gebhart/patrepeval huggingface dataset:
Cold Shock of a Hyperthermophilic Archaeon: Pyrococcus furiosus Exhibits Multiple Responses to a Suboptimal Growth Temperature with a Key Role for Membrane-Bound Glycoproteins (2004)

The hyperthermophilic archaeon, Pyrococcus furiosus, was grown on maltose near its optimal growth temperature, 95 degrees C, and at the lower end of the temperature range for significant growth, 72 degrees C. In addition, cultures were shocked by rapidly dropping the temperature from 95 to 72 degrees C. This resulted in a 5-h lag phase, during which time little growth occurred. Transcriptional analyses using whole-genome DNA microarrays representing 2,065 open reading frames (ORFs) in the P. furiosus genome showed that cells undergo three very different responses at 72 degrees C: an early shock (1 to 2 h), a late shock (5 h), and an adapted response (occurring after many generations at 72 degrees C). Each response involved the up-regulation in the expression of more than 30 ORFs unique to that response. These included proteins involved in translation, solute transport, amino acid biosynthesis, and tungsten and intermediary carbon metabolism, as well as numerous conserved-hypothetical and/or membrane-associated proteins. Two major membrane proteins were evident after one-dimensional sodium dodecyl sulfate-gel analysis of cold-adapted cells, and staining revealed them to be glycoproteins. Their cold-induced expression evident from the DNA microarray analysis was confirmed by quantitative PCR. Termed CipA (PF0190) and CipB (PF1408), both appear to be solute-binding proteins. While the archaea do not contain members of the bacterial cold shock protein (Csp) family, they all contain homologs of CipA and CipB. These proteins are also related phylogenetically to some cold-responsive genes recently identified in certain bacteria. The Cip proteins may represent a general prokaryotic-type cold response mechanism that is present even in hyperthermophilic archaea.
Design of the Boeing 777 electric system (2003)

The Boeing 777 electric system is being designed to take advantage of technologically proven concepts, as well as new concepts, in order to provide a fully automated state-of-the-art system. The system is comprised of two independent electrical systems, the main and the backup. Automation of the system is performed by the state-of-the-art, microprocessor-based control units. These units perform system control, protection, and built-in-test functions. Each control unit has redundant two-way communications through the ARINC 629 communications bus. By using this communication bus, the number of discrete wires previously required for similar systems has been significantly reduced, thereby allowing considerable reduction of the interface circuits and reduction in weight.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
AN INTEGRATED OPTICAL DETECTOR FOR MICROFABRICATED ELECTRICAL FIELD FLOW FRACTIONATION SYSTEM (2003)

This paper addresses the fabrication and testing of a polymer optical waveguide detector for a micro electrical field flow fractionation system. This study involves fabrication of a monolithically integrated p-electrical FFF channel and a waveguide detector.
Molecular Biomarker–Based Screening for Early Detection of Cervical Cancer (2001)

This method appears to be a robust and reliable means of detecting cervical dysplasia and is now being evaluated in additional clinical studies.
Silver-Palladium Surfaces Inhibit Biofilm Formation (2009)

Undesired biofilm formation is a major concern in many areas. In the present study, we investigated biofilm-inhibiting properties of a silver-palladium surface that kills bacteria by generating microelectric fields and electrochemical redox processes. For evaluation of the biofilm inhibition efficacy and study of the biofilm inhibition mechanism, the silver-sensitive Escherichia coli J53 and the silver-resistant E. coli J53[pMG101] strains were used as model organisms, and batch and flow chamber setups were used as model systems. In the case of the silver-sensitive strain, the silver-palladium surfaces killed the bacteria and prevented biofilm formation under conditions of low or high bacterial load. In the case of the silver-resistant strain, the silver-palladium surfaces killed surface-associated bacteria and prevented biofilm formation under conditions of low bacterial load, whereas under conditions of high bacterial load, biofilm formation occurred upon a layer of surface-associated dead bacteria.
Cancer/testis antigen CT45: Analysis of mRNA and protein expression in human cancer (2009)

CT45 is a cancer/testis gene that we previously identified by massively parallel signature sequencing. Encoded by a multigene family on chromosome X, CT45 showed restricted mRNA expression to normal testis and various cancers. In this study, monoclonal antibodies were generated against recombinant CT45 protein, and CT45 protein expression in normal and tumor tissues was evaluated by immunohistochemical analysis. In adult normal tissue, CT45 expression was restricted to testicular germ cells, detected as a nuclear protein mainly at the stage of primary spermatocytes. In tumors, CT45 protein expression correlated with the mRNA levels detected by quantitative RT-PCR, and most lung cancer and ovarian cancers with CT45 mRNA at levels >1% of testicular expression were CT45 protein-positive. In positive cases, CT45 showed expression patterns that ranged from diffuse strong staining to heterogeneous and patchy expression. In lung cancer, CT45 expression was least frequent in adenocarcinoma, more frequent in squamous cell carcinoma and neuroendocrine tumors. Using tissue microarrays, 376 lung cancer, 219 ovarian cancer and 155 breast cancer were evaluated for CT45 protein expression. The expression frequency was highest in ovarian cancer (37%), followed by lung cancer (13%) and lowest in breast cancer (<5%). Given the focal nature of CT45 expression in many cases, these numbers represented the minimal frequency of expression in these tumor types. In summary, the expression frequency and characteristics of CT45 expression are similar to other CT cancer vaccine targets currently in clinical trials, e.g., NY-ESO-1 and MAGE-A, suggesting CT45 as a potentially useful cancer target.
The presence of active von Willebrand factor under various pathological conditions (2007)

Freshly secreted VWF consists of ultra-large multimers that interact spontaneously with platelets at the endothelial cell surface. Proteolysis of ultra-large VWF by a member of the disintegrin and metalloprotease with thrombospondin motif family (ADAMTS13) reduces both multimeric size and accessibility of platelet-adhesion sites. The resulting VWF molecules circulate as inactive multimers, which regain their platelet-adhesion capacity upon binding to the subendothelial matrix, in particular under conditions of high shear. Unfortunately, mechanisms responsible for suppression of circulating plasma levels of active VWF are hampered in a number of pathological conditions, leading to VWF-platelet aggregates associated with thrombotic complications or thrombocytopenia. A recently developed assay allowed us to monitor the presence of circulating active VWF and we found that several diseases are characterized by increased levels. Further analysis provided insight into mechanisms contributing to the presence of active VWF, which revealed that beta2-glycoprotein I may act as a natural regulator of VWF-platelet interactions.
Dissecting the in Vivo Metabolic Potential of Two Human Gut Acetogens (2010)

Fermenting microbial communities generate hydrogen; its removal through the production of acetate, methane, or hydrogen sulfide modulates the efficiency of energy extraction from available nutrients in many ecosystems. We noted that pathway components for acetogenesis are more abundantly and consistently represented in the gut microbiomes of monozygotic twins and their mothers than components for methanogenesis or sulfate reduction and subsequently analyzed the metabolic potential of two sequenced human gut acetogens, Blautia hydrogenotrophica and Marvinbryantia formatexigens in vitro and in the intestines of gnotobiotic mice harboring a prominent saccharolytic bacterium. To do so, we developed a generally applicable method for multiplex sequencing of expressed microbial mRNAs (microbial RNA-Seq) and, together with mass spectrometry of metabolites, showed that these organisms have distinct patterns of substrate utilization. B. hydrogenotrophica targets aliphatic and aromatic amino acids. It increases the efficiency of fermentation by consuming reducing equivalents, thereby maintaining a high NAD(+)/NADH ratio and boosting acetate production. In contrast, M. formatexigens consumes oligosaccharides, does not impact the redox state of the gut, and boosts the yield of succinate. These findings have strategic implications for those who wish to manipulate the hydrogen economy of gut microbial communities in ways that modulate energy harvest.
MCMC for Wind Power Simulation (2008)

This paper contributes a Markov chain Monte Carlo (MCMC) method for the direct generation of synthetic time series of wind power output. It is shown that obtaining a stochastic model directly in the wind power domain leads to reduced number of states and to lower order of the Markov chain at equal power data resolution. The estimation quality of the stochastic model is positively influenced since in the power domain, a lower number of independent parameters is estimated from a given amount of recorded data. The simulation results prove that this method offers excellent fit for both the probability density function and the autocorrelation function of the generated wind power time series. The method is a first step toward simple stochastic black-box models for wind generation.
Effect of tendon orientation on MR imaging signal intensity: a manifestation of the "magic angle" phenomenon. (1991)

To determine whether orientation in the static field may be responsible for the frequent occurrence of increased signal intensity within normal tendons at magnetic resonance (MR) imaging, seven healthy volunteers were imaged by means of a 1.5-T unit and standard clinical pulse sequences. The wrist, ankle, and shoulder regions were evaluated with local coils. Imaging was performed with tendon orientations ranging from 0 degree to 90 degrees in relation to the constant magnetic induction field (B0). Markedly increased intratendinous signal intensity was observed at the "magic angle" of 55 degrees, intermediate signal intensity was observed at 45 degrees and 65 degrees, and no signal intensity was observed at 0 degree and 90 degrees. Signal intensity was evident only when a short echo time was used. The authors believe that tendon orientation greatly affects tendon signal intensity in vivo. Increased signal intensity due to the magic angle effect may be misdiagnosed as tendinous degeneration, tendinitis, or frank tear.
Secondary structure content of the HDV ribozyme in 95% formamide (1996)

The Hepatitis Delta Virus (HDV) ribozyme self-cleaving activity in 20 M formamide solutions is unique. Does this catalytic activity result from the conservation of its tertiary structure in 20 M formamide? We followed the ribozyme structure in formamide solutions by monitoring the amount of bound Ethidium Bromide (EB). We were able to measure the quantity of dye bound using time-resolved fluorescence spectroscopy, as an estimate of the ribozyme double helical content. This method, calibrated by using oligonucleotides with defined tertiary structure and denaturing solvents, parallels NMR and UV measurements as a function of temperature. Measurements with the HDV ribozyme lead to three conclusions: (a) both the precursor and product RNAs are structured to 24 M (95% w/w) formamide or 4 M H2O solutions which is equivalent to 4 M H2O; (b) the HDV ribozyme is the only RNA sequence investigated in this study that retains so much structure in formamide; and (c) DNA analogs of formamide resistant HDV ribozyme sequences lose their structure at less than 15 M formamide. Thus, the structural integrity of the HDV ribozyme is an intrinsic property of the RNA molecule and its sequence.
Biosynthesis and expression of the disialoganglioside GD2, a relevant target antigen on small cell lung carcinoma for monoclonal antibody-mediated cytolysis. (1986)

Monoclonal antibodies (MAbs) 126 (immunoglobulin M) and 14.18 (immunoglobulin G3) react strongly with the cell surface of small cell carcinoma of the lungs (SCCL) and are unreactive with most normal tissues and other neoplasms with the notable exception of tumors derived from cells of neural crest origin. These MAbs react specifically with the oligosaccharide portion of the disialoganglioside GD2. Analysis of total gangliosides from cultured cell lines derived from SCCL indicates that GD2 is a predominant ganglioside. A comparison of the reactivities of MAbs against GD2 with those directed against gangliosides GM2 and GD3, each differing from GD2 by a single sugar residue, clearly indicates that GD2 is preferentially expressed by cultured cells derived from SCCL. Membranes isolated from these cells exhibit GD2 synthetase activity which specifically converts the precursor GD3 to GD2 in the presence of uridine diphosphate-N-acetyl galactosamine as the glycosyl donor. We present evidence that in SCCL, GD2 serves as a relevant target antigen for monoclonal antibody-mediated cytolysis. Specifically, we demonstrate that MAb 14.18 (immunoglobulin G3), can lyse small cell carcinoma of the lung targets by either complement- or antibody-dependent cellular cytotoxicity.
Genomic imbalances pinpoint potential oncogenes and tumor suppressors in Wilms tumors (2016)

This study confirmed the presence of CNAs previously related to WT and characterized new CNAs found only in few cases. The later were found in higher frequency in relapsed cases, suggesting that they could be associated with WT progression.
Site-specific gene correction of a point mutation in human iPS cells derived from an adult patient with sickle cell disease (2011)

Human induced pluripotent stem cells (iPSCs) bearing monogenic mutations have great potential for modeling disease phenotypes, screening candidate drugs, and cell replacement therapy provided the underlying disease-causing mutation can be corrected. Here, we report a homologous recombination-based approach to precisely correct the sickle cell disease (SCD) mutation in patient-derived iPSCs with 2 mutated β-globin alleles (β(s)/β(s)). Using a gene-targeting plasmid containing a loxP-flanked drug-resistant gene cassette to assist selection of rare targeted clones and zinc finger nucleases engineered to specifically stimulate homologous recombination at the β(s) locus, we achieved precise conversion of 1 mutated β(s) to the wild-type β(A) in SCD iPSCs. However, the resulting co-integration of the selection gene cassette into the first intron suppressed the corrected allele transcription. After Cre recombinase-mediated excision of this loxP-flanked selection gene cassette, we obtained "secondary" gene-corrected β(s)/β(A) heterozygous iPSCs that express at 25% to 40% level of the wild-type transcript when differentiated into erythrocytes. These data demonstrate that single nucleotide substitution in the human genome is feasible using human iPSCs. This study also provides a new strategy for gene therapy of monogenic diseases using patient-specific iPSCs, even if the underlying disease-causing mutation is not expressed in iPSCs.
T1/ST2 expression on Th2 cells negatively regulates allergic pulmonary inflammation (2007)

The transmembrane form of T1/ST2 (ST2) is a specific marker on murine Th2 cells that have been generated in vitro, or isolated from sites of allergic type 2 inflammation. Despite the association of ST2 with Th2 cells, to date no obligate role for ST2 in type 2 responses in vivo has been described. We have specifically addressed the role of ST2 on T cells by generation of ST2(-/-) mice crossed with ovalbumin (OVA) T cell receptor-transgenic mice. OVA-specific ST2(-/-) cells had normal cytokine responses to T cell activation after in vitro Th2 differentiation, but OVA stimulation of IL-5 was increased. Transfer of OVA-specific ST2(-/-) Th2 cells into BALB/c mice caused exacerbated pulmonary inflammation with occluded airways, elevated airway hyper-responsiveness and increased susceptibility to methacholine challenge that was associated with mortalities of recipient mice. The increased pulmonary inflammation in OVA-specific ST2(-/-) Th2 cell recipients was associated with selective differences in pulmonary levels of Th2 cytokines compared with OVA-specific ST2(+) Th2 cell recipients. Recipients of OVA-specific ST2(-/-) Th2 cells had a significant increase in eosinophils and a significant reduction in F4/80(hi) macrophages in the lungs. This is the first demonstration of a role for ST2 expression on Th2 cells down-regulating pulmonary inflammation. These data have major implications for the targeting of ST2 as a therapy for allergic airway disorders.
Selective Lesioning of the Basal Forebrain Cholinergic System by Intraventricular 192 IgG–saporin: Behavioural, Biochemical and Stereological Studies in the Rat (1995)

The elucidation of the functional role of the basal forebrain cholinergic system will require access to a highly specific and efficient cholinergic neurotoxin. Recently, selective depletion of the nerve growth factor (NGF) receptor-bearing cholinergic neurons in the rat basal forebrain and a dramatic loss of cholinergic innervation in the related cortical regions have been obtained following intraventricular injection of a newly introduced immunotoxin, 192 IgG-saporin. Here we extend these initial findings and report that administration of increasing doses (1.25, 2.5, 5.0 or 10 micrograms) of the 192 IgG-saporin conjugate into the lateral ventricles of adult rats induced dose-dependent impairments in the water maze task and passive avoidance retention, but only weak and inconsistent effects on locomotor activity. These behavioural changes were paralleled by a reduction in choline acetyltransferase activity in hippocampus and several cortical areas (up to 97%) and selective depletions of NGF receptor-positive cholinergic neurons in the septal-diagonal band area and nucleus basalis magnocellularis (up to 99%). By contrast, the non-cholinergic parvalbumin-containing neurons in the septum were completely spared, and other cholinergic projection systems (such as in the striatum, thalamus, brainstem and spinal cord) were unaffected even at the highest dose. The observed changes in the water maze and passive avoidance tasks, as well as the cholinergic cell loss, were maintained up to at least 8 months following the intraventricular injection of a single dose (5 micrograms) of the immunotoxin. The results confirm the usefulness of the 192 IgG-saporin toxin for selective and profound lesions of the basal forebrain cholinergic neurons and provide further support for a role of the basal forebrain cholinergic system in cognitive functions.
One‐Pot Reaction Cascades Using Star Polymers with Core‐Confined Catalysts (2005)

My stars! Star polymers that contain otherwise incompatible acid or base catalysts, such as para-toluenesulfonic acid or 4-(dialkylamino)pyridines moieties, at their sterically restricted cores (see scheme) are readily prepared. Homogeneous catalysis using these star polymers can perform reaction cascades in the same pot and is demonstrated with an acid-catalyzed deprotection and the nucleophilic amine-catalyzed Baylis–Hillman reaction.
The Immunoglobulins of Cold-Blooded Vertebrates (2014)

Although lymphocyte-like cells secreting somatically-recombining receptors have been identified in the jawless fishes (hagfish and lamprey), the cartilaginous fishes (sharks, skates, rays and chimaera) are the most phylogenetically distant group relative to mammals in which bona fide immunoglobulins (Igs) have been found. Studies of the antibodies and humoral immune responses of cartilaginous fishes and other cold-blooded vertebrates (bony fishes, amphibians and reptiles) are not only revealing information about the emergence and roles of the different Ig heavy and light chain isotypes, but also the evolution of specialised adaptive features such as isotype switching, somatic hypermutation and affinity maturation. It is becoming increasingly apparent that while the adaptive immune response in these vertebrate lineages arose a long time ago, it is most definitely not primitive and has evolved to become complex and sophisticated. This review will summarise what is currently known about the immunoglobulins of cold-blooded vertebrates and highlight the differences, and commonalities, between these and more "conventional" mammalian species.
An efficient logic emulation system (1993)

The Realizer, is a logic emulation system that automatically configures a network of field-programmable gate arrays (FPGAs) to implement large digital logic designs, is presented. Logic and interconnect are separated to achieve optimum FPGA utilization. Its interconnection architecture, called the partial crossbar, greatly reduces system-level placement and routing complexity, achieves bounded interconnect delay, scales linearly with pin count, and allows hierarchical expansion to systems with hundreds of thousands of FPGA devices in a fast and uniform way. An actual multiboard system has been built, using 42 Xilinx XC3090 FPGAs for logic. Several designs, including a 32-b CPU datapath, have been automatically realized and operated at speed. They demonstrate very good FPGA utilization. The Realizer has applications in logic verification and prototyping, simulation, architecture development, and special-purpose execution.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interleukin-6 (IL-6) as an anti-inflammatory cytokine: induction of circulating IL-1 receptor antagonist and soluble tumor necrosis factor receptor p55 (1994)

The aim of this study was to investigate whether interleukin (IL)-6 induces the production of IL-1 and tumor necrosis factor (TNF) antagonists. Serial plasma samples were obtained from cancer patients participating in phase I and II trials of recombinant IL-6 administered as a 120-hour continuous intravenous (IV) infusion. Plasma IL-1 receptor antagonist (IL-1Ra) and soluble TNF receptor p55 (TNFsRp55) levels were measured by specific radioimmunoassays (RIAs). IL-1Ra levels increased rapidly, reaching peak values (9.6 +/- 1.7 ng/mL) within 2 to 4 hours of beginning treatment. Thereafter, levels promptly declined, reaching near baseline within 24 hours despite continuation of IL-6. TNFsRp55 plasma levels increased within 4 to 8 hours after initiating treatment and increased progressively throughout the duration of therapy. IL-1 beta and TNF-alpha plasma levels were below the detection limit in all samples tested. Peripheral blood mononuclear cells (PBMC) exposed to IL-6 produced only small amounts (1.56 +/- 0.3 ng/mL) of IL-1Ra, even in the presence of exogenous soluble IL-6 receptor (gp80). TNFsRp55 levels measured in the supernatants of IL-6- stimulated PBMC were below the detection limit of the assay. Macrophages generated by culturing monocytes in granulocyte-macrophage colony-stimulating factor (GM-CSF) were much more responsive to IL-6 than freshly isolated unfractionated or adherent PBMC and synthesized almost as much IL-1Ra when stimulated with IL-6 as with endotoxin. These results suggest that the antinflammatory properties of IL-6 may be due; in part, to the induction of IL-1Ra synthesis and the release of soluble TNF receptors. Our findings also suggest that tissue macrophages may be an important source of IL-6-induced IL-1Ra.