gebhart/patrepeval huggingface dataset:
Growth factor production by human colon carcinoma cell lines. (1989)

Conditioned media collected under serum-free conditions over 24 to 48 h from 18 human colon adenocarcinoma cell lines were analyzed for transforming growth factor, types alpha and beta (TGF-alpha and -beta), and platelet-derived growth factor in assays for anchorage-independent growth and radioreceptor competition. Detectable levels of TGF-alpha, TGF-beta, and platelet-derived growth factor were produced by 17, 16, and 6 cell lines, respectively. Three liters of conditioned medium from highly tumorigenic (HT-29, DLD-1, and SW620) and nontumorigenic (SKCO-1) colon cell lines and from nonneoplastic rat kidney (NRK-52E) and small intestinal (IEC-6) epithelial cells were purified by high-performance liquid chromatography and assayed for TGF-alpha- and TGF-beta-like activity. The highly tumorigenic colon cell lines produced 10- to 45-fold (soft agar), 19- to 90-fold (radioreceptor), and 4- to 35-fold (radioimmunoassay) more TGF-alpha activity compared to the nonneoplastic rat intestinal (IEC) epithelial cells. NRK-52E did not produce detectable TGF-alpha activity. Radioimmunoassay analysis of peak fractions revealed only TGF-alpha immunoreactivity; epidermal growth factor was not detected. Levels of TGF-beta-like material in the colon carcinoma populations were comparable (HT-29) or elevated (DLD-1, SW620) only 3- to 4-fold (soft agar) or 1- to 3-fold (radioreceptor binding) compared to IEC cells or NRK-52E. Growth factor production is an ubiquitous property of colon carcinoma cell lines maintained in vitro and is consistent with this class of molecule, playing a contributory role in regulating cell growth.
Quantitative chemical exchange saturation transfer (qCEST) MRI – RF spillover effect‐corrected omega plot for simultaneous determination of labile proton fraction ratio and exchange rate (2014)

Chemical exchange saturation transfer (CEST) MRI is sensitive to dilute proteins and peptides as well as microenvironmental properties. However, the complexity of the CEST MRI effect, which varies with the labile proton content, exchange rate and experimental conditions, underscores the need for developing quantitative CEST (qCEST) analysis. Towards this goal, it has been shown that omega plot is capable of quantifying paramagnetic CEST MRI. However, the use of the omega plot is somewhat limited for diamagnetic CEST (DIACEST) MRI because it is more susceptible to direct radio frequency (RF) saturation (spillover) owing to the relatively small chemical shift. Recently, it has been found that, for dilute DIACEST agents that undergo slow to intermediate chemical exchange, the spillover effect varies little with the labile proton ratio and exchange rate. Therefore, we postulated that the omega plot analysis can be improved if RF spillover effect could be estimated and taken into account. Specifically, simulation showed that both labile proton ratio and exchange rate derived using the spillover effect-corrected omega plot were in good agreement with simulated values. In addition, the modified omega plot was confirmed experimentally, and we showed that the derived labile proton ratio increased linearly with creatine concentration (p < 0.01), with little difference in their exchange rate (p = 0.32). In summary, our study extends the conventional omega plot for quantitative analysis of DIACEST MRI.
PDGF, CSF-1, and EGF induce tyrosine phosphorylation of p120, a pp60src transformation-associated substrate. (1991)

Transformation by activated pp60c-src has been correlated by genetic analysis with the tyrosine phosphorylation of a 120 kilodalton (kDa) protein, p120. We now demonstrate tyrosine phosphorylation of p120 following stimulation of cells by growth factors whose receptors have intrinsic tyrosine-specific protein kinase activity. Stimulation of quiescent NIH3T3 cells with platelet-derived growth factor (PDGF) resulted in the tyrosine phosphorylation of p120 that was maximal by 5 min and returned to background levels by 30 min. p120 was also phosphorylated on tyrosine after addition of colony-stimulating factor 1 (CSF-1) or epidermal growth factor (EGF) to NIH3T3 cells engineered to express high levels of their respective receptors. Two additional src substrates, p110 and p85, were analysed under identical assay conditions. PDGF, CSF-1, and EGF induced only a minimal increase in the tyrosine phosphorylation of p85 and no change in the phosphorylation of p110. Thus, the marked ligand-induced tyrosine phosphorylation of p120 was a property not shared by the other src substrates examined. Immunoblotting with antibodies to p120 and the ras GTPase activating protein, GAP, suggests that p120 and GAP are unrelated. In addition, the amino acid sequences of four cyanogen bromide peptides derived from p120 showed no homology to GAP or to sequences in either the PIR or Swiss-Prot databases. These data suggest that tyrosine phosphorylation of p120 may contribute to both signal transduction through growth factor receptors and pp60src induced transformation.
Spatiotemporal coherent control using shaped, temporally focused pulses (2005)

In most coherent control experiments with femtosecond pulses, the temporal shape of the pulses is maintained throughout the interaction region. Here we show how pulses can be controlled such that their shapes vary rapidly even when propagating very short distances of a few micrometers. This changing pulse shape has a significant effect on coherent nonlinear optical processes. Here we study third-harmonic generation induced by a coherently controlled excitation pulse whose temporal profile changes along the axial coordinate.We show how such manipulations can be used to improve the axial resolution in a multiphoton optical microscope.
Karabaşlı çinte (Emberiza melanocephala Scopoli, 1769)’nin ekolojik niş modeli ve Türkiye’deki durumu (2015)

Türlerin coğrafik dağılımlarının bilinmesi, biyolojik çeşitliliğin korunması ve yönetilmesi açısından son derece önemlidir. Tür dağılımlarını tam olarak belirlemek için çoğu taksonda sınırlı sayıda veri bulunmakta olup mevcut dağılımları ve iklimsel değişimler neticesinde nasıl dağılım gösterecekleri konusunda ekolog ve doğa korumacılar genel olarak coğrafi bilgi sistemleri ile çeşitli dağılım modelleri yapmakta ve taksonların dağılımlarını ortaya çıkarmaktadır. Bu çalışmada Türkiye’de geniş dağılım gösteren Karabaşlı çinte (Emberiza melanocephala Scopoli, 1769)’nin dağılım alanının sıcaklık ve yağış parametrelerine bağlı değişimi DivaGIS programında DOMAIN yöntemi kullanılarak analiz edilmiştir. Bu sonuçlara göre Karabaşlı çinte popülasyonları özellikle Güneydoğu Anadolu Bölgesi ile İç Anadolu bozkırları ve Ege ve Akdeniz Bölgesi’ndeki meşeliklerde geniş yayılış göstermekte olup alpin kuşakta görülmemekle birlikte, Karadeniz Bölgesi’nin kıyılarında artış göstereceği tahmin edilmektedir.
Site-specific Recombination in Phage Lambda (1983)

INTRODUCTION Cells lysogenic for λ carry a quiescent form of the viral chromosome called prophage. The prophage differs from the DNA of viral particles in two important ways: (1) The ends of the prophage and of the viral particle DNA are at different points in the nucleotide sequence, and (2) the prophage ends are covalently joined to host DNA. Campbell (1962) proposed that viral particle DNA is converted to prophage by the joining of the ends followed by insertion of the resulting circular molecule into the host DNA. Insertion occurs by reciprocal recombination at specific sites (attachment or att sites) in each chromosome (Fig. 1). This proposal has received extensive experimental support and, indeed, was generally accepted when the first edition of this book was written (see Gottesman and Weisberg 1971). A stable lysogen is formed when an infecting viral particle succeeds both in repressing lytic functions and in inserting its DNA. The inserted prophage is then replicated as part of the bacterial chromosome. In the rare event that repression is not followed by insertion (abortive lysogeny), the viral chromosome cannot replicate and so is lost by dilution as the host cell divides. Excision of the prophage from the chromosome is rare during normal bacterial growth but occurs readily following repressor inactivation. If the repressor is inactivated only briefly (abortive or transient derepression), prophage excision can occur without lytic growth. The excised DNA is then frequently lost as the cell divides (prophage curing). Intricate controls ensure that insertion occurs only...
A revised set of potentials for β‐turn formation in proteins (1994)

Three thousand eight hundred ninety-nine beta-turns have been identified and classified using a nonhomologous data set of 205 protein chains. These were used to derive beta-turn positional potentials for turn types I' and II' for the first time and to provide updated potentials for formation of the more common types I, II, and VIII. Many of the sequence preferences for each of the 4 positions in turns can be rationalized in terms of the formation of stabilizing hydrogen bonds, preferences for amino acids to adopt a particular conformation in phi, psi space, and the involvement of turn types I' and II' in beta-hairpins. Only 1,632 (42%) of the turns occur in isolation; the remainder have at least 1 residue in common with another turn and have hence been classified as multiple turns. Several types of multiple turn have been identified and analyzed.
Conopressin Affects Excitability, Firing, and Action Potential Shape Through Stimulation of Transient and Persistent Inward Currents in Mulluscan Neurons (1998)

The molluscan vasopressin/oxytocin-related neuropeptide conopressin activates two persistent inward currents in neurons from the anterior lobe of the right cerebral ganglion of Lymnaea stagnalis that are involved in the control of male copulatory behavior. The low-voltage-activated (LVA) current is activated at a wide range of membrane potentials, its amplitude being only weakly voltage dependent. The high-voltage-activated (HVA) current is activated at potentials positive to -40 mV only and shows a steep voltage dependence. Occurrence of both currents varies from cell to cell, some expressing both and others only the HVA current. In most neurons that have the LVA current, a conopressin-independent persistent inward current (INSR) is found that resembles the HVA current in its voltage dependence. The functional importance of the LVA and HVA currents was studied under current-clamp conditions in isolated anterior lobe neurons. In cells exhibiting both current types, the effect of activation of the LVA current alone was investigated as follows: previously recorded LVA current profiles were injected into the neurons, and the effects were compared with responses induced by conopressin. Both treatments resulted in a strong depolarization and firing activity. No differences in firing frequency and burst duration were observed, indicating that activation of the LVA current is sufficient to evoke bursts. In cells exhibiting only the HVA current, the effect of conopressin on the response to a depolarizing stimulus was tested. Conopressin reversibly increased the number of action potentials generated by the stimulus, suggesting that the HVA current enhances excitability and counteracts accommodation. Conopressin enhanced action potential broadening during depolarizing stimuli in many neurons. Voltage-clamp experiments performed under ion-selective conditions revealed the presence of transient sodium and calcium currents. Using the action potential clamp technique, it was shown that both currents contribute to the action potential. The calcium current, which is activated mainly during the repolarizing phase of the action potential, is augmented by conopressin. Thus conopressin may directly modulate the shape of the action potential. In summary, conopressin may act simultaneously on multiple inward currents in anterior lobe neurons of Lymnaea to affect firing activity, excitability, and action potential shape.
Electrical conductivity and dielectric constant measurements of liquid crystal–gold nanoparticle composites (2006)

Abstract The behaviour of the anisotropic electrical conductivity of liquid crystal–gold nanoparticle (LC‐GNP) composites consisting of a commercially available room temperature nematic compound doped with alkylthiol‐capped GNPs has been investigated. The nematic–isotropic transition of the composite decreases nearly linearly with increasing X, the concentration of GNP (in weight %) at a rate of about 1°C /weight %. The inclusion of GNPs increases the electrical conductivity of the system with the value increasing by more than two orders of magnitude for X = 5%. However, the anisotropy in conductivity, defined as the ratio of the conductivity along (σ∥) and orthogonal (σ⊥) to the director shows a much smaller but definite decrease as X increases.
Comparison of drive currents in metal-oxide-semiconductor field-effect transistors made of Si, Ge, GaAs, InGaAs, and InAs channels (2010)

In this study, the effect of using high-electron-mobility channel materials, such as GaAs, InAs, and InGaAs, on drive current in n-channel metal-oxide-semiconductor (nMOS) and p-channel metal-oxide-semiconductor devices is studied. Relative to silicon, these materials have lower electron effective mass, which leads to lower inversion capacitance (Cinv) due to their lower density of states. Despite their lower Cinv, high-electron mobility channel materials are shown to be promising alternatives to silicon in delivering higher drive current in nMOS devices.
Palladium(II)-mediated 11C-carbonylative coupling of diaryliodonium salts with organostannanes—a new, mild and rapid synthesis of aryl [11C]ketones (2000)

Palladium(II)-mediated [11C]carbonylative coupling of diaryliodonium salts with aryltributylstannanes for 1 min in DME–water (4∶1 v/v) at RT gives a new mild and rapid route to aryl [11C]ketones. Substituted aryltributylstannanes couple with diphenyliodonium bromide to give substituted [11C]benzophenones in generally very high radiochemical yield (>98%, decay-corrected), while diphenyliodonium tosylates, bearing one or two substituents in one ring, couple with phenyltributylstannane to give a mixture of substituted (30–43%) and unsubstituted [11C]benzophenone (47–66%). These reactions are highly attractive for introducing cyclotron-produced carbon-11 (t1/2 = 20.4 min) into prospective radiotracers for application in medical imaging with positron emission tomography.
Novel Vip3-Related Protein from Bacillus thuringiensis (2005)

A novel vip3-related gene was identified in Bacillus thuringiensis. This novel gene is 2,406 bp long and codes for a 91-kDa protein (801 amino acids). This novel protein exhibits between 61 and 62% similarity with Vip3A proteins and is designated Vip3Ba1. Vip3Ba1 has several specific features. Differences between Vip3Ba1 and the Vip3A proteins are spread throughout the sequence but are more frequent in the C-terminal part from amino acid 456 onward. The regions containing the two proteolytic processing sites, which are highly conserved among the Vip3A toxins, are markedly different in Vip3Ba1. The pattern DCCEE (Asp Cys Cys Glu Glu) is repeated four times between position 463 and 483 in Vip3Ba1, generating the sequence 463-DCCEEDCCEEDCCEEDCCEE-483. This sequence, which is rich in negatively charged amino acids, also contains 73% of the cysteines present in Vip3Ba1. This repeated sequence is not present in Vip3A proteins. The Vip3Ba1protein was produced in Escherichia coli and tested against Ostrinia nubilalis and Plutella xylostella, and it generated significant growth delays but had no larvicidal effect, indicating that its host range might be different than that of Vip3A proteins.
Molecular cloning and nucleotide sequencing of the 3'-terminal genomic RNA of the porcine reproductive and respiratory syndrome virus (1994)

The genomic RNA of a porcine reproductive and respiratory syndrome virus (PRRSV) isolate from the U.S.A., VR 2385 (ATCC), was copied into cDNA after priming with oligo(dT) and cloned into phage lambda. The cDNA clones representing the 3'-terminal genomic RNA of the virus were isolated and sequenced. The genome is a positive-stranded, polyadenylated RNA with an estimated size of 15 kb. Analysis of the resulting sequence identified three complete open reading frames (ORFs) with the potential to encode polypeptides with predicted M(r)s of 22.2K (ORF 5), 19.1K (ORF 6) and 13.6K (ORF 7). ORF 7, which is closest to the 3' end, is predicted to encode a highly basic nucleocapsid protein displaying 58% amino acid identity to the corresponding protein of the Lelystad virus (LV), a European PRRSV isolate. ORFs 6 and 5, preceding ORF 7, are each predicted to encode proteins containing several hydrophobic domains that are thought to be membrane-associated. The VR 2385 ORF 6 protein is the most conserved structural protein. It has 78% amino acid identity to the equivalent LV protein, and ORF 5 shares only 54% of its amino acid sequence. Northern blot analysis revealed a 3'-coterminal nested set of six subgenomic RNAs in VR 2385 virus-infected CRL 11171 cells. Our results indicate that VR 2385, like LV, is a member of the newly proposed arterivirus group. However, the striking genetic variation and the difference in pathogenicity between LV and VR 2385 suggest that the viruses causing PRRS in the U.S.A. and Europe are highly variable and they may represent different genotypes.
Temporal sparsity exploiting nonlocal regularization for 4D computed tomography reconstruction (2016)

X-ray imaging applications in medical and material sciences are frequently limited by the number of tomographic projections collected. The inversion of the limited projection data is an ill-posed problem and needs regularization. Traditional spatial regularization is not well adapted to the dynamic nature of time-lapse tomography since it discards the redundancy of the temporal information. In this paper, we propose a novel iterative reconstruction algorithm with a nonlocal regularization term to account for time-evolving datasets. The aim of the proposed nonlocal penalty is to collect the maximum relevant information in the spatial and temporal domains. With the proposed sparsity seeking approach in the temporal space, the computational complexity of the classical nonlocal regularizer is substantially reduced (at least by one order of magnitude). The presented reconstruction method can be directly applied to various big data 4D (x, y, z+time) tomographic experiments in many fields. We apply the proposed technique to modelled data and to real dynamic X-ray microtomography (XMT) data of high resolution. Compared to the classical spatio-temporal nonlocal regularization approach, the proposed method delivers reconstructed images of improved resolution and higher contrast while remaining significantly less computationally demanding.
Fusing points and lines for high performance tracking (2005)

This paper addresses the problem of real-time 3D model-based tracking by combining point-based and edge-based tracking systems. We present a careful analysis of the properties of these two sensor systems and show that this leads to some non -trivial design choices that collectively yield extremely high performance. In particular, we present a method for integrating the two systems and robustly combining the pose estimates they produce. Further we show how on-line learning can be used to improve the performance of feature tracking. Finally, to aid real-time performance, we introduce the FAST feature detector which can perform full-frame feature detection at 400Hz. The combination of these techniques results in a system which is capable of tracking average prediction errors of 200 pixels. This level of robustness allows us to track very rapid motions, such as 50deg camera shake at 6Hz
Determination of mercaptans by negative ion mass spectrometry (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of mercaptans by negative ion mass spectrometryHans. Knof, Robert. Large, and Georg. AlbersCite this: Anal. Chem. 1976, 48, 14, 2120–2123Publication Date (Print):December 1, 1976Publication History Published online1 May 2002Published inissue 1 December 1976https://doi.org/10.1021/ac50008a017RIGHTS & PERMISSIONSArticle Views63Altmetric-Citations10LEARN 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 InReddit PDF (411 KB) Get e-Alertsclose Get e-Alerts
Leptin Acts on Human Marrow Stromal Cells to Enhance Differentiation to Osteoblasts and to Inhibit Differentiation to Adipocytes1 (1999)

Both bone mass and serum leptin levels are increased in obesity. Because osteoblasts and adipocytes arise from a common precursor in bone marrow, we assessed the effects of human recombinant leptin on a conditionally immortalized human marrow stromal cell line, hMS2-12, with the potential to differentiate to either the osteoblast or adipocyte phenotypes. By RT-PCR and Western immunoblot analysis, the hMS2-12 cells expressed messenger RNA (mRNA) and protein for the leptin receptor. Leptin did not affect hMS2-12 cell proliferation, but resulted in dose- and time-dependent increases in mRNA and protein levels of alkaline phosphatase, type I collagen, and osteocalcin, and in a 59% increase in mineralized matrix. Leptin increased mRNA levels of lipoprotein lipase at 3 days, but decreased mRNA levels of adipsin and leptin at 9 days and decreased lipid droplet formation by 50%. Leptin did not affect the expression of Cbfa1 or peroxisome proliferator-activated receptor-gamma2, transcription factors involved in commitment to the osteoblast and adipocyte pathways, respectively. Thus, leptin acts on human marrow stromal cells to enhance osteoblast differentiation and to inhibit adipocyte differentiation. Our data support the hypothesis that leptin is a previously unrecognized, physiological regulator of these two differentiation pathways, acting primarily on maturation of stromal cells into both lineages.