gebhart/patrepeval huggingface dataset:
Increased synthesis of secreted proteins induces expression of glucose-regulated proteins in butyrate-treated Chinese hamster ovary cells (1989)

The effects of increased synthesis of secreted proteins expressed from stably integrated heterologous genes in Chinese hamster ovary (CHO) cells following treatment with sodium butyrate was studied. Butyrate treatment increased expression of mRNA transcribed from the adenovirus major late promoter in combination with the SV40 enhancer for Factor VIII, von Willebrand factor, and erythropoietin. Increased levels of mRNA were compared to increases in intracellular primary translation product and secreted protein. While von Willebrand factor and erythropoietin were efficiently secreted, Factor VIII was not. Increased expression of all these proteins induced expression of the glucose-regulated proteins, GRP78 and GRP94. However, increased Factor VIII synthesis was correlated with an 80-fold increase in GRP78 mRNA and a 10-fold increase in GRP94 mRNA. These data suggest that elevated levels of newly synthesized secretion-competent protein as well as misfolded protein induce the glucose-regulated proteins.
Vascular endothelial growth factor receptor-2-blocking antibody potentiates radiation-induced long-term control of human tumor xenografts. (2001)

Antiangiogenic therapy can enhance radiation-induced tumor growth inhibition. However, the effects of combined antiangiogenic and radiation therapy on long-term tumor control and normal tissue response have not been reported. We treated mice bearing two different human tumor xenografts with anti-vascular endothelial growth factor receptor-2 antibody (DC101) and five dose fractions of local radiation and followed them for at least 6 months. DC101 significantly decreased the dose of radiation necessary to control 50% of tumors locally. The decrease was 1.7- and 1.3-fold for the moderately radiosensitive small cell lung carcinoma 54A and the highly radioresistant glioblastoma multiforme U87, respectively. In contrast to tumors, no increase in skin radiation reaction by the antibody was detected. Surprisingly, 44% of mice bearing 54A tumor developed clear ascites after DC101 treatment at its highest dose; this was fatal to 20% of mice. This adverse effect was seen only in mice that received whole-body irradiation 1 day before tumor implantation. The encouraging results on two human tumor xenografts suggest that vascular endothelial growth factor receptor-2 blockade merits further investigation to assess its potential as an enhancer of radiation therapy in the clinic.
A Synthetic Heparanase Inhibitor Reduces Proteinuria in Passive Heymann Nephritis (2004)

The β-D-endoglycosidase heparanase has been proposed to be important in the pathogenesis of proteinuria by acting to selectively degrade the negatively charged side chains of heparan sulfate proteoglycans (HSPG) within the glomerular basement membrane (GBM). A loss of the negatively charged HSPG may result in alteration of the permselective properties of the GBM, loss of glomerular epithelial and endothelial cell anchor points, and liberation of growth factors. This study examined the effect of PI-88, a sulfated oligosaccharide heparanase inhibitor, on renal function, glomerular ultrastructure, and proteinuria. Continuous PI-88 infusion at 25 mg/kg per d did not adversely affect animal behavior, growth, or GFR. Cortical tubular vacuolation, however, was observed by light microscopy, and GBM thickness was significantly reduced in these animals (P < 0.0002). Tissue distribution studies using [35S]-labeled PI-88 revealed high levels of radioactivity in the kidney after a single subcutaneous injection of 25 mg/kg, suggesting protracted accumulation; moreover, active PI-88 was detected in urine. In passive Heymann nephritis, PI-88 delivered as a continuous infusion at 25 mg/kg per d significantly reduced autologous-phase proteinuria, at day 14 (P < 0.009), in the absence of altered sheep antibody deposition, C5b-9 deposition, and circulating rat anti-sheep antibody titers. Glomerular vascular endothelial growth factor and fibroblast growth factor expression was unaffected by PI-88 administration. However, PI-88 administration significantly prevented glomerular HSPG loss as demonstrated by quantitative immunofluorescence studies (P < 0.0001) in the absence of altered agrin distribution. These data therefore confirm the importance of heparanase in the development of proteinuria.
Serum Levels of TNF‐α, IFN‐γ, IL‐6, IL‐8,IL‐12, IL‐17, and IL‐18 in Patients With Active Psoriasis andCorrelation With Disease Severity (2005)

Recent progress in the understanding of psoriasis has shown that the regulation of local and systemic cytokines plays an important role in its pathogenesis. The most often used psoriasis score is the psoriasis area and severity index (PASI). A simple laboratory test from a blood sample would be an attractive, patient-independent, and observer-independent marker of disease severity. To this end, we evaluated the association of serum levels of some proinflammatory cytokines in vivo and their correlation with severity of psoriasis. The serum levels of cytokines levels were determined with the use of the ELISA method. All mean values except IL-17 levels of patients were significantly higher than those of controls. There was a significant correlation between serum levels of IFN-gamma, IL-12, IL-17, and IL-18, and severity of the disease. Psoriasis can be described as a T-cell-mediated disease, with a complex role for a variety of cytokines, which has led to the development of new immunomodulatory therapies. In this study, serum TNF-alpha, IFN-gamma, IL-6, IL-8, IL-12, and IL-18 levels were significantly higher in active psoriatic patients than in controls. Furthermore, high levels of IFN-gamma, IL-12, and IL-18 correlated with the clinical severity and activity of psoriasis, and those measurements of serum levels of these cytokines may be objective parameters for the disease severity.
Degradation of Atrazine in Estuarine Water/Sediment Systems and Soils (1982)

Abstract Herbicides have been postulated as a cause of the disappearance of submerged aquatic vegetation in the Chesapeake Bay. This research was undertaken to determine the longevity of 2‐chloro‐4‐ethylamino‐6‐isopropylamino‐ s ‐triazine (atrazine) in two estuarine water/sediment microcosm systems and two agricultural soil systems over an 80‐d period under aerobic and low‐O 2 conditions. Atrazine degradation proceeded more rapidly in the estuarine systems than in the soil systems. The disappearance of atrazine from the estuarine water was relatively rapid, with the half‐life (50% remaining in the water column) of the parent compound ranging from 3 to 12 d. Atrazine half‐life was determined to be 15 and 20 d for the two estuarine sediments and 330 and 385 d for the two agricultural soils. Hydroxyatrazine (2‐hydroxy‐4‐ethylamino‐6‐isopropylamino‐ s ‐triazine) was the major short‐term metabolite in both the estuarine and terrestrial systems. By the 21st day of the experiment, the percent of total extracted residues corresponding to atrazine and hydroxyatrazine were: 65, 20 and 10, 85 for the two estuarine systems; and 66, 29 and 93, 5 for the two soil systems. Decreased O 2 levels had little effect on atrazine degradation in the experimental systems. The rapid degradation of atrazine to hydroxyatrazine in estuarine water and sediment indicates a low probability for the accumulation of atrazine in the estuary.
Hrs, a FYVE finger protein localized to early endosomes, is implicated in vesicular traffic and required for ventral folding morphogenesis (1999)

Hrs is an early endosomal protein homologous to Vps27p, a yeast protein required for vesicular trafficking. Hrs has a FYVE double zinc finger domain, which specifically binds phosphatidylinositol(3)-phosphate and is conserved in several proteins involved in vesicular traffic. To understand the physiological role of Hrs, we generated mice carrying a null mutation of the gene. Hrs homozygous mutant embryos developed with their ventral region outside of the yolk sac, had two independent bilateral heart tubes (cardia bifida), lacked a foregut, and died around embryonic day 11 (E11). These phenotypes arise from a defect in ventral folding morphogenesis that occurs normally around E8.0. Significant apoptosis was detected in the ventral region of mutant embryos within the definitive endoderm, suggesting an important role of this germ layer in ventral folding morphogenesis. Abnormally enlarged early endosomes were detected in the mutants in several tissues including definitive endoderm, suggesting that a deficiency in vesicular transport via early endosomes underlies the mutant phenotype. The vesicular localization of Hrs was disrupted in cells treated with wortmannin, implicating Hrs in the phosphatidylinositol 3-kinase pathway of membrane trafficking.
Facile synthesis of highly stable and well-dispersed mesoporous ZrO2/carbon composites with high performance in oxidative dehydrogenation of ethylbenzene (2010)

Highly ordered mesoporous ZrO(2)/carbon (FDU-15) composites have been synthesized via a facile evaporation induced triconstituent co-assembly (EISA) approach by using Pluronic F127 as a template and zirconium oxychloride octahydrate and resol as Zr and carbon sources. The synthesized mesoporous composites exhibit a highly ordered two-dimensional (2-D) hexagonal mesostructure with relatively high specific surface areas (up to 947 m(2) g(-1)), pore sizes around 3.8 nm and high pore volumes (up to 0.71 cm(3) g(-1)). The results clearly show that the crystalline zirconia nanoparticles (ca. 1.9-3.9 nm) are well-dispersed in amorphous matrices of the ordered mesoporous carbon FDU-15 materials, which construct the nanocomposites. The ordered mesostructures of the obtained ZrO(2)/FDU-15 composites can be well-retained even at the high pyrolysis temperature (up to 900 degrees C), suggesting a high thermal stability. The zirconia content of the ZrO(2)/FDU-15 composites can be tunable in a wide range (up to 47%). Moreover, the resultant mesoporous ZrO(2)/FDU-15 composites exhibit high catalytic activity in oxidative dehydrogenation (ODH) of ethylbenzene (EB) to styrene (ST), with high ethylbenzene conversion (59.6%) and styrene selectivity (90.4%), which is mainly attributed to the synergistic catalytic effect between the oxygen-containing groups located on the carbon pore walls and weakly basic sites of the nanocrystalline ZrO(2). Furthermore, the high specific surface areas and opening pore channels are also responsible for their high catalytic activity. Therefore, it is a very promising catalyst material in styrene production on an industrial scale.
Galactosylation of human IgG monoclonal anti-D produced by EBV-transformed B-lymphoblastoid cell lines is dependent on culture method and affects Fc receptor-mediated functional activity. (1994)

Human monoclonal antibodies to the Rh D blood group antigen were produced by EBV-transformed B cell lines grown in serum-free medium in low density (LD) static cultures or high density (HD) hollow fiber bioreactors. Glycosylation analysis of the purified IgG was determined by the binding of anti-GlcNAc monoclonal antibody (GN7) and by analysis of oligosaccharides released by hydrazinolysis. The LD MAbs had only trace levels of agalactosyl oligosaccharides (G0), the major species (> 70%) being digalactosyl structures (G2). The HD MAbs, by contrast, contained about 10% G0 and relatively high levels (over 50%) of monogalactosyl (G1) oligosaccharides. beta 1-4 galactosyltransferase activity in the LD cell lines was similar to that found previously for other EBV-transformed B cell lines. The predominant oligosaccharides of an IgG3 anti-D, BRAD-3, contained bisecting N-acetylglucosamine. In functional assays with Fc receptor (Fc gamma R) positive effector cells, the highly galactosylated LD form of BRAD-3 was more active than the HD form in monocyte (Fc gamma RI) and K cell (Fc gamma RIII) mediated lysis of erythrocytes in ADCC assays, although these preparations showed no difference in Fc gamma RI-mediated rosette formation with U937 cells. One MAb, JAC10, was over 10-fold less active than two other IgG1 MAbs, 2B6 and BRAD-5, at mediating lysis of erythrocytes by Fc gamma RIII+ K cells; differences in sialylation may have contributed to this heterogeneity.(ABSTRACT TRUNCATED AT 250 WORDS)
Synthesis and Performance of Novel Hydrogels Coatings for Implantable Glucose Sensors (2008)

Novel hydrogel polymers were prepared, characterized, coated on implantable glucose sensors, and tested in vitro and in vivo. The effects of 2,3-dihydroxypropyl methacrylate (DHPMA) on the swelling, morphology, glass transition (Tg), and water structure were studied. The results show that the degree of swelling increases with increasing DHPMA content. Scanning electron microscopy (SEM) studies identified uniform, porous structures in samples containing 60–90 mol % DHPMA. Glass-transition temperatures did not change significantly with DHPMA content, but the ratio of freezing to nonfreezing water tended to increase with DHPMA content. Sensors coated with different hydrogels were prepared and in vitro evaluations were performed. The 80% DHPMA hydrogels exhibited optimum sensitivity, response, and stability when coated directly onto the sensor or top of a polyurethane (PU) layer. The histology results show that 80% DHPMA samples exhibit reduced fibrosis and reduced inflammation, resulting in a longer functional life.
ROLE OF INTERLEUKIN-6 IN EXPERIMENTAL CANCER CACHEXIA (1993)

Journal of Immunotherapy with Emphasis on Tumor Immunology: January 1993 - Volume 13 - Issue 1 - p 73
Expression and regulation of the PD-L1 immunoinhibitory molecule on microvascular endothelial cells. (2002)

These data show the expression of a novel B7-like molecule on murine ECs that is mediated by IFN-alpha, -beta, and -gamma, and suggest a potential pathway by which ECs may modulate T-cell function.
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs (2013)

Supplementary data are available at Bioinformatics online.
Lactic Acid Bacteria and Human Health (1990)

Although claims for health and nutritional benefits have been made for lactic acid bacteria in fermented dairy products for nearly a century, the nutritional and therapeutic value of these organisms is still controversial. This article will review the scientific basis of these claims. There are numerous studies showing fermentation of food with lactobacilli increase the quantity, availability, digestibility, and assimilability of nutrients. The basis for this conclusion comes from direct measurements of vitamin synthesis and from increased feed efficiency when fermented products are fed to animals. There have been a number of studies showing that various fermented dairy products lower serum cholesterol levels in humans and animals. These studies are reviewed and the validity of these findings are assessed. A summary of the evidence indicating that lactase deficient individuals can eat yogurt and the mechanisms involved in this toleration is reviewed. The role of fermented dairy products in inhibiting tumor growth and chemically induced tumors in animals is discussed and the possible mechanisms involved in this protective effect are reviewed. Fermented dairy products and lypholized lactobacilli preparations have been shown to be useful in treating and preventing various intestinal infections including; salmonellosis, shigellosis and antibiotic induced diarrhea. In this context a specific lactobacillus designated GG has been shown to be useful in treating recurring diarrhea caused by a toxin produced by Clostridium difficile.
Self-expanding Biliary Stents: Preliminary Clinical Experience (1989)

Nine self-expanding metallic stents were implanted in 7 patients to relieve biliary obstruction. One patient had a benign stricture and 6 patients had malignant stenoses. The stent was inserted percutaneously on a 7 F delivery catheter in 6 patients. Endoscopic transpapillary implantation was performed in one patient. After release the stent expanded to a diameter of 8-10 mm. The correct position was checked by fluoroscopy and cholangiography. In addition, percutaneous cholangioscopy was carried out in 6 patients. No complications were observed within 30 days. Clinical improvement was seen in all patients. After a mean follow-up period of 11 weeks (range: 3-17) 6 of the 7 patients are still alive with no evidence of biliary reobstruction. One patient died of disseminated malignancy. The initial results are promising. The wide-bore diameter, the macroporous configuration and the small surface area of the implanted self-expanding stents would seem to be associated with lower rates of infection, clogging and migration as compared with conventional endoprostheses. Further trials are warranted to determine the future role of self-expanding stents in biliary obstruction.
Performance analysis of coded cooperation diversity (2004)

In a multi-user environment, coded cooperation creates transmit diversity for small mobiles (e.g. handsets) that cannot support more than one antenna. Coded cooperation allows these mobiles to share their antennas via a simple and effective coding method. In this work we present an analytical methodology for evaluating the performance of coded cooperation. We develop tight bounds for bit and block error capabilities, showing in the process that coded cooperation achieves maximal diversity. We demonstrate the validity of these bounds via simulations.
The Effect of Particle Size of Whole-Grain Flour on Plasma Glucose, Insulin, Glucagon and Thyroid-Stimulating Hormone in Humans (1999)

The particle size of whole grain wheat flour did not substantially affect glycemic responses.
Construction of a Dual Chain Pseudotetrameric Chicken Avidin by Combining Two Circularly Permuted Avidins (2004)

Two distinct circularly permuted forms of chicken avidin were designed with the aim of constructing a fusion avidin containing two biotin-binding sites in one polypeptide. The old N and C termini of wild-type avidin were connected to each other via a glycine/serine-rich linker, and the new termini were introduced into two different loops. This enabled the creation of the desired fusion construct using a short linker peptide between the two different circularly permuted subunits. The circularly permuted avidins (circularly permuted avidin 5 --> 4 and circularly permuted avidin 6 --> 5) and their fusion, pseudotetrameric dual chain avidin, were biologically active, i.e. showed biotin binding, and also displayed structural characteristics similar to those of wild-type avidin. Dual chain avidin facilitates the development of dual affinity avidins by allowing adjustment of the ligand-binding properties in half of the binding sites independent of the other half. In addition, the subunit fusion strategy described in this study can be used, where applicable, to modify oligomeric proteins in general.
Expansion of Human Embryonic Stem Cells In Vitro (2008)

This unit describes a protocol for the large-scale expansion of karyotypically normal human embryonic stem cells (hESCs). hESCs can be maintained indefinitely as dense colonies that are mechanically cut into pieces, which are subsequently transferred to fresh organ culture dishes seeded with primary mouse embryonic fibroblasts (MEFs). hESCs can also be enzymatically passaged (bulk culture); however, over time, this style of culturing may lead to the acquisition of chromosomal abnormalities. Nevertheless, enzymatic passaging can be used for short periods (up to 25 passages) without the appearance of cells with abnormal karyotypes.
Significant expression of IGFBP2 in breast cancer compared with benign lesions (2005)

IGFBP2 mitogenic signals of autocrine/paracrine regulatory mechanisms may be responsible for the growth of breast carcinomas and IGFBP2 may be an independent indicator of malignancy.
Optimization of the performance of a thin film permalloy magnetoresistive sensor (1984)

Basic factors influencing the sensitivity of resistance sensors of magnetic field have been determined. The relation of these factors and sensor geometric form, taking into account the field non-uniformity, has been investigated numerically and experimentally. After introduction of new mathematical model of a sensor, the optimization for the two modes - for limited dissipated power and for limited supply voltage has been carried out. It has been concluded that for a given film thickness and a gap between the sensor paths (depending on the manufacturing technology) there exists an optimal value of a path width and an angle between the path and anisotropy axis. The sensor sensitivity reaches maximum in this optimum point.
Crystal Structure of a Subcomplex of Human Transcription Factor TFIID Formed by TATA Binding Protein-associated Factors hTAF4 (hTAFII135) and hTAF12 (hTAFII20) (2002)

The crystal structure is presented of a complex formed by the interacting domains from two subunits of the general transcription factor TFIID, the human TATA binding protein-associated factors hTAF4 (hTAF(II)135) and hTAF12 (hTAF(II)20). In agreement with predictions, hTAF12 forms a histone fold that is very similar to that of histone H2B, yet unexpected differences are observed between the structures of the hTAF12 interaction domain of hTAF4 and histone H2A. Most importantly, the hTAF4 fragment forms only the first two helices of a classical histone fold, which are followed by a 26-residue disordered region. This indicates that either full-length TAF4 contains an unusually long connecting loop between its second and third helix, and this helix is not required for stable interaction with TAF12, or that TAF4 represents a novel class of partial histone fold motifs. Structural models and structure-based sequence alignments support a role for TAF4b and hSTAF42/yADA1 as alternative partners for TAF12 and are consistent with the formation of nucleosome-like histone-fold octamers through interaction of TAF12 with a TAF6-TAF9 tetramer, yet argue against involvement of TAF12-containing histone-fold pairs in DNA binding.
A previously undescribed pathway for pyrimidine catabolism (2006)

The b1012 operon of Escherichia coli K-12, which is composed of seven unidentified ORFs, is one of the most highly expressed operons under control of nitrogen regulatory protein C. Examination of strains with lesions in this operon on Biolog Phenotype MicroArray (PM3) plates and subsequent growth tests indicated that they failed to use uridine or uracil as the sole nitrogen source and that the parental strain could use them at room temperature but not at 37 degrees C. A strain carrying an ntrB(Con) mutation, which elevates transcription of genes under nitrogen regulatory protein C control, could also grow on thymidine as the sole nitrogen source, whereas strains with lesions in the b1012 operon could not. Growth-yield experiments indicated that both nitrogens of uridine and thymidine were available. Studies with [(14)C]uridine indicated that a three-carbon waste product from the pyrimidine ring was excreted. After trimethylsilylation and gas chromatography, the waste product was identified by mass spectrometry as 3-hydroxypropionic acid. In agreement with this finding, 2-methyl-3-hydroxypropionic acid was released from thymidine. Both the number of available nitrogens and the waste products distinguished the pathway encoded by the b1012 operon from pyrimidine catabolic pathways described previously. We propose that the genes of this operon be named rutA-G for pyrimidine utilization. The product of the divergently transcribed gene, b1013, is a tetracycline repressor family regulator that controls transcription of the b1012 operon negatively.