gebhart/patrepeval huggingface dataset:
Streptococcus suistype 2 infections in pigs in the Netherlands (part two) (1987)

Since 1983 some pig breeding and fattening farms in the Netherlands have been faced with a considerable mortality in pigs due to Streptococcus suis type 2 infections. The most predominant clinical feature of S. suis type 2 infection is meningitis, although sudden deaths often occur. It was noted that some affected farms had imported breeding stock from the United Kingdom. Tonsils of slaughter pigs were collected from herds with and without a history of S. suis type 2 infections. Bacteriological examination was done by using an elective-selective medium. No significant difference was found in carrier rates of S. suis type 2 between clinically healthy and affected herds (38% vs. 45%). A cohort study was carried out by regular bacteriological examination of tonsil biopsies on a farm with a high incidence of streptococcal meningitis. Twenty-seven percent of the pigs were carriers of S. suis type 2 at nine weeks of age. Possible methods for disease control are discussed.
An Ancient Yeast for Young Geneticists: A Primer on theSchizosaccharomyces pombeModel System (2015)

The fission yeast Schizosaccharomyces pombe is an important model organism for the study of eukaryotic molecular and cellular biology. Studies of S. pombe, together with studies of its distant cousin, Saccharomyces cerevisiae, have led to the discovery of genes involved in fundamental mechanisms of transcription, translation, DNA replication, cell cycle control, and signal transduction, to name but a few processes. However, since the divergence of the two species approximately 350 million years ago, S. pombe appears to have evolved less rapidly than S. cerevisiae so that it retains more characteristics of the common ancient yeast ancestor, causing it to share more features with metazoan cells. This Primer introduces S. pombe by describing the yeast itself, providing a brief description of the origins of fission yeast research, and illustrating some genetic and bioinformatics tools used to study protein function in fission yeast. In addition, a section on some key differences between S. pombe and S. cerevisiae is included for readers with some familiarity with budding yeast research but who may have an interest in developing research projects using S. pombe.
Role of Protein Kinase C α in Nerve Growth Factor‐Induced Arachidonic Acid Release from PC12 Cells (1996)

Nerve growth factor (NGF) increases arachidonic acid (AA) release by PC12 pheochromocytoma cells. To explore the role of protein kinase C (PKC) in this action of NGF, PKC was down-regulated by long-term treatment of the cells with phorbol 12-myristate 13-acetate (PMA). Such prolonged exposure to PMA (1 microM) resulted in the inhibition of NGF-induced AA release. Moreover, pretreatment of PC12 cells with the protein kinase inhibitor staurosporine or with calphostin C, a specific inhibitor of PKC, also blocks the increase of AA release induced by NGF. These data, as well as that PMA alone can induce AA release in PC12 cells, suggest that PKC is necessary for NGF-induced AA release. Immunoblot analysis of whole cell lysates by using antibodies against various PKC isoforms revealed that our PC12 cells contained PKCs alpha, delta, epsilon, and zeta. PMA down-regulation depleted PKCs alpha, delta, and epsilon, and partially depleted zeta. To see which isoform was involved in NGF-induced AA release, an isoform-specific PKC inhibitor was used. GO 6976, a compound that inhibits PKCs alpha and beta specifically, blocked NGF-induced AA release. In addition, thymeleatoxin, a specific activator of PKCs alpha, beta, and gamma, induced AA release from PC12 cells in amounts comparable with those seen with NGF. Taken together, these data suggest that PKC alpha plays a role in NGF-induced AA release.
Hematologic Disorders Associated with Hepatitis C Virus Infection and Their Management (2003)

More than 4 million people in the United States are infected with hepatitis C virus (HCV). During the next 20-30 years, the burden of HCV-related mortality and morbidity will likely double. To date, the most effective treatment for chronic HCV infection is the combination of either interferon (IFN)-alpha or pegylated IFN-alpha and ribavirin. For a sustained virologic response, treatment adherence and dose maintenance are essential. However, both IFN-alpha and ribavirin induce hematologic toxicity, such as anemia, neutropenia, and thrombocytopenia, which can compromise treatment adherence and dose maintenance and could, therefore, potentially influence outcomes. Although there are currently no approved treatments for hematologic complications of HCV therapy, studies have shown that hematopoietic growth factors can provide significant benefits. This review highlights the pharmacology, risks, and benefits of recombinant hematopoietic growth factor therapy in HCV-infected patients.
Noninvasive diffuse optical monitoring of head and neck tumor blood flow and oxygenation during radiation delivery (2012)

This study explored using a novel diffuse correlation spectroscopy (DCS) flow-oximeter to noninvasively monitor blood flow and oxygenation changes in head and neck tumors during radiation delivery. A fiber-optic probe connected to the DCS flow-oximeter was placed on the surface of the radiologically/clinically involved cervical lymph node. The DCS flow-oximeter in the treatment room was remotely operated by a computer in the control room. From the early measurements, abnormal signals were observed when the optical device was placed in close proximity to the radiation beams. Through phantom tests, the artifacts were shown to be caused by scattered x rays and consequentially avoided by moving the optical device away from the x-ray beams. Eleven patients with head and neck tumors were continually measured once a week over a treatment period of seven weeks, although there were some missing data due to the patient related events. Large inter-patient variations in tumor hemodynamic responses were observed during radiation delivery. A significant increase in tumor blood flow was observed at the first week of treatment, which may be a physiologic response to hypoxia created by radiation oxygen consumption. Only small and insignificant changes were found in tumor blood oxygenation, suggesting that oxygen utilizations in tumors during the short period of fractional radiation deliveries were either minimal or balanced by other effects such as blood flow regulation. Further investigations in a large patient population are needed to correlate the individual hemodynamic responses with the clinical outcomes for determining the prognostic value of optical measurements.
Localization of the glucocorticoid receptor in discrete clusters in the cell nucleus (1995)

The cell nucleus is highly organized. Many nuclear functions are localized in discrete domains, suggesting that compartmentalization is an important aspect of the regulation and coordination of nuclear functions. We investigated the subnuclear distribution of the glucocorticoid receptor, a hormone-dependent transcription factor. By immunofluorescent labeling and confocal microscopy we found that after stimulation with the agonist dexamethasone the glucocorticoid receptor is concentrated in 1,000-2,000 clusters in the nucleoplasm. This distribution was observed in several cell types and with three different antibodies against the glucocorticoid receptor. A similar subnuclear distribution of glucocorticoid receptors was found after treatment of cells with the antagonist RU486, suggesting that the association of the glucocorticoid receptor in clusters does not require transformation of the receptor to a state that is able to activate transcription. By dual labeling we found that most dexamethasone-induced receptor clusters do not colocalize with sites of pre-mRNA synthesis. We also show that RNA polymerase II is localized in a large number of clusters in the nucleus. Glucocorticoid receptor clusters did not significantly colocalize with these RNA polymerase II clusters or with domains containing the splicing factor SC-35. Taken together, these results suggest that most clustered glucocorticoid receptor molecules are not directly involved in activation of transcription.
Ab initio protein structure prediction using a combined hierarchical approach (1999)

As part of the third Critical Assessment of Structure Prediction meeting (CASP3), we predict the three-dimensional structures for 13 proteins using a hierarchical approach. First, all possible compact conformations of a protein sequence are enumerated using a highly simplified tetrahedral lattice model. We select a large subset of these conformations using a lattice-based scoring function and build detailed all-atom models incorporating predicted secondary structure. A combined all-atom knowledge-based scoring function is then used to select three smaller subsets from these all-atom models. Finally, a consensus-based distance geometry procedure is used to generate the best conformations from each of the all-atom subsets. With this method, we are able to predict the global topology/shape for all or a large part of the sequence for six out of the thirteen proteins. For two other proteins, the topology/shape for shorter fragments are predicted. This represents a marked improvement in ab initio prediction since CASP was first instigated in 1994. Proteins Suppl 1999;3:194–198. © 1999 Wiley-Liss, Inc.
Comparison of disposition behavior and de‐coppering effect of triethylenetetramine in animal model for Wilson's disease (long‐evans cinnamon rat) with normal Wistar rat (1992)

The disposition behaviors and de-coppering effect of triethylenetetramine dihydrochloride (trientine), a selective chelating agent for copper and an 'orphan drug' for Wilson's disease, have been evaluated in an animal model, Long-Evans Cinnamon (LEC) rats, and normal rats (Wistar). In LEC rats, urinary excretion of trientine was remarkably lower than that of Wistar rats. The absorption rates from the jejunal loop and in vitro metabolism in the liver S9 fraction (supernatant of 9000 x g) were approximately the same for both strains. The decline of urinary excretion of trientine in LEC rats is thought to be due mainly to the lowering of the functional activity of the kidney, because urinary excretion of creatinine and phenolsulfonphthalein were significantly lower in LEC rats than those in Wistar rats. Both acceleration of urinary excretion of copper and reduction of hepatic copper levels were observed with treatment of trientine in LEC rats aged 6 weeks. In LEC rats aged 13 weeks, however, no de-coppering effect from the liver was observed, though urinary excretion of copper was increased. These results suggest that trientine has a pharmacological effect in disease state, especially in the early stages of hepatitis.
Packaging Cells Based on Inducible Gene Amplification for the Production of Adeno-Associated Virus Vectors (1998)

Although vectors based on adeno-associated virus (AAV) offer several unique advantages, their usage has been hampered by the difficulties encountered in vector production. In this report, we describe a new AAV packaging system based on inducible amplification of integrated helper and vector constructs containing the simian virus 40 (SV40) replication origin. The packaging and producer cell lines developed express SV40 T antigen under the control of the reverse tetracycline transactivator system, which allows inducible amplification of chromosomal loci linked to the SV40 origin. Culturing these cells in the presence of doxycycline followed by adenovirus infection resulted in helper and vector gene amplification as well as higher vector titers. Clonal producer cell lines generated vector titers that were 10 times higher than those obtained by standard methods, with approximately 10(4) vector particles produced per cell. These stocks were free of detectable replication-competent virus. The lack of a transfection step combined with the reproducibility of stable producer lines makes this packaging method ideally suited for the large-scale production of vector stocks for human gene therapy.
Purification of ras GTPase activating protein from bovine brain. (1988)

In cytosolic extracts of bovine brain, we detected ras GTPase activating protein (GAP) activity that stimulated the GTP hydrolytic activity of normal c-Ha-ras p21 but not that of the oncogenic [Val12]p21 variant. GAP was purified 19,500-fold by a five-column procedure involving DEAE-Sephacel, Sepharose 6B, orange dye and green dye matrices, and Mono Q resins. A single major protein band of 125 kDa was observed on NaDodSO4/polyacrylamide gels that correlated with the elution of GAP activity on Mono Q. Purified GAP was devoid of inherent GTP hydrolytic activity, suggesting that it was a regulator of ras intrinsic GTPase activity. Under submaximal velocity conditions, the second-order rate constant of GTP hydrolysis at 24 degrees C for p21-GTP + GAP (4.5 X 10(6) M-1.sec-1) was at least 1000-fold greater than that for [Val12]p21-GTP + GAP (less than 3 X 10(3) M-1.sec-1).
The VMP network adapter board (NAB): high-performance network communication for multiprocessors (1988)

High performance computer communication between multiprocessor nodes requires significant improvements over conventional host-to-network adapters. Current host-to-network adapter interfaces impose excessive processing, system bus and interrupt overhead on a multiprocessor host. Current network adapters are either limited in function, wasting key host resources such as the system bus and the processors, or else intelligent but too slow, because of complex transport protocols and because of an inadequate internal memory architecture. Conventional transport protocols are too complex for hardware implementation and too slow without it.
Self-Assembled Polymer Membrane Capsules Inflated by Osmotic Pressure (2004)

We fabricate and characterize capsules that are composite membranes, made of a polymer network stabilized by adsorption to colloids and inflated by osmotic pressure from internal free polyelectrolyte; here, poly-l-lysine forms the network and inflates the capsules. To assess these capsules' properties and structure, we deform capsules using microcantilevers and use finite element modeling to describe these deformations. Additional experimental tests confirm the model's validity. These capsules' resilient response to mechanical forces indicates that loading and shear should be good triggers for the release of contents via deformation. The osmotic pressure inflating these capsules has the potential to trigger release of contents via deflation in response to changes in the capsules' environment; we demonstrate addition of salt as a trigger for deflating capsules. Because these capsules have a variety of release triggers available and the technique used to fabricate them is very flexible and allows high encapsulation efficiency, these capsules have very high potential for application in many areas.
Multivalent Scaffolds for Affinity Maturation of Small Molecule Cell Surface Binders and Their Application to Prostate Tumor Targeting (2008)

Adamantane scaffolds for affinity maturation of prostate cancer specific ligands of low molecular mass are described. These scaffolds are modular and can be used for conjugation of up to three ligands and an additional effector molecule by standard peptide coupling techniques. The potential of the scaffolds is demonstrated with the multimerization of GPI 1, a prostate cancer specific small molecule. A detailed study of multimerized GPI conjugates with near-infrared fluorophores and their binding properties to different prostate cancer cell lines shows the specific binding of these conjugates to cell types positive for prostate specific membrane antigen (PSMA). We demonstrate that these conjugates allow the sensitive imaging of prostate cancer cells with NIR methodology and suggest that our adamantane scaffolds might be generally useful for affinity maturation of small molecules targeting cell surface epitopes.
Random access quantum information processors using multimode circuit quantum electrodynamics (2017)

Qubit connectivity is an important property of a quantum processor, with an ideal processor having random access-the ability of arbitrary qubit pairs to interact directly. This a challenge with superconducting circuits, as state-of-the-art architectures rely on only nearest-neighbor coupling. Here, we implement a random access superconducting quantum information processor, demonstrating universal operations on a nine-qubit memory, with a Josephson junction transmon circuit serving as the central processor. The quantum memory uses the eigenmodes of a linear array of coupled superconducting resonators. We selectively stimulate vacuum Rabi oscillations between the transmon and individual eigenmodes through parametric flux modulation of the transmon frequency. Utilizing these oscillations, we perform a universal set of quantum gates on 38 arbitrary pairs of modes and prepare multimode entangled states, all using only two control lines. We thus achieve hardware-efficient random access multi-qubit control in an architecture compatible with long-lived microwave cavity-based quantum memories.
Singlet molecular oxygen in the Haber-Weiss reaction. (1994)

Characteristic chemiluminescence emission of singlet (1 delta g) molecular oxygen at 1268 nm is reported from a Haber-Weiss reaction. The reaction consists of mixing aqueous hydrogen peroxide with a solution of potassium superoxide, solubilized by 18-crown-6 ether in carbon tetrachloride or in dry acetonitrile at room temperature. Since the discovery of the enzyme superoxide dismutase by J.M. McCord and I. Fridovich [(1968) J. Biol. Chem. 243, 5733-5760], the identity of the reactive oxidant in superoxide-generating systems in biology has remained a chemical mystery. The results presented here suggest strongly that the reactive species is singlet oxygen generated via the Haber-Weiss reaction and not, as usually assumed, the hydroxyl radical, .OH, generated by the same reaction.
Peripheral Blood Corticotropin-Releasing Factor, Adrenocorticotropic Hormone and Cytokine (Interleukin Beta, Interleukin 6, Tumor Necrosis Factor Alpha) Levels after High- and Low-Dose Total-Body Irradiation in Humans (1994)

Total-body irradiation (TBI) induces an increase in levels of granulocytes and cortisol in blood. To explore the underlying mechanisms, we studied 26 patients who had TBI prior to bone marrow transplantation. Our findings suggest that only a high dose of TBI (10 Gy) was capable of activating the hypothalamo-pituitary area since corticotropin-releasing factor and blood adrenocorticotropic hormone levels increased at the end of the TBI. There was a concomitant increase in the levels of interleukin 6 and tumor necrosis factor in blood, suggesting that these cytokines might activate the hypothalamo-pituitary adrenal axis. Interleukin 1 was not detected. Since vascular injury is common after radiation treatment, it is possible that interleukin 6 was secreted by endothelial cells. The exact mechanisms of the production of cytokines induced by ionizing radiation remain to be determined.
A Specific Product of Phosphatidylinositol 3-Kinase Directly Activates the Protein Kinase Akt through Its Pleckstrin Homology Domain (1997)

Phosphatidylinositol (PI) 3-kinase is a cytoplasmic signaling molecule that is recruited to activated growth factor receptors after growth factor stimulation of cells. Activation of PI 3-kinase results in increased intracellular levels of 3' phosphorylated inositol phospholipids and the induction of signaling responses, including the activation of the protein kinase Akt, which is also known as RAC-PK or PKB. We tested the possibility that the phospholipid products of PI 3-kinase directly mediate the activation of Akt. We have previously described a constitutively active PI 3-kinase, p110, which can stimulate Akt activity. We used purified p110 protein to generate a series of 3' phosphorylated inositol phospholipids and tested whether any of these lipids could activate Akt in vitro. Phospholipid vesicles containing PI3,4 bisphosphate (P2) specifically activated Akt in vitro. By contrast, the presence of phospholipid vesicles containing PI3P or PI3,4,5P3 failed to increase the kinase activity of Akt. Akt could also be activated by synthetic dipalmitoylated PI3,4P2 or after enzymatic conversion of PI3,4,5P3 into PI3,4P2 with the signaling inositol polyphosphate 5' phosphatase SIP. We show that PI3,4P2-mediated activation is dependent on a functional pleckstrin homology domain in Akt, since a point mutation in the pleckstrin homology domain abrogated the response to PI3,4P2. Our findings show that a phospholipid product of PI 3-kinase can directly stimulate an enzyme known to be an important mediator of PI 3-kinase signaling.
Detection of a Schroedinger's Cat State in an rf-SQUID (2000)

We present experimental evidence for a coherent superposition of macroscopically distinct flux states in an rf-SQUID. When the external flux Phi_x applied to the SQUID is near 1/2 of a flux quantum Phi_0, the SQUID has two nearly degenerate configurations: the zero- and one-fluxoid states, corresponding to a few microamperes of current flowing clockwise or counterclockwise, respectively. The system is modeled as a particle in a double-well potential where each well represents a distinct fluxoid state (0 or 1) and the barrier between the wells can be controlled in situ. For low damping and a sufficiently high barrier, the system has a set of quantized energy levels localized in each well. The relative energies of these levels can be varied with Phi_x. External microwaves are used to pump the system from the well-localized ground state of one well into one of a pair of excited states nearer the top of the barrier. We spectroscopically map out the energy of these levels in the neighborhood of their degeneracy point by varying Phi_x as well as the barrier height. We find a splitting between the two states at this point, when both states are below the classical energy barrier, indicating that the system attains a coherent superposition of flux basis states that are macroscopically distinct in that their mean fluxes differ by more than 1/4 Phi_0 and their currents differ by several microamperes.
The effects of shift work on nurses: implications for Australian hospitals. (1988)

This review of Australian and international research on the effects of shift work on nurses reveals that there is neither a wide nor a growing body of information on shift work in nursing. Shift work in nursing has been the subject of only three substantial studies overseas, and none in Australia. Although research indicates that there are negative physiological, psychological and social consequences associated with shift work, it is not possible at the current time to favour any single shift or roster system, particularly in nursing where empirical research is wanting.