gebhart/patrepeval huggingface dataset:
Regulation of Telomerase Activity in Immortal Cell Lines (1996)

Telomerase is a ribonucleoprotein whose activity has been detected in germ line cells, immortal cells, and most cancer cells. Except in stem cells, which have a low level of telomerase activity, its activity is absent from normal somatic tissues. Understanding the regulation of telomerase activity is critical for the development of potential tools for the diagnosis and treatment of cancer. Using the telomeric repeat amplification protocol, we found that immortal, telomerase-positive, pseudodiploid human cells (HT1080 and HL60 cells) sorted by flow repressed in quiescent cells. This was true whether quiescence was induced by contact inhibition (NIH 3T3 mouse cells), growth factor removal (bromodeoxyuridine-blocked mouse myoblasts), reexpression of cellular senescence (the reversibly immortalized IDH4 cells), or irreversible cell differentiation (HL60 promyelocytic leukemia cells and C2C12 mouse myoblasts). Taken together, these results indicate that telomerase is active throughout the cell in dividing, immortal cells but that its activity is repressed in cells that exit the cell cycle. This suggests that quiescent stem cells that have the potential to express telomerase may remain unaffected by potential antitelomerase cancer therapies.
Use of the 10-Day-Old Chick Embryo Model for Studying Angiogenesis (2003)

The development of new vessels plays a critical role in a number of physiological and pathological events such as embryonic development, wound healing, arthritis, and tumor growth and metastasis (1–4). One area that has received considerable attention is determining the role that integrins play in angiogenesis. Recently, we demonstrated that integrin αvβ3 was highly expressed on angiogenic blood vessels associated with a variety of solid tumors and during granulation tissue formation (5,6). Importantly, little if any αvβ3 was detected on quiescent vessels (5,6). In addition, antagonists of αvβ3 were shown to specifically inhibit angiogenesis in vivo. These findings suggest an important role for integrin αvβ3 during neovascularization. Thus, a great deal of attention has been focused on understanding the cellular and molecular mechanisms by which integrins regulate angiogenesis. Angiogenesis can be defined as the process by which new blood vessels form from pre-existing vessels. This process is similar to, but not identical with vasculogenesis, in which new blood vessels arise from blood islands and precursor cells called angioblasts (1–3). Thus, an in-depth understanding of the molecules that regulate this complex biological process is of fundamental importance in both basic and clinical research. In fact, recent advances in our understanding of the molecular and biochemical events that facilitate angiogenesis have provided insight into cellular invasion in general as well as the development of novel strategies for the treatment of neovascular diseases (5,7–11).
Dehydrogenation vs Oxygenation in Photosensitized Oxidation of 9-Substituted 10-Methyl-9,10-dihydroacridine in the Presence of Scandium Ion (2002)

Photooxidation of 9-substituted 10-methyl-9,10-dihydroacridine (AcrHR) with oxygen occurs efficiently in the presence of 9,10-dicyanoanthracene (DCA) and scandium triflate [Sc(OTf)3] under visible light irradiation in oxygen-saturated acetonitrile (MeCN) to yield the 9-substituted 10-methylacridinium ion (AcrR+) and H2O2 or the 10-methylacridinium ion (AcrH+) and the oxygenated products of R such as ROOH, depending on the type of substitutent R. No DCA-photosensitized oxidation of AcrHR occurs in the absence of Sc3+ under otherwise the same experimental conditions. The observed selectivities for the C(9)−H vs C(9)−C bond cleavage of AcrHR in the DCA-photosensitized oxidation of AcrHR in the presence of Sc(OTf)3 agree with those for the cleavage of radical cations of AcrHR (AcrHR•+) depending on the type of substituent R. Such product selectivities, being consistent with the electron-transfer oxidation of AcrHR, combined with quantum yield determination, the 1O2 phosphorescence decay dynamics, and the detection of radical ion intermediates in the laser-flash photolysis experiments reveal the electron-transfer radical chain mechanism for the DCA-photosensitized oxidation of AcrHR initiated by photoinduced electron transfer from AcrHR to the singlet excited state of DCA.
Primary structure of the Escherichia coli serotype K30 capsular polysaccharide (1980)

Methylation, 1H nuclear magnetic resonance, and bacteriophage degradation results indicate that the Escherichia coli serotype K30 capsular polysaccharide consists of leads to 2)-alpha-D-Manp-(1 leads to 3)-beta-D-Galp-(1 leads to chains carrying beta-D-GlcUAp-(1 leads to 3)-alpha-D-Galp-(1 leads to branches at position 3 of the mannoses.
Molecular Gating of Silicon Nanowire Field-Effect Transistors with Nonpolar Analytes (2011)

Silicon nanowire field-effect transistors (Si NW FETs) have been used as powerful sensors for chemical and biological species. The detection of polar species has been attributed to variations in the electric field at the conduction channel due to molecular gating with polar molecules. However, the detection of nonpolar analytes with Si NW FETs has not been well understood to date. In this paper, we experimentally study the detection of nonpolar species and model the detection process based on changes in the carrier mobility, voltage threshold, off-current, off-voltage, and subthreshold swing of the Si NW FET. We attribute the detection of the nonpolar species to molecular gating, due to two indirect effects: (i) a change in the dielectric medium close to the Si NW surface and (ii) a change in the charged surface states at the functionality of the Si NW surface. The contribution of these two effects to the overall measured sensing signal is determined and discussed. The results provide a launching pad for real-world sensing applications, such as environmental monitoring, homeland security, food quality control, and medicine.
Noise robust linear dynamic system for phase unwrapping and smoothing (2011)

Phase unwrapping techniques remove the modulus 2 π ambiguities of wrapped phase maps. The present work shows a first-order feedback system for phase unwrapping and smoothing. This system is a fast phase unwrapping system which also allows filtering some noise since in deed it is an Infinite Impulse Response (IIR) low-pass filter. In other words, our system is capable of low-pass filtering the wrapped phase as the unwrapping process proceeds. We demonstrate the temporal stability of this unwrapping feedback system, as well as its low-pass filtering capabilities. Our system even outperforms the most common and used unwrapping methods that we tested, such as the Flynn's method, the Goldstain's method, and the Ghiglia least-squares method (weighted or unweighted). The comparisons with these methods show that our system filters-out some noise while preserving the dynamic range of the phase-data. Its application areas may cover: optical metrology, synthetic aperture radar systems, magnetic resonance, and those imaging systems where information is obtained as a demodulated wrapped phase map.
Identification of nucleolin and nucleophosmin as genotoxic stress-responsive RNA-binding proteins (2002)

Genotoxic stress (DNA damage) can elicit multiple responses in mammalian cells, including the activation of numerous cascades of signal transduction that result in the activation of cellular genes involved in growth control, DNA repair and apoptosis. In an earlier report, we have shown that DNA-damaging agents can also induce the RNA-binding activity of several specific proteins that favor a double stem-loop RNA structure. Here we report the purification and identification of nucleophosmin (NPM) and nucleolin as two genotoxic stress-responsive RNA-binding proteins. UV radiation induces the protein expression levels and RNA-binding activity of NPM while nucleolin RNA-binding activity increases after UV or ionizing radiation exposure. Moreover, we have identified 40 mRNA ligands that are potentially regulated by nucleolin, several of which are stress-responsive transcripts. In addition, our data indicate that activation of nucleolin RNA-binding activity by genotoxic stress is mediated by stress-activated protein kinase p38. Our findings suggest that activation of the RNA-binding properties of nucleolin and NPM is part of the cellular response to genotoxic stress.
A subspace approach to single channel signal separation using maximum likelihood weighting filters (2004)

Our goal is to extract multiple source signals when only a single observation channel is available. We propose a new signal separation algorithm based on a subspace decomposition. The observation is transformed into subspaces of interest with different sets of basis functions. A flexible model for density estimation allows an accurate modeling of the distributions of the source signals in the subspaces, and we develop a filtering technique using a maximum likelihood (ML) approach to match the observed single channel data with the decomposition. Our experimental results show good separation performance on simulated mixtures of two music signals as well as two voice signals.
Free Radical Sensor Based on CdSe Quantum Dots with Added 4-Amino-2,2,6,6-Tetramethylpiperidine Oxide Functionality (2006)

The association and resulting fluorescence quenching of CdSe quantum dots by 4-amino-2,2,6,6-tetramethylpiperidine oxide (4-amino-TEMPO), a persistent nitroxide, have been examined using electron paramagnetic resonance (EPR) and fluorescence spectroscopy. EPR data suggest binding constants around (8 +/- 4) x 10(6) M(-1) for green (2.4-2.5 nm) nanoparticles, and the application of Job's method indicates that the preferred mode of binding involves one or two quencher molecules per quantum dot, although more quenchers could bind at high concentrations of 4-amino-TEMPO. Fluorescence quenching by 4-amino-TEMPO is at least 3 orders of magnitude more efficient than by TEMPO itself, reflecting the strong binding confirmed by the EPR data. Stern-Volmer plots are nonlinear and in light of the EPR data probably reflect ready accessibility of the CdSe surface to one or two 4-amino-TEMPO molecules, while additional quenchers can only bind if they displace trioctylphosphine oxide ligands. Quantum dot-4-amino-TEMPO complexes can be used as free radical sensors, since the fluorescence (quenched by the nitroxide) is readily restored when radicals are trapped to form alkoxyamines.
A new function for a phosphotyrosine phosphatase: linking GRB2-Sos to a receptor tyrosine kinase. (1994)

Autophosphorylated growth factor receptors provide binding sites for the src homology 2 domains of intracellular signaling molecules. In response to epidermal growth factor (EGF), the activated EGF receptor binds to a complex containing the signaling protein GRB2 and the Ras guanine nucleotide-releasing factor Sos, leading to activation of the Ras signaling pathway. We have investigated whether the platelet-derived growth factor (PDGF) receptor binds GRB2-Sos. In contrast with the EGF receptor, the GRB2 does not bind to the PDGF receptor directly. Instead, PDGF stimulation induces the formation of a complex containing GRB2; 70-, 80-, and 110-kDa tyrosine-phosphorylated proteins; and the PDGF receptor. Moreover, GRB2 binds directly to the 70-kDa protein but not to the PDGF receptor. Using a panel of PDGF beta-receptor mutants with altered tyrosine phosphorylation sites, we identified Tyr-1009 in the PDGF receptor as required for GRB2 binding. Binding is inhibited by a phosphopeptide containing a YXNX motif. The protein tyrosine phosphatase Syp/PTP1D/SHPTP2/PTP2C is approximately 70 kDa, binds to the PDGF receptor via Tyr-1009, and contains several YXNX sequences. We found that the 70-kDa protein that binds to the PDGF receptor and to GRB2 comigrates with Syp and is recognized by anti-Syp antibodies. Furthermore, both GRB2 and Sos coimmunoprecipitate with Syp from lysates of PDGF-stimulated cells, and GRB2 binds directly to tyrosine-phosphorylated Syp in vitro. These results indicate that GRB2 interacts with different growth factor receptors by different mechanisms and the cytoplasmic phosphotyrosine phosphatase Syp acts as an adapter between the PDGF receptor and the GRB2-Sos complex.
C-Reactive Protein in Ischemic Stroke (2001)

CRP is a marker of increased 1-year risk in ischemic stroke. CRP at discharge is better related to later outcome and could be of greater utility for risk stratification. These findings are consistent with the hypothesis that elevated CRP may predict future cardiovascular events or death.
Induction of experimental autoimmune sialoadenitis by immunization of PL/J mice with carbonic anhydrase II. (1995)

Experimental autoimmune sialoadenitis was induced in PL/J (H-2u) mice by intradermal immunization with human carbonic anhydrase II (CAII) and adjuvant containing monophosphoryl lipid A and trehalose diorynomycolate. Mice immunized with CAII showed a significant increase in the number and size of foci with lymphocytic infiltration in the salivary gland compared with mice immunized with adjuvant alone and untreated mice. In mice immunized with CAII, lymphocytic foci were observed around intercalated and intralobular ducts in the salivary glands, resulting in atrophy and replacement of acinar units. The epithelial cells of salivary ducts adjacent to the lymphocytic foci showed both degenerative and regenerative changes. Similar lymphocytic infiltrations were observed in the pancreas and kidney of a few mice immunized with CAII. Among several mouse strains with different H-2 haplotypes (p, q, r, s, and u), strains bearing H-2s and H-2u were susceptible to CAII-induced sialoadenitis. These results indicate that sialoadenitis induced by the immunization of CAII in mice may serve as a disease model of Sjögren's syndrome and that CAII or its derived peptides in association with the MHC may be one Ag recognized by an autoimmune response in this syndrome.
Childhood anaplastic large cell lymphoma has a high incidence of ALK gene rearrangement as determined by immunohistochemical staining and fluorescent in situ hybridisation: a genetic and pathological correlation* (2005)

Anaplastic large cell lymphoma (ALCL) comprises 10-15% of childhood non-Hodgkin lymphomas (NHL). Systemic ALCL is highly associated with anaplastic lymphoma kinase (ALK) gene translocations with over-expression of ALK protein. We studied ALK rearrangements using fluorescence in situ hybridisation (FISH) and ALK immunohistochemical staining in 43 paediatric systemic ALCLs. FISH (performed on 35 cases) identified a translocation in 29 cases (83%). Immunohistochemistry identified ALK over-expression in 42/43 cases (97%) with the single ALK-negative case demonstrating an ALK rearrangement by FISH, indicating 100% incidence of ALK translocations.
Rapid detection of chromosome aneuploidies in uncultured amniocytes by using fluorescence in situ hybridization (FISH). (1992)

Herein we report the results of the first major prospective study directly comparing aneuploidy detection by fluorescence in situ hybridization of interphase nuclei with the results obtained by cytogenetic analysis. We constructed probes derived from specific subregions of human chromosomes 21, 18, 13, X, and Y that give a single copy-like signal when used in conjunction with suppression hybridization. A total of 526 independent amniotic fluid samples were analyzed in a blind fashion. All five probes were analyzed on 117 samples, while subsets of these five probes were used on the remaining samples (because of insufficient sample size), for a total of over 900 autosomal hybridization reactions and over 400 sex chromosome hybridization reactions. In this blind series, 21 of 21 abnormal samples were correctly identified. The remaining samples were correctly classified as disomic for these five chromosomes. The combination of chromosome-specific probe sets composed primarily of cosmid contigs and optimized hybridization/detection allowed accurate chromosome enumeration in uncultured human amniotic fluid cells, consistent with the results obtained by traditional cytogenetic analysis.
Computing generalized inverse systems using matrix pencil methods (2001)

We address the numerically reliable computation of generalized inverses of rational matrices in descriptor state-space representation. We put particular emphasis on two classes of inverses: the weak generalized inverse and the Moore-Penrose pseudoinverse. By combining the underlying computational techniques, other types of inverses of rational matrices can be computed as well. The main computational ingredient to determine generalized inverses is the orthogonal reduction of the system matrix pencil to appropriate Kronecker-like forms.
The house that JAK/STAT built (1997)

An international workshop on "Cytokines, Signaling and the Jak/Stat Pathway' organized by Peter C. Heinrich of the Klinikum der RWTH Aachen under the auspices of DFG-Forschergruppe was held in Aachen, Germany, on 4-5 October 1996. In this review David Levy notes that even though some diagrams shown at the meeting displayed more arrows than there were meeting participants, remarkable progress has been made in the unraveling of the complexities of cytokine signal transduction. The central issue in the field of cytokine signaling is specificity, and this issue was addressed through experimental results from biochemical, molecular, and genetic studies of signal transduction pathways.
Increased Anatomical Specificity for Neuromodulation Using Modulated Focused Ultrasound (2014)

Thesis (Master's)--University of Washington, 2014
Levels of α7 integrin and laminin-α2 are increased following prednisone treatment in themdxmouse and GRMD dog models of Duchenne muscular dystrophy (2013)

Duchenne muscular dystrophy (DMD) is a fatal neuromuscular disease for which there is no cure and limited treatment options. Prednisone is currently the first line treatment option for DMD and studies have demonstrated that it improves muscle strength. Although prednisone has been used for the treatment of DMD for decades, the mechanism of action of this drug remains unclear. Recent studies have shown that the α7β1 integrin is a major modifier of disease progression in mouse models of DMD and is therefore a target for drug-based therapies. In this study we examined whether prednisone increased α7β1 integrin levels in mdx mouse and GRMD dog models and myogenic cells from humans with DMD. Our results show that prednisone promotes an increase in α7 integrin protein in cultured myogenic cells and in the muscle of mdx and GRMD animal models of DMD. The prednisone-mediated increase in α7 integrin was associated with increased laminin-α2 in prednisone-treated dystrophin-deficient muscle. Together, our results suggest that prednisone acts in part through increased merosin in the muscle basal lamina and through sarcolemmal stabilization of α7β1 integrin in dystrophin-deficient muscle. These results indicate that therapies that target an increase in muscle α7β1 integrin, its signaling pathways and/or laminin could be therapeutic in DMD.
On-chip Raman analysis of heterogeneous catalytic reaction in supercritical CO2: phase behaviour monitoring and activity profiling (2008)

Raman spectroscopy on a chip based Si/glass microreactor allows fast and simultaneous analysis of concentration profiles and phase behaviour of a heterogeneously catalyzed reaction at high pressure.
Detection of aneuploidy in chromosomes X, Y, 13, 18 and 21 by QF-PCR in 662 selected pregnancies at risk (2000)

A quantitative fluorescent-polymerase chain reaction (QF-PCR) test system with different short tandem repeat (STR) markers of the X chromosome (SBMA, DXS8377 and DXS1283E) together with the amelogenin locus (AMXY) was developed for the rapid detection of sex chromosome aneuploidies on uncultured amniotic fluids. The samples (n = 662) were also tested with STRs specific for chromosomes 13, 18 or 21, with two STRs used for each chromosome. In uninformative cases, an additional STR marker was applied. The QF-PCR data were compared with the results of conventional cytogenetics. One dark red stained specimen showed an artificial PCR pattern, probably due to maternal contamination. Six sex chromosome aberrations (four 45,X, one 47,XXY, one mosaic 47,XXY/46,XX) were identified as aneuploid by STRs specific for chromosome X and AMXY. One pregnancy with a mosaic 45, X/46,XX karyotype was not detected by the assay. In all, 12 cases with a numerical aberration involving either chromosome 18 or 21 or with a triploidy were correctly diagnosed by QF-PCR. No information was obtained in one fetal sample with a trisomy 18 due to an uncertain result for two of the three applied STRs specific for chromosome 18 and an uninformative third STR marker. Two samples with an unbalanced Robertsonian translocation could be identified by QF-PCR as trisomic for chromosomes 13 and 21 respectively. The results show an excellent agreement between QF-PCR and cytogenetics with regard to sex chromosome and autosomal aneuploidy detection in prenatal diagnosis.
The Medusa Applications Environment (1994)

We envisage that most of the traffic in our system will not involve direct human interactions but will instead involve agents whose purpose is to examine video and will be agents for face recognition, for interpreting gestures and spoken and so on. These agents will often have real-time requirements which differ fiom those of direct human and it is important that all these different are supported equally Medusa is a peer to peer architecture for controlling networked multimedia devices. This paper describes the audio olll behalf of human For example sofmre model presented to the applications programmer. Active objects called Wes are used to represent cameras, displays, format converters and so on. Data canflow from module to module on connections between them. We introduce two key ideas: jhdy, connections between modules are simple, reliable and by our and unbujjiered. More complex connections are represented by special intermediate modules. Secondly, security is direct peripherals,,, including capabilities then using hierarchies of proxy modules to seTyers, as well as networked Each of restrict access. Keywora!~: multimedia, distributed the direct peripherals is a computer built afoullcl an ARM processor which is connected to an input or output systems, pmgramming paradigms, A IU networks The upon which the Medusa project is is a collection of Provided with unfoeeable cm-, microphones, loudspe&m and multimedia file
Biological Changes in the Annulus Fibrosus in Patients With Low-Back Pain (1982)

The anterior annulus from patients undergoing surgery for low-back pain was compared with the same region removed at autopsy. Collagen, proteoglycan, and water content were measured in different regions across the annulus. Water and proteoglycan contents increased from the outer to the inner annulus, whereas the collagen contents declined. Quantitative differences were found between agematched surgical and autopsy specimens. Discs from most patients showed lowered proteoglycan contents, and a few of these showed high water contents. Loss of collagen in isolated areas of the annulus was demonstrated in some patients. Collagen loss occurred most frequently in the lumbosacral disc, whereas changes in proteoglycan and water were more frequent higher in the lumbar region. No qualitative changes in collagen types were detected immunochemically. In many patients, the levels of proteoglycan which aggregated in vitro were extremely low. Changes in hexosamine molar ratio of disc proteoglycan and in the length of the chondroitin sulfate side chains were observed with aging in this group of patients.