gebhart/patrepeval huggingface dataset:
T Cellâ€“Macrophage Interactions and Granuloma Formation in Vasculitis (2014)

Granuloma formation, bringing into close proximity highly activated macrophages and T cells, is a typical event in inflammatory blood vessel diseases, and is noted in the name of several of the vasculitides. It is not known whether specific properties of the microenvironment in the blood vessel wall or the immediate surroundings of blood vessels contribute to granuloma formation and, in some cases, generation of multinucleated giant cells. Granulomas provide a specialized niche to optimize macrophage-T cell interactions, strongly activating both cell types. This is mirrored by the intensity of the systemic inflammation encountered in patients with vasculitis, often presenting with malaise, weight loss, fever, and strongly upregulated acute phase responses. As a sophisticated and highly organized structure, granulomas can serve as an ideal site to induce differentiation and maturation of T cells. The granulomas possibly seed aberrant Th1 and Th17 cells into the circulation, which are known to be the main pathogenic cells in vasculitis. Through the induction of memory T cells, aberrant innate immune responses can imprint the host immune system for decades to come and promote chronicity of the disease process. Improved understanding of T cell-macrophage interactions will redefine pathogenic models in the vasculitides and provide new avenues for immunomodulatory therapy.
Neoplastic differentiation: Interaction of simian virus 40 and polyoma virus with murine teratocarcinoma cells in vitro (1975)

The host-virus interactions of Simian virus 40 (SV40) and polyoma virus (Py) with cell lines established from a teratocarcinoma were studied. The cells utilized in this study were the multipotential stem cell of the teratocarcinoma, embryonal carcinoma, and differentiated cells derived from embryonal carcinoma. Several lines of differentiated cells were established in vitro which included parietal yolk sac, epithelial, and spindle cell types. Embryonal carcinoma cells are not susceptible to infection by either SV40 or Py virus. However, differentiated cells are susceptible to infection by these viruses. The differentiated cells are permissive for Py virus replication and nonpermissive for SV40. Several continuously growing cell lines have been established from the SV40 infected cultures which express T antigen in 100% of the cells. The results indicate that undifferentiated embryonal carcinoma cells and their differentiated progeny respond quite differently to challenge with these two oncogenic DNA viruses.
Protection of the gastric mucosa by linoleic acid--a nutrient essential fatty acid. (1987)

We studied whether linoleic acid, a precursor for arachidonic acid and prostaglandins, could protect the gastric mucosa against ethanol-induced injury. Fasted male rats received intragastric pretreatment with 1 ml of one of: a) solubilizer; b) solubilized linoleic acid (74 mg); or c) solubilized oleic acid (74 mg) (a nonessential fatty acid). One hour later, 2 ml 100% ethanol was given intragastrically. Three hours after ethanol administration, the gastric mucosa was assessed for gross necrosis and for histologic changes. Three hours after ethanol administration in solubilizer, pretreated-group gross mucosal necrosis involved 35 +/- 3% of total mucosal area, while deep histologic necrosis involved 52 +/- 4% of the mucosal strip length. Pretreatment with linoleic acid (but not oleic acid) significantly reduced gross histologic necrosis, to 2.3 +/- 0.5%, and deep histologic necrosis to 4 +/- 2% (both p less than 0.001 versus solubilizer group). The protective action of linoleic acid was significantly reduced (greater than 10-fold) by pretreatment with indomethacin (prostaglandins synthetase inhibitor), suggesting prostaglandins as mediators of protection. The present study showed that effective protection of the gastric mucosa against ethanol injury can be achieved by intragastric administration of linoleic acid, a dietary essential fatty acid.
Expression of the IP3R1 promoter‐driven nls‐lacZ transgene in Purkinje cell parasagittal arrays of developing mouse cerebellum (2010)

The cerebellar Purkinje cell monolayer is organized into heterogeneous Purkinje cell compartments that have different molecular compositions. Here we describe a transgenic mouse line, 1NM13, that shows heterogeneous transgene expression in parasagittal Purkinje cell arrays. The transgene consists of a nuclear localization signal (nls) fused to the beta-galactosidase (lacZ) composite gene driven by the type 1 inositol 1,4,5-trisphosphate receptor (IP(3)R1) gene promoter. IP(3)R1-nls-lacZ transgene expression was detected at a single Purkinje cell level over the surface of a whole-mount X-gal-stained cerebellum because of nuclear accumulation of the nls-lacZ activity. Developing cerebella of 1NM13 mice showed stripe-like X-gal staining patterns of parasagittal Purkinje cell subsets. The X-gal stripe pattern was likely determined by an intrinsic property as early as E15 and showed increasing complexity with cerebellar development. The X-gal stripe pattern was reminiscent of, but not identical to, the stripe pattern of zebrin II immunoreactivity. We designated the symmetrical X-gal-positive (transgene-positive, Tg(+)) Purkinje cell stripes about the midline as vermal Tg1(+), Tg2(a, b)(+) and Tg3(a, b)(+) stripes and hemispheric Tg4(a, b)(+), Tg5(a, b)(+), Tg6(a, b, c)(+), and Tg7(a, b)(+) stripes, where a, b, and c indicate substripes. We also assigned three parafloccular substripes Tg8(a, b, c)(+). The boundaries of X-gal stripes at P5 were consistent with raphes in the Purkinje cell layer through which granule cells migrate, suggesting a possible association of the X-gal stripes with raphe formation. Our results indicate that 1NM13 is a good mouse model with a reproducible and clear marker for the compartmentalization of Purkinje cell arrays.
Targeting BCL11A and KLF1 For The Treatment Of Sickle Cell Disease and β-Thalassemia In Vitro using Antisense Oligonucleotides (2013)

Abstract Sickle cell anemia (SCD) is a hereditary blood disorder in which red blood cells (RBC) become sickle-shaped and block blood vessels, leading to painful vaso-occlusive episodes. Sickling occurs because of a point-mutation in the β-globin gene of hemoglobin. Fetal hemoglobin (HbF, α2γ2) is the main oxygen transport protein with greater oxygen binding affinity in the fetus during the last months of embryonic development and the first few months of life after birth. HbF inhibits sickling by interfering with the polymerization of hemoglobin S. Higher HbF levels in SCD correlate with better survival and because HbF production can be reactivated pharmacologically in adults, it can be used for the treatment of SCD as well as β-thalassemia. In β-thalassemia, there is reduced or absent synthesis of the β-globin gene, causing ineffective erythropoiesis. B-cell lymphoma/leukemia 11A (BCL11A) is a transcription factor in the zinc-finger protein family and is expressed in B cells and erythroid cells. BCL11A represses fetal hemoglobin expression by binding to the GGCCCGG motif in the β-globin promoter region. Erythroid Kruppel-like factor (KLF1) is an erythroid-specific transcription factor that regulates β-globin expression through direct interaction with its promoter and indirectly regulates γ-globin expression through the regulation of BCL11A. By reducing the expression of BCL11A and KLF1, we can promote production of HbF through the upregulation of γ-globin expression. To demonstrate upregulation of γ-globin mRNA expression in vitro, we used MEL-h-b-BAC line#7 cells, a murine erythroleukemic cell line harboring the entire human beta globin locus and expressing mouse BCL11A and KLF1 (Tim Townes, Univ. of Alabama at Birmingham). Antisense oligonucleotides (ASOs) targeting mouse BCL11A or mouse KLF1 were added to the cells in a dose-dependent manner. Seven days later, with free uptake of the ASOs into the cells, we observed dose-dependent reduction of mouse BCL11A mRNA (IC50 = 0.7 μM) and mouse KLF1 mRNA (IC50 = 3 μM). Consequently, we observed a 300 +/- 8% upregulation of human γ-globin mRNA expression after achieving ∼90% reduction in BCL11A mRNA expression after ASO treatment compared to the untreated control cells. Similarly, KLF1 ASO treatment caused a 500 +/- 58% up regulation of human γ-globin mRNA expression after achieving ∼80% mRNA reduction in KLF expression. These data indicate that targeting BCL11A and/or KLF1 with ASO treatment can cause an increase in γ-globin expression that is necessary for the upregulation of fetal hemoglobin and may be used for the treatment of sickle-cell anemia and β-thalassemia. Disclosures: Peralta: Isis Pharmaceuticals, Inc.: Employment. Low: Isis Pharmaceuticals, Inc.: Employment. Kim: Isis Pharmaceuticals, Inc.: Employment. Murray: Isis Pharmaceuticals, Inc.: Employment. Guo: Isis Pharmaceuticals, Inc.: Employment. Freier: Isis Pharmaceuticals, Inc.: Employment. Townes: University of Alabama at Birmingham: Employment. Hung: Isis Pharmaceuticals, Inc.: Employment.
Irinotecan Plus Oxaliplatin and Leucovorin-Modulated Fluorouracil in Advanced Pancreatic Cancer—A Groupe Tumeurs Digestives of the Fédération Nationale des Centres de Lutte Contre le Cancer Study (2005)

With a good safety profile, a promising response rate, and an improvement in QOL, Folfirinox will be further assessed in a phase III trial.
Surface Chemistry of Gold Nanoparticles Produced by Laser Ablation in Aqueous Media (2004)

The femtosecond laser ablation of a gold target in aqueous solutions has been used to produce colloidal Au nanoparticles with controlled surface chemistry. A detailed chemical analysis showed that the nanoparticles formed were partially oxidized by the oxygen present in solution. The hydroxylation of these Au−O compounds, followed by a proton loss to give surface Au−O-, resulted in the negative charging of the nanoparticles. The partial oxidation of the gold nanoparticle surface enhances its chemical reactivity and consequently has a strong impact on its growth. In particular, the oxidized surface reacted efficiently with Cl- and OH- to augment its net surface charge. This limited the coalescence of the particles, due to electrostatic repulsion, and led to a significant reduction of their size. Taking advantage of the repulsion effect, efficient size control was achieved using different salts (7 ± 5 nm for 10 mM KCl, 5.5 ± 4 nm for 10 mM NaCl, 8 ± 5 nm for NaOH, pH 9.4), a considerable improvement comparatively to particles prepared in deionized water, using identical ablation conditions, where particles of 1−250 nm were produced. The partially oxidized gold surface was also suitable for surface modification through both covalent and electrostatic interactions during particle formation. Using solutions of N-propylamine, we showed an efficient control of nanoparticle size (5−8 ± 4−7 nm) by the involvement of these interactions. The results obtained help to develop methodologies for the control of laser-ablation-based nanoparticle growth and the functionalization of nanoparticle surfaces by specific interactions.
Purification and characterization of recombinant human leukocyte interferon (IFLrA) with monoclonal antibodies. (1981)

Recombinant human leukocyte interferon produced in bacteria (IFLrA) was purified to homogeneity with the use of monoclonal antibodies against leukocyte interferon. The purified interferon exhibited a single band of Mr = approximately 19,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Amino acid analysis and the NH2-terminal sequence were consistent with the sequence predicted from the DNA. Some of the purified product contained NH2-terminal methionine; the terminal methionine was removed from the rest of the chains.
Liquid Corn and Fish Fertilizers Are Good Options for Fertigation in Blackberry Cultivars Grown in an Organic Production System (2015)

The impact of organic fertilizer source on the growth, fruit quality, and yield of blackberry ( Rubus L. subgenus Rubus Watson) cultivars (Marion and Black Diamond) grown in a machine-harvested, organic production system for the processed market was evaluated from 2011 to 2013. The planting was established in Spring 2010 using approved practices for organic production and was certified in 2012. Plants were irrigated using a dripline under a woven polyethylene groundcover (weed mat) installed for weed management. Two sources of liquid fertilizer were evaluated: 1) a corn steep liquor and fish waste digestion blend (“corn”; 2.5N–1.1P–1.2K); and 2) a fish solubles and molasses blend (“fish”; 4N–0P–1.7K). Fertilizers were applied by fertigation through the drip system at rates of 56 kg·ha −1 nitrogen (N) per year in 2011–12 and 90 kg·ha −1 N in 2013. The impact of fertigation on drip system performance was evaluated with two maintenance options, “flushing” and “no flushing” of the driplines. Total yield differed among years, whereas fruit soluble solids concentration and firmness as well as floricane biomass at pruning showed a year × cultivar interaction. ‘Black Diamond’ had greater total yield and average fruit weight than ‘Marion’, but produced a greater proportion unmarketable fruit. There was no effect of fertilizer source on yield, fruit quality, primocane length, or primocanes/plant in any year with the exception of fruit weight, which was greater with corn than with fish. ‘Marion’ had a greater floricane biomass when fertilized with fish than with corn. Soil nutrients were within the recommended range, except for boron (B), which was below recommended levels. Only soil nitrate-N was affected by fertilizer source, which was greater in ‘Marion’ than in ‘Black Diamond’ when fertilized with fish. Primocane leaf tissue nutrient concentrations were within recommended levels for all nutrients, except for calcium (Ca) and B, which were below recommended standards in both cultivars. Primocane leaf potassium (K) and zinc (Zn) concentrations were greater with fish than with corn. There was no fertilizer source or maintenance effect on emitter flow rate of the drip system in either year. However, flow rates decreased an average of 4.5% in the first year and 19% in the second year. Overall, there were no differences between the fertilizers on plant growth, yield, or fruit quality, and both fertilizers were suitable for planting establishment.
Incorporating background frequency improves entropy-based residue conservation measures (2006)

Our results suggest that the application of appropriate background frequency information may lead to more biologically relevant results in many areas of bioinformatics.
A New Calculus for the Treatment of Optical Systems IV (1942)

Part IV is divided into two sections. The first is devoted to some additions to the general theory developed in Part I, and the second section to the derivation of the matrices representing two optical elements which were not treated in Parts II and III: (1) plates possessing circular dichroism, and (2) plates cut from crystals of such low symmetry that the principal axes of absorption and refraction are not parallel. In case (2), the discussion is limited to monoclinic and triclinic crystals which do not possess optical activity.
Common-path interferometer for frequency-domain optical coherence tomography (2003)

A Michelson-type spectral interferometer that uses a common beam path for the reference and the sample arms is described. This optical arrangement is more compact and stable than the more commonly used dual-arm interferometer and is well suited for frequency-domain optical coherence tomography of biological samples. With a 16-bit CCD camera, the instrument has sufficient dynamic range and resolution for imaging to depths of 2 mm in scattering biological materials. Images obtained with this spectral interferometer are presented, including cross-sectional images in a Xenopus laevis tadpole.
Air-Stable Single-Source Precursors for the Synthesis of Chalcogenide Semiconductor Nanoparticles (2001)

Bis(hexylmethyldithio-/diselenocarbamato)cadmium(II)/zinc(II) (M(E2CNMenHex)2 [M = Zn, Cd; E = S, Se]) have been used as single-source precursors for the preparation of TOPO-capped CdS, CdSe, ZnS, and ZnSe nanoparticles. The precursors are stable for long periods of time and pyrolyse cleanly to give high yields of nanocrystals. The nanoparticles were of high quality, close to monodispersed, and showed quantum confinement with characteristic close to band edge luminescence in their emission spectra. The broad diffraction in the XRD pattern and diffuse diffraction rings of the SAED pattern are typical of nanometric size particles. The TEM micrographs showed well-defined, close to spherical particles and the lattice fringes in the HRTEM images confirmed the crystalline nature. The presence of a strong phosphorus peak in the EDAX spectra is indicative of TOPO or TOPE (E = S or Se) bound to the surface.
Stem Cell Research: A Target Article Collection Part III - Determining Moral Status (2002)

In this chapter, I review some of the background thinking concerning matters of moral status that I had developed in previous years and that I would now bring to the work of the Human Embryo Research Panel. Two ideas were at the forefront of my thinking. First, that biology usually offers not decisive "events" but only continuous processes of development. Second, in making status determinations we do not so much "identify" a point on a developmental continuum where moral respect should be accorded as "choose" that point. These choices are "balancing decisions" in which the community of moral agents weighs its interests in protecting an entity against the burdens of doing so. After illustrating these two contentions, I consider some of the reasons why thinkers on the "right" and "left" of our bioethics debates have resisted or missed this basic insight.
U.S. Lighting Market Characterization Volume II: Energy Efficient Lighting Technology Options (2005)

Multiyear study to evaluate light sources and identify opportunities for saving energy. This report looks broadly at energy-efficient options in lighting and identifies leading opportunities.
Serotonin Receptor Activation Inhibits Sodium Current and Dendritic Excitability in Prefrontal Cortex via a Protein Kinase C-Dependent Mechanism (2002)

The serotonin (5-HT) innervation of the prefrontal cortex (PFC) exerts a powerful modulatory influence on neuronal activity in this cortical region, although the mechanisms through which 5-HT modulates cellular activity are unclear. Voltage-dependent Na+ channels are one potential target of 5-HT receptor signaling that have wide-ranging effects on activity. Molecular and electrophysiological studies were used to test this potential linkage. Single cell RT-PCR profiling revealed that the vast majority of pyramidal neurons expressed detectable levels of 5-HT2a and/or 5-HT2c receptor mRNA with half of the cells expressing both mRNAs. Whole-cell voltage-clamp recordings of dissociated pyramidal neurons showed that 5-HT2a/c receptor activation reduced rapidly inactivating Na+ currents by reducing maximal current amplitude and shifting fast inactivation voltage dependence. These effects were mediated by G(q) activation of phospholipase C, leading to activation of protein kinase C (PKC). 5-HT2a/c receptor stimulation also reduced the amplitude of persistent Na+ current without altering its activation voltage dependence. This modulation was also mediated by PKC. Although 5-HT(2a,c) receptor activation did not affect somatic action potentials of layer V pyramidal neurons in PFC slices, it did reduce the amplitude of action potentials backpropagating into the apical dendrite. These findings show that 5-HT2a,c receptor activation reduces dendritic excitability and may negatively modulate activity-dependent dendritic synaptic plasticity.
Zinc and DNA Binding Properties of a Novel LIM Homeodomain Protein Isl-2 (1994)

LIM homeodomain proteins are a family of recently characterized proteins which contain, in addition to a homeodomain, two tandem repeats of conserved Cys-His motifs termed as LIM domains. We have recently isolated several clones from a chinook salmon pituitary cDNA library that encode two novel LIM homeodomain proteins, Isl-2 and Isl-3, which are structurally related to rat Isl-1. In the present study, we used the salmon Isl-2 to determine the role of LIM domains in DNA binding. Several glutathione S-transferase (GST) fusion proteins containing either full length Isl-2 or various portions of this protein were expressed in bacteria. Zinc blot analysis reveals that the LIM domains produced in bacteria are capable of binding zinc. Gel shift analysis indicates that all homeodomain-containing fusion proteins are able to bind to a TAAT target sequence while the fusion proteins containing only the LIM domain are not. In contrast to a previous observation that the LIM domains of rat Isl-1 have an inhibitory role in DNA binding, full length salmon Isl-2 containing both the LIM domains and a homeodomain can bind to a TAAT target sequence. To further examine the role of LIM domains in DNA binding, several GST fusion proteins were used to select specific target DNA sequences from a pool of randomly incorporated oligonucleotides. Specific target DNAs were selected by fusion proteins containing the homeodomain or the full length Isl-2, but not by LIM domain only fusion proteins, indicating that the LIM domain alone is not involved in DNA binding. The selected target DNAs were cloned and sequenced. They revealed two classes of consensus, C/TTAATG/TG/A and C/TTAAGTG, for both the homeodomain and full length Isl-2. The two classes of consensus competed with each other for binding to the homeodomain. The equilibrium dissociation constants for DNA binding, estimated by Scatchard analysis, were similar for the homeodomain and full length Isl-2.(ABSTRACT TRUNCATED AT 400 WORDS)
Genetic engineering of vein grafts resistant to atherosclerosis. (1995)

Previously, researchers have speculated that genetic engineering can improve the long-term function of vascular grafts which are prone to atherosclerosis and occlusion. In this study, we demonstrated that an intraoperative gene therapy approach using antisense oligodeoxynucleotide blockage of medial smooth muscle cell proliferation can prevent the accelerated atherosclerosis that is responsible for autologous vein graft failure. Selective blockade of the expression of genes for two cell cycle regulatory proteins, proliferating cell nuclear antigen and cell division cycle 2 kinase, was achieved in the smooth muscle cells of rabbit jugular veins grafted into the carotid arteries. This alteration of gene expression successfully redirected vein graft biology away from neointimal hyperplasia and toward medial hypertrophy, yielding conduits that more closely resembled normal arteries. More importantly, these genetically engineered grafts proved resistant to diet-induced atherosclerosis. These findings establish the feasibility of developing genetically engineered bioprostheses that are resistant to failure and better suited to the long-term treatment of occlusive vascular disease.
Effects of lysine vasopressin and glypressin on the fibrinolytic system in cirrhosis. (1979)

In eight patients with cirrhosis of the liver and portal hypertension an intravenous infusion of lysine vasopressin induced a rapid increase in the plasma level of the fibrinolytic proenzyme plasminogen activator. In contrast, triglycyl lysine vasopressin (glypressin; GVP), in a dose known to lower portal venous pressure, produced no fibrinolytic response. This lack of fibrinolytic response represents an advantage of GVP over lysine vasopressin in addition to its longer in vivo half-life and lower cardiotoxicity. Clinical trials of GVP in the treatment of bleeding oesophageal varices are needed.