gebhart/patrepeval huggingface dataset:
Cell Surface Targeting of Heat Shock Protein gp96 Induces Dendritic Cell Maturation and Antitumor Immunity (2001)

gp96 is a residential heat shock protein of the endoplasmic reticulum that has been implicated in the activation of dendritic cells (DCs) for the initiation of adaptive immunity. By genetic targeting of gp96 onto the cell surface, we demonstrate that direct access of gp96 to DCs induces their maturation, resulting in secretion of proinflammatory cytokines IL-1beta, IL-12, and chemokine monocyte chemoattractant protein-1 and up-regulation of the expression of MHC class I, MHC class II, CD80, CD86, and CD40. Furthermore, surface expression of gp96 on tumor cells renders them regressive via a T lymphocyte-dependent mechanism. This work reinforces the notion that gp96 is an endogenous DC activator and unveils that the context in which Ag is delivered to the immune system, in this case surface expression of gp96, has profound influence on immunity. It also establishes a principle of bridging innate and adaptive immunity for cancer immunotherapy by surface targeting of an intracellular heat shock protein.
Partial External Biliary Diversion in Children With Progressive Familial Intrahepatic Cholestasis and Alagille Disease (2009)

At median follow-up of 3.1 years after PEBD, pruritus has been relieved in 75%. Bile salts level and growth are improved in most patients. Longer follow-up is needed to determine whether PEBD can postpone or avoid the demand for liver transplantation.
Comparing the effects of Bentonite & Calendula on the improvement of infantile diaper dermatitis: A randomized controlled trial (2015)

Our results showed that in comparison with Calendula, Bentonite had faster healing effect and was more effective on the improvement of infantile diaper dermatitis (IRCT ID: IRCT 2012112811593N1).
A cryptic T cell epitope on the apical membrane antigen 1 of Plasmodium chabaudi adami can prime for an anamnestic antibody response: implications for malaria vaccine design (1997)

We have investigated the proliferative and Th cell responses to the Plasmodium chabaudi adami DS homologue of the Plasmodium falciparum apical membrane Ag 1 (AMA-1), a leading malaria vaccine candidate. Immunodominant T cell epitopes were defined following immunization of BALB/c mice with Escherichia coli-expressed, refolded P. c. adami DS AMA-1 recombinant protein and testing cells from the draining lymph nodes for responses against a series of overlapping peptides spanning P. c. adami AMA-1. A limited number of major T cell sites were identified in both conserved and variable regions of the protein. Several cryptic epitopes that evoked T cell responses following immunization with peptides, but not after protein immunization, were also identified. Adoptive transfer of a T cell line specific for a conserved cryptic epitope (corresponding to residues 31-50) provided help for an anti-AMA-1 protein-specific Ab response following in vivo challenge with P. c. adami parasitized RBC, such that AMA-1-specific Abs appeared more rapidly in recipient mice than in controls. Furthermore, T cells specific for cryptic epitopes afforded partial protection against P. c. adami infection in nude mice. The identification of conserved cryptic Th cell epitopes has important implications for malaria vaccine design.
Endocarditis Due to Rare and Fastidious Bacteria (2001)

The etiologic diagnosis of infective endocarditis is easily made in the presence of continuous bacteremia with gram-positive cocci. However, the blood culture may contain a bacterium rarely associated with endocarditis, such as Lactobacillus spp., Klebsiella spp., or nontoxigenic Corynebacterium, Salmonella, Gemella, Campylobacter, Aeromonas, Yersinia, Nocardia, Pasteurella, Listeria, or Erysipelothrix spp., that requires further investigation to establish the relationship with endocarditis, or the blood culture may be uninformative despite a supportive clinical evaluation. In the latter case, the etiologic agents are either fastidious extracellular or intracellular bacteria. Fastidious extracellular bacteria such as Abiotrophia, HACEK group bacteria, Clostridium, Brucella, Legionella, Mycobacterium, and Bartonella spp. need supplemented media, prolonged incubation time, and special culture conditions. Intracellular bacteria such as Coxiella burnetii cannot be isolated routinely. The two most prevalent etiologic agents of culture-negative endocarditis are C. burnetti and Bartonella spp. Their diagnosis is usually carried out serologically. A systemic pathologic examination of excised heart valves including periodic acid-Schiff (PAS) staining and molecular methods has allowed the identification of Whipple's bacillus endocarditis. Pathologic examination of the valve using special staining, such as Warthin-Starry, Gimenez, and PAS, and broad-spectrum PCR should be performed systematically when no etiologic diagnosis is evident through routine laboratory evaluation.
Localization of an 11 beta hydroxysteroid dehydrogenase activity to the distal nephron. Evidence for the existence of two species of dehydrogenase in the rat kidney. (1992)

An 11 beta hydroxysteroid dehydrogenase (11 beta HSD) activity has been localized in the rat kidney by a histochemical technique which links steroid metabolism with the production of a color reaction. Oxidation of 11 beta-hydroxyandrostenedione was observed in cortical distal convoluted tubules and in medullary collecting ducts. Carbenoxolone abolished staining, no reaction was obtained with androstenedione hydroxylated at the 17 or 19 position, and oxidation of 11 beta-hydroxyandrostenedione was nicotinamide-adenine dinucleotide (NAD) dependent. These results demonstrate the presence of a dehydrogenase activity separate from the nicotinamide-adenine dinucleotide phosphate (NADP)-dependent 11 beta hydroxysteroid dehydrogenase recently purified and cloned from rat liver. We have named this activity 11 beta HSD2 to distinguish it from the NADP-dependent 11 beta HSD. Histological studies showed that 11 beta HSD2 activity does not correlate with the immunocytochemical localization of the previously defined 11 beta HSD enzyme, but rather the 11 beta HSD2 activity is localized in the distal tubules of the rat kidney. In this respect 11 beta HSD2 colocalizes with the mineralocorticoid receptor. No reaction product was obtained using cortisol or corticosterone as substrate with either NAD or NADP as cofactor. Furthermore incubation of tissue sections with 11 beta androstenedione in the presence of deoxycorticosterone completely inhibited cytochemical staining. We interpret these results as evidence of 20 reductase activity which uses the reduced cofactor at the expense of the color reaction. These results support the crucial role played by an 11 beta hydroxysteroid dehydrogenase in the local protection of type I receptors in mineralocorticoid selective tissues.
Membrane Insertion of the Heptameric Staphylococcal α-Toxin Pore (2001)

Staphylococcal alpha-toxin forms heptameric pores on eukaryotic cells. After binding to the cell membrane in its monomeric form, the toxin first assembles into a heptameric pre-pore. Subsequently, the pre-pore transforms into the final pore by membrane insertion of an amphipathic beta-barrel, which comprises the "central loop" domains of all heptamer subunits. The process of membrane insertion was analyzed here using a set of functionally altered toxin mutants. The results show that insertion may be initiated within an individual protomer when its NH2 terminus activates its central loop. The activated state is then shared with the central loops of the residual heptamer subunits, which results in cooperative membrane penetration. This cooperation of the central loops commences while these are still remote from the lipid bilayer. Nevertheless, it is subject to modulation by the target membrane, which therefore acts across a distance much like an allosteric effector. However, while allosteric transitions usually are reversible, membrane insertion of alpha-toxin is an irreversible event, and we show here that it can proceed to completion in a domino-like fashion when triggered by as little as a single foreign atom within the entire heptamer.
Conditional Inhibition of the Mitogen-activated Protein Kinase Cascade by Wortmannin (1997)

Phosphoinositide (PI) 3-kinase and the mitogen-activated protein (MAP) kinase cascades are activated by many of the same ligands. Several groups have reported involvement of PI 3-kinase in the activation of Erk1 and Erk2, whereas many other groups have shown that activation of Erk1 and Erk2 is not sensitive to inhibitors of PI 3-kinase such as wortmannin. Here we show that wortmannin inhibition of the MAP kinase pathway is cell type- and ligand-specific. Wortmannin blocks platelet-derived growth factor (PDGF)-dependent activation of Raf-1 and the MAP kinase cascade in Chinese hamster ovary cells, which have few PDGF receptors, but has no significant effect on Erk activation in Swiss 3T3 cells, which have high levels of PDGF receptors. However, wortmannin blocks activation of Erk proteins if Swiss 3T3 cells are stimulated with lower, physiological levels of PDGF. These results suggest that PI 3-kinase is in an efficient pathway for activation of MAP kinase, but that MAP kinase can be stimulated by a redundant pathway when a large number of receptors are activated. We present evidence that a protein kinase C family member downstream of phospholipase Cgamma is involved in the redundant pathway.
Over 10 W Output Linearly-Polarized Single-Stage Fiber Laser Oscillating Above 1160 nm Using Yb-Doped Polarization-Maintaining Solid Photonic Bandgap Fiber (2011)

We propose an all-fiber linearly-polarized single-stage fiber laser oscillating above 1160 nm employing a low-loss Yb-doped polarization-maintaining solid photonic bandgap fiber (Yb-PM-SPGF) as a laser source for a yellow-orange frequency-doubling laser. We also present a new fabrication method for Yb-PM-SPBGF to reduce fiber attenuation in its photonic bandgap for increasing laser output power and improving slope efficiency. The attenuation of a fabricated Yb-PM-SPBGF is below 20 dB/km at 1180 nm, which is as low as that of a conventional Yb-doped fiber. All-fiber linearly-polarized single-stage fiber laser oscillating at 1180 nm using the fabricated Yb-PM-SPBGF is demonstrated. ASE and parasitic lasing in the wavelength range from 1030 nm to 1130 nm are suppressed and eliminated thanks to the filtering effect of the fiber. A 10.8 W output power is successfully achieved with a slope efficiency of 56% and a conversion efficiency of 50% by high-power 976 nm pumping. A spectral width of less than 0.05 nm, a polarization extinction ratio of more than 20 dB and nearly diffraction limited beam quality in output light are achieved. These results indicate that our proposed fiber laser can realize a compact and high-power yellow-orange frequency-doubling laser.
Long‐term open‐label preliminary study of the safety and efficacy of leflunomide in patients with polyarticular‐course juvenile rheumatoid arthritis (2005)

In this open-label study of JRA patients who either failed to respond to, or were intolerant of, methotrexate, the majority met the ACR Pedi 30 response criteria at week 26. The response was durable, since 53% of patients who entered into the extension phase (maximum 30 months) responded at the end of this phase. Our findings support the further study of the role of leflunomide in the treatment of polyarticular-course JRA.
On Reusing Test Access Mechanisms for Debug Data Transfer in SoC Post-Silicon Validation (2008)

One of the main difficulties in post-silicon validation is the limited debug access bandwidth to internal signals. At the same time, SoC devices often contain dedicated bus-based test access mechanisms (TAMs) that are used to transfer test data between external testers and embedded cores. In this paper, we propose to reuse these precious TAM resources for real-time debug data transfer in post-silicon validation. This strategy significantly increases debug bandwidth with negligible routing overhead. To support different TAM architectures and debug scenarios, design for debug (DfD) structures are introduced at both core test wrapper level and system level. Simulation results demonstrate the effectiveness of the proposed approach at low DfD cost.
Growth regulation of human breast and ovarian tumor cells by heregulin: Evidence for the requirement of ErbB2 as a critical component in mediating heregulin responsiveness. (1996)

Alterations in the expression of the epidermal growth factor (EGF) receptor ErbB family are frequently encountered in a number of human cancers. Two of these receptors, ErbB3 and ErbB4, are known to bind a family of related proteins termed heregulins (HRGs) or neu differentiation factors. In biologically relevant systems, interaction of HRG with ErbB3 or ErbB4 results in the transactivation of ErbB2. In this report, we show that ErbB2 is a critical component in mediating HRG responsiveness in a panel of human breast and ovarian tumor cell lines. Because HRGs have been reported to elicit diverse biological effects on cultured cells, including growth stimulation, growth inhibition, and induction of differentiation, we systematically examined the effect of rHRG beta 1 on tumor cell proliferation. HRG binding studies were performed with a panel of breast and ovarian tumor cell lines expressing a range of levels of ErbB2. The biological responses to HRG were also compared to EGF and to the growth-inhibitory anti-ErbB2 antibody, 4D5. In most cases, HRG stimulation of DNA synthesis correlated with positive effects on cell cycle progression and cell number and with enhancement of colony formation in soft agar. On each cell line tested, the HRG effects were distinguishable from EGF and 4D5. Our findings indicate that HRG induces cell proliferation in a number of tumor cell lines. In addition, we show that methods for measuring cell proliferation, as well as experimental conditions, are critical for determining HRGs effect on tumor cell growth in vitro.
Dynamics of entangled linear polymer melts:  A molecular-dynamics simulation (1990)

We present an extensive molecular-dynamics simulation for a bead spring model of a melt of linear polymers. The number of monomers N covers the range from N=5 to N=400. Since the entanglement length Ne is found to be approximately 35, our chains cover the crossover from the nonentangled to the entangled regime. The Rouse model provides an excellent description for short chains N&amp;lt;Ne, while the dynamics of the long chains can be described by the reptation model. By mapping the model chains onto chemical species we give estimates of the times and distances of onset of the slowing down in motion due to reptation. Comparison to neutron spin-echo data confirm our mapping procedure, resolving a discrepancy between various experiments. By considering the primitive chain we are able to directly visualize the confinement to a tube. Analyzing the Rouse mode relaxation allows us to exclude the generalized Rouse models, while the original reptation prediction gives a good description of the data.
Advances in Genome Editing and Application to the Generation of Genetically Modified Rat Models (2021)

The rat has been extensively used as a small animal model. Many genetically engineered rat models have emerged in the last two decades, and the advent of gene-specific nucleases has accelerated their generation in recent years. This review covers the techniques and advances used to generate genetically engineered rat lines and their application to the development of rat models more broadly, such as conditional knockouts and reporter gene strains. In addition, genome-editing techniques that remain to be explored in the rat are discussed. The review also focuses more particularly on two areas in which extensive work has been done: human genetic diseases and immune system analysis. Models are thoroughly described in these two areas and highlight the competitive advantages of rat models over available corresponding mouse versions. The objective of this review is to provide a comprehensive description of the advantages and potential of rat models for addressing specific scientific questions and to characterize the best genome-engineering tools for developing new projects.
Possible role of cytosolic free calcium concentrations in mediating insulin resistance of obesity and hyperinsulinemia. (1988)

Insulin- and glyburide-stimulated changes in cytosolic free calcium concentrations [( Ca2+]i) were studied in gluteal adipocytes obtained from six obese women (139 +/- 3% ideal body wt) and six healthy, normal weight age- and sex-matched controls. Biopsies were performed after an overnight fast and twice (at 3 and 6 h) during an insulin infusion (40 mU/m2 per min) (euglycemic clamp). In adipocytes obtained from normal subjects before insulin infusion, insulin (10 ng/ml) increased [Ca2+]i from 146 +/- 26 nM to 391 +/- 66 nM. Similar increases were evoked by 2 microM glyburide (329 +/- 41 nM). After 3 h of insulin infusion, basal [Ca2+]i rose to 234 +/- 21 nM, but the responses to insulin and glyburide were completely abolished. In vitro insulin-stimulated 2-deoxyglucose uptake was reduced by insulin and glucose infusion (25% stimulation before infusion, 5.4% at 3 h, and 0.85% at 6 h of infusion). In obese patients, basal adipocyte [Ca2+]i was increased (203 +/- 14 nM, P less than 0.05 vs. normals). The [Ca2+]i response demonstrated resistance to insulin (230 +/- 23 nM) and glyburide (249 +/- 19 nM) stimulation. Continuous insulin infusion increased basal [Ca2+]i (244 +/- 24 nM) and there was no response to either insulin or glyburide at 3 and 6 h of study. Rat adipocytes were preincubated with 1-10 mM glucose and 10 ng/ml insulin for 24 h. Measurements of 2-deoxyglucose uptake demonstrated insulin resistance in these cells. Under these experimental conditions, increased levels of [Ca2+]i that were no longer responsive to insulin were demonstrated. Verapamil in the preincubation medium prevented the development of insulin resistance.
<title>Practical evaluation of optical-proximity effect correction by EDM methodology</title> (1995)

Practical evaluation method for optical proximity effect correction (OPC) feasibility is newly proposed using EDM (Exposure-Defocus and Mask fabrication latitude) methodology. In this method, printed image on a wafer is characterized by process latitude functions derived from EDM methodology in terms of exposure latitude, depth of focus, and mask line width latitude. In this paper, effectiveness of the process latitude functions will be verified by applying them to intraproximity effect evaluation for isolated lines and angled lines, and also to interproximity effect evaluation for T-shaped patterns and lines &amp; spaces (L/S) patterns in i-line lithography.
Direct injection of hepatitis B virus DNA into liver induced hepatitis in adult rats. (1991)

Hepatitis B virus (HBV) surface antigen (HBsAg) genes were injected directly into the liver of adult rats with non-histone chromosomal protein high mobility group 1 by the hemagglutinating B virus of Japan (Sendai virus)-liposome method (Kato, K., Nakanishi, M., Kaneda, Y., Uchida, T., and Okada, Y. (1991) J. Biol. Chem. 266, 3361-3364). Immunohistochemical analysis showed that HBV surface antigen was expressed by the hepatocytes in vivo. On successive injections of the HBsAg genes, the antibody to HBV surface polypeptides was produced in the rats, and characteristic pathological changes of lymphocytic focal necrosis and denaturation of hepatic cells were observed in the liver of all the rats. We conclude that hepatitis is caused by the direct injection of HBsAg genes.
Unconventional Geophysics for Unconventional Plays (2010)

Abstract In conventional plays the role of the geophysicist is primarily that of locating and delineating the resource. This is most commonly accomplished through the use of active source seismic exploration. In this classic case it is the responsibility of the geophysicist to identify the structures associated with the trap and migration pathways of the resource. In the last twenty years this role has been expanded through the applicability of direct hydrocarbon indicators where, particularly in the Gulf of Mexico, the resource itself can often be identified using seismic exploration. In the case of unconventional resources neither the trap nor the presence of hydrocarbons are unknowns. The source rock, reservoir and trap are continuous and well defined. As such it would be easy to dismiss the geophysicist's role as diminished to one where his primary responsibilities are secondary concerns, such as hazard avoidance through the location of faults. However, in practice, the role of the unconventional geophysicist is much more complex and multi-dimensional. Access to resource in an unconventional rock is largely controlled by exposure to the rock, i.e. how efficiently it can be hydraulically fractured. The unconventional geophysicist can contribute to the understanding of how to best access the resource by studying the finer scale heterogeneities in the rock which are manifested indirectly through various seismic attributes such as anisotropy and curvature, and directly measured through microseismic monitoring of hydraulic stimulations.
Genetic Structure of Human Populations (2002)

We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations. Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.
Network Security In a Heterogeneous Environment (1994)

This paper provides a framework for enhancing the security of networks, large and small. It delves into the problems faced when adding new network-security mechanisms. It also defines a process that can be used to determine what security mechanisms are required, and where to place them, within a network. A large portion of the paper describes the types of mechanisms that are available, and provides examples of AT&T network-security products.
Allergen‐induced inflammation and airway epithelial and smooth muscle cell proliferation: role of Jun N‐terminal kinase (2003)

Chronic cellular inflammation and airway wall remodelling with subepithelial fibrosis and airway smooth muscle (ASM) cell hyperplasia are features of chronic asthma. Jun N-terminal kinase (JNK) may be implicated in these processes by regulating the transcriptional activity of activator protein (AP)-1. We examined the effects of an inhibitor of JNK, SP600125 (anthra [1,9-cd] pyrazole-6 (2 H)-one), in a model of chronic allergic inflammation in the rat. Rats sensitised to ovalbumin (OA) were exposed to OA-aerosol every third day on six occasions and were treated with SP600125 (30 mg kg-1 b.i.d; 360 mg in total) for 12 days, starting after the second through to the sixth OA exposure. We measured eosinophilic and T-cell inflammation in the airways, proliferation of ASM cells and epithelial cells by incorporation of bromodeoxyuridine (BrdU), and bronchial responsiveness to acetylcholine. SP600125 significantly reduced the number of eosinophils (P<0.05) and lymphocytes (P<0.05) in bronchoalveolar lavage fluid, suppressed eosinophilic (P<0.05) and CD2+ T-cell (P<0.05) infiltration within the bronchial submucosa, and the increased DNA incorporation in ASM (P<0.05) and epithelial cell incorporation (P<0.05). SP600125 did not alter bronchial hyper-responsiveness observed after chronic allergen exposure. Pathways regulated by JNK positively regulate ASM cell proliferation and allergic cellular inflammation following chronic allergen exposure.