gebhart/patrepeval huggingface dataset:
Nucleotide Sequences and Modifications That Determine RIG-I/RNA Binding and Signaling Activities (2009)

Cytoplasmic viral RNAs with 5' triphosphates (5'ppp) are detected by the RNA helicase RIG-I, initiating downstream signaling and alpha/beta interferon (IFN-alpha/beta) expression that establish an antiviral state. We demonstrate here that the hepatitis C virus (HCV) 3' untranslated region (UTR) RNA has greater activity as an immune stimulator than several flavivirus UTR RNAs. We confirmed that the HCV 3'-UTR poly(U/UC) region is the determinant for robust activation of RIG-I-mediated innate immune signaling and that its antisense sequence, poly(AG/A), is an equivalent RIG-I activator. The poly(U/UC) region of the fulminant HCV JFH-1 strain was a relatively weak activator, while the antisense JFH-1 strain poly(AG/A) RNA was very potent. Poly(U/UC) activity does not require primary nucleotide sequence adjacency to the 5'ppp, suggesting that RIG-I recognizes two independent RNA domains. Whereas poly(U) 50-nt or poly(A) 50-nt sequences were minimally active, inserting a single C or G nucleotide, respectively, into these RNAs increased IFN-beta expression. Poly(U/UC) RNAs transcribed in vitro using modified uridine 2' fluoro or pseudouridine ribonucleotides lacked signaling activity while functioning as competitive inhibitors of RIG-I binding and IFN-beta expression. Nucleotide base and ribose modifications that convert activator RNAs into competitive inhibitors of RIG-I signaling may be useful as modulators of RIG-I-mediated innate immune responses and as tools to dissect the RNA binding and conformational events associated with signaling.
Polymers for holographic recording: VI. Some basic ideas for modelling the kinetics of the recording process (1997)

The diffusion mechanism for hologram formation in multicomponent polymerizable systems undergoing photocrosslinking was examined. The nonlinear diffusion equation was solved to predict the behaviour of the recording system. The results show the crucial importance of the competition between diffusion and photochemical reaction. They account for the reciprocity failure and nonlinearity and reveal the interdependence of the physicochemical, optical and photonic parameters. The experimental results obtained with a model recording system are in better than qualitative agreement with this theoretical approach.
Probabilistic analysis of gene expression measurements from heterogeneous tissues (2010)

timo.p.erkkila@tut.fi; harri.lahdesmaki@tut.fi
GLI1 is regulated through Smoothened-independent mechanisms in neoplastic pancreatic ducts and mediates PDAC cell survival and transformation (2009)

Pancreatic ductal adenocarcinoma (PDAC) is characterized by the deregulation of the hedgehog signaling pathway. The Sonic Hedgehog ligand (Shh), absent in the normal pancreas, is highly expressed in pancreatic tumors and is sufficient to induce neoplastic precursor lesions in mouse models. We investigated the mechanism of Shh signaling in PDAC carcinogenesis by genetically ablating the canonical bottleneck of hedgehog signaling, the transmembrane protein Smoothened (Smo), in the pancreatic epithelium of PDAC-susceptible mice. We report that multistage development of PDAC tumors is not affected by the deletion of Smo in the pancreas, demonstrating that autocrine Shh-Ptch-Smo signaling is not required in pancreatic ductal cells for PDAC progression. However, the expression of Gli target genes is maintained in Smo-negative ducts, implicating alternative means of regulating Gli transcription in the neoplastic ductal epithelium. In PDAC tumor cells, we find that Gli transcription is decoupled from upstream Shh-Ptch-Smo signaling and is regulated by TGF-beta and KRAS, and we show that Gli1 is required both for survival and for the KRAS-mediated transformed phenotype of cultured PDAC cancer cells.
Translation of ODC mRNA and Polyamine Transport Are Suppressed inras-Transformed CREF Cells by Depleting Translation Initiation Factor 4E (1997)

Rapid tumor growth and metastasis require increased polyamine metabolism, which is coordinately regulated by ornithine decarboxylase (ODC) and the polyamine transporter. Both activities are stimulated by ras signalling and are dependent upon protein biosynthesis. T24ras oncogene expression in rat embryo fibroblasts (CREFT24) induces cellular transformation and malignancy, in part, by stimulating the rate-limiting translation initiation factor, eIF-4E. CREFT24 expressing antisense RNA to eIF-4E (AS4E) have markedly decreased tumor growth rates and metastatic capacity, without altered monolayer growth rates. Herein, we demonstrate that in AS4E, ODC is translationally suppressed resulting in decreased ODC activity. Additionally, exogenous polyamine uptake is suppressed in AS4E cells indicating that AS4E can neither generate nor import the polyamines necessary to support rapid tumor growth. These data provide evidence that eIF-4E is the link between ras-induced malignancy and increased polyamine metabolism and support the hypothesis that eIF-4E plays a pivotal role in mediating ras-induced malignancy.
Power dependence of upconversion luminescence (1999)

Spectroscopic data are of essential value for understanding the excitation mechanisms in luminescent and laser materials. Special attention has been devoted to the investigation of upconversion-induced luminescence, partly because of the availability of near-infrared pump sources for the excitation of visible luminescence and laser emission and partly because these mechanisms can introduce a loss channel for devices emitting in the infrared region. Typical upconversion processes are pump excited-state absorption (ESA) and energy-transfer upconversion (ETU). For the interpretation of short-wavelength luminescence, it is often assumed that the order n of the upconversion process, i.e. the number n of pump photons required to excite the emitting state, is indicated by the slope of the luminescence intensity versus pump power in double-logarithmic representation. However, a saturation of upconversion luminescence with rising pump power was already observed 30 years ago. We show theoretically by assuming the simplest possible rate-equation model that the experimentally observed decrease in power dependence of an upconversion luminescence with rising pump power is purely determined by the competition between linear decay and upconversion processes for the depletion of the intermediate excited states. An upconversion luminescence which is excited by the subsequent absorption of n photons has a dependence on absorbed pump power P which may range from Pn in the limes of infinitely short lifetimes of the intermediate excited states down to P1 for the upper state and less than P1 for the intermediate states in the limes of infinitely strong upconversion rates. Whereas the upper limes is valid universally, the lower limes for the intermediate states depends on whether the excitation is achieved via ETU or ESA and whether the states decay predominantly via ground-state luminescence or multiphonon relaxation into the next lower-lying state. These results allow for the interpretation of a measured power dependence of multiphoton-excited luminescence with respect to the order of the process and its physical origin and strength. We have verified experimentally the convergence into both limes by upconversion luminescence in Cs3Lu2Cl9:1% Er3+ and Cs3Er2Cl9.
Confocal photothermal flow cytometry in vivo (2005)

The new experimental design of an integrated flow cytometry (FC) is presented, combining high-resolution transmission digital microscopy (TDM) with photothermal (PT), photoacoustic (PA), and fluorescence techniques. We used phantom in vitro to verify this concept with moving living cells, and micro- and nanoparticles. The transistion in vivo study was realized by using unique rat mesentery model for real-time detection of circulating red and white blood cells. The adaptation of confocal schematics to PT microscopy to provide 3-D measurement is discussed. We demonstrated that simulataneous transmission, PT and fluorescent imaging provide the basis for nanodiagnostics and nanotherpeutics in vivo with gold nanoparticles as PT probes and sensitizers as well as identification cells with specific absorbing endogenous and exogenous structures. First attempt to use in parallel PA methods with detection PA signals from single live cells are presented. Potential applications of integrated FC are discussed, including identification of selected cells with different natural absorptive properties, characterization of bioflow (e.g., velocity profile), and PT nanotherapeutics and nanodiagnostics of metastatic cells with gold nanoparticles.
Buoyant Density of the Hepatitis A Virus-Like Particle in Cesium Chloride (1974)

We recently visualized by immune electron microscopy a virus-like particle in the stools of patients with hepatitis A. The particle measured approximately 27 nm in diameter and morphologically resembled a picornavirus or parvovirus. To further characterize this particle, we have determined its buoyant density in cesium chloride (CsCl) by ultracentrifugation. Hepatitis A particles from three positive stool specimens were isopycnically banded in separate experiments, and the gradient fractions were examined for particles by immune electron microscopy by using hepatitis A convalescent sera. In each experiment, the particles were observed in a normal distribution about a peak fraction with a mean density of approximately 1.4 g/cm(3). The buoyant density of 1.4 g/cm(3) in CsCl together with its morphology and the reported resistance of hepatitis virus to acid, ether, and heat suggest that this particle is parvovirus-like.
Controlling the Water Content of Biomass Fast Pyrolysis Oil (2007)

Several methods to control the water content of pyrolysis oil from fast pyrolysis of biomass were evaluated experimentally. Parameters varied were the operating temperature of the condenser, the gas load of the condenser, and the moisture content of the feedstock. Experiments were performed in a continuous bench scale plant (1 kg/h intake) equipped with a fluidized bed reactor. Pine wood with moisture contents between 0 wt % and 20 wt % (as-received basis) was used as feedstock. The mass balance closure was between 94 wt % and 102 wt %, and the reproducibility of yields of identical experiments was good. Increasing the condenser temperature (15−90 °C) and increasing the gas load (2.0−4.1 kg of gases/kg of vapors in the condenser feed) of the condenser are both well suited to control the water content. However, decreasing the water content by these measures always results in a loss of organic vapors, leading to a lower oil yield in the condenser. Deep drying of the feedstock is beneficial; a lower moisture content of the feed results in less loss of organic vapors for the same water content of pyrolysis oil. Experimental results were compared with the predictions of an equilibrium flash condensation model. Predictions of this equilibrium model are in good agreement with the experimental results. All input parameters of the model (reactor yields and composition of the organics in pyrolysis oil) can be measured, or are known, with sufficient accuracy.
Inhibition of T Helper Cell Type 2 Cell Differentiation and Immunoglobulin E Response by Ligand-Activated Vα14 Natural Killer T Cells (1999)

Murine Valpha14 natural killer T (NKT) cells are thought to play a crucial role in various immune responses, including infectious, allergic, and autoimmune diseases. Because Valpha14 NKT cells produce large amounts of both interleukin (IL)-4 and interferon (IFN)-gamma upon in vivo stimulation with a specific ligand, alpha-galactosylceramide (alpha-GalCer), or after treatment with anti-CD3 antibody, a regulatory role on helper T (Th) cell differentiation has been proposed for these cells. However, the identity of the cytokine produced by Valpha14 NKT cells that play a dominant role on the Th cell differentiation still remains controversial. Here, we demonstrate by using Valpha14 NKT-deficient mice that Valpha14 NKT cells are dispensable for the induction of antigen-specific immunoglobulin (Ig)E responses induced by ovalbumin immunization or Nippostrongylus brasiliensis infection. However, upon in vivo activation with alpha-GalCer, Valpha14 NKT cells are found to suppress antigen-specific IgE production. The suppression appeared to be IgE specific, and was not detected in either Valpha14 NKT- or IFN-gamma-deficient mice. Consistent with these results, we also found that ligand-activated Valpha14 NKT cells inhibited Th2 cell differentiation in an in vitro induction culture system. Thus, it is likely that activated Valpha14 NKT cells exert a potent inhibitory effect on Th2 cell differentiation and subsequent IgE production by producing a large amount of IFN-gamma. In marked contrast, our studies have revealed that IL-4 produced by Valpha14 NKT cells has only a minor effect on Th2 cell differentiation.
CdS/CdTe Solar Cells Containing Directly Deposited CdSxTe1-x Alloy Layers: Preprint (2011)

A CdSxTe1-x layer forms by interdiffusion of CdS and CdTe during the fabrication of thin-film CdTe photovoltaic (PV) devices. The CdSxTe1-x layer is thought to be important because it relieves strain at the CdS/CdTe interface that would otherwise exist due to the 10% lattice mismatch between these two materials. Our previous work [1] has indicated that the electrical junction is located in thisinterdiffused CdSxTe1-x region. Further understanding, however, is essential to predict the role of this CdSxTe1-x layer in the operation of CdS/CdTe devices. In this study, CdSxTe1-x alloy films were deposited by radio-frequency (RF) magnetron sputtering and co-evaporation from CdTe and CdS sources. Both RF-magnetron-sputtered and co-evaporated CdSxTe1-x films of lower S content (x<0.3) have acubic zincblende (ZB) structure akin to CdTe, whereas those of higher S content have a hexagonal wurtzite (WZ) structure like that of CdS. Films become less preferentially oriented as a result of a CdCl2 heat treatment (HT) at~400 degrees C for 5 min. Films sputtered in a 1% O2/Ar ambient are amorphous as deposited, but show CdTe ZB, CdS WZ, and CdTe oxide phases after a CdCl2 HT. Filmssputtered in O2 partial pressure have a much wider bandgap than expected. This may be explained by nanocrystalline size effects seen previously [2] for sputtered oxygenated CdS (CdS:O) films. Initial PV device results show that the introduction of a directly-deposited CdSxTe1-x alloy layer into the device structure produces devices of comparable performance to those without the alloy layer whena CdCl2 HT is performed. Further investigation is required to determine whether the CdCl2 heat treatment step can be altered or eliminated through direct deposition of the alloy layer.
Functional expression of the murine Thy-1.2 gene in transfected human T cells. (1986)

The interaction of certain mAbs with the Thy-1 molecules of murine T lymphocytes leads to cell activation and proliferation. To examine the signal transduction mechanism underlying this process and to determine what, if any, relationship exists between Thy-1-dependent triggering and T cell activation mediated through the T3-antigen receptor (T3-Ti) complex, a genomic clone of murine Thy-1.2 was isolated and transfected into the human T cell tumor, Jurkat. The transfected gene was actively transcribed in these human cells and high levels of Thy-1.2 glycoprotein were found on the cell membrane. Although certain mAbs to Thy-1.2 failed to bind to the Thy-1 transfected Jurkat cells, several known mitogenic anti-Thy-1 mAbs did react, and in the presence of phorbol ester, induced IL-2 secretion. One Thy-1+ transfectant out of five failed to produce IL-2 in response to anti-T3/Ti antibodies even though it retained the ability to increase intracytoplasmic calcium concentration [( Ca2+]i) in response to these ligands. A Thy-1 negative revertant of this cell regained anti-T3/Ti reactivity, suggesting a regulatory defect in signal transmission via T3/Ti in the original transfectant. These data confirm the ability of Thy-1 to act as an activation receptor for T cells. They reveal a potential role for changes in [Ca2+]i in this process, in common with other pathways of T cell activation, but also indicate a more complex series of events is involved.
Reliability of sensors based on nanowire networks (2012)

Nanowires have a great potential in many industrial applications, including electronics and sensors. Palladium nanowire network-based hydrogen sensors have been found to outperform their counterparts that consist of an individual nanowire or palladium thin or thick films. However, reliability issues that affect these sensors still need to be addressed. This article considers hydrogen gas sensors based on a nanowire network with a square lattice structure. A general model for describing the reliability behavior of this network is proposed. It is shown that the reliability function can be imposed by considering a network of nanowires rather than a single nanowire. Among many other applications, the presented results can also be used to assess the reliability of any nanosystem/ nanodevice where the proposed model is a reasonable choice. What distinguishes the work presented in this article from related work are the unique difficulties that the nanocomponents introduce to the evaluation of reliability and the way reliability is defined over cycles of hydrogen gas.
Critical evaluation of stability constants for alpha-hydroxycarboxylic acid complexes with protons and metal ions and the accompanying enthalpy changesPart I: Aromatic ortho-hydroxycarboxylic acids (Technical Report) (1997)

Abstract
Topical cannabinoid antinociception: synergy with spinal sites (2003)

Analgesic effects of cannabimimetic compounds have been known to be related to their central effects. Cannabinoid receptors also exist in the periphery but their role in pain perception has been remained to be clarified. Therefore, we assessed topical antinociceptive effects of WIN 55, 212-2, a mixed CB(1) and CB(2) receptors agonist, in mice using tail-flick test. Immersion of the tail of mouse into the WIN 55, 212-2 solution produced dose-dependent antinociception. This antinociceptive activity was limited to the portion of the tail exposed to WIN 55, 212-2. The antinociceptive response was dependent on duration of exposure to WIN 55, 212-2 solution. The topical antinociceptive effects of WIN 55, 212-2 were dose dependently blocked by topical pretreatment of CB(1) receptor-selective antagonist, AM 251. Thus, topical antinociceptive action of WIN 55, 212-2 involve CB(1) receptors. Intrathecal (i.th.) administration of WIN 55, 212-2 produced a dose-dependent antinociceptive effect. Interestingly, ineffective i.th. doses of WIN 55, 212-2 produced a marked antinociception when combined with topical application of WIN 55, 212-2 and topical antinociceptive effect was potentiated. The dose-response curve of i.th. WIN 55, 212-2 was shifted to the left 15-fold by topical WIN 55, 212-2. This finding suggests that there is an antinociceptive synergy between peripheral and spinal sites of cannabinoid action and it also implicates that local activation of cannabinoid system may regulate pain initiation in cutaneous tissue. Our findings support that cannabinoid system participates in buffering the emerging pain signals at the peripheral sites in addition to their spinal and supraspinal sites of action. In addition, an antinociceptive synergy between topical and spinal cannabinoid actions exists. These results also indicate that topically administered cannabinoid agonists may reduce pain without the dysphoric side effects and abuse potential of centrally acting cannabimimetic drugs.
Tandem repeating of the expression cartridge--a novel strategy to enhance the expression efficiency of cloned gene in Escherichia coli. (1996)

A novel strategy to enhance the expression efficiency of cloned target gene in Escherichia coli was developed. The whole expression cartridge, consisting of promoter, SD sequence, target gene and transcription terminator, was tandem repeatedly engineered into a expression plasmid. Consequently, the copy number of specific gene was increased substantially, leading to the improvement of expression efficiency. Using this approach, a recombinant plasmid, designed as pLYD, was constructed and transformated into the Escherichia coli strain DH5 alpha. Upon induction, the desired protein was synthesized in a considerable level and accumulated up to 63% of the total cell proteins. The present study revealed that tandem repeating of expression cartridge provided a convenient means to improve expression level efficiently.
Advances in Immuno–Positron Emission Tomography: Antibodies for Molecular Imaging in Oncology (2012)

Identification of cancer cell-surface biomarkers and advances in antibody engineering have led to a sharp increase in the development of therapeutic antibodies. These same advances have led to a new generation of radiolabeled antibodies and antibody fragments that can be used as cancer-specific imaging agents, allowing quantitative imaging of cell-surface protein expression in vivo. Immuno-positron emission tomography (immunoPET) imaging with intact antibodies has shown success clinically in diagnosing and staging cancer. Engineered antibody fragments, such as diabodies, minibodies, and single-chain Fv (scFv) -Fc, have been successfully employed for immunoPET imaging of cancer cell-surface biomarkers in preclinical models and are poised to bring same-day imaging into clinical development. ImmunoPET can potentially provide a noninvasive approach for obtaining target-specific information useful for titrating doses for radioimmunotherapy, for patient risk stratification and selection of targeted therapies, for evaluating response to therapy, and for predicting adverse effects, thus contributing to the ongoing development of personalized cancer treatment.
Differences in the antigenic expression of immunomodulatory mannoprotein constituents on yeast and mycelial forms of Candida albicans (1990)

The expression of a strongly immunomodulatory mannoprotein complex (GMP) in the different forms of growth of the human commensal and opportunistic pathogen Candida albicans was studied using a monoclonal antibody (mAb AF1) directed against an oligosaccharide epitope of GMP. Immunofluorescence revealed that the surface of the yeast cells was highly reactive with mAb AF1, but that the reactivity was greatly reduced or disappeared during mycelial conversion. This modulation was shared by a number of strains of C. albicans, and was not solely a temperature- or nutrition-dependent phenomenon. Hypha-deficient strains (A12 and CA2) did not show variations of surface fluorescence under environmental conditions which were permissive for hyphal conversion (incubation in N-acetylglucosamine or Lee's medium, at 37 degrees C). GMP extracts from yeast and mycelial forms of the fungus were separated into three chromatographically distinct, high molecular mass mannoprotein fractions (F1, F2 and F3), which were tested individually by indirect ELISA for mAb AF1 recognition. All yeast-derived constituents and two (F2 and F3) of the hyphal mannoproteins were recognized by the mAb. The low or absent reactivity of the F1 constituent from hyphal cells was confirmed by immunoblots. Irrespective of their source (yeast or mycelial), all fractions reacted to a similar extent with a polyclonal anti-Candida serum. Overall, the data suggest changes in epitope specificity and/or confinement of reactive constituents in the inner wall layers as possible mechanisms of modulated expression of mAb AF1-reactive epitope during mycelial conversion.