gebhart/patrepeval huggingface dataset:
VEGF-Trap: A VEGF blocker with potent antitumor effects (2002)

Vascular endothelial growth factor (VEGF) plays a critical role during normal embryonic angiogenesis and also in the pathological angiogenesis that occurs in a number of diseases, including cancer. Initial attempts to block VEGF by using a humanized monoclonal antibody are beginning to show promise in human cancer patients, underscoring the importance of optimizing VEGF blockade. Previous studies have found that one of the most effective ways to block the VEGF-signaling pathway is to prevent VEGF from binding to its normal receptors by administering decoy-soluble receptors. The highest-affinity VEGF blocker described to date is a soluble decoy receptor created by fusing the first three Ig domains of VEGF receptor 1 to an Ig constant region; however, this fusion protein has very poor in vivo pharmacokinetic properties. By determining the requirements to maintain high affinity while extending in vivo half life, we were able to engineer a very potent high-affinity VEGF blocker that has markedly enhanced pharmacokinetic properties. This VEGF-Trap effectively suppresses tumor growth and vascularization in vivo, resulting in stunted and almost completely avascular tumors. VEGF-Trap-mediated blockade may be superior to that achieved by other agents, such as monoclonal antibodies targeted against the VEGF receptor.
Optimal control of unsteady compressible viscous flows (2002)

Abstract The control of complex, unsteady flows is a pacing technology for advances in fluid mechanics. Recently, optimal control theory has become popular as a means of predicting best case controls that can guide the design of practical flow control systems. However, most of the prior work in this area has focused on incompressible flow which precludes many of the important physical flow phenomena that must be controlled in practice including the coupling of fluid dynamics, acoustics, and heat transfer. This paper presents the formulation and numerical solution of a class of optimal boundary control problems governed by the unsteady two‐dimensional compressible Navier–Stokes equations. Fundamental issues including the choice of the control space and the associated regularization term in the objective function, as well as issues in the gradient computation via the adjoint equation method are discussed. Numerical results are presented for a model problem consisting of two counter‐rotating viscous vortices above an infinite wall which, due to the self‐induced velocity field, propagate downward and interact with the wall. The wall boundary control is the temporal and spatial distribution of wall‐normal velocity. Optimal controls for objective functions that target kinetic energy, heat transfer, and wall shear stress are presented along with the influence of control regularization for each case. Copyright © 2002 John Wiley &amp; Sons, Ltd.
Nuclease Stability of LNA Oligonucleotides and LNA-DNA Chimeras (2003)

The stabilizing properties of LNA and alpha-L-LNA oligonucleotides against endo- and 3'-exonucleases have been evaluated.
The genetic origins of neoplasia (1995)

The last 15 years have witnessed a conceptual breakthrough in our understanding of the molecular and genetic basis of the origins of neoplasia in humans. This happened methodically, experiment by experiment, with no one observation yielding the entire picture. Over time, a large number of observations slowly came together, and, for that reason, we often do not give enough credit to the science, or the scientists, for this remarkable achievement. Mutations in three broad categories of genes have been shown to contribute to the origins and progression of neoplasia in humans: the oncogenes, the tumor suppressor genes, and the mutator genes. Almost 100 different oncogenes have been identified in animals and humans and shown to contain mutations in a wide variety of tumors. Most of these oncogenes were discovered with the use of retro viruses that insert adjacent to an oncogene and activate it or capture the oncogene in a
Synthesis of well‐defined polychlorostyrenes by living radical polymerization with 4‐methoxy‐2,2,6,6‐tetramethylpiperidine‐1‐oxyl (1997)

Radical polymerization of 2-, 3-, and 4-chlorostyrenes (ClSts) was investigated with benzoyl peroxide (BPO) as an initiator, in the presence of 4-methoxy-2,2,6,6-tetramethylpiperidine-1-oxyl (MTEMPO). The polymerization was performed in bulk for 3.5 h at 95°C and then continued for a defined time at 125°C to give the corresponding poly(ClSt)s with narrow polydispersity in high yield. It was found that the polymerization proceeded in accordance with a living mechanism in all cases, because the molecular weight of the resulting polymers was proportional to the conversion, and inversely proportional to the initial concentration of MTEMPO. Furthermore, the polymers obtained from 2- and 3-ClSts quantitatively act as initiators for the polymerization in the living radical manner, of styrene to give the corresponding block copolymers, except for poly(4-ClSt). The thermal stability of the living poly(ClSt)s was found to decrease in the order of 2- > 3- > 4-ClSt on the basis of the results of their postpolymerizations. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 2371–2378, 1997
Developmental expression of perlecan during murine embryogenesis (1997)

Perlecan is a modular heparan sulfate proteoglycan that is an intrinsic constituent of all basement membranes and extracellular matrices. Because of its strategic position and unique structure, perlecan has been implicated in modulating the activity of various growth factors required for normal development and tissue homeostasis. To gain insights into the potential function of perlecan in vivo, we examined the spatiotemporal distribution of its mRNA and protein core during murine embryogenesis. We utilized a new affinity-purified antibody that recognizes specifically the protein core of perlecan together with an in situ RT-PCR approach to perform a systematic analysis of perlecan expression and deposition during murine ontogeny. Perlecan appeared early (E10.5) in tissues of vasculogenesis including heart, pericardium, and major blood vessels. Its early expression coincided with the development of the cardiovascular system. Subsequently (E11-13), the greatest deposition of perlecan occurred within the developing cartilage, especially the cartilage undergoing endochondral ossification, where it remained elevated throughout all the developmental stages, and up to adulthood. Interestingly, the mRNA levels of perlecan were always higher in all the vascularized tissues, principally within endothelial cells, while chondrocytes displayed relatively low mRNA levels. This suggests a higher biosynthesis and turnover rates in the blood vessels vis-à-vis those of cartilaginous and other mesenchymal tissues. During later stages of development (E13-17.5) perlecan mRNA levels progressively increased and its expression correlated with the onset of tissue differentiation of various parenchymal organs including the developing kidneys, lungs, liver, spleen, and gastrointestinal tract. The central nervous system showed no perlecan expression with the exception of the calvaria and choroid plexus. Collectively, the results indicate that perlecan may play crucial roles not only in vasculogenesis but also in the maturation and maintenance of differentiated tissues, including cartilage.
Vienna-Fortran/HPF extensions for sparse and irregular problems and their compilation (1997)

Vienna Fortran, High Performance Fortran (HPF), and other data parallel languages have been introduced to allow the programming of massively parallel distributed-memory machines (DMMP) at a relatively high level of abstraction, based on the SPMD paradigm. Their main features include directives to express the distribution of data and computations across the processors of a machine. In this paper, we use Vienna-Fortran as a general framework for dealing with sparse data structures. We describe new methods for the representation and distribution of such data on DMMPs, and propose simple language features that permit the user to characterize a matrix as "sparse" and specify the associated representation. Together with the data distribution for the matrix, this enables the complier and runtime system to translate sequential sparse code into explicitly parallel message-passing code. We develop new compilation and runtime techniques, which focus on achieving storage economy and reducing communication overhead in the target program. The overall result is a powerful mechanism for dealing efficiently with sparse matrices in data parallel languages and their compilers for DMMPs.
cDNA cloning and expression of bovine aspartyl (asparaginyl) beta-hydroxylase. (1992)

Aspartyl (asparaginyl) beta-hydroxylase which specifically hydroxylates 1 Asp or Asn residue in certain epidermal growth factor-like domains of a number of proteins, has been previously purified to apparent homogeneity from detergent-solubilized bovine liver microsomes (Wang, Q., VanDusen, W. J., Petroski, C. J., Garsky, V. M., Stern, A. M., and Friedman, P. A. (1991) J. Biol. Chem. 266, 14004-14010). Three oligonucleotides, corresponding to three amino acid sequences of the purified hydroxylase, were used to screen bovine cDNA libraries. Several overlapping positive cDNA clones containing a full length open reading frame of 754 amino acids encoding a 85-kDa protein were isolated, and a cDNA, containing the full length open reading frame, was constructed from two of these clones. The resulting clone was then transcribed and translated in vitro to produce recombinant protein which possessed Asp beta-hydroxylase activity. These results constitute proof that the protein purified from bovine liver is an Asp beta-hydroxylase. Comparisons of deduced amino acid sequences of two other alpha-ketoglutarate-dependent dioxygenases, prolyl-4-hydroxylase and lysyl hydroxylase, with that of Asp beta-hydroxylase showed no significant homologies. Indeed, Asp beta-hydroxylase appears to be unique as no striking homology was found with known protein sequences. Furthermore, structural predictions derived from the deduced amino acid sequence are in accord with earlier Stokes' radius and sedimentation coefficient determinations of the enzyme, suggesting that the enzyme contains a relatively compact carboxyl-terminal catalytic domain and an extended amino terminus. This amino-terminal region has a potential transmembrane type II signal-anchor domain that could direct the catalytic domain into the lumen of the endoplasmic reticulum.
176. Carbazoles, carbolines, and related compounds. Part III. Quinindoline derivatives (1948)

S. J. Holt and V. Petrow, J. Chem. Soc., 1948, 922 DOI: 10.1039/JR9480000922
The carbonic anhydrase II gene, a gene regulated by thyroid hormone and erythropoietin, is repressed by the v-erbA oncogene in erythrocytic cells. (1990)

The v-erbA oncogene encodes an altered form of the nuclear receptor of the thyroid hormone triiodothyronine (T3). This altered receptor is unable to bind T3, and blocks the differentiation of chicken erythrocyte progenitor cells. To identify the cellular target genes of v-ErbA in the transformed cells, we analysed the expression of several genes in normal erythrocytic cells exposed to T3, and found that the gene encoding carbonic anhydrase II is transcriptionally activated by the hormone. In contrast, this gene is repressed in erythroleukemic cells transformed by the v-erbA product. To investigate in more details the effects of v-ErbA, we constructed a mutant of v-ErbA in which we restored the ability to bind T3. This mutant developed its oncogenicity only in the absence of T3. Upon binding of T3, the transformed cells differentiated and immediately expressed the carbonic anhydrase II gene. These data show that v-ErbA directly inhibits the transcription of the carbonic anhydrase II gene, presumably by competing with normal T3 receptors. The carbonic anhydrase II gene is the first identified target gene of the v-ErbA oncoprotein in erythroleukemic cells.
Relative contributions of passive equilibrium and active transport to the distribution of chloride in mammalian cortical neurons (1988)

1. Active and passive factors affecting the chloride gradient of cortical neurons were assessed using intracellular recordings from neurons in slices of cingulate cortex maintained in vitro. The chloride equilibrium potential (ECl-) was estimated indirectly from the reversal potentials of responses to perisomatic gamma-aminobutyric acid (GABA) application and the Cl(-)-dependent inhibitory postsynaptic potential (IPSP). Under control conditions the mean resting potential (Vm; -69.7 mV) was not significantly different than the mean IPSP reversal potential (EIPSP; -70.1 mV). 2. Increasing the external potassium concentration ([K+]o) from 1 to 10 mM shifted the mean EIPSP from -80.4 to -61.8 mV. The mean EIPSP was approximately equal to the mean Vm at all [K+]oS. The conditions of Donnan equilibrium are not met in [K+]o less than 10 mM. 3. Polarization of Vm up to 20 mV away from EIPSP for 4 min with maintained current injection had no significant effect on EIPSP. 4. The GABA reversal potential was maintained 37-52 mV less negative than Vm after equilibration in saline in which the external chloride concentration had been reduced from 133 to 5 mM by substitution with isethionate. Vm and input resistance were not significantly different from control values in cells recorded under these conditions. 5. We conclude that Cl- is not passively distributed in cortical neurons, perhaps due to a low resting Cl- permeability. 6. Impalement with electrodes containing 2 M KCl resulted in a rapid 10 mV depolarizing shift in EIPSP that then remained relatively constant. Intracellular iontophoresis of Cl- resulted in a further depolarizing shift of EIPSP of 5-10 mV that returned to control in less than 1 min. The time course of recovery of IPSP amplitude could be fit with a single exponential having a mean time constant of 6.9 +/- 1.5 s and was independent of the amount of Cl- injected or stimulation frequency. 7. Reductions in temperature from 37 to 32 degrees C significantly increased the mean time constant of IPSP recovery from Cl- injection to 11.1 +/- 3.3 s, corresponding to Q10 = 2.6.(ABSTRACT TRUNCATED AT 400 WORDS)
Prosthetic joint infections: update in diagnosis and treatment (2005)

The pathogenesis of prosthetic joint infection is related to microorganisms growing in biofilms, rendering these infections difficult to diagnose and to eradicate. Low-grade infections in particular are difficult to distinguish from aseptic failure, often presenting only with early loosening and persisting pain, or no clinical signs of infection at all. A combination of preoperative and intraoperative tests is usually needed for an accurate diagnosis of infection of prosthetic joint infections. Successful treatment requires adequate surgical procedure combined with long-term antimicrobial therapy, ideally with an agent acting on adhering stationary- phase microorganisms. In this article, epidemiology, pathogenesis, diagnosis and treatment of prosthetic joint infections are reviewed.
Cytokinin oxidase: Biochemical features and physiological significance (1994)

The catabolism of cytokinin in plant tissues appears to be due, in large part, to the activity of a specific enzyme, cytokinin oxidase. This enzyme catalyses the oxidation of cytokinin substrates bearing unsaturated isoprenoid side chains, using molecular oxygen as the oxidant. In general, substrate specificity is highly conserved and cytokinin substrates bearing saturated or cyclic side chains do not serve as substrates for most cytokinin oxidases tested to date. Despite variation in molecular properties of the enzyme from a number of higher plants, oxygen is always required for the reaction. Cytokinin oxidases from several sources have been shown to be glycosylated. Cytokinin oxidase activity appears to be universally inhibited by cytokinin‐active urea derivatives. Auxin has been reported to act as an allosteric regulator which increases activity of the enzyme. Cytokinin oxidase activity is subject to tight regulation. Levels of the enzyme are controlled by a mechanism sensitive to cytokinin supply. The up‐regulation of cytokinin oxidase expression in response to exogenous application of cytokinin suggests that the metabolic fate of exogenously applied cytokinins may not accurately mimic that of the endogenous compounds. Cytokinin oxidase is believed to be a copper‐containing amine oxidase (EC 1.4.3.6). Considerable evidence strongly supports a common mechanism for amine oxidases. It is possible that advances in understanding of other amine oxidases could be extrapolated to increase our understanding of cytokinin oxidase at the molecular level. This is discussed with reference to what is currently known about the catalytic mechanism of the enzyme. The possibility of pyrroloquinoline quinone, or a closely related compound, as a redox cofactor of cytokinin oxidase is considered, as are the implications of the glycosylated nature of the enzyme for its regulation and compartmentalisation within the cell.
Cyclohexane Carboxylate and Benzoate Formation from Crotonate in Syntrophus aciditrophicus (2006)

ABSTRACT The anaerobic, syntrophic bacterium Syntrophus aciditrophicus grown in pure culture produced 1.4 ± 0.24 mol of acetate and 0.16 ± 0.02 mol of cyclohexane carboxylate per mole of crotonate metabolized. [U- 13 C]crotonate was metabolized to [1,2- 13 C]acetate and [1,2,3,4,5,7- 13 C]cyclohexane carboxylate. Cultures grown with unlabeled crotonate and [ 13 C]sodium bicarbonate formed [6- 13 C]cyclohexane carboxylate. Trimethylsilyl (TMS) derivatives of cyclohexane carboxylate, cyclohex-1-ene carboxylate, benzoate, pimelate, glutarate, 3-hydroxybutyrate, and acetoacetate were detected as intermediates by comparison of retention times and mass spectral profiles to authentic standards. With [U- 13 C]crotonate, the m/z -15 ion of TMS-derivatized glutarate, 3-hydroxybutyrate, and acetoacetate each increased by +4 mass units, and the m/z -15 ion of TMS-derivatized pimelate, cyclohex-1-ene carboxylate, benzoate, and cyclohexane carboxylate each increased by +6 mass units. With [ 13 C]sodium bicarbonate and unlabeled crotonate, the m/z -15 ion of TMS derivatives of glutarate, pimelate, cyclohex-1-ene carboxylate, benzoate, and cyclohexane carboxylate each increased by +1 mass unit, suggesting that carboxylation occurred after the synthesis of a four-carbon intermediate. With [1,2- 13 C]acetate and unlabeled crotonate, the m/z -15 ion of TMS-derivatized 3-hydroxybutyrate, acetoacetate, and glutarate each increased by +0, +2, and +4 mass units, respectively, and the m/z -15 ion of TMS-derivatized pimelate, cyclohex-1-ene carboxylate, benzoate, cyclohexane carboxylate, and 2-hydroxycyclohexane carboxylate each increased by +0, +2, +4, and +6 mass units. The data are consistent with a pathway for cyclohexane carboxylate formation involving the condensation of two-carbon units derived from crotonate degradation with CO 2 addition, rather than the use of the intact four-carbon skeleton of crotonate.
Analysis of the role of leukocyte function-associated antigen-1 in activation of human influenza virus-specific T cell clones. (1990)

The role of leukocyte function-associated Ag-1 (LFA-1) in intercellular adhesion is well documented. Previously, we demonstrated that the LFA-1 molecule (CD11a/CD18) can also regulate the induction of proliferation of peripheral blood T cells. In these studies, we observed opposite effects of antibodies against CD11a (LFA-1-alpha-chain) or CD18 (LFA-1-beta-chain). Here, we determined the effects of anti-CD11a and anti-CD18 mAb on proliferation of cloned influenza virus-specific T cells. Anti-CD18 mAb had similar inhibiting effects on the proliferative response of T cell clones induced by immobilized anti-CD3 mAb as it had on the response of peripheral blood T cells. In contrast to its costimulatory effect on resting peripheral blood T cells, anti-CD11a mAb did not increase the proliferation of cloned T cells. Similar differences in effects of anti-CD11a and anti-CD18 mAb were observed when proliferation of the T cell clones was induced by immobilized anti-TCR mAb. When proliferation was induced by influenza virus presented by monocytes as APC, both anti-CD11a and anti-CD18 mAb inhibited T cell proliferation. However, when EBV-transformed B cells were used as APC, neither anti-CD11a nor anti-CD18 mAb inhibited proliferation. These results demonstrate that the effects of antibodies against CD11a (LFA-1-alpha) or CD18 (LFA-1-beta) on T cell proliferation depend on 1) the stage of activation of the T cells, 2) the activation stimulus and its requirement for intercellular adhesion involving LFA-1, and 3) the type of cell used to present Ag.
Factor V Leiden Inhibits Fibrinolysis In Vivo (2004)

fV(Leiden) inhibits fibrinolysis in vivo, suggesting an additional pathway by which this mutation promotes thrombosis.
Dipole Localization for Identification of Neuronal Generators in Independent Neighboring Interictal EEG Spike Foci (2001)

We showed that dipoles in close proximity but with different orientations projected two negative maxima on scalp EEG in three patients with extratemporal localization-related epilepsy. Equivalent current dipole analysis of individual interictal spikes can provide useful information about the epileptogenic zone in these patients.
Dynamic properties of silica aerogels as deduced from specific-heat and thermal-conductivity measurements (1992)

The specific heat ${\mathit{C}}_{\mathit{p}}$ and the thermal conductivity \ensuremath{\lambda} of a series of base-catalyzed silica aerogels have been measured at temperatures between 0.05 and 20 K. The results confirm that the different length-scale regions observed in the aerogel structure are reflected in the dynamic behavior of these materials. The analysis of the ${\mathit{C}}_{\mathit{p}}$ and \ensuremath{\lambda} data reveals three different temperature regimes where the contributions of phonon, fracton, and particle modes can be separated and identified. In particular, we discuss the crossover behavior linking the phonon and the fracton regime and we consider the possibility of two spectral dimensions characterizing the fracton modes. Our data imply important differences between the physical mechanisms dominating the low-temperature behavior of aerogels and dense glasses, respectively. From our analysis we also conclude that the low-temperature properties of amorphous ${\mathrm{SiO}}_{2}$ are most likely not due to fractal behavior.
Pro‐apoptotic effect of endogenous H 2 S on human aorta smooth muscle cells (2006)

Cystathionine gamma-lyase (CSE) is a key enzyme in the trans-sulfuration pathway, which uses L-cysteine to produce hydrogen sulfide (H2S). The CSE/H2S system has been shown to play an important role in regulating cellular functions in different systems. In the present study, we overexpressed CSE in human aorta smooth muscle cells (HASMCs) using a recombinant defective adenovirus containing CSE gene (Ad-CSE). Infection of HASMCs with Ad-CSE resulted in a significant increase in the expression of CSE protein and H2S production. Ad-CSE transfection inhibited cell growth and stimulated apoptosis, as evidenced by cell viability assay, Hoechst 33258 staining, TUNEL, and caspase 3 activation. CSE-mediated apoptosis was associated with an increased ERK and p38 MAPK activation, up-regulation of p21(Cip/WAK-1), and down-regulation of cyclin D1 expression. After inhibiting endogenous background CSE gene expression, direct administration of H2S at 100 microM induced apoptosis of HASMCs. The other two endproducts of CSE-catalyzed enzymatic reaction, ammonium and pyruvate, failed to do so. These results demonstrate that overexpression of CSE stimulates SMC apoptosis due to an increased endogenous production of H2S. Adenovirus-mediated transfer of CSE gene may provide a novel therapeutic approach in treating vascular diseases linked to abnormal cellular proliferation and vascular remodeling.