gebhart/patrepeval huggingface dataset:
Stimulation of Lipolysis and Hormone-sensitive Lipase via the Extracellular Signal-regulated Kinase Pathway (2001)

Hormonally stimulated lipolysis occurs by activation of cyclic AMP-dependent protein kinase (PKA) which phosphorylates hormone-sensitive lipase (HSL) and increases adipocyte lipolysis. Evidence suggests that catecholamines not only can activate PKA, but also the mitogen-activated protein kinase pathway and extracellular signal-regulated kinase (ERK). We now demonstrate that two different inhibitors of MEK, the upstream activator of ERK, block catecholamine- and beta(3)-stimulated lipolysis by approximately 30%. Furthermore, treatment of adipocytes with dioctanoylglycerol, which activates ERK, increases lipolysis, although MEK inhibitors decrease dioctanoylglycerol-stimulated activation of lipolysis. Using a tamoxifen regulatable Raf system expressed in 3T3-L1 preadipocytes, exposure to tamoxifen causes a 14-fold activation of ERK within 15-30 min and results in approximately 2-fold increase in HSL activity. In addition, when differentiated 3T3-L1 cells expressing the regulatable Raf were exposed to tamoxifen, a 2-fold increase in lipolysis is observed. HSL is a substrate of activated ERK and site-directed mutagenesis of putative ERK consensus phosphorylation sites in HSL identified Ser(600) as the site phosphorylated by active ERK. When S600A HSL was expressed in 3T3-L1 cells expressing the regulatable Raf, tamoxifen treatment fails to increase its activity. Thus, activation of the ERK pathway appears to be able to regulate adipocyte lipolysis by phosphorylating HSL on Ser(600) and increasing the activity of HSL.
CLV3 Is Localized to the Extracellular Space, Where It Activates the Arabidopsis CLAVATA Stem Cell Signaling Pathway (2002)

Plant growth and development depends on the activity of a continuously replenished pool of stem cells within the shoot apical meristem to supply cells for organogenesis. In Arabidopsis, the stem cell-specific protein CLAVATA3 (CLV3) acts cell nonautonomously to restrict the size of the stem cell population, but the hypothesis that CLV3 acts as an extracellular signaling molecule has not been tested. We used genetic and immunological assays to show that CLV3 localizes to the apoplast and that export to the extracellular space is required for its function in activating the CLV1/CLV2 receptor complex. Apoplastic localization allows CLV3 to signal from the stem cell population to the organizing center in the underlying cells.
Heterogeneous expression of melanoma-associated antigens and HLA-A2 in metastatic melanoma in vivo (1998)

MART-1/MelanA and Pmel17/gp100 are melanoma-associated antigens (MAAs) that can be recognized by tumor-infiltrating lymphocytes (TILs) capable of mediating successful adoptive therapy in vivo. Analysis of melanoma cell lines in vitro has demonstrated that heterogeneous antigen expression in the context of class I MHC is a significant co-factor in determining the recognition of melanoma targets by cytotoxic lymphocytes (CTLs). In this study, 217 specimens from 103 patients with metastatic melanoma were examined for the expression of MART-1/MelanA (monoclonal antibody [MAb] M27C10) and Pmel17/gp100 (HMB45 MAb) by immuno-histochemistry. Marked heterogeneity in the expression of both MAAs was confirmed by analysis of the percentage of positively staining tumor cells or the average intensity of tumor staining. We also noted heterogeneity of expression among multiple lesions taken from different anatomic sites within a patient. A dissociation was noted in the detection of MART-1 and gp100 in some lesions, with gp100 being undetectable in 24% of the lesions and MART-1 being undetectable in 11%. In several cases, loss of one MAA was not associated with loss of the other MAA, suggesting that MART-1 can represent a useful additional marker for the diagnosis of melanoma in gp100 (HMB45)-negative lesions. Of the 217 specimens, 155 were obtained from HLA-A*0201 patients, of which 6% were negative for HLA-A2, 8% were negative for MART-1/MelanA and 21% were negative for Pmel17/gp100. The potential significance of our findings is illustrated by a case study in which a patient with melanoma experienced rapid tumor progression in association with loss of either MAA or HLA expression in several lesions.
Effects of intravenous immunoglobulin on platelet count and antiplatelet antibody disposition in a rat model of immune thrombocytopenia (2002)

Experiments were conducted to investigate the effects of intravenous immunoglobulin (IVIG) in a rat model of immune thrombocytopenia (ITP). Rats were pretreated with 0 to 2 g/kg IVIG and then challenged with an antiplatelet antibody (7E3, 8 mg/kg). IVIG effects on 7E3-induced thrombocytopenia and on 7E3 pharmacokinetics were determined. IVIG pretreatment led to significant changes in the degree and time-course of 7E3-induced thrombocytopenia (P = .031). Nadir percent platelet counts were 121% to 279% greater in animals treated with IVIG (0.4-2 g/kg) than in animals receiving 7E3 alone. IVIG treatment also led to dose-dependent increases in 7E3 clearance (P &lt; .001), with more than 2-fold increases in 7E3 clearance seen following the highest dose of IVIG. In vitro experiments showed that IVIG effects on platelet count are not likely due to anti-idiotypic inhibition of 7E3-platelet binding and that IVIG did not directly bind to 7E3. Consequently, IVIG-7E3 binding cannot explain the increase of 7E3 clearance following IVIG treatment. We propose that the observed increase in 7E3 clearance with IVIG therapy is due to saturation of the FcRn salvage receptor for IgG. The importance of the effect of IVIG on 7E3 clearance to the prevention of thrombocytopenia in these animals is unclear at present; nonetheless, these data provide experimental support for a new mechanism of IVIG action in ITP (ie, IVIG-mediated increases in antiplatelet antibody elimination). This model of ITP will be useful for further investigations of IVIG mechanism of action and for development of new therapies for ITP.
T-ray computed tomography (2002)

We demonstrate a tomographic imaging modality that uses pulsed terahertz (THz) radiation to probe the optical properties of three-dimensional (3D) structures in the far-infrared. This THz-wave computed tomography (T-ray CT) system provides sectional images of objects in a manner analogous to conventional CT techniques such as x-ray CT. The transmitted amplitude and phase of broadband pulses of THz radiation are measured at multiple projection angles. The filtered backprojection algorithm is then used to reconstruct the target object, including both its 3D structure and its frequency-dependent far-infrared optical properties.
Effects of β6 amino acid hydrophobicity on stability and solubility of hemoglobin tetramers (1993)

The relationship between different amino acids at the beta 6 position of hemoglobin and tetramer stability was addressed by a site-directed mutagenesis approach. Precipitation rates during mechanical agitation of oxyhemoglobins with Gln, Ala, Val, Leu and Trp at the beta 6 position increased 2, 5, 13, 21 and 53 times, respectively, compared with that for Hb A. There was a linear relationship between the log of the precipitation rate constant and amino acid hydrophobicity at the beta 6 position, suggesting that enhanced precipitation of oxy Hb S during mechanical agitation results in part from increased hydrophobicity of beta 6 Val. Deoxyhemoglobin solubility increased in the order of beta 6 Ile, Leu, Val, Trp, Gln, Ala and Glu suggesting that hydrophobic interactions between beta 6 Val and the acceptor site of another hemoglobin molecule during deoxy-Hb S polymerization not only depend on hydrophobicity but also on stereospecificity of the amino acid side chain at the beta 6 position. Furthermore, our results indicate that hydrophobic amino acids at the beta 6 position which promote tetramer instability in the oxy form do not necessarily promote polymerization in the deoxy form.
Standardless Semiquantitative Analysis of Metals Using Single-Shot Laser Ablation Inductively Coupled Plasma Time-of-Flight Mass Spectrometry (2001)

A method has been developed that allows the accurate, standardless measurement of the elemental composition of metal samples from single laser ablation (LA) pulses. This technique provides a fast, low-sample-consumption means for the characterization of samples having a range of matrixes. The method directly compares adjusted elemental signals with the total mass spectrometric signal to produce relative percent composition information. Three mathematical techniques were used to determine the accuracy and precision of single-shot LA measurement. Comparison of the techniques showed that a linear regression calculation, which plots individual elemental signals as a function of the summed signal for all elements in the sample on a point-by-point basis during a laser ablation transient proved superior. The simultaneous extraction capability of time-of-flight mass spectrometry permits the sampling of all analytes from any temporal position within the transient laser ablation pulse, thereby reducing quantitation error. A typical concentration dynamic range of 3 orders of magnitude, from 0.1 to 100%, was achieved. However, by measuring low-abundance isotopes for matrix elements, the dynamic range of the technique was extended to 4 orders of magnitude. The new technique is largely immune to sample matrix effects commonly experienced in laser ablation. By performing a complete elemental analysis from a single ablation pulse, high spatial resolution should be achieved.
Post‐transcriptional defects in tobacco chloroplast mutants lacking the cytochrome b6/f complex (2000)

A variety of post-transcriptional mechanisms govern the synthesis and assembly of photosynthetic protein complexes in chloroplasts. To test whether such mechanisms are conserved between photosynthetic algae and vascular plants, we have interrupted the chloroplast petA, petB and petD genes of tobacco, which encode three subunits of the cytochrome b6/f complex, and compared our results to those previously obtained with Chlamydomonas reinhardtii. As expected, the mutants exhibited high chlorophyll fluorescence, consistent with the loss of a functional cytochrome b6/f complex. Unlike the corresponding mutants of Chlamydomonas, however, cytochrome f was barely detectable in the DeltapetB or DeltapetD mutants. The amounts of petB- and petD-containing mRNAs were reduced in the mutants compared to wild-type plants, but the remaining mRNA was normally associated with polysomes. In contrast, there was a decrease in polysome association of the polycistronic petA mRNA in the DeltapetB and DeltapetD mutants, suggesting that the synthesis of cytochrome f may be decreased in the absence of cytochrome b6 or SUIV. These results are discussed in light of the translational autoregulation model that has been proposed for cytochrome b6/f complex assembly in Chlamydomonas.
Superresolution imaging via ptychography (2011)

Coherent diffractive imaging of objects is made considerably more practicable by using ptychography, where a set of diffraction patterns replaces a single measurement and introduces a high degree of redundancy into the recorded data. Here we demonstrate that this redundancy allows diffraction patterns to be extrapolated beyond the aperture of the recording device, leading to superresolved images, improving the limit on the finest feature separation by more than a factor of 3.
Aliphatic β-Chlorovinyl Aldoximes1a (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAliphatic β-Chlorovinyl Aldoximes1aWalter R. Benson and Albert E. PohlandCite this: J. Org. Chem. 1965, 30, 4, 1126–1129Publication Date (Print):April 1, 1965Publication History Published online1 May 2002Published inissue 1 April 1965https://doi.org/10.1021/jo01015a043RIGHTS & PERMISSIONSArticle Views224Altmetric-Citations23LEARN 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 (539 KB) Get e-Alertsclose Get e-Alerts
Acoustic correlates of user response to error in human-computer dialogues (2004)

Using tagged data from the DARPA Communicator Project, we investigate acoustic features of user responses to system errors. We measure acoustic parameters such as energy, fundamental frequency, sub-band energy, ratios of voiced, unvoiced and silent regions of speech, fundamental frequency slope, spectral slope, and spectral center of gravity. We investigate different types of user responses to the errors, including frustration and various types of corrections. It is confirmed that the most prominent acoustic parameter for responses to the errors is fundamental frequency maximum and range, while other features are found to be salient for specific reaction types. More interestingly, acoustic characteristics of user responses to the errors are found to be different depending on whether the responses are the initial or continued responses to the errors. Similarly, normal user responses can differ acoustically depending on whether or not they were preceded by responses to error. We also present results on automatic classification of error response types using these features.
NaYF4 nanocrystals with TOPO ligands: synthesis-dependent structural and luminescent properties (2013)

A comprehensive characterization of NaYF4 nanocrystals synthesized in trioctylphosphine oxide has been reported in order to present an effective method of monodisperse, small, hexagonal nanocrystal synthesis in a high boiling organic solvent via a co-thermolysis pathway. We observed the influence of temperature, Na/Y precursors ratio and time of the synthesis on the nanocrystals size, shape and crystal structure. For that purpose, we characterized the structure of as-synthesized nanocrystals by X-ray diffraction and transmission electron microscopy. Moreover, all nanocrystals were doped with Eu(3+) ions, which were used as an optical crystal field probe. We applied photoluminescence, PL excitation and absorbance spectra to determine the influence of crystal symmetry, surface to volume ratio and ligands on the optical properties of doped Eu(3+) ions. It was found that trioctylphosphine oxide reduces the free-energy barrier and stimulates the NaYF4 crystallization in the hexagonal phase, even at relatively low temperature. A similar effect was observed when the excess of sodium trifluoroacetate precursors was used. Moreover, the presented nanocrystal evolution within synthesis time confirmed that at suitable conditions NaYF4 crystallized in the hexagonal phase within less than 5 min. Optical spectroscopy investigations confirmed the high quality of small β-NaYF4:Eu(3+) nanocrystals, which are promising candidates for e.g. optical markers in the visible wavelength range.
Chitosanase from Streptomyces sp. strain N174: a comparative review of its structure and function (1997)

Novel information on the structure and function of chitosanase, which hydrolyzes the beta-1,4-glycosidic linkage of chitosan, has accumulated in recent years. The cloning of the chitosanase gene from Streptomyces sp. strain N174 and the establishment of an efficient expression system using Streptomyces lividans TK24 have contributed to these advances. Amino acid sequence comparisons of the chitosanases that have been sequenced to date revealed a significant homology in the N-terminal module. From energy minimization based on the X-ray crystal structure of Streptomyces sp. strain N174 chitosanase, the substrate binding cleft of this enzyme was estimated to be composed of six monosaccharide binding subsites. The hydrolytic reaction takes place at the center of the binding cleft with an inverting mechanism. Site-directed mutagenesis of the carboxylic amino acid residues that are conserved revealed that Glu-22 and Asp-40 are the catalytic residues. The tryptophan residues in the chitosanase do not participate directly in the substrate binding but stabilize the protein structure by interacting with hydrophobic and carboxylic side chains of the other amino acid residues. Structural and functional similarities were found between chitosanase, barley chitinase, bacteriophage T4 lysozyme, and goose egg white lysozyme, even though these proteins share no sequence similarities. This information can be helpful for the design of new chitinolytic enzymes that can be applied to carbohydrate engineering, biological control of phytopathogens, and other fields including chitinous polysaccharide degradation.
Lectin‐like oxidized LDL receptor‐1 (LOX‐1) supports adhesion of mononuclear leukocytes and a monocyte‐like cell line THP‐1 cells under static and flow conditions (2001)

Adhesion of mononuclear leukocytes to vascular endothelial cells appears one of the initial steps in the process of atherogenesis and inflammation. We examined if LOX-1, an endothelial scavenger receptor with C-type lectin-like structure, can support adhesion of mononuclear leukocytes. Under a static condition, CHO-K1 cells stably expressing LOX-1 showed more prominent adhesion of human peripheral blood mononuclear leukocytes and THP-1 cells than untransfected CHO-K1 cells, in a temperature-independent fashion. Mononuclear leukocytes also adhered to plastic plates precoated with recombinant soluble LOX-1 extracellular domain. A neutralizing anti-LOX-1 monoclonal antibody, as well as oxidized low-density lipoprotein, significantly blocked adhesion of THP-1 cells to CHO-K1 cells overexpressing LOX-1 and bovine aortic endothelial cells. Under a flow condition, increased numbers of THP-1 cells showed rolling with reduced velocities on LOX-1-expressing CHO-K1 cells, compared with those on untransfected CHO-K1 cells. Taken together, LOX-1 can work as a cell surface receptor for mononuclear leukocytes under both static and flow conditions.
Intragenic Crop Improvement:  Combining the Benefits of Traditional Breeding and Genetic Engineering (2007)

New crop varieties are developed by applying traditional breeding methods that rely on random genome modifications. These varieties combine multiple traits that support farm efficiency and acceptable yields but also contain genes associated with the production of toxins, allergens, and/or antinutritional compounds that were not considered during the selection process. Furthermore, existing cultivars frequently lack the functional genes required for specific sensory traits and the formation of health-promoting antioxidants. One new method efficiently addresses some of these issues by either silencing undesirable genes or enhancing the expression of genes that are linked to dormant beneficial traits. Rather than incorporating foreign DNA into the plant's genome, these methods transform crops with plant-derived transfer (P-) DNAs that consist of only native genetic elements. The genetic modification can be characterized molecularly so that any inadvertent transfer of undesirable DNA, as may be the case with traditional methods, is excluded. A recently developed intragenic potato plant is silenced for the polyphenol oxidase, dikinase R1, and phosphorylase-L genes in a tuber-specific manner. French fries derived from these tubers lack discolorations, display an enhanced potato flavor, and produce greatly reduced amounts of the suspected carcinogen acrylamide. It is argued that intragenic modification is unlikely to trigger phenotypic, biochemical, or physiological variation that is new to the species. Similarly, the targeted traits are similar to those that breeders select for and often have a history of domestication and reduced fitness. For these reasons, an updated regulatory system is proposed whereby intragenic crops are considered as low risk and should be cleared for commercial release in a timely and cost-effective manner. By using modern techniques to modify the same genetic material that is used by breeders, intragenic approaches may be perceived as an acceptable extension of traditional methods in crop improvement.
The mRNA Poly(A)-Binding Protein: Localization, Abundance, and RNA-Binding Specificity (1994)

The poly(A)-binding protein (PABP) binds to the messenger (mRNA) 3'-poly(A) tail found on most eukaryotic mRNAs and together with the poly(A) tail has been implicated in governing the stability and the translation of mRNA. In order to further understand the role of the PABP in these processes, we have undertaken a detailed analysis of the cellular localization, the abundance, and the RNA-binding properties of the human PABP (hPABP). We raised monoclonal antibodies against the 70-kDa hPABP and confocal immunofluorescence microscopy with these antibodies reveals that it is localized exclusively to the cytoplasm. The hPABP exhibits a very low turnover rate in these cells and quantitative immunoblotting experiments demonstrated that growing HeLa cells contain a surprisingly high number of approximately 8 x 10(6) PABP molecules per cell, which corresponds to an intracellular concentration of about 4 microM. In an in vitro selection/amplification assay from random sequence oligonucleotide pools the hPABP selects oligo(rA)-rich sequences and it binds oligo(rA)25 with an apparent Kd of 7 nM. The hPABP binds to unrelated RNA sequences with an about 100-fold lower affinity (Kd > or = 0.5 microM). The abundance of the hPABP indicates that there is an approximately three-fold excess of the protein over binding sites on cytoplasmic poly(A). This excess and the high concentration of the hPABP, which is three orders of magnitude above its Kd for oligo(rA)25, suggest that the hPABP may bind to additional, lower affinity binding sites in vivo.
Design of Digital Notch Filters (1974)

It is shown that a second-order digital notch filter is uniquely characterized by two distinct parameters, the notch frequency and the 3-dB rejection bandwidth. As a result, such a filter can be realized using only two multipliers. Methods are outlined to design a notch filter for a prescribed notch frequency and a prescribed 3-dB rejection bandwidth, along with procedures for postdesign adjustment of these parameters. All two-multiplier, canonic and noncanonic, notch filter configurations are developed using the multiplier extraction approach. These networks are then compared with regard to the effect of internal multiplication roundoff errors. Results of computer simulation of the notch filter configurations are also included.
Circulating cytokines in Norwegian patients with psoriatic arthritis determined by a multiplex cytokine array system (2006)

Our findings suggest that these factors modulate PsA pathology and the articular involvement in a synergistic manner. Identifying factors could be used in the development of clinical diagnostic tests, which are valuable to guide evidence-based diagnosis and disease management of PsA.
BIS-(N,N-DIALKYLAMINO)-ALKOXYPHOSPHINES AS A NEW CLASS OF PHOSPHITE COUPLING AGENT FOR THE SYNTHESIS OF OLIGONUCLEOTIDES (1984)

Abstract A new class of bifunctional phosphitylating agent which is stable but readily activatable for the efficient synthesis of oligonucleotides is described.