gebhart/patrepeval huggingface dataset:
Beclin 1, an autophagy gene essential for early embryonic development, is a haploinsufficient tumor suppressor (2003)

The biochemical properties of beclin 1 suggest a role in two fundamentally important cell biological pathways: autophagy and apoptosis. We show here that beclin 1-/- mutant mice die early in embryogenesis and beclin 1+/- mutant mice suffer from a high incidence of spontaneous tumors. These tumors continue to express wild-type beclin 1 mRNA and protein, establishing that beclin 1 is a haploinsufficient tumor suppressor gene. Beclin 1-/- embryonic stem cells have a severely altered autophagic response, whereas their apoptotic response to serum withdrawal or UV light is normal. These results demonstrate that beclin 1 is a critical component of mammalian autophagy and establish a role for autophagy in tumor suppression. They both provide a biological explanation for recent evidence implicating beclin 1 in human cancer and suggest that mutations in other genes operating in this pathway may contribute to tumor formation through deregulation of autophagy.
A scalable control system for a superconducting adiabatic quantum optimization processor (2010)

We have designed, fabricated and operated a scalable system for applying independently programmable time-independent, and limited time-dependent flux biases to control superconducting devices in an integrated circuit. Here we report on the operation of a system designed to supply 64 flux biases to devices in a circuit designed to be a unit cell for a superconducting adiabatic quantum optimization system. The system requires six digital address lines, two power lines, and a handful of global analog lines.
Multispectral analysis of the temporal evolution of cerebral ischemia in the rat brain (2000)

A major difficulty in staging and predicting ischemic brain injury by magnetic resonance (MR) imaging is the time-varying nature of the MR parameters within the ischemic lesion. A new multispectral (MS) approach is described to characterize cerebral ischemia in a time-independent fashion. MS analysis of five MR parameters (mean diffusivity, diffusion anisotropy, T2, proton density, and perfusion) was employed to characterize the progression of ischemic lesion in the rat brain following 60 minutes of transient focal ischemia. k-Means (KM) and fuzzy c-means (FCM) classification methods were employed to define the acute and subacute ischemic lesion. KM produced an estimate of lesion volume that was highly correlated with postmortem infarct volume, independent of the age of the lesion. Overall classification rates for KM exceeded FCM at acute and subacute time points as follows: KM, 90.5%, 94.4%, and 95. 9%; FCM, 82.4%, 90.6%, and 82.6% (for 45 minutes, 180 minutes, and 24-120 hours post MCAO groups). MS analysis also offers a formal method of combining diffusion and perfusion parameters to provide an estimate of the ischemic penumbra (KM classification rate = 70.3%). J. Magn. Reson. Imaging 2000;12:842-858.
Pore formation associated with the tail-tip protein pb2 of bacteriophage T5. (1990)

Upon binding of bacteriophage T5 tails to purified FhuA receptor protein the tail-tip protein pb2 became extremely sensitive to trypsin and other proteases. However, when T5 tails were bound to FhuA integrated into liposomes, pb2 was found to retain some resistance to trypsin. Electron microscopic examination of tail-liposome complexes supported the idea that trypsin resistance of pb2 in such complexes was caused by insertion of the tail-tip into the liposomes. pb2 was isolated from tails by treatment with sodium dodecyl sulfate and was further purified by gel filtration using a fast protein liquid chromatography system. pb2 obtained with this procedure was most likely monomeric. It was extremely sensitive to trypsin. When reconstituted into black lipid bilayer membranes, it formed pores with an average single-channel conductance of 4.6 nanosiemens in 1 M KCl. Zero-current potential measurements showed only a very slight preference, if any, for cations over anions. The data are compatible with pb2 forming a large water-filled transmembrane channel. The functioning during infection of pb2 in cytoplasmic membrane depolarization and phage DNA uptake into the cell is discussed.
Relative Amino Acid Composition Signatures of Organisms and Environments (2013)

Our results suggest that relative amino acid composition can be used as a signature of an environment. In addition, we observed that the relative amino acid composition of organisms is not highly determined by environment, reinforcing previous studies that find GC content to be the major factor correlating to amino acid composition in living organisms.
Lactone; XIII.1Phasentransfer-Oxidation nach Grignardierung: Eine einfache Synthese γ,γ-disubstituierter γ-Butyrolactone aus γ-Butyrolacton (1987)

Lactones; XIII. Grignard Reaction Followed by Phase-Transfer Oxidation: A Convenient Synthesis of γ,γ-Disubstituted γ-Butyrolactones from γ-Butyrolactone Grignard Reaction of γ-butyrolactones, followed by oxidation of the resulting reaction mixture produces symmetrically γ,γ-dialkylared diarylated γ-butyrolactones. Phase transfer oxidation with potassium permanganate in benzene/water proves to be the best out of twelve examined oxidation methods. The synthesis is unsuccessful with sterically hindered or oxidizable Grignard reagents.
The Transcriptional Coactivator Cbp Interacts with β-Catenin to Activate Gene Expression (2000)

Beta-catenin plays a pivotal role in the transcriptional activation of Wnt-responsive genes by binding to TCF/LEF transcription factors. Although it has been suggested that the COOH-terminal region of beta-catenin functions as an activation domain, the mechanisms of activation remain unclear. To screen for potential transcriptional coactivators that bind to the COOH-terminal region of beta-catenin, we used a novel yeast two-hybrid system, the Ras recruitment system (RRS) that detects protein-protein interactions at the inner surface of the plasma membrane. Using this system, we isolated the CREB-binding protein (CBP). Armadillo (Arm) repeat 10 to the COOH terminus of beta-catenin is involved in binding to CBP, whereas beta-catenin interacts directly with the CREB-binding domain of CBP. Beta-catenin synergizes with CBP to stimulate the activity of a synthetic reporter in vivo. Conversely, beta-catenin-dependent transcriptional activation is repressed by E1A, an antagonist of CBP function, but not by an E1A mutant that does not bind to CBP. The activation of Wnt target genes such as siamois and Xnr3 in Xenopus embryos is also sensitive to E1A. These findings suggest that CBP provides a link between beta-catenin and the transcriptional machinery, and possibly mediates the oncogenic function of beta-catenin.
On the relationship between digital Hilbert transformers and certain low-pass filters (1975)

Designs of symmetric Hilbert transformers are shown to be easily derived from corresponding designs for symmetric half-band low-pass filters, and vice versa. The latter filter type is particularly useful for interpolation or smoothing in sample-rate alteration.
Sol−Gel Synthesis, Electrochemical Characterization, and Stability Testing of Ti0.7W0.3O2Nanoparticles for Catalyst Support Applications in Proton-Exchange Membrane Fuel Cells (2010)

The materials currently used in proton-exchange membrane fuel cells (PEMFCs) require complex control of operating conditions to make them sufficiently durable to permit commercial deployment. One of the major materials challenges to allow simplification of fuel cell operating strategies is the discovery of catalyst supports that are much more stable to oxidative decomposition than currently used carbon blacks. Here we report the synthesis and characterization of Ti(0.7)W(0.3)O2 nanoparticles (approximately 50 nm diameter), a promising doped metal oxide that is a candidate for such a durable catalyst support. The synthesized nanoparticles were platinized, characterized by electrochemical testing, and evaluated for stability under PEMFC and other oxidizing acidic conditions. Ti(0.7)W(0.3)O2 nanoparticles show no evidence of decomposition when heated in a Nafion solution for 3 weeks at 80 °C. In contrast, when heated in sulfuric, nitric, perchloric, or hydrochloric acid, the oxide reacts to form salts such as titanylsulfatehydrate from sulfuric acid. Electrochemical tests show that rates of hydrogen oxidation and oxygen reduction by platinum nanoparticles supported on Ti(0.7)W(0.3)O2 are comparable to those of commercial Pt on carbon black.
Expression Patterns and Promoter Activity of the Cold-Regulated Gene ci21A of Potato (1997)

Storage of potato (Solanum tuberosum) tubers at 4 degrees C is associated with the accumulation of several transcripts. DNA sequence analysis of cDNA clone CI21, which corresponds to one of the cold-induced transcripts, revealed high homology to transcripts of tomato (Lycopersicon esculentum) and wild potato (Solanum chacoense) induced by ripening and water stress. Two homologous, nonallelic genes, ci21A and ci21B, were isolated and sequenced. Northern blot analysis showed that CI21 transcripts were present at the highest levels in cold-stored tubers, at lower levels in stems and roots, and at the lowest levels in leaves and tubers stored at room temperature. Treatment with abscisic acid, heat, and a high concentration of salt had no marked effect on CI21 transcript levels in tubers and leaves. Drought was the only stress treatment that induced CI21 transcripts in leaves, but it did not do so in tubers. Western blot analysis detected CI21 protein only in tubers. Chimeric gene constructs between the putative ci21A promoter region and the uidA reporter gene were tested in transgenic potato plants for induction of beta-glucuronidase activity by low temperature. A 2-fold increase of beta-glucuronidase activity in response to tuber storage at 4 degrees C was observed for fragments between 380 and 2000 bp of the ci21A promoter region.
PIG-tailed membrane proteins. (1994)

Some membrane proteins are associated with the plasma membrane solely through a glycolipid moiety (GPI anchor). The GPI anchor is composed of a core structure of phosphatidylinositol attached to a glycan chain which, in turn, is attached to the C-terminus of the protein. The GPI-anchored protein can be released from the cell surface by the action of GPI-specific phospholipases C and D. In protozoa, GPI anchors represent the predominant mechanism for integrating cell-surface proteins into the lipid bilayer. Addition of a glycolipid anchor to a nascent protein requires a C-terminal hydrophobic signal sequence on the protein which is rapidly exchanged for a pre-assembled anchor. GPI anchors may have roles in protein targeting, cell signalling and in the uptake of small molecules (potocytosis). The human disease 'paroxysmal nocturnal haemoglobinuria' represents a defect in biosynthesis of the GPI anchor. Other lipid post-translational modifications of proteins are also recognized as important in regulating protein function (myristoylation, palmitoylation, prenylation).
Space-time block-coded OFDMA with linear precoding for multirate services (2002)

Relying on space-time linearly precoded orthogonal frequency-division multiple access (OFDMA) and exploiting both transmit and receive antenna diversity, we design herein multirate transceivers that guarantee deterministic symbol recovery with diversity gains regardless of the (possibly unknown) frequency-selective finite impulse response (FIR) channels and multiuser interference. Our approach is based on a three-level design of user codes: the top level (based on OFDMA) handles multiuser interference, the middle level (based on space-time block coding) results in space-time diversity gains, and the lower level (based on linear precoding) mitigates intersymbol interference (ISI). In a multiuser/multirate setting, with two transmit and a single receive antenna, our designs achieve guaranteed diversity gains, whereas the use of two receive antennas could potentially double the capacity of the system (in terms of maximum number of users or achievable transmission rates) under favorable conditions (such as no frequency offset). Simulations illustrate the merits of our approach.
Characterization of a microscale cyclical electrical field flow fractionation system (2006)

A microscale cyclical electrical field flow fractionation (CyElFFF) channel is characterized with regard to the effect of various operating parameters and comparison made to recent theoretical developments. Challenges associated with various operating conditions are reported along with some of the optimized operating parameters. The effect of retention wall choice, an offset voltage, relaxation steps, and flow rates, along with the basic operating parameters of voltage, frequency, and electrophoretic mobility are reported. Retention of polystyrene nanoparticle standards is accomplished and the first separations using this technique in a microscale system are also demonstrated. Relaxation steps and offset voltages are found to be effective in eliminating early peaks and in improving plate heights. Plate heights were also found to decrease with increasing flow rates, which is the opposite of the behavior seen in most existing chromatographic systems. The experimental results are compared to the analytical and empirical models of CyElFFF and found to be compatible. Suggestions are made for improving the separation and analysis methods used with CyElFFF.
Expression of PDGF, VEGF and their receptors in non-small cell lung tumor cell lines (1996)

Cell lines derived from non-small cell carcinomas of the lung (NSCLC) often express a variety of polypeptide growth factors able to activate receptors that encode tyrosine kinases. These receptors initiate numerous biological responses, including cell proliferation, and constitutive activation can result in cellular transformation. Consequently, it is possible that the aberrant growth properties of NSCLC cell lines is due at least in part to the action of mutated or perpetually activated receptor tyrosine kinases (RTK)s. As a first step in the process of testing this hypothesis we set out to examine the different RTKs expressed in NSCLC cell lines. A small group of NSCLC cell lines was screened for the expression of RTKs using a reverse transcriptase PCR approach with nested degenerate primers. We found four different RTKs expressed: the fibroblast growth factor receptor (FGFR) type III, the FGFR type IV, the platelet-derived growth factor beta receptor (beta PDGFR) and Flk-1/KDR, one of the receptors that binds vascular endothelial growth factor (VEGF). Since Flk-1/KDR and the beta PDGFR are not usually expressed in epithelial cells, we verified that they are expressed in NSCLC by Northern and Western blot analysis. To assess the incidence of expression of these RTKs in NSCLC cell lines a larger panel of cell lines was examined by Western blot analysis. The beta PDGFR was expressed in 30% (3/10) of the cell lines examined, while Flk-1/KDR was expressed in 10% (1/10). We also examined the expression of ligands for these RTKs. PDGF-A, PDGF-B and VEGF were expressed in 89%, 0% and 78%, respectively. While the high incidence of ligand expression made it likely that receptor and growth factor would be coexpressed, we found that in most instances this was not the case. Furthermore, in the cell lines in which the RTK and its ligand were coexpressed, we were unable to detect a functional autocrine loop. These studies indicate that while NSCLC cell lines aberrantly express various RTKs and growth factors, this does not always result in the establishment of an autocrine loop. These findings suggest that growth factors such as PDGF and VEGF act in a paracrine manner to contribute to the growth, survival and angiogenic program of a lung tumor.
A Comparative Study of Protocols for Mouse Embryonic Stem Cell Culturing (2013)

Most stem cell laboratories still rely on old culture methods to support the expansion and maintenance of mouse embryonic stem (ES) cells. These involve growing cells on mouse embryonic fibroblast feeder cells or on gelatin in media supplemented with fetal bovine serum and leukemia inhibitory factor (LIF). However, these techniques have several drawbacks including the need for feeder-cells and/or use of undefined media containing animal derived components. Culture of stem cells under undefined conditions can induce spontaneous differentiation and reduce reproducibility of experiments. In recent years several new ES cell culture protocols, using more well-defined conditions, have been published and we have compared the standard culture protocols with two of the newly described ones: 1) growing cells in semi-adherence in a medium containing two small molecule inhibitors (CHIR99021, PD0325901) and; 2) growing cells in a spheroid suspension culture in a defined medium containing LIF and bFGF. Two feeder-dependent mouse ES (mES) cell lines and two cell lines adapted to feeder-independent growth were used in the study. The overall aim has not only been to compare self-renewal and differentiation capacity, but also ease-of-use and cost efficiency. We show that mES cells when grown adherently proliferate much faster than when grown in suspension as free-floating spheres, independent of media used. Although all the tested culture protocols could maintain sustained pluripotency after prolonged culturing, our data confirm previous reports showing that the media containing two chemical inhibitors generate more pure stem cell cultures with negligible signs of spontaneous differentiation as compared to standard mES media. Furthermore, we show that this medium effectively rescues and cleans up cultures that have started to deteriorate, as well as allow for effective adaption of feeder-dependent mES cell lines to be maintained in feeder-free conditions.
Mechanical properties of aerogel-like thin films used for MEMS (2004)

We have investigated a novel material, thin-film aerogel, for use in microelectromechanical systems (MEMS) and determined its mechanical properties on the microscale. Fabrication processes, including photolithography and etching, have been developed to build the overhanging cantilevers and bridges used for the measurement. Young's modulus for the deposited aerogel material has been measured from the resonant frequencies of those microstructures. A nanoindentation test allows us to estimate not only Young's modulus but also the hardness of the thin-film aerogel deposited on a silicon wafer. These results show that the aerogel has unique properties in a MEMS not found with other materials.
Expression and characterization of glycoprotein gp35 of hepatitis C virus using recombinant vaccinia virus (1992)

Complementary DNA clones corresponding to one of the putative structural regions of the hepatitis C virus (HCV) genome were obtained from sera of non-A non-B hepatitis patients. The putative envelope gene was expressed by using a recombinant vaccinia virus carrying this region of the HCV genome. In cells infected with the recombinant vaccinia virus, a glycosylated protein with an M(r) of about 35K (gp35) was specifically detected by convalescent sera from hepatitis C patients. The sera from rabbits immunized with this recombinant vaccinia virus reacted to the gp35 produced in insect cells and also to gp35 which was translated in vitro in the glycosylated and processed form. The gp35 was used to detect antibodies in sera of only 7 to 23% of HCV patients at various stages of HCV disease. These results suggest that the gp35 of HCV may not have high antigenicity in humans.
Creation and X-ray Structure Analysis of the Tumor Necrosis Factor Receptor-1-selective Mutant of a Tumor Necrosis Factor-α Antagonist (2007)

Tumor necrosis factor-alpha (TNF) induces inflammatory response predominantly through the TNF receptor-1 (TNFR1). Thus, blocking the binding of TNF to TNFR1 is an important strategy for the treatment of many inflammatory diseases, such as hepatitis and rheumatoid arthritis. In this study, we identified a TNFR1-selective antagonistic mutant TNF from a phage library displaying structural human TNF variants in which each one of the six amino acid residues at the receptor-binding site (amino acids at positions 84-89) was replaced with other amino acids. Consequently, a TNFR1-selective antagonistic mutant TNF (R1antTNF), containing mutations A84S, V85T, S86T, Y87H, Q88N, and T89Q, was isolated from the library. The R1antTNF did not activate TNFR1-mediated responses, although its affinity for the TNFR1 was almost similar to that of the human wild-type TNF (wtTNF). Additionally, the R1antTNF neutralized the TNFR1-mediated bioactivity of wtTNF without influencing its TNFR2-mediated bioactivity and inhibited hepatic injury in an experimental hepatitis model. To understand the mechanism underlying the antagonistic activity of R1antTNF, we analyzed this mutant using the surface plasmon resonance spectroscopy and x-ray crystallography. Kinetic association/dissociation parameters of the R1antTNF were higher than those of the wtTNF, indicating very fast bond dissociation. Furthermore, x-ray crystallographic analysis of R1antTNF suggested that the mutation Y87H changed the binding mode from the hydrophobic to the electrostatic interaction, which may be one of the reasons why R1antTNF behaved as an antagonist. Our studies demonstrate the feasibility of generating TNF receptor subtype-specific antagonist by extensive substitution of amino acids of the wild-type ligand protein.
Gout: new insights into an old disease (2006)

Gout is an autoinflammatory disorder associated with deposition of monosodium urate (MSU) crystals in joints and periarticular tissues. Recent advances suggest that the innate immune system may drive the gouty inflammatory response to MSU. These findings prompt questions concerning how the innate immune system recognizes MSU and the identities of the receptors involved. In this issue of the JCI, Chen et al. show that the IL-1 receptor and its signaling protein myeloid differentiation primary response protein 88 (MyD88) but not the "classical" innate immune receptors, TLRs, are central for MSU-induced inflammation (see the related article beginning on page 2262).
Botulinum toxin-A therapy for palmar and plantar hyperhidrosis. (2002)

In an open study regarding focal hyperhidrosis, we injected 45-65 mouse units of botulinum toxin A (Btx-A) per palm and 100 per sole intracutaneously to 28 hands and 6 feet. We observed patients for up to 10 months to evaluate the efficacy and tolerability of Btx-A for palmar and plantar hyperhidrosis. The mean sweat production significantly declined for both palmar and plantar hyperhidrosis quantitatively on the first month of therapy (P < 0.01). One patient had transient muscle weakness and mild thenar atrophy interfering with her daily activities for 10 days. Injections were otherwise tolerated well by the patients. In this trial Btx-A injection is found to be an effective and safe method of treatment for palmar and plantar hyperhidrosis.