gebhart/patrepeval huggingface dataset:
Insulin-induced phosphorylation of the 46- and 52-kDa Shc proteins. (1993)

The products of the shc gene appear to be substrates for activated oncogenic tyrosine kinases, such as v-Src and v-Fps and activated tyrosine kinase receptors like the epidermal growth factor (EGF) and platelet-derived growth factor (PDGF) receptors. We investigated whether the Shc proteins are targets for the activated insulin receptor tyrosine kinase. Here we show that the 46- and 52-kDa Shc proteins are rapidly phosphorylated upon insulin receptor activation in fibroblasts expressing elevated levels of human insulin receptors. Furthermore, we observed insulin-induced association of a 23-kDa protein with the Shc proteins. These effects on Shc proteins are similar to those observed after EGF and PDGF treatment. In contrast to the observed Shc-EGF receptor association, we did not detect association between the Shc proteins and the insulin receptor. We conclude that the Shc proteins are common elements in a signal transduction pathway that is shared by EGF, PDGF, and insulin.
GlycoMod – A software tool for determining glycosylation compositions from mass spectrometric data (2001)

GlycoMod (http://www.expasy.ch/tools/glycomod/) is a software tool designed to find all possible compositions of a glycan structure from its experimentally determined mass. The program can be used to predict the composition of any glycoprotein-derived oligosaccharide comprised of either underivatised, methylated or acetylated monosaccharides, or with a derivatised reducing terminus. The composition of a glycan attached to a peptide can be computed if the sequence or mass of the peptide is known. In addition, if the protein is known and is contained in the SWISS-PROT or TrEMBL databases, the program will match the experimentally determined masses against all the predicted protease-produced peptides (including any post-translational modifications annotated in these databases) which have the potential to be glycosylated with either N- or O-linked oligosaccharides. Since many possible glycan compositions can be generated from the same mass, the program can apply compositional constraints to the output if the user supplies either known or suspected monosaccharide constituents. Furthermore, known oligosaccharide structural constraints on monosaccharide composition are also incorporated into the program to limit the output.
Skin ageing: changes of physical properties of human skin in vivo (2001)

We have investigated in vivo the change with age of various parameters that describe the physical properties of skin. The parameters were derived from pressure/displacement curves obtained by applying reduced pressure to a small area of skin and measuring the resulting displacement by 20 MHz scan echography. By fitting the pressure/displacement curves to a theoretical model, the following skin parameters were obtained: E, Young's modulus or stiffness (in Pascals); sigma(0), the initial stress (in Pascals); and the unrestored energy ratio (UER), an index related to cutaneous non-elasticity. These parameters, which are used in mechanics to define the intrinsic physical characteristics of materials, were measured for the first time on volar forearm skin of 206 male and female subjects, aged between 6 months and 90 years. The results showed that skin thickness increases until maturity and decreases for women over 50-60 years old, Young's modulus E increases linearly with age, and ageing is divided into two phases for natural stress, sigma(0) and the non-elasticity index UER. Natural stress sigma(0) increases until maturity and then rapidly decreases. The non-elasticity index decreases until puberty and steadily increases after puberty. This new procedure provides a simple quantitative assessment of the physical properties of the skin, revealing that the skin becomes thinner, stiffer, less tense and elastic with ageing.
Argus: Low-Cost, Comprehensive Error Detection in Simple Cores (2008)

Argus, a novel approach for detecting errors in simple processor cores, dynamically verifies the correctness of the four tasks performed by a von Neumann core: control flow, data flow, computation, and memory access. Argus detects transient and permanent errors, with far lower impact on performance and chip area than previous techniques.
Outbreak of West Nile Virus Infection, Volgograd Region, Russia, 1999 (2001)

From July 25 to October 1, 1999, 826 patients were admitted to Volgograd Region, Russia, hospitals with acute aseptic meningoencephalitis, meningitis, or fever consistent with arboviral infection. Of 84 cases of meningoencephalitis, 40 were fatal. Fourteen brain specimens were positive in reverse transcriptase-polymerase chain reaction assays, confirming the presence of West Nile/Kunjin virus.
Superparamagnetic Fe3O4 nanocrystals@graphene composites for energy storage devices (2011)

In this paper, a Fe3O4 nanocrystals@graphene composite (FGC) was synthesized via a chemical deposition method by using graphene oxide as a precursor. We also investigate the structures, physicochemical properties and applications of FGCs, involving superparamagnetic performance, and use as supercapacitors and lithium ion battery (LIBs). The results showed that the Fe3O4 NCs were formed and incorporated onto the surface of the graphene sheets. The composite material FGC with a micrometre scale structure possessed similar size as the graphene sheets and exhibited superparamagnetic behavior at room temperature. The supercapacitance values of the FGC composites were enlarged compared with those of the graphene sheets or Fe3O4 NCs, which is attributed to the interaction between the Fe3O4 NCs and the graphene sheets. Meanwhile, a superior rechargeable stability of FGCs used as an anode material in LIBs can be observed.
DNA-Templated Formation of a Helical Cyanine Dye J-Aggregate (2000)

UV−vis and CD spectroscopy reveal that a tricationic cyanine dye spontaneously assembles into a helical J-aggregate in the presence of a double-helical DNA template. The stability of the J-aggregate is strongly dependent on the dye concentration and DNA length in a manner that reflects a high degree of cooperativity in formation of the aggregate. Slight changes in environmental conditions such as temperature and ionic strength result in interconversion between J- and H-aggregates. The aggregate likely consists of dimeric units assembled in an offset, face-to-face orientation within the minor groove of the DNA template, analogous to an earlier report of H-aggregation on DNA by a related cyanine dye. A model is proposed that relates the two aggregate structures by translation of one monomer from a given dimer along the floor of the minor groove. This translation requires adjacent monomers to also translate, leading to the observed cooperativity.
Intranasal Sufentanil for Preoperative Sedation (1988)

Department of Anethesiology, University Hospital, Antwerp, and Department of Clinical Research and Development, Jannsen Pharmaceutica, Beerse, Belgium
Estimation of cell size from pulse shape in flow cytofluorometry. (1976)

The fluorescence pulse widths (pulse duration) generated by fluorochromed cells in a flow-through cytofluorometer provide useful information regarding cell (or nuclear) size and possibly other morphologic features. Simple fixed thresholds just above background noise can be used to identify these pulses, but measurements are then strongly affected by random noise and will vary as a result of both pulse amplitude and pulse shape. In this paper, we propose two alternative, amplitude-independent estimates of pulse width. The first is based on a threshold at some fraction of pulse height, or on a pair of thresholds scaled to some fixed central fraction of the total integrated intensity. The second is based on the ratio of pulse area to peak height. The quantitative properties of these width estimators is studied with simulated fluorescence pulses and with experimental specimens of fluorchromed polystyrene spheres, pollen and spores of known different diameters. The results indicated that absolute particle diameters can be measured within a precision of approximately 1 mu using instruments for flow cytofluorometry.
Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet (2012)

The natural four-letter genetic alphabet, comprised of just two base pairs (dA-dT and dG-dC), is conserved throughout all life, and its expansion by the development of a third, unnatural base pair has emerged as a central goal of chemical and synthetic biology. We recently developed a class of candidate unnatural base pairs, exemplified by the pair formed between d5SICS and dNaM. Here, we examine the PCR amplification of DNA containing one or more d5SICS-dNaM pairs in a wide variety of sequence contexts. Under standard conditions, we show that this DNA may be amplified with high efficiency and greater than 99.9% fidelity. To more rigorously explore potential sequence effects, we used deep sequencing to characterize a library of templates containing the unnatural base pair as a function of amplification. We found that the unnatural base pair is efficiently replicated with high fidelity in virtually all sequence contexts. The results show that, for PCR and PCR-based applications, d5SICS-dNaM is functionally equivalent to a natural base pair, and when combined with dA-dT and dG-dC, it provides a fully functional six-letter genetic alphabet.
Human Mesenchymal Stem Cell Grafts Enhance Normal and Impaired Wound Healing by Recruiting Existing Endogenous Tissue Stem/Progenitor Cells (2012)

Mesenchymal stem cells (MSCs) have been investigated as a clinical therapy to promote tissue repair. However, the disappearance of grafted cells soon after engraftment suggests a possible role as initiators of repair rather than effectors. We evaluated the relative contribution of grafted human MSCs and host stem/progenitor cells in promoting wound healing by using a novel asymmetric wound model in normal and impaired healing diabetic (db/db) mice to discriminate between the effect of direct engraftment and the subsequent systemic response. Experimental animals received paired wounds, with one wound receiving human mesenchymal stem cells (hMSCs) and the other wound receiving vehicle to assess local and systemic effects, respectively. Control animals received vehicle in both wounds. Grafted hMSCs significantly improved healing in both normal and impaired healing animals; produced significant elevation of signals such as Wnt3a, vascular endothelial growth factor, and platelet-derived growth factor receptor-α; and increased the number of pre-existing host MSCs recruited to the wound bed. Improvement was also seen in both the grafted and nongrafted sides, suggesting a systemic response to hMSC engraftment. Healing was enhanced despite the rapid loss of hMSCs, suggesting that mobilizing the host response is the major outcome of grafting MSCs to tissue repair. We validate that hMSCs evoke a host response that is clinically relevant, and we suggest that therapeutic efforts should focus on maximizing the mobilization of host MSCs.
The effect of hepatic progenitor cells on experimental hepatocellular carcinoma in the regenerating liver (2013)

HPCs have a marked effect on HCC cells in vitro and appear to stimulate the growth and malignant potential of experimental HCC tumors.
Trade Aid: Taking Fair Trade into the Future (2009)

Geoff White contemplated issues that were all in a day's work for him: a global economy spiralling into serious recession, competitive challenges for the fair trade dollar, and a balancing act between commercial business principles and social mission. White considered expanding Christchurch-based Trade Aid into Australia and restructuring company ownership to give its economically disadvantaged trading partners a stake in the company, despite these issues. Can Trade Aid's global leadership in social value creation be continued despite the expected dramatic drop in retail spending?
<title>Fabrication and properties of refractive micro-optical beam-shaping elements</title> (1999)

Several algorithms can be used in order to calculate a phase function that shapes a light beam into a certain intensity distribution. In cases of smooth phase functions, e.g. for the conversion of a Gaussian beam into a flat top distribution, the optical element can be realized by a smooth surface profile without 2 pi jumps. Even though the disadvantages of diffractive elements are well known, often the limitations of the fabrication technologies permit the realization of only diffractive elements. For the beam shaping elements in micro optics, methods exist which allow the fabrication of smooth surface profiles. Such refractive elements have the advantages of a wavelength independent behavior and a conversion efficiency of nearly 100% as known from refractive lenses. In some cases, the design of refractive result in thick surface profiles and the fabrication technique do not fit to this. Therefore, the objective of the paper is to show some possibilities to make the design meet the fabrication capabilities. We used lithographic and etch techniques as well as replication technologies for the fabrication. The basis of the presented technology is gray tone technique, the generation of a proper pre-form, and its correction in order to achieve maximum coincidence with the desired surface profile. Several refractive beam shaping elements have been realized.
Continual Production of Phosphatidic Acid by Phospholipase D Is Essential for Antigen-stimulated Membrane Ruffling in Cultured Mast Cells (2002)

Phospholipase Ds (PLDs) are regulated enzymes that generate phosphatidic acid (PA), a putative second messenger implicated in the regulation of vesicular trafficking and cytoskeletal reorganization. Mast cells, when stimulated with antigen, show a dramatic alteration in their cytoskeleton and also release their secretory granules by exocytosis. Butan-1-ol, which diverts the production of PA generated by PLD to the corresponding phosphatidylalcohol, was found to inhibit membrane ruffling when added together with antigen or when added after antigen. Inhibition by butan-1-ol was completely reversible because removal of butan-1-ol restored membrane ruffling. Measurements of PLD activation by antigen indicate a requirement for continual PA production during membrane ruffling, which was maintained for at least 30 min. PLD1 and PLD2 are both expressed in mast cells and green fluorescent protein-tagged proteins were used to identify PLD2 localizing to membrane ruffles of antigen-stimulated mast cells together with endogenous ADP ribosylation factor 6 (ARF6). In contrast, green fluorescent protein-PLD1 localized to intracellular vesicles and remained in this location after stimulation with antigen. Membrane ruffling was independent of exocytosis of secretory granules because phorbol 12-myristate 13-acetate increased membrane ruffling in the absence of exocytosis. Antigen or phorbol 12-myristate 13-acetate stimulation increased both PLD1 and PLD2 activity when expressed individually in RBL-2H3 cells. Although basal activity of PLD2-overexpressing cells is very high, membrane ruffling was still dependent on antigen stimulation. In permeabilized cells, antigen-stimulated phosphatidylinositol(4,5)bisphosphate synthesis was dependent on both ARF6 and PA generated from PLD. We conclude that both activation of ARF6 by antigen and a continual PLD2 activity are essential for local phosphatidylinositol(4,5)bisphosphate generation that regulates dynamic actin cytoskeletal rearrangements.
In vivo flow cytometry: A horizon of opportunities (2011)

Flow cytometry (FCM) has been a fundamental tool of biological discovery for many years. Invasive extraction of cells from a living organism, however, may lead to changes in cell properties and prevents studying cells in their native environment. These problems can be overcome by use of in vivo FCM, which provides detection and imaging of circulating normal and abnormal cells directly in blood or lymph flow. The goal of this review is to provide a brief history, features, and challenges of this new generation of FCM methods and instruments. Spectrum of possibilities of in vivo FCM in biological science (e.g., cell metabolism, immune function, or apoptosis) and medical fields (e.g., cancer, infection, and cardiovascular disorder) including integrated photoacoustic-photothermal theranostics of circulating abnormal cells are discussed with focus on recent advances of this new platform.
[Recent data on somatomedins (insulin-like growth factors) (author's transl)]. (1980)

Data on somatomedins have resulted from the convergence of two initially distinct lines of research relating to the two major aspects of their biological activities, their effects on cartilage growth and their insulin-like action. Human serum has yielded three factors, SM-A, SM-C and NSILA-S. The latter comprises two very similar polypeptides, IGF I and IGF II which structurally closely resemble proinsulin. A fourth factor, MSA, has been isolated from calf serum and from conditioned medium of a rat liver cell strain. All these chemically and biologically closely related factors have a molecular weight of approximately 7 500 but circulate in a form with much higher molecular weight owing to their binding to specific carrier proteins. Over the past five years, the use of purified somatomedins has led to rapid progress in the elucidation of the physiology of these hormones. In this review, present knowledge of somatomedins is analysed in the following terms: physiochemical properties, circulating forms, action on growth, insulin-like activity, interaction with receptors, immunological characteristics, biosynthesis and hormonal regulation of their blood level. Results obtained in our laboratory from rat liver organ culture are discussed: the action of culture media on cartilage sulphation, the detection of a protein which specifically binds NSILA-S and SM-A and its use in a competitive protein binding assay for somatomedins in biological fluids.
Biallelic mutation of SOCS-1 impairs JAK2 degradation and sustains phospho-JAK2 action in the MedB-1 mediastinal lymphoma line (2004)

Primary mediastinal B-cell lymphoma (PMBL) is a well-defined subtype of diffuse large B-cell lymphoma. Molecular cytogenetics revealed frequent gains of 9p24. JAK2, mapping in this region, is presently regarded as a candidate oncogene because expression profiling showed high Janus kinase-2 (JAK2) transcript levels and JAK2 was found to be constitutively phosphorylated in mediastinal B-cell lymphomas. We confirm that in the MedB-1 mediastinal B-cell line, harboring a trisomy 9, JAK2 transcription is elevated and the product is highly phosphorylated. However, JAK2 is not overexpressed at the protein level. On top, JAK2 protein turnover is even delayed. This unexpected finding coincides with a biallelic mutation of the suppressor of cytokine signaling-1 (SOCS-1) gene in this cell, which abrogates SOCS box function of the protein. Ectopic expression of wild-type (wt) SOCS-1 in MedB-1 leads to growth arrest and dramatic reduction of phospho-JAK2 and its downstream partner phospho-signal transducer and activator of transcription-5 (phospho-STAT5). Ultimately, the target gene cyclin D1 is repressed in transfectants while RB1, which is silenced in MedB-1, is induced. We conclude that, in MedB-1, action of phospho-JAK2 is sustained due to defective SOCS-1. Hence, SOCS-1 qualifies as a novel tumor suppressor. Of note, SOCS-1 mutations are also present in the parental tumor of MedB-1 and were detected in 9 of 20 PMBLs.
PHOTOPHYSICAL AND PHOTOBIOLOGICAL PROPERTIES OF DIPORPHYRIN ETHERS (1991)

Spectral properties of several diporphyrin ethers were assessed in different solvents and after accumulation by leukemia L1210 cells in vitro. To facilitate studies in a variety of solvents, both tetramethylesters of the diporphyrin ethers and free acids were employed. For comparison, studies on the corresponding porphyrin monomers were also carried out. The joining of two porphyrins by an ether linkage had several consequences. We observed a blue shift in the Soret band of the ethers, but not of the corresponding simple porphyrins, in protic solvents. This phenomenon is likely related to ether aggregation under conditions which promote H-bonding. The presence of an ether linkage was associated with enhanced fluorescence at 630-640 nm and decreased fluorescence lifetimes and yields, especially in protic solvents. The ether linkage was unaffected by intracellular enzymes, but porphyrin esters were readily hydrolyzed upon accumulation by L1210 cells. The joining of two hematoporphyrin molecules by an ether linkage promoted dye accumulation by L1210 cells. In contrast, accumulation of mesoporphyrin and protoporphyrin was thereby retarded.
Endocytosis of folate-protein conjugates: ultrastructural localization in kb cells (1993)

It has been demonstrated that proteins covalently conjugated to folic acid may be taken up by cells via endocytosis after binding to a folate binding protein (FBP) in the cell membrane. The proteins taken up in this manner remain catalytically active and they may modify physiological processes occurring in the cytosol. Confocal fluorescence microscopy of KB cells incubated with FITC-bovine serum albumin-folic acid conjugates showed that after uptake, the conjugates resided in large vesicular structures. The purpose of the present study was to determine the subcellular localization of protein-folic acid conjugates in KB cells using folic acid-bovine serum albumin-colloidal gold (F-BSA-CG) as a tracer. F-BSA-CG conjugates were taken up via uncoated pits or caveolae, and resided primarily in multivesicular bodies (MVBs) and other tubular endosomes at early time points (15-60 min). At later time points (6 hours), conjugates were still contained in MVBs but some were also found in secondary lysosomes or free in the cytoplasm. Coincubation of KB cells with transferrin-colloidal gold (TF-CG) and F-BSA-CG resulted in colocalization of TF-CG and F-BSA-CG within endosomal elements at times later than 15 minutes, indicating that the caveolae-mediated F-BSA-CG endocytic pathway converged with a pathway utilized by clathrin-coated pits.
An Anti-oncogenic Role for Decorin (2000)

The leucine-rich proteoglycan decorin interacts with the epidermal growth factor receptor and triggers a signaling pathway that leads to growth suppression. We find that decorin causes a functional inactivation of the oncogenic ErbB2 protein in breast carcinoma cells. Upon de novo expression of decorin, the ErbB2 protein is reduced by approximately 40%, whereas its degree of tyrosyl phosphorylation is almost completely abrogated. Both co-culture experiments or experiments with recombinant decorin demonstrate an initial induction of ErbB2 tyrosine kinase, followed by a profound and long-lasting down-regulation of its activity. This leads to growth inhibition and cytodifferentiation of mammary tumor cells and a concurrent suppression of their tumorigenic potential in vivo. These decorin-mediated effects appear to involve the activation of ErbB4, which in turn would block the phosphorylation of heterodimers containing either ErbB2 or ErbB3. These results provide an explanation for the heightened decorin levels around invasive carcinomas and suggest that decorin may function as a natural antagonist of neoplastic cells enriched in ErbB2.
Applications of ultrashort pulse propagation in Bragg gratings for wavelength-division multiplexing and code-division multiple access (1998)

We discuss theoretical and experimental studies on the propagation of ultrashort pulses through fiber Bragg gratings. We also consider several applications in optical communications to be found by combining ultrashort pulses and fiber Bragg gratings: a multiwavelength source for wavelength-division-multiplexed systems and a means for implementing optical code-division multiple access.