gebhart/patrepeval huggingface dataset:
Cytokines, Inflammation, and Pain (2007)

Cytokines are small secreted proteins released by cells have a specific effect on the interactions and communications between cells. Cytokine is a general name; other names include lymphokine (cytokines made by lymphocytes), monokine (cytokines made by monocytes), chemokine (cytokines with chemotactic activities), and interleukin (cytokines made by one leukocyte and acting on other leukocytes). Cytokines may act on the cells that secrete them (autocrine action), on nearby cells (paracrine action), or in some instances on distant cells (endocrine action). There are both pro-inflammatory cytokines and anti-inflammatory cytokines. There is significant evidence showing that certain cytokines/chemokines are involved in not only the initiation but also the persistence of pathologic pain by directly activating nociceptive sensory neurons. Certain inflammatory cytokines are also involved in nerve-injury/inflammation-induced central sensitization, and are related to the development of contralateral hyperalgesia/allodynia. The discussion presented in this chapter describes several key pro-inflammatory cytokines/chemokines and anti-inflammatory cytokines, their relation with pathological pain in animals and human patients, and possible underlying mechanisms.
High Titers of Cytopathic Virus in Plasma of Patients with Symptomatic Primary HIV-1 Infection (1991)

Primary, symptomatic HIV-1 infection is associated with high titers of cytopathic, replication-competent viral strains, and during such infection potential infectivity is enhanced. Effective control of HIV-1 replication during primary infection implies the activation of clinically important mechanisms of immune defense that merit further examination in relation to the development of antiviral therapy and vaccines.
Interactive tactile maps, visual disability, and accessibility of building interiors (1999)

Objectives: To test the feasibility of interactive tactile maps as a public intervention for the effects of severe vision loss on the loss of travel independence in building interiors. Methods: An ...
Technologies for exascale systems (2011)

To satisfy the economic drive for ever more powerful computers to handle scientific and business applications, new technologies are needed to overcome the limitations of current approaches. New memory technologies will address the need for greater amounts of data in close proximity to the processors. Three-dimensional silicon integration will allow more cache and function to be integrated with the processor while allowing more than 1,000 times higher bandwidth communications at low power per channel using local interconnects between Si die layers and between die stacks. Integrated silicon nanophotonics will provide low-power and high-bandwidth optical interconnections between different parts of the system on a chip, board, and rack levels. Highly efficient power delivery and advanced liquid cooling will reduce the electrical demand and facility costs. A combination of these technologies will likely be required to build exascale systems that meet the combined challenges of a practical power constraint on the order of 20 MW with sufficient reliability and at a reasonable cost.
Effect of recombinant human granulocyte colony-stimulating factor on hematopoiesis of normal dogs and on hematopoietic recovery after otherwise lethal total body irradiation (1989)

This study was designed to test whether recombinant human G-CSF (rh G- CSF) affects hematopoiesis in normal dogs and, if so, to test the effects of G-CSF in dogs given otherwise lethal total body irradiation (TBI). Rh G-CSF given subcutaneously at 10 or 100 micrograms/kg/d for 14 days to two normal dogs increased peripheral blood neutrophils eight to tenfold and monocytes four to sixfold above controls. Lymphocyte counts remained unchanged at the lower dose and increased threefold at the higher dose of rh G-CSF. No significant changes were observed in eosinophil, platelet, reticulocyte, or hematocrit levels. After 2 weeks of treatment with rh G-CSF, bone marrow displayed myeloid hyperplasia and left-shifted granulocytopoiesis. After discontinuation of rh G-CSF, peripheral leukocyte counts returned to control levels within three days. Five dogs administered 400 cGy TBI at 10 cGy/min from two opposing 60Co sources and no marrow infusion or growth factor, all developed profound pancytopenia and died between 17 and 23 days after TBI with infections secondary to marrow aplasia. Four of five dogs treated within two hours after 400 cGy TBI with 100 micrograms rh G- CSF/kg/d subcutaneously twice a day for 21 days showed complete and sustained endogenous hematopoietic recovery. In contrast, five dogs irradiated with 400 cGy TBI and treated with 100 micrograms rh G- CSF/kg/d starting on day 7 after TBI, all died between days 17 and 20 after TBI with infections secondary to marrow aplasia. Rh G-CSF, if administered shortly after irradiation, can reverse the otherwise lethal myelosuppressive effect of radiation exposure.
Microwave sterilization of plastic tissue culture vessels for reuse (1982)

A simple protocol has been developed for recycling plastic tissue culture vessels. The killing properties of microwaves were used to decontaminate plastic tissue culture vessels for reuse. Nine bacterial cultures, four gram-negative and five gram-positive genera, including two Bacillus species, were used to artificially contaminate tissue culture vessels. The microwaves produced by a "home-type" microwave oven (2.45 gHz) were able to decontaminate the vessels with a 3-min exposure. The same exposure time was also used to completely inactivate the following three test viruses: polio type 1, parainfluenza type 1 (Sendai), and bacteriophage T4. The recycling procedure did not reduce the attachment and proliferation of the following cell types: primary chicken and turkey embryo, HEp-2, Vero, BGMK, and MK-2.
Linear Rheology of Polyolefin-Based Bottlebrush Polymers (2015)

Two series of polyolefin-based bottlebrush polymers were synthesized using ring-opening metathesis polymerization of norbornenyl-functionalized macromonomers to compare the rheology of systems with and without the presence of side chain entanglement. The first series of bottlebrushes includes atactic polypropylene (aPP) branches with a fixed length of Mbranch = 2.05 kg/mol and variable backbone degree of polymerization ranging from 11 to 732 (Mw = 22–1500 kg/mol). The branches in this series are shorter than the entanglement molecular weight of aPP (Mbranch/Me ≈ 0.5). The second series utilizes poly(ethylene-alt-propylene) (PEP) branches with Mbranch = 6.7 kg/mol and variable backbone degree of polymerization ranging from 13 to 627 (Mw = 89–4200 kg/mol). The branches in this series exceed the entanglement molecular weight of PEP (Mbranch/Me ≈ 3.5). The linear viscoelastic responses of each sample were examined using small-amplitude oscillatory shear measurements, and dynamic master curves were constructed by time–temperature superposition. Master curves of all aPP bottlebrush polymers exhibited relaxation spectra devoid of any entanglement plateau, despite their high molecular weight. Master curves of the PEP bottlebrushes displayed rubbery plateau regions at short relaxation times, indicating successful entanglement formation between PEP branches. The scaling behavior of the master curves reveals a transient power law scaling throughout the relaxation process. The dynamics are more Zimm-like at early relaxation times and become increasingly Rouse-like at long relaxation times. This transition arises due to the changing conformational character of bottlebrushes at different length scales. Finally, plots of the phase angle versus complex modulus revealed additional intrinsic characteristics of the bottlebrush polymers: (i) the presence of two distinct relaxation processes corresponding to the motion of side chains and of the backbone and (ii) the onset of thermorheological complexity as the glass transition temperature was approached. These two observations represent inherent material properties that are individually governed by the macromolecular architecture and by the monomer scale chemistry, respectively.
The Roles of the Subunits in the Function of the Calcium Channel (1991)

Dihydropyridine-sensitive voltage-dependent L-type calcium channels are critical to excitation-secretion and excitation-contraction coupling. The channel molecule is a complex of the main, pore-forming subunit alpha 1 and four additional subunits: alpha 2, delta, beta, and gamma (alpha 2 and delta are encoded by a single messenger RNA). The alpha 1 subunit messenger RNA alone directs expression of functional calcium channels in Xenopus oocytes, and coexpression of the alpha 2/delta and beta subunits enhances the amplitude of the current. The alpha 2, delta, and gamma subunits also have pronounced effects on its macroscopic characteristics, such as kinetics, voltage dependence of activation and inactivation, and enhancement by a dihydropyridine agonist. In some cases, specific modulatory functions can be assigned to individual subunits, whereas in other cases the different subunits appear to act in concert to modulate the properties of the channel.
Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia (2004)

Clostridium cellulolyticum ATCC 35319 is a non-ruminal mesophilic cellulolytic bacterium originally isolated from decayed grass. As with most truly cellulolytic clostridia, C. cellulolyticum possesses an extracellular multi-enzymatic complex, the cellulosome. The catalytic components of the cellulosome release soluble cello-oligosaccharides from cellulose providing the primary carbon substrates to support bacterial growth. As most cellulolytic bacteria, C. cellulolyticum was initially characterised by limited carbon consumption and subsequent limited growth in comparison to other saccharolytic clostridia. The first metabolic studies performed in batch cultures suggested nutrient(s) limitation and/or by-product(s) inhibition as the reasons for this limited growth. In most recent investigations using chemostat cultures, metabolic flux analysis suggests a self-intoxication of bacterial metabolism resulting from an inefficiently regulated carbon flow. The investigation of C. cellulolyticum physiology with cellobiose, as a model of soluble cellodextrin, and with pure cellulose, as a carbon source more closely related to lignocellulosic compounds, strengthen the idea of a bacterium particularly well adapted, and even restricted, to a cellulolytic lifestyle. The metabolic flux analysis from continuous cultures revealed that (i) in comparison to cellobiose, the cellulose hydrolysis by the cellulosome introduces an extra regulation of entering carbon flow resulting in globally lower metabolic fluxes on cellulose than on cellobiose, (ii) the glucose 1-phosphate/glucose 6-phosphate branch point controls the carbon flow directed towards glycolysis and dissipates carbon excess towards the formation of cellodextrins, glycogen and exopolysaccharides, (iii) the pyruvate/acetyl-CoA metabolic node is essential to the regulation of electronic and energetic fluxes. This in-depth analysis of C. cellulolyticum metabolism has permitted the first attempt to engineer metabolically a cellulolytic microorganism.
Efficient Cellular Transformation by the Met Oncoprotein Requires a Functional Grb2 Binding Site and Correlates with Phosphorylation of the Grb2-associated Proteins, Cbl and Gab1 (1997)

The Tpr-Met oncoprotein consists of the catalytic kinase domain of the hepatocyte growth factor/scatter factor receptor tyrosine kinase (Met) fused downstream from sequences encoded by the tpr gene. Tpr-Met is a member of a family of tyrosine kinase oncoproteins generated following genomic rearrangement and has constitutive kinase activity. We have previously demonstrated that a single carboxyl-terminal tyrosine residue, Tyr489, is essential for efficient transformation of Fr3T3 fibroblasts by Tpr-Met and forms a multisubstrate binding site for Grb2, phosphatidylinositol 3' kinase, phospholipase Cgamma, SHP2, and an unknown protein of 110 kDa. A mutant Tpr-Met protein that selectively fails to bind Grb2 has reduced transforming activity, implicating pathways downstream of Grb2 in Tpr-Met mediated cell transformation. We show here that the 110-kDa Tpr-Met substrate corresponds to the recently identified Grb2-associated protein, Gab1. Moreover, we show that tyrosine phosphorylation of the Cbl protooncogene product as well as Gab1 required Tyr489 and correlated with the ability of Tpr-Met to associate with Grb2 and to transform cells, providing evidence that pathways downstream of Gab1 and/or Cbl may play a role in Tpr-Met-mediated cell transformation.
A dominant mutation to ricin resistance in Chinese hamster ovary cells induces UDP-GlcNAc:glycopeptide beta-4-N-acetylglucosaminyltransferase III activity. (1984)

A biochemical basis for the LEC10 mutant phenotype of Chinese hamster ovary cells has been identified. Independent LEC10 mutants, originally selected for resistance to the toxicity of ricin, have been shown to exhibit reduced binding of 125I-ricin at the cell surface. Although this is indicative of structural changes in cell-surface carbohydrates, labeling of plasma membranes with galactose oxidase/[3H]borohydride revealed no significant differences between mutant and parental cells. Alterations in the carbohydrates synthesized by LEC10 cells were, however, resolved by lectin-affinity chromatography of glycopeptides from the G glycoprotein of vesicular stomatitis virus (VSV) grown in LEC10. LEC10/VSV glycopeptides contain a fraction which is not bound to concanavalin A-Sepharose but is strongly retarded on E-PHA (erythroagglutinin from Proteus vulgaris)-agarose. In contrast, CHO/VSV glycopeptides or those from a LEC 10 revertant (R.LEC 10/VSV) do not contain carbohydrates with these properties. High-field 1H NMR spectroscopy of the novel LEC10/VSV carbohydrates showed that they are complex, biantennary structures containing N-acetylglucosamine in beta(1,4)-linkage to the beta-linked core mannose residue. The presence of these structures correlates with the expression of the enzyme responsible for the addition of this "bisecting" GlcNAc residue, UDP-GlcNAc:glycopeptide beta-4-N-acetylglucosaminyltransferase III (GlcNAc-TIII). Parental Chinese hamster ovary cells and the LEC10 revertant possess no detectable GlcNAc-TIII activity. The combined evidence suggests that the LEC10 mutation induces the expression of the GlcNAc-TIII enzyme in Chinese hamster ovary cells.
Isolation of a novel human alpha (1,3)fucosyltransferase gene and molecular comparison to the human Lewis blood group alpha (1,3/1,4)fucosyltransferase gene. Syntenic, homologous, nonallelic genes encoding enzymes with distinct acceptor substrate specificities. (1992)

Biochemical and genetic evidence indicates that the human genome may encode four or more distinct GDP-fucose:beta-D-N-acetylglucosaminide 3-alpha-L-fucosyltransferase (alpha(1,3)fucosyltransferase) activities. Genes encoding two of these activities have been previously isolated. These correspond to an alpha(1,3/1,4)fucosyltransferase thought to represent the human Lewis blood group locus and an alpha(1,3)fucosyltransferase expressed in the myeloid lineage. We report here the molecular cloning and expression of a third human alpha(1,3)fucosyltransferase gene, homologous to but distinct from the two previously reported human fucosyltransferase genes. When expressed in transfected mammalian cells, this gene determines expression of a fucosyltransferase capable of using N-acetyllactosamine to form the Lewis x epitope, and alpha(2,3)sialyl-N-acetyllactosamine to construct the sialyl Lewis x moiety. This enzyme shares 91% amino acid sequence identity with the human Lewis blood group alpha(1,3/1,4)fucosyltransferase, yet exhibits only trace amounts of alpha(1,4)fucosyltransferase activity. Polymerase chain reaction analyses were used to demonstrate that the gene is syntenic to the Lewis locus on chromosome 19. These analyses also excluded the possibility that this DNA segment represents an allele of the Lewis locus that encodes alpha(1,3)fucosyltransferase but not alpha(1,4)fucosyltransferase activity. These results are consistent with the hypothesis that this gene encodes the human "plasma type" alpha(1,3)fucosyltransferase, and suggest a molecular basis for a family of human alpha(1,3)fucosyltransferase genes.
Convolutional Neural Networks for Sentence Classification (2014)

We report on a series of experiments with convolutional neural networks (CNN) trained on top of pre-trained word vectors for sentence-level classification tasks. We show that a simple CNN with little hyperparameter tuning and static vectors achieves excellent results on multiple benchmarks. Learning task-specific vectors through fine-tuning offers further gains in performance. We additionally propose a simple modification to the architecture to allow for the use of both task-specific and static vectors. The CNN models discussed herein improve upon the state of the art on 4 out of 7 tasks, which include sentiment analysis and question classification.
Observations on the Intranasal Vaccination of Pregnant Cattle Against Infectious Bovine Rhinotracheitis and Parainfluenza-3 Virus Infection (1973)

SUMMARY A modified live-virus ( mlv ) vaccine for infectious bovine rhinotracheitis ( ibr ) was administered intranasally ( i.n .) to one group of 371 cattle, and an mlv-ibr vaccine combined with mlv -parainfluenza-3 ( pi -3) vaccine was administered i.n . to another group of 371 cattle. Of 157 pregnant cattle in the group given ibr vaccine alone, 4 (2.5%) aborted. Of 221 pregnant cattle in the group given ibr-pi -3 vaccine, 3 (1.4%) aborted. The abortions could not be attributed to the vaccination, and each vaccine was judged safe for pregnant cattle. Of the 742 cattle vaccinated, 566 were seronegative to ibr prior to vaccination; 558 (98.6%) of these had detectable ibr antibody 4 to 5 weeks after vaccination. Adverse postvaccinal reactions were not observed in 11 herds, but cattle in 1 herd given ibr-pi -3 vaccine experienced increased body temperatures, excessive nasal discharge, and slightly decreased milk production after vaccination.
Molecular cloning of a novel non-receptor tyrosine kinase, HYL (hematopoietic consensus tyrosine-lacking kinase). (1994)

We identified a novel non-receptor tyrosine kinase from a human megakaryoblastic cell line, UT-7, by means of a PCR-based cloning method. The HYL gene contained a SH2 and SH3 domain and a tyrosine kinase catalytic domain. The deduced amino acid sequence of the protein encoded by this gene was most homologous to CSK (c-src kinase). This gene and CSK shared some unique structural properties such as the absence of a myristylation signal and phosphorylation sites of tyrosine residues corresponding to tyrosines 416 and 527 of chicken p60c-src. Unlike CSK, the SH3 domain of HYL was unique since the ALYDY motif was absent. Northern blot analysis revealed a 2.2 kb transcript in various myeloid cell lines but not in adult tissues except for the brain and the lung, whereas CSK mRNA was ubiquitously expressed. The expression of HYL was upregulated when these myeloid cells were differentiated by induction with phorbol myristate acetate. We named this gene, hematopoietic consensus tyrosine-lacking kinase, HYL. The HYL gene was assigned to chromosome 19 at band p13. It is suggested that HYL plays a significant role in the signal transduction of hematopoietic cells.
Design of a Serial Communication Protocol and Bus Interface Chip for tactile Communications. (1999)

Tactile communication requires rapid data transfer along a common bus. The developed communication protocol and application-specific interface chip enable precise control of multiple tactile transmitters (tactors) to convey information to military users. This extrapolation of the Tactile Situation Awareness System developed by the Naval Aerospace Medical Research Laboratory uses a serial data bus and individual interface chips to communicate commands with a minimum number of conductors. This thesis develops the communication protocol and the design of the Tactor Interface Chip (TIC). This work also includes a computer-driven tactile array controller and Parallel Port Data Modulator for TIC testing and demonstration
Architecture with designer atoms: Simple theoretical considerations (2000)

The distinct electronic states of assemblies of metallic quantum dots are discussed in a simple approximation where each dot is mimicked as an "atom" that carries one valence electron. Because of their large size, the charging energy of the dots, I = energy required to add another electron, is much smaller than for ordinary atoms. The Coulomb blocking of charge migration is therefore easier to overcome. For the theory, however, this is a challenge, because ionic states, which are typically higher in energy, come down, so the density of electronic states is high, and special methods need to be adapted. Quantum dots are prepared by wet chemical methods and accordingly are not quite identical. They will have a size distribution that can be narrow (when the dots can be assembled into an ordered array) or broad. Other sources of disorder are packing imperfections, which are characteristic of a wider size distribution, ligand deformations, and chemical unevenness. Two experimental control parameters are the size of the dots and the spacing between them. We discuss the combined effects of the low charging energy and disorder and examine the distinct electronic phases that can be realized.
Homozygosity for prion protein alleles encoding glutamine-171 renders sheep susceptible to natural scrapie. (1994)

Natural scrapie has been viewed both as a recessive trait and as a contagious disease modulated by a host locus. To address this conundrum, we determined the structure of the sheep prion protein (PrP) gene, which contains three exons and extends over 20 kb of DNA. In the United States 86.4% of scrapie cases occur in Suffolk sheep, and within this breed 49 +/- 6% (+/- S.D., n = 69) of healthy animals carry one or more PrP alleles encoding Arg (R)-171. Four scrapie-affected sheep were homozygous for wild-type PrP open reading frames encoding the alternative Gln (Q)-171 allele. Analysis of additional cases revealed that all were Q/Q-171 homozygotes (n = 31), yielding a probability of 0.000004 that PrP genotype is unrelated to susceptibility. These data imply that homozygosity for Q-171 codons is necessary but not sufficient for the development of natural scrapie, echo reports of recessive manifestation, and parallel over-representation of PRNP codon 129 homozygotes in Creutzfeldt-Jakob disease of humans. Whereas progress has been substantial regarding experimental scrapie in rodents, the occurrence and spread of disease in flocks of sheep has remained enigmatic. Appreciation of the relationship between codon 171 genotype and susceptibility may help define the molecular basis of natural scrapie.
Cyclic ADP-ribose (cADPR) and Nicotinic Acid Adenine Dinucleotide Phosphate (NAADP): Novel Regulators of Ca 2+-Signaling and Cell Function (2002)

Ca2+ ions are involved in the regulation of many diverse functions in animal and plant cells, e.g. muscle contraction, secretion of neurotransmitters, hormones and enzymes, fertilization of oocytes, and lymphocyte activation and proliferation. The intracellular Ca2+ concentration can be increased by different molecular mechanisms, such as Ca2+ influx from the extracellular space or Ca2+ release from intracellular Ca2+ stores. Release from intracellular Ca2+ stores is accomplished by the small molecular compounds D-myo-inositol 1,4,5-trisphosphate (InsP3), cyclic ADP-ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate (NAADP). This review concentrates on (i) receptor-mediated formation of cADPR by ADP-ribosyl cyclases, (ii) intracellular and extracellular effects of cADPR in a variety of cell types, and (iii) cADPR in the nucleus. Though our understanding of the role of NAADP is still unclear in many aspects, important recent findings are reviewed, e.g. Ca2+ release activity and binding studies in mammalian cell types.