gebhart/patrepeval huggingface dataset:
p38 and Extracellular Signal-Regulated Kinases Regulate the Myogenic Program at Multiple Steps (2000)

The extracellular signals which regulate the myogenic program are transduced to the nucleus by mitogen-activated protein kinases (MAPKs). We have investigated the role of two MAPKs, p38 and extracellular signal-regulated kinase (ERK), whose activities undergo significant changes during muscle differentiation. p38 is rapidly activated in myocytes induced to differentiate. This activation differs from those triggered by stress and cytokines, because it is not linked to Jun-N-terminal kinase stimulation and is maintained during the whole process of myotube formation. Moreover, p38 activation is independent of a parallel promyogenic pathway stimulated by insulin-like growth factor 1. Inhibition of p38 prevents the differentiation program in myogenic cell lines and human primary myocytes. Conversely, deliberate activation of endogenous p38 stimulates muscle differentiation even in the presence of antimyogenic cues. Much evidence indicates that p38 is an activator of MyoD: (i) p38 kinase activity is required for the expression of MyoD-responsive genes, (ii) enforced induction of p38 stimulates the transcriptional activity of a Gal4-MyoD fusion protein and allows efficient activation of chromatin-integrated reporters by MyoD, and (iii) MyoD-dependent myogenic conversion is reduced in mouse embryonic fibroblasts derived from p38alpha(-/-) embryos. Activation of p38 also enhances the transcriptional activities of myocyte enhancer binding factor 2A (MEF2A) and MEF2C by direct phosphorylation. With MEF2C, selective phosphorylation of one residue (Thr293) is a tissue-specific activating signal in differentiating myocytes. Finally, ERK shows a biphasic activation profile, with peaks of activity in undifferentiated myoblasts and postmitotic myotubes. Importantly, activation of ERK is inhibitory toward myogenic transcription in myoblasts but contributes to the activation of myogenic transcription and regulates postmitotic responses (i.e., hypertrophic growth) in myotubes.
Electrospray‐assisted laser desorption/ionization and tandem mass spectrometry of peptides and proteins (2007)

Abstract We have constructed an electrospray‐assisted laser desorption/ionization (ELDI) source which utilizes a nitrogen laser pulse to desorb intact molecules from matrix‐containing sample solution droplets, followed by electrospray ionization (ESI) post‐ionization. The ELDI source is coupled to a quadrupole ion trap mass spectrometer and allows sampling under ambient conditions. Preliminary data showed that ELDI produces ESI‐like multiply charged peptides and proteins up to 29 kDa carbonic anhydrase and 66 kDa bovine albumin from single‐protein solutions, as well as from complex digest mixtures. The generated multiply charged polypeptides enable efficient tandem mass spectrometric (MS/MS)‐based peptide sequencing. ELDI‐MS/MS of protein digests and small intact proteins was performed both by collisionally activated dissociation (CAD) and by nozzle‐skimmer dissociation (NSD). ELDI‐MS/MS may be a useful tool for protein sequencing analysis and top‐down proteomics study, and may complement matrix‐assisted laser desorption/ionization (MALDI)‐based measurements. Copyright © 2007 John Wiley & Sons, Ltd.
A review of the pharmacokinetics and pharmacodynamics of combination carboplatin/paclitaxel. (1997)

The combination of carboplatin and paclitaxel (Taxol; Bristol-Myers Squibb Company, Princeton, NJ) has been found to be highly active, to offer convenience of administration and better potential for dose escalation, and to produce less nonhematologic toxicity than standard therapy with cisplatin plus paclitaxel. Increased myelosuppression was anticipated to be a disadvantage of the carboplatin/paclitaxel combination, although it was expected to affect mainly platelets. Studies to date of the paclitaxel/carboplatin combination suggest the combination has a relatively benign effect on platelets compared with single-agent carboplatin. Previous pharmacokinetic studies have suggested that the measured area under the plasma carboplatin concentration-time curve is significantly less than that predicted by dosing formulas based on glomerular filtration rates. Newer evidence, however, contradicts these findings. This review examines the evidence of both a pharmacodynamic and a pharmacokinetic interaction between carboplatin and paclitaxel that has a sparing effect on platelets. It further assesses methodologic differences in methods used to estimate glomerular filtration. Paclitaxel appears to offer some protective effect for carboplatin-induced thrombocytopenia, although the two drugs do not interact pharmacokinetically. The apparent deviations of the achieved carboplatin area under the plasma concentration-time curve from that predicted by a dosing formula are thought to be due to differences in the methodology used to estimate renal function and measure creatinine. Any interaction between the two drugs most likely occurs at the level of the megakaryocyte.
Enhancement of Activity and Sulfur Resistance of CeO<sub>2</sub> Supported on TiO<sub>2</sub>–SiO<sub>2</sub> for the Selective Catalytic Reduction of NO by NH<sub>3</sub> (2012)

A series of novel metal-oxide-supported CeO(2) catalysts were prepared via the wet impregnation method, and their NH(3)-SCR activities were investigated. The Ce/TiO(2)-SiO(2) catalyst with a Ti/Si mass ratio of 3/1 exhibited superior NH(3)-SCR activity and high N(2) selectivity in the temperature range of 250-450 °C. The characterization results revealed that the activity enhancement was correlated with the properties of the support material. Cerium was highly dispersed on the TiO(2)-SiO(2) binary metal oxide support, and the interaction of Ti and Si resulted in greater conversion of Ce(4+) to Ce(3+) on the surface of the catalyst compared to that on the single metal oxide supports. As a result of in the increased number of acid sites on Ce/TiO(2)-SiO(2) that resulted from the addition of SiO(2), the NH(3) adsorption capacity was significantly improved. All of these factors played significant roles in the high SCR activity. More importantly, Ce/TiO(2)-SiO(2) exhibited strong resistance to SO(2) and H(2)O poisoning. After the addition of SiO(2), the number of Lewis-acid sites was not decreased, but the number of Brønsted-acid sites on the TiO(2)-SiO(2) carrier was increased. The introduction of SiO(2) further weakened the alkalinity over the surface of the Ce/TiO(2)-SiO(2) catalyst, which resulted in sulfate not easily accumulating on the surface of the Ce/TiO(2)-SiO(2) catalyst in comparison with Ce/TiO(2).
An in vivo brain–bacteria interface: the developing brain as a key regulator of innate immunity (2020)

Infections have numerous effects on the brain. However, possible roles of the brain in protecting against infection, and the developmental origin and role of brain signaling in immune response, are largely unknown. We exploited a unique <i>Xenopus</i> embryonic model to reveal control of innate immune response to pathogenic <i>E. coli</i> by the developing brain. Using survival assays, morphological analysis of innate immune cells and apoptosis, and RNA-seq, we analyzed combinations of infection, brain removal, and tail-regenerative response. Without a brain, survival of embryos injected with bacteria decreased significantly. The protective effect of the developing brain was mediated by decrease of the infection-induced damage and of apoptosis, and increase of macrophage migration, as well as suppression of the transcriptional consequences of the infection, all of which decrease susceptibility to pathogen. Functional and pharmacological assays implicated dopamine signaling in the bacteria-brain-immune crosstalk. Our data establish a model that reveals the very early brain to be a central player in innate immunity, identify the developmental origins of brain-immune interactions, and suggest several targets for immune therapies.
Conformational preferences of oligopeptides rich in α‐aminoisobutyric acid. I. Observation of a 3<sub>10</sub>/α‐helical transition upon sequence permutation (1991)

The solution conformation of peptides rich in the alpha, alpha-dialkylated amino acid Aib has proven to be a subtle problem, not because of helix/coil transitions, but rather because of alpha-helical/3(10)-helical competition. A special series of peptides containing 75% Aib has been synthesized that feature identical amino acid composition but differing sequences; they are sequence permutation isomers. Nuclear magnetic resonance hydrogen-bonding studies reveal that there is a sequence permutation induced transition between the two alternative helical forms within this set. The implications for the design and conformational prediction of helical Aib-rich peptides are discussed.
Sensitive and Specific Identification of<i>Neospora caninum</i>Infection of Cattle Based on Detection of Serum Antibodies to Recombinant Ncp29 (2002)

Neosporosis is an economically important disease of dairy cattle caused by the protozoan Neospora caninum. Diagnostic tests for neosporosis are complicated by the potential for cross-reaction of antibodies to antigens that are similar between N. caninum and closely related parasites Toxoplasma gondii and Sarcocystis cruzi. To provide a sensitive and specific assay for detecting antibodies to N. caninum in the serum of infected animals, we have investigated a recombinant form of the antigen known as Ncp29 (rNcp29), which is a major surface protein of the parasite. Ncp29 is encoded by a gene that is homologous to the SAG1 gene previously characterized from T. gondii. An enzyme-linked immunosorbent assay (ELISA) was used to screen animals for the presence of serum antibodies specific to rNcp29. The rNcp29 ELISA readily distinguished between cattle known to be infected with N. caninum (optical density [OD] > 1.2 at 1:500 or greater dilution) and negative controls (OD < 0.5 at 1:500). Additionally, sera from animals that were infected with T. gondii or S. cruzi were negative. The rNcp29 ELISA developed here provides a specific and sensitive assay for detecting neosporosis in cattle.
Cold Radiofrequency Plasma Treatment Modifies Wettability and Germination Speed of Plant Seeds (2012)

We report the possibility to modify the wetting properties of the surfaces of a diversity of seeds including: lentils (Lens culinaris), beans (Phaseolus vulgaris) and wheat (Triticum, species C9) by cold radiofrequency air plasma treatment. Air plasma treatment leads to the dramatic decrease in the apparent contact angle. Moreover, the speed of germination and yield (germination rate) of seeds can be modified by preliminary plasma treatment. The change in the wetting properties of seeds is at least partially due to oxidation of their surface under plasma treatment. Significant growth of the peaks corresponding to the nitrogen containing groups in the mass spectra of air plasma treated seeds was registered by TOF-SIMS spectroscopy.
Chemistry and physical properties of estolides (2011)

Estolides are a developing class of natural and synthetic compounds that have been synthesized from hydroxy oils like castor and lesquerella or by the condensation of fatty acids across the olefin of a second fatty acid. Castor and lesquerella estolides are derived from either their triglycerides or their free fatty acids utilizing their hydroxyl moiety to establish the estolide bond. The triglyceride estolides have pour points of 9 to –36ºC but suffer poor oxidative stability with RPVOT times of 29 – 52 minutes even with 1% of an anti-oxidant package incorporated into the samples. In contrast to the triglyceride estolides of castor and lesquerella, the estolides from lesquerolic and ricinoleic acids have very good pour points of –36 to –54ºC. Estolides derived from the acid catalyzed condensation of oleic acid with a variety of fatty acids can be made in good yield and posses a wide range of physical properties. Of particular interest are the saturated capped estolides of oleic that have both good low temperature properties (pour point –5 to – 39ºC) and good oxidative stability. Estolides from meadowfoam fatty acids do not have good low temperature properties but have been extensively used in cosmetics where they provide good moisturizing properties.
A Study of Gongqing Wangming (_??__??__??__??_) (2004)

Gongqing Wangming is a kind of capital punishment procedure for Governors-general and Governors (_??__??_) without getting emperor's sanction by using Wangming Qipai (_??__??__??__??_). It can bethought to come from the expedient measure in military affairs.In the Yongzheng (_??__??_) era, it was the expedient measure for capital cases which was chosen to hasten the execution of the death penalty. However, it was only the method accepted with the limitation after troublesome procedure, which was possible to impose a serious punishment in comparison with the Cane punishment (_??__??_) of the same time.In the early Qianlong (_??__??_) era, the emperor made Governorsgeneral and Governors use properly the Cane punishment and the capital punishment by the statute law to impose a punishment corresponding to the crime. So they had to grope for the new method in the case using the Cane punishment to hasten the execution of the death penalty. As coping with this situation, some methods to hasten the execution of the death penalty were groped on each step of capital punishment procedure. One of them was an Imperial ordinance at 1761 and 1764 that establishes to use Gongqing Wangming in the case of murdering parents or grandparents. It was established as the method to impose quickly the capital punishment by the statute law.After the mid-Qianlong era, the case of Gongqing Wangming increased since establishing to use it in the case of murdering parents or grandparents. On the one hand the emperor and the government officials worked for establishing in advance, on the other hand they used it as the expedient measure. Occasionally, the established method was born of such practice. These were activities about an aptitude for procedure in the whole of the bureaucracy system, and establishing was the process that took root of those in the fixed method. "The system" of Gongqing Wangming was established by repeating trial and error with an uncertain limit during the historical change, as the form that it didn't contend gradually for the kernel. There is a feature in holding fluidity in system at all time.The function of difference in punishment by the elements of procedure was produced from the increase and establishment of Gongqing Wangming after the mid-Qianlong era, and contributed to making it stabilize an established method. As the stability of established method rose from such an interaction, the expedient function to hasten the execution of the death penalty changed into the function of difference in punishment in the established method of Gongqing Wangming. One of the reasons why Gongqing Wangming became to be used only in the part of establishment at the end of Qing dynasty is a decrease of the expedient function in "the system" of Gongqing Wangming.
Pilot-Channel Aided SIC for Uplink WCDMA Systems over Multipath Fading Channels (2005)

In this paper, we examine the performance of the pilot-channel aided successive interference cancellation scheme in asynchronous WCDMA systems over multipath fading channels. Three types of cancellation-ordering method are compared where the cancellation order is decided based on either average power or instantaneous RAKE output strength with various updating rate. The scheme performs pilot-channel signal removal before data detection to alleviate the interferences from other users ’ pilot channels and thus can achieve better performance on user data detection. With the investigation and comparison through computer simulations, the scheme with three types of ordering method are shown to perform variously due to different grouping interval and power distribution ratio over both AWGN and Rayleigh fading channels.
Fouling Mechanisms in Axial Compressors (2012)

Fouling of compressor blades is an important mechanism leading to performance deterioration in gas turbines over time. Fouling is caused by the adherence of particles to airfoils and annulus surfaces. Particles that cause fouling are typically smaller than 2 to 10 microns. Smoke, oil mists, carbon, and sea salts are common examples. Fouling can be controlled by appropriate air filtration systems, and can often be reversed to some degree by detergent washing of components. The adherence of particles is impacted by oil or water mists. The result is a build up of material that causes increased surface roughness and to some degree changes the shape of the airfoil (if the material build up forms thicker layers of deposits), with subsequent deterioration in performance. Fouling mechanisms are evaluated based on observed data, and a discussion on fouling susceptibility is provided. A particular emphasis will be on the capabilities of modern air filtration systems.
A physiological signature of sound meaning in dementia (2016)

The meaning of sensory objects is often behaviourally and biologically salient and decoding of semantic salience is potentially vulnerable in dementia. However, it remains unclear how sensory semantic processing is linked to physiological mechanisms for coding object salience and how that linkage is affected by neurodegenerative diseases. Here we addressed this issue using the paradigm of complex sounds. We used pupillometry to compare physiological responses to real versus synthetic nonverbal sounds in patients with canonical dementia syndromes (behavioural variant frontotemporal dementia - bvFTD, semantic dementia - SD; progressive nonfluent aphasia - PNFA; typical Alzheimer's disease - AD) relative to healthy older individuals. Nonverbal auditory semantic competence was assessed using a novel within-modality sound classification task and neuroanatomical associations of pupillary responses were assessed using voxel-based morphometry (VBM) of patients' brain MR images. After taking affective stimulus factors into account, patients with SD and AD showed significantly increased pupil responses to real versus synthetic sounds relative to healthy controls. The bvFTD, SD and AD groups had a nonverbal auditory semantic deficit relative to healthy controls and nonverbal auditory semantic performance was inversely correlated with the magnitude of the enhanced pupil response to real versus synthetic sounds across the patient cohort. A region of interest analysis demonstrated neuroanatomical associations of overall pupil reactivity and differential pupil reactivity to sound semantic content in superior colliculus and left anterior temporal cortex respectively. Our findings suggest that autonomic coding of auditory semantic ambiguity in the setting of a damaged semantic system may constitute a novel physiological signature of neurodegenerative diseases.
Mechanisms of Chromosome Number Evolution in Yeast (2011)

The whole-genome duplication (WGD) that occurred during yeast evolution changed the basal number of chromosomes from 8 to 16. However, the number of chromosomes in post-WGD species now ranges between 10 and 16, and the number in non-WGD species (Zygosaccharomyces, Kluyveromyces, Lachancea, and Ashbya) ranges between 6 and 8. To study the mechanism by which chromosome number changes, we traced the ancestry of centromeres and telomeres in each species. We observe only two mechanisms by which the number of chromosomes has decreased, as indicated by the loss of a centromere. The most frequent mechanism, seen 8 times, is telomere-to-telomere fusion between two chromosomes with the concomitant death of one centromere. The other mechanism, seen once, involves the breakage of a chromosome at its centromere, followed by the fusion of the two arms to the telomeres of two other chromosomes. The only mechanism by which chromosome number has increased in these species is WGD. Translocations and inversions have cycled telomere locations, internalizing some previously telomeric genes and creating novel telomeric locations. Comparison of centromere structures shows that the length of the CDEII region is variable between species but uniform within species. We trace the complete rearrangement history of the Lachancea kluyveri genome since its common ancestor with Saccharomyces and propose that its exceptionally low level of rearrangement is a consequence of the loss of the non-homologous end joining (NHEJ) DNA repair pathway in this species.
EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae (2016)

Saccharomyces cerevisiae is widely used in the biotechnology industry for production of ethanol, recombinant proteins, food ingredients and other chemicals. In order to generate highly producing and stable strains, genome integration of genes encoding metabolic pathway enzymes is the preferred option. However, integration of pathway genes in single or few copies, especially those encoding rate-controlling steps, is often not sufficient to sustain high metabolic fluxes. By exploiting the sequence diversity in the long terminal repeats (LTR) of Ty retrotransposons, we developed a new set of integrative vectors, EasyCloneMulti, that enables multiple and simultaneous integration of genes in S. cerevisiae. By creating vector backbones that combine consensus sequences that aim at targeting subsets of Ty sequences and a quickly degrading selective marker, integrations at multiple genomic loci and a range of expression levels were obtained, as assessed with the green fluorescent protein (GFP) reporter system. The EasyCloneMulti vector set was applied to balance the expression of the rate-controlling step in the β-alanine pathway for biosynthesis of 3-hydroxypropionic acid (3HP). The best 3HP producing clone, with 5.45 g.L(-1) of 3HP, produced 11 times more 3HP than the lowest producing clone, which demonstrates the capability of EasyCloneMulti vectors to impact metabolic pathway enzyme activity.
Concurrent three-dimensional characterization of the refractive-index and residual-stress distributions in optical fibers (2012)

A three-dimensional index-stress distribution (3DISD) measurement method for determining concurrently the refractive-index distributions (RIDs) and residual-stress distributions (RSDs) in optical fibers is presented. The method combines the quantitative-phase microscopy technique, the Brace-Köhler compensator technique, and computed tomography principles. These techniques are implemented on a common apparatus to enable concurrent characterization of the RID and the RSD. Measurements are performed on Corning SMF-28 fiber in an unperturbed section and in a section exposed to CO(2) laser radiation. The concurrent measurements allow for the first accurate comparison of the collocated RID and RSD. The resolutions of the refractive index and stress are estimated to be 2.34×10(-5) and 0.35 MPa, respectively.
The effects of beta-endorphin and enkephalins on protein biosynthesis in a eukaryotic cell-free system. Inhibition of phenylalanyl-tRNA synthetase. (1980)

The effects of beta-endorphin and various enkephalins on protein synthesis in eukaryotic cell-free systems have been examined. Beta-Endorphin, Leu-enkephalin, and Met-enkephalin inhibit the incorporation of radioactive leucine into globin in the presence of reticulocyte poly(A)+ RNA and of radioactive phenylalanine into polyphenylalanine in the presence of poly(U); however, the poly(U)-dependent synthesis of polyphenylalanine from Phe-tRNA is not inhibited. the aminoacylation of tRNAPhe is markedly inhibited by enkephalin, indicating that the sensitive component is Phe-tRNA synthetase. Other aminoacyl-tRNA synthetases are not significantly affected. The interaction between enkephalin and Phe-tRNA synthetase is reversible; activity is restored by dialysis of enzyme-enkephalin reaction mixtures. Morphine, vasopressin and analogues of vasopressin, and enkephalin analogues such as [D-Ala2,D-Leu5]enkephalin and [D-Ala2,Met]enkephalinamide have no effect on translation. The results suggest that the effects on protein synthesis are probably not related to opiate effects.