gebhart/patrepeval huggingface dataset:
Vascular Endothelial Growth Factor (VEGF) and Its Receptor (VEGFR) Signaling in Angiogenesis: A Crucial Target for Anti- and Pro-Angiogenic Therapies (2011)

The vascular endothelial growth factor (VEGF) and its receptor (VEGFR) have been shown to play major roles not only in physiological but also in most pathological angiogenesis, such as cancer. VEGF belongs to the PDGF supergene family characterized by 8 conserved cysteines and functions as a homodimer structure. VEGF-A regulates angiogenesis and vascular permeability by activating 2 receptors, VEGFR-1 (Flt-1) and VEGFR-2 (KDR/Flk1 in mice). On the other hand, VEGF-C/VEGF-D and their receptor, VEGFR-3 (Flt-4), mainly regulate lymphangiogenesis. The VEGF family includes other interesting variants, one of which is the virally encoded VEGF-E and another is specifically expressed in the venom of the habu snake (Trimeresurus flavoviridis). VEGFRs are distantly related to the PDGFR family; however, they are unique with respect to their structure and signaling system. Unlike members of the PDGFR family that strongly stimulate the PI3K-Akt pathway toward cell proliferation, VEGFR-2, the major signal transducer for angiogenesis, preferentially utilizes the PLCγ-PKC-MAPK pathway for signaling. The VEGF-VEGFR system is an important target for anti-angiogenic therapy in cancer and is also an attractive system for pro-angiogenic therapy in the treatment of neuronal degeneration and ischemic diseases.
Human cystathionine β-synthase cDNA: sequence, alternative splicing and expression in cultured cells (1993)

Cystathionine beta-synthase (CBS) deficiency is the major cause of homocystinuria in humans. The most frequent symptoms of homocystinuria include: dislocated optic lenses, vascular disorders, skeletal abnormalities and mental retardation. Patients with this deficiency have elevated levels of homocyst(e)ine, methionine and low cysteine in their body fluids. These abnormal levels often partially or fully normalize upon treatment with pharmacological doses of vitamin B6. To investigate the molecular and biochemical basis for these conditions, it was necessary to determine the nucleotide and polypeptide sequence of CBS. We report here the human CBS cDNA sequence of 2,554 nucleotides encoding the CBS subunit of 551 amino acids. An intron of 214 bp appears to be retained in the 3'-untranslated region of most of the fibroblast and liver mRNA. We also report a frequent Mspl polymorphism in the 3'-untranslated sequence and two synonymous mutations in the coding region: 699C/T (Y233Y) and 1080C/T (A360A). The amino acid sequence similarity of human and rat CBS is greater than 90%; the enzyme also exhibits 52% similarity to O-acetylserine(thiol)-lyase from bacteria and plants. Lastly, we demonstrate that expression of the human enzyme in CHO cells yields enzymatically active protein of the expected size with a half-life of approximately 14 hrs.
Augmentation of HIV-1-specific T helper cell responses in chronic HIV-1 infection by therapeutic immunization (2003)

HIV-1-specific T helper cell responses can be successfully increased by therapeutic immunization in individuals with chronic infection on suppressive ART. Further studies will be needed to determine whether the augmentation of these responses correlate with long-term clinical benefits.
Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA (2009)

DNA sequences determined from ancient organisms have high error rates, primarily due to uracil bases created by cytosine deamination. We use synthetic oligonucleotides, as well as DNA extracted from mammoth and Neandertal remains, to show that treatment with uracil-DNA-glycosylase and endonuclease VIII removes uracil residues from ancient DNA and repairs most of the resulting abasic sites, leaving undamaged parts of the DNA fragments intact. Neandertal DNA sequences determined with this protocol have greatly increased accuracy. In addition, our results demonstrate that Neandertal DNA retains in vivo patterns of CpG methylation, potentially allowing future studies of gene inactivation and imprinting in ancient organisms.
Mutational analysis of nucleoside diphosphate kinase from Pseudomonas aeruginosa: characterization of critical amino acid residues involved in exopolysaccharide alginate synthesis (1996)

We report the utilization of site-directed and random mutagenesis procedures in the gene encoding nucleoside diphosphate kinase (ndk) from Pseudomonas aeruginosa in order to examine the role of Ndk in the production of alginate by this organism. Cellular levels of the 16-kDa form of the Ndk enzyme are greatly reduced in P. aeruginosa 8830 with a knockout mutation in the algR2 gene (8830R2::Cm); this strain is also defective in the production of the exopolysaccharide alginate. In this study, we isolated four mutations in ndk (Ala-14-->Pro [Ala14Pro], Gly21Val, His117Gln, and Ala125Arg) which resulted in the loss of Ndk biochemical activity; hyperexpression of any of these four mutant genes did not restore alginate production to 8830R2::Cm. We identified six additional amino acid residues (Ser-43, Ala-56, Ser-69, Glu-80, Gly-91, and Asp-135) whose alteration resulted in the inability of Ndk to complement alginate production. After hyperproduction in 8830R2::Cm, it was determined that each of these six mutant Ndks was biochemically active. However, in four cases, the in vivo levels of Ndk were reduced, which consequently affected the growth of 8830R2::Cm in the presence of Tween 20. Two mutant Ndk proteins which could not complement the alginate synthesis defect in 8830R2::Cm were not affected in any characteristic examined in the present study. All of the mutant Ndks characterized which were still biochemically active formed membrane complexes with Pk, resulting in GTP synthesis. Two of the four Ndk activity mutants (His117Gln and Ala125Arg) identified were capable of being truncated to 12 kDa and formed a membrane complex with Pk; however, the complexes formed were inactive for GTP synthesis. The other two Ndk activity mutants could be truncated to 12 kDa but were not detected in membrane fractions. These results further our understanding of the role of Ndk in alginate synthesis and identify amino acid residues in Ndk which have not previously been studied as critical to this process.
Liver failure induces a systemic inflammatory response. Prevention by recombinant N-terminal bactericidal/permeability-increasing protein. (1995)

The observed increased susceptibility of patients with fulminant hepatic failure for local and systemic infections has been hypothesized to be due to a failure for the hepatic clearance function and subsequent leaking of endogenous endotoxins into the systemic circulation. However, experimental evidence for such a systemic inflammation during liver failure due to endogenous endotoxemia is lacking. Therefore, we designed a study to clarify whether circulating endotoxins due to liver failure could lead to the development of systemic inflammations. In a rat model for liver failure induced by a two-thirds partial hepatectomy, we evaluated the course of circulating tumor necrosis factor and interleukin-6, changes in blood chemistry and hemodynamics, and histopathological changes in the lungs. Partially hepatectomized animals, but not sham-operated animals, demonstrated cardiac failure, increased levels of creatinin and urea, metabolic acidosis, high plasma levels of tumor necrosis factor and interleukin-6, and an influx of PMNs in the lungs-together indicating the development of a systemic inflammatory response. Continuous infusion of recombinant N-terminal bactericidal/permeability-increasing protein (rBPI23), a well described endotoxin-neutralizing protein, prevented these inflammatory reactions. Ex vivo experiments with rat plasma samples confirmed the presence of circulating endotoxins in partially hepatectomized rats as opposed to those treated with rBPI23. Thus, our results indicate that the early phase of liver failure induces a systemic inflammatory response triggered by circulating endotoxins, which can be prevented by perioperative infusion of rBPI23.
Erratum: “GaN evaporation in molecular beam epitaxy environment” [Appl. Phys. Lett. 74, 1854 (1999)] (1999)

First Page
Novel Photochemical Rearrangement of Styrylfurans (1999)

A conrotatory photocyclization, a novel [1,9] hydrogen shift, and a lateral ring opening are involved in the rearrangement of a series of 2-(4-alkylstyryl)furans 1 to 5-(3-alkylbutadienyl)benzo[b]furans 2 in dichloromethane. These novel photochemical rearrangements occur with good yields of isolated products.
Synthesis Based on Affinity Separation (SAS): Separation of Products Having Barbituric Acid Tag from Untagged Compounds by Using Hydrogen Bond Interaction (2001)

A new method is described for affinity purification of synthetic compounds based on molecular recognition between bis(2,6-diaminopyridine)amide of isophthalic acid and a barbituric acid derivative. The desired compounds possessing the barbituric acid derivative as a tag were readily isolated from the reaction mixture by the following procedure. After each reaction cycle, the reaction mixture was applied to the polystyrene column possessing bis(2,6-diaminopyridine)amide of isophthalic acid as an artificial receptor. The compound possessing the barbituric acid tag was selectively adsorbed on the column, whereas other impurities without the tag such as excess reagents and byproducts were washed off. Subsequent desorption with CH2Cl2-MeOH (1 : 1) afforded the desired compound with high purity. This new strategy was applied to the synthesis of a heterocycle, peptides, and oligosaccharides.
Infiltration-processed, functionally graded materials for microceramic componenets (2010)

A three-dimensional micro ceramic functionally graded material (FGM) has been fabricated by an infiltration process. The proposed technique offers an effective way to tailor the composition and microstructure of ceramic micro components. The process involves soft lithography, colloidal powder processing and the infiltration of yttria stabilized zirconia with a pre-ceramic polymer solution. Analyses by SEM, BSE and EDS have revealed the existence of concentration gradients, the Si and C content decreasing with increasing of the sample depth. The resultant micro part has a homogeneous core encased with a graded and layer of YSZ / SiC.
Graph-based analysis of nonreciprocity in coupled-mode systems (2015)

In this work we derive the general conditions for obtaining nonreciprocity in multi-mode parametrically-coupled systems. The results can be applied to a broad variety of optical, microwave, and hybrid systems including recent electro- and opto-mechanical devices. In deriving these results, we use a graph-based methodology to derive the scattering matrix. This approach naturally expresses the terms in the scattering coefficients as separate graphs corresponding to distinct coupling paths between modes such that it is evident that nonreciprocity arises as a consequence of multi-path interference and dissipation in key ancillary modes. These concepts facilitate the construction of new devices in which several other characteristics might also be simultaneously optimized. As an example, we synthesize a novel three-mode unilateral amplifier design by use of graphs. Finally, we analyze the isolation generated in a common parametric multi-mode system, the DC-SQUID.
Combined (Thalamotomy and Stimulation) Stereotactic Surgery of the VIM Thalamic Nucleus for Bilateral Parkinson Disease (1987)

Stereotactic thalamotomy of the thalamic nucleus ventralis intermedius (VIM) is routinely used for movement disorders. During this procedure, it has been observed that high-frequency (100 Hz) stimulation of VIM was able to stop the extrapyramidal tremor. In patients with bilateral tremor of extrapyramidal origin, who were resistant to drug therapy, the therapeutic protocol associated (1) a radiofrequency VIM thalamotomy for the most disabled side, and (2) a continuous VIM stimulation for the other side using stereotactically implanted electrodes, connected to subcutaneous stimulators. VIM thalamotomy relieved the tremor in all operated cases. Side effects were mild and regressive. VIM stimulation strongly decreased the tremor but failed to suppress it as completely as thalamotomy did. This was due in part to the fact that programmable stimulator frequency rate is limited to 130 Hz, while it appeared that the optimal stimulation frequency was 200 Hz. This therapeutic protocol appears to be of interest for patients with bilateral extrapyramidal movement disorders.
<title>Marble cutting with cw CO<formula><inf><roman>2</roman></inf></formula> laser</title> (1995)

In this paper we present results of marble cutting with high power CO2 laser. The dependence of various parameters such as thickness of marble, laser power, cutting speed, assist gas and its pressure on cutting process was studied. Structural properties of marble like crystal size have been found to affect the cut quality. The average severance energy (P/vt, P = laser power, v = cutting speed, t = thickness) for marble was approximately found to be 9.0 J/mm2. This agrees very closely with the calculated value based on energy balance.
A Peripheral Site of Action for the Attenuation of Baroreflex-Mediated Bradycardia by Intravenous μ-Opioid Agonists (2000)

We previously reported that i.v. DAMGO (Tyr-D-Ala-Gly-NMePhe-Gly-ol), a selective mu-opioid agonist, causes an increase in blood pressure with no change in heart rate in unanesthetized sheep and subsequently demonstrated that DAMGO attenuates baroreflex-mediated bradycardia. To determine the site and mechanism by which mu-agonists inhibit baroreflex sensitivity, we have carried out further investigations by using DAMGO and another mu-agonist, DALDA (Tyr-D-Arg-Phe-Lys-NH2). The bradycardic response to norepinephrine (NE) was significantly blunted after i.v. DAMGO or DALDA in both nonpregnant and pregnant sheep. In contrast, the tachycardic response to sodium nitroprusside (SNP) remained unchanged in the presence of DAMGO or DALDA. In view of the highly restricted distribution of DALDA across the blood-brain barrier (BBB), we hypothesized that the blunting of reflex-mediated bradycardia by mu-opioid agonists can occur peripherally. Pretreatment with the quaternary opioid antagonist, naloxone methiodide (NM), completely blocked the attenuation of baroreflex sensitivity by DAMGO and DALDA in both nonpregnant and pregnant animals. These data suggest that in addition to central mechanisms, mu-opioid agonists can inhibit baroreflex sensitivity at a peripheral site, most likely by inhibiting vagal influence on heart-rate control rather than by acting directly at baroreceptors.
The pH-dependent bilayer destabilization by an amphipathic peptide (1987)

A 30-residue amphipathic peptide was designed to interact with uncharged bilayers in a pH-dependent fashion. This was achieved by a pH-induced random coil-alpha-helical transition, exposing a hydrophobic face in the peptide. The repeat unit of the peptide, glutamic acid-alanine-leucine-alanine (GALA), positioned glutamic acid residues on the same face of the helix, and at pH 7.5, charge repulsion between aligned Glu destabilized the helix. A tryptophan was included at the N-terminal as a fluorescence probe. The rate and extent of peptide-induced leakage of contents from large, unilamellar vesicles composed of egg phosphatidylcholine were dependent on pH. At pH 5.0 with a lipid/peptide mole ratio of 500/1, 100% leakage of vesicle contents occurred within 1 min. However, no leakage of vesicle contents occurred at pH 7.5. Circular dichroism measurements indicated that the molar ellipticity at 222 nm changed from about -4000 deg cm2 dmol-1 at pH 7.6 to -11,500 deg cm2 dmol-1 at pH 5.1, indicating a substantial increase in helical content as the pH was reduced. Changes in molar ellipticity were most significant over the same pH range where a maximum change in the extent and rate of leakage occurred. The tryptophan fluorescence emission spectra and the circular dichroism spectra of the peptide, in the presence of lipid, suggest that GALA did not associate with the bilayer at neutral pH. A change in the circular dichroism spectrum and a blue shift of the maximum of the tryptophan fluorescence emission spectra at pH 5.0, in the presence of lipid, indicated an association of GALA with the bilayer.(ABSTRACT TRUNCATED AT 250 WORDS)
wingless signal and Zeste-white 3 kinase trigger opposing changes in the intracellular distribution of Armadillo (1994)

wingless/wnt-1 signaling directs cell fate during development. Genetic analysis in Drosophila identified genes that may encode components of the wingless signal transduction system. Drosophila Armadillo, homolog of vertebrate beta-catenin, is required for wingless signaling. Unlike armadillo RNA, Armadillo protein accumulates non-uniformly in different cells of each embryonic segment. We found that cells alter their intracellular distribution of Armadillo in response to Wingless signal, accumulating increased levels of cytoplasmic Armadillo relative to those of membrane-associated protein. Levels of cytoplasmic Armadillo are also regulated by Zeste-White 3 kinase. Analysis of double mutants demonstrates that Armadillo's role in wingless signaling is direct, and that Armadillo functions downstream of both wingless and zeste-white 3. We present a model for the role of Armadillo stripes in transduction of wingless signal.
European Hematology Association - 20th Annual Congress (June 11-14,2015 - Vienna, Austria) (2015)

The Annual Congress of the European Hematology Association, now in its 20th year, brought together specialists in all areas of hematology research to present new data on ongoing research and share innovative ideas to aid in the treatment and diagnosis of many hematological diseases. Clinical and translational research was presented along with technological advancement in diagnostics and risk-assessment strategies. The congress afforded attendees time for networking with representatives from many disciplines associated with hematological research, including academia, industry and patient advocacy groups. This report will cover the most interesting presentations relating to therapeutics for a range of hematological conditions.
An Ankle-Foot Orthosis Powered by Artificial Pneumatic Muscles (2005)

We developed a pneumatically powered orthosis for the human ankle joint. The orthosis consisted of a carbon fiber shell, hinge joint, and two artificial pneumatic muscles. One artificial pneumatic muscle provided plantar flexion torque and the second one provided dorsiflexion torque. Computer software adjusted air pressure in each artificial muscle independently so that artificial muscle force was proportional to rectified low-pass-filtered electromyography (EMG) amplitude (i.e., proportional myoelectric control). Tibialis anterior EMG activated the artificial dorsiflexor and soleus EMG activated the artificial plantar flexor. We collected joint kinematic and artificial muscle force data as one healthy participant walked on a treadmill with the orthosis. Peak plantar flexor torque provided by the orthosis was 70 Nm, and peak dorsiflexor torque provided by the orthosis was 38 Nm. The orthosis could be useful for basic science studies on human locomotion or possibly for gait rehabilitation after neurological injury.
Prolonged and effective blockade of tumor necrosis factor activity through adenovirus-mediated gene transfer. (1994)

A chimeric protein capable of binding and neutralizing tumor necrosis factor (TNF) and lymphotoxin was expressed in mice transduced with a replication-incompetent adenoviral vector into which a TNF inhibitor gene had been engineered. Within 3 days following the injection of 10(9) infectious particles, the TNF inhibitor concentration exceeded 1 mg/ml of plasma; this level of expression was maintained for at least 4 weeks, and detectable TNF inhibitory activity was measured 6 weeks after injection of the recombinant virus. Introduction of the artificial gene produced a phenotypic effect comparable to homozygous deletion of the 55-kDa TNF receptor, in that animals were rendered highly susceptible to infection by Listeria monocytogenes, whereas control animals receiving a replication-incompetent virus coding for beta-galactosidase were capable of resisting Listeria challenge. Adenovirus-mediated transfer of a gene encoding a TNF inhibitor offers a practical means of imposing effective, long-term blockade of TNF activity in vivo for investigational and therapeutic purposes.
Characterization of a bacterial tyrosine ammonia lyase, a biosynthetic enzyme for the photoactive yellow protein (2002)

During genome sequence analysis of Rhodobacter capsulatus, nearby open reading frames were found that encode a photoactive yellow protein (PYP) and a hypothetical biosynthetic enzyme for its chromophore, a tyrosine ammonia lyase (TAL). We isolated the TAL gene, overproduced the recombinant protein in Escherichia coli, and after purification analyzed the enzyme for its activity. The catalytic efficiency for tyrosine was shown to be approximately 150 times larger than for phenylalanine, suggesting that the enzyme could in fact be involved in biosynthesis of the PYP chromophore. To our knowledge it is the first time this type of enzyme has been found in bacteria.
On the Nature of the "Copper Effect" in the Stille Cross-Coupling (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOn the Nature of the "Copper Effect" in the Stille Cross-CouplingVittorio Farina, Suresh Kapadia, Bala Krishnan, Chenjie Wang, and Lanny S. LiebeskindCite this: J. Org. Chem. 1994, 59, 20, 5905–5911Publication Date (Print):October 1, 1994Publication History Published online1 May 2002Published inissue 1 October 1994https://pubs.acs.org/doi/10.1021/jo00099a018https://doi.org/10.1021/jo00099a018research-articleACS PublicationsRequest reuse permissionsArticle Views5732Altmetric-Citations464LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
In situ characterization of qubit control lines: a qubit as a vector network analyzer (2017)

We present a technique to measure the transfer function of a control line using a qubit as a vector network analyzer. Our method requires coupling the line under test to the the longitudinal component of the Hamiltonian of the qubit and the ability to induce Rabi oscillations through simultaneous driving of the transversal component. We used this technique to characterize the 'flux' control of a superconducting Transmon qubit in the range of 8 to 400\,MHz. Our method can be used for the qubit 'flux' line calibration to increase the fidelity of entangling gates for the quantum processor. The qubit can be also used as a microscopic probe of the electro-magnetic fields on a chip.