gebhart/patrepeval huggingface dataset:
Phosphoinositide-binding peptides derived from the sequences of gelsolin and villin. (1992)

The polyphosphoinositides phosphatidylinositol 4-monophosphate (PIP) and phosphatidylinositol 4,5-bisphosphate (PIP2) inactivate the actin filament-severing proteins villin and gelsolin and dissociate them from monomeric and polymeric actin. A potential polyphosphoinositide- (PPI) binding site of human plasma gelsolin regulating filament severing has been localized to the region between residues 150-169 and to the corresponding region in villin which occurs in the second of six homologous domains present in both proteins. Synthetic peptides based on these sequences bind tightly to both PIP and PIP2, in either micelles or bilayer vesicles, compete with gelsolin for binding to PPIs, and dissociate gelsolin-PIP2 complexes, restoring severing activity to the protein. These peptides also bind with moderate affinity to F-actin, suggesting that inactivation of the severing function of the intact proteins by PPIs results from competition between actin and PPIs for a critical binding site on gelsolin-villin. The PPI-binding peptides contain numerous basic amino acids, but their effects on PPIs are far greater than those of Arg or Lys oligomers, a highly basic peptide derived from the calmodulin-binding site of myristoylated, alanine-rich kinase C substrate protein, or the 5-kDa actin-binding protein thymosin beta-4, suggesting that specific aspects of the primary and secondary structure of these basic peptides are important for their interaction with the acidic headgroups of PPIs. In addition to elucidating the structure of PIP2-binding sites in gelsolin, the results describe a sensitive assay for phosphoinositide-binding molecules based on their ability to prevent inhibition of gelsolin function.
Cardiac PET-CT (2007)

Integrated positron emission tomography computed tomography (PET/CT) scanners allow a true integration of the structure and function of the heart. Myocardial perfusion PET provides a high sensitivity (91%) and specificity (89%) for the diagnosis of obstructive coronary artery disease (CAD). But, as with single photon emission CT, relative perfusion PET often uncovers only the territory subtended by the most severe coronary stenosis, leading to underestimation of the extent of CAD. In contrast, quantitative PET provides a noninvasive assessment of myocardial blood flow and coronary flow reserve and improves detection of preclinical and multivessel coronary atherosclerosis. Similarly, CT coronary angiography is an accurate means to image the entire continuum of anatomic coronary atherosclerosis from nonobstructive to obstructive CAD. However, not all coronary stenoses are hemodynamically significant and <50% of the patients with obstructive CAD on CT angiography demonstrate stress induced perfusion defects. Stress PET data complement the anatomic information on the CT angiogram by providing instant readings about the ischemic burden of coronary stenoses. Thus, combined PET/CT may be potentially superior to CT angiography alone for the guiding revascularization decisions. Further, fusion of the PET and CT angiogram images allows identification of the culprit stenosis in patients presenting with chest pain. Finally, the advances in molecular imaging and image fusion may soon make noninvasive detection of vulnerable coronary plaques a clinical reality. In summary, integrated PET/CT is a powerful new noninvasive modality that offers the potential for refined diagnosis and management of the entire spectrum of coronary atherosclerosis.
Measurements and analyses of substrate noise waveform in mixed signal IC environment (2003)

A transition controllable noise source is developed in a 0.4 /spl mu/m CMOS, P-substrate N-well technology, for experimental studies on substrate noise properties in a mixed signal IC environment. The number of active logic elements, transition directions, and delays can be controlled. Measured substrate noise waveforms with 100 ps time resolution show that peaks in substrate voltage, reflecting logic transition frequencies, have a time constant a few times larger than the switching time. Analyses with equivalent circuits make it clear that this process results from charge transfer between parasitic capacitance of entire logic circuits and an external supply, through supply/return parasitic impedance.
Castration-Induced Apoptosis in the Rat Ventral Prostate Is Associated with Increased Expression of Genes Encoding Insulin-Like Growth Factor Binding Proteins 2, 3, 4 and 5 (1998)

Insulin-like growth factor binding proteins (IGFBPs) have recently been demonstrated to act as regulators of apoptosis in vitro in both prostate and breast cancer cell lines. We show here that gene expression of IGFBP-2,-3,-4 and -5 increase rapidly in the rat ventral prostate following castration. Increases in IGFBP mRNA levels were detectable by Northern blotting by 6 hours and reached 5 to 10 fold of control levels at 72 hours after castration. Apoptosis in the ventral prostate, as detected in situ by the TUNEL method, was also induced as early as 6 hours after castration. TRPM-2/clusterin, a gene known to be associated with involution of the prostate, was not detected in sham castrated controls but was expressed by 24 hours following androgen ablation. IGF-I mRNA levels increased to 160% of control values within 6 hours following castration, then decreased gradually over the next 72 hours to 35% of control. Affinity labelling experiments demonstrated that IGF-I receptor levels increased initially after castration with peak binding at 24 hours, then declined to levels lower than control. These results suggest that rapid induction of IGFBPs in the rat ventral prostate following androgen ablation may play a role in apoptosis and involution of the prostate gland.
On PVT-data, well treatment, and prepartion of input data for an isothermal gas-water-foam version of MULKOM (1988)

MULKOM is a multi-dimensional numerical model for simulating the coupled mass and heat transport of multiphase fluids in permeable media. Originally developed for geothermal reservoir simulation, MULKOM features a modular architecture which facilitates applications to a variety of flow systems of interest in subsurface resource recovery storage. The notes assembled in this report are intended to assist in applications of a particular version of MULKOM adapted for isothermal flow of gas-water-foam mixtures. Not all of these three phases need be present; for example, systems containing only gas and water may be simulated by setting foam saturation (volume fraction of foam) to a very small value. It is emphasized that the version of MULKOM described here is under continuing development; the chief shortcoming at the present time being the treatment of foam as an indestructible phase rather than as an emulsion of gas surfactant solution with texture changing in response to flow. The section on PVT treatment highlights the correlations used to calculate thermophysical properties of the foam and gas phases, and gives detailed specifications of the relative permeability treatment used. This section on well treatment describes the formulation for production and injection wells with multi-layer completions operating under combined rate and pressure constraints. Subsequently, a detailed description of input formats for specifying simulation problems is given. The appendices include statements of the governing equations for multiphase flow solved by the MULKOM simulator in continuum as well as in discretized form. 18 refs., 2 figs., 1 tab.
Surgical Maneuvers Enhance Molecular Detection of Circulating Tumor Cells During Gastric Cancer Surgery (2001)

A high incidence of positive CEA-mRNA was found in the blood during gastric cancer surgery. Surgical maneuvers are a possible cause of hematogenous metastasis. The authors found that patients with positive CEA-mRNA had a high risk of blood-borne metastasis even after curative resection.
The Relationship Between Religion and Adjustment to College. (1995)

Although the overall incidence of and mortality rate associated with burn injury have decreased in recent decades, burns remain a significant source of morbidity and mortality in children. Children with major burns require emergent resuscitation. Resuscitation is similar to that for adults, including pain control, airway management, and administration of intravenous fluid. However, in pediatrics, fluid resuscitation is needed for burns greater than or equal to 15% of total body surface area (TBSA) compared with burns greater than or equal to 20% TBSA for adults. Unique to pediatrics is the additional assessment for non-accidental injury and accurate calculation of the percentage of total burned surface area (TBSA) in children with changing body proportions are crucial to determine resuscitation parameters, prognosis, and disposition.
A Computational Reaction−Diffusion Model for the Analysis of Transport-Limited Kinetics (1999)

Optical, evanescent wave biosensors have become popular tools for quantitatively characterizing the kinetic properties of biomolecular interactions. Analyzing data from biosensor experiments, however, is often complicated when mass-transfer influences the detection kinetics. We present a computational, transport-kinetic model that can be used to analyze transport-limited biosensor data. This model describes a typical biosensor experiment in which a soluble analyte diffuses through a flow chamber and binds to a receptor immobilized on the transducer surface. Analyte transport in the flow chamber is described by the diffusion equation while the kinetics of analyte-surface association and dissociation are captured by a reactive boundary condition at the sensor surface. Numerical integration of the model equations and nonlinear least-squares fitting are used to compare model kinetic data to experimental results and generate estimates for the rate constants that describe analyte detection. To demonstrate the feasibility of this model, we use it to analyze data collected for the binding of fluorescently labeled trinitrobenzene to immobilized monoclonal anti-TNT antibodies. A successful analysis of this antigen-antibody interaction is presented for data collected with a fluorescence-based fiber-optic immunoassay. The results of this analysis are compared with the results obtained with existing methods for analyzing diffusion-limited kinetic data.
Effect of Omega-3 Fatty Acids on Growth of a Rat Mammary Tumor2 (1984)

The effect of administering marine oil that was rich in omega-3 fatty acids on tumor growth was studied in female inbred F344 rats that received transplants of R3230AC mammary adenocarcinoma. Four groups of rats were maintained on a normal rat chow diet containing 5% fat, and marine oil supplementation was started 1 week prior to transplantation of the tumors. The marine oil provided 17, 33, and 67 mg of 5, 8, 11, 14, 17-eicosapentaenoic acid (EPA) and 16, 32, and 64 mg 4, 7, 10, 13, 16, 19-docosahexaenoic acid (DHA) a day. A significant reduction in weight (g) and volume (cm3) of the rat R3230AC mammary tumor was observed after 4 weeks of treatment. EPA (20:5 omega-3) and DHA (22:6 omega-3) were found in choline phospholipid fractions of mammary tumors from rats given marine oil. Both tumor content and synthesis in vitro of prostaglandins of two series were inhibited in the marine oil-treated groups. These data indicated that the mechanism underlying inhibition of mammary tumorigenesis may be linked, in part, to the inhibitory effect of both EPA and DHA on arachidonic acid metabolism.
A Direct Method for Site‐Specific Protein Acetylation (2011)

Radicals at work: Radical-mediated thiol-ene addition of the thiol group of Cys to N-vinylacetamide gives acetyl-thialysine (KSAc), a near-perfect mimic of acetyl-lysine (see picture). The reaction is highly efficient with near quantitative conversion obtained in short reaction times. The generated KSAc is functionally identical or similar to its native counterpart.
Niemann-Pick disease type C (2010)

Niemann-Pick C disease (NP-C) is a neurovisceral atypical lysosomal lipid storage disorder with an estimated minimal incidence of 1/120,000 live births. The broad clinical spectrum ranges from a neonatal rapidly fatal disorder to an adult-onset chronic neurodegenerative disease. The neurological involvement defines the disease severity in most patients but is typically preceded by systemic signs (cholestatic jaundice in the neonatal period or isolated spleno- or hepatosplenomegaly in infancy or childhood). The first neurological symptoms vary with age of onset: delay in developmental motor milestones (early infantile period), gait problems, falls, clumsiness, cataplexy, school problems (late infantile and juvenile period), and ataxia not unfrequently following initial psychiatric disturbances (adult form). The most characteristic sign is vertical supranuclear gaze palsy. The neurological disorder consists mainly of cerebellar ataxia, dysarthria, dysphagia, and progressive dementia. Cataplexy, seizures and dystonia are other common features. NP-C is transmitted in an autosomal recessive manner and is caused by mutations of either the NPC1 (95% of families) or the NPC2 genes. The exact functions of the NPC1 and NPC2 proteins are still unclear. NP-C is currently described as a cellular cholesterol trafficking defect but in the brain, the prominently stored lipids are gangliosides. Clinical examination should include comprehensive neurological and ophthalmological evaluations. The primary laboratory diagnosis requires living skin fibroblasts to demonstrate accumulation of unesterified cholesterol in perinuclear vesicles (lysosomes) after staining with filipin. Pronounced abnormalities are observed in about 80% of the cases, mild to moderate alterations in the remainder ("variant" biochemical phenotype). Genotyping of patients is useful to confirm the diagnosis in the latter patients and essential for future prenatal diagnosis. The differential diagnosis may include other lipidoses; idiopathic neonatal hepatitis and other causes of cholestatic icterus should be considered in neonates, and conditions with cerebellar ataxia, dystonia, cataplexy and supranuclear gaze palsy in older children and adults. Symptomatic management of patients is crucial. A first product, miglustat, has been granted marketing authorization in Europe and several other countries for specific treatment of the neurological manifestations. The prognosis largely correlates with the age at onset of the neurological manifestations.
Improved ATM kinase inhibitor KU-60019 radiosensitizes glioma cells, compromises insulin, AKT and ERK prosurvival signaling, and inhibits migration and invasion (2009)

Ataxia telangiectasia (A-T) mutated (ATM) is critical for cell cycle checkpoints and DNA repair. Thus, specific small molecule inhibitors targeting ATM could perhaps be developed into efficient radiosensitizers. Recently, a specific inhibitor of the ATM kinase, KU-55933, was shown to radiosensitize human cancer cells. Herein, we report on an improved analogue of KU-55933 (KU-60019) with K(i) and IC(50) values half of those of KU-55933. KU-60019 is 10-fold more effective than KU-55933 at blocking radiation-induced phosphorylation of key ATM targets in human glioma cells. As expected, KU-60019 is a highly effective radiosensitizer of human glioma cells. A-T fibroblasts were not radiosensitized by KU-60019, strongly suggesting that the ATM kinase is specifically targeted. Furthermore, KU-60019 reduced basal S473 AKT phosphorylation, suggesting that the ATM kinase might regulate a protein phosphatase acting on AKT. In line with this finding, the effect of KU-60019 on AKT phosphorylation was countered by low levels of okadaic acid, a phosphatase inhibitor, and A-T cells were impaired in S473 AKT phosphorylation in response to radiation and insulin and unresponsive to KU-60019. We also show that KU-60019 inhibits glioma cell migration and invasion in vitro, suggesting that glioma growth and motility might be controlled by ATM via AKT. Inhibitors of MEK and AKT did not further radiosensitize cells treated with KU-60019, supporting the idea that KU-60019 interferes with prosurvival signaling separate from its radiosensitizing properties. Altogether, KU-60019 inhibits the DNA damage response, reduces AKT phosphorylation and prosurvival signaling, inhibits migration and invasion, and effectively radiosensitizes human glioma cells.
A circadian clock in macrophages controls inflammatory immune responses (2009)

Time of day-dependent variations of immune system parameters are ubiquitous phenomena in immunology. The circadian clock has been attributed with coordinating these variations on multiple levels; however, their molecular basis is little understood. Here, we systematically investigated the link between the circadian clock and rhythmic immune functions. We show that spleen, lymph nodes, and peritoneal macrophages of mice contain intrinsic circadian clockworks that operate autonomously even ex vivo. These clocks regulate circadian rhythms in inflammatory innate immune functions: Isolated spleen cells stimulated with bacterial endotoxin at different circadian times display circadian rhythms in TNF-alpha and IL-6 secretion. Interestingly, we found that these rhythms are not driven by systemic glucocorticoid variations nor are they due to the detected circadian fluctuation in the cellular constitution of the spleen. Rather, a local circadian clock operative in splenic macrophages likely governs these oscillations as indicated by endotoxin stimulation experiments in rhythmic primary cell cultures. On the molecular level, we show that >8% of the macrophage transcriptome oscillates in a circadian fashion, including many important regulators for pathogen recognition and cytokine secretion. As such, understanding the cross-talk between the circadian clock and the immune system provides insights into the timing mechanism of physiological and pathophysiological immune functions.
Monte Carlo simulations of hydrogen storage in carbon nanotubes (2002)

The storage capacities of porous materials made up of carbon nanotubes are estimated by Monte Carlo simulations for the specific case of hydrogen in the pressure domain from 0.1 to 20 MPa at temperatures of 293, 150 and 77 K. The use of these materials in devices for hydrogen storage is discussed on the basis of the simulation results.
TNF-alpha convertase enzyme from human arthritis-affected cartilage: isolation of cDNA by differential display, expression of the active enzyme, and regulation of TNF-alpha. (1998)

A snake venom-like protease isolated by a differential display screen between normal and osteoarthritis (OA)-affected cartilage (designated as cSVP) has a cDNA sequence identical to TNF-alpha convertase enzyme (TACE). TACE shows the presence of an unknown prodomain, a cysteine switch, a catalytic domain, a zinc binding region, a disintegrin region, an EGF-like domain, a transmembrane domain, and a unique cytoplasmic region. A TACE construct harboring the signal + prodomain + catalytic region (TACE-SPCdeltaDETCy), expressed in baculovirus could cleave preferentially (approximately 12-fold) the TNF-specific peptide over the matrix metalloproteases peptide in vitro. This recombinant protein also cleaved the natural substrate GST-ProTNF-alpha to TNF-alpha (17 kDa) in vitro. The mRNA for TACE, which is broadly distributed and differentially expressed in a variety of human tissues, is up-regulated in arthritis-affected cartilage, but not normal cartilage. OA-affected cartilage also expressed TNF-alpha mRNA that was not detected in normal cartilage. The OA-affected cartilage (in explant assays) spontaneously released TNF-alpha and IL-8 in ex vivo conditions. Addition of TNF-alphaR fused to IgG Fc fragment (TNF-alphaR:Fc) in the presence or absence of soluble IL-1R (with which it acted additively) significantly attenuated the spontaneous/autocrine release of articular IL-8 in this assay. These experiments demonstrate a functional paracrine/autocrine role of TNF-alpha in OA-affected cartilage that may depend, in part, on up-regulated levels of chondrocyte-derived TACE.
Emission-line widths and stellar-wind flows in T Tauri stars (1986)

We report on spectra of T Tauri stars taken with the IPCS on the Isaac Newton Telescope at the Observatorio del Roque de los Muchachos at a dispersion of 17 Å mm−1. These were taken in order to determine emission-line widths and hence flow velocities in the winds of these stars following the successful modelling of the wind from RU Lupi using such data. Line widths in RW Aur suggest a similar pattern to the wind flow as in RU Lupi with velocities rising in the inner chromosphere of the star and then entering a ‘ballistic’ zone. The wind from DF Tau is also similar but velocities are generally much lower and the lines sharper. The pattern may also be the same in V380 Ori but in DI Cep, on the other hand, the wind also accelerates in the outer chromosphere with He Iλ5876 Å being the broadest line.
High-Contrast Solid-State Electrochromic Devices of Viologen-Bridged Polysilsesquioxane Nanoparticles Fabricated by Layer-by-Layer Assembly (2009)

Water-soluble silsesquioxane nanoparticles (NPs) incorporating viologen groups (PXV; 1,1'-bis[3-(trimethoxysilyl)propyl]-4,4'-bipyridinium iodide) have been synthesized by sol-gel polymerization. The electrochromic properties of the bulk film fabricated by layer-by-layer (LbL) assembly have been examined, along with their incorporation into solid-state devices. The orange LbL films show high thermal stability and exhibit a maximum UV-vis absorption at 550 nm. Electrochromic switching of the NPs in liquid electrolyte as well as in the solid state was evaluated by a kinetic study via measurement of the change in transmission (% T) at the maximum contrast. Cyclic voltammograms of the PXV NP LbL films exhibit a reversible reduction at -0.6 V vs Ag/AgCl in a 0.1 M NaClO4(aq) solution, revealing good electrochromic stability, with a color change from orange to dark purple-blue at applied potentials ranging from -0.7 to -1.3 V. Cathodically coloring PXV NP solid-state devices exhibit a switching time of a few seconds between the purple-blue reduced state and the orange oxidized state, showing a contrast of 50% at 550 nm and a coloration efficiency of 205 cm2/C. Their solubility and fairly fast electrochromic switching ( approximately 3 s) at low switching voltages (between 0 and 3.0 V), along with their stability under atmospheric conditions, make PXV NPs good candidates for electrochromic displays.
Lactose Solubility and Lactose Crystal Formation (1926)

The experiments reported and results quoted in this paper on lactose solubility refer particularly to lactose solubility in the presence of sucrose and milk colloids as compared with lactose solubility in water.