gebhart/patrepeval huggingface dataset:
Pharmacological survey of recombinant hirudin. (1988)

The pharmacological properties of a genetically engineered recombinant hirudin (r-hirudin) were studied in animal experiments. r-Hirudin proved to be a well tolerated substance. I.v. injection of up to 200 mg/kg did not lead to perceptible functional or morphological changes. There were no treatment-related effects on the cardiovascular system of dogs and rats after administration of up to 10 mg/kg. After long-term treatment (4 weeks, 1.0 mg/kg daily), no r-hirudin-related histopathological, haematological or biochemical changes could be found. Formation of antibodies was not detectable. Absorption, distribution, and elimination of r-hirudin were studied in dogs and rats. Pharmacokinetics could be best described by an open two-compartment model with first-order kinetics. After i.v. injection in dogs, r-hirudin is distributed into the extracellular space and eliminated through the kidneys in active form by glomerular filtration. After i.v. administration, a half-life of about 1 h was estimated; s.c. administration prolonged the apparent half-life. Pulmonary absorption was shown. Enteral absorption, placental transfer as well as transfer through the fetal integument were very low. r-Hirudin did not pass the blood-brain barrier. The efficacy of r-hirudin in preventing both venous and arterial thrombosis, vascular shunt occlusion or disseminated intravascular coagulation was demonstrated in rats. Depending on the dose, r-hirudin was able to prevent or reduce stasis-induced venous thrombosis, prolong the patency of an extracorporeal arteriovenous shunt, reduce the incidence of arterial thrombosis caused by vascular wall lesions as well as of microthrombosis induced by thrombin infusion.(ABSTRACT TRUNCATED AT 250 WORDS)
GILZ Promotes Production of Peripherally Induced Treg Cells and Mediates the Crosstalk between Glucocorticoids and TGF-β Signaling (2014)

Regulatory T (Treg) cells expressing the transcription factor forkhead box P3 (FoxP3) control immune responses and prevent autoimmunity. Treatment with glucocorticoids (GCs) has been shown to increase Treg cell frequency, but the mechanisms of their action on Treg cell induction are largely unknown. Here, we report that glucocorticoid-induced leucine zipper (GILZ), a protein induced by GCs, promotes Treg cell production. In mice, GILZ overexpression causes an increase in Treg cell number, whereas GILZ deficiency results in impaired generation of peripheral Treg cells (pTreg), associated with increased spontaneous and experimental intestinal inflammation. Mechanistically, we found that GILZ is required for GCs to cooperate with TGF-β in FoxP3 induction, while it enhances TGF-β signaling by binding to and promoting Smad2 phosphorylation and activation of FoxP3 expression. Thus, our results establish an essential GILZ-mediated link between the anti-inflammatory action of GCs and the regulation of TGF-β-dependent pTreg production.
Symmetry modes and stiffnesses for bimanual rehabilitation (2011)

Bimanual rehabilitation devices show promise for use in low cost trainers for home use. To gain a better understanding of the symmetry modes and coupling stiffnesses that would be beneficial for home use bimanual trainers, we conducted a haptic tracking task. Participants used one hand to recreate the trajectory applied by a robot to the other hand using three bimanual symmetry modes. The participants recreated visual symmetry and joint space (mirror) symmetry more easily than point mirror symmetry. Joint space symmetry was the easiest mode when the trajectory was an increasing chirp frequency function. The stiffness between the robot and one hand affected the coordination between both hands and stiffnesses of 200-700 N/m enabled better tracking than 50 N/m.
Gastrointestinal Absorption of Intact Proteins (1988)

There is now no reasonable doubt that small quantities of intact proteins do cross the gastrointestinal tract in animals and adult humans, and that this is a physiologically normal process required for antigen sampling by subepithelial immune tissue in the gut. It is too small to be nutritionally significant in terms of gross acquisition of amino-nitrogen, but since it has important implications relating to dietary composition it must receive consideration from nutritionists. The process of intact protein absorption occurs without eliciting harmful consequences for most individuals, but it appears likely that a small number of people absorbing these "normal" amounts may react idiosyncratically; also, some individuals may absorb excessive amounts, and they may suffer clinically significant consequences. Likewise, individuals with diminished absorption of intact protein may be at risk. Normal absorption probably occurs predominantly by transcellular endocytosis with some possible contribution by a route between cells; increased net entry of protein to the circulation may reflect (a) increased paracellular (intercellular) passage, (b) increased transcellular passage, and/or (c) decreased lysosomal proteolysis. Tests to distinguish among these possibilities are strongly desirable. Intact protein absorption may be involved in the pathogenesis of inflammatory bowel disease, "food allergies," and other diseases, including even major psychiatric disorders, but the current evidence is mainly indirect and suggestive. Great caution and careful objective studies are needed to establish whether such relationships with disease do exist and to unravel the underlying basic physiological mechanisms. Now that interest has developed in the assessment of intestinal permeability to small- and medium-sized molecules, it is hoped that equally simple methods for studying macromolecular permeability will be developed and applied. Therapeutic methods for enhancing intact polypeptide absorption would be valuable for vaccine and peptide drug administration by the oral route. Therapeutic reduction of the process may be relevant in food-sensitive patients.
Growth and metabolism in somatotropin-treated steers: I. Growth, serum chemistry and carcass weights (1990)

Growth, feed conversion, serum chemistry and gross slaughter characteristics were determined in 20 steers (initially 9 mo of age, 231 +/- 18 kg) receiving daily injections of either saline (S) or recombinantly derived bovine somatotropin (rBST, 20.6 mg/d) for 112 d. Live weight gains were 15% greater for steers treated with rBST than for those treated with S. Feed intake was not different between S- and rBST-treated steers; thus, feed conversion was 12% more efficient in rBST steers. Scanogram backfat measurements were not affected by treatments. Serum electrolytes, protein, glucose and most enzyme activities were similar in S and rBST steers. Serum urea, creatinine and cholesterol (toward the end of treatment) concentrations, however, were lower (P less than .05) in rBST steers, suggesting that nitrogen retention was increased and lipid turnover was decreased by rBST. Total (P less than .1) and conjugated (P less than .05) bilirubin concentrations and glutamate-pyruvate transaminase activity (P less than .05) were lower in rBST steers. Carcass weights were not altered, but dressing percentages were lower (P less than .05) in rBST steers. This indicated that weight gain response to rBST was primarily in noncarcass components; further examination showed that this gain was predominantly in gut fill (approximately 2/3 of the greater live weight gain in rBST steers). Alternative protocols, such as administering the hormone to younger animals and (or) for a longer duration, may be necessary in order to achieve desirable responses in carcass growth.
Open Microscopy Environment (2006)

Summary form only given. The Open Microscopy Environment (OME) is a framework for the management and analysis of image data and metadata in biological microscopy. Biological microscopy images can be collected in many different ways, and may represent many different kinds of information which changes continually with evolving technology and experimental goals. A framework that fully encompasses biological microscopy in scope cannot rely on a fixed data model - it must be designed to accommodate ever-changing informatics needs. The challenge posed by a fluid data model is similar to one addressed by the semantic web, principally support for arbitrary or user-defined semantics and ontologies. However, an analysis framework faces additional challenges besides the management of semantics: definition of analytic units as transforms between semantic constructs, definition of aggregates of analytic units to represent work flows, interfaces to algorithm implementations, and maintenance of data provenance or history. A collaborative scientific environment also demands that these locally defined semantics and transforms be fully transportable for subsequent review or analysis. OME incorporates these components in a database-backed system targeted at end-user biologists. This presentation will briefly describe the various components of OME: the semantic layer (Semantic Types - STs), the analytical un its used to transform between STs (Analysis Modules), the units of work flow (Analysis Chains), the work-flow processor (Analysis Engine), and the transportability layer (OME XML). An example of a complex work flow will also be presented illustrating how this system is used for automated image classification.
Ectopic Germinal Center Formation in Rheumatoid Synovitis (2003)

Synovial inflammation in rheumatoid arthritis is closely related to the formation of ectopic lymphoid microstructures. In synovial tissue from some patients, one finds seemingly diffuse infiltrates; in others, T cells and B cells cluster in aggregates with interdigitating dendritic cells (DCs) but no follicular DCs (FDCs). In a third group, T cell/B cell follicles with germinal center (GC) reactions are generated. Within a given patient, aggregates and GCs are mutually exclusive and stable over time. Because antigen storage capacity, lymphoid density, and three-dimensional topography of GCs optimize immune responses, synovial GCs should play a crucial role in the breakdown of self-tolerance. We have identified factors critical for ectopic GCs, thereby transforming the synovial inflammatory process. Tissues with GCs produced 10- to 20-fold higher amounts of the chemokines CXCL13 and CCL21. CXCL13 derived from three sources, endothelial cells, synovial fibroblasts, and FDC networks. The level of CXCL13 transcripts strongly predicted GCs; however, some tissues had high levels of CXCL13 but lacked GCs. Tissue expression of LT-beta emerged as a second key factor. LT-beta protein was detected on follicular center and mantle zone B cells. Multivariate regression analysis identified CXCL13 and LT-beta as the only cytokines predicting GCs. Remarkably, LT-alpha did not contribute independently. The contribution of B cells to ectopic lymphoid organogenesis was not limited to LT-beta production. Rather, synovial tissue B cells were critical in regulating T cell activation. In adoptive transfer experiments in human synovium-SCID mouse chimeras, activation of synovium-derived CD4 T cells was strictly dependent on T cell/B cell follicles. Depletion of synovial tissue B cells abrogated T cell function, and non-B cell antigen-presenting cells could not maintain T cell stimulation. Unexpectedly, GC function in the rheumatoid lesion was also dependent on CD8 T cells. The majority of T cell receptors derived from CD8 T cells were shared between distinct GCs. Depletion of CD8 T cells disrupted synovial GCs, FDC networks disappeared, and transcription of LT-beta, IgG, and Igkappa declined. Follicle-sustaining CD8 T cells were located at the edge of or within the mantle zone. Cell-cell communication in the mantle zone, including CD8 T cells, appears to be critical for ectopic GC formation in rheumatoid synovitis.
Acquiring robot skills via reinforcement learning (1994)

Skill acquisition is a difficult , yet important problem in robot performance. The authors focus on two skills, namely robotic assembly and balancing and on two classic tasks to develop these skills via learning: the peg-in hole insertion task, and the ball balancing task. A stochastic real-valued (SRV) reinforcement learning algorithm is described and used for learning control and the authors show how it can be used with nonlinear multilayer ANNs. In the peg-in-hole insertion task the SRV network successfully learns to insert to insert a peg into a hole with extremely low clearance, in spite of high sensor noise. In the ball balancing task the SRV network successfully learns to balance the ball with minimal feedback.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cigarette Smoke Inhibits Human Bronchial Epithelial Cell Repair Processes (2001)

By interfering with the ability of airway epithelial cells to support repair processes, cigarette smoke could contribute to alterations of airway structures and functions that characterize chronic obstructive pulmonary disease (COPD). The current study assessed the ability of cigarette smoke extract (CSE) to alter human airway epithelial cell chemotaxis, proliferation, and contraction of three-dimensional collagen gels, a model of extracellular matrix remodeling. The volatile components contained in cigarette smoke, acetaldehyde and acrolein, were able to inhibit all three processes. Nonvolatile components contained within lyophilized CSE also inhibited chemotaxis but displayed no activity in the other two bioassays. CSE also inhibited the ability of airway epithelial cells to release transforming growth factor (TGF)-beta and fibronectin. Exogenous fibronectin was unable to restore epithelial cell contraction of collagen gels. Exogenous TGF-beta partially restored the ability of airway epithelial cells to contract collagen gels and to produce fibronectin. This supports a role for inhibition of TGF-beta release in mediating the inhibitory effects of cigarette smoke. Taken together, the results of the current study suggest that epithelial cells present in the airways of smokers may be altered in their ability to support repair responses, which may contribute to architectural disruptions present in the airways in COPD associated with cigarette smoking.
The beneficial endophyte Trichoderma hamatum isolate DIS 219b promotes growth and delays the onset of the drought response in Theobroma cacao (2009)

Theobroma cacao (cacao) is cultivated in tropical climates and is exposed to drought stress. The impact of the endophytic fungus Trichoderma hamatum isolate DIS 219b on cacao's response to drought was studied. Colonization by DIS 219b delayed drought-induced changes in stomatal conductance, net photosynthesis, and green fluorescence emissions. The altered expression of 19 expressed sequence tags (ESTs) (seven in leaves and 17 in roots with some overlap) by drought was detected using quantitative real-time reverse transcription PCR. Roots tended to respond earlier to drought than leaves, with the drought-induced changes in expression of seven ESTs being observed after 7 d of withholding water. Changes in gene expression in leaves were not observed until after 10 d of withholding water. DIS 219b colonization delayed the drought-altered expression of all seven ESTs responsive to drought in leaves by > or = 3 d, but had less influence on the expression pattern of the drought-responsive ESTs in roots. DIS 219b colonization had minimal direct influence on the expression of drought-responsive ESTs in 32-d-old seedlings. By contrast, DIS 219b colonization of 9-d-old seedlings altered expression of drought-responsive ESTs, sometimes in patterns opposite of that observed in response to drought. Drought induced an increase in the concentration of many amino acids in cacao leaves, while DIS 219b colonization caused a decrease in aspartic acid and glutamic acid concentrations and an increase in alanine and gamma-aminobutyric acid concentrations. With or without exposure to drought conditions, colonization by DIS 219b promoted seedling growth, the most consistent effects being an increase in root fresh weight, root dry weight, and root water content. Colonized seedlings were slower to wilt in response to drought as measured by a decrease in the leaf angle drop. The primary direct effect of DIS 219b colonization was promotion of root growth, regardless of water status, and an increase in water content which it is proposed caused a delay in many aspects of the drought response of cacao.
Pim-1 levels determine the size of early B lymphoid compartments in bone marrow. (1993)

The mouse proto-oncogene Pim-1, which encodes two cytoplasmic serine-threonine-specific protein kinases, is frequently activated by proviral insertion in murine leukemia virus-induced hematopoietic tumors. Transgenic mice overexpressing Pim-1 show a low incidence of spontaneous T cell lymphomas, whereas null mutant mice lack an obvious phenotype. We have analyzed the early B lymphoid compartment from both null mutant and E mu-Pim-1 transgenic mice. The level of Pim-1 expression appears to be a determining factor in the ability of these cells to respond to the growth factors interleukin 7 (IL-7) and SF (steel factor). The impaired response in null mutant mice could be rescued by introduction of a functional Pim-1 transgene. Moreover, overexpression of Pim-1 facilitates the derivation of primitive lymphoid cell lines that are dependent on combined stimulation with IL-7 and SF or insulin-like growth factor 1. These results for the first time identify the involvement of Pim-1 in a normal cellular function, as an important regulator of early B lymphopoiesis in mice.
Synthesis of Ru, Rh and Pd complexes immobilized on modified supports. Investigation of the hydrogenation of cinnamaldehyde (1996)

Preparation de catalyseurs a base de complexes du Ru, Rh et du Pd sur supports modifies. Proprietes dans l'hydrogenation du cinnamaldehyde. L'hydrogenation de l'aldehyde cinnamique a ete effectuee en presence de catalyseurs a base de Ru, Rh, ou de Pd. Les solides ont ete obtenus par fixation echange de complexes organometalliques sur des supports organiques ou mineraux modifies. Il a ete montre que la selectivite en alcool insature pouvait etre augmentee par des supports a caractere basique contenant des groupements amines, aliphatiques ou heterocycliques. D'autre part, il a ete observe que les complexes de ruthenium conduisent a des catalyseurs plus selectifs que ceux obtenus a partir du rhodium ou de palladium.
TR60 and TR80 tumor necrosis factor (TNF)-receptors can independently mediate cytolysis. (1993)

The human rhabdomyosarcoma cell line KYM-1 coexpresses high numbers of both tumor necrosis factor-alpha (TNF) receptors, TR60 and TR80, and is highly sensitive to TNF-induced cytotoxicity. We show here that each receptor type can mediate cytotoxicity on its own on selective stimulation. This was achieved using receptor specific antibodies, able to compete with ligand binding to the respective receptor molecules. Thus, the TR60-specific monoclonal antibody H398 was strongly agonistic, i.e., cytotoxic, in the presence of a secondary cross-linking immunoglobulin. Selective stimulation of TR80 by antibody-mediated receptor crosslinking also induced strong cytotoxicity in KYM-1 cells. Interestingly, when both receptor subsets were stimulated in parallel by limited receptor cross-linking, additive cytolytic effects were observed. In each case the respective Fab fragments showed no agonistic activity. When the natural ligand TNF was used to induce cytolysis, blocking studies with receptor specific Fab fragments indicated that the main cytotoxic effect of TNF is mediated via TR60, although these receptors represent only about 8% of the total TNF receptor number.
The sequence and de novo assembly of the giant panda genome (2009)

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.
Tube-Super Dielectric Materials: Electrostatic Capacitors with Energy Density Greater than 200 J·cm−3 (2015)

The construction and performance of a second generation of super dielectric material based electrostatic capacitors (EC), with energy density greater than 200 J·cm<sup>-</sup>³, which rival the best reported energy density of electric double layer capacitors (EDLC), also known as supercapacitors, are reported. The first generation super dielectric materials (SDM) are multi-material mixtures with dielectric constants greater than 1.0 × 10⁵, composed of a porous, electrically insulating powder filled with a polarizable, ion-containing liquid. Second-generation SDMs (TSDM), introduced here, are anodic titania nanotube arrays filled with concentrated aqueous salt solutions. Capacitors using TiO₂ based TSDM were found to have dielectric constants at ~0 Hz greater than 10⁷ in all cases, a maximum operating voltage of greater than 2 volts and remarkable energy density that surpasses the highest previously reported for EC capacitors by approximately one order of magnitude. A simple model based on the classic ponderable media model was shown to be largely consistent with data from nine EC type capacitors employing TSDM.
Necdin Promotes GABAergic Neuron Differentiation in Cooperation with Dlx Homeodomain Proteins (2006)

Necdin, a member of the MAGE (melanoma antigen) protein family, is expressed predominantly in terminally differentiated neurons. The necdin gene NDN is maternally imprinted and expressed only from the paternal allele, the deficiency of which is implicated in the pathogenesis of the neurodevelopmental disorder Prader-Willi syndrome. Necdin binds to its homologous MAGE protein MAGE-D1 (also known as NRAGE or Dlxin-1), which interacts with Msx (msh homeobox) and Dlx (distal-less homeobox) family homeodomain transcription factors. Members of the Dlx homeobox gene family are involved in the differentiation and specification of forebrain GABAergic neurons. Here we demonstrate that necdin associates with Dlx homeodomain proteins via MAGE-D1 to promote the differentiation of GABAergic neurons in mouse embryonic forebrain. Immunohistochemical analysis revealed that necdin was coexpressed with Dlx2, Dlx5, or MAGE-D1 in a subpopulation of embryonic forebrain cells. Necdin bound to Dlx2 and Dlx5 via MAGE-D1 and enhanced Dlx2-dependent activation of the Wnt1 (wingless-type MMTV integration site family) promoter. Necdin significantly increased the populations of cells expressing the GABAergic neuron markers calbindin D-28k and glutamic acid decarboxylase when overexpressed by electroporation in cultured forebrain slices. In this assay, Dlx5N, a truncated Dlx5 mutant that competes with Dlx2 to bind MAGE-D1, diminished the effect of necdin on GABAergic neuron differentiation. Furthermore, mutant mice lacking the paternal necdin allele showed a significant reduction in the differentiation of forebrain GABAergic neurons in vivo and in vitro. These results suggest that paternally expressed necdin facilitates the differentiation and specification of GABAergic neurons in cooperation with Dlx homeodomain proteins.