gebhart/patrepeval huggingface dataset:
Y RNA fragment in extracellular vesicles confers cardioprotection via modulation of IL ‐10 expression and secretion (2017)

Cardiosphere-derived cells (CDCs) reduce myocardial infarct size via secreted extracellular vesicles (CDC-EVs), including exosomes, which alter macrophage polarization. We questioned whether short non-coding RNA species of unknown function within CDC-EVs contribute to cardioprotection. The most abundant RNA species in CDC-EVs is a Y RNA fragment (EV-YF1); its relative abundance in CDC-EVs correlates with CDC potency <i>in vivo</i> Fluorescently labeled EV-YF1 is actively transferred from CDCs to target macrophages via CDC-EVs. Direct transfection of macrophages with EV-YF1 induced transcription and secretion of IL-10. When cocultured with rat cardiomyocytes, EV-YF1-primed macrophages were potently cytoprotective toward oxidatively stressed cardiomyocytes through induction of IL-10. <i>In vivo,</i> intracoronary injection of EV-YF1 following ischemia/reperfusion reduced infarct size. A fragment of Y RNA, highly enriched in CDC-EVs, alters <i>Il10</i> gene expression and enhances IL-10 protein secretion. The demonstration that EV-YF1 confers cardioprotection highlights the potential importance of diverse exosomal contents of unknown function, above and beyond the usual suspects (e.g., microRNAs and proteins).
On computational properties of chains of recurrences (2001)

Backward and mixed chains of recurrences are introduced. A complete set of chains of recurrences manipulation tools is described. Applications of these tools, related to the safety and numeric stability of chained computations are given.
Enhancement of fcgamma receptor-mediated phagocytosis by transforming mutants of Cbl. (1999)

Phagocytosis mediated by FcgammaR plays an important role in host defense. The molecular events involved in this process have not been completely defined. The adapter protein Cbl has been implicated in FcgammaR signaling, but the function of Cbl in phagocytosis is unknown. Here we show that overexpression of the transforming mutants of Cbl, Cbl-70Z, and v-Cbl, but not wild-type (wt) Cbl, enhance phagocytosis mediated by FcgammaR in COS cells. Cbl-70Z, but not Cbl-wt, also enhanced FcgammaR-mediated phagocytosis in P388D1 murine macrophage cells. Cbl-70Z did not affect tyrosine phosphorylation or in vitro kinase activity of Syk, indicating that Syk may not be the direct target of Cbl-70Z in the enhancement of phagocytosis. A point mutation (G306E) in the phosphotyrosine domain of Cbl-70Z, as well as a C-terminal 67-aa deletion, partially abolished the enhancing effect on FcgammaR-mediated phagocytosis. A double mutant of Cbl-70Z containing both the G306E mutation and the C-terminal deletion completely lacked the ability to enhance phagocytosis. Thus, both the phosphotyrosine binding domain and the carboxyl-terminal tail were required for optimal enhancement of phagocytosis by Cbl-70Z. Functional phosphatidylinositol 3-kinase was required for Cbl-70Z to enhance phagocytosis, since wortmannin, a phosphatidylinositol 3-kinase inhibitor, inhibited FcgammaR-mediated phagocytosis in the presence of Cbl-70Z. These studies demonstrate that mutants of Cbl can modulate the phagocytic pathway mediated by FcgammaR and imply a functional involvement of c-Cbl in Fcgamma receptor-mediated phagocytosis.
Velocity model building by semblance maximization of modulated-shot gathers (2007)

Abstract In recent years, wave-equation migration has greatly enhanced imaging in complex velocity models. However, velocity model building is still dependent on ray-theory approximations. We propose a full wave-equation methodology for velocity model building based on the nonlinear inversion of a semblance criterion with respect to the velocity field. A newly described type of migration, called the modulated-shot migration, is used to obtain the necessary gathers, which are indexed in surface angle. The semblance of these gathers, after spatial averaging, is used as the cost function. This methodology is shown to successfully image the Marmousi model and the subsalt part of the Sigsbee model, especially in terms of focusing, which is as good as with the true model, but also in terms of depthing which is enhanced compared with the initial model. Realistic constraints are used in terms of minimum frequency, maximum offset, and crudeness of the starting model. A key point in the success of this methodology is the multiscale approach wherein the iterations are started on a coarse scale, and ended at a finer scale.
Silencing the epidermal growth factor receptor gene with RNAi may be developed as a potential therapy for non small cell lung cancer (2005)

Lung cancer has emerged as a leading cause of cancer death in the world. Non-small cell lung cancer (NSCLC) accounts for 75-80% of all lung cancers. Current therapies are ineffective, thus new approaches are needed to improve the therapeutic ratio. Double stranded RNA (dsRNA)-mediated RNA interference (RNAi) has shown promise in gene silencing, the potential of which in developing new methods for the therapy of NSCLC needs to be tested. We report here RNAi induced effective silencing of the epidermal growth factor receptor (EGFR) gene, which is over expressed in NSCLC. NSCLC cell lines A549 and SPC-A1 were transfected with sequence- specific dsRNA as well as various controls. Immune fluorescent labeling and flow cytometry were used to monitor the reduction in the production of EGFR protein. Quantitative reverse-transcriptase PCR was used to detect the level of EGFR mRNA. Cell count, colony assay, scratch assay, MTT assay in vitro and tumor growth assay in athymic nude mice in vivo were used to assess the functional effects of EGFR silencing on tumor cell growth and proliferation. Our data showed transfection of NSCLC cells with dsRNA resulted in sequence specific silencing of EGFR with 71.31% and 71.78 % decreases in EGFR protein production and 37.04% and 54.92% in mRNA transcription in A549 and SPC-A1 cells respectively. The decrease in EGFR protein production caused significant growth inhibition, i.e.: reducing the total cell numbers by 85.0% and 78.3%, and colony forming numbers by 63.3% and 66.8%. These effects greatly retarded the migration of NSCLC cells by more than 80% both at 24 h and at 48 h, and enhanced chemo-sensitivity to cisplatin by four-fold in A549 cells and seven-fold in SPC-A1. Furthermore, dsRNA specific for EGFR inhibited tumor growth in vivo both in size by 75.06% and in weight by 73.08%. Our data demonstrate a new therapeutic effect of sequence specific suppression of EGFR gene expression by RNAi, enabling inhibition of tumor proliferation and growth. However, in vivo use of dsRNA for gene transfer to tumor cells would be limited because dsRNA would be quickly degraded once delivered in vivo. We thus tested a new bovine lentiviral vector and showed lentivector-mediated RNAi effects were efficient and specific. Combining RNAi with this gene delivery system may enable us to develop RNAi for silencing EGFR into an effective therapy for NSCLC.
Improving lactose digestion and symptoms of lactose intolerance with a novel galacto-oligosaccharide (RP-G28): a randomized, double-blind clinical trial (2013)

Efficacy trends and favorable safety/tolerability findings suggest that RP-G28 appears to be a potentially useful approach for improving lactose digestion and LI symptoms. The concurrent reduction in abdominal pain and improved overall tolerance could be a meaningful benefit to lactose intolerant individuals.
Solid-Phase Extraction and Solid-State Spectroscopy for Monitoring Water Pollution (1991)

Abstract Research results are described which bring out the potential of using commercially available solid-phase extraction membranes and solid-state spectroscopy for monitoring water pollution. The membranes are used to preconcentrate pollutants by sorption from aqueous solution followed by nondestructive spectroscopic measurements. Solid-state fluorescence measurements using EmporeTM C18 membranes were employed in the laboratory for concept validation studies. Tabs from the membranes were suspended in solutions containing parts per billion (ppb) concentrations of anthracene for specific periods of time. The tabs were withdrawn, allowed to dry briefly in air, and then examined for fluorescence. The potential exists for at least semiquantitative analysis. The method is relatively simple. Use of extraction membranes in B dip-stick mode is new, as is the use of the membranes with solid-state fluorescence spectroscopy. Limitations are being defined. Key Words: solid-phase extractionsolid-state spectroscopyground water monitoringfluorescenceanthracene
Programmed Death (PD)-1-Deficient Mice Are Extremely Sensitive to Murine Hepatitis Virus Strain-3 (MHV-3) Infection (2011)

The inhibitory receptor programmed death-1 (PD-1) has the capacity to maintain peripheral tolerance and limit immunopathological damage; however, its precise role in fulminant viral hepatitis (FH) has yet to be described. Here, we investigated the functional mechanisms of PD-1 as related to FH pathogenesis induced by the murine hepatitis virus strain-3 (MHV-3). High levels of PD-1-positive CD4(+), CD8(+) T cells, NK cells and macrophages were observed in liver, spleen, lymph node and thymus tissues following MHV-3 infection. PD-1-deficient mice exhibited significantly higher expression of the effector molecule which initiates fibrinogen deposition, fibrinogen-like protein 2 (FGL2), than did their wild-type (WT) littermates. As a result, more severe tissue damage was produced and mortality rates were higher. Fluorescence double-staining revealed that FGL2 and PD-1 were not co-expressed on the same cells, while quantitative RT-PCR demonstrated that higher levels of IFN-γ and TNF-α mRNA transcription occurred in PD-1-deficient mice in response to MHV-3 infection. Conversely, in vivo blockade of IFN-γ and TNF-α led to efficient inhibition of FGL2 expression, greatly attenuated the development of tissue lesions, and ultimately reduced mortality. Thus, the up-regulation of FGL2 in PD-1-deficient mice was determined to be mediated by IFN-γ and TNF-α. Taken together, our results suggest that PD-1 signaling plays an essential role in decreasing the immunopathological damage induced by MHV-3 and that manipulation of this signal might be a useful strategy for FH immunotherapy.
Development of T H 1 CD4 + T Cells Through IL-12 Produced by Listeria -Induced Macrophages (1993)

Development of the appropriate CD4+ T helper (TH) subset during an immune response is important for disease resolution. With the use of naïve, ovalbumin-specific alpha beta T cell receptor transgenic T cell, it was found that heat-killed Listeria monocytogenes induced TH1 development in vitro through macrophage production of interleukin-12 (IL-12). Moreover, inhibition of macrophage production of IL-12 may explain the ability of IL-10 to suppress TH1 development. Murine immune responses to L. monocytogenes in vivo are of the appropriate TH1 phenotype. Therefore, this regulatory pathway may have evolved to enable innate immune cells, through interactions with microbial pathogens, to direct development of specific immunity toward the appropriate TH phenotype.
Ferromagnetic resonance in a suspension of single-domain particles (1994)

The theory of ferromagnetic resonance (FMR) in an assembly of single-domain uniaxially anisotropic particles is being applied to suspensions. The approach used has, as its basis, the independent-grain model once proposed for the description of FMR in polycrystals. We surmise that the basic assumptions of this model are also appropriate for composites of fine magnetic particles. With regard to the specific properties of the systems in question, we extend the model taking into account (i) the thermofluctuational effects (superparamagnetism) and (ii) the orientational mobility of the particles which leads to the change of the orientational distribution of their anisotropy axes under the influence of the applied field. The joint action of these effects imparts some specific features to the FMR spectra of a magnetic suspension. For example, in a certain temperature range two peak absorption lines must occur.
HMM-based efficient sketch recognition (2005)

Current sketch recognition systems treat sketches as images or a collection of strokes, rather than viewing sketching as an interactive and incremental process. We show how viewing sketching as an interactive process allows us to recognize sketches using Hidden Markov Models. We report results of a user study indicating that in certain domains people draw objects using consistent stroke orderings. We show how this consistency, when present, can be used to perform sketch recognition efficiently. This novel approach enables us to have polynomial time algorithms for sketch recognition and segmentation, unlike conventional methods with exponential complexity.
Digital storage and transmission of cardiovascular images: what are the costs, benefits and timetable for conversion? (1996)

A new word has recently appeared in the lexicon of computers, the pedabyte, which refers to a digital storage unit of 1 quadrillion (1 000 000 000 000 000) bytes of information. For those of us who remember the Neanderthal era of digital storage using punch cards (1970s) or floppy disks (early 1980s), this number, representing a million gigabytes, is truly staggering. Nevertheless, it is approxi- mately the magnitude of digital storage needed to record one year's worth of echocardiographic and angiographic data from the Cleveland Clinic Heart Center. Despite the daunting challenges, there remains little doubt that digital storage of all cardiovascular imag- ing studies will become feasible over the next several years. Indeed, many authorities confi- dently predict that a decade from now, digital imaging will be the main method used to store all medical images. What forces are driving this massive conversion from analogue to digi- tal storage? What advantages will digital imag- ing bring to the cardiovascular practitioner and how much will such systems cost? How can such an enormous quantity of data be stored, retrieved, and transmitted around a hospital? This review will try to answer the "why", "how", and (perhaps most impor- tantly) "when" of digital cardiac image stor- age.
Effects of triiodo-thyronine on angiotensin-induced cardiomyocyte hypertrophy: reversal of increased β-myosin heavy chain gene expression (2006)

Thyroid hormone-induced cardiac hypertrophy is similar to that observed in physiological hypertrophy, which is associated with high cardiac contractility and increased alpha-myosin heavy chain (alpha-MHC, the high ATPase activity isoform) expression. In contrast, angiotensin II (Ang II) induces an increase in myocardial mass with a compromised contractility accompanied by a shift from alpha-MHC to the fetal isoform beta-MHC (the low ATPase activity isoform), which is considered as a pathological hypertrophy and inevitably leads to the development of heart failure. The present study is designed to assess the effect of thyroid hormone on angiotensin II-induced hypertrophic growth of cardiomyocytes in vitro. Cardiomyocytes were prepared from hearts of neonatal Wistar rats. The effects of Ang II and 3,3',5-triiodo-thyronine (T3) on incorporations of [3H]-thymine and [3H]-leucine, MHC isoform mRNA expression, PKC activity, and PKC isoform protein expression were studied. Ang II enhanced [3H]-leucine incorporation, beta-MHC mRNA expression, PKC activity, and PKCepsilon expression and inhibited alpha-MHC mRNA expression in cardiomyocytes. T3 treatment prevented Ang II-induced increases in PKC activity, PKCepsilon, and beta-MHC mRNA overexpression and favored alpha-MHC mRNA expression. Thyroid hormone appears to be able to reprogram gene expression in Ang II-induced cardiac hypertrophy, and a PKC signal pathway may be involved in such remodeling process.
Characterization and Localization of New Antifungal Cysteine-Rich Proteins fromBeta vulgaris (1995)

Two novel antifungal proteins, AX1 and AX2, were isolated from leaves of sugar beet infected with Cercospora beticola. AX1 (MW = 5078 +/- 3D) and AX2 (MW = 5193 +/- 3D) were N-terminally sequenced and identified as monomeric, basic proteins consisting of 46 amino acid residues, of which eight are cysteines. Both AX proteins strongly inhibit growth of C. beticola and other filamentous fungi, but have little or no effect against bacteria. Based on primary sequence homology (24 to 46% identity), they are related to the superfamily of gamma-thionins, which have been isolated recently from seeds of monocotyledons and Brassicaceae. Specific antibodies were raised against the AX proteins after conjugation to diphtheria toxoid. Using immunoblotting and immunohistology, we detected high concentrations of AX proteins extracellularly in cell walls and in globular bodies around necrotic lesions in sugar beet leaves infected with C. beticola, suggesting that AX proteins are involved in antifungal defense. Furthermore, AX proteins or serologically related proteins were detected in xylem, stomata, and stomatal cells as well as in sugar beet styles.
Multiple Actions of Pituitary Adenylyl Cyclase Activating Peptide in Nervous System Development and Regeneration (2002)

Pituitary adenylyl cyclase activating peptide (PACAP) is widely expressed in the embryonic brain at the onset of neurogenesis, and is strongly upregulated in several models of nerve injury. Moreover, high-affinity PACAP receptors are expressed in proliferative zones in the embryonic and postnatal nervous system suggesting that PACAP regulates the development of both neuronal and glial precursors. Tissue culture studies indicate that PACAP exerts a variety of growth factor-like actions that depend on the origin of the cell population and developmental stage. These effects include regulation of proliferation, survival, maturation, neurite outgrowth, and expression of trophic factors, cytokines and trk receptors. The presence of other growth factors can also markedly affect these actions of PACAP, for example, reversing PACAP's effect from proliferative to antiproliferative. In vivo models now provide additional evidence that PACAP acts in neural development and regeneration.
High-Throughput Fluorescent Tagging of Full-Length Arabidopsis Gene Products in Planta (2004)

We developed a high-throughput methodology, termed fluorescent tagging of full-length proteins (FTFLP), to analyze expression patterns and subcellular localization of Arabidopsis gene products in planta. Determination of these parameters is a logical first step in functional characterization of the approximately one-third of all known Arabidopsis genes that encode novel proteins of unknown function. Our FTFLP-based approach offers two significant advantages: first, it produces internally-tagged full-length proteins that are likely to exhibit native intracellular localization, and second, it yields information about the tissue specificity of gene expression by the use of native promoters. To demonstrate how FTFLP may be used for characterization of the Arabidopsis proteome, we tagged a series of known proteins with diverse subcellular targeting patterns as well as several proteins with unknown function and unassigned subcellular localization.
Identification of a Toxic Mechanism of the Plasticizers, Phtahlic Acid Esters, which are Putative Endocrine Disrupters: Time-dependent Increase in Quinolinic Acid and Its Metabolites in… (2002)

We have reported that the administration of di(2-ethylhexyl)phthalate (DEHP) increased the formations of quinolinic acid (QA) and its lower metabolites on the tryptophan-niacin pathway. To discover the mechanism involved in disruption of the tryptophan-niacin pathway by DEHP, we assessed the daily urinary excretion of QA and its lower metabolites, and enzyme activities on the tryptophan-niacin pathway. Rats were fed with a niacin-free, 20% casein diet or the same diet supplemented with 0.1% DEHP or 0.043% phthalic acid and 0.067% 2-ethylhexanol added for 21 days. Feeding of DEHP increased the urinary excretions of QA and its lower metabolites in a time-dependent manner, and the increase of these excretions reached a peak at 11 days, but feeding of phthalic acid and 2-ethylhexanol had no effect. Feeding of DEHP, however, did not affect any enzyme activity including alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD), affecting the formation of QA, on the tryptophan-niacin pathway.
Semiconducting polymer-buckminsterfullerene heterojunctions: Diodes, photodiodes, and photovoltaic cells (1993)

The characterization of rectifying heterojunctions (diodes) fabricated from a semiconducting polymer, a soluble derivative of poly(phenylene-vinylene), and buckminsterfullerene, C60, are reported. Rectification ratios in the current versus voltage characteristics exceed 104. When illuminated, the devices exhibit a large photoresponse as a result of photoinduced electron transfer across the heterojunction interface from the semiconducting polymer (donor) onto C60 (acceptor). The photodiode and photovoltaic responses are characterized. Photoinduced electron transfer across the donor-accepted rectifying heterojunction offers potential for photodetector and for solar cell applications.
Surface plasmon generation and light transmission by isolated nanoholes and arrays of nanoholes in thin metal films (2005)

Extensive 3-D finite-difference time-domain simulations are carried out to elucidate the nature of surface plasmon polaritons (SPPs) and localized surface plasmon polaritons (LSPs) generated by nanoscale holes in thin metallic films interacting with light. Both isolated nanoholes and square arrays of nanoholes in gold films are considered. For isolated nanoholes, we expand on an earlier discussion of Yin et al. [Appl. Phys. Lett. 85, 467-469 (2004)] on the origins of fringe patterns in the film and the role of nearfield scanning optical microscope probe interactions. The associated light transmission of a single nanohole is enhanced when a LSP excitation of the nanohole itself is excited. Periodic arrays of nanoholes exhibit more complex behavior, with light transmission peaks exhibiting distinct minima and maxima that can be very well described with Fano lineshape models. This behavior is correlated with the coupling of SPP Bloch waves and more directly transmitted waves through the holes.
A solvent replenishment solution for managing evaporation of biochemical reactions in air-matrix digital microfluidics devices (2014)

Digital microfluidics (DMF) is a powerful technique for sample preparation and analysis for a broad range of biological and chemical applications. In many cases, it is desirable to carry out DMF on an open surface, such that the matrix surrounding the droplets is ambient air. However, the utility of the air-matrix DMF format has been severely limited by problems with droplet evaporation, especially when the droplet-based biochemical reactions require high temperatures for long periods of time. We present a simple solution for managing evaporation in air-matrix DMF: just-in-time replenishment of the reaction volume using droplets of solvent. We demonstrate that this solution enables DMF-mediated execution of several different biochemical reactions (RNA fragmentation, first-strand cDNA synthesis, and PCR) over a range of temperatures (4-95 °C) and incubation times (up to 1 h or more) without use of oil, humidifying chambers, or off-chip heating modules. Reaction volumes and temperatures were maintained roughly constant over the course of each experiment, such that the reaction kinetics and products generated by the air-matrix DMF device were comparable to those of conventional benchscale reactions. This simple yet effective solution for evaporation management is an important advance in developing air-matrix DMF for a wide variety of new, high-impact applications, particularly in the biomedical sciences.
Regulation of matrix metalloprotease activity in malignant mesothelioma cell lines by growth factors (2003)

This study shows, for the first time, the broad extent of regulation of MMPs by various growth factors in malignant mesothelioma cells.