gebhart/patrepeval huggingface dataset:
Diesel engine dynamics modeling based on heat release rate identification (2011)

Heat release rate is one of the important factors affecting diesel engine characteristics. This paper presents a diesel engine dynamics model based on identification of heat release rate. Instantaneous engine speed and cylinder pressure can be obtained by numerical simulation of air intake and exhaust properties, in-cylinder combustion process and crank rotational dynamics by using the identification results. Simulation results of the engine speed and cylinder pressure well coincide with experimental ones for different external loads and nominal engine speed.
An overview of the suitability of hydrogel-forming polymers for extrusion-based 3D-printing (2015)

In this review hydrogel-forming polymers that are suitable for extrusion-based 3D printing are evaluated.
Cyanuric acid hydrolase: evolutionary innovation by structural concatenation (2013)

The cyanuric acid hydrolase, AtzD, is the founding member of a newly identified family of ring-opening amidases. We report the first X-ray structure for this family, which is a novel fold (termed the 'Toblerone' fold) that likely evolved via the concatenation of monomers of the trimeric YjgF superfamily and the acquisition of a metal binding site. Structures of AtzD with bound substrate (cyanuric acid) and inhibitors (phosphate, barbituric acid and melamine), along with mutagenesis studies, allowed the identification of the active site. The AtzD monomer, active site and substrate all possess threefold rotational symmetry, to the extent that the active site possesses three potential Ser-Lys catalytic dyads. A single catalytic dyad (Ser85-Lys42) is hypothesized, based on biochemical evidence and crystallographic data. A plausible catalytic mechanism based on these observations is also presented. A comparison with a homology model of the related barbiturase, Bar, was used to infer the active-site residues responsible for substrate specificity, and the phylogeny of the 68 AtzD-like enzymes in the database were analysed in light of this structure-function relationship.
Comparative effects of hepatocyte growth factor and epidermal growth factor on motility, morphology, mitogenesis, and signal transduction of primary rat hepatocytes (1994)

Hepatocyte growth factor (HGF) and epidermal growth factor (EGF) are major hepatocyte mitogens, but HGF, also known as scatter factor (SF), has also been shown as a potent motogen for epithelial and endothelial cells. The mechanisms by which HGF is a stronger motogen compared to other mitogens are not understood. Here we report a comparative study of the effect of the two growth factors on cultured primary rat hepatocytes regarding their differential effects on morphology, mitogenicity, and motility as well as the phosphorylation of cytoskeletal-associated proteins. Using three different motility assays, both HGF and EGF increased the motility of hepatocytes, but HGF consistently elicited a significantly greater motility response than EGF. Additionally, HGF induced a more flattened, highly spread morphology compared to EGF. To examine if HGF and EGF phosphorylated different cytoskeletal elements as signal transduction targets in view of the observed variation in morphology and motility, primary cultures of 32P-loaded rat hepatocytes were stimulated by either HGF or EGF for up to 60 min. Both mitogens rapidly stimulated four isoforms of MAP kinase with similar kinetics and also rapidly facilitated the phosphorylation of cytoskeletal-associated F-actin. Two cytoskeletal-associated proteins, however, were observed to undergo rapid phosphorylation by HGF and not EGF during the time points described. One protein of 28 kDa was observed to become phosphorylated fivefold over controls, while the EGF-stimulated cells showed only a slight increase in the phosphorylation of this protein. Another protein with an apparent mwt of 42 kDa was phosphorylated 20-fold at 1 min and remained phosphorylated over 50-fold over control up to the 60 min time point. This protein was observed to become phosphorylated by EGF only after 10 min, and to a lesser extent (20-fold). Taken together, the data suggest that HGF and EGF stimulate divergent as well as redundant signal transduction pathways in the hepatocyte cytoskeleton, and this may result in unique HGF- or EGF-specific motility, morphology, and mitogenicity in hepatocytes.
[Intraglomerular coagulation and fibrinolysis in human primary glomerular diseases]. (1991)

It is a well known fact that intraglomerular coagulation plays an important role in the development of human primary glomerular diseases. However, the precise mechanism of intraglomerular coagulation, and intraglomerular coagulability and/or fibrinolytic activity remains obscure. The present study was aimed to elucidate the role of the intraglomerular coagulation and fibrinolysis in human primary glomerular diseases. Subjects enrolled in this study were 27 patients with minimal change nephrotic syndrome (MCNS), 14 patients with focal glomerular sclerosis (FGS), 36 patients with membranous nephropathy (MN), 161 patients with mesangial proliferative glomerulonephritis (mesPGN), 9 patients with membranoproliferative glomerulonephritis (MPGN), and 40 healthy volunteers as controls. Normal human renal cortex as controls of isolated intraglomerular plasminogen activator activity (PAA) was obtained at the time of nephrectomy from the normal pole of kidneys removed because of an opposite pole tumor. Urinary urokinase (UK), fibrinopeptide A (FPA) and fibrinopeptide B beta 15-42 (B beta 15-42) antigens were measured by RIA. Urinary tissue plasminogen activator (t-PA) antigen was measured by ELISA. Urinary fibrin/fibrinogen degradation products (FDP) were measured by latex agglutination method. Moreover, PAA was measured by 125I-fibrin films. The following results were obtained: 1) In primary glomerular diseases, levels of urinary UK and t-PA were significantly lower than those in healthy volunteers, 2) Urinary UK and t-PA showed gradual decrease along with the development of mesangial proliferation, 3) Urinary UK and t-PA were significantly correlated with both the urinary FPA and B beta 15-42, 4) In mesPGN and FGS, PAA was significantly lower than that in normal controls, 5) PAA was significantly correlated with urinary UK, t-PA, FPA and B beta 15-42, 6) Urinary UK and t-PA in the patients with urinary FDP were significantly lower than those in patients without urinary FDP, 7) Urinary UK, t-PA and PAA were significantly lower in patients with intraglomerular fibrin deposition than those in patients without fibrin depositions. These findings suggest that the decrease of urinary UK and t-PA levels and the diminution of isolated intraglomerular plasminogen activator activity contribute to the progression of primary glomerular diseases.
Heavy-Ion Accelerators (1977)

Various types of heavy-ion accelerators, such as several cyclotrons and synchrotrous, are discussed in detail with regard to their applications, properties, and components.
Insulin and vasopressin elicit inhibition of cholera-toxin-stimulated adenylate cyclase activity in both hepatocytes and the P9 immortalized hepatocyte cell line through an action involving protein kinase C (1995)

Incubation of hepatocytes or the SV40-DNA-immortalized hepatocyte P9 cell line with cholera toxin led to a time-dependent activation of adenylate cyclase activity, which occurred after a defined lag period. When added together with cholera toxin, each of the hormones insulin and vasopressin was capable of attenuating the maximum stimulatory effect achieved by cholera toxin over a period of 60 min through a process which could be blocked by the compounds staurosporine and chelerythrine. Attenuating effects on cholera-toxin-stimulated adenylate cyclase activity could also be elicited by using either the protein kinase C (PKC)-stimulating phorbol ester PMA (phorbol 12-myristate 13-acetate) or the protein phosphatase inhibitor okadaic acid. Alkaline phosphatase treatment of membranes reversed the inhibitory effect of PMA. Cholera toxin also stimulated the adenylate cyclase activity of intact CHO (Chinese-hamster ovary) and NIH-3T3 cells, but this activity was insensitive to the addition of PMA. Overexpression of various PKC isoforms in CHO cell lines did not confer sensitivity to inhibition by PMA upon cholera-toxin-stimulated adenylate cyclase activity. Rather, overexpression of the gamma isoform of PKC allowed PMA to stimulate adenylate cyclase activity in CHO cells. It is suggested that the PKC-mediated phosphorylation of a membrane protein attenuates cholera-toxin-stimulated adenylate cyclase activity in hepatocytes and P9 cells. The cellular selectivity of such an action may be due to the target for this inhibitory action of PKC being a particular isoform of adenylate cyclase which provides the major activity in hepatocytes and P9 cells, but not in either CHO or NIH-3T3 cells.
Isolation and Characterization of the Plasma Hyaluronan-Binding Protein (PHBP) Gene (HABP2) (1997)

PHBP is a novel human plasma hyaluronan-binding protein that shows significant homology in amino acid sequence to hepatocyte growth factor activator. Two overlapping clones that encode the human plasma hyaluronan-binding protein (PHBP) gene (HABP2) were isolated and characterized. The PHBP gene spans 35 kb and is composed of 13 exons from 37 to 1,394 bp in size with consensus splice sites. The gene's regulatory sequences contain putative promoter elements, but no typical TATA box. Some exons of this gene showed significant similarities to those of coagulation factor XII, tissue-type plasminogen activator, and urokinase genes in nucleotide length and in intron phasing. We also report the chromosome mapping of this gene by fluorescence in situ hybridization (FISH) using a genomic DNA fragment as a probe. The PHBP gene (HABP2) was located on chromosome 10q25-q26.
Nonequilibrium Thermodynamics and Nonlinear Kinetics in a Cellular Signaling Switch (2005)

We develop a rigorous nonequilibrium thermodynamics for an open system of nonlinear biochemical reactions responsible for cell signal processing. We show that the quality of the biological switch consisting of a phosphorylation-dephosphorylation cycle, such as those in protein kinase cascade, is controlled by the available intracellular free energy from the adenosine triphosphate (ATP) hydrolysis in vivo: DeltaG=k(B)Tln(([ATP]/K(eq)[ADP]), where K(eq) is the equilibrium constant. The model reveals the correlation between the performance of the switch and the level of DeltaG. The result demonstrates the importance of nonequilibrium thermodynamics in analyzing biological information processing, provides its energetic cost, establishes an interplay between signal transduction and energy metabolism in cells, and suggests a biological function for phosphoenergetics in the ubiquitous phosphorylation signaling.
Conceptual basis of the selective activation of bis(dialkylamino)methoxyphosphines by weak acids and its application toward the preparation of deoxynucleoside phosphoramidites in situ (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConceptual basis of the selective activation of bis(dialkylamino)methoxyphosphines by weak acids and its application toward the preparation of deoxynucleoside phosphoramidites in situMichael F. Moore and Serge L. BeaucageCite this: J. Org. Chem. 1985, 50, 12, 2019–2025Publication Date (Print):June 1, 1985Publication History Published online1 May 2002Published inissue 1 June 1985https://pubs.acs.org/doi/10.1021/jo00212a003https://doi.org/10.1021/jo00212a003research-articleACS PublicationsRequest reuse permissionsArticle Views383Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Design of an optimizing, dynamically retargetable compiler for common Lisp (1986)

We outline the components of a retargetable cross-compiler for the Common Lisp language. A description is given of a method for modeling the various hardware features in the compiler's database, and a breakdown is shown of the compiler itself into various machine-independent and machine-dependent modules. A novel feature of this development is the dynamic nature of the retargeting: Databases for multiple hardware architectures are a standard part of the compiler, and the internal interfaces used by the compiler are such that the machine-dependent modules may be instantly switched from one to another. Examples of generated code in several environments will be given to demonstrate the high quality of the output available, even under this very modular approach.
The Characteristics of Extracellular Protein Secretion by Staphylococcus aureus (Wood 46) and their Relationship to the Regulation of  -Toxin Formation (1977)

Summary: The progress of secretion of α-toxin and total extracellular protein by Staphylococcus aureus (Wood 46), grown aerobically at 37°C, in a 3 % (w/v) tryptone soya broth medium supplemented with vitamins was followed. Exoprotein was secreted at a high rate by intact bacteria during the exponential phase (to 9 h) and into the post-exponential phase. After 18 h, when exoprotein accounted for 33% of the total protein in the culture, no further exoprotein was secreted although the bacterial density continued to increase at a low rate beyond this time. During the phase of active secretion, α-toxin represented a constant proportion of total exoprotein, the differential rate of synthesis of which increased by a factor of four after the end of exponential growth. Concomitant with the increase in the differential rate of exoprotein formation there was a fourfold increase in the intracellular concentration of RNA precursor material.
Similar Efficacy from Specific and Non-Specific Mineralocorticoid Receptor Antagonist Treatment of Muscular Dystrophy Mice (2016)

These data suggest that spironolactone and eplerenone show similar effects in dystrophic mice and support the clinical development of MR antagonists for treating skeletal muscles in Duchenne muscular dystrophy.
Purification and properties of an acid lipase from <i>Penicillium roqueforti</i> (1983)

REFERENCES The extracellular acid lipase produced by Penicillium roqueforti strain 1173 was purified by precipitation with 50 % ethanol, DEAE Sephadex A 50 ion exchange chromatography and 2 successive treatments with SP Sephadex C 50. An ~ 400-fold purification with a 35 % yield was obtained. The enzyme was active from pH 1·7–10·5, with an optimum activity pH of 6·5 at 20 °C and 6·0 at 30 °C. A second minor optimum appeared close to pH 2·5 and there was a minimum activity at pH 3·6. In the presence of 0·1 M-CaCl 2 at 30 °C, the optimum was at pH 5·5, also the pH value where inhibition by CaCl 2 was least (9%). The pH stability curve at 30 °C showed no discontinuities and had a maximum between pH 3·7 and 6·0. At pH 6·5 activity at 5 °C represented 37 % of the maximum value, which was reached at 35–40 °C and the apparent activation energy was about 5·42 kcal mol -1 . Between pH 4·0 and 7·0, the ratio of hydrolysis velocity at 30 °C compared to that at 20 °C ranged from 2·1 to 1·2. At pH 6·0, the enzyme began to be inactivated at temperatures above 35 °C with decimal destruction times (D values) of 150, 29 and 4 min for respective temperatures of 40, 45 and 50 °C. In terms of substrate specificity the maximum activity was obtained with tricaproin whilst with tributyrin, tricaprylin, butter oil and triolein relative velocities were 22, 6·7, 3·0 and 1·5% respectively of that for tricaproin whilst Tween 20 and triacetin were 2·5 and 2% respectively.
Vasodilatory effects and coexistence of calcitonin gene‐related peptide (CGRP) and substance P in sensory nerves of cat dental pulp (1987)

Substance P (SP)- and calcitonin gene-related peptide (CGRP)-immunoreactivity (-IR) were localized by immunohistochemistry in the same nerve cell bodies in the trigeminal ganglia as well as in nerve terminals of the dental pulp. The distribution of SP- and CGRP-IR nerves were identical in the dental pulp and mainly associated with blood vessels. The level of CGRP-IR in the dental pulp, as measured by radio-immunoassay (RIA), was 1.4 +/- 0.2 pmol g-1 wet wt, which is in the same range as that found for substance P. Local intra-arterial infusion of synthetic CGRP and substance P produced vasodilatation in the dental pulp as measured by both laser Doppler flowmetry and an 125I clearance technique. The CGRP was effective as a vasodilator when infused in the femtomole per minute range, and SP in the picomole range. The effect of CGRP (50 fmol min-1) was 10 times larger when given after SP (15 pmol min-1) than before it. Since the two peptides coexist in the same neurons, it is suggested that they both contribute to the vasodilation seen upon antidromic stimulation of sensory nerves.
Development of a Shape-Memory-Alloy Actuated Biomimetic Hydrofoil (2002)

The development and testing of a biomimetic active hydrofoil that utilizes Shape-Memory-Alloy (SMA) actuator technology is presented. This work is the second stage in the development of a vehicle that has a skeletal structure similar to that of aquatic animals and SMA actuators for muscles. The current work describes the development and testing of a six-segment demonstration vehicle and the control schemes used. Each SMA actuation element consists of a thin wire that joins together two adjacent vertebrae segments of the hydrofoil skeleton and induces relative movement of one with respect to the other. Controlled heating and cooling of the wire sets generates bi-directional rotation of the vertebrae, which in turn causes a change in the shape of the hydrofoil. Each SMA wire is embedded in an elastic water channel that facilitatesfast active SMA cooling via forced water circulation. This hydrofoil was able to deform to several shapes mimicking aquatic animal swimming, with controlled oscillation frequencies of up to 1 Hz, with 1/2 Hz oscillation producing the largest body motion amplitudes.
The impact of RF front-end characteristics on the spectral regrowth of communications signals (2005)

The nonlinear characteristic of an RF front-end results in in-band distortion and spectral regrowth of digitally modulated signals with distortion being dependent on the statistical variation of the signal. In this paper, the interaction of the nonlinear response with the signal is explored using a time-averaged autocorrelation analysis applied to several limiter-amplifier models having characteristics ranging from soft-to-hard amplitude limiting. The analysis is verified by comparing measured and predicted adjacent channel power rejection for a code-division multiple-access amplifier.
Epigenetic dysregulation of leukaemic <scp>HOX</scp> code in <i><scp>MLL</scp></i>‐rearranged leukaemia mouse model (2013)

HOX genes are frequently dysregulated in human leukaemia with the gene rearrangement between mixed lineage leukaemia (MLL) and partner genes. The resultant MLL fusion proteins are known to mediate leukaemia through disruption of the normal epigenetic regulation at the target gene loci. To elucidate the pathogenic role of MLL fusion proteins in HOX dysregulation in leukaemia, we generated a novel haematopoietic lineage-specific Mll-Een knock-in mouse model using a Cre-mediated inversion strategy. The Mll(Een) (/+) invertor mice developed acute myeloid leukaemia, with organomegaly of the spleen, liver and mesenteric lymph nodes caused by infiltration of blast cells. Using Mll-Een-expressing leukaemic cell lines derived from bone marrow of Mll(Een) (/+) mutant mice, we showed that induction of Hox genes in leukaemic cells was associated with hypomethylated promoter regions and an aberrant active chromatin state at the Hox loci. Knock-down of Prmt1 was insufficient to reverse the active chromatin status and the hypomethylated Hox loci, suggesting that Prmt1-mediated histone arginine methylation was only partially involved in the maintenance of Hox expression in leukaemic cells. Furthermore, in vivo analysis of bone marrow cells of Mll(Een) (/+) mice revealed a Hox expression profile similar to that of wild-type haematopoietic stem cells. The leukaemic Hox profile was highly correlated with aberrant hypomethylation of Hox promoters in the mutant mice, which highlights the importance of DNA methylation in leukaemogenic mechanisms induced by MLL fusion proteins. Our results point to the involvement of dynamic epigenetic regulations in the maintenance of the stem cell-like HOX code that initiates leukaemic stem cells in MLL-rearranged leukaemia. This provides insights for the development of alternative strategies for leukaemia treatment.
Proteomic identification of novel proteins associated with Lewy bodies (2008)

The manifestation of Lewy bodies (LB) in the brain is a hallmark of Parkinson's disease. Here, we present a comprehensive analysis of protein elements in Lewy bodies by comparative mass spectrometry. Cortical LB inclusions were enriched by sucrose gradient centrifugation from postmortem brains, and a negative control sample was prepared from specimen without LB pathology. Whereas approximately 550 proteins were identified in the LB-enriched sample by mass spectrometry, quantitative comparison with the control sample revealed that approximately 40 proteins were co-enriched with alpha-synuclein, the major component in Lewy bodies. As expected, the list of proteins included previously reported constituents, such as those involved in protein folding, membrane trafficking and oxidative stress. More interestingly, we discovered in the LB-enriched sample several kinases (MAPKK1/MEK1, protein kinase C, and doublecortin-like kinase), a novel deubiquitinating enzyme (otubain 1), and numerous ubiquitin ligases (KPC and SCF). The proteomic studies provide enzyme candidates to investigate the regulation of alpha-synuclein and/or other LB proteins, which may contribute to the formation of Lewy bodies and the toxicity of alpha-synuclein in the related neurodegenerative disorders.