gebhart/patrepeval huggingface dataset:
Heterologous Expression of Toxins from Bacterial Toxin-Antitoxin Systems in Eukaryotic Cells: Strategies and Applications (2016)

Toxin-antitoxin (TA) systems are found in nearly all prokaryotic genomes and usually consist of a pair of co-transcribed genes, one of which encodes a stable toxin and the other, its cognate labile antitoxin. Certain environmental and physiological cues trigger the degradation of the antitoxin, causing activation of the toxin, leading either to the death or stasis of the host cell. TA systems have a variety of functions in the bacterial cell, including acting as mediators of programmed cell death, the induction of a dormant state known as persistence and the stable maintenance of plasmids and other mobile genetic elements. Some bacterial TA systems are functional when expressed in eukaryotic cells and this has led to several innovative applications, which are the subject of this review. Here, we look at how bacterial TA systems have been utilized for the genetic manipulation of yeasts and other eukaryotes, for the containment of genetically modified organisms, and for the engineering of high expression eukaryotic cell lines. We also examine how TA systems have been adopted as an important tool in developmental biology research for the ablation of specific cells and the potential for utility of TA systems in antiviral and anticancer gene therapies.
Spin injection in thermally assisted magnetic random access memory (2005)

An integrated thermal, micromagnetic, spin-momentum-transfer (SMT) model was developed to study the effect of SMT on the programming current required for thermally assisted magnetic random access memory (MRAM). The thermal portion of the model is used to compute Joule heating by the spin-polarized current, and it is based on a Crank–Nicolson inhomogeneous heat equation solver. The magnetic portion of the model is based on a micromagnetic Langevin dynamic Landau–Lifshitz–Gilbert solver including SMT torque. Simulations of thermally assisted magnetization reversal of 0.09-μm MRAM elements, heated by passing current through the barrier separating the pinned and free layers, were performed. The free layer of the MRAM elements was switched using a magnetic field at fixed heating-SMT current bias. Results suggest that a spin-polarized heating current can be used to lower the programming current required to write thermally assisted MRAM if the direction of the heating current is properly synchronized with the reversal field.
High quality document image compression with “DjVu” (1998)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
Clinical Features, Pathophysiology, and Treatment of Levodopa-Induced Dyskinesias in Parkinson’s Disease (2012)

Dyskinetic disorders are characterized by excess of motor activity that may interfere with normal movement control. In patients with Parkinson's disease, the chronic levodopa treatment induces dyskinetic movements known as levodopa-induced dyskinesias (LID). This paper analyzed the pathophysiology, clinical manifestations, pharmacological treatments, and surgical procedures to treat hyperkinetic disorders. Surgery is currently the only treatment available for Parkinson's disease that may improve both parkinsonian motor syndrome and LID. However, this paper shows the different mechanisms involved are not well understood.
Retorting of Green River oil shale under high-pressure hydrogen atmospheres (1977)

Studies have been carried out on 31- and 24-gallons-of-oil-per-ton oil shale from the Green River Formation to study the effects of pressure, sweep gas rate, and heating rate during batch-wise retorting in a hydrogen atmosphere. The studies were performed in a vertical pressure retort which was heated at a predetermined fixed rate to a final bed temperature of approximately 1,000/sup 0/F. The hydrogen sweep gas was passed downward through the shale bed during the experiments. The effects of pressure ranging from atmospheric to 1,500 psig, nominal heating rates ranging from 25 to 250/sup 0/F/h, and hydrogen sweep gas rates ranging from 10 to 120 scf/h/ft/sup 2/ of bed cross-section have been studied. Oil, gas, water, and spent shale yields are reported along with analyses of product oil, gas, and spent shale. Organic carbon utilization is also reported. Heating rate showed an effect on oil yield for the atmospheric runs; this effect was not noticed under the higher pressure runs. For the run conditions reported, no effect was noticed with variance of hydrogen sweep rate. Oil yields showed a marked increase with increasing hydrogen pressures. The oil produced showed a decrease in oxygen, sulfur, carbon/hydrogen ratio, pour point, viscosity, specific gravity,more » and average boiling range with increasing hydrogen pressures. Nitrogen content of the oil showed an increase with increasing hydrogen pressures. Other effects noted with increasing hydrogen pressures were increased carbon utilization and increased water production. 14 figures, 11 tables.« less
Introducing novel FDD and FDM in MC-CDMA to enhance performance (2002)

This paper presents a method of efficiently incorporating frequency division duplex (FDD) and frequency division multiplexing (FDM) into MC-CDMA systems to exploit frequency diversity and reduce multiple access interference (MAI). The approach used in the novel FDD/MC-CDMA is to break the total available bandwidth into subbands and interleave the subbands used for the downlink and uplink. It is shown that this technique significantly improves the performance relative to an MC-CDMA system employing a traditional FDD scheme where the spectrum is divided into a single uplink block and a single downlink block. Furthermore, FDM is introduced in the novel FDD scheme to reduce MAI in MC-CDMA (without any loss in the capacity of the overall system).
Quantitative Analysis of Carbohydrate−Protein Interactions Using Glycan Microarrays:  Determination of Surface and Solution Dissociation Constants (2007)

Carbohydrate-protein interactions on surface and in solution were quantitatively measured by a glycan microarray. Assessing carbohydrate affinities is typically difficult due to weak affinities and limited sources of structurally complex glycans. We described here a sensitive, high-throughput, and convenient glycan microarray technology for the simultaneous determination of a wide variety of parameters in a single experiment using small amounts of materials. Assay systems based on this technology were developed to analyze multivalent interactions and determine the surface dissociation constant (KD,surf) for surface-coated mannose derivatives with mannose binding lectins and antibodies. Competition experiments that employed monovalent ligands in solution yielded KD and Ki values in solution similar to equilibrium binding constants obtained in titration microcalorimetry and surface plasmon resonance experiments.
Fabrication of porous synthetic polymer scaffolds for tissue engineering (2014)

Tissue engineering provides a novel and promising approach to replace damaged tissue with an artificial substitute. Porous synthetic biodegradable polymers are the preferred materials for this substitution due to their microstructure, biocompatibility, biodegradability, and low cost. As a crucial element in tissue engineering, a scaffold acts as an artificial extracellular matrix (ECM) and provides support for cell migration, differentiation, and reproduction. The fabrication of viable scaffolds, however, has been a challenge in both clinical and academic settings. Methods such as solvent casting/particle leaching, thermally induced phase separation (TIPS), electrospinning, gas foaming, and rapid prototyping (additive manufacturing) have been developed or introduced for scaffold fabrication. Each method has its own advantages and disadvantages. In this review, the commonly used synthetic polymer scaffold fabrication methods will be introduced and discussed in detail, and recent progress regarding scaffold fabrication—such as combining different scaffold fabrication methods, combining various materials, and improving current scaffold fabrication methods—will be reviewed as well.
Production of transgenic merino sheep by microinjection of ovine metallothionein-ovine growth hormone fusion genes (1989)

Seven transgenic Merino sheep have been produced by the technique of pronuclear microinjection. Two different Sheep Metallothionein-1a-Sheep Growth Hormone fusion genes were used. Four of the transgenic sheep, all of which contained the gene MTsGH5, did not express the transgene. The remaining three sheep carrying the second fusion gene, MTsGH9, expressed the gene at high levels in a variety of tissues and had elevated blood levels of sheep growth hormone.
Molecular events in the organization of renal tubular epithelium: from nephrogenesis to regeneration (1989)

Information from studies of embryonic nephrons and established renal tubular cell lines in culture can be integrated to derive a picture of how the renal tubule develops and regenerates after acute injury. During development, the formation of a morphologically polarized epithelium from committed nephric mesenchymal cells requires an external signal for mitogenesis and differentiation. Polypeptide growth factors, in some cases mediated through oncogene expression, act in an autocrine or paracrine fashion to stimulate the production of extracellular matrix proteins that probably provide the earliest orientation signal for the cell. Interaction of these proteins with cell surface receptors leads to early organization of the cytoskeletal actin network, which is the major scaffolding for further differentiation and for definition of plasma membrane domains. The formation of cell-cell contacts via specialized adhesion molecules integrates the epithelium into a polarized monolayer and maintains its fence function, i.e., separation of plasma membrane domains. Microtubules probably participate in the delivery of vesicles to specific plasma membrane domains and in the spatial organization of intracellular organelles. Following acute renal injury, this sequence of events appears to be reversed, resulting in partial or complete loss of differentiated features. Regeneration seems to follow the same pattern of sequential differentiation steps as nephrogenesis. The integrity of the epithelium is restored by reestablishing only those stages of differentiation that have been lost. Where cell death occurs, mitogenesis in adjacent cells restores the continuity of the epithelium and the entire sequence of differentiation events is initiated in the newly generated cells.
The factors affecting transformation efficiency of coryneform bacteria by electroporation. (1995)

High-voltage electroporation was performed to transfer plasmid DNA of pXZ10145 into different kinds of corynebacteria strains. A number of factors that affected transformation efficiency were investigated. Cells grown in the presence of 4% glycine and harvested in the early exponential growth phase (OD600 was about 0.2) were much more easily transformed. Transformation efficiency up to 8 x 10(6) transformants per microgram of plasmid DNA with homologously derived DNA was obtained. If heterologously derived DNA was used, transformation efficiency was 10(2) to 10(3) times lower than the former one.
Bone Marrow Toxicity Associated with 5-Fluorocytosine Therapy (1977)

Bone marrow toxicity occurred in 4 of 15 patients treated with 5-fluorocytosine (5-FC) for serious fungal infections. The development of marrow toxicity appeared to be related to serum 5-FC levels of 125 mug/ml or greater. In three patients, accumulation of toxic levels of 5-FC was related to diminished renal function. One patient with acute renal failure and prolonged high levels of 5-FC developed marrow aplasia and died of bacterial sepsis. Three patients experienced leukopenia, which was readily reversed when the dosage of 5-FC was decreased and the serum concentration was lowered. With careful monitoring of serum 5-FC concentration and renal function, the dose-related toxic effects of 5-FC on the marrow can be avoided.
Lipocalin-type prostaglandin D synthase/β-trace is a major amyloid β-chaperone in human cerebrospinal fluid (2007)

The conformational change in amyloid beta (Abeta) peptide from its monomeric form to aggregates is crucial in the pathogenesis of Alzheimer's disease (AD). In the healthy brain, some unidentified chaperones appear to prevent the aggregation of Abeta. Here we reported that lipocalin-type prostaglandin D synthase (L-PGDS)/beta-trace, the most abundant cerebrospinal fluid (CSF) protein produced in the brain, was localized in amyloid plaques in both AD patients and AD-model Tg2576 mice. Surface plasmon resonance analysis revealed that L-PGDS/beta-trace tightly bound to Abeta monomers and fibrils with high affinity (K(D) = 18-50 nM) and that L-PGDS/beta-trace recognized residues 25-28 in Abeta, which is the key region for its conformational change to a beta-sheet structure. The results of a thioflavin T fluorescence assay to monitor Abeta aggregation disclosed that L-PGDS/beta-trace inhibited the spontaneous aggregation of Abeta (1-40) and Abeta (1-42) within its physiological range (1-5 microM) in CSF. L-PGDS/beta-trace also prevented the seed-dependent aggregation of 50 microM Abeta with K(i) of 0.75 microM. Moreover, the inhibitory activity toward Abeta (1-40) aggregation in human CSF was decreased by 60% when L-PGDS/beta-trace was removed from the CSF by immunoaffinity chromatography. The deposition of Abeta after intraventricular infusion of Abeta (1-42) was 3.5-fold higher in L-PGDS-deficient mice and reduced to 23% in L-PGDS-overexpressing mice as compared with their wild-type levels. These data indicate that L-PGDS/beta-trace is a major endogenous Abeta-chaperone in the brain and suggest that the disturbance of this function may be involved in the onset and progression of AD. Our findings may provide a diagnostic and therapeutic approach for AD.
Toxicity of infliximab in the course of treatment of Crohn’s disease (2005)

Infliximab is a monoclonal antibody directed against the pro-inflammatory mediator TNF-α, which was approved in the US in 1998 for treatment-resistant Crohn’s disease. Since that time, the indications have dramatically expanded to include rheumatoid arthritis, ankylosing spondylitis, psoriasis and most recently, active ulcerative colitis. Although the safety profile in the initial studies was quite favourable, subsequent studies have shown that a small percentage of patients reported severe side effects, including pneumonia, tuberculosis, lymphoma, drug-induced lupus and hepatotoxicity. Although these complications are rare, it is important to properly screen patients for predisposing conditions before beginning treatment. Furthermore, concurrent use of other immunosuppresive agents, such as 6-mercaptopurine, may reduce the incidence of less serious side effects, such as arthralgias, myopathies and other antibody-associated diseases. Since its approval, infliximab has revolutionised the treatment of Crohn’s disease and has shown benefit in a variety of other inflammatory conditions, but significant toxicities can occur that necessitate thorough screening protocols and periodic clinical evaluation.
[Cytofluorometric analysis of tumor cell size and follicle formation of B-cell lymphomas]. (1995)

In order to investigate the size variation of neoplastic B cells (NBC) from lymph nodes of patients with B-cell lymphomas (BCL), we carried out two-dimensional analysis by flow cytometry (FCM) using the forward light scatter (FLS) and the fluorescence intensity (FI) of surface immunoglobulin light chain (sIgL). NBC were identified as having the homogeneous characteristics of both FLS and tumor-restricted sIgL (kappa or lambda). The FLS variation of NBC was then analyzed using CD3+ T-cells as a scale control. The results closely coincided with the cell types determined by the pathologic diagnosis. Secondly, we used FCM to investigate how strongly NBC express VLA-4 alpha and LFA-1 alpha, which seemed to play important roles in neoplastic follicle formation. The expression intensities of these molecules were classified into three grades (-, + & ++). The results were presented in the order of VLA-4 alpha and LFA-1 alpha; follicular 8/15 (++/++), 6/15 (++/+), 1/15 (+/++), partially follicular 3/5 (+/++), 2/5 (+/+), diffuse 2/16 (++/-), 6/16 (+/++), 8/16 (+/+), B-CLL 8/8 (-/+ or -). These findings suggest that follicular lymphomas are phenotypically distinguishable from diffuse lymphomas.
Characterization of a novel self-associating Mr 40,000 platelet glycoprotein [see comments] (1991)

A novel platelet glycoprotein has been purified and characterized. This glycoprotein, designated Pltgp40, is an acidic sialylated 40,000-dalton protein that bears both O-linked and N-linked oligosaccharides. Treatment of Pltgp40 with neuraminidase resulted in a 5,000-dalton reduction in its Mr and a 1.5 Unit alkaline shift in the isoelectric point, indicating the presence of a large number of sialic acid residues. A similar size reduction and change in pl were observed after treatment of Pltgp40 with O-glycanase showing that sialic acids are present on O-linked oligosaccharides. Digestion of Pltgp40 with N-glycanase reduced the Mr to approximately 20,000 daltons but did not affect the isoelectric point, suggesting that Pltgp40 contains six to seven nonsialylated N-linked carbohydrate chains. High Mr proteins were observed in affinity purified Pltgp40 and were identified as detergent-stable protein oligomers consisting of multiple 40,000-dalton monomers. Immunodepletion and direct binding studies indicated that Pltgp40 was not equivalent to Ig Fc receptor type II, another 40,000-dalton glycoprotein expressed on platelets. However, Pltgp40 copurified with Fc receptor type II when platelet extracts were loaded onto human IgG affinity columns, raising the possibility that Pltgp40 may associate with Fc receptors or Fc receptor-lg complexes. Amino acid sequence analysis of the N-terminus of Pltgp40 was performed and confirmed that Pltgp40 is a novel platelet glycoprotein. Epitopes on Pltgp40 appear to be widely expressed because monoclonal antibodies against Pltgp40 also reacted with a variety of myeloid, lymphoid, and epithelial cells. Pltgp40 was detected on activated but not resting platelets, indicating that Pltgp40 is a platelet activation marker.
Endothelial Progenitor Cell Vascular Endothelial Growth Factor Gene Transfer for Vascular Regeneration (2002)

In vitro, VEGF EPC gene transfer enhances EPC proliferation, adhesion, and incorporation into endothelial cell monolayers. In vivo, gene-modified EPCs facilitate the strategy of cell transplantation to augment naturally impaired neovascularization in an animal model of experimentally induced limb ischemia.
Pyrolysis Kinetics for the Conversion of a Polymer into an Amorphous Silicon Oxycarbide Ceramic (2002)

We present experimental and analytical results for the pyrolysis reactions underlying the conversion of a cross‐linked polymer into an amorphous ceramic material. The activation energies, obtained from thermogravimetric data, and chemical analysis of the volatiles by mass spectroscopy are used to identify the reaction pathways. The reaction is determined to be first‐order, which is consistent with its solid‐state nature. The magnitude of the weight loss is analyzed to calculate the number of molecular sites in the polymer that participate in the reaction. The experiments were conducted on a polymer made from silsesquioxanes that convert into silicon oxycarbide ceramics on pyrolysis. The results show that &lt;2.5% of the silicon atoms in the polymer are removed as volatile silanes, and less than one‐half of the carbon atoms are lost as methane. These results are a first step in understanding the molecular basis for the ceramic yield, as well as the evolution of the nanostructure as the material changes from an organic into a ceramic state by reactions that can occur at &lt;850°C.
Median-joining networks for inferring intraspecific phylogenies (1999)

Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.
A comparison of range-Doppler and wavenumber domain SAR focusing algorithms (1992)

Focusing of SAR data requires a space-variant two-dimensional correlation. Different algorithms are compared with each other in terms of their focusing quality and their ability to handle the space-variance of the correlation kernel: the range-Doppler approach with and without secondary range compression, modified range-Doppler algorithms, and four versions of the wavenumber domain processor. The phase aberrations of the different algorithms are given in analytic form. Numerical examples are presented for Seasat and ERS-1. A novel systems theoretical derivation of the wavenumber domain algorithm is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Novel Engagement of CD14 and Multiple Toll-Like Receptors by Group B Streptococci (2001)

Group B streptococcus (GBS) imposes a major health threat to newborn infants. Little is known about the molecular basis of GBS-induced sepsis. Both heat-inactivated whole GBS bacteria and a heat-labile soluble factor released by GBS during growth (GBS-F) induce nuclear translocation of NF-kappaB, the secretion of TNF-alpha, and the formation of NO in mouse macrophages. Macrophages from mice with a targeted disruption of MyD88 failed to secrete TNF-alpha in response to both heat-inactivated whole bacteria and GBS-F, suggesting that Toll-like receptors (TLRs) are involved in different aspects of GBS recognition. Immune cell activation by whole bacteria differed profoundly from that by secreted GBS-F. Whole GBS activated macrophages independently of TLR2 and TLR6, whereas a response to the secreted GBS-F was not observed in macrophages from TLR2-deficient animals. In addition to TLR2, TLR6 and CD14 expression were essential for GBS-F responses, whereas TLR1 and TLR4 or MD-2 did not appear to be involved. Heat lability distinguished GBS-F from peptidoglycan and lipoproteins. GBS mutants deficient in capsular polysaccharide or beta-hemolysin had GBS-F activity comparable to that of wild-type streptococci. We suggest that CD14 and TLR2 and TLR6 function as coreceptors for secreted microbial products derived from GBS and that cell wall components of GBS are recognized by TLRs distinct from TLR1, 2, 4, or 6.