gebhart/patrepeval huggingface dataset:
Common γ-Chain-Dependent Signals Confer Selective Survival of Eosinophils in the Murine Small Intestine (2009)

Abstract Eosinophils are potent effector cells that are recruited to sites of inflammation. However, in some tissues, in particular in the gastrointestinal tract, eosinophils constitute an abundant leukocyte population also under homeostatic conditions. The lack of suitable isolation protocols restricted the analysis of these cells to histological assessment of cell numbers while important aspects of their phenotype, turnover, and functions remain unresolved. In this study, we report a protocol that allows the quantitative isolation of intestinal eosinophils. We characterized small intestinal eosinophils by flow cytometry as SSChighCD11b+CD11c+CCR3+Siglec-F+ cells. Intestinal eosinophils resembled eosinophils isolated from thymus and uterus but differed from eosinophils isolated from lung or blood. Eosinophils in intestine, thymus, and uterus showed in vivo a markedly higher life time compared with eosinophils present in lung and blood measured by incorporation of BrdU. This indicates that under steady-state conditions homeostasis of eosinophils is controlled by regulation of cell survival. Intestinal eosinophils are severely reduced in the intestines of Rag-2/common γ-chain double-deficient mice but not Rag-2-deficient mice, correlating with differential expression of GM-CSF and CCL11 in both mouse strains. Moreover, under steady-state conditions, intestinal eosinophils constitutively express high levels of the common γ-chain transcripts compared with lung eosinophils as well as eosinophils present under inflammatory conditions. These observations reveal a hitherto unrecognized diversity in phenotypic and functional properties of eosinophils and suggest that tissue-specific common γ-chain-dependent signals might profoundly affect eosinophil function and homeostasis.
Structure and function of chicken interleukin-1 beta mutants: uncoupling of receptor binding and in vivo biological activity (2016)

Receptor-binding and subsequent signal-activation of interleukin-1 beta (IL-1β) are essential to immune and proinflammatory responses. We mutated 12 residues to identify sites important for biological activity and/or receptor binding. Four of these mutants with mutations in loop 9 (T117A, E118K, E118A, E118R) displayed significantly reduced biological activity. Neither T117A nor E118K mutants substantially affected receptor binding, whereas both mutants lack the IL-1β signaling in vitro but can antagonize wild-type (WT) IL-1β. Crystal structures of T117A, E118A, and E118K revealed that the secondary structure or surface charge of loop 9 is dramatically altered compared with that of wild-type chicken IL-1β. Molecular dynamics simulations of IL-1β bound to its receptor (IL-1RI) and receptor accessory protein (IL-1RAcP) revealed that loop 9 lies in a pocket that is formed at the IL-1RI/IL-1RAcP interface. This pocket is also observed in the human ternary structure. The conformations of above mutants in loop 9 may disrupt structural packing and therefore the stability in a chicken IL-1β/IL-1RI/IL-1RAcP signaling complex. We identify the hot spots in IL-1β that are essential to immune responses and elucidate a mechanism by which IL-1β activity can be inhibited. These findings should aid in the development of new therapeutics that neutralize IL-1 activity.
Thermodynamics of Hydrogen Generation from Methane for Domestic Polymer Electrolyte Fuel Cell Systems (2003)

Abstract Low temperature fuel cells such as the Polymer Electrolyte Fuel Cell (PEFC) are preferably used for domestic applications because of their moderate operating conditions. Using the existing distribution system, natural gas is used as a source for a hydrogen rich gas to power this fuel cell type. The high requirements on the fuel gas quality as well as high conversion efficiencies for the small local gas processing units are critical aspects in the evaluation of decentralized fuel cell systems. In the present paper, three typical gas processing methods are evaluated for the supply of a hydrogen rich gas for PEFCs: steam reforming, partial oxidation, and autothermic conversion. All three processes are studied in detail by varying the relevant process parameters: temperature, pressure, steam to fuel ratio, and oxygen to fuel ratio. The results are graphically displayed in numerous nomograms. With the help of these graphs, regions of stable operation and the sensitivity to the operational parameters are discussed. For all three gas processing methods, the graphs generated display methane conversion, the hydrogen yield, and the yields of unwanted components, i.e., carbon monoxide and solid carbon. Although only steady‐state operating conditions were simulated, critical modes of operation, which might occur during start‐up or transient operation can easily be identified. For instance, operating conditions where soot is generated have to be avoided under all circumstances. All simulations were done with the Gibb's reactor model of a commercial simulation program. The Gibb's reactor model was found to be a suitable tool, since the simulated results compared well with reported literature data. According to the simulation results, the methane‐steam‐reforming process appears to be favorable for application to PEFCs. Methane conversion and hydrogen yields are highest for this process while the yield of CO is relatively low.
La canalisation des fragments de fission (1969)

Abstract On a étudié la canalisation des fragments de fission dans les métaux, en particulier dans le platine et le tungstène. On montre que cette canalisation est très importante, et que les conditions de canalisation pour les fragments de fission sont plus strictes que pour les particules plus légères, comme les particules α. La bonne définition des images obtenues par “canaligraphie” permet de penser que cette technique sera trés utile pour I'étude des défauts cristallins dans les métaux. THE CHANNELING OF FISSION FRAGMENTS The channeling of fission fragments in metals is studied, in particular in platinum and tungsten. It is shown that this channeling is very important, and that the conditions of channeling for fission fragments are more rigorous than for lighter particles, such as α particles. The good resolution of images obtained by “channelography” suggests that this technique will be very useful in the study of crystalline defects in metals.
Procainamide Is a Specific Inhibitor of DNA Methyltransferase 1 (2005)

CpG island hypermethylation occurs in most cases of cancer, typically resulting in the transcriptional silencing of critical cancer genes. Procainamide has been shown to inhibit DNA methyltransferase activity and reactivate silenced gene expression in cancer cells by reversing CpG island hypermethylation. We report here that procainamide specifically inhibits the hemimethylase activity of DNA methyltransferase 1 (DNMT1), the mammalian enzyme thought to be responsible for maintaining DNA methylation patterns during replication. At micromolar concentrations, procainamide was found to be a partial competitive inhibitor of DNMT1, reducing the affinity of the enzyme for its two substrates, hemimethylated DNA and S-adenosyl-l-methionine. By doing so, procainamide significantly decreased the processivity of DNMT1 on hemimethylated DNA. Procainamide was not a potent inhibitor of the de novo methyltransferases DNMT3a and DNMT3b2. As further evidence of the specificity of procainamide for DNMT1, procainamide failed to lower genomic 5-methyl-2'-deoxycytidine levels in HCT116 colorectal cancer cells when DNMT1 was genetically deleted but significantly reduced genomic 5-methyl-2'-deoxycytidine content in parental HCT116 cells and in HCT116 cells where DNMT3b was genetically deleted. Because many reports have strongly linked DNMT1 with epigenetic alterations in carcinogenesis, procainamide may be a useful drug in the prevention of cancer.
SEKİZİNCİ SINIF ÖĞRENCİLERİNİN NOKTALAMA İŞARETLERİNİ UYGULAMA DÜZEYİ (2012)

Oz Bu calismanin amaci sekizinci sinif ogrencilerinin sik kullanilan noktalama isaretlerini dogru uygulayabilme duzeyini belirlemektir. Calisma yedi noktalama isaretinin (nokta, iki nokta, uc nokta, noktali virgul, virgul, soru isareti, unlem) uygulanmasiyla ilgili ayrintili sonuclar sunmaya yoneliktir. Arastirma, 2010-2011 egitim ogretim yilinda Aksaray'da ogrenim goren 208 sekizinci sinif ogrencisi, yedi noktalama isareti ve bu isaretlerle ilgili toplam yirmi kural ile sinirlidir. Arastirmada tarama modeli kullanilmistir. Sekizinci sinif ogrencilerinin noktalama isaretlerini uygulayabilmede basari duzeyini belirlemek icin arac olarak dort farkli test kullanilmistir. Arastirmada elde edilen veriler, SPSS 15.0 kullanilarak betimsel istatistik analizi ve bagimsiz t-testi ile cozumlenmistir. Dort farkli testten olusan arastirma sonuclarina gore dogru cevaplarin en fazla oldugu test coktan secmeli, en az oldugu ise dikte uygulamasidir. Kiz ogrenciler, erkeklere gore daha fazla dogru cevap vermistir. Dershaneye giden ogrenciler, dershaneye gitmeyen ogrencilere gore daha fazla dogru cevap vermistir. Ogrencilerin uygulamada en fazla dogru cevap verdikleri isaret soru isareti, en az dogru cevap verdikleri isaret ise noktali virguldur. Ogrencilerin noktalama isaretlerini dogru ogrenip ogrenmedikleri farkli tekniklerle denetlenmeli ve uygun teknikler secilerek isaretlerin islevleri kavratilmalidir. Anahtar Kelimeler: Turkce ogretimi, noktalama kurallari, noktalama isaretleri.
Role of MYC in Medulloblastoma (2013)

Since its discovery as an oncogene carried by the avian acute leukemia virus MC29 in myelocytomatosis (Roussel et al. 1979) and its cloning (Vennstrom et al. 1982), c-MYC (MYC), as well as its paralogs MYCN and MYCL1, has been shown to play essential roles in cycling progenitor cells born from proliferating zones during embryonic development, and in all proliferating cells after birth. MYC deletion induces cell-cycle exit or cell death, depending on the cell type and milieu, whereas MYC and MYCN amplification or overexpression promotes cell proliferation and occurs in many cancers. Here, we review the relationship of MYC family proteins to the four molecularly distinct medulloblastoma subgroups, discuss the possible roles MYC plays in each of these subgroups and in the developing cells of the posterior fossa, and speculate on possible therapeutic strategies targeting MYC.
Revisiting Annie Hall: Exploring Jewish Identity on the Silver Screen (2018)

In 1978
Transient kinetics of heparin-catalyzed protease inactivation by antithrombin III. The reaction step limiting heparin turnover in thrombin neutralization. (1986)

The intrinsic protein fluorescence quenching which accompanies the heparin-accelerated inhibition of thrombin (T) by antithrombin III (AT) was resolved into a heparin-independent component associated with formation of the product T-AT complex and a component associated with an AT conformational change linked to heparin dissociation. To determine whether dissociation of heparin from the product T-AT complex limits the rate at which heparin can turn over catalytically, the kinetics of protein fluorescence quenching during the reaction of thrombin with AT X heparin complex (AT X H) were investigated by stopped-flow fluorimetry under pseudo-first order conditions ([AT X H]o much greater than [T]o). Both fluorescence components were quenched in a single exponential reaction with a hyperbolic dependence of the first order rate constant (kobs) on [AT X H]o. An indistinguishable hyperbolic dependence of kobs on [AT X H]o was measured by displacement of p-aminobenzamidine from the T active site, with both signals extrapolating to a limiting rate constant of 5 s-1. These results indicate that heparin dissociation occurs concomitant with T-AT complex formation at the limiting 5 s-1 rate constant. In reasonable agreement with this value, a kcat of 2.3 s-1 was determined for heparin turnover at catalytic concentrations. We conclude that formation of the T-AT complex is the primary rate-limiting step in heparin catalytic turnover and that this reaction is accompanied by a change in conformation of the AT component resulting in facile heparin dissociation.
Description and dosimetric verification of the <scp>PEREGRINE</scp> Monte Carlo dose calculation system for photon beams incident on a water phantom (2001)

PEREGRINE is a three-dimensional Monte Carlo dose calculation system written specifically for radiotherapy. This paper describes the implementation and overall dosimetric accuracy of PEREGRINE physics algorithms, beam model, and beam commissioning procedure. Particle-interaction data, tracking geometries, scoring, variance reduction, and statistical analysis are described. The BEAM code system is used to model the treatment-independent accelerator head, resulting in the identification of primary and scattered photon sources and an electron contaminant source. The magnitude of the electron source is increased to improve agreement with measurements in the buildup region in the largest fields. Published measurements provide an estimate of backscatter on monitor chamber response. Commissioning consists of selecting the electron beam energy, determining the scale factor that defines dose per monitor unit, and describing treatment-dependent beam modifiers. We compare calculations with measurements in a water phantom for open fields, wedges, blocks, and a multileaf collimator for 6 and 18 MV Varian Clinac 2100C photon beams. All calculations are reported as dose per monitor unit. Aside from backscatter estimates, no additional, field-specific normalization is included in comparisons with measurements. Maximum discrepancies were less than either 2% of the maximum dose or 1.2 mm in isodose position for all field sizes and beam modifiers.
Use of amorphous silicon tandem junction solar cells for hydrogen production in a photoelectrochemical cell (2006)

We report the use of amorphous silicon (a-Si) tandem junctions as part of an integral "hybrid" photoelectrochemical (PEC) cell to produce hydrogen directly from water using sunlight. The device configuration consists of stainless steel (SS)/ni<sub>2</sub>pni<sub>1</sub>p/ZnO/WO<sub>3</sub>. When the device is immersed in an electrolyte and illuminated, O<sub>2</sub> is evolved at the WO<sub>3</sub>/electrolyte interface and H<sub>2</sub> is produced at the counter electrode. A voltage >1.23V is required to split water; typically 1.6-1.8V are needed, taking account of losses in a practical water-splitting system. We use a-Si tandem cells, deposited by plasma-enhanced chemical vapor deposition, to supply this voltage. Current matching in the two a-Si subcells is achieved by altering the thicknesses of the two layers (i<sub>1</sub> and i<sub>2</sub>) while keeping their band gaps at ~1.75eV, which results in a device with an open circuit voltage >1.6V, short circuit current density (J<sub>sc</sub>) >6mA/cm<sup>2</sup> (on SS substrates), and a fill factor >0.6. Deposition on a textured SnO<sub>2</sub> coated glass has resulted in J<sub>sc</sub> >9mA/cm<sup>2</sup>. Photoactive WO<sub>3</sub> films, deposited using the RF sputtering technique, have achieved photocurrents >3mA/cm<sup>2</sup> at 1.6V vs. saturated calomel electrode (SCE). The PEC device operates at the point at which the WO<sub>3</sub> photocurrent IV curve and the a-Si (filtered by WO<sub>3</sub>) light IV curve cross, leading to operating currents of 2.5mA/cm<sup>2</sup> and solar-to-hydrogen (STH) conversion efficiency of >3%.
Thermal characteristics of submicron vias studied by scanning Joule expansion microscopy (2000)

Thermal characteristics of submicron vias strongly impact reliability of multilevel VLSI interconnects. The magnitude and spatial distribution of the temperature rise around a via are important to accurately estimate interconnect lifetime under electromigration (EM), which is temperature dependent. Localized temperature rise can cause stress gradients inside the via structures and can also lead to thermal failures under high current stress conditions, such as electrostatic discharge (ESD) events. This letter reports the first use of a novel thermometry technique, scanning Joule expansion microscopy, to study the steady state and dynamic thermal behavior of small geometry vias under sinusoidal and pulsed current stress. Measurement of the spatial distribution of temperature rise around a submicron via is reported with sub-0.1 μm resolution, along with other thermal characteristics including the thermal time constant.
Biochemical and Structural Characterization of the <i>trans</i>-Enoyl-CoA Reductase from <i>Treponema denticola</i> (2012)

The production of fatty acids is an important cellular pathway for both cellular function and the development of engineered pathways for the synthesis of advanced biofuels. Despite the conserved reaction chemistry of various fatty acid synthase systems, the individual isozymes that catalyze these steps are quite diverse in their structural and biochemical features and are important for controlling differences at the cellular level. One of the key steps in the fatty acid elongation cycle is the enoyl-ACP (CoA) reductase function that drives the equilibrium forward toward chain extension. In this work, we report the structural and biochemical characterization of the trans-enoyl-CoA reductase from Treponema denticola (tdTer), which has been utilized for the engineering of synthetic biofuel pathways with an order of magnitude increase in product titers compared to those of pathways constructed with other enoyl-CoA reductase components. The crystal structure of tdTer was determined to 2.00 Å resolution and shows that the Ter enzymes are distinct from members of the FabI, FabK, and FabL families but are highly similar to members of the FabV family. Further biochemical studies show that tdTer uses an ordered bi-bi mechanism initiated by binding of the NADH redox cofactor, which is consistent with the behavior of other enoyl-ACP (CoA) reductases. Mutagenesis of the substrate binding loop, characterization of enzyme activity with respect to crotonyl-CoA, hexenoyl-CoA, and dodecenoyl-CoA substrates, and product inhibition by lauroyl-CoA suggest that this region is important for controlling chain length specificity, with the major portal playing a more important role for longer chain length substrates.
Intensification of protein extraction from soybean processing materials using hydrodynamic cavitation (2017)

High pressure homogenisation (HPH) has been investigated for its potential to aid the aqueous extraction of protein and other components from soybeans. HPH treatments (50–125 MPa) were applied to soy slurry and okara, the diluted waste stream from soybase production. Extraction yields of oil, protein and solids were calculated, and the feasibility of the technology was assessed. The most productive HPH treatment investigated improved extraction yields of protein up to 82% with a single pass of soy slurry at 100 MPa. In comparison, a maximal protein extraction yield of 70% has been achieved previously using ultrasound at lab-scale for 15 min (20 kHz, 65 W according to manual, 13 mm probe tip) (Preece et al., in press). Results showed a particle size reduction upon HPH and disruption of intact cells, confirmed via confocal laser scanning microscopy. Multiple HPH passes of soy slurry caused an increase in dynamic viscosity and a small increase in particle size probably due to cell wall swelling, resulting in decreased separation efficiency and consequently a reduced extraction yield. HPH offers extraction assistance, with more promising results reported in comparison to ultrasound-assisted extraction of soybean processing materials. Improvement of current soybean processing is desirable on an industrial level to better use available raw materials and reduce waste production. This study shows the effects of a technology already widely employed in industry for other benefits, such as fine emulsion production and microbial cell disruption. High pressure homogenisation was carried out on a lab-scale on soybean processing materials which were prepared in a pilot plant, with similar feed compositions to those produced at an industrial scale.
Strategies for analysing and improving the expression and quality of recombinant proteins made in mammalian cells (2009)

The production of monoclonal antibodies and other recombinant proteins is one of the highest growth areas in the pharmaceutical industry. Mammalian cells are used to manufacture the majority of biotherapeutics, largely due to their ability to perform complex post-translational modifications. Although significant progress has been made recently in improving product yields and protein quality, many challenges still lie ahead to achieve consistently high yields while avoiding potentially damaging protein modifications. The present review first considers the strategies used to analyse and improve recombinant protein expression of industrial cell lines, with an emphasis on proteomic technologies. Next, cellular and environmental influences on protein production and quality are examined, and strategies for improvements in product yield and quality are reviewed. The analytical techniques required to detect these protein changes are also described, together with prospects for assay improvements.
Experimental evaluation of wireless simulation assumptions (2004)

All analytical and simulation research on ad~hoc wireless networks must necessarily model radio propagation using simplifying assumptions. We provide a comprehensive review of six assumptions that are still part of many ad hoc network simulation studies, despite increasing awareness of the need to represent more realistic features, including hills, obstacles, link asymmetries, and unpredictable fading. We use an extensive set of measurements from a large outdoor routing experiment to demonstrate the weakness of these assumptions, and show how these assumptions cause simulation results to differ significantly from experimental results. We close with a series of recommendations for researchers, whether they develop protocols, analytic models, or simulators for ad~hoc wireless networks.
Eddy current coil interaction with a right-angled conductive wedge (2005)

The time-harmonic electromagnetic field in an electrically conductive right-angled wedge due to an inductive excitation by circular coil in air has been calculated. Using a formulation in Cartesian coordinates, the problem domain is truncated in a dimension whose axis is normal to a wedge face, and an approximate series solution found using elementary functions satisfying Maxwell's equations in the quasi-static limit. The coil impedance variation with position and frequency is calculated and compared with measurements made on a coil near the edge of a large aluminium block which approximates the effect of a conductive quarter-space. The comparison between theory and experiment shows very close agreement.