gebhart/patrepeval huggingface dataset:
Dominant-Negative Notch3 Receptor Inhibits Mitogen-Activated Protein Kinase Pathway and the Growth of Human Lung Cancers (2005)

Notch3 is a member of an evolutionarily conserved family of cell surface receptors important in cell-fate determination in both vertebrates and invertebrates. Significant data support the role of Notch pathway in cancer development, although the conflicting role of Notch signaling pathways in tumorigenesis suggests that its action is highly context-dependent. Furthermore, although Notch receptors signal primarily through the regulation of hairy enhancer of split (HES) and HES-related (HRT) genes, they are known to crosstalk with other signaling pathways, including the epidermal growth factor (EGF) and the mitogen-activated protein kinase pathways. Whereas much is known about the role of Notch1 in human cancer, the role of Notch3 in epithelial tumors, such as lung carcinomas, has not been well established. In this study, we show that Notch3 is expressed in 80 of 207 (39%) resected human lung tumors and that its expression is positively correlated with EGF receptor expression. Inhibition of the Notch3 pathway using a dominant-negative receptor dramatically reduces growth in soft agar and increases growth factor dependence. We also find that Notch inhibition increases sensitivity to EGF receptor tyrosine kinase inhibition and decrease in phosphorylation of the mitogen-activated protein kinase. These observations support a role for Notch3 signaling in lung cancer, and one potential mechanism of maintaining the neoplastic phenotype is through the modulation of the EGF pathway.
In Vivo Bactofection: Listeria Can Function as a DNA-Cancer Vaccine (2006)

The development of an effective therapeutic vaccine to induce cancer-specific immunity remains an unsolved yet pressing priority requiring novel vaccine strategies. Here we have generated a series of vaccines in which bacteria deliver a plasmid encoding a tumor antigen under the control of a mammalian promoter in an attempt to induce an antitumor immune response. Utilizing a plasmid release mechanism involving the suicide of the carrier bacteria, we were able to engineer Listeria monocytogenes to induce antitumor immunity to a physiologically relevant tumor antigen, the cervical cancer oncoprotein E7. In a mouse model of cervical cancer, we were able to slow tumor growth and induce an effector CD8(+) T-cell response against the immunodominant epitope for E7. The CD8(+) T cells generated could both home to and penetrate the tumor. This is the first demonstration of in vivo efficacy of bactofection vectors in treating solid tumors. However, although this delivery system was more effective than administering plasmid alone, it was not as effective as L. monocytogenes engineered to deliver the E7 protein in impacting on established tumor growth.
Novel synthesis of some new pyrimido[1,6‐a]pyrimidine and pyrazolo[1,5‐a]pyrimidine derivatives (2011)

Abstract An easy and efficient route for synthesis of some pyrimido[1,6‐ a ]pyrimidine and pyrazolo[1,5‐ a ]pyrimidine derivatives was described through the reaction of sodium salts of formyl ketones with 6‐aminothiouracil and 5‐aminopyrazole derivatives, respectively. The characterization of the reaction products was confirmed by using elemental analysis and spectral data. J. Heterocyclic Chem., (2012).
Reflex Responses from the Main Pulmonary Artery and Bifurcation in Anaesthetised Dogs (2000)

This study was undertaken to determine the reflex cardiovascular and respiratory responses to discrete stimulation of pulmonary arterial baroreceptors using a preparation in which secondary modulation of responses from other reflexes was prevented. Dogs were anaesthetised with -chloralose, artificially ventilated, the chests widely opened and a cardiopulmonary bypass established. The main pulmonary arterial trunk, bifurcation and extrapulmonary arteries as far as the first lobar arteries on each side were vascularly isolated and perfused through the left pulmonary artery and drained via the right artery through a Starling resistance which controlled pulmonary arterial pressure. Pressures distending systemic baroreceptors and reflexogenic regions in the heart were controlled. Reflex vascular responses were assessed from changes in perfusion pressures to a vascularly isolated hind limb and to the remainder of the subdiaphragmatic systemic circulation, both of which were perfused at constant flows. Respiratory responses were assessed from recordings of efferent phrenic nerve activity. Increases in pulmonary arterial pressure consistently evoked increases in both perfusion pressures and in phrenic nerve activity. Both vascular and respiratory responses were obtained when pulmonary arterial pressure was increased to above about 30 mmHg. Responses increased at higher levels of pulmonary arterial pressures. In 13 dogs increases in pulmonary arterial pressure to 45 mmHg increased systemic perfusion pressure by 24 +/- 7 mmHg (mean +/- S.E.M.) from 162 +/- 11 mmHg. Setting carotid sinus pressure at different levels did not influence the vascular response to changes in pulmonary arterial pressure. The presence of a negative intrathoracic pressure of -20 mmHg resulted in larger vascular responses being obtained at lower levels of pulmonary arterial pressure. This indicates that the reflex may be more effective in the intact closed-chest animal. These results demonstrate that stimulation of pulmonary arterial baroreceptors evokes a pressor reflex and augments respiratory drive. This reflex is likely to be elicited in circumstances where pulmonary arterial pressure increases and the negative excursions of intrathoracic pressure become greater. They are likely, therefore, to be involved in the cardio-respiratory response to exercise as well as in pathological states such as pulmonary hypertension or restrictive or obstructive lung disease.
Cell-specific expression of the carrot EP2 lipid transfer protein gene. (1991)

A cDNA corresponding to a 10-kD protein, designated extracellular protein 2 (EP2), that is secreted by embryogenic cell cultures of carrot was obtained by expression screening. The derived protein sequence and antisera against heterologous plant lipid transfer proteins identified the EP2 protein as a lipid transfer protein. Protein gel blot analysis showed that the EP2 protein is present in cell walls and conditioned medium of cell cultures. RNA gel blot analysis revealed that the EP2 gene is expressed in embryogenic cell cultures, the shoot apex of seedlings, developing flowers, and maturing seeds. In situ hybridization showed expression of the EP2 gene in protoderm cells of somatic and zygotic embryos and transient expression in epidermis cells of leaf primordia and all flower organs. In the shoot apical meristem, expression is found in the tunica and lateral zone. In maturing seeds, the EP2 gene is expressed in the outer epidermis of the integument, the seed coat, and the pericarp epidermis, as well as transiently in between both mericarps. Based on the extracellular location of the EP2 protein and the expression pattern of the encoding gene, we propose a role for plant lipid transfer proteins in the transport of cutin monomers through the extracellular matrix to sites of cutin synthesis.
Synthesis and Characterization of Oxetane‐Functionalized Phosphorescent Ir(III)‐Complexes (2009)

Abstract In order to incorporate iridium(III) complexes covalently into an oxetane‐bearing hole‐transporting matrix, a new oxetane‐equipped acetoacetate derivative was introduced as an ancillary ligand. Model complexes with an analogical nonpolymerizable ligand were also prepared in order to perform comparative investigations. Therefore, a series of bis ‐cyclometalated Ir(III) complexes, showing orange (C⁁N‐ligand, coumarin 6) and green (C⁁N‐ligand, phenylpyridine) emission were synthesized and fully characterized. The emission maxima are 569 nm for the orange and 518 nm for the green‐emitting Ir(III) complexes. Entirely solution processed devices, based on crosslinkable hole‐conductors, partially doped with the described orange and green Ir(III) emitters, respectively, were fabricated and tested. magnified image
The Problem of Persistent Platelet Activation in Acute Coronary Syndromes and Following Percutaneous Coronary Intervention (2008)

Platelets play a central role in the atherosclerotic inflammatory response, thrombotic vascular occlusion, microembolization, vasoconstriction, and plaque progression. Persistent platelet activation poses a serious problem among patients with acute coronary syndromes (ACS) and those who have undergone percutaneous coronary intervention (PCI), placing them at risk for ischemic events and subacute stent thrombosis. Patients undergoing PCI are at risk for further ischemic events because of procedure-related platelet activation as well as the inherent persistent platelet hyperreactivity and enhanced thrombin generation associated with ACS. Persistent platelet activation following an acute coronary event and/or PCI supports incorporating antiplatelet strategies into the standard medical management of such patients. In this clinical setting, antiplatelet therapies are capable of improving outcomes. Aspirin, thienopyridines, and glycoprotein IIb/IIIa inhibitors, the 3 major pharmacologic approaches to persistent platelet activation, target various levels of the hemostatic pathways and thrombus formation.
Caspase-9 Activation Results in Downstream Caspase-8 Activation and Bid Cleavage in 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine-Induced Parkinson's Disease (2001)

Parkinson's disease (PD) and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) toxicity are both associated with dopaminergic neuron death in the substantia nigra (SN). Apoptosis has been implicated in this cell loss; however, whether or not it is a major component of disease pathology remains controversial. Caspases are a major class of proteases involved in the apoptotic process. To evaluate the role of caspases in PD, we analyzed caspase activation in MPTP-treated mice, in cultured dopaminergic cells, and in postmortem PD brain tissue. MPTP was found to elicit not only the activation of the effector caspase-3 but also the initiators caspase-8 and caspase-9, mitochondrial cytochrome c release, and Bid cleavage in the SN of wild-type mice. These changes were attenuated in transgenic mice neuronally expressing the general caspase inhibitor protein baculoviral p35. These mice also displayed increased resistance to the cytotoxic effects of the drug. MPTP-associated toxicity in culture was found temporally to involve cytochrome c release, activation of caspase-9, caspase-3, and caspase-8, and Bid cleavage. Caspase-9 inhibition prevented the activation of both caspase-3 and caspase-8 and also inhibited Bid cleavage, but not cytochrome c release. Activated caspase-8 and caspase-9 were immunologically detectable within MPP(+)-treated mesencephalic dopaminergic neurons, dopaminergic nigral neurons from MPTP-treated mice, and autopsied Parkinsonian tissue from late-onset sporadic cases of the disease. These data demonstrate that MPTP-mediated activation of caspase-9 via cytochrome c release results in the activation of caspase-8 and Bid cleavage, which we speculate may be involved in the amplification of caspase-mediated dopaminergic cell death. These data suggest that caspase inhibitors constitute a plausible therapeutic for PD.
Cyclin E-induced S phase without activation of the pRb/E2F pathway. (1997)

In cells of higher eukaryotes, cyclin D-dependent kinases Cdk4 and Cdk6 and, possibly, cyclin E-dependent Cdk2 positively regulate the G1- to S-phase transition, by phosphorylating the retinoblastoma protein (pRb), thereby releasing E2F transcription factors that control S-phase genes. Here we performed microinjection and transfection experiments using rat R12 fibroblasts, their derivatives conditionally overexpressing cyclins D1 or E, and human U-2-OS cells, to explore the action of G1 cyclins and the relationship of E2F and cyclin E in S-phase induction. We demonstrate that ectopic expression of cyclin E, but not cyclin D1, can override G1 arrest imposed by either the p16INK4a Cdk inhibitor specific for Cdk4 and Cdk6 or a novel phosphorylation-deficient mutant pRb. Several complementary approaches to assess E2F activation, including quantitative reporter assays in live cells, showed that the cyclin E-induced S phase and completion of the cell division cycle can occur in the absence of E2F-mediated transactivation. Together with the ability of cyclin E to overcome a G1 block induced by expression of dominant-negative mutant DP-1, a heterodimeric partner of E2Fs, these results provide evidence for a cyclin E-controlled S phase-promoting event in somatic cells downstream of or parallel to phosphorylation of pRb and independent of E2F activation. They furthermore indicate that a lack of E2F-mediated transactivation can be compensated by hyperactivation of this cyclin E-controlled event.
Immunochemistry of viruses : the basis for serodiagnosis and vaccines (1985)

Content Headings: Chapter 1 . The structure of viral epitopes (M.H.V. van Regenmortel). Chapter 2 . Influence of glycosylation on antigenicity of viral proteins (H.-D. Klenk). Chapter 3 . Processing and presentation of viral antigens (K.P. Williams and J.A. Smith). Chapter 4 . Local immune response to viruses (W.F. Muller, R. Garofalo and P.L. Ogra). Chapter 5 . Viruses and autoimmunity (R.S. Fujinami). Chapter 6 . Use of synthetic peptides as diagnostic reagents in virology (S. Modrow and H. Wolf). Chapter 7 . Production of viral antigens in prokaryotic and eukaryotic cells (T. Rutgers, T. Cabez and M. De Wilde). Chapter 8 . Live recombinant viral vaccines (J. Tartaglia and E. Paoletti). Chapter 9 . Picornaviruses (F. Brown). Chapter 10 . Antigenic structure of influenza viruses (G.M. Air and W.G. Laver). Chapter 11 . Immunochemistry of paramyxoviruses (R. Ray and R.W. Compans). Chapter 12 . Arenaviridae and Bunyaviridae (K.E. Wright, C. Schmaljohn, A. Schmaljohn and M.J. Buchmeier). Chapter 13 . Antigenic structure of togaviruses (J.T. Roehrig). Chapter 14 . The antigenic structure of flaviviruses (F.X. Heinz and J.T. Roehrig). Chapter 15 . Lentiviruses (S.D. Putney and R.C. Montelaro). Chapter 16 . Rhabdoviruses (E. Celis). Chapter 17 . Antigenic structure of coronaviruses (W. Spaan, D. Cavanagh and M.C. Horzinek). Chapter 18 . Antigenic and structural features of reoviruses (J.A. Cohen, W.V. Williams, D.B. Weiner and M.I. Greene) Chapter 19 . Hepadnaviruses (A.R. Neurath and Y. Thanavala). Chapter 20 . Herpes simplex virus (M.I. Muggerridge, S.R. Roberts, V.J. Isola, G.H. Cohen and R.J. Eisenberg). Chapter 21 . Poxviruses (Y. Ichihashi). Chapter 22 . Plant viruses (M.H.V. van Regenmortel). Chapter 23 . Bacteriophages (J.L. Carrascosa and E. Kellenberger). Imprint: Elsevier Amsterdam
Salmon: Accurate, Versatile and Ultrafast Quantification from RNA-seq Data using Lightweight-Alignment (2018)

Transcript quantification is a central task in the analysis of RNA-seq data. Accurate computational methods for the quantification of transcript abundances are essential for downstream analysis. However, most existing approaches are much slower than is necessary for their degree of accuracy. We introduce Salmon, a novel method and software tool for transcript quantification that exhibits state-of-the-art accuracy while being significantly faster than most other tools. Salmon achieves this through the combined application of a two-phase inference procedure, a reduced data representation, and a novel lightweight read alignment algorithm. Salmon is written in C++11, and is available under the GPL v3 license as open-source software at https://combine-lab.github.io/salmon.
Replication and Resolution of Telomeres in Yeast (1983)

The ends of eukaryotic chromosomes are complex DNA structures called telomeres. The main function of a telomere is to provide a stable DNA terminus that is fully replicatable. The details of telomere structure and function are as yet unknown, largely because of the difficulty of cloning a protected DNA end. It has recently been shown that the ends of the Tetrahymena linear rDNA plasmid will function as telomeres on linear plasmids in yeast (Szostak and Blackburn 1982). Linear molecules with two Tetrahymena rDNA ends were constructed in vitro; these molecules were able to replicate in yeast, where they were maintained in a linear form. These linear plasmids were used to clone yeast telomeres, which appear to have several structural similarities to Tetrahymena telomeres.
Exploiting Nonlinear Recurrence and Fractal Scaling Properties for Voice Disorder Detection (2007)

Abstract Background: Voice disorders affect patients profoundly, and acoustic tools can potentially measure voice function objectively. Disordered sustained vowels exhibit wide-ranging phenomena, from nearly periodic to highly complex, aperiodic vibrations, and increased "breathiness". Modelling and surrogate data studies have shown significant nonlinear and non-Gaussian random properties in these sounds. Nonetheless, existing tools are limited to analysing voices displaying near periodicity, and do not account for this inherent biophysical nonlinearity and non-Gaussian randomness, often using linear signal processing methods insensitive to these properties. They do not directly measure the two main biophysical symptoms of disorder: complex nonlinear aperiodicity, and turbulent, aeroacoustic, non-Gaussian randomness. Often these tools cannot be applied to more severe disordered voices, limiting their clinical usefulness. Methods: This paper introduces two new tools to speech analysis: recurrence and fractal scaling, which overcome the range limitations of existing tools by addressing directly these two symptoms of disorder, together reproducing a "hoarseness" diagram. A simple bootstrapped classifier then uses these two features to distinguish normal from disordered voices. Results: On a large database of subjects with a wide variety of voice disorders, these new techniques can distinguish normal from disordered cases, using quadratic discriminant analysis, to overall correct classification performance of 91.8% plus or minus 2.0%. The true positive classification performance is 95.4% plus or minus 3.2%, and the true negative performance is 91.5% plus or minus 2.3% (95% confidence). This is shown to outperform all combinations of the most popular classical tools. Conclusions: Given the very large number of arbitrary parameters and computational complexity of existing techniques, these new techniques are far simpler and yet achieve clinically useful classification performance using only a basic classification technique. They do so by exploiting the inherent nonlinearity and turbulent randomness in disordered voice signals. They are widely applicable to the whole range of disordered voice phenomena by design. These new measures could therefore be used for a variety of practical clinical purposes.
Mitochondrial DNA decrease in subcutaneous adipose tissue of HIV-infected individuals with peripheral lipoatrophy (2001)

Lipodystrophy with peripheral fat wasting following treatment with NRTI-containing HAART is associated with a decrease in subcutaneous adipose tissue mtDNA content.
Localization of VEGF and expression of its receptors flit and KDR in human placenta throughout pregnancy (1996)

Vascular endothelial growth factor (VEGF) is a potent secreted angiogenic growth factor. Its action is mediated through the tyrosine kinase receptors flt and KDR. We here examine, in detail, the distribution of this ligand and its receptors in human placentae throughout gestation. In the first trimester, in-situ hybridization revealed uneven distribution of flt mRNA around the villous trophoblast indicating spatial regulation. Temporal regulation of flt was observed with no flt mRNA expression detected in villi from mid-gestational placenta, while low levels were found in term villi. Extravillous trophoblast was found to contain both mRNA encoding flt and flt-like immunoreactivity throughout pregnancy. In contrast, KDR mRNA was found only in association with endothelial cells. Within the decidua the anti-flt antibody stained multiple cell types during the first trimester of pregnancy but only the extravillous trophoblast later in gestation. VEGF immunoreactivity tended to co-localize with the staining for flt. These results indicate that VEGF may exert an important role within both the placental villi and the maternal decidua in relation to the growth, differentiation and migration of trophoblast and that this is mediated primarily through the spatial and temporal regulation of the flt receptor rather than the KDR receptor.
Block copolymers of ethylene oxide and propylene oxide (pluronics) as immunomodulators and antitumour agents. (1991)

Block copolymers of ethylene oxide and propylene oxide (pluronics) are nontoxic water-soluble membranotropic surfactants available as polymers with various compositions, molecular masses, number, and arrangement of blocks. In vivo experiments are reported which demonstrate that these polymers and their functional derivatives stimulate the production of anti-sheep-erythrocyte antibodies in mice. The introduction of reactive (hydroperoxide) groups into the polymers by chemical modification or by solubilization of low-molecular-mass hydroperoxides alters the properties of these immunostimulators. In vitro experiments revealed that these modified polymers enhance the activity of natural killer cells without reducing their viability. It is proposed that the immunomodulatory properties of pluronics and their derivatives play an important role in the antitumour activity of these substances in vivo.
Lactate Utilization Is Regulated by the FadR-Type Regulator LldR in Pseudomonas aeruginosa (2012)

NAD-independent L-lactate dehydrogenase (l-iLDH) and NAD-independent D-lactate dehydrogenase (D-iLDH) activities are induced coordinately by either enantiomer of lactate in Pseudomonas strains. Inspection of the genomic sequences of different Pseudomonas strains revealed that the lldPDE operon comprises 3 genes, lldP (encoding a lactate permease), lldD (encoding an L-iLDH), and lldE (encoding a D-iLDH). Cotranscription of lldP, lldD, and lldE in Pseudomonas aeruginosa strain XMG starts with the base, C, that is located 138 bp upstream of the lldP ATG start codon. The lldPDE operon is located adjacent to lldR (encoding an FadR-type regulator, LldR). The gel mobility shift assays revealed that the purified His-tagged LldR binds to the upstream region of lldP. An XMG mutant strain that constitutively expresses D-iLDH and L-iLDH was found to contain a mutation in lldR that leads to an Ile23-to-serine substitution in the LldR protein. The mutated protein, LldR(M), lost its DNA-binding activity. A motif with a hyphenated dyad symmetry (TGGTCTTACCA) was identified as essential for the binding of LldR to the upstream region of lldP by using site-directed mutagenesis. L-Lactate and D-lactate interfered with the DNA-binding activity of LldR. Thus, L-iLDH and D-iLDH were expressed when the operon was induced in the presence of L-lactate or D-lactate.
Mechanical and thermal properties of dragline silk from the spider Nephila clavipes (1994)

Abstract Dragline silk from the spider, Nephila clavipes , was characterized by thermal analysis (TGA, DSC, DMA), computational modeling, scanning electron microscopy and by quasi‐static as well as high rates of strain. Thermal stability to about 230°C was observed by TGA, two transitions by DMA, −75°C, representative of localized motion in the amorphous domain, and a main chain motion associated with partial melt at 210°C. Tensile tests indicated average initial modulus, ultimate tensile strength and ultimate tensile strain of 22 GPa, 1.1 GPa and 9%, respectively. The corresponding properties of the best fibers tested were 60 GPa, 2.9 GPa and 11%, respectively. High strain rates (&gt;50,000%/sec) indicated similar mechanical properties to the average values indicated above. Microscopy showed compressive and tensile strains to failure of 34%. Computational modeling yielded a crystal modulus of 200 GPa.