gebhart/patrepeval huggingface dataset:
Isolation and Characterization of GBP28, a Novel Gelatin-Binding Protein Purified from Human Plasma (1996)

By use of its affinity to gelatin-Cellulofine, a novel protein, GBP28 (gelatin-binding protein of 28 kDa), was obtained from human plasma. GBP28 bound to gelatin-Cellulofine could be eluted with 1 M NaCl. By analysis of its amino-terminal amino acid sequences and the peptides obtained by protease digestion, GBP28 was identified as a novel protein. After repeated gel chromatography of the 1 M NaCl eluate from gelatin-Cellulofine, about 50 micrograms of GBP28 was purified from 500 ml of human plasma. On gel chromatography, the protein migrated as a molecule of about 420 kDa. On SDS-PAGE, its molecular mass was 28 kDa under reducing conditions and 68 kDa under nonreducing conditions. Recently, human mRNA specific to adipose tissue, cDNA clone apM1, has been registered [Maeda, K., Okubo, K., Shimomura, I., Funahashi, T., Matsuzawa, Y., and Matsubara, K. (1996) Biochem. Biophys. Res. Commun. 221, 286-289]. The assumed amino acid sequence of cDNA clone apM1 contained all the sequences of GBP28 and its peptides. Therefore, it is evident that the cDNA clone apM1 encodes GBP28 and the protein is specific to adipose tissue. The clone encodes a polypeptide of 244 amino acids with a secretory signal sequence at the amino terminus, a small non-helical region, a stretch of 22 collagen repeats and a globular domain. Thus, GBP28 appears to belong to a family of proteins possessing a collagen-like domain through which they form homo-trimers, which further combine to make oligomeric complexes. Although its biological function is presently unclear, its adipocyte-specific expression suggests that GBP28 may function as an endogenous factor involved in lipid catabolism and storage or whole body metabolism.
Identification of Protein Expression Signatures Associated with Helicobacter pylori Infection and Gastric Adenocarcinoma Using Recombinant Antibody Microarrays (2006)

Antibody microarray based technology is a powerful emerging tool in proteomics, target discovery, and differential analysis. Here, we report the first study where recombinant antibody fragments have been used to construct large scale antibody microarrays, composed of 127 different antibodies against mostly immunoregulatory antigens. The arrays were based on single framework recombinant antibody fragments (SinFabs) designed for high on-chip stability and functionality and were used for the analysis of malignant and normal stomach tissue samples from Helicobacter pylori-positive and -negative patients. Our results demonstrate that distinct tumor- as well as infection-associated protein expression signatures could be identified from these complex tissue proteomes, as well as biomarkers such as IL-9, IL-11, and MCP-4, previously not found in these diseases. In a longer perspective, this study may improve the understanding of H. pylori-induced stomach cancer and lead to development of improved diagnostics.
Cloning and characterization of a gene encoding pig epidermal growth factor (1991)

A portion of the pig epidermal growth factor (EGF) gene has been isolated and characterized. The nucleotide sequencies of exons 20 and 21, which encode the EGF region of the precursor protein, show 85% similarity with the human EGF gene sequence. In addition, conservation of the intron-exon boundaries between the two species was generally observed. Although the pig exon 21 appeared to lack a single nucleotide at its 5' end relative to the human gene, sequences obtained by direct amplification of the genomic DNA around the 5' end of this exon using the polymerase chain reaction, and from a pig EGF cDNA recombinant isolated from a kidney library, indicated that the deletion was probably a cloning artifact. Comparison of the predicted amino acid sequence of pig EGF with that of EGF from other species, as well as with several other polypeptides which bind to the EGF receptor, indicated conservation of Gly18, Tyr37, Gly39 and Arg41 in addition to all six cysteine residues and Leu47, which are known to be critical for biological activity. A synthetic gene encoding the predicted amino acid sequence of pig EGF was expressed in yeast. The recombinant polypeptide was shown to compete with 125I-labelled mouse EGF for binding to cells and to stimulate DNA synthesis in quiescent monolayers of Swiss 3T3 cells.
Diversity Oriented Fluorescence Library Approach (DOFLA) for Live Cell Imaging Probe Development (2014)

A cell is the smallest functional unit of life. All forms of life rely on cellular processes to maintain normal functions, and changes in cell function induced by metabolic disturbances, physicochemical damage, infection, or abnormal gene expression may cause disease. To understand basic biology and to develop therapeutics for diseases, researchers need to study live cells. Along with advances in fluorescence microscopy and in vitro cell culture, live-cell imaging has become an essential tool in modern biology for the study of molecular and cellular events. Although researchers have often used fluorescent proteins to visualize cell-type-specific markers, this method requires genetic manipulations, which may not be appropriate in nontransgenic cells. Immunodetection of cellular markers requires the use of xenogenic antibodies, which may not detect intracellular markers in live cells. One option for overcoming these problems is the use of fluorescent small molecules targeted to specific cell types, which can enter live cells and interact with molecules of interest. We have used combinatorial chemistry to develop a large number of fluorescent small molecules as new imaging probes even without prior information about the probes' binding targets and mechanism, a strategy that we call the diversity oriented fluorescence library approach (DOFLA). We have used DOFLA to produce novel sensors and probes that detect a variety of biological and chemical molecules in vivo as well as in vitro. In this Account, we describe a series of fluorescent small molecules developed using DOFLA that bind specifically to particular cell types. These molecules provide new ways to detect and isolate these cells. The fluorescent probes CDy1, CDg4, and CDb8 tag embryonic stem cells and induced pluripotent stem cells but not fibroblasts or germ-line cells. CDr3 binds to an intracellular neural stem cell marker, fatty acid binding protein 7, which allows researchers to separate neural stem cells from embryonic stems cells and more differentiated cells such as neurons and glia. In addition, we have developed CDr10, which distinguishes microglia from neurons and glia. CDy2 stains myocytes much more brightly than myoblasts because of the increase in mitochondrial membrane potential during myogenesis. GY and PiY selectively stain α and β cells of pancreatic islets, respectively. Histamine Blue binds directly to histamine and stains basophils and macrophages containing high quantities of histamine. Glutathione Green allows researchers to measure the level of glutathione in cells and tissues by binding to glutathione and then triggering a hypsochromic shift. We have also developed a set of compounds that bind to cancer cells based on the cell type of origin and biocompatible surface-enhanced Raman spectroscopy (SERS) nanotags for cancer detection. In addition to discussing these new probes and their cell-type specificity, we also describe their applications in new assays, cell characterization, and pathology studies.
Gain enhancement methods for printed circuit antennas (1985)

Resonance conditions for a substrate-superstrate printed antenna geometry which allow for large antenna gain are presented. Asymptotic formulas for gain, beamwidth, and bandwidth are given, and the bandwidth limitation of the method is discussed. The method is extended to produce narrow patterns about the horizon, and directive patterns at two different angles.
Fractals and chaos in geology and geophysics (1993)

This book introduces the fundamental concepts of fractal geometry and chaotic dynamics. These concepts are then related to a variety of geological and geophysical problems, illustrating just what chaos theory and fractals really tell us and how they can be applied to the earth sciences. Petroleum and mineral reserves, earthquakes, mantle convection and magnetic field generation are among the earth's properties that come under scrutiny. This is the first book that covers these topics at an accessible level; the concepts are introduced at the lowest possible level of mathematics and are consistently understandable, so that the reader requires only a background in basic physics and mathematics. Problems are also included for the reader to solve.
A novel end-effector design for robotics in image-guided needle procedures (2006)

Such a switch-able and flexible mode for a robotic arm could overcome much of the current limitations for automated needle placements for mobile targets, and could mitigate risks from breathing or patient motion with a rigid needle gripper in place.
Pseudo homogeneous catalyst layer model for polymer electrolyte fuel cell (1991)

We have developed a relatively simple one-dimensional model for the cathode catalyst layer. This model explains certain observed polarization curve features at higher current densities. These features include a change in linear slope, instead of a sharp limiting current feature, and a lower than expected ratio of current density measured using O{sub 2} relative to air. Diffusional paths, ionic resistance, and catalyst sites are intimately coupled in a pseudohomogeneous layer using effective'' parameters. 3 refs., 7 figs.
Detection of the Engine Anti-Knock Additive Methylcyclopentadienyl Manganese Tricarbonyl (MMT) from Unleaded Gasoline in Soil by Diffuse Reflectance Infrared Fourier Transform Spectroscopy and Mass Spectrometry (1995)

Soil samples were washed with dilute solutions of the toxic anti-knock fuel additive methylcyclopentadienyl manganese tricarbonyl (MMT) in hexanes and commercial unleaded gasoline. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) was then used to detect the v(CO) modes of MMT, and subsequently 13 CO-enriched MMT, in the soil samples. The presence of MMT in the soils was further confirmed by mass spectrometry. Concentrations corresponding to ∼10 ppm Mn in soil could be detected by DRIFTS of the dry samples, and, most interestingly, there was no evidence of significant MMT decomposition over a period of eight months. Apparently, MMT is stabilized by physisorption onto the soils. In the absence of such stabilization, however, MMT undergoes photolytic and thermal decomposition in a matter of minutes. These results suggest the possibility of longer-term environmental problems associated with gasoline spills containing MMT than was previously suspected.
Development of (18)F-fluoroethylcholine for cancer imaging with PET: synthesis, biochemistry, and prostate cancer imaging. (2002)

The synthesis of (18)F-FECh was easy and reliable. (18)F-FECh PET was very effective in detecting prostate cancer in patients. The chemical trap, consisting of active transport of (18)F-FECh and formation of phosphoryl-(18)F-FECh, seemed to be involved in the uptake mechanism of (18)F-FECh in tumors.
Nicotinic receptors in circuit excitability and epilepsy (2002)

Neuronal nicotinic acetylcholine receptors belong to the family of excitatory ligand-gated channels and result from the assembly of five subunits. Functional heteromeric nictonic receptors are present in the hippocampus and neocortex, thalamus, mesolimbic dopamine system and brainstem motor nuclei, where they may play a role, respectively, in memory, sensory processing, addiction and motor control. Some forms of autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE) have been found to be associated with mutations in the genes coding for the alpha 4 or beta2 subunits of the nicotinic receptor. Mutant receptors display an increased acetylcholine sensitivity with respect to normal receptors. Since the thalamus and the cortex are strongly innervated by cholinergic neurons projecting from the brainstem and basal forebrain, an unbalance between excitation and inhibition, brought about by the presence of mutant receptors, could generate seizures by facilitating and synchronizing spontaneous oscillations in thalamo-cortical circuits.
Oligoribonucleotide circularization by 'template-mediated' ligation with T4 RNA ligase: Synthesis of circular hammerhead ribozymes (1998)

Circular hammerhead ribozymes were synthesized from linear oligoribonucleotides using T4 RNA ligase. Some of the precursors could not be efficiently circularized under standard conditions. For these molecules, the use of a DNA template allowed their efficient circularization. The template was designed to prevent the precursor from folding into an unsuitable structure. The template allowed circular ribozymes as small as 15 nucleotides in length to be efficiently synthesized at concentrations as high as 50 microM in the ligation reaction. The circular products retained their biological activity.
Effectiveness of temporal pattern in the input to a ganglion: Inhibition in the cardiac ganglion of spiny lobsters (1969)

Abstract (1) The single inhibitor axon of one side, going to the cardiac ganglion of Panulirus in a preparation with the central nervous system removed, was stimulated at a constant mean frequency but with different temporal fine structure. In particular, inhibitory trains with uniform intervals are compared with trains of alternately short and long intervals (“paired pulses”). Different ratios of short to long interval were used and, besides pairs, groups of up to 8 shocks. (2) Sixteen different measures of the inhibitory effect upon various aspects of the electroneurogram of the heart beat are compared. Some are more sensitive, others are more consistent. (3) Pattern sensitivity is found, that is the heart beat slows to different extents for different temporal structures. Trains of uniform intervals were generally more effective than any other pattern. Bursts of 7 or 8 are less effective than shorter bursts with the same minimum and mean interval. (4) The same burst has a different effect according to the phase of the heart cycle at which it arrives; the later the arrival the greater the effect. At the optimal phase and impulse interval, the minimum number of impulses for a just noticeable inhibitory effect (5–10%) is about 4. (5) In some preparations aging was associated with a reversal from inhibition to acceleration and such changes were not necessarily in parallel for different stimulus patterns. (6) On present evidence it cannot be said that the pattern sensitivity is explained by the effect of conditioning shock‐test shock interval on the synaptic response to the test shock. (7) Evidence does not yet permit evaluation of the possible role of pattern sensitivity under normal conditions. The significance at presetn is the finding that in a nearly ideal preparation for testing, a postsynaptic neuron can “read,” i.e., respond differently to the same mean frequency according to temporal fine structure.
Survival and Development of Larval Onchocerca volvulus in Diffusion Chambers Implanted in Primate and Rodent Hosts (1993)

Third-stage larvae (L3) of Onchocerca volvulus were implanted in diffusion chambers in chimpanzees, mangabey monkeys, rhesus monkeys, squirrel monkeys, and inbred strains of mice, jirds, and rats for 3-63 days. At different times during the experimental period, larvae were recovered and assessed for their viability and development. Survival and growth rates were equal regardless of whether the implanted larvae were fresh or cryopreserved. Survival and growth rates of the larvae did not differ among the primate and rodent hosts tested, with the exception of squirrel monkeys and rats, which were resistant to infection. Molting from L3 to fourth-stage larvae began on day 3 and continued through day 14 in the primates and rodents. The primate and rodent models developed in the present study will be useful for the study of the immunology and chemotherapy of onchocerciasis.
Purification of core-binding factor, a protein that binds the conserved core site in murine leukemia virus enhancers. (1992)

The Moloney murine leukemia virus causes thymic leukemias when injected into newborn mice. A major genetic determinant of the thymic disease specificity of the Moloney virus genetically maps to two protein binding sites in the Moloney virus enhancer, the leukemia virus factor b site and the adjacent core site. Point mutations introduced into either of these sites significantly shifts the disease specificity of the Moloney virus from thymic leukemia to erythroleukemia (N. A. Speck, B. Renjifo, E. Golemis, T. Frederickson, J. Hartley, and N. Hopkins, Genes Dev. 4:233-242, 1990). We have purified several polypeptides that bind to the core site in the Moloney virus enhancer. These proteins were purified from calf thymus nuclear extracts by selective pH denaturation, followed by chromatography on heparin-Sepharose, nonspecific double-stranded DNA-cellulose, and core oligonucleotide-coupled affinity columns. We have achieved greater than 13,000-fold purification of the core-binding factors (CBFs), with an overall yield of approximately 19%. Analysis of purified protein fractions by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis reveals more than 10 polypeptides. Each of the polypeptides was recovered from an SDS-polyacrylamide gel, and those in the molecular size range of 19 to 35 kDa were demonstrated to have core-binding activity. The purified CBFs were shown by DNase I footprint analyses to bind the core site in the Moloney virus enhancer specifically, and also to core motifs in the enhancers from a simian immunodeficiency virus, the immunoglobulin mu chain, and T-cell receptor gamma-chain genes.
Automated partitioning of hierarchically specified digital systems (1982)

This paper describes a heuristic algorithm for automatically partitioning digital systems. High- level information contained within a hierarchical design is used to increase the effectiveness of this algorithm. This algorithm uses a constructive process to build a physical design of a hierarchically specified logic design. An iterative improvement step is then done.
Abstract 10826: GBT1118, a Potent Allosteric Modifier of Hemoglobin Oxygen Affinity Increases Tolerance to Hypoxia in Mice (2015)

Introduction: Adaptation to hypoxia involves several mechanisms that influence oxygen (O2) transport and utilization, including a reduction in hemoglobin (Hb) O2 affinity to favor the release of O2 to tissues. Paradoxically, increased Hb O2 affinity has been observed to have beneficial effects during severe hypoxia. Hypothesis: This study was designed to test the hypothesis that pharmacologically increasing Hb O2 affinity with GBT1118 can augment O2 transport during severe hypoxia (10 and 5% O2). Method: Mice were orally dosed with GBT1118 (70 or 140 mg/kg) or only vehicle (Control), and Hb O2 affinity was determined by hemoximetry. During hypoxia, changes in systemic and microvascular hemodynamics, tissue partial pressure of O2 (PO2) and tissue hypoxia were evaluated. At each timepoint, mice with adequate systolic blood pressure (BP) were counted as survived and mice with severe hypotension (BP ≤60 mmHg) were counted as non-survived and were euthanized. Results: Similar trends were observed at 10 and 5% O2 hypoxia. GBT1118 at 70 and 140 mg/kg decreased the P50 (PO2 at which blood is 50% saturated with O2) by 29 and 35 mmHg, respectively. During 5% O2 hypoxia, GBT1118 at 70 and 140 mg/kg increased SaO2 from 40% (Control) to 57% (70mg/kg) and 80% (140mg/kg), respectively. Moreover, mean BP and heart rate (HR) decreased to 50 mmHg and 375 bpm in control mice, whereas GBT1118-dosed mice sustained higher mean BP and HR in a dose-dependent fashion and improved survival (Figure 1). In addition, GBT1118 preserved microvascular blood flow and tissue oxygenation; consequently, GBT1118 reduced heart and brain hypoxic areas compared with control groups during hypoxia. Conclusion: Under severe hypoxia, GBT1118-mediated increase in Hb O2 affinity increases SaO2. At the tissue level, local milieu allows for efficient O2 extraction leading to improved oxygenation as measured by decreased lactic acidosis, improved cardiovascular function and ultimately, survival.
A simplified assay for the arylamine N-acetyltransferase 2 polymorphism validated by phenotyping with isoniazid. (1997)

Human arylamine N-acetyltransferase (NAT) activity is determined by two distinct genes, NAT1 and NAT2, and the classical acetylation polymorphism in NAT2 has been associated with a variety of disorders, including lupus erythematosus and arylamine induced cancers. Over 50% of the white population exhibit a slow acetylator phenotype. The genetic basis of the defect has been identified and several DNA based assays are available for genotyping studies. We present here a simplified, rapid PCR based assay for the identification of the major slow acetylator genotypes and validate it using isoniazid as probe drug. This assay was 100% predictive of phenotype. The three genotypes (homozygous mutated, heterozygous, and homozygous rapid) corresponded to a trimodal distribution of Ac-INH/INH metabolic ratios (slow, intermediate, and rapid) without overlapping.
Powder based superdielectric materials for novel Capacitor design (2017)

This thesis is part of a continuing effort to improve upon the performance and fabrication methods of powder-based superdielectric material (PSDM) capacitors. This thesis reports the performance as a function of discharge time for very thin films of aqueous NaCl solution-saturated silica gel films spread within holes of a very thin (16 μm) polymer sheet. The most significant finding is that these PSDM capacitors have unprecedented, functional dielectric values for this thickness and excellent power and energy densities (≈90 J/cmᶟ). Earlier PSDM studies indicated that thicknesses ˃300 μm PSDMs have extremely high dielectric values. However, performance of these capacitors extrapolated to very thin dielectric layers was still unknown. This study recorded dielectric values of up to 1x10⁹ for layers on the order of ten microns-thick. In addition, this study provides unique required engineering data regarding the performance of SDM as a function of discharge time. In summation, PSDM capacitors were successfully tested as a function of frequency and form factor for various thicknesses.
Purification and Application of Serum IgM from Turbot (Scophthalmus maximus) (2008)

An immunoglobulin M(IgM) was purified from serum of turbot with ammonium sulfate precipitation,followed with Sepharose-4B column chromatography and DEAE-Sepharose Fast Flow column chromatogsaphy.SOS-PAGE electrophoresis showd that the purified lgM was composed of 76 kD heavy chains and 27 kD light chains.Antiserum against the purified IgM was prepared by repeatedly immunized New Zealand rabbits with the purified protein.Western blot analysis showed that the heavy chain of the purified IgM reacted well with the rabbit antiserum while the light chain hardly reacted with it.An indirect ELISA method was established using the specific antiserum as second antibody.Turbot was immunized with formalin-killed Vibrio anguillarum cells via intraperitoneal injection.The specific antibody was determined with the indirect ELISA.Specific antibody could be detected in a week after immunization.The titer of the antibody reached to a peak in three weeks,and maintained a high level till thirteen weeks.