gebhart/patrepeval huggingface dataset:
Substance P, calcitonin gene related peptide and PGE2 co-released from the mouse colon: a new model to study nociceptive and inflammatory responses in viscera, in vitro (2001)

Visceral inflammation is thought to play an important role in the sensitization of low and high threshold mechanosensory and polymodal afferents and to recruit silent nociceptors. Yet, little is known about the potential role of the mediators involved in nociceptor sensitization to mechanical stimulation as compared to heat sensitization in the skin. In the present study we developed a new isolated preparation of the mouse colon which allowed to apply controlled mechanical distensions. Excised segments of colon from CD mice were immersed in synthetic interstitial fluid (SIF) exposing the serosal surface during 5 min to different types of noxious stimuli; the increase in neuropeptide and PGE(2) release were analyzed (by EIA technique). Capsaicin, heat and pH 5.2 were able to induce significant increases in calcitonin gene related peptide (CGRP) release (14.6-, 5.1-, and 2.3-fold over baseline), however, only capsaicin induced a significant increase in substance P (SP) levels (1.8-fold over baseline). When pH 3.4 was used, a massive liberation of both CGRP and SP was obtained (14- and 15-fold from baseline) which was Ca(2+)-independent and not recovering, suggesting unphysiological release. Mechanical distensions in the noxious range (45, 60 and 90 mmHg) evoked a long-linear graded release of CGRP (1.3-, 1.6- and 2.6-fold over baseline) and of PGE(2) (1.9- 3.8-, 12.3-fold over baseline). Only the 90 mmHg distension evoked a significant increase of SP (1.9-fold over baseline). We conclude that the mouse colon preparation is a suitable model to study inflammatory and nociceptive mechanisms in viscera. Furthermore, a potentially important and yet unexplored role of PGE(2) in noxious visceral distension has been revealed.
Protection against Fatal Sindbis Virus Encephalitis by Beclin, a Novel Bcl-2-Interacting Protein (2020)

bcl-2, the prototypic cellular antiapoptotic gene, decreases Sindbis virus replication and Sindbis virus-induced apoptosis in mouse brains, resulting in protection against lethal encephalitis. To investigate potential mechanisms by which Bcl-2 protects against central nervous system Sindbis virus infection, we performed a yeast two-hybrid screen to identify Bcl-2-interacting gene products in an adult mouse brain library. We identified a novel 60-kDa coiled-coil protein, Beclin, which we confirmed interacts with Bcl-2 in mammalian cells, using fluorescence resonance energy transfer microscopy. To examine the role of Beclin in Sindbis virus pathogenesis, we constructed recombinant Sindbis virus chimeras that express full-length human Beclin (SIN/beclin), Beclin lacking the putative Bcl-2-binding domain (SIN/beclinΔBcl-2BD), or Beclin containing a premature stop codon near the 5′ terminus (SIN/beclinstop). The survival of mice infected with SIN/beclin was significantly higher (71%) than the survival of mice infected with SIN/beclinΔBcl-2BD (9%) or SIN/beclinstop (7%) (P < 0.001). The brains of mice infected with SIN/beclin had fewer Sindbis virus RNA-positive cells, fewer apoptotic cells, and lower viral titers than the brains of mice infected with SIN/beclinΔBcl-2BD or SIN/beclinstop. These findings demonstrate that Beclin is a novel Bcl-2-interacting cellular protein that may play a role in antiviral host defense.
Ferredoxin:NADPH oxidoreductase is recruited to thylakoids by binding to a polyproline type II helix in a pH-dependent manner (2010)

Ferredoxin:NADPH oxidoreductase (FNR) is a key enzyme of photosynthetic electron transport required for generation of reduction equivalents. Recently, two proteins were found to be involved in membrane-anchoring of FNR by specific interaction via a conserved Ser/Pro-rich motif: Tic62 and Trol. Our crystallographic study reveals that the FNR-binding motif, which forms a polyproline type II helix, induces self-assembly of two FNR monomers into a back-to-back dimer. Because binding occurs opposite to the FNR active sites, its activity is not affected by the interaction. Surface plasmon resonance analyses disclose a high affinity of FNR to the binding motif, which is strongly increased under acidic conditions. The pH of the chloroplast stroma changes dependent on the light conditions from neutral to slightly acidic in complete darkness or to alkaline at saturating light conditions. Recruiting of FNR to the thylakoids could therefore represent a regulatory mechanism to adapt FNR availability/activity to photosynthetic electron flow.
Optimization study of stacked micro-channel heat sinks for micro-electronic cooling (2003)

With smaller inlet flow velocity, a micro-channel stack requires less pumping power to remove a certain amount of heat than a single-layered micro-channel, because it provides a larger heat transfer area. A simple thermal resistance network model was developed to evaluate the overall thermal performance of a stacked micro-channel heat sink. Based on this simple model, in this study, a single objective minimization of overall thermal resistance is carried out using genetic algorithms. The aspect ratio, fin thickness and the ratio of channel width to fin thickness are the variables to be optimized, subject to constraints of maximum pressure drop (4 bar) and maximum volumetric flow rate (1000 ml/min). During the optimization, the overall dimensions, number of layers and pumping power (product of pressure drop and flow rate) are fixed. The study indicates that reduction in thermal resistance can be achieved by optimizing the channel configuration. The effects of number of layers in the stack, pumping power per unit area, and the channel length are investigated.
DILUTE EMULSIONS AND THEIR EFFECT ON THE BREAKUP OF THE LIQUID SHEET PRODUCED BY FLAT-FAN SPRAY NOZZLES (1999)

Studies of the effect of dilute emulsions on spray formation by flat-fan nozzles have shown that the presence of emulsion particles changes the mechanism of liquid sheet breakup. Perforations in the liquid sheet occur at a position that is dependent on the nature and the concentration of the emulsified components. It has been suggested that perforations occur with particles of low wettability and when the liquid sheet thickness equals the particle diameter. We examined this by (1) investigating the relationship between the length of the liquid sheet and the diameter of the emulsion particles, (2) evaluating the effect of adding surfactants to the dilute emulsion on spray formation, and (3) considering how nozzle size and liquid pressure influence the breakup mechanism. It is suggested that the wettability of particles may be correlated with their ability to cause perforations if their interfacial tension is not at equilibrium. However, perforations did not appear at the position when the particle diameter was equal to the sheet thickness. It is suggested that the emulsion particles interact with the local perturbations within the flow. These perturbations grow, causing a hole to develop in the sheet. Adding surfactants to dilute emulsions resulted in a reduction in emulsion particle size, a change in the number of emulsion particles, or a change in the number of perturbations. These changes were associated with a change in spray droplet size.
Local corneal thickness changes after small-incision cataract surgery (2006)

A nasal-temporal difference in corneal thickness was found preoperatively in all patients. Phacoemulsification through a temporal limbal-corneal incision caused an increase in corneal thickness along the horizontal meridian 1 day after surgery. The prolonged corneal thickening at 3.0 mm eccentricity temporally could be a result of the proximity to the incision site.
Efficient isotopic tryptophan labeling of membrane proteins by an indole controlled process conduct (2013)

A protocol for the efficient isotopic labeling of large G protein-coupled receptors with tryptophan in Escherichia coli as expression host was developed that sufficiently suppressed the naturally occurring L-tryptophan indole lyase, which cleaves tryptophan into indole, pyruvate, and ammonia resulting in scrambling of the isotopic label in the protein. Indole produced by the tryptophanase is naturally used as messenger for cell-cell communication. Detailed analysis of different process conducts led to the optimal expression strategy, which mimicked cell-cell communication by the addition of indole during expression. Discrete concentrations of indole and (15) N2 -L-tryptophan at dedicated time points in the fermentation drastically increased the isotopic labeling efficiency. Isotope scrambling was only observed in glutamine, asparagine, and arginine side chains but not in the backbone. This strategy allows producing specifically tryptophan labeled membrane proteins at high concentrations avoiding the disadvantages of the often low yields of auxotrophic E. coli strains. In the fermentation process carried out according to this protocol, we produced ∼15 mg of tryptophan labeled neuropeptide Y receptor type 2 per liter medium.
Analysis of the pharmacokinetic/pharmacodynamic relationship of a small molecule CXCR3 antagonist, NBI‐74330, using a murine CXCR3 internalization assay (2007)

The CXCR3 receptor internalization assay provides a robust method for determining agonist potency orders, antagonist affinity estimates and PK/PD analyses, which discriminate between dosing regimens for the CXCR3 antagonist NBI-74330.
Human Endothelial Cells as an Alternative to DH82 Cells for Isolation of <i>Ehrlichia chaffeensis</i>, <i>E. canis</i>, and <i>Rickettsi rickettsii</i> (1993)

Ehrlichia chaffeensis, etiologic agent of human ehrlichiosis, and Rickettsia rickettsii, etiologic agent of Rocky Mountain spotted fever (RMSF), are both tick-borne agents that cause nonspecific symptoms that may be indistinguishable from each other early in the course of infection. E. canis is a canine pathogen closely related to E. chaffeensis and was initially suspected of being the causative agent of human ehrlichiosis. If a febrile illness is reported, after tick exposure, neither ehrlichiosis nor RMSF can be immediately ruled out. When attempts are made to isolate the agent from blood, a very limited amount of blood is often available; we, therefore, sought a tissue-culture cell line that would support the growth of both R. rickettsii and E. chaffeensis. A newly established human microvascular endothelial immortal cell line (CDC/EU.HMEC-1) was evaluated for supporting the growth of both agents. Our results demonstrate that HMEC-1 supports the growth of R. rickettsii, E. chaffeensis, and E. canis and may be a useful tool for the isolation of these agents.
Location Mention Detection in Tweets and Microblogs (2016)

The automatic identification of location expressions in social media text is an actively researched task. We present a novel approach to detection mentions of locations in the texts of microblogs and social media. We propose an approach based on Noun Phrase extraction and n-gram based matching instead of the traditional methods using Named Entity Recognition (NER) or Conditional Random Fields (CRF), arguing that our method is better suited to noisy microblog text. Our proposed system is comprised of several individual modules to detect addresses, Points of Interest (e.g. hospitals or universities), distance and direction markers; and location names (e.g. suburbs or countries). Our system won the ALTA 2014 Twitter Location Detection shared task with an F-score of 0.792 for detecting location expressions in a test set of 1,000 tweets, demonstrating its efficacy for this task. A number of directions for future work are discussed.
Crystallization kinetics of poly‐ε‐caprolactone from poly‐ε‐caprolactone/poly(vinyl chloride) solutions (1973)

Abstract The polymer–polymer solution of poly(vinyl chloride) and poly‐ε‐caprolactone yields an excellent system for studying the crystallization kinetics of a crystallizable component from a polymer–polymer solution. Unlike previous studies of isotactic–atactic polystyrene solutions for which the glass transition temperature is invariant with composition, this system exhibits a marked dependence of T g on the composition. The experimental data dE ⅓ (modulus)/ dt (psi ⅓ /min) were obtained over a composition range of 40 to 70 wt‐% poly‐ε‐caprolactone. With the appropriate modification of the spherulitic growth rate equation, the expression approximated a reasonable fit of the experimental data. This demonstrates a marked dependence of the crystallization rate on concentration. Secondary observations of this investigation show a slower crystallization rate for high molecular weight poly‐ε‐caprolactone and a slow secondary crystallization step. Both homopolymer poly‐ε‐caprolactone and poly‐ε‐caprolactone in the poly‐ε‐caprolactone/poly(vinyl chloride) solution show a slow (relative to the nucleation‐controlled step) crystallization stage considered to involve a slow diffusion mechanism.
Immunization with<i>Staphylococcus aureus</i>iron regulated surface determinant B (IsdB) confers protection via Th17/IL17 pathway in a murine sepsis model (2012)

We have previously shown that IsdB, a conserved protein expressed by Staphylococcus aureus, induces a robust antibody response which correlates with protection in a murine challenge model. Here we investigate the role of cellular immunity in IsdB mediated protection using lymphocyte deficient SCID mice. As opposed to WT CB-17 mice the CB-17 SCID mice were not protected against a lethal challenge of S. aureus after active and passive immunizations with IsdB. Adoptive transfer of in vitro isolated lymphocyte subsets revealed that reconstituting mice with IsdB specific CD3+ or CD4+ T-cells conferred antigen specific protection while CD8(+) T-cells, CD19(+) B-cells and plasma cells (CD138(high)B220(int)CD19(lo)) alone were not protective. A combination of CD3(+) T-cells plus CD19(+) B-cells conferred protection in CB-17 SCID mice, whereas bovine serum albumin (BSA) immune lymphocytes did not confer protection. Active immunization experiments indicated that IsdB immunized Jh mice (B-cell deficient) were protected against lethal challenge, while nude (T-cell deficient) mice were not. In vitro assays indicated that isolated IsdB specific splenocytes from immunized mice produced abundant IL-17A, much less IFN-γ and no detectable IL-4. IL-23 deficient mice were not protected from a lethal challenge by IsdB vaccination, pointing to a critical role for CD4(+) Th17 in IsdB-mediated vaccination. Neutralizing IL-17A, but not IL-22 in vivo significantly increased mortality in IsdB immunized mice; whereas, neutralizing IFN-γ did not alter IsdB-mediated protection. These findings suggest that IL-17A producing Th17 cells play an essential role in IsdB vaccine-mediated defense against invasive S. aureus infection in mice.
Localization of EphA4 in axon terminals and dendritic spines of adult rat hippocampus (2007)

Eph receptors and their ephrin ligands assume various roles during central nervous system development. Several of these proteins are also expressed in the mature brain, and notably in the hippocampus, where EphA4 and ephrins have been shown to influence dendritic spine morphology and long-term potentiation (LTP). To examine the cellular and subcellular localization of EphA4 in adult rat ventral hippocampus, we used light and electron microscopic immunocytochemistry with a specific polyclonal antibody against EphA4. After immunoperoxidase labeling, EphA4 immunoreactivity was found to be enriched in the neuropil layers of CA1, CA3, and dentate gyrus. In all examined layers of these regions, myelinated axons, small astrocytic leaflets, unmyelinated axons, dendritic spines, and axon terminals were immunolabeled in increasing order of frequency. Neuronal cell bodies and dendritic branches were immunonegative. EphA4-labeled dendritic spines and axon terminals corresponded to 9-19% and 25-40% of the total number of spines and axon terminals, respectively. Most labeled spines were innervated by unlabeled terminals, but synaptic contacts between two labeled elements were seen. The vast majority of synaptic junctions made by labeled elements was asymmetrical and displayed features of excitatory synapses. Immunogold labeling of EphA4 was located mostly on the plasma membrane of axons, dendritic spines, and axon terminals, supporting its availability for surface interactions with ephrins. The dual preferential labeling of EphA4 on pre- or postsynaptic specializations of excitatory synapses in adult rat hippocampus is consistent with roles for this receptor in synaptic plasticity and LTP.
Attainment of the Theoretical Yield of Carbon from Biomass (2000)

Previous work has shown that very high yields of charcoal are obtained when pyrolysis of the biomass feedstock is conducted at elevated pressure in a closed vessel, wherein the pyrolytic vapors are held captive and in contact with the solid products of pyrolysis. In this paper, we show that, for some biomass species, the yield of carbon produced by this process effectively attains the theoretical value predicted to exist when thermochemical equilibrium is realized. Various agricultural wastes (e.g., kukui nut, macadamia nut, and pecan shells) and tropical species (e.g., eucalyptus, leucaena, and bamboo) offer higher yields of carbon than the hardwoods traditionally employed by industry in the U.S. and Europe. Moreover, the yields of carbon from oat and rice hulls and from sunflower seed hulls are nearly as high as the yields of carbon from hardwoods. There is a correlation between the yield of carbon and the acid-insoluble lignin content of the feed. Charcoal briquettes made from agricultural wastes and lump charcoal from tropical species are promising sources of renewable carbon for use in the smelting of metal ores.
Hot-tearing of Al-Li alloys in DC casting. (1993)

The prevention of hot-tearing in the commercial Al-Li alloys ingots (150mm×350mm) produced by DC casting was studied. Crack started at the caved part of ingot surface which was contaminated by oxide. The molten metal surface was ventilated by Ar gas to inhibit the generation and contamination of oxide. The stress by solidification shrinkage was reduced by decreasing casting speed, because the faster casting speed caused larger shrinkage. But the pouring temperature and coolant flow rate had no influence. No crack was detected in 2024 alloy. Shrinkage of Al-Li alloys was larger than 2024 alloy, and that was the one of the reasons why Al-Li alloy easily cracked. The faster casting speed causes the deeper sump.
Sarcomatoid Renal Cell Carcinoma: A Comprehensive Review of the Biology and Current Treatment Strategies (2012)

Recent advancements in the molecular characterization of renal cell carcinoma altered the classification system and now kidney cancer is divided into several distinct histologic subtypes. Although once a separate histologic category, sarcomatoid renal cell carcinoma is no longer considered a separate tumor type because it can occur with all histologic subtypes. Limited research on tumors with sarcomatoid change has led to minimal progress in the understanding and treatment of these tumors. Because the sarcomatoid variant of renal cell carcinoma can account for approximately one in six cases of advanced kidney cancer, we hope to familiarize clinicians with these tumors by describing the historic background, histologic features, molecular characterization, diagnosis, prognosis, treatment strategies, and active clinical trials of this aggressive type of tumor.
Estimation of channel statistics for iterative detection of OFDM signals (2005)

Maximum likelihood sequence estimation for orthogonal frequency division multiplexing (OFDM) transmissions over unknown multipath fading channels is analytically infeasible for lack of efficient methods to maximize the likelihood function. A practical solution to this problem has been recently proposed in the context of space-time block-coded OFDM by resorting to the expectation-maximization (EM) algorithm. The resulting detector operates iteratively, exploiting knowledge of the channel statistics and the operating signal-to-noise ratio (SNR). In this work, we address the problem of estimating the above quantities and propose a recursive solution based on ad hoc reasoning. Simulations indicate that the EM detector employing the estimated SNR and channel statistics has better performance than other schemes operating in a mismatched mode. Also, the performance loss with respect to a system with perfect channel knowledge is negligible at SNR values of practical interest.
Human Immunodeficiency Virus Type 1 gp120 Induces Abnormal Maturation and Functional Alterations of Dendritic Cells: a Novel Mechanism for AIDS Pathogenesis (2004)

Dendritic cells (DCs) play a crucial role in bridging innate and acquired immune responses to pathogens. In human immunodeficiency virus type 1 (HIV-1) infection, immature DCs (iDCs) are also main targets for HIV-1 at the mucosal level. In this study, we evaluated the effects of HIV-1-DC interactions on the maturation and functional activity of these cells. Exposure of human monocyte-derived iDCs to either aldrithiol-2-inactivated HIV-1 or gp120 led to an upmodulation of activation markers indicative of functional maturation. Despite their phenotype, these cells retained antigen uptake capacity and showed an impaired ability to secrete cytokines or chemokines and to induce T-cell proliferation. Although gp120 did not interfere with DC differentiation, the capacity of these cells to produce interleukin-12 (IL-12) upon maturation was markedly reduced. Likewise, iDCs stimulated by classical maturation factors in the presence of gp120 lacked allostimulatory capacity and did not produce IL-12, in spite of their phenotype typical of activated DCs. Exogenous addition of IL-12 restores the allostimulatory capacity of gp120-exposed DCs. The finding that gp120 induces abnormal maturation of DCs linked to profound suppression of their activities unravels a novel mechanism by which HIV can lead to immune dysfunction in AIDS patients.
Glucosinolate Metabolites Required for an <i>Arabidopsis</i> Innate Immune Response (2008)

The perception of pathogen or microbe-associated molecular pattern molecules by plants triggers a basal defense response analogous to animal innate immunity and is defined partly by the deposition of the glucan polymer callose at the cell wall at the site of pathogen contact. Transcriptional and metabolic profiling in Arabidopsis mutants, coupled with the monitoring of pathogen-triggered callose deposition, have identified major roles in pathogen response for the plant hormone ethylene and the secondary metabolite 4-methoxy-indol-3-ylmethylglucosinolate. Two genes, PEN2 and PEN3, are also necessary for resistance to pathogens and are required for both callose deposition and glucosinolate activation, suggesting that the pathogen-triggered callose response is required for resistance to microbial pathogens. Our study shows that well-studied plant metabolites, previously identified as important in avoiding damage by herbivores, are also required as a component of the plant defense response against microbial pathogens.
Four-Port Bimanual Vitrectomy (1986)

A further subdivision of functions during vitrectomy surgery has been enabled. By means of a separate, suture-secured fiberoptic endoilluminator and a modified infusion cannula located in the inferior quadrants, two superior sclerotomies are kept free for the use of a variety of simple and complex instruments, alone or in combination. Included among these are vitreous scissors, forceps, picks, spatulas, diathermy probes, and endophotocoagulators.
Innovations in Optical Communication Infrastructure Technologies (2011)

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