gebhart/patrepeval huggingface dataset:
Distinct 19 S and 20 S subcomplexes of the 26 S proteasome and their distribution in the nucleus and the cytoplasm. (1994)

The 26 S proteolytic complex ("26 S proteasome") is a macromolecular assembly thought to be involved in ATP- and ubiquitin-dependent protein degradation in the cytoplasm of higher eukaryotic cells. This complex is composed of one 20 S cylinder particle (multicatalytic proteinase, 20 S proteasome) and two cap-shaped 19 S particles comprising a set of polypeptides in the M(r) range of 35,000-110,000. Here we show that cell supernatant fractions contain both these two subunit complexes as distinct particles as well as assembled to 26 S proteasomes. We have separated and purified all three forms from Xenopus laevis oocytes and have determined their peptidase and protease activities. Using various antibodies specific for either a constitutive p52 polypeptide of the 19 S cap complex or for proteins of the 20 S cylinder particle, we have immunolocalized these complexes in both the cytoplasm and the nucleus of diverse species and cell types. The occurrence of all three forms, the 26 S proteasome, the 20 S cylinder particle, and the 19 S cap complex in the nucleoplasm has also been demonstrated in analyses of isolated giant nuclei from Xenopus oocytes. In addition, we show that the 19 S and 20 S subcomplexes can be released from 26 S proteasomes by ATP depletion and that readdition of ATP to 19 S and 20 S particles in cell extracts leads to the reformation of 26 S proteasomes. We discuss that all three particles (19 S, 20 S, and 26 S) exist in a dynamic equilibrium in both cell compartments and serve cytoplasmic as well as nucleus-specific functions.
The Numerical Range of a Simple Compression (2017)

The numerical range of a contraction acting on L(C2) is identified, so allowing one to exhibit a hermitian projection that is not ultrahermitian. An explicit formula for the norm of the associated operator κm translates into a family of inequalities in four complex variables.
Low-power prediction based data transfer architecture (2006)

The energy dissipation of on-chip buses is becoming one of the main bottlenecks in current integrated circuits. This paper proposes a prediction-based technique to reduce data bus power dissipation. This technique uses value prediction to speculate the next value to transfer over the data bus. Two identical predictors are placed on the two ends of the bus. If the sender predictor accurately predicts the data to be transferred, data is not transmitted, and the bus energy dissipation is reduced. After implementing the proposed architecture in a 70nm CMOS technology, and using a representative subset of SPEC2K benchmarks, an average of 41% of the bus transitions were eliminated, which led to a 31% average overall energy reduction
Measurement of on-chip waveforms and pulse propagation in digital GaAs integrated circuits by picosecond electro-optic sampling (1986)

We demonstrate precise measurement of sub-100 ps rise time on-chip electrical waveforms and of pulse propagation in digital GaAs integrated circuits with the use of picosecond electro-optic sampling. These experiments yield the first non-invasive measurement of single-gate propagation delays via direct and precise observation of on-chip waveforms at the input and output of individual logic gates internal to an integrated circuit.
Crystal structure of saposin B reveals a dimeric shell for lipid binding (2002)

Saposin B is a small, nonenzymatic glycosphingolipid activator protein required for the breakdown of cerebroside sulfates (sulfatides) within the lysosome. The protein can extract target lipids from membranes, forming soluble protein-lipid complexes that are recognized by arylsulfatase A. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity.
Impaired intestinal barrier integrity in the colon of patients with irritable bowel syndrome: involvement of soluble mediators (2008)

Our study shows that colonic soluble mediators are able to reproduce functional (permeability) and molecular (ZO-1 mRNA expression) alterations observed in IBS patients. These findings might pave the way both to identify novel biomarkers as well as new therapeutic targets in IBS.
A kinetic study of the 1,3-cycloaddition of benzonitrile oxides to para-substituted β-aminocinnamonitriles (1990)

Stable arylnitrile oxides undergo 1,3-cycloaddition to β-aminocinnamonitriles at the CN or the CC bond, which gives rise to 3,5-disubstituted 1,2,4-oxadiazoles or 3,5-diaryl-4-cyanoisoxazoles, respectively, by parallel reactions in different solvents. Overall kinetics were measured at temperatures in the range 50–90 °C; product selectivities were determined by HPLC rate coefficients for the parallel reactions were, thus, obtained. Rates were enhanced by increasing the solvent polarity. Hammett plots for substitution on the nitrile oxide benzene ring were V-shaped; those for substitution on the enaminonitrile benzene ring had negative ρ-values.
Sex hormone levels correlate with the activity of cytokine‐secreting cells <i>in vivo</i> (2000)

This work examines the correlation between serum levels of oestrogen, progesterone and dehydroepiandrosterone sulphate (DHEA-S) and the number of human peripheral blood cells actively secreting interleukin (IL)-2, IL-4, IL-6, IL-10, tumour necrosis factor-alpha (TNF-alpha) or interferon-gamma (IFN-gamma) in vivo. Simultaneous assessment of serum hormone levels and cytokine-secreting cell activity throughout the menstrual cycle showed that the number of peripheral blood mononuclear cells (PBMC) able to secrete IL-4 in response to stimulation correlated significantly (P < 0.0001) with oestrogen levels and fluctuated with the menstrual cycle in pre-menopausal women. The activity of IFN-gamma-secreting cells, on the other hand, varied as a function of serum DHEA-S levels in pre-menopausal women (P < 0.0001). Similarly, the number of cells secreting IFN-gamma in men correlated with serum DHEA-S levels (P < 0.001). In contrast, post-menopausal women had fewer cells actively secreting cytokines and the activity of these cells did not correlate with sex hormone levels. These results suggest that sex hormones may modulate cytokine production in vivo and contribute to gender-related differences in normal and pathological immune responses.
<i>In Vitro</i> Imaging and <i>in Vivo</i> Liver Targeting with Carbohydrate Capped Quantum Dots (2009)

PEGylated quantum dots (QDs) capped with d-mannose, d-galactose, and d-galactosamine have been synthesized. The stable, high quantum yield fluorescence of QDs was exploited to study specific carbohydrate-protein interactions in vitro and in vivo.
Solid tumor models for the assessment of different treatment modalities: I. Radiation-induced changes in growth rate characteristics of a solid tumor model. (1975)

A computer program has been developed to quantitatively evaluate changes in tumor growth rates of a solid tumor model (hepatoma 3924A) after a series of radiation doses from 375 R to 3750 R. The computer-derived growth curves are simulated from the volumes of the individual tumors rather than from the mean tumor volume at any specific time point after treatment. The ability to generate data from a family of tumor growth curves permits a more precise evaluation of therapeutic effects on tumors than can be obtained with conventional methods. The quantitative determination of equivalent amounts of radiation needed to produce comparable 5-fluorouracil-induced changes in tumor growth rate has been made. The ability to determine quantitatively radiotherapeutic and chemotherapy equivalents on these solid tumor models has direct implications in regard to our effort to improve the treatment of cancer. At present no specific solid tumor or groups of solid tumors have provided all of the necessary information for clinical utilization in therapeutic scheduling of different forms of cancer treatment. Since solid tumors comprise the majority of human cancer, one of the primary objectives of these studies has been the establishment of a solid tumor model that could serve both as a system for devising improved therapeutic scheduling and for a better understanding of solid tumors.
Loudspeakers on Damped Pipes (2000)

First Locanthi's horn analog is shown to be well suited for modeling transmission-line loudspeaker systems. The circuit can accommodate arbitrary flare shapes and allows damping to be included as any combination of series and parallel losses. Four empirical parameters are then developed to simulate the effects of lining or stuffing. Finally three optimized transmission-line geometries are presented, which can be described in terms of generalized alignments using familiar Thiele-Small parameters. Using one of these new alignments, a transmission line can match the frequency response and efficiency of a comparable closed box, but with reduced cone excursion.
Thermomechanical fatigue of solder joints: a new comprehensive test method (1989)

A comprehensive method for testing solder joints under conditions of thermomechanical fatigue is presented. The method involves simultaneous imposition of temperature cycles and strain on discrete solder joints in a shear orientation. The stress, microstructure, and number of cycles to failure were monitored. Cycles to failure were determined by a continuous electrical detection method. 60Sn-40Pb and 40Sn-40In-20Pb solder joints were tested using the proposed method at 20% shear strain. The 60Sn-40Pb alloy has a shorter fatigue lifetime than 40Sn-40In-20Pb. This is attributed to heterogeneous coarsening strain in a small area of the 60Sn-40Pb microstructure. In contrast, the 40Sn-40In-20Pb microstructure becomes refined. The heterogeneous coarsening also results in cyclic softening in 60Sn-Pb, which was not observed in 40Sn-40In-20Pb. Failures initiated within the coarsened band in 60Sn-40Pb at Sn-Sn grain boundaries or phase boundaries. In contrast, failures initiated at the surface of 40Sn-40In-20Pb joints and propagated through both phases of the microstructure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Distinct epitopes on the T cell antigen receptor of HPB-ALL tumor cells identified by monoclonal antibodies. (1986)

The T cell antigen receptor is a approximately 90,000 dalton disulfide linked heterodimer that is non-covalently associated with the CD3 complex. Prior studies have demonstrated that anti-CD3 or -Ti antibodies can mimic antigen and induce cellular proliferation and the secretion of lymphokines. An early event in activation via CD3/Ti is a rapid increase in concentration of intracellular Ca2+ levels. In the present studies, we have produced a panel of monoclonal antibodies (MAb) against the Ti expressed on HPB-ALL tumor cells. All MAb immunoprecipitate a approximately 90,000 dalton disulfide linked heterodimer and induced co-modulation of Ti and CD3. On the basis of competitive binding studies, four distinct epitopes on the Ti of HPB-ALL were identified with MAb L38, L39, L41, and L42. These epitopes were additionally discriminated on the basis of reactivity with normal polyclonal T cell populations and functional effects on HPB-ALL. L39 reacted with a monomorphic epitope present on approximately 2 to 5% of peripheral blood T lymphocytes from all donors examined and was specifically mitogenic for peripheral blood T cells expressing this epitope. L39+ T cells in blood included both CD4+ and CD8+ lymphocytes. In contrast, L38, L41, and L42 failed to react with peripheral blood T cells and were not mitogenic for peripheral blood lymphocytes. Anti-Leu-4, L38, L39, and L41 MAb all induced a rapid increase in (Ca2+)i in HPB-ALL tumor cells, similar to previous findings with anti-CD3 and anti-Ti MAb against various tumor cells and peripheral blood T cells. In contrast, L42 MAb did not induce a substantial increase in (Ca2+)i. Failure of L42 to induce a substantial increased (Ca2+)i could not be attributed to the apparent titer, avidity, or isotype of the antibody. These findings suggest that induction of increased (Ca2+)i upon binding of Ti is epitope dependent. Furthermore, these data demonstrate that several distinct public and private epitopes can be identified on the T cell antigen receptor.
Hydrogen Storage in the Giant‐Pore Metal–Organic Frameworks MIL‐100 and MIL‐101 (2006)

Eine große Wasserstoff-Speicherkapazität bei der Temperatur von flüssigem Stickstoff zeigt das metall-organische Gerüst MIL-101. In der Zeotyp-Architektur dieses porösen Feststoffs (siehe Bild) ist jeder Schnittpunkt zwischen den Käfigen von einem Supertetraeder besetzt, das aus Trimeren von Chromoktaedern besteht, die mithilfe von Benzol-1,4-dicarboxylat-Liganden aufgebaut wurden. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2006/z600105_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Sorption and partial molar volume of gases in poly (dimethyl siloxane) (1990)

Abstract Sorption of N 2 , O 2 , Ar, CH 4 , CO 2 , C 2 H 4 , and C 2 H 6 in poly (dimethyl siloxane) liquid and rubber and the dilation of the polymers due to sorption of the gases are studied at 25°C under pressures up to 50 atm. In the liquid, the sorption isotherms for low‐solubility and high‐solubility gases are described by Henry's law and the Flory–Huggins equation, respectively. Gas sorption in the rubber, which contains a 29 wt % silica filler, follows the dual‐mode sorption model, though marked hysteresis is observed in the sorption of O 2 and CH 4 . The dilation isotherms increase linearly or exponentially in both polymers with increasing pressure. Considering that gas molecules adsorbed into micropores of the filler particles do not participate in the dilation, partial molar volumes of the dissolved gases in the rubber are determined from data of sorption and dilation. The values are nearly equal to the partial molar volumes in the liquid (48–60 cm 3 /mol).
Acute hypoxia influences collagen and matrix metalloproteinase expression by human keratoconus cells in vitro (2017)

Keratoconus (KC) is a progressive corneal ectasia linked to thinning of the central cornea. Hard contact lenses, rigid gas permeable lenses, and scleral lenses are the primary treatment modalities for early to mid- stages of KC to correct refractive error and astigmatism that develops as a result of an irregular corneal structure. These treatments are associated with significant drawbacks, including reduced availability of the tear film and oxygen to the corneal epithelium and stroma. However, it remains unknown whether hypoxia affects corneal integrity in the KC pathobiology. A number of studies have associated elevated oxidative stress with KC both in vitro and ex vivo. We hypothesized that KC-derived corneal fibroblasts are more susceptible to hypoxia-induced oxidative stress compared to healthy controls leading to exacerbation of corneal thinning in KC. This study investigated the effects of hypoxia on ECM secretion, assembly, and matrix metalloproteinase (MMP) expression in human corneal fibroblasts from healthy controls (HCFs) and KC patients (HKCs) in vitro. HCFs and HKCs were cultured in 3D constructs for 3 weeks and maintained or transferred to normoxic (21% O2) or hypoxic (2% O2) conditions, respectively, for 1 additional week. At the 4 week time-point, constructs were isolated and probed for Collagen I, III, and V, keratocan and MMP-1, -2, -3, -9, and -13, as well as hypoxia markers, hypoxia inducible factor-1α and lactoferrin. Conditioned media was also collected and probed for Collagen I, III, and V by Western blot. Thickness of the ECM assembled by HCFs and HKCs was measured using immunofluorescence microscopy. Results showed that hypoxia significantly reduced Collagen I secretion in HKCs, as well as upregulated the expression of MMP-1 and -2 with no significant effects on MMP-3, -9, or -13. ECM thickness was reduced in both cell types following 1 week in a low oxygen environment. Our study shows that hypoxia influences collagen and MMP expression by HKCs, which may have consequential effects on ECM structure in the context of KC.
Structure and Physiological Actions of Ghrelin (2013)

Ghrelin is a gastric peptide hormone, discovered as being the endogenous ligand of growth hormone secretagogue receptor. Ghrelin is a 28 amino acid peptide presenting a unique n-octanoylation modification on its serine in position 3, catalyzed by ghrelin O-acyl transferase. Ghrelin is mainly produced by a subset of stomach cells and also by the hypothalamus, the pituitary, and other tissues. Transcriptional, translational, and posttranslational processes generate ghrelin and ghrelin-related peptides. Homo- and heterodimers of growth hormone secretagogue receptor, and as yet unidentified receptors, are assumed to mediate the biological effects of acyl ghrelin and desacyl ghrelin, respectively. Ghrelin exerts wide physiological actions throughout the body, including growth hormone secretion, appetite and food intake, gastric secretion and gastrointestinal motility, glucose homeostasis, cardiovascular functions, anti-inflammatory functions, reproductive functions, and bone formation. This review focuses on presenting the current understanding of ghrelin and growth hormone secretagogue receptor biology, as well as the main physiological effects of ghrelin.
Formation, Transformation, and Decomposition of Y <sub>2</sub> TeO <sub>6</sub> (1988)

A metastable modification of Y 2 TeO 6 crystallizes at 770°C to 870°C at a heating rate of 10°C·min −1 in air from an amorphous material prepared by the simultaneous hydrolysis of yttrium and tellurium alkoxides. It has a tetragonal unit cell with a=1.0428 nm and c=1.7524 nm. The tetragonal‐to‐hexagonal phase transformation occurs at 920° to 960°C. Hexagonal Y 2 TeO 6 decomposes into Y 6 TeO 12 and TeO 3 ↑ at 1220° to 1320°C; only Y 6 TeO 12 is obtained as the decomposition product. Both modifications of Y 2 TeO 6 are built up by octahedral TeO 6 groups.
Voltage-jump relaxation kinetics for wild-type and chimeric beta subunits of neuronal nicotinic receptors. (1996)

We have studied the voltage-jump relaxation currents for a series of neuronal nicotinic acetylcholine receptors resulting from the coexpression of wild-type and chimeric beta 4/beta 2 subunits with alpha 3 subunits in Xenopus oocytes. With acetylcholine as the agonist, the wild-type alpha 3 beta 4 receptors displayed five- to eightfold slower voltage-jump relaxations than did the wild-type alpha 3 beta 2 receptors. In both cases, the relaxations could best be described by two exponential components of approximately equal amplitudes over a wide range of [ACh]'s. Relaxation rate constants increased with [ACh] and saturated at 20- to 30-fold lower concentrations for the alpha 3 beta 2 receptor than for the alpha 3 beta 4 receptor, as observed previously for the peak steady state conductance. Furthermore, the chimeric beta 4/beta 2 subunits showed a transition in the concentration dependence of the rate constants in the region between residues 94 and 109, analogous to our previous observation with steady state conductances. However, our experiments with a series of beta-subunit chimeras did not localize residues that govern the absolute value of the kinetic parameters. Hill coefficients for the relaxations also differed from those previously measured for steady state responses. The data reinforce previous conclusions that the region between residues 94 and 109 on the beta subunit plays a role in binding agonist but also show that other regions of the receptor control gating kinetics subsequent to the binding step.
Saporin as a Commercial Reagent: Its Uses and Unexpected Impacts in the Biological Sciences—Tools from the Plant Kingdom (2022)

Saporin is a ribosome-inactivating protein that can cause inhibition of protein synthesis and causes cell death when delivered inside a cell. Development of commercial Saporin results in a technology termed 'molecular surgery', with Saporin as the scalpel. Its low toxicity (it has no efficient method of cell entry) and sturdy structure make Saporin a safe and simple molecule for many purposes. The most popular applications use experimental molecules that deliver Saporin via an add-on targeting molecule. These add-ons come in several forms: peptides, protein ligands, antibodies, even DNA fragments that mimic cell-binding ligands. Cells that do not express the targeted cell surface marker will not be affected. This review will highlight some newer efforts and discuss significant and unexpected impacts on science that molecular surgery has yielded over the last almost four decades. There are remarkable changes in fields such as the Neurosciences with models for Alzheimer's Disease and epilepsy, and game-changing effects in the study of pain and itch. Many other uses are also discussed to record the wide-reaching impact of Saporin in research and drug development.
Low-dielectric-constant cross-linking polymers: Film electrets with excellent charge stability (1999)

The cross-linking low-dielectric-constant polymers benzocyclobutene (BCB) and perfluorocyclobutene (PFCB) are identified as film electrets with excellent charge stability, comparable to the members of the polytetrafluoroethylene family. BCB and PFCB films can be easily prepared on substrates by spin coating. The onset of molecular motion at the high- and low-temperature glass-like transitions is revealed by dielectric dilatometry. BCB and PFCB electret films exhibit remarkable stability regarding both negative and positive charging. They enlarge the family of charge electrets and may thus become interesting for miniaturized electret devices.
MANAGEMENT OF OIL SANDS TAILINGS (2002)

ABSTRACT In Alberta, oil sands bitumen is utilized for synthetic crude oil (SCO) production by surface mining, bitumen extraction followed by primary (coking) and secondary (catalytic hydrotreating) upgrading processes. SCO is further refined in specially designed or slightly modified conventional refineries into transportation fuels. Oil sands tailings, composed of water, sands, silt, clay and residual bitumen, is produced as a byproduct of the bitumen extraction process. The tailings have poor consolidation and water release characteristics. For twenty years, significant research has been performed to improve the consolidation and water release characteristics of the tailings. Several processes were developed for the management of oil sands tailings, resulting in different recovered water characteristics, consolidation rates and consolidated solid characteristics. These processes may affect the performance of the overall plant operations. Apex Engineering Inc. (AEI) has been developing a process for the same purpose. In this process oil sands tailings are treated with Ca(OH)2 lime and CO2 and thickened using a suitable thickener. The combination of chemical treatment and the use of a thickener results in the release of process water in short retention times without accumulation of any ions in the recovered water. This makes it possible to recycle the recovered water, probably after a chemical treatment, as warm as possible, which improves the thermal efficiency of the extraction process. The AEI Process can be applied in many different fashions for the management of different fractions of the tailings effluent, depending on the overall plant operating priorities.