gebhart/patrepeval huggingface dataset:
Purification and some properties of streptococcal protein G, a novel IgG-binding reagent. (1984)

Protein G, a bacterial cell wall protein with affinity for immunoglobulin G (IgG), has been isolated from a human group G streptococcal strain (G148). Bacterial surface proteins were solubilized by enzymatic digestion with papain. Protein G was isolated by sequential use of ion-exchange chromatography on DEAE-cellulose, gel filtration on Sephadex G-100, and affinity chromatography on Sepharose 4B-coupled IgG. The presence of protein G in various pools and fractions during the isolation was followed by their ability to inhibit the binding of radio-labeled IgG to G148 bacteria. A highly purified protein G was obtained. On polyacrylamide gel electrophoresis in sodium dodecyl sulfate, the apparent m.w. was 30,000, and on agarose gel electrophoresis the purified protein gave rise to a single band in the alpha 1-region. Protein G was found to bind all human IgG subclasses and also rabbit, mouse, and goat IgG. On the IgG molecule, the Fc part appears mainly responsible for the interaction with protein G, although a low degree interaction was also recorded for Fab fragments. IgM, IgA, and IgD, however, showed no binding to protein G. This novel IgG-binding reagent promises to be of theoretical and practical interest in immunologic research.
Reduced Cardiotoxicity and Preserved Antitumor Efficacy of Liposome-Encapsulated Doxorubicin and Cyclophosphamide Compared With Conventional Doxorubicin and Cyclophosphamide in a Randomized, Multicenter Trial of Metastatic Breast Cancer (2001)

Myocet improves the therapeutic index of doxorubicin by significantly reducing cardiotoxicity and grade 4 neutropenia and provides comparable antitumor efficacy, when used in combination with cyclophosphamide as first-line therapy for MBC.
Functional Nicotinic Acetylcholine Receptors That Mediate Ganglionic Transmission in Cardiac Parasympathetic Neurons (2000)

Nicotinic acetylcholine receptors (nAChRs) mediate ganglionic transmission in the peripheral autonomic nervous system in mammals. Functional neuronal nAChRs have been shown to assemble from a combination of alpha and beta subunits, including alpha3, alpha5, alpha7, beta2, and beta4 in RNA-injected oocytes, but the subunit composition of functional neuronal nAChRs in vivo in mammals remains unknown. We examined the subunit composition of functional nAChRs in the intracardiac parasympathetic ganglion in a physiologically intact system in vivo. We report here that localized perfusion of the canine intracardiac ganglion in situ with an antagonist specific for nAChRs containing an alpha3/beta2 subunit interface (alpha-conotoxin MII 100-200 nm) resulted in reversible attenuation of the sinus cycle length (SCL) response by approximately 70% to electrical stimulation of the preganglionic vagus nerve. Perfusion with antagonist specific for receptors containing an alpha3/beta4 subunit interface (alpha-conotoxin AuIB 1 micrometer) resulted in attenuation in SCL responses (approximately 20%) compared with baseline when applied by itself, but not in animals pretreated with alpha-conotoxin MII. Perfusion of the ganglion with alpha-bungarotoxin (1 micrometer, which blocks alpha7 receptors) caused a reduction in SCL response by approximately 30% compared with baseline when perfused on its own and when added after blockade with MII and AuIB. Perfusion with hexamethonium bromide resulted in complete blockade of ganglionic transmission, confirming total perfusion of the ganglion and the nicotinic nature of ganglionic transmission at this synapse. Immunohistochemistry using monoclonal antibodies against specific nicotinic subunits confirmed the presence of alpha3, alpha7, beta2, and beta4 subunits. We conclude that functional ganglionic transmission in the canine intracardiac ganglion is mediated primarily by receptors containing an alpha3/beta2 subunit interface, with a smaller contribution by receptors containing alpha7 nAChRs. Despite the presence of beta4 subunits in functional channels, a contribution of a distinct alpha3/beta4 receptor population that does not include an alpha3/beta2 subunit interface was less clear.
Expression of keratinocyte growth factor receptor correlates with expansive growth and early stage of gastric cancer (2006)

The keratinocyte growth factor receptor, also known as KGFR/FGFR2 IIIb, is mainly localized in epithelial cells, and participates in the proliferation of these cells. In contrast, a recent study has revealed that the overexpression of KGFR in salivary adenocarcinoma induces growth inhibition, cell differentiation and apoptosis. We attempted to clarify the expression and role of KGFR in normal and cancerous human gastric tissues and cancer cell lines. Reverse-transcription polymerase chain reaction and Western blot analyses showed KGFR mRNA and its protein expression in NUGC-4, KATO-III and MKN-7 gastric cancer cell lines, but not in the NS-8 cell line. Immunohistochemically, KGFR immunoreactivity was weakly detected in the luminal surface of normal gastric epithelial cells. In addition, KGFR immunoreactivity was strongly detected in the nucleus and cytoplasm of many parietal cells. In gastric cancer tissue, KGFR was expressed in the cell membrane and cytoplasm of cancer cells in 46 of 126 (36.5%) cases. KGFR expression in gastric cancer cells was significantly associated with early-type macroscopic findings, shallow invasion of the gastric wall and expansive growth type. KGFR expression tended to correlate with a good prognosis in gastric cancer. These findings indicate that KGFR expression plays important roles in the differentiation of normal gastric epithelial cells and parietal cell functions. Furthermore, a decreased expression level or the non-expression of KGFR in gastric cancer cells may be associated with the proliferation and invasion of gastric cancer cells and a poor prognosis for the patient.
Non‐additive effects of multiple amino acid substitutions on antigen‐antibody recognition (1992)

Synthetic peptides have been used to mimic the main antigenic site of foot-and-mouth disease virus (FMDV) of serotype C and of several variant isolates. This region includes multiple continuous B cell epitopes. The effect of single amino acid replacements, individually or in combination, on antigen specificity has been evaluated using monoclonal antibodies. Quantitative enzyme immunodot assays have shown that both additive and non-additive effects of multiple replacements occur in continuous B cell epitopes, with regard to antibody recognition. Antigenically critical single replacements may be compensated by other, non-critical replacements. Thus, the role of a single amino acid on antibody recognition depends on the sequence context in the antigenic domain. The non-additive effects of multiple replacements may modulate the extent of antigenic diversification of highly variable RNA viruses, and keep viruses confined within antigenic groups by precluding linear antigenic divergence.
Nucleotide sequence of the polyhedron envelope protein gene region of the Lymantria dispar nuclear polyhedrosis virus (1992)

A 6.4 kb region from the Lymantria dispar multicapsid nuclear polyhedrosis virus (LdMNPV) genome was sequenced and found to contain open reading frames (ORFs) homologous to the polyhedron envelope (PE) protein coding sequence, and the C-terminal half of ORF 1, which is a gene located upstream of the PE protein gene in other baculoviruses. The proteins predicted from the LdMNPV genes encoding the PE protein, and ORF 1 demonstrated 27 and 34% amino acid sequence identity, respectively, with the corresponding genes in the Autographa californica multicapsid nuclear polyhedrosis virus.
Overexpression of the rat inducible 70-kD heat stress protein in a transgenic mouse increases the resistance of the heart to ischemic injury. (1995)

Myocardial protection and changes in gene expression follow whole body heat stress. Circumstantial evidence suggests that an inducible 70-kD heat shock protein (hsp70i), increased markedly by whole body heat stress, contributes to the protection. Transgenic mouse lines were constructed with a cytomegalovirus enhancer and beta-actin promoter driving rat hsp70i expression in heterozygote animals. Unstressed, transgene positive mice expressed higher levels of myocardial hsp70i than transgene negative mice after whole body heat stress. This high level of expression occurred without apparent detrimental effect. The hearts harvested from transgene positive mice and transgene negative littermates were Langendorff perfused and subjected to 20 min of warm (37 degrees C) zero-flow ischemia and up to 120 min of reflow while contractile recovery and creatine kinase efflux were measured. Myocardial infarction was demarcated by triphenyltetrazolium. In transgene positive compared with transgene negative hearts, the zone of infarction was reduced by 40%, contractile function at 30 min of reflow was doubled, and efflux of creatine kinase was reduced by approximately 50%. Our findings suggest for the first time that increased myocardial hsp70i expression results in protection of the heart against ischemic injury and that the antiischemic properties of hsp70i have possible therapeutic relevance.
DESPOT: Online POMDP Planning with Regularization (2013)

POMDPs provide a principled framework for planning under uncertainty, but are computationally intractable, due to the “curse of dimensionality ” and the “curse of history”. This paper presents an online POMDP algorithm that alleviates these difficulties by focusing the search on a set of randomly sampled scenarios. A Determinized Sparse Partially Observable Tree (DESPOT) compactly captures the execution of all policies on these scenarios. Our Regularized DESPOT (R-DESPOT) algorithm searches the DESPOT for a policy, while optimally balancing the size of the policy and its estimated value obtained under the sampled scenarios. We give an output-sensitive performance bound for all policies derived from a DESPOT, and show that R-DESPOT works well if a small optimal policy exists. We also give an anytime algorithm that approximates R-DESPOT. Experiments show strong results, compared with two of the fastest online POMDP algorithms. Source code along with experimental settings are available at
Interleukin-6 Induces S100A9 Expression in Colonic Epithelial Cells through STAT3 Activation in Experimental Ulcerative Colitis (2012)

Elevated S100A9 expression in CECs mediated by an IL-6/STAT3 signaling cascade may play an important role in the development of colitis.
Reversible Inhibition of α-Synuclein Fibrillization by Dopaminochrome-mediated Conformational Alterations (2005)

Previous studies demonstrated that alpha-synuclein (alpha-syn) fibrillization is inhibited by dopamine, and studies to understand the molecular basis of this process were conducted (Conway, K. A., Rochet, J. C., Bieganski, R. M., and Lansbury, P. T., Jr. (2001) Science 294, 1346-1349). Dopamine inhibition of alpha-syn fibrillization generated exclusively spherical oligomers that depended on dopamine autoxidation but not alpha-syn oxidation, because mutagenesis of Met, His, and Tyr residues in alpha-syn did not abrogate this inhibition. However, truncation of alpha-syn at residue 125 restored the ability of alpha-syn to fibrillize in the presence of dopamine. Mutagenesis and competition studies with specific synthetic peptides identified alpha-syn residues 125-129 (i.e. YEMPS) as an important region in the dopamine-induced inhibition of alpha-syn fibrillization. Significantly, the dopamine oxidation product dopaminochrome was identified as a specific inhibitor of alpha-syn fibrillization. Dopaminochrome promotes the formation of spherical oligomers by inducing conformational changes, as these oligomers regained the ability to fibrillize by simple denaturation/renaturation. Taken together, these data indicate that dopamine inhibits alpha-syn fibrillization by inducing structural changes in alpha-syn that can occur through the interaction of dopaminochrome with the 125YEMPS129 motif of alpha-syn. These results suggest that the dopamine autoxidation can prevent alpha-syn fibrillization in dopaminergic neurons through a novel mechanism. Thus, decreased dopamine levels in substantia nigra neurons might promote alpha-syn aggregation in Parkinson's disease.
Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish (2013)

Gene modifications in animal models have been greatly facilitated through the application of targeted genome editing tools. The prokaryotic CRISPR/Cas9 type II genome editing system has recently been applied in cell lines and vertebrates. However, we still have very limited information about the efficiency of mutagenesis, germline transmission rates and off-target effects in genomes of model organisms. We now demonstrate that CRISPR/Cas9 mutagenesis in zebrafish is highly efficient, reaching up to 86.0%, and is heritable. The efficiency of the CRISPR/Cas9 system further facilitated the targeted knock-in of a protein tag provided by a donor oligonucleotide with knock-in efficiencies of 3.5-15.6%. Mutation rates at potential off-target sites are only 1.1-2.5%, demonstrating the specificity of the CRISPR/Cas9 system. The ease and efficiency of the CRISPR/Cas9 system with limited off-target effects make it a powerful genome engineering tool for in vivo studies.
Unliganded Thyroid Hormone Receptor α Can Target TATA-Binding Protein for Transcriptional Repression (1996)

Unliganded human thyroid hormone receptor alpha (hTR alpha) can repress transcription by inhibiting the formation of a functional preinitiation complex (PIC) on promoters bearing thyroid hormone receptor (TR)-binding elements. Here we demonstrate that hTR alpha directly contacts the TATA-binding protein (TBP) and that preincubation of hTR alpha with TBP completely alleviates TR-mediated repression in vitro. Using stepwise preassembled PICs, we show that hTR alpha targets either the TBP/TFIIA or the TBP/TFIIA/TFIIB steps of PIC assembly for repression. We also show that the repression domain of hTR alpha maps to the C-terminal ligand-binding region and that direct TR-TBP interactions can be inhibited by thyroid hormone. Together, these results suggest a model in which unliganded hTR alpha contacts promoter-bound TBP and interferes with later steps in the initiation of transcription.
Simple, rapid spectrophotometry of urinary N-acetyl-beta-D-glucosaminidase, with use of a new chromogenic substrate. (1983)

Abstract We have developed a new spectrophotometric assay for urinary N-acetyl-beta-D-glucosaminidase (NAGase) with use of sodio m-cresolsulfonphthaleinyl N-acetyl-beta-D-glucosaminide (MCP-NAG). MCP-NAG was synthesized from acetochloro-glucosamine and m-cresolsulfonphthalein (MCP) in four steps. MCP-NAG reacts well with NAGase (Km = 0.41 mmol/L) and is highly water soluble. The absorption maximum and molar absorptivity of the aglycone MCP are 580 nm and 40 670, respectively. Spectral overlap of interfering substances at 580 nm is almost negligible, so that the urine blank can be omitted from the assay procedure. The high molar absorptivity of MCP gives sufficient analytical sensitivity at a reaction time of 15 min. The correlation between the MCP-NAG method (y) and the fluorimetric method (x) involving 4-methylumbelliferyl N-acetyl-beta-D-glucosaminide is represented by the equation y = 0.995x - 0.669 (r = 0.991). Thus, the present method provides practical advantages over conventional methods, for use in the routine laboratory.
Production of Lewis x Tetrasaccharides by Metabolically Engineered Escherichia coli (2006)

Two tetrasaccharides carrying the trisaccharidic Lewis x motif on a GlcNAc or a Gal residue were produced on the gram-scale by high-cell-density cultures of metabolically engineered Escherichia coli strains that overexpressed the Helicobacter pylori futA gene for alpha-3 fucosyltransferase and the Neisseria meningitidis lgtB gene for beta-4 galactosyltransferase. The first compound Galbeta-4(Fucalpha-3)GlcNAcbeta-4GlcNAc was produced by glycosylation of chitinbiose, which was endogenously generated in the bacterial cytoplasm by the successive action of the rhizobial chitin-synthase NodC and the Bacillus circulans chitinase A1, whose genes were additionally expressed in the E. coli strain. The second compound, Galbeta-4(Fucalpha-3)GlcNAcbeta-3Gal, was produced from exogenously added Gal by a strain that was deficient in galactokinase activity and overexpressed the additional N. meningitidis lgtA gene for beta-3 N-acetylglucosaminyltransferase.
3D Mesh Labeling via Deep Convolutional Neural Networks (2015)

This article presents a novel approach for 3D mesh labeling by using deep Convolutional Neural Networks (CNNs). Many previous methods on 3D mesh labeling achieve impressive performances by using predefined geometric features. However, the generalization abilities of such low-level features, which are heuristically designed to process specific meshes, are often insufficient to handle all types of meshes. To address this problem, we propose to learn a robust mesh representation that can adapt to various 3D meshes by using CNNs. In our approach, CNNs are first trained in a supervised manner by using a large pool of classical geometric features. In the training process, these low-level features are nonlinearly combined and hierarchically compressed to generate a compact and effective representation for each triangle on the mesh. Based on the trained CNNs and the mesh representations, a label vector is initialized for each triangle to indicate its probabilities of belonging to various object parts. Eventually, a graph-based mesh-labeling algorithm is adopted to optimize the labels of triangles by considering the label consistencies. Experimental results on several public benchmarks show that the proposed approach is robust for various 3D meshes, and outperforms state-of-the-art approaches as well as classic learning algorithms in recognizing mesh labels.
Effective targeting of the tumor microenvironment for cancer therapy. (2012)

Measurement of HA is a viable biomarker approach for predicting antitumor response in animal models to the HA-depleting agent, PEGPH20.
Functions of signal and signal-anchor sequences are determined by the balance between the hydrophobic segment and the N-terminal charge. (1992)

The signal sequence of secretory proteins and the signal-anchor sequence of type II membrane proteins initiate the translocation of the following polypeptide segments, whereas the signal-anchor sequence of cytochrome P-450-type membrane proteins mediates the membrane insertion of the polypeptide via a signal-recognition particle-dependent mechanism but does not lead to the translocation of the following C-terminal sequences. To establish the structural requirements for the function of signal and signal-anchor sequences, we constructed chimeric proteins containing artificial topogenic sequences in which the N-terminal net charge and the length of the hydrophobic segment were systematically altered. Utilizing an in vitro translation-translocation system, we found that hydrophobic segments consisting of 7-10 leucine residues functioned as signal sequences whereas segments with 12-15 leucine residues showed different topogenic functions, behaving as signal sequences or P-450-type signal-anchor sequences, depending on the N-terminal charge. From these observations, we propose that the function of N-terminal topogenic sequences depends on a balance between the N-terminal charge and the length of the following hydrophobic segment.
Immunohistochemical and ultrastructural detection of advanced glycation end products in atherosclerotic lesions of human aorta with a novel specific monoclonal antibody. (1995)

To elucidate the deposition of advanced glycation end products (AGEs) in aortic atherosclerosis, aortic walls were obtained from 25 autopsy cases and examined immunohistochemically and immunoelectron microscopically with a monoclonal antibody specific for AGEs, 6D12. Among the autopsy cases, atherosclerotic lesions were found in the aortas of 22 cases and were composed of diffuse intimal thickening, fatty streaks, atherosclerotic plaques, and/or complicated lesions. In these cases, intracellular AGE accumulation was demonstrated in the intimal lesions of aortic atherosclerosis in 12 cases. Compared with the diffuse intimal thickening, intracellular AGE accumulation was marked in the fatty streaks and atherosclerotic plaques. Immunohistochemical double staining with 6D12 and monoclonal antibodies for macrophages or muscle actin or a polyclonal antibody for scavenger receptors demonstrated that the AGE accumulation in macrophages or their related foam cells was marked in the diffuse intimal thickening and fatty streak lesions and that almost all macrophages and macrophage-derived foam cells possessed scavenger receptors. Immunoelectron microscopic observation revealed the localization of 6D12-positive reaction in lysosomal lipid vacuoles or electron-dense granules of the foam cells. These results indicate that AGE accumulation occurs in macrophages, smooth muscle cells, and their related foam cells.
Contributions of the cornea and the lens to the aberrations of the human eye (1998)

The relative contributions of optical aberrations of the cornea and the crystalline lens to the final image quality of the human eye were studied. The aberrations of the entire eye were obtained from pairs of double-pass retinal images, and the aberrations of the cornea were obtained from videokeratographic data. Third-order spherical aberration and coma were significantly larger for the cornea than for the complete eye, indicating a significant role of the lens in compensating for corneal aberrations. In a second experiment retinal images were recorded in an eye before and after we neutralized the aberrations of the cornea by having the subjects wear swimming goggles filled with saline water, providing a direct estimate of the optical performance of the crystalline lens.
Development of long-length SmBCO coated conductors using a batch-type reactive co-evaporation method (2008)

In order to fabricate long-length high temperature superconducting coated conductors, we have employed a batch-type reactive co-evaporation process for the deposition of a SmBCO layer on the IBAD-MgO substrate of LaMnO3/epi-MgO/IBAD-MgO/Y2O3/Al2O3/Hastelloy. Critical current densities (Jc) of SmBCO coated conductors were investigated with respect to their composition ratios. Higher Jc was obtained in the Sm-rich, Ba-poor and Cu-rich composition region, compared to the stoichiometric region. The highest critical transition temperature (Tc) of the SmBCO coated conductor was ∼94 K with a narrower transition width of about 0.5 K. A 93 m long SmBCO layer was deposited on a 4 mm wide IBAD-MgO substrate for 90 min. Although some differences in the appearance of pores and Cu oxide precipitates between both ends of the deposited tape exist, the deposited SmBCO layer was dense and biaxially textured. The growth of a highly textured SmBCO layer was maintained up to the thickness of 2.2 µm. A minimum Ic of 305 A/cm-w was achieved at the 27 m section of the 93 m long SmBCO coated conductor at 77 K in self-field.
Base- and Sugar-Modified Cytidine MonophosphateN-Acetylneuraminic Acid (CMP-Neu5Ac) Analogues - Synthesis and Studies with α(2-6)-Sialyltransferase from Rat Liver (2000)

The reaction of sialyl phosphites 1, 22a-d, 28, 39, and 45 with acyl-protected riboside 5-phosphorous acids 2a,b and 23 directly furnished, without addition of a catalyst, under phosphite/phosphate exchange the corresponding β-configured sialyl riboside monophosphates 3a,b, 24a-d, 29, 46, and 47. The synthesis of the starting materials, formation of the products, and their treatment with sodium methanolate in methanol and subsequent hydrolysis of the sialic acid ester moiety to provide the unprotected target molecules 4a,b, 25a-d, 30, 48, and 49 is described. Investigations with α(2-6)-sialyltransferase from rat liver showed that base replacement in CMP-Neu5Ac (4a,b) is not tolerated by the enzyme but that modifications of the 5-, 8-, or 9-position of the neuraminic acid residue (25a-d, 30, 48, 49) are tolerated.