for labelling mpc have been devised, but none of these has proven to be completely reliable in firmly establishing the origin of myogenic cells. The use of tritiated thymidine to label DNA in proliferating mpc (which are not specifically distinguishable at the time) and the subsequent location of their labelled progeny in myotube nuclei has revealed a great deal of data on the timing of myogenesis, but not about the nature of mpc themselves. DNA synthesis can also be detected by antibodies to the thymidine analogue, bromodeoxyuridine, and also by antibody staining for proliferating nuclear cell antigen. Like tritiated thymidine, these other markers are not specific for muscle but are general markers for DNA synthesis. In situ hybridisation of various muscle-specific genetic markers and their products has been informative, as has immunolabelling of myogenin, MyoD1 and desmin. Desmin labelling has been particularly instructive in identifying mpc because it is one of the first muscle-specific proteins to be produced in mpc. This review covers some of the techniques mentioned above and their usefulness in determining the early events in myogenesis.
The function of vitamin B12 in the metabolism of propionate by the protozoan Ochromonas malhamensis (1962)

Research Article| May 01 1962 The function of vitamin B12 in the metabolism of propionate by the protozoan Ochromonas malhamensis HRV ARNSTEIN; HRV ARNSTEIN Search for other works by this author on: This Site PubMed Google Scholar AM WHITE AM WHITE Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1962) 83 (2): 264–270. https://doi.org/10.1042/bj0830264 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation HRV ARNSTEIN, AM WHITE; The function of vitamin B12 in the metabolism of propionate by the protozoan Ochromonas malhamensis. Biochem J 1 May 1962; 83 (2): 264–270. doi: https://doi.org/10.1042/bj0830264 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1962 The Biochemical Society1962 Article PDF first page preview Close Modal You do not currently have access to this content.
Programming gene expression in developing epidermis (1994)

As the major proteins of adult keratinocytes, keratins provide biochemical markers for exploring mouse epidermal embryogenesis. Here, we used a modified method of whole-mount in situ hybridization to track skin-specific expression of endogenous keratin mRNAs throughout embryogenesis. To monitor transcriptional regulation, we coupled this with beta-galactosidase expression of a human epidermal keratin promoter-driven transgene. These studies have radically changed our perception of how the program of gene expression becomes established during epidermal development. Specifically, we have discovered that (1) basal keratin (K5 and K14) genes are first detected at E9.5 in a highly regional fashion, and surprisingly as early as the single layered ectodermal stage; (2) the early patterns do not correlate with morphogenesis per se, but rather with regional variations in the embryonic origin of underlying mesenchyme, supporting morphogenetic criteria that early inductive cues are mesenchymal; (3) epidermal keratin genes are expressed in periderm, supporting the notion that this layer arises from ectodermal stratification, even though it is simple epithelial-like in morphology and is subsequently sloughed during development; (4) later embryonic patterns of K5 and K14 gene expression parallel proliferative capacity and not stratification; and (5) K1 and K10 mRNAs are first detected as early as E13.5, and their patterns correlate with differentiation and not stratification. These patterns of epidermal gene expression led us to explore whether potential transcriptional regulators of these genes are expressed similarly. We show that AP2 (but not Sp1) cRNAs hybridize in a pattern similar to, but preceding that of basal keratin cRNAs. Finally, using gene expression in cultured cells, we demonstrate that AP2 has a strong inductive effect on basal keratin expression in a cellular environment that does not normally possess AP2 activity.
Structure‐based prediction of binding peptides to MHC class I molecules: Application to a broad range of MHC alleles (2000)

Specific binding of antigenic peptides to major histocompatibility complex (MHC) class I molecules is a prerequisite for their recognition by cytotoxic T-cells. Prediction of MHC-binding peptides must therefore be incorporated in any predictive algorithm attempting to identify immunodominant T-cell epitopes, based on the amino acid sequence of the protein antigen. Development of predictive algorithms based on experimental binding data requires experimental testing of a very large number of peptides. A complementary approach relies on the structural conservation observed in crystallographically solved peptide-MHC complexes. By this approach, the peptide structure in the MHC groove is used as a template upon which peptide candidates are threaded, and their compatibility to bind is evaluated by statistical pairwise potentials. Our original algorithm based on this approach used the pairwise potential table of Miyazawa and Jernigan (Miyazawa S, Jernigan RL, 1996, J Mol Biol 256:623-644) and succeeded to correctly identify good binders only for MHC molecules with hydrophobic binding pockets, probably because of the high emphasis of hydrophobic interactions in this table. A recently developed pairwise potential table by Betancourt and Thirumalai (Betancourt MR, Thirumalai D, 1999, Protein Sci 8:361-369) that is based on the Miyazawa and Jernigan table describes the hydrophilic interactions more appropriately. In this paper, we demonstrate how the use of this table, together with a new definition of MHC contact residues by which only residues that contribute exclusively to sequence specific binding are included, allows the development of an improved algorithm that can be applied to a wide range of MHC class I alleles.
The cxc chemokine cCAF stimulates differentiation of fibroblasts into myofibroblasts and accelerates wound closure (2002)

Chemokines are small cytokines primarily known for their roles in inflammation. More recently, however, they have been implicated in processes involved in development of the granulation tissue of wounds, but little is known about their functions during this process. Fibroblasts play key roles in this phase of healing: some fibroblasts differentiate into myofibroblasts, alpha-smooth muscle actin (SMA)-producing cells that are important in wound closure and contraction. Here we show that the CXC chemokine chicken chemotactic and angiogenic factor (cCAF) stimulates fibroblasts to produce high levels of alpha-SMA and to contract collagen gels more effectively than do normal fibroblasts, both characteristic properties of myofibroblasts. Specific inhibition of alpha-SMA expression resulted in abrogation of cCAF-induced contraction. Furthermore, application of cCAF to wounds in vivo increases the number of myofibroblasts present in the granulation tissue and accelerates wound closure and contraction. We also show that these effects in culture and in vivo can be achieved by a peptide containing the NH2-terminal 15 amino acids of the cCAF protein and that inhibition of alpha-SMA expression also results in inhibition of N-peptide-induced collagen gel contraction. We propose that chemokines are major contributors for the differentiation of fibroblasts into myofibroblasts during formation of the repair tissue. Because myofibroblasts are important in many pathological conditions, and because chemokines and their receptors are amenable to pharmacological manipulations, chemokine stimulation of myofibroblast differentiation may have implications for modulation of functions of these cells in vivo.
Central corneal thickness determined with optical coherence tomography in various types of glaucoma (2000)

Because of thinner CCT in patients with LTG, PEX, and POAG this may result in underestimation of IOP, whereas thicker corneas may lead to an overestimation of IOP in subjects with OH. By determining CCT with OCT, a new and precise technique to measure CCT, this study emphasises the need for a combined measurement of IOP and CCT in order to obtain exact IOP readings.
Pharmacokinetics of L/105, a New Rifamycin, in Rats and Dogs, after Oral Administration (1983)

The absorption and tissue distribution of a new rifamycin, L/105, which chemically is 4-deoxy-4'-methylpyrido [1',2'-1,2]imidazo [5,4 C] rifamycin SV, were studied in rats after oral administration of 100 mg/kg. This study showed that L/105, contrary to what was observed for rifampicin, was practically not absorbed: neither serum nor significant tissue levels were evidenced. Also in dogs, after oral administration of L/105 in a single dose (25 mg/kg) and a multiple dosage (10 mg/kg/day, for 8 days), no traces of the compound were detected in the serum. The elimination was investigated in the rat: the highest recovery of L/105 (more than 50% of the administered dose) was in feces after 72 h, hardly any traces were found in urine.
The Quality of Chimpanzee T-Cell Activation and Simian Immunodeficiency Virus/Human Immunodeficiency Virus Susceptibility Achieved via Antibody-Mediated T-Cell Receptor/CD3 Stimulation Is a Function of the Anti-CD3 Antibody Isotype (2008)

While human immunodeficiency virus type 1 (HIV-1) infection is associated with hyperimmune activation and systemic depletion of CD4(+) T cells, simian immunodeficiency virus (SIV) infection in sooty mangabeys or chimpanzees does not exhibit these hallmarks. Control of immune activation is thought to be one of the major components that govern species-dependent differences in the disease pathogenesis. A previous study introduced the idea that the resistance of chimpanzees to SIVcpz infection-induced hyperimmune activation could be the result of the expression of select sialic acid-recognizing immunoglobulin (Ig)-like lectin (Siglec) superfamily members by chimpanzee T cells. Siglecs, which are absent on human T cells, were thought to control levels of T-cell activation in chimpanzees and were thus suggested as a cause for the pathogenic differences in the course of SIVcpz or HIV-1 infection. As in human models of T-cell activation, stimulation had been attempted using an anti-CD3 monoclonal antibody (MAb) (UCHT1; isotype IgG1), but despite efficient binding, UCHT1 failed to activate chimpanzee T cells, an activation block that could be partially overcome by MAb-induced Siglec-5 internalization. We herein demonstrate that anti-CD3 MAb-mediated chimpanzee T-cell activation is a function of the anti-CD3 MAb isotype and is not governed by Siglec expression. While IgG1 anti-CD3 MAbs fail to stimulate chimpanzee T cells, IgG2a anti-CD3 MAbs activate chimpanzee T cells in the absence of Siglec manipulations. Our results thus imply that prior to studying possible differences between human and chimpanzee T-cell activation, a relevant model of chimpanzee T cell activation needs to be established.
Applications of pox virus vectors to vaccination: an update. (1996)

Recombinant pox viruses have been generated for vaccination against heterologous pathogens. Amongst these, the following are notable examples. (i) The engineering of the Copenhagen strain of vaccinia virus to express the rabies virus glycoprotein. When applied in baits, this recombinant has been shown to vaccinate the red fox in Europe and raccoons in the United States, stemming the spread of rabies virus infection in the wild. (ii) A fowlpox-based recombinant expressing the Newcastle disease virus fusion and hemagglutinin glycoproteins has been shown to protect commercial broiler chickens for their lifetime when the vaccine was administered at 1 day of age, even in the presence of maternal immunity against either the Newcastle disease virus or the pox vector. (iii) Recombinants of canarypox virus, which is restricted for replication to avian species, have provided protection against rabies virus challenge in cats and dogs, against canine distemper virus, feline leukemia virus, and equine influenza virus disease. In humans, canarypox virus-based recombinants expressing antigens from rabies virus, Japanese encephalitis virus, and HIV have been shown to be safe and immunogenic. (iv) A highly attenuated vaccinia derivative, NYVAC, has been engineered to express antigens from both animal and human pathogens. Safety and immunogenicity of NYVAC-based recombinants expressing the rabies virus glycoprotein, a polyprotein from Japanese encephalitis virus, and seven antigens from Plasmodium falciparum have been demonstrated to be safe and immunogenic in early human vaccine studies.
The Atr and Atm protein kinases associate with different sites along meiotically pairing chromosomes. (1996)

A number of cell-cycle checkpoint genes have been shown to play important roles in meiosis. We have characterized the human and mouse counterpart of the Schizosaccharomyces pombe Rad3 protein, named Atr (for ataxia-telangiectasia- and rad3-related), and the protein that is mutated in ataxia-telangiectasia, Atm. We demonstrate that ATR mRNA and protein are expressed in human and mouse testis. More detailed analysis of specific cells in seminiferous tubules shows localization of Atr to the nuclei of cells in the process of meiosis I. Using immunoprecipitation and immunoblot analysis, we show that Atr and Atm proteins are approximately 300 and 350 kD relative molecular mass, respectively, and further demonstrate that both proteins have associated protein kinase activity. Further, we demonstrate that Atr and Atm interact directly with meiotic chromosomes and show complementary localization patterns on synapsing chromosomes. Atr is found at sites along unpaired or asynapsed chromosomal axes, whereas Atm is found along synapsed chromosomal axes. This is the first demonstration of a nuclear association of Atr and Atm proteins with meiotic chromosomes and suggests a direct role for these proteins in recognizing and responding to DNA strand interruptions that occur during meiotic recombination.
Compositional Human Pose Regression (2017)

Regression based methods are not performing as well as detection based methods for human pose estimation. A central problem is that the structural information in the pose is not well exploited in the previous regression methods. In this work, we propose a structure-aware regression approach. It adopts a reparameterized pose representation using bones instead of joints. It exploits the joint connection structure to define a compositional loss function that encodes the long range interactions in the pose. It is simple, effective, and general for both 2D and 3D pose estimation in a unified setting. Comprehensive evaluation validates the effectiveness of our approach. It significantly advances the state-of-the-art on Human3.6M [20] and is competitive with state-of-the-art results on MPII [3].
Porous Chitosan-Silica Hybrid Microspheres as a Potential Catalyst (2004)

Chitosan/silica hybrids were synthesized and shaped as microspheres, which may or may not present a core/shell structure, depending on the experimental conditions. The core is constituted by a homogeneous hybrid, while the shell is pure silica. The amino groups of the biopolymer are still accessible as active sites for heterogeneous catalysis.
Remote Sensing of Algal Bloom Dynamics (1996)

mhe last decade has seen rapid advances in two technologybased approaches to the study of algal biology: the use of remote sensing, which quantitatively measures light reflected from the surface of the earth, as a tool to study regional-scale aquatic ecosystem dynamics, and the refinement of techniques to identify and quantify algal pigments. Although research in remote sensing has been driven by the ongoing development of new sensors, advances in pigment analysis have essentially evolved from continual research in algal population dynamics, ecology, and physiology. Recent innovative results in both
Cyclophilin A Is a Secreted Growth Factor Induced by Oxidative Stress (2000)

Reactive oxygen species have been implicated in the pathogenesis of atherosclerosis, hypertension, and restenosis, in part by promoting vascular smooth muscle cell (VSMC) growth. Many VSMC growth factors are secreted by VSMC and act in an autocrine manner. Here we demonstrate that cyclophilin A (CyPA), a member of the immunophilin family, is secreted by VSMCs in response to oxidative stress and mediates extracellular signal-regulated kinase (ERK1/2) activation and VSMC growth by reactive oxygen species. Human recombinant CyPA can mimic the effects of secreted CyPA to stimulate ERK1/2 and cell growth. The peptidyl-prolyl isomerase activity is required for ERK1/2 activation by CyPA. In vivo, CyPA expression and secretion are increased by oxidative stress and vascular injury. These findings are the first to identify CyPA as a secreted redox-sensitive mediator, establish CyPA as a VSMC growth factor, and suggest an important role for CyPA and enzymes with peptidyl-prolyl isomerase activity in the pathogenesis of vascular diseases.
Analysis of reflectometry density profile measurements in JET (1993)

A multichannel microwave reflectometer system is used to measure the electron density profile at JET. A new measurement technique is described which gives continuous information on the electron profile in time. Profile measurements using swept-frequency measurements are combined with accurate measurements of the evolution of the density using fixed-frequency operation. The analysis of the data can be carried out routinely for each discharge at JET. The method includes estimates for the uncertainties on the measurements, corrections for finite sweep on the data and relativistic effects. The results compare well with other measurements of the electron density in JET.
Optical Vehicle-to-Vehicle Communication System Using LED Transmitter and Camera Receiver (2014)

This paper introduces an optical vehicle-to-vehicle (V2V) communication system based on an optical wireless communication technology using an LED transmitter and a camera receiver, which employs a special CMOS image sensor, i.e, an optical communication image sensor (OCI). The OCI has a “communication pixel (CPx)” that can promptly respond to light intensity variations and an output circuit of a “flag image” in which only high-intensity light sources, such as LEDs, have emerged. The OCI that employs these two technologies provides capabilities for a 10-Mb/s optical signal reception and real-time LED detection to the camera receiver. The optical V2V communication system consisting of the LED transmitters mounted on a leading vehicle and the camera receiver mounted on a following vehicle is constructed, and various experiments are conducted under real driving and outdoor lighting conditions. Due to the LED detection method using the flag image, the camera receiver correctly detects LEDs, in real time, in challenging outdoor conditions. Furthermore, between two vehicles, various vehicle internal data (such as speed) and image data (320 × 240, color) are transmitted successfully, and the 13.0-fps image data reception is achieved while driving outside.