gebhart/patrepeval huggingface dataset:
Production of proteoglycans by human lung fibroblasts (IMR-90) maintained in a low concentration of serum (1982)

Maintenance of fibroblasts in 0.5% serum results in viable but non-proliferative cells that may be analogous to fibroblasts in vivo. The synthesis of proteoglycans by human embryo lung fibroblasts in Eagle's minimal essential medium with 0.5% newborn-bovine serum or with 10% serum has been compared. A similar amount of [35S]sulphate-labelled glycosaminoglycan per cell was secreted by fibroblasts in 10% or 0.5% serum. 35SO42-incorporation into sulphated glycosaminoglycans was enhanced in 0.5% serum when expressed per mg of cell protein, but [3H]glucosamine incorporation was decreased. The charge density of these glycosaminoglycans was not changed as determined by ion-exchange chromatography. It was concluded that decreased protein/ cell resulted in an apparent increase in 35S-labelled glycosaminoglycan synthesis/mg of cell protein, whereas decreased uptake of [3H]glucosamine resulted in a decrease in their glucosamine labelling. The proteoglycans secreted by fibroblasts in 0.5% serum were similar in glycosaminoglycan composition, chain length and buoyant density to the dermatan sulphate proteoglycan, which is the major secreted component of cells in 10% serum. Larger heparan sulphate and chondroitin sulphate proteoglycans, which comprise about 40% of the total secreted proteoglycans of cultures in 10% serum, were greatly diminished in the medium of cultures in 0.5% serum. The proteoglycan profile of medium from density-inhibited cultures in 10% serum resembles that of proliferating cultures, indicating that lack of proliferation was not responsible for the alteration. The dermatan sulphate proteoglycan, participating in extracellular matrix structure, may be the primary tissue product of lung fibroblasts in vivo.
Epstein-Barr virus infection induces lupus autoimmunity. (2006)

Systemic lupus erythematosus (SLE or lupus) is a systemic autoimmune disease characterized by a constellation of varied clinical presentations, although the nearly universal presence of autoantibodies is a salient unifying feature. Ongoing research efforts focus on understanding the complex combination of genetic and environmental factors that lead to SLE in select individuals. Our previous work has demonstrated that years before diagnosis abnormal autoantibody responses are present in the sera of patients who will subsequently develop lupus and, further, that the initial targets of two of these key responses (anti-Sm B' and anti-60 kD Ro alone) have been identified for some patients. Indeed, our results suggest that the first lupus-specific autoantibodies arise from particular antibodies directed against Epstein-Barr virus Nuclear Antigen-1 (EBNA-1) and that infection with Epstein-Barr virus (EBV) is an environmental risk factor for lupus. The predicted sequence of events is normal immunity, followed by Epstein- Barr virus infection, the generation of anti-EBNA-1 antibodies, then followed by those particular anti-EBNA-1 antibodies that also bind lupus-specific autoantigens (Sm or Ro), followed by the development of more complex autoimmune responses, and, finally, culminating in clinical disease. Studies from others and those underway suggest that lupus patients have unusual immune responses to Epstein-Barr virus. In aggregate, these results are consistent with an immune response against Epstein-Barr virus being important in at least some patients for the initiation of lupus autoimmunity.
Capillary protein leak syndrome appears to explain fluid retention in cancer patients who receive docetaxel treatment. (1998)

Docetaxel appears to induce an initial enhancement of fluid filtration followed by a capillary protein leakage that leads to edema formation.
Crystal Engineering of NLO Materials Based on Metal−Organic Coordination Networks (2002)

Crystal engineering, the ability to predict and control the packing of molecular building units in the solid state, has attracted much attention over the past three decades owing to its potential exploitation for the synthesis of technologically important materials. We present here the development of crystal-engineering strategies toward the synthesis of noncentrosymmetric infinite coordination networks for use as second-order nonlinear optical (NLO) materials. Work performed mainly in our laboratory has demonstrated that noncentrosymmetric solids based on infinite networks can be rationally synthesized by combining unsymmetrical bridging ligands and metal centers with well-defined coordination geometries. Specifically, coordination networks based on 3D diamondoid and 2D grid structures can be successfully engineered with a high degree of probability and predictability to crystallize in noncentrosymmetric space groups. We have also included noncentrosymmetric solids based on 1D chains and related helical structures for comparison.
Three-dimensional synthetic aperture integral imaging (2002)

We propose synthetic aperture integral imaging, in which an effectively enlarged aperture (or field of view) is obtained by movement of small integral imaging system. This system substantially increases the field of view and the viewing resolution. The feasibility of our approach is experimentally demonstrated. To the best of our knowledge, this is the first time the synthetic aperture technique has been applied to three-dimensional integral imaging.
Stage III follicular lymphoma: durable remissions with a combined chemotherapy-radiotherapy regimen. (1987)

From 1975 to 1982, 74 patients with stage III follicular lymphoma were treated with a combined modality protocol which included chemotherapy with cyclophosphamide, doxorubicin, vincristine, prednisone, and bleomycin (CHOP-Bleo), and radiotherapy to involved regions. This program resulted in a complete remission (CR) rate of 81%, a 5-year survival of 75%, and 5-year relapse-free survival (RFS) of 52% for all patients. Analysis of potential factors affecting treatment outcome revealed a significantly better CR rate for patients with small cleaved cell type (97%) than for patients with mixed (73%) or large-cell (57%) histologies. The 5-year survival was significantly better for patients with small cleaved (91%) and mixed (84%) cell types than for large cell (40%). In addition, bulky abdominal disease and elevated serum lactate dehydrogenase (LDH) were significant adverse prognostic factors for CR and for survival. Toxicity was moderate. No secondary leukemias have occurred. This combined modality regimen resulted in prolonged remission and potential cure for over half of patients who achieved CR, and is particularly encouraging for those with follicular small cleaved and mixed histologies.
One Rule to Grow Them All: A General Theory of Neuronal Branching and Its Practical Application (2010)

Understanding the principles governing axonal and dendritic branching is essential for unravelling the functionality of single neurons and the way in which they connect. Nevertheless, no formalism has yet been described which can capture the general features of neuronal branching. Here we propose such a formalism, which is derived from the expression of dendritic arborizations as locally optimized graphs. Inspired by Ramón y Cajal's laws of conservation of cytoplasm and conduction time in neural circuitry, we show that this graphical representation can be used to optimize these variables. This approach allows us to generate synthetic branching geometries which replicate morphological features of any tested neuron. The essential structure of a neuronal tree is thereby captured by the density profile of its spanning field and by a single parameter, a balancing factor weighing the costs for material and conduction time. This balancing factor determines a neuron's electrotonic compartmentalization. Additions to this rule, when required in the construction process, can be directly attributed to developmental processes or a neuron's computational role within its neural circuit. The simulations presented here are implemented in an open-source software package, the "TREES toolbox," which provides a general set of tools for analyzing, manipulating, and generating dendritic structure, including a tool to create synthetic members of any particular cell group and an approach for a model-based supervised automatic morphological reconstruction from fluorescent image stacks. These approaches provide new insights into the constraints governing dendritic architectures. They also provide a novel framework for modelling and analyzing neuronal branching structures and for constructing realistic synthetic neural networks.
New Approaches to Sepsis: Molecular Diagnostics and Biomarkers (2012)

Sepsis is among the most common causes of death in hospitals. It arises from the host response to infection. Currently, diagnosis relies on nonspecific physiological criteria and culture-based pathogen detection. This results in diagnostic uncertainty, therapeutic delays, the mis- and overuse of antibiotics, and the failure to identify patients who might benefit from immunomodulatory therapies. There is a need for new sepsis biomarkers that can aid in therapeutic decision making and add information about screening, diagnosis, risk stratification, and monitoring of the response to therapy. The host response involves hundreds of mediators and single molecules, many of which have been proposed as biomarkers. It is, however, unlikely that one single biomarker is able to satisfy all the needs and expectations for sepsis research and management. Among biomarkers that are measurable by assays approved for clinical use, procalcitonin (PCT) has shown some usefulness as an infection marker and for antibiotic stewardship. Other possible new approaches consist of molecular strategies to improve pathogen detection and molecular diagnostics and prognostics based on transcriptomic, proteomic, or metabolic profiling. Novel approaches to sepsis promise to transform sepsis from a physiologic syndrome into a group of distinct biochemical disorders and help in the development of better diagnostic tools and effective adjunctive sepsis therapies.
Maintenance of Correction of the Modified Lapidus Procedure With a First Metatarsal to Intermediate Cuneiform Cross-Screw Technique (2019)

Level IV, retrospective case series.
Metal Binding to Bipyridine-Modified PNA (2006)

Substitution of natural nucleobases in PNA oligomers with ligands is a strategy for directing metal ion incorporation to specific locations within a PNA duplex. In this study, we have synthesized PNA oligomers that contain up to three adjacent bipyridine ligands and examined the interaction with Ni2+ and Cu2+ of these oligomers and of duplexes formed from them. Variable-temperature UV spectroscopy showed that duplexes containing one terminal pair of bipyridine ligands are more stable upon metal binding than their nonmodified counterparts. While binding of one metal ion to duplexes that contain two adjacent bipyridine pairs makes the duplexes more stable, additional metal ions lower the duplex stability, with electrostatic repulsions being, most likely, an important contributor to the destabilization. UV titrations showed that the presence of several bipyridine ligands in close proximity of each other in PNA oligomers exerts a chelate effect. A supramolecular chelate effect occurs when several bipyridines are brought next to each other by hybridization of PNA duplexes. EPR spectroscopy studies indicate that even when two Cu2+ ions coordinate to a PNA duplex in which two bipyridine pairs are next to each other, the two metal-ligand complexes that form in the duplex are far enough from each other that the dipolar coupling is very weak. EXAFS and XANES show that the Ni2+-bipyridine bond lengths are typical for [Ni(bipy)2]2+ and [Ni(bipy)3]2+ complexes.
A Zoogloea sp. associated with blooms of Anabaena flos-aquae (1978)

Bacteria were found attached to the heterocysts of Aphanizomenon flos-aquae and embedded within the mucilage of both anabaena flos-aquae and Microcystis aeruginosa in freshwater plankton. Electron microscopy of thin sections preceding the peak of an Anabaena flos-aquae bloom showed that the density of bacterial cells was 7.4 X 10(5) cells/ml in the planktonic macroenvironment and 2.6 X 10(11) cells/ml within the microenvironment of cyanobacterial mucilage. The bacteria occurred in aggregates and isolation required that these be dispersed by homogenizing at 50 000 rpm with glass beads. This procedure yielded a single bacterial isolate from blooms of Anabaena flos-aquae during 2 consecutive years. The isolate was flagellated, catalase- and oxidase-positive. Gram-negative, and rod-shaped to pleomorphic. Observation that the isolate required a pH greater than 8 for consistent growth, could not grow alone on liquid media but could grow alone on the corresponding solid media, could grow in liquid media only in the presence of Anabaena, formed tough mucilagenous colonies on solid media only in the presence of Anabaena extract, and rapidly assimilated but did not respire extracellular 14C-labelled organic matter produced by Anabaena suggested that the occurrence of the bacterium in cyanobacterial mucilage was not coincidental but reflected an obligatory bacterial requirement for the biological or physicochemical microenvironment of the mucilage. The bacterial isolate occurred in three growth forms. Either as a planktonic swarmer cell (which showed a positive chemotactic response to the cyanobacterium) embedded in cyanobacterial mucilage, or embedded in its own mucilage derived, in part, from a low molecular weight (below 1300) carbohydrate secreted by the cyanobacterium. These cultural, biochemical, and ecological characteristics suggest that the isolate is a new species in the genus Zoogloea and of potential importance in phytoplankton ecology.
Reviews of books (1992)

Journal Article Reviews of books Get access The Margins of City Life: Explorations on the French Urban Frontier, 1815–51. By John. MerrimanOxford: Oxford University Press. 1991. x + 318 pp. £35. ISBN 0 19 50638 0. ROGER MAGRAW ROGER MAGRAW Warwick University Search for other works by this author on: Oxford Academic Google Scholar French History, Volume 6, Issue 4, December 1992, Pages 484–485, https://doi.org/10.1093/fh/6.4.484 Published: 01 December 1992
Adoptive T Cell Immunotherapy of Human Uveal Melanoma Targeting gp100 (2000)

HLA-A*0201-restricted CTL against human gp100 were isolated from HLA-A*0201/K(b) (A2/K(b))-transgenic mice immunized with recombinant canarypox virus (ALVAC-gp100). These CTL strongly responded to the gp100(154-162) epitope, in the context of both the chimeric A2/K(b) and the wild-type HLA-A*0201- molecule, and efficiently lysed human HLA-A*0201(+), gp100(+) melanoma cells in vitro. The capacity of the CTL to eradicate these tumors in vivo was analyzed in A2/K(b)-transgenic transgenic mice that had received a tumorigenic dose of human uveal melanoma cells in the anterior chamber of the eye. This immune-privileged site offered the unique opportunity to graft xenogeneic tumors into immunocompetent A2/K(b)-transgenic mice, a host in which they otherwise would not grow. Importantly, systemic (i.v.) administration of the A2/K(b)-transgenic gp100(154-162)-specific CTL resulted in rapid elimination of the intraocular uveal melanomas, indicating that anti-tumor CTL are capable of homing to the eye and exerting their tumoricidal effector function. Flow cytometry analysis of ocular cell suspensions with HLA-A*0201-gp100(154-162) tetrameric complexes confirmed the homing of adoptively transferred CTL. Therefore, the immune-privileged state of the eye permitted the outgrowth of xenogeneic uveal melanoma cells, but did not protect these tumors against adoptive immunotherapy with highly potent anti-tumor CTL. These data constitute the first direct indication that immunotherapy of human uveal melanoma may be feasible.
Cloning of cDNA encoding Drosophila poly(ADP-ribose) polymerase: leucine zipper in the auto-modification domain. (1993)

We have isolated cDNA clones for a Drosophila poly(ADP-ribose) polymerase (PARP; EC 2.4.2.30) by screening a lambda gt11 cDNA library with a Drosophila partial cDNA fragment. The Drosophila PARP probe was obtained by the polymerase chain reaction with heterologous primers deduced from conserved amino acids in the mammalian, chicken, amphibian, and fish sequences. The Drosophila PARP mRNA is 3.2 kb in length and is expressed in the early stages of development. The PARP protein of 994 amino acids contains two zinc-finger motifs and an NAD-binding motif, which are conserved among different species. Interestingly, the heptad leucine repeat in an alpha-helix was found in Drosophila PARP. Alignments of the auto-modification domains of various species showed the repeated hydrophobic amino acids on the same face of the helix that make the coiled-coil configuration in the mammalian and chicken sequences. The presence of a leucine-zipper motif in the auto-modification domain suggests that this motif might be responsible for protein-protein interaction between PARP and physiological acceptors. PARP may have novel functions, possibly involving its homo- and/or heterodimerization with other nuclear leucine-zipper proteins and its regulation by ADP-ribosylation.
Harnessing chaos for image synthesis (1988)

Chaotic dynamics can be used to model shapes and render textures in digital images. This paper addresses the problem of how to model geometrically shapes and textures of two dimensional images using iterated function systems. The successful solution to this problem is demonstrated by the production and processing of synthetic images encoded from color photographs. The solution is achieved using two algorithms: (1) an interactive geometric modeling algorithm for finding iterated function system codes; and (2) a random iteration algorithm for computing the geometry and texture of images defined by iterated function system codes. Also, the underlying mathematical framework, where these two algorithms have their roots, is outlined. The algorithms are illustrated by showing how they can be used to produce images of clouds, mist and surf, seascapes and landscapes and even faces, all modeled from original photographs. The reasons for developing iterated function systems algorithms include their ability to produce complicated images and textures from small databases, and their potential for highly parallel implementation.
A Replicating RNA Molecule Suitable for a Detailed Analysis of Extracellular Evolution and Replication (1972)

The aim of the present study is to make available a replicating molecule of known sequence. Accordingly, we sought a molecule that has the following properties: (a) replicates in vitro in a manner similar to phage Qbeta RNA; (b) produces antiparallel complementary strands that can be separated from one another; and (c) is small enough to yield its sequence with reasonable effort. We report here the isolation of a replicating RNA molecule that contains 218 nucleotides and possesses the other features desired for a definitive analysis of the replicating mechanism. Despite its small size, this molecule can mutate to previously determined phenotypes. It will, therefore, permit the precise identification of the base changes required to mutate from one phenotype to another in the course of extracellular Darwinian selection experiments.
COP9: a new genetic locus involved in light-regulated development and gene expression in arabidopsis. (1992)

We report here the identification and characterization of a new Arabidopsis light-regulatory locus, COP9, mutation that leads to a constitutive photomorphogenic phenotype. Dark-grown cop9 seedlings exhibit many morphological characteristics of light-grown seedlings, including short hypocotyls and open and enlarged cotyledons with cell-type and chloroplast differentiation. Furthermore, the cop9 mutation leads to high-level expression of light-inducible genes in the absence of light, probably by altering the promoter activities of these genes. These properties imply that the mutation in the COP9 locus uncouples the light/dark signals from morphogenesis and light-regulated gene expression. In addition, light-grown cop9 mutants are severely dwarfed and are unable to reach maturation and flowering. This adult-lethal phenotype indicates that the COP9 locus also plays a critical role for normal development of the light-grown plant. Similar to cop1 mutants, but not det1, the cop9 mutants show (1) no effect on the phytochrome control of seed germination and (2) deficiency in the dark-adaptive change of expression of light-regulated genes. Our results suggest that the cop9 and cop1 mutations result in the same range of phenotypes and therefore COP9 and COP1 loci may encode closely related components in the same regulatory pathway.
Characterization of mesenchymal stem cells isolated from murine bone marrow by negative selection (2003)

Abstract Mesenchymal stem cells (MSCs) are typically enriched from bone marrow via isolation of the plastic adherent, fibroblastoid cell fraction. However, plastic adherent cultures elaborated from murine bone marrow are an admixture of fibroblastoid and hematopoietic cell types. Here we report a reliable method based on immunodepletion to fractionate fibroblastoid cells from hematopoietic cells within plastic adherent murine marrow cultures. The immunodepleted cells expressed the antigens Sca‐1, CD29, CD44, CD81, CD106, and the stem cell marker nucleostemin (NST) but not CD11b, CD31, CD34, CD45, CD48, CD90, CD117, CD135, or the transcription factor Oct‐4. They were also capable of differentiating into adipocytes, chondrocytes, and osteoblasts in vitro as well as osteoblasts/osteocytes in vivo. Therefore, immunodepletion yields a cell population devoid of hematopoietic and endothelial cells that is phenotypically and functionally equivalent to MSCs. The immunodepleted cells exhibited a population doubling time of approximately 5–7 days in culture. Poor growth was due to the dramatic down regulation of many genes involved in cell proliferation and cell cycle progression as a result of immunodepletion. Exposure of immunodepleted cells to fibroblast growth factor 2 (FGF2) but not insulin‐like growth factor (IGF), murine stem cell factor, or leukemia inhibitory factor (LIF) significantly increased their growth rate. Moreover, 82% of the transcripts down regulated by immunodepletion remain unaltered in the presence of FGF2. Exposure to the later also reversibly inhibited the ability of the immunodepleted cells to differentiate into adipocytes, chondrocytes, and osteoblasts in vitro. Therefore, FGF2 appears to function as a mitogen and self‐maintenance factor for murine MSCs enriched from bone marrow by negative selection. © 2003 Wiley‐Liss, Inc.