gebhart/patrepeval huggingface dataset:
mTOR Inhibition Induces Compensatory, Therapeutically Targetable MEK Activation in Renal Cell Carcinoma (2014)

Rapamycin derivatives allosterically targeting mTOR are currently FDA approved to treat advanced renal cell carcinoma (RCC), and catalytic inhibitors of mTOR/PI3K are now in clinical trials for treating various solid tumors. We sought to investigate the relative efficacy of allosteric versus catalytic mTOR inhibition, evaluate the crosstalk between the mTOR and MEK/ERK pathways, as well as the therapeutic potential of dual mTOR and MEK inhibition in RCC. Pharmacologic (rapamycin and BEZ235) and genetic manipulation of the mTOR pathway were evaluated by in vitro assays as monotherapy as well as in combination with MEK inhibition (GSK1120212). Catalytic mTOR inhibition with BEZ235 decreased proliferation and increased apoptosis better than allosteric mTOR inhibition with rapamycin. While mTOR inhibition upregulated MEK/ERK signaling, concurrent inhibition of both pathways had enhanced therapeutic efficacy. Finally, primary RCC tumors could be classified into subgroups [(I) MEK activated, (II) Dual MEK and mTOR activated, (III) Not activated, and (IV) mTOR activated] based on their relative activation of the PI3K/mTOR and MEK pathways. Patients with mTOR only activated tumors had the worst prognosis. In summary, dual targeting of the mTOR and MEK pathways in RCC can enhance therapeutic efficacy and primary RCC can be subclassified based on their relative levels of mTOR and MEK activation with potential therapeutic implications.
An Endoplasmic Reticulum-Targeting Signal Sequence Enhances the Immunogenicity of an Immunorecessive Simian Virus 40 Large T Antigen Cytotoxic T-Lymphocyte Epitope (1998)

An immunological hierarchy among three H-2Db-restricted cytotoxic T lymphocyte (CTL) determinants in simian virus 40 (SV40) large T antigen (Tag) was described previously: determinants I and II/III are immunodominant, whereas determinant V is immunorecessive. To assess the immunogenicity of each determinant individually and define mechanisms that contribute to the immunorecessive nature of determinant V, we constructed a panel of recombinant vaccinia viruses (rVVs) expressing minigenes encoding these determinants in various polypeptide contexts. We found the following. (i) Immunization of mice with an rVV encoding full-length SV40 Tag resulted in priming for CTL responses to determinants I and II/III but not determinant V. (ii) rVVs encoding peptide I or II/III in the cytosol or targeted to the endoplasmic reticulum (ER) were highly antigenic and immunogenic. (iii) rVVs encoding peptide V minigenes were antigenic and immunogenic if the peptide was targeted to the ER, expressed in the cytosol with short flanking sequences, or expressed from within a self-protein, murine dihydrofolate reductase. (iv) Presentation of the nonflanked peptide V (preceded by a Met codon only) could be enhanced by using a potent inhibitor of the proteasome. (v) H-2Db-epitope V peptide complexes decayed more rapidly than complexes containing epitope I or II/III peptides. In brefeldin A blocking experiments, functional epitope V complexes were detected longer on targets expressing ER-targeted epitope V than on targets expressing forms of epitope V dependent on the transporter associated with antigen processing. Therefore, limited formation of relatively unstable cell surface H-2Db complexes most likely contributes to the immunorecessive nature of epitope V within SV40 Tag. Increasing the delivery of epitope V peptide to the major histocompatibility complex class I presentation pathway by ER targeting dramatically enhanced the immunogenicity of epitope V.
The cloning and sequence analysis of the aspC and tyrB genes from Escherichia coli K12. Comparison of the primary structures of the aspartate aminotransferase and aromatic aminotransferase of E. coli with those of the pig aspartate aminotransferase isoenzymes (1986)

In this paper we describe the cloning and sequence analysis of the tyrB and aspC genes from Escherichia coli K12, which encode the aromatic aminotransferase and aspartate aminotransferase respectively. The tyrB gene was isolated from a cosmid carrying the nearby dnaB gene, identified by its ability to complement a dnaB lesion. Deletion and linker insertion analysis located the tyrB gene to a 1.7-kilobase NruI-HindIII-digest fragment. Sequence analysis revealed a gene encoding a 43 000 Da polypeptide. The gene starts with a GTG codon and is closely followed by a structure resembling a rho independent terminator. The aspC gene was cloned by screening gene banks, prepared from a prototrophic E. coli K12 strain, for plasmids able to complement the aspC tyrB lesions in the aminotransferase-deficient strain HW225. Sub-cloning and deletion analysis located the aspC gene on a 1.8-kilobase HincII-StuI-digest fragment. Sequence analysis revealed the presence of a gene encoding a 43 000 Da protein, the sequence of which is identical with that previously obtained for the aspartate aminotransferase from E. coli B. Considerable overproduction of the two enzymes was demonstrated. We compared the deduced protein sequences with those of the pig mitochondrial and cytoplasmic aspartate aminotransferases. From the extensive homology observed we are able to propose that the two E. coli enzymes possess subunit structures, subunit interactions and coenzyme-binding and substrate-binding sites that are very similar both to each other and to those of the mammalian enzymes and therefore must also have very similar catalytic mechanisms. Comparison of the aspC and tyrB gene sequences reveals that they appear to have diverged as much as is possible within the constraints of functionality and codon usage.
Test-to-Failure of crystalline silicon modules (2010)

Accelerated lifetime testing of five crystalline silicon module designs was carried out according to the Terrestrial Photovoltaic Module Accelerated Test-to-Failure Protocol. This protocol compares the reliability of various module constructions on a quantitative basis. The modules under test are subdivided into three accelerated lifetime testing paths: 85°C/85% relative humidity with system bias, thermal cycling between -40°C and 85°C, and a path that alternates between damp heat and thermal cycling. The most severe stressor is damp heat with system bias applied to simulate the voltages that modules experience when connected in an array. Positive 600 V applied to the active layer with respect to the grounded module frame accelerates corrosion of the silver grid fingers and degrades the silicon nitride antireflective coating on the cells. Dark I-V curve fitting indicates increased series resistance and saturation current around the maximum power point; however, an improvement in junction recombination characteristics is obtained. Severe shunt paths and cell-metallization interface failures are seen developing in the silicon cells as determined by electroluminescence, thermal imaging, and I-V curves in the case of negative 600 V bias applied to the active layer. Ability to withstand electrolytic corrosion, moisture ingress, and ion drift under system voltage bias are differentiated according to module design. The results are discussed in light of relevance to field failures.
Identification of Insertion Deletion Mutations from Deep Targeted Resequencing (2013)

Taking advantage of the deep targeted sequencing capabilities of next generation sequencers, we have developed a novel two step insertion deletion (indel) detection algorithm (IDA) that can determine indels from single read sequences with high computational efficiency and sensitivity when indels are fractionally less compared to wild type reference sequence. First, it identifies candidate indel positions utilizing specific sequence alignment artifacts produced by rapid alignment programs. Second, it confirms the location of the candidate indel by using the Smith-Waterman (SW) algorithm on a restricted subset of Sequence reads. We demonstrate that IDA is applicable to indels of varying sizes from deep targeted sequencing data at low fractions where the indel is diluted by wild type sequence. Our algorithm is useful in detecting indel variants present at variable allelic frequencies such as may occur in heterozygotes and mixed normal-tumor tissue.
Identification and molecular characterization of a novel Salmonella enteritidis pathogenicity islet encoding an ABC transporter (1999)

Using a newly constructed minitransposon with a phoA reporter gene in a Salmonella enteritidis phoN mutant, we have identified an iron- and pH-inducible lipoprotein gene sfbA, which is a component of a novel ABC-type transporter system required for virulence. This gene is located on a 4 kb Salmonella-specific chromosomal segment, which constitutes a new pathogenicity islet. This islet encodes an outer membrane protein, OmpX, and contains the operon designated sfbABC (Salmonella ferric binding) encoding a putative periplasmic iron-binding lipoprotein SfbA, a nucleotide-binding ATPase SfbB and a cytoplasmic permease SfbC, as predicted by their characteristic signature sequences. Inactivation of the sfbA gene resulted in a mutant that is avirulent and induces protective immunity in BALB/c mice. The wild-type phenotype could be restored by in vivo complementation with the sfbABC operon. This novel transporter might be involved in iron uptake in Salmonella.
Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments (2015)

Plasma consists of DNA released from multiple tissues within the body. Using genome-wide bisulfite sequencing of plasma DNA and deconvolution of the sequencing data with reference to methylation profiles of different tissues, we developed a general approach for studying the major tissue contributors to the circulating DNA pool. We tested this method in pregnant women, patients with hepatocellular carcinoma, and subjects following bone marrow and liver transplantation. In most subjects, white blood cells were the predominant contributors to the circulating DNA pool. The placental contributions in the plasma of pregnant women correlated with the proportional contributions as revealed by fetal-specific genetic markers. The graft-derived contributions to the plasma in the transplant recipients correlated with those determined using donor-specific genetic markers. Patients with hepatocellular carcinoma showed elevated plasma DNA contributions from the liver, which correlated with measurements made using tumor-associated copy number aberrations. In hepatocellular carcinoma patients and in pregnant women exhibiting copy number aberrations in plasma, comparison of methylation deconvolution results using genomic regions with different copy number status pinpointed the tissue type responsible for the aberrations. In a pregnant woman diagnosed as having follicular lymphoma during pregnancy, methylation deconvolution indicated a grossly elevated contribution from B cells into the plasma DNA pool and localized B cells as the origin of the copy number aberrations observed in plasma. This method may serve as a powerful tool for assessing a wide range of physiological and pathological conditions based on the identification of perturbed proportional contributions of different tissues into plasma.
Recent Advances on Surface Engineering of Magnetic Iron Oxide Nanoparticles and Their Biomedical Applications (2007)

Magnetic nanoparticles with appropriate surface coatings are increasingly being used clinically for various biomedical applications, such as magnetic resonance imaging, hyperthermia, drug delivery, tissue repair, cell and tissue targeting and transfection. This is because of the nontoxicity and biocompatibility demand that mainly iron oxide-based materials are predominantly used, despite some attempts to develop 'more magnetic nanomaterials' based on cobalt, nickel, gadolinium and other compounds. For all these applications, the material used for surface coating of the magnetic particles must not only be nontoxic and biocompatible but also allow a targetable delivery with particle localization in a specific area. Magnetic nanoparticles can bind to drugs and an external magnetic field can be applied to trap them in the target site. By attaching the targeting molecules, such as proteins or antibodies, at particles surfaces, the latter may be directed to any cell, tissue or tumor in the body. In this review, different polymers/molecules that can be used for nanoparticle coating to stabilize the suspensions of magnetic nanoparticles under in vitro and in vivo situations are discussed. Some selected proteins/targeting ligands that could be used for derivatizing magnetic nanoparticles are also explored. We have reviewed the various biomedical applications with some of the most recent uses of magnetic nanoparticles for early detection of cancer, diabetes and atherosclerosis.
Recombinant Staphylokinase Variants With Altered Immunoreactivity (1996)

SakSTAR contains three immunodominant epitopes, two of which were eliminated by site-directed mutagenesis, yielding combination mutants with relatively maintained specific activities that were not recognized by a significant fraction of the antibodies elicited in patients by treatment with wildtype SakSTAR. These mutants appear to be suitable for more detailed investigation of their thrombolytic and antigenic properties.
PPP BSD Compression Protocol (1996)

This document describes the use of the Unix Compress compression
protocol for compressing PPP encapsulated packets. This memo provides
information for the Internet community. This memo does not specify an
Internet standard of any kind.
Crystallization of Amorphous Components in Spray-Dried Powders (2007)

Spray-dried powders are typically produced as amorphous particles. Long storage of the particles tends to crystallize the powders, a reaction affected by moisture, time, and temperature. This work has examined partial crystallization from amorphous spray-dried powders by moisture sorption. Powders of citrus fiber with hibiscus extract, maltodextrin, coffee, tea, skim milk, and sucrose were produced with a laboratory-scale spray dryer. The powders were exposed to ambient temperature and various relative humidities, with weight measurements recorded over time. It has been found that, in different materials, the amorphous to crystalline state change is observed at varying rates depending on the relative humidities and molecular weights. This observation may be associated with all amorphous spray-dried materials.
Market Efficiency: A Theoretical Distinction and So What? (2005)

With the aid of some simplifying assumptions, the capital asset pricing model comes to dramatic conclusions about practical matters, such as how to choose an investment portfolio and how to value financial assets. As illustrated in this article, when one particular, clearly unrealistic CAPM assumption is replaced by a more real-world version, some of the dramatic, practical conclusions of CAPM no longer follow. This result has implications for financial practice, research, and pedagogy.
Functional Isolation and Characterization of Human Hematopoietic Stem Cells (1995)

Hematopoietic cells differentiate in steps marked by the acquisition or loss of specific phenotypic characteristics. Human bone marrow cells that were responsive to the early-acting cytokines Kit ligand and interleukin-3 were forced to a metabolic death. The subfraction remaining represented 1 in 10(5) bone marrow mononuclear cells, were determined to be quiescent by cell cycle analysis, and had a stem cell immunophenotype. The cells were highly enriched for long-term culture-initiating cells, were capable of secondary colony formation, and produced both myeloid and lymphoid progeny. Thus, this technically simple strategy led to the efficient purification of cells with characteristics of hematopoietic stem cells.
A SNoW-Based Face Detector (1999)

A novel learning approach for human face detection using a network of linear units is presented. The SNoW learning architecture is a sparse network of linear functions over a pre-defined or incrementally learned feature space and is specifically tailored for learning in the presence of a very large number of features. A wide range of face images in different poses, with different expressions and under different lighting conditions are used as a training set to capture the variations of human faces. Experimental results on commonly used benchmark data sets of a wide range of face images show that the SNoW-based approach outperforms methods that use neural networks, Bayesian methods, support vector machines and others. Furthermore, learning and evaluation using the SNoW-based method are significantly more efficient than with other methods.
Potent and specific inhibition of p60v-src protein kinase both in vivo and in vitro by radicicol. (1992)

A fungal metabolite, radicicol, with a macrocyclic ring induced the reversal of transformed phenotypes of v-src-transformed fibroblasts (Rous sarcoma virus-transformed 3Y1 rat fibroblast) at a quite low concentration of 0.1 microgram/ml. Actin stress fibers reappeared in the transformed cells after treatment with radicicol. Radicicol reduced the intracellular level of autophosphorylation of p60v-src as well as the level of other tyrosine-phosphorylated proteins in a dose-dependent manner. In vitro kinase assay revealed that radicicol effectively inhibited not only autophosphorylation but also transphosphorylation activities of purified p60v-src with a concentration producing 50% inhibition of 0.1 microgram/ml. However, radicicol showed no inhibitory effect on protein kinase C or protein kinase A. These results suggest that radicicol is a novel and specific protein-tyrosine kinase inhibitor and that the decreased level of tyrosine kinase activity of p60v-src causes reversion of transformed phenotypes of Rous sarcoma virus-transformed 3Y1 rat fibroblast. Furthermore, differentiation of Friend leukemia cells, which is one of the known characteristic phenomena associated with the inhibition of tyrosine kinase, was also induced in the concentration range of 0.05-0.5 microgram/ml, suggesting that the agent is useful for the analysis of differentiation as well as the kinase-mediated signal transduction.
CD4 + CD25 + regulatory T cells control CD8 + T-cell effector differentiation by modulating IL-2 homeostasis (2011)

CD4(+)CD25(+) regulatory T cells (Treg) play a crucial role in the regulation of immune responses. Although many mechanisms of Treg suppression in vitro have been described, the mechanisms by which Treg modulate CD8(+) T cell differentiation and effector function in vivo are more poorly defined. It has been proposed, in many instances, that modulation of cytokine homeostasis could be an important mechanism by which Treg regulate adaptive immunity; however, direct experimental evidence is sparse. Here we demonstrate that CD4(+)CD25(+) Treg, by critically regulating IL-2 homeostasis, modulate CD8(+) T-cell effector differentiation. Expansion and effector differentiation of CD8(+) T cells is promoted by autocrine IL-2 but, by competing for IL-2, Treg limit CD8(+) effector differentiation. Furthermore, a regulatory loop exists between Treg and CD8(+) effector T cells, where IL-2 produced during CD8(+) T-cell effector differentiation promotes Treg expansion.
A steroid-inducible gene expression system for plant cells. (1991)

Promoters that allow the selective induction of gene expression in vivo constitute an important methodology in eukaryotic organisms such as yeast and the fruit fly, but to date no such system has been described for higher plants. Given the fact that mammalian steroid receptors can function as hormone-dependent inducers of gene expression in heterologous systems, the feasibility of using mammalian steroid hormones as selective inducers of plant gene expression was investigated. Here it is shown that the glucocorticoid receptor expressed in plant cells is capable of activating a test gene linked to glucocorticoid response elements, providing the transfected plant cells are treated with glucocorticoid hormone. Nanomolar concentrations of glucocorticoids are sufficient to induce gene expression more than 150-fold, without causing detectable alterations in the physiology of the cultured plant cells. These findings indicate that glucocorticoid induction of steroid-responsive promoters should provide a general method for regulating gene expression in plant cells and imply that such a system might ultimately function in whole plants such as Arabidopsis thaliana.
Binding of the proteoglycan decorin to collagen type VI. (1992)

We have examined the interactions between the small dermatan sulfate proteoglycan decorin and collagen types I-VI using solid phase binding assays. The results of these studies showed that 125I-decorin bound most efficiently to collagen type VI in a time- and concentration-dependent manner. Furthermore, this interaction was specific and of moderately high affinity (Kd approximately 3 x 10(-7) M). Binding of decorin to collagen type VI appears to involve the decorin core protein rather than the glycosaminoglycan side chains, since the isolated core protein as well as a recombinant fusion protein containing a major segment (65%) of the human decorin core protein inhibited binding of 125I-decorin to collagen type VI. Other related proteoglycans and their respective core proteins also inhibited the binding of 125I-decorin to collagen type VI, whereas unrelated proteins and isolated glycosaminoglycan chains were without effect. In addition to decorin, collagen type II was also shown to bind to immobilized collagen type VI. Both interactions were effectively inhibited by preincubation of the immobilized collagen VI with decorin or collagen type II. These results suggested that the collagen type VI molecule has binding sites for collagen type II and decorin which are located in close proximity on the collagen type VI molecule. Possible functional roles of these interactions are discussed.
Operative Strategie bei septischen Komplikationen im Abdomen (1994)

Bei der abdominalen Sepsis ist die chirurgische Herdsanierung (Fokussanierung) für die Prognose weiterhin von entscheidender Bedeutung. Therapieprinzipien bei umschriebenen Infektionen (lokale Peritonitis) sind die Fokussanierung durch einzeitiges offenes Vorgehen (z.B. Cholezystitis, Divertikulitis) und die Fokussanierung durch perkutane Drainagesysteme (z.B. Abszesse parenchymatöser Organe, Galleleck). Bei der infizierten Pankreasnekrose bietet sich die Fokussanierung durch Drainage und Kompartimentbildung an. Durch die extraperitoneale Kompartimentbildung der Pankreasloge kann das infizierte Sekret ohne Kontamination der primär nicht infizierten Bauchhöhle nach auβen abgeleitet werden. Bei der diffusen Peritonitis umfaβt die chirurgische Therapie die Versorgung der Infektionsquelle sowie die Therapie der existierenden Peritonitis und der Infektionsfolgen. Dabei kommt der Fokussanierung im oberen Gastrointestinaltrakt und rechten Oberbauch wegen der technisch schwierigen Versorgungsmöglichkeit eine besondere Bedeutung zu. Die chirurgische Weiterbehandlung in Form von programmierten Relaparotomien oder einer primär offenen Behandlung (Laparostoma) richtet sich nach dem Verschmutzungsgrad der Bauchhöhle und dem Allgemeinzustand des Patienten.
hnRNP PROTEINS AND THE BIOGENESIS OF mRNA (1993)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More