gebhart/patrepeval huggingface dataset:
The Human Gene of a Protein That Modifies Na <sup>+</sup> - <scp>d</scp> -Glucose Co-Transport (1996)

Recently, a cDNA (pRS1) was cloned from pig kidney cortex that encodes a membrane-associated protein involved in Na(+)-coupled sugar transport. pRS1 alters sugar transport by SGLT1 from rabbit intestine or by SMIT from dog kidney which is homologous to SGLT1. In contrast, pRS1 does not influence transporters from other genetic families. We report the cloning of the intronless human gene hRS1 (6,743 bp), which encodes a 617-amino-acid protein with 74% amino acid identity to pRS1. By fluorescence in situ hybridization, hRS1 was localized to chromosome 1p36.1. The localization to one chromosome and Southern blot analysis of restricted genomic DNA suggest that there is only one RS1-homologous gene in humans. Functionality of hRS1 was demonstrated by co-expression experiments of hRS1 and SGLT1 from human intestine in oocytes from Xenopus laevis. They show that hRS1-protein inhibits Na(+)-D-glucose co-transport expressed by human SGLT1 by decreasing both the Vmax and the apparent Km value of the transporter. The analysis of the 5'-noncoding sequence of hRS1 revealed different enhancer consensus sequences that are absent in the SGLT1 gene, e.g., several consensus sequences for steroid-binding proteins.
FPGA acceleration of the pair-HMMs forward algorithm for DNA sequence analysis (2015)

Many DNA sequence analysis tools have been developed to turn the massive raw DNA sequencing data generated by NGS (Next Generation Sequencing) platforms into biologically meaningful information. The pair-HMMs forward algorithm is widely used to calculate the overall alignment probability needed by a number of DNA analysis tools. In this paper, we propose a novel systolic array design to accelerate the pair-HMMs forward algorithm on FPGAs. A number of architectural features have been implemented to improve the performance of the design, such as early exit points to increase the utilization of the array for small sequence sizes, as well as on-chip buffering to enable the processing of long sequences effectively. We present an implementation of the design on the Convey supercomputing platform. Experimental results show that the FPGA implementation of the pair-HMMs forward algorithm is up to 67x faster, compared to software-only execution.
Supercritical phase fischer‐tropsch synthesis: Catalyst pore‐size effect (1992)

Abstract The Fischer‐Tropsch synthesis reaction was conducted in a supercritical fluid medium using a fixed‐bed reactor. Tailor‐made catalyst supports which had sharp pore diameter distributions were prepared by the p H swing method. The relationships between the catalyst pore structure and the catalytic activity or the product distribution were studied. The influence of the catalyst pore size on the mass transfer of reactants and products was also characterized. The catalyst pore size affected not only catalytic activity but also product selectivity. The diffusion of reactants inside the catalyst pellets in the supercritical fluid media was simulated and the effects of catalyst pore size and catalyst particle size on catalytic performances were consistent with simulation results.
Preparation of polyacetylenes bearing an amino group and their application to chirality assignment of carboxylic acids by circular dichroism (1997)

Five phenylacetylenes bearing an amino group such as 4-amino (1), 3-amino (2), 4-N,N-dimethylamino (3), 4-aminomethyl (4), and 4-N,N-diisopropylamino-methyl (5) group on the phenyl group, 4-pyridylacetylene (6), and 2-pyridylacetylene (7) were synthesized and polymerized with [Rh(nbd)Cl]2 (nbd: norbornadiene). Monomer 5 showed the highest polymerizability and afforded quantitatively a fibrous polymer, whereas the other monomers showed lower reactivity and the resulting polymers were powdery. Although most polymers were not soluble in common organic solvents such as tetrahydrofuran (THF), chloroform, acetonitrile, and dimethyl sulfoxide, some polymers were soluble in the presence of carboxylic acids. Among the polyphenylacetylene derivatives, only poly-5 having a stable, highly cis-transoidal stereoregular structure exhibited an induced circular dichroism (ICD) in the UV-visible region, probably due to a prevailing one-handed helical conformation upon complexation with optically active carboxylic and α-hydroxy acids such as mandelic acid, lactic acid, and 2-phenylbutyric acid in THF, the sign of which reflected the absolute configuration of the acids. Therefore, poly-5 can be used as a novel probe for determining the chirality of acids. The α-hydroxy acids of the same configuration gave the same sign in induced Cotton effect in THF. However, carboxylic acids used in the present study showed the opposite signs to those of the α-hydroxy acids when their absolute configurations were same. The magnitude of the ICDs seems to depend on the bulkiness of the α-hydroxy acids. On the contrary, other poly(phenylacetylenes) bearing an amino group and poly(pyridylacetylenes) did not show any ICD in the presence of optically active acids, probably because of either low basicity for the acid-base complexation or low stereoregularity of the polymers. Chirality 9:593–600, 1997. © 1997 Wiley-Liss, Inc.
A coordinated phosphorylation by Lats and CK1 regulates YAP stability through SCF<sup>β-TRCP</sup> (2010)

The Yes-associated protein (YAP) transcription coactivator is a key regulator of organ size and a candidate human oncogene. YAP is inhibited by the Hippo pathway kinase cascade, at least in part via phosphorylation of Ser 127, which results in YAP 14-3-3 binding and cytoplasmic retention. Here we report that YAP is phosphorylated by Lats on all of the five consensus HXRXXS motifs. Phosphorylation of Ser 381 in one of them primes YAP for subsequent phosphorylation by CK1delta/epsilon in a phosphodegron. The phosphorylated phosphodegron then recruits the SCF(beta-TRCP) E3 ubiquitin ligase, which catalyzes YAP ubiquitination, ultimately leading to YAP degradation. The phosphodegron-mediated degradation and the Ser 127 phosphorylation-dependent translocation coordinately suppress YAP oncogenic activity. Our study identified CK1delta/epsilon as new regulators of YAP and uncovered an intricate mechanism of YAP regulation by the Hippo pathway via both S127 phosphorylation-mediated spatial regulation (nuclear-cytoplasmic shuttling) and the phosphodegron-mediated temporal regulation (degradation).
Design, Synthesis, Biological Evaluation, and Structure–Activity Relationships of Substituted Phenyl 4-(2-Oxoimidazolidin-1-yl)benzenesulfonates as New Tubulin Inhibitors Mimicking Combretastatin A-4 (2011)

Sixty-one phenyl 4-(2-oxoimidazolidin-1-yl)benzenesulfonates (PIB-SOs) and 13 of their tetrahydro-2-oxopyrimidin-1(2H)-yl analogues (PPB-SOs) were prepared and biologically evaluated. The antiproliferative activities of PIB-SOs on 16 cancer cell lines are in the nanomolar range and unaffected in cancer cells resistant to colchicine, paclitaxel, and vinblastine or overexpressing the P-glycoprotein. None of the PPB-SOs exhibit significant antiproliferative activity. PIB-SOs block the cell cycle progression in the G(2)/M phase and bind to the colchicine-binding site on β-tubulin leading to cytoskeleton disruption and cell death. Chick chorioallantoic membrane tumor assays show that compounds 36, 44, and 45 efficiently block angiogenesis and tumor growth at least at similar levels as combretastatin A-4 (CA-4) and exhibit low to very low toxicity on the chick embryos. PIB-SOs were subjected to CoMFA and CoMSIA analyses to establish quantitative structure-activity relationships.
Outflow facility studies in the perfused bovine aqueous outflow pathways (1988)

We have recently developed a technique for constant pressure perfusion of the aqueous outflow pathway of the eye. Our preliminary studies, conducted in the calf eye, show surprisingly that the manipulations necessary for preparing the outflow pathways and attached corneoscleral shell for perfusion do not greatly disrupt normal aqueous outflow physiology and anatomy according to the following criteria: 1. facility of outflow is similar before and during outflow pathway perfusion 2. as in the intact eye, facility of outflow decreases with increased IOP 3. removal of outflow resistance tissue greatly increases facility of outflow 4. morphology of outflow tissues remains normal Use of the perfused outflow pathway model may enable the creation of valuable in vitro preparations which may provide much needed information about the pathogenesis of primary open-angle glaucoma.
A low-noise low-voltage CT ΔΣ modulator with digital compensation of excess loop delay (2005)

The implementation of a 3/sup rd/-order 50MS/s CT /spl Delta//spl Sigma/ modulator with 5 levels of quantization, for a CDMA2k receiver, is presented. Its 9nVrms//spl radic/Hz input referred noise produces 80dB of DR in a 600kHz BW for signals as low as 70mVrms. It draws 4mA from a single 1.5V supply, uses a 90nm CMOS process and occupies 0.25mm/sup 2/.
Crystal Structure of<i>Tritrichomonas foetus</i>Inosine-5‘-monophosphate Dehydrogenase and the Enzyme−Product Complex (1997)

Inosine-5'-monophosphate dehydrogenase (IMPDH) is an attractive drug target for the control of parasitic infections. The enzyme catalyzes the oxidation of inosine monophosphate (IMP) to xanthosine monophosphate (XMP), the committed step in de novo guanosine monophosphate (GMP) biosynthesis. We have determined the crystal structures of IMPDH from the protozoan parasite Tritrichomonas foetus in the apo form at 2.3 A resolution and the enzyme-XMP complex at 2.6 A resolution. Each monomer of this tetrameric enzyme is comprised of two domains, the largest of which includes an eight-stranded parallel beta/alpha-barrel that contains the enzyme active site at the C termini of the barrel beta-strands. A second domain, comprised of residues 102-220, is disordered in the crystal. IMPDH is expected to be active as a tetramer, since the active site cavity is formed by strands from adjacent subunits. An intrasubunit disulfide bond, seen in the crystal structure, may stabilize the protein in a less active form, as high concentrations of reducing agent have been shown to increase enzyme activity. Disorder at the active site suggests that a high degree of flexibility may be inherent in the catalytic function of IMPDH. Unlike IMPDH from other species, the T. foetus enzyme has a single arginine that is largely responsible for coordinating the substrate phosphate in the active site. This structural uniqueness may facilitate structure-based identification and design of compounds that specifically inhibit the parasite enzyme.
Accuracy and precision of the Cholestech LDX System in monitoring blood lipid levels (2002)

Journal Article Accuracy and precision of the Cholestech LDX System in monitoring blood lipid levels Get access Jennifer Santee, Pharm.D. Jennifer Santee, Pharm.D. Clinical Assistant Professor Division of Pharmacy Practice, M3-C19 Medical School Building, School of Pharmacy, University of Missouri–Kansas City, 2411 Holmes, Kansas City, MO 64108 (santeej@umkc.edu) Search for other works by this author on: Oxford Academic Google Scholar American Journal of Health-System Pharmacy, Volume 59, Issue 18, 15 September 2002, Pages 1774–1779, https://doi.org/10.1093/ajhp/59.18.1774 Published: 15 September 2002
PCR Method for Detection of Adenovirus in Urine of Healthy and Human Immunodeficiency Virus-Infected Individuals (1998)

Adenoviruses (AdV) cause diseases that range from localized, self-limited illnesses to fatal infections in immunocompromised patients. Culture is assumed to be sensitive but requires viable virus and up to 3 weeks for detection, and it can be inhibited by bacterial contamination. A new PCR method amplifying a region of the hexon gene was developed in order to detect AdV in urine more rapidly and with greater sensitivity than obtainable by culture technology. All 18 serotypes tested were detected. Quantitatively, with optimized urine processing, AdV PCR detected 0.2 PFU/ml (serotype 11) and 10 DNA copies/ml (serotype 2). Serially collected urine samples from human immunodeficiency virus (HIV)-infected patients with concurrent cytomegalovirus retinitis were divided into three groups: AdV culture-positive samples, AdV culture-negative or bacterially contaminated samples from patients with a history of AdV culture-positive urines, and AdV culture-negative samples from patients without a history of AdV culture positivity. Urine samples from healthy adults were also tested by culture and PCR to screen for asymptomatic shedding. Amplification was assessed with and without prior DNA purification. AdV was detected by PCR in 90% of culture-positive urines (100% of unclotted samples, e.g., those culture positive after storage for PCR testing), 71% of culture-negative or bacterially contaminated urines from AdV-infected patients, and 28% from AdV culture-negative patients. Healthy volunteers were culture negative for AdV, and 96% were PCR negative. The new AdV PCR method is rapid and sensitive and can detect viral DNA in samples for which culturing is problematic. The role of AdV replication during HIV infection merits further investigation with sensitive tools such as PCR.
PSI: An Innovative Method to Determine and to Classify Particles during the Thermal Spray Process (2008)

Abstract Coatings produced by thermal spray processes are determined by particle parameters, which can be investigated using various diagnostic systems. With the newly developed PSI (Particle Shape Imaging) four (velocity, size, shape and position) important particle parameters can be measured and evaluated. The data acquisition system consists of two separate optical setups, thus a single particle produces two pictures in the lower and upper area of an ICCD-Camera. These pictures are evaluated by assigning specially developed shape and size parameters to the particles, which in combination with the velocity can be used to predict the coating quality. This instrument can be used to determine the optimum spray parameters (i.e. find the optimal distance between substrate and thermal spray system) and to survey the coating process. A newly developed, mobile PSI-System will allow operation at industrial and research thermal spray facilities.
Deflation Techniques for an Implicitly Restarted Arnoldi Iteration (1996)

A deflation procedure is introduced that is designed to improve the convergence of an implicitly restarted Arnoldi iteration for computing a few eigenvalues of a large matrix. As the iteration progresses, the Ritz value approximations of the eigenvalues converge at different rates. A numerically stable scheme is introduced that implicitly deflates the converged approximations from the iteration. We present two forms of implicit deflation. The first, a locking operation, decouples converged Ritz values and associated vectors from the active part of the iteration. The second, a purging operation, removes unwanted but converged Ritz pairs. Convergence of the iteration is improved and a reduction in computational effort is also achieved. The deflation strategies make it possible to compute multiple or clustered eigenvalues with a single vector restart method. A block method is not required. These schemes are analyzed with respect to numerical stability, and computational results are presented.
Optical detection methods for mass spectrometry of macroions (2004)

Detection of macroions has been a challenge in the field of mass spectrometry. Conventional ionization-based detectors, relying on production and multiplication of secondary electrons, are restricted to detection for charged particles of m/z < 1 x 10(6). While both energy-sensitive and charge-sensitive detectors have been developed recently to overcome the limitation, they are not yet in common use. Photon-sensitive detectors are suggested to be an alternative, with which detection of macroions (or charged particles) by either elastic light scattering (ELS) or laser-induced fluorescence (LIF) has been possible. In this article, we provide a critical review on the developments of novel optical detection methods for mass spectrometry of macroions, including both micron-sized and nano-sized synthetic polymers as well as high-mass biomolecules. Design and development of new spectrometers making possible observations of the mass spectra of macroions with sizes in the range of 10-10(3) nm or masses in the range of 1-10(6) MDa are illustrated. The potential and promise of this optical approach toward macroion detection with high efficiency are discussed in practical aspects.
Beam Modelling for Treatment Planning of Scanned Proton Beams (2008)

Scanned proton beams offer the possibility to take full advantage of the dose deposition properties of proton beams, i.e. the limited range and sharp peak at the end of the range, the Bragg peak. By actively scanning the proton beam, laterally by scanning magnets and longitudinally by shifting the energy, the position of the Bragg peak can be controlled in all three dimensions, thereby enabling high dose delivery to the target volume only. A typical scanned proton beam line consists of a pair of scanning magnets to perform the lateral beam scanning and possibly a range shifter and a multi-leaf collimator (MLC). Part of this thesis deals with the development of control, supervision and verification methods for the scanned proton beam line at the The Svedberg laboratory in Uppsala, Sweden. Radiotherapy is preceded by treatment planning, where one of the main objectives is predicting the dose to the patient. The dose is calculated by a dose calculation engine and the accuracy of the results is of course dependent on the accuracy and sophistication of the transport and interaction models of the dose engine itself. But, for the dose distribution calculation to have any bearing on the reality, it needs to be started with relevant input in accordance with the beam that is emitted from the treatment machine. This input is provided by the beam model. As such, the beam model is the link between the reality (the treatment machine) and the treatment planning system. The beam model contains methods to characterise the treatment machine and provides the dose calculation with the reconstructed beam phase space, in some convenient representation. In order for a beam model to be applicable in a treatment planning system, its methods have to be general. In this thesis, a beam model for a scanned proton beam is developed. The beam model contains models and descriptions of the beam modifying elements of a scanned proton beam line. Based on a well-defined set of generally applicable characterisation measurements, ten beam model parameters are extracted, describing the basic properties of the beam, i.e. the energy spectrum, the radial and the angular distributions and the nominal direction. Optional beam modifying elements such as a range shifter and an MLC are modelled by dedicated Monte Carlo calculation algorithms. The algorithm that describes the MLC contains a parameterisation of collimator scatter, in which the rather complex phase space of collimator scattered protons has been parameterised by a set of analytical functions. Dose calculations based on the phase space reconstructed by the beam model are in good agreement with experimental data. This holds both for the dose distribution of the elementary pencil beam, reflecting the modelling of the basic properties of the scanned beam, as well as for complete calculations of collimated scanned fields.
Interleukin-1 plays a major role in vascular inflammation and atherosclerosis in male apolipoprotein E-knockout mice (2005)

Our results demonstrate that the IL-1/IL-1Ra ratio plays a critical role in the pathogenic mechanisms leading to vascular inflammation and atherosclerosis in ApoE -/- mice.
Glycosylation of the Epidermal Growth Factor Receptor and Its Relationship to Membrane Transport and Ligand Binding1 (1988)

Journal Article Glycosylation of the Epidermal Growth Factor Receptor and Its Relationship to Membrane Transport and Ligand Binding Get access Shinobu Gamou, Shinobu Gamou Department of Molecular Biology, Keio University School of MedicineShinjuku-ku, Tokyo 160 Search for other works by this author on: Oxford Academic PubMed Google Scholar Nobuyoshi Shimizu Nobuyoshi Shimizu 2 Department of Molecular Biology, Keio University School of MedicineShinjuku-ku, Tokyo 160 2To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Biochemistry, Volume 104, Issue 3, September 1988, Pages 388–396, https://doi.org/10.1093/oxfordjournals.jbchem.a122478 Published: 01 September 1988 Article history Received: 17 March 1988 Published: 01 September 1988
Molecular characterization of recombinant human adenosine receptors (1996)

The four human adenosine receptors (ARs), A1, A2A, A2B, and A3, have been stably expressed in mammalian cells. Radioligand binding properties were examined for all four subtypes, including, for the first time the A2BAR. The A1AR-selective radioligand, [3H]8-cyclopentyl-1,3-dipropylxanthine ([3H]CPX; A1; KD = 2 nM) also can be used to characterize recombinant A2BAR (KD = 40 nM). Theophylline and enprofylline both bind to A2BAR with KI of 7 μM, well within the therapeutic ranges of these compounds used to treat asthma. We have identified C8-(N-methylisopropyl)-amino-N6-(5′-endohydroxy)-endonorbornan-2-yl-9-methyladenine (WRC-0571) as the most selective antagonist of A1AR. Recombinant ARs have been extended with hexahistidine (H) and the FLAG (F) epitope to make H/F-A1 and H/F-A2A receptors that have been purified to near homogeneity under conditions that preserve radioligand binding. [3H]Adenosine binds to purified H/F-A1AR-G protein complexes with a KD of 0.95 ± 0.3 nM; binding is not affected by the adenosine deaminase inhibitor, erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA). Phosphoaminoacid analysis of H/F-A1AR and H/F-A2AAR purified from mammalian cells incubated in [32P]phosphate indicates that both receptors are phosphorylated on serine residues. Monoclonal antibodies were raised by using the purified H/F-A2AAR as an antigen. Antibodies with higher affinity than antipeptide antisera were generated and used for Western blotting and rat brain immunocytochemistry. Drug Dev. Res. 39:243–252, 1996. © 1997 Wiley-Liss, Inc.
The potential of nestin-expressing hair follicle stem cells in regenerative medicine (2007)

The hair follicle bulge area is an abundant, easily accessible source of actively growing pluripotent adult stem cells. Nestin, a protein marker for neural stem cells, is also expressed in follicle stem cells and their immediate, differentiated progeny. Green fluorescent protein (GFP), whose expression is driven by the nestin regulatory element in transgenic mice, serves to mark hair follicle stem cells. The pluripotent nestin-driven GFP stem cells are positive for the stem cell marker CD34, but negative for keratinocyte marker keratin 15, suggesting their relatively undifferentiated state. These cells can differentiate into neurons, glia, keratinocytes, smooth muscle cells and melanocytes in vitro. In vivo studies show that nestin-driven GFP hair follicle stem cells can differentiate into blood vessels and neural tissue after transplantation to the subcutis of nude mice. Hair follicle stem cells implanted into the gap region of a severed sciatic or tibial nerve greatly enhance the rate of nerve regeneration and the restoration of nerve function. The follicle cells transdifferentiate largely into Schwann cells, which are known to support neuron regrowth. The transplanted mice regain the ability to walk normally. Thus, hair follicle stem cells provide an effective, accessible, autologous source of stem cells for treatment of peripheral nerve injury.