gebhart/patrepeval huggingface dataset:
The optimization of protein‐solvent interactions: Thermostability and the role of hydrophobic and electrostatic interactions (1995)

Protein-solvent interactions were analyzed using an optimization parameter based on the ratio of the solvent-accessible area in the native and the unfolded protein structure. The calculations were performed for a set of 183 nonhomologous proteins with known three-dimensional structure available in the Protein Data Bank. The dependence of the total solvent-accessible surface area on the protein molecular mass was analyzed. It was shown that there is no difference between the monomeric and oligomeric proteins with respect to the solvent-accessible area. The results also suggested that for proteins with molecular mass above some critical mass, which is about 28 kDa, a formation of domain structure or subunit aggregation into oligomers is preferred rather than a further enlargement of a single domain structure. An analysis of the optimization of both protein-solvent and charge-charge interactions was performed for 14 proteins from thermophilic organisms. The comparison of the optimization parameters calculated for proteins from thermophiles and mesophiles showed that the former are generally characterized by a high degree of optimization of the hydrophobic interactions or, in cases where the optimization of the hydrophobic interactions is not sufficiently high, by highly optimized charge-charge interactions.
Charged Polymer/Nanoparticle Mixtures: Monte Carlo Simulations (2002)

We used Monte-Carlo simulations to study the formation of complexes between charged polymers (or polyelectrolytes) with oppositely charged spherical nanoparticles. We presented the model, the Monte Carlo numerical method and investigated the effects of the ionic concentration of the solution, polyelectrolyte rigidity (or flexibility), linear charge density, and surface charge of the nanoparticles. Polyelectrolyte adsorption is controlled by several competing effects. On the one hand, rigidity and electrostatic repulsion force the polyelectrolyte to adopt extended conformations and limit the number of monomers which may be attached to the nanoparticles. On the other hand, electrostatic attractive interactions between the particle and the polyelectrolyte monomers force the chain to undergo a structural transition and collapse at the particle surface. By increasing the intrinsic rigidity, we observed a transition from disordered and strongly bound complexes to a situation where the polymer touches the particles over a finite length, while passing by the formation of a solenoid conformation. We found that the critical ionic concentration at which adsorption/desorption is observed rapidly increases with the increase of the nanoparticle surface charge density in good agreement with experimental data dealing with the formation of complexes between micelles and oppositely charged polyelectrolytes. Adsorption is also promoted by decreasing the chain stiffness or decreasing the salt concentration for a given chain length.
Guidelines for management of patients with chronic heart failure in Australia (2001)

Chronic heart failure (CHF) affects approximately 1% of people aged 50-59 years, and this high prevalence increases dramatically with age. CHF is a common reason for hospital admission and general practitioner consultation in the elderly. Common causes of CHF are ischaemic heart disease, hypertension and idiopathic dilated cardiomyopathy. Diagnosis of CHF is based on clinical features and objective measurement of ventricular function (eg, echocardiography). Management is directed at prevention, retarding disease progression, relief of symptoms and prolonging survival. Non-pharmacological approaches include exercise, home-based support and risk-factor modification. Angiotensin-converting enzyme (ACE) inhibitors are the cornerstone of pharmacological therapy to prevent disease progression and prolong survival. beta-Blockers prolong survival when added to ACE inhibitors in symptomatic patients. Diuretics provide symptom relief and restoration or maintenance of euvolaemia. Spironolactone, angiotensin II receptor antagonists and digoxin may be useful in some patients. Surgical approaches in highly selected patients may include myocardial revascularisation, insertion of devices and cardiac transplantation.
Single- and Triaxis Piezoelectric-Bimorph Accelerometers (2008)

This paper describes the novel single- and triaxis piezoelectric-bimorph accelerometers that are built on parylene beams with ZnO films. The unamplified sensitivity and the minimum detectable signal of the fabricated single-axis accelerometer are measured to be 7.0 mV/g and 0.01 g, respectively, over a frequency range from 60 Hz to subhertz. The linearity of the sensitivity as a function of acceleration is measured to be 0.9% in the full scale. A highly symmetric quad-beam bimorph structure with a single proof mass is used for triaxis acceleration sensing and is demonstrated to produce high sensitivity, low cross-axial sensitivity, and good linearity, all in a compact size. The unamplified sensitivities of the X-, Y-, and Z-axis electrodes (of the triaxis accelerometer) in response to the accelerations in X-, Y-, and Z-axes are 0.93, 1.13, and 0.88 mV/g, respectively. The worst-case minimum detectable signal of the triaxis accelerometer is measured to be 0.04 g over a bandwidth ranging from subhertz to 100 Hz. The cross-axial sensitivity among the X-, Y-, and Z-axis electrodes is less than 15% in the triaxis accelerometer. The theoretical analyses of the charge sensitivities and resonant frequencies along with the effects of residual stress on the charge sensitivities are presented for both the single- and triaxis accelerometers.
HD-Zip proteins: members of an Arabidopsis homeodomain protein superfamily. (1992)

Homeobox genes encode a large family of homeodomain proteins in animal systems. To test whether such genes are also abundant in higher plants, degenerate oligonucleotides complementary to sequences encoding the recognition helix (helix three) of the homeodomain were used to screen genomic and cDNA libraries from the plant Arabidopsis thaliana. Analysis of 8 of the 41 cDNAs isolated revealed that each encodes a presumptive homeodomain; interestingly, most of these clones also contain a leucine zipper motif tightly linked to the homeodomain. It is concluded that Arabidopsis encodes a large family of homeodomain proteins, including members that contain a homeodomain/leucine-zipper (HD-Zip) motif.
Ghrelin-a new gastroprotective factor in gastric mucosa. (2004)

Ghrelin, a novel peptide expressed in the gastrointestinal tract, especially in the gastric mucosa, exerts several biological activities including the stimulation of appetite and food intake, the stimulation of intestinal motility and the release of growth hormone. The aim of this study was to examine the expression of ghrelin in gastric mucosa after its exposure to ethanol and its effects on gastric lesions induced by ethanol with and without pretreatment with indomethacin. Acute gastric lesions were induced by intragastric administration of 75% ethanol in rats pretreated with saline-vehicle or ghrelin injected intraperitoneally (i.p.) without or with i.p. pretreatment with indomethacin. At the end of experiments, the rats were anesthetized, the stomach was exposed to measure gastric blood flow (GBF), to determine the area of gastric lesions and to take biopsy samples from the oxyntic mucosa for determination of transcripts of ghrelin, tumor necrosis alpha (TNF-alpha) and transforming growth factor alpha (TGFalpha) using RT-PCR and to assess the generation of PGE(2) by RIA. Exposure of gastric mucosa to 75% ethanol resulted in numerous mucosal lesions of an area of about 115 mm(2) and in the increase of mucosal expression of TNF-alpha, PGE(2), TGFalpha and ghrelin with concomitant decrease in GBF. Exogenous ghrelin reduced dose-dependently acute gastric lesions with simultaneous attenuation of GBF and a decrease in the expression of TNF-alpha but not TGFalpha. Pretreatment with indometahcin, which suppressed the generation of PGE(2) by about 85%, augmented ethanol-induced gastric lesions and eliminated the ghrelin-induced protection of mucosa against ethanol. We conclude that ghrelin, whose mucosal expression is enhanced after exposure to ethanol, exhibits a strong gastroprotection, at least in part, due to its anti-inflammatory action mediated by prostaglandins.
Compression Artifact Reduction by Overlapped-Block Transform Coefficient Estimation With Block Similarity (2013)

Block transform coded images usually suffer from annoying artifacts at low bit rates, caused by the coarse quantization of transform coefficients. In this paper, we propose a new method to reduce compression artifacts by the overlapped-block transform coefficient estimation from non-local blocks. In the proposed method, the discrete cosine transform coefficients of each block are estimated by adaptively fusing two prediction values based on their reliabilities. One prediction is the quantized values of coefficients decoded from the compressed bitstream, whose reliability is determined by quantization steps. The other prediction is the weighted average of the coefficients in nonlocal blocks, whose reliability depends on the variance of the coefficients in these blocks. The weights are used to distinguish the effectiveness of the coefficients in nonlocal blocks to predict original coefficients and are determined by block similarity in transform domain. To solve the optimization problem, the overlapped blocks are divided into several subsets. Each subset contains nonoverlapped blocks covering the whole image and is optimized independently. Therefore, the overall optimization is reduced to a set of sub-optimization problems, which can be easily solved. Finally, we provide a strategy for parameter selection based on the compression levels. Experimental results show that the proposed method can remarkably reduce compression artifacts and significantly improve both the subjective and objective qualities of block transform coded images.
Discovery of 2-((3-Amino-4-methylphenyl)amino)-N-(2-methyl-5-(3-(trifluoromethyl)benzamido)phenyl)-4-(methylamino)pyrimidine-5-carboxamide (CHMFL-ABL-053) as a Potent, Selective, and Orally Available BCR-ABL/SRC/p38 Kinase Inhibitor for Chronic Myeloid Leukemia (2016)

Starting from a dihydropyrimidopyrimidine core scaffold based compound 27 (GNF-7), we discovered a highly potent (ABL1: IC50 of 70 nM) and selective (S score (1) = 0.02) BCR-ABL inhibitor 18a (CHMFL-ABL-053). Compound 18a did not exhibit apparent inhibitory activity against c-KIT kinase, which is the common target of currently clinically used BCR-ABL inhibitors. Through significant suppression of the BCR-ABL autophosphorylation (EC50 about 100 nM) and downstream mediators such as STAT5, Crkl, and ERK's phosphorylation, 18a inhibited the proliferation of CML cell lines K562 (GI50 = 14 nM), KU812 (GI50 = 25 nM), and MEG-01 (GI50 = 16 nM). A pharmacokinetic study revealed that 18a had over 4 h of half-life and 24% bioavailability in rats. A 50 mg/kg/day dosage treatment could almost completely suppress tumor progression in the K562 cells inoculated xenograft mouse model. As a potential useful drug candidate for CML, 18a is under extensive preclinical safety evaluation now.
SDP: Session Description Protocol (2021)

This memo defines the Session Description Protocol (SDP). SDP is intended for describing multimedia sessions for the purposes of session announcement, session invitation, and other forms of multimedia session initiation. This document obsoletes RFC 4566.
Protein kinase C involvement in focal adhesion formation (1992)

Matrix molecules such as fibronectin can promote cell attachment, spreading and focal adhesion formation. Although some interactions of fibronectin with cell surface receptors have now been identified, the consequent activation of intracellular messenger systems by cell/matrix interactions have still to be elucidated. We show here that the kinase inhibitors H7 and HA1004 reduce focal adhesion and stress fiber formation in response to fibronectin in a dose-dependent manner, and that activators of protein kinase C can promote their formation under conditions where they do not normally form. Fibroblasts spread within 1h on substrata composed of fibronectin and formed focal adhesions by 3h, as monitored by interference reflection microscopy (IRM) and by labeling for talin, vinculin and integrin beta 1 subunits. In addition, stress fibers were visible. When cells were allowed to spread for 1h and then treated with kinase inhibitors H7 and HA1004 for 2h, IRM indicated a reduction in focal adhesion formation at concentrations where protein kinase C (PKC) should be inhibited. In contrast, focal adhesions formed normally at concentrations of these inhibitors where cyclic AMP- or cyclic GMP-dependent kinases should be inactivated. Inhibition of PKC, but not that of cyclic AMP- or cyclic GMP-dependent kinases, also prevented the formation of stress fibers and induced a dispersal of talin and vinculin, but not integrin beta 1 subunits, from small condensations present at 1h. Consistent with the reduction in focal adhesion formation when PKC was inhibited, activation of PKC by 30 minutes of treatment with phorbol esters induced focal adhesion formation in cells spread for 3h on substrata composed of the cell-binding (RGD-containing) fragment of fibronectin, while untreated cells or those treated with inactive phorbol esters did not form these structures.
Biological properties of recombinant chicken interferon‐γ (1996)

Supernatants of the chicken T cell line 855 contain antiviral and macrophage activating factor activity and strongly activate transcription of the guanylate binding protein (GBP) gene in chicken cells. To characterize the cytokine responsible for the GBP-inducing activity, we chose a cDNA expression cloning strategy in COS cells. Sequencing a positive clone revealed that it encode chicken interferon-gamma (ChIFN-gamma). Histidine-tagged ChIFN-gamma was expressed in Escherichia coli and purified by nickel chelate affinity chromatography. ChIFN-gamma from COS cells and E. coli both potently induced GBP RNA synthesis but were rather poor antiviral agents. In macrophages, recombinant ChIFN-strongly stimulated secretion of nitric oxide and enhanced expression of major histocompatibility complex class II antigen. A rabbit antiserum to E. coli derived ChIFN-gamma effectively neutralized the macrophage-activating factor activity secreted by concanavalin A-induced spleen cells and various T cell lines, suggesting that IFN-gamma is the major macrophage-activating factor of the chicken.
Human IL-18 Receptor and ST2L Are Stable and Selective Markers for the Respective Type 1 and Type 2 Circulating Lymphocytes (2001)

CD4(+) (Th) and CD8(+) (Tc) T and NK lymphocytes can be divided into type 1 and 2 subsets according to their cytokine secretion profile. Studies on the role of lymphocyte subsets in human diseases have been hampered by the lack of stable surface markers to define them. Recently, we reported that ST2L and IL-18R are stably expressed on murine Th2 and Th1 cells, respectively. In this study, we generated Abs to human homologues of ST2L and IL-18R and tested them against Th1/Th2, Tc1/Tc2, and NK1/NK2 lines and PBMCs from healthy individuals. We show for the first time that ST2L and IL-18R are stable selective cell surface markers for human Th2/Tc2/NK2 and Th1/Tc1/NK1 lymphocytes, respectively. We then investigated PBMCs from HIV-infected patients and HIV-negative individuals, to test whether Abs to these two surface markers could be used directly to monitor lymphocyte subset distribution in human diseases. We found a clear Th1 to Th2 shift in the HIV-infected individuals, thus settling a long-standing controversy and include, for the first time, Tc and NK cells as well. Therefore, these cell surface molecules could serve as important determinants of the immune status of human diseases in general, and thereby could be useful for therapeutic monitoring and intervention.
Painful prosthesis: approaching the patient with persistent pain following total hip and knee arthroplasty. (2013)

The cause of pain needs always to be indentified and removed whenever possible. Implant revision is indicated only when septic or aseptic loosening is diagnosed. Current evidence has shown that peri-and/or post-operative administration of bisphosphonates may have a role in pain management and periprosthetic bone loss prevention.
Characteristics of micromachined switches at microwave frequencies (2002)

This article reviews the fundamental characteristics of micromechanical membrane switches operating at microwave frequencies. The construction and theory of operation of capacitive membrane switches is reviewed. Measurement and modeling of the electromechanical and microwave properties of these switches are presented. The inherent advantages of these switches relative to semiconductor switches is discussed.
Central tachykinins: mediators of defence reaction and stress reactions (1995)

The tachykinins substance P, neurokinin A, and neurokinin B are natural agonists for NK1, NK2, and NK3 receptors, respectively. Evidence from biochemical, neurophysiological, pharmacological, and molecular biology studies indicates that the tachykinin-containing pathways within the brain contribute to central cardiovascular and endocrine regulation and to the control of motor activity. The hypothalamus, which represents a site for the integration of central neuroendocrine and autonomic processes, is rich in tachykinin nerve endings and tachykinin receptors. Stimulation of periventricular or hypothalamic NK1 receptors in conscious rats induces an integrated cardiovascular, behavioural, and endocrine response. The cardiovascular response is associated with increased sympathoadrenal activity and comprises an increase in blood pressure and heart rate, mesenteric and renal vasoconstriction, and hind-limb vasodilatation. The behavioural response consists of increased locomotion and grooming behaviour. This response pattern is consistent with an integrated stress response to nociceptive stimuli and pain in rodents. Several studies have demonstrated rapid changes in substance P levels and its receptors in distinct brain areas following acute stress. These data indicate that substance P and other tachykinins, in addition to serving as nociceptive and pain transmitters in the spinal cord, may act in the brain as neurotransmitters--neuromodulators within the neuronal circuits mediating central stress responses.
Morphology of Particles in Sizefractionated Na- Montmorillonites (1968)

Abstract Electron microscopy of particles in size fractions (0·5–1·0 μ , 0·1–0·5 μ , 0·05–0·1 μ and &lt; 0·05 μ e.s.d.) obtained by centrifugation of Na-saturated montmorillonites from Wyoming (two samples); Chambers, Arizona; and Fayette County, Texas, has shown details of particle morphology. The finest fraction of each montmorillonite consists predominantly of very thin, separate flakes whereas all coarser fractions, totalling 80 per cent or more by weight of the samples studied, are composed of microaggregates. For all the samples, preferred orientation is best developed in specimens formed from flakes of the finest fractions. Microaggregates are stable in dilute suspension although they swell to give large interlayer spacings, but can be disrupted into smaller, thinner flakes by ultrasonic vibration. Differences in dispersion behavior between separate flakes and microaggregates are not due to differences in interlayer charge or chemical composition, which are very small between fractions of each sample, but are thought to be due to the interlocking of flakes in microaggregates during crystal growth, which prevents their complete separation in dilute suspension.
Increased intake of calcium reverses vitamin B12 malabsorption induced by metformin. (2000)

Patients receiving metformin have diminished B12 absorption and low serum total vitamin B12 and TCII-B12 levels because of a calcium-dependent ileal membrane antagonism, an effect reversed with supplemental calcium.
ChemInform Abstract: C‐NUCLEOSIDE SYNTHESIS. 10. SYNTHESIS OF 2′‐METHYLATED PYRIMIDINE C‐NUCLEOSIDES (1980)

Abstract Synthesis of 2′‐Methylated Pyrimidine C‐Nucleosides.
Organization of hydroxyapatite crystals within collagen fibrils (1986)

Transmission electron micrographs of individual mineralized collagen fibrils show that hydroxyapatite crystals are located mainly within the fibrils at the level of the gap regions. The plate-shaped crystals are observed to be more or less uniformly stacked across the fibril diameter. We therefore suggest that the crystals are primarily located in 'grooves' created by contiguous adjacent gaps. The proposal is consistent with the observed crystal distribution in the fibril and with their average widths, which are almost 10-times greater than an individual gap diameter.
Functional Interplay between Acetylation and Methylation of the RelA Subunit of NF-κB (2010)

Posttranslational modifications of the RelA subunit of NF-kappaB, including acetylation and methylation, play a key role in controlling the strength and duration of its nuclear activity. Whether these modifications are functionally linked is largely unknown. Here, we show that the acetylation of lysine 310 of RelA impairs the Set9-mediated methylation of lysines 314 and 315, which is important for the ubiquitination and degradation of chromatin-associated RelA. Abolishing the acetylation of lysine 310 either by the deacetylase SIRT1 or by mutating lysine 310 to arginine enhances methylation. Conversely, enhancing the acetylation of lysine 310 by depleting SIRT1 or by replacing lysine 310 with acetyl-mimetic glutamine inhibits methylation, thereby decreasing ubiquitination, prolonging the stability of chromatin-associated RelA, and enhancing the transcriptional activity of NF-kappaB. The acetylation of lysine 310 of RelA interferes with its interaction with Set9. Based on structural modeling of the SET domain of Set9 with RelA, we propose that the positive charge of lysine 310 is critical for the binding of RelA to a negatively charged "exosite" within the SET domain of Set9. Together, these findings demonstrate for the first time an interplay between RelA acetylation and methylation and also provide a novel mechanism for the regulation of lysine methylation by acetylation.
The International Workshop on Meibomian Gland Dysfunction: Executive Summary (2011)

DOI:10.1167/iovs.10-6997a Investigative Ophthalmology & Visual Science, Special Issue 2011, Vol. 52, No. 4 Copyright 2011 The Association for Research in Vision and Ophthalmology, Inc. 1922 ドライアイ疾患の原因としては、マイボーム腺機能不全 (MGD)がおそらく最も多い。この疾患によって数百万人 もの健康と幸福が損なわれているにもかかわらず、MGD の定 義、分類、診断、治療について世界的なコンセンサスはない。 そうしたコンセンサスに達する目的で、非営利団体である Tear Film and Ocular Surface Society( TFOS; http://www. tearfilm.org)が International Workshop on Meibomian Gland Dysfunction(国際マイボーム腺機能不全ワークショップ、 www.tearfilm.org/mgdworkshop/index.html)を起ち上げた。こ のワークショップの目的は以下の通りである: