gebhart/patrepeval huggingface dataset:
Treatment with anti‐inflammatory drugs in community‐acquired pneumonia (2012)

Pneumonia exhibits a broad range of severity, from mildly symptomatic at one end to fulminant septic shock and death at the other. Although an adequate inflammatory response is necessary for the clearance of microorganisms, excessive inflammation can lead to ongoing local and systemic damage. Because of this extended inflammatory response despite appropriate antibiotic therapy, as well as increasing antibiotic resistance, adjuvant therapy for pneumonia that can favourably modify the immune response has become an increasingly relevant approach to improve prognosis. Different adjuvant treatment options for pneumonia have recently been proposed. Promising treatment options include corticosteroids, statins, macrolides and Toll-like receptor antagonists. The aim of this review is to summarize the inflammatory response during pneumonia and discuss the current knowledge and future perspectives regarding the anti-inflammatory treatment options for patients with pneumonia.
Development of Efficient UV-LED Phosphor Coatings for Energy Saving Solid State Lighting (2006)

The University of Georgia, in collaboration with GE Global Research, has investigated the relevant quenching mechanism of phosphor coatings used in white light devices based on UV LEDs. The final goal of the project was the design and fabrication of a high-efficacy white light UV-LED device through improved geometry and optimized phosphor coatings. At the end of the research period, which was extended to seamlessly carry over the research to a follow-up program, we have demonstrated a two-fold improvement in the conversion efficiency of a white light LED device, where the increase efficacy is due to both improved phosphor quantum efficiency and lamp geometry. Working prototypes have been displayed at DOE sponsored meetings and during the final presentation at the DOE Headquarters in Washington, DC. During the first phase of the project, a fundamental understanding of quenching processes in UV-LEDs was obtained, and the relationships that describe the performance of the phosphor as a function of photon flux, temperature, and phosphor composition were established. In the second phase of the project, these findings were then implemented to design the improved UV-LED lamp. In addition, our research provides a road map for the design of efficient white light LEDs, which will be an important asset during a follow-up project led by GE.
Levodopa‐induced modulation of subthalamic beta oscillations during self‐paced movements in patients with Parkinson's disease (2005)

Excessive synchronization of neural activity in the beta frequency band ( approximately 20 Hz) within basal ganglia circuits might contribute to the paucity and slowness of movement in Parkinson's disease (PD). Treatment with dopaminergic drugs reduces the background level of beta frequency band synchronization in the subthalamic nucleus (STN), but has not been shown to increase the proportion of beta activity that is suppressed before voluntary movement in PD. We assessed changes in the event-related desynchronization (ERD) in the beta frequency band of local field potential signals from the region of the STN in 14 patients with PD as they performed self-paced movements of a joystick before and after levodopa administration. The dopamine precursor, levodopa, increased the duration and magnitude of the premovement beta ERD, but did not alter postmovement synchronization in the beta band. Both the latency and magnitude of the beta ERD inversely correlated with the degree of motor impairment. These findings suggest that the beta ERD recorded in the STN area reflects motor-preparative processes that are at least partly dependent on dopaminergic activity within the basal ganglia.
Entry and Selection Methods for Specifying Dates (1989)

Experienced and inexperienced computer users specified event dates using seven different human-computer interaction methods (three entry and four selection methods). Both groups were faster and more accurate when using the three entry methods than the four selection methods. The rank order of performance with these methods was about the same for both groups of participants. The number of keystrokes required by each method was a good predictor of participants' performance time. It was found that decomposing selection tasks into separate fields is advisable.
Redox Regulation of Plant Homeodomain Transcription Factors (2002)

Several families of plant transcription factors contain a conserved DNA binding motif known as the homeodomain. In two of these families, named Hd-Zip and glabra2, the homeodomain is associated with a leucine zipper-like dimerization motif. A group of Hd-Zip proteins, namely Hd-ZipII, contain a set of conserved cysteines within the dimerization motif and adjacent to it. Incubation of one of these proteins, Hahb-10, in the presence of thiol-reducing agents such as dithiothreitol or reduced glutathione produced a significant increase in DNA binding. Under such conditions, the protein migrated as a monomer in non-reducing SDS-polyacrylamide gels. Under oxidizing conditions, a significant proportion of the protein migrated as dimers, suggesting the formation of intermolecular disulfide bonds. A similar behavior was observed for the glabra2 protein HAHR1, which also contains two conserved cysteines within its dimerization domain. Site-directed mutagenesis of the cysteines to serines indicated that each of them has different roles in the activation of the proteins. Purified thioredoxin was able to direct the NADPH-dependent activation of Hahb-10 and HAHR1 in the presence of thioredoxin reductase. The results suggest that redox conditions may operate to regulate the activity of these groups of plant transcription factors within plant cells.
FR104, an Antagonist Anti-CD28 Monovalent Fab’ Antibody, Prevents Alloimmunization and Allows Calcineurin Inhibitor Minimization in Nonhuman Primate Renal Allograft (2014)

Selective targeting of CD28 might represent an effective immunomodulation strategy by preventing T cell costimulation, while favoring coinhibition since inhibitory signals transmitted through CTLA-4; PD-L1 and B7 would not be affected. We previously showed in vitro and in vivo that anti-CD28 antagonists suppress effector T cells while enhancing regulatory T cell (Treg) suppression and immune tolerance. Here, we evaluate FR104, a novel antagonist pegylated anti-CD28 Fab' antibody fragment, in nonhuman primate renal allotransplantation. FR104, in association with low doses of tacrolimus or with rapamycin in a steroid-free therapy, prevents acute rejection and alloantibody development and prolongs allograft survival. However, when FR104 was associated with mycophenolate mofetil and steroids, half of the recipients rejected their grafts prematurely. Finally, we observed an accumulation of Helios-negative Tregs in the blood and within the graft after FR104 therapy, confirmed by Treg-specific demethylated region DNA analysis. In conclusion, FR104 reinforces immunosuppression in calcineurin inhibitor (CNI)-low or CNI-free protocols, without the need of steroids. Accumulation of intragraft Tregs suggested the promotion of immunoregulatory mechanisms. Selective CD28 antagonists might become an alternative CNI-sparing strategy to B7 antagonists for kidney transplant recipients.
Synthesis of Cross-Linked Starch with Acrylic Acid (2002)

アミロペクチンからなるワキシコーンスターチを用いてアクリル酸デンプンを合成し，さらに架橋することによりデンプンの機能化を検討した．高置換度のアクリル酸デンプンは，ピリジン中でデンプンにアクリル酸無水物を作用させることによって得られた．高置換度アクリル酸デンプンを用いた重合では，分枝構造による立体障害などによって架橋ポリマーを得ることができなかったが，高置換度アクリル酸デンプンとアクリル酸とを共重合すると，架橋反応物が得られた．この共重合体の架橋部分は重合度の低いアクリル酸重合体であり，生分解性ポリマーの原料として用いることができると思われる．一方，低置換度アクリル酸デンプンとアクリル酸との共重合では，架橋デンプンは得られなかった．
Suppression of Hepatocyte Growth Factor Production Impairs the Ability of Adipose-Derived Stem Cells to Promote Ischemic Tissue Revascularization (2007)

The use of adipose-derived stem/stromal cells (ASCs) for promoting repair of tissues is a promising potential therapy, but the mechanisms of their action are not fully understood. We and others previously demonstrated accelerated reperfusion and tissue salvage by ASCs in peripheral ischemia models and have shown that ASCs secrete physiologically relevant levels of hepatocyte growth factor (HGF) and vascular endothelial growth factor. The specific contribution of HGF to ASC potency was determined by silencing HGF expression. RNA interference was used to downregulate HGF expression. A dual-cassette lentiviral construct expressing green fluorescent protein (GFP) and either a small hairpin RNA specifically targeted to HGF mRNA (shHGF) or an inactive control sequence (shCtrl) were used to stably transduce ASCs (ASC-shHGF and ASC-shCtrl, respectively). Transduced ASC-shHGF secreted >80% less HGF, which led to a reduced ability to promote survival, proliferation, and migration of mature and progenitor endothelial cells in vitro. ASC-shHGF were also significantly impaired, compared with ASC-shCtrl, in their ability to promote reperfusion in a mouse hindlimb ischemia model. The diminished ability of ASCs with silenced HGF to promote reperfusion of ischemic tissues was reflected by reduced densities of capillaries in reperfused tissues. In addition, fewer GFP(+) cells were detected at 3 weeks in ischemic limbs of mice treated with ASC-shHGF compared with those treated with ASC-shCtrl. These results indicate that production of HGF is important for the potency of ASCs. This finding directly supports the emerging concept that local factor secretion by donor cells is a key element of cell-based therapies. Disclosure of potential conflicts of interest is found at the end of this article.
Acute and subacute inflammation of the optic nerve and its sheath: clinical features in Chinese patients. (2012)

Optic perineuritis and neuromyelitis optica-related optic neuritis were more commonly encountered in our study of Hong Kong Chinese patients than in Caucasian populations. Even in Chinese patients with 'typical' optic neuritis, neuro-imaging and further investigations may be warranted to exclude optic perineuritis/neuromyelitis optica, since Chinese ethnicity is itself an atypical feature. Where neuro-imaging is not readily available, intravenous methylprednisolone may be considered as initial treatment to cover both optic neuritis/optic perineuritis in patients with severe visual loss.
Mode spectrum of waveguides using a transverse S-matrix resonance method (2003)

An S-matrix representation of longitudinal discontinuities is used to investigate the mode spectrum of waveguides. The numerical advantages and disadvantages of the method are described. As an example, field plots for the first modes of a T-septum guide are shown. Monomode bandwidth characteristics for a simple T-septum guide are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fluorescence guided excimer laser ablation of intervertebral discs in vitro (1991)

Laser induced fluorescence of intervertebral discs was investigated in this study for the first time in order to develop a fluorescence guided percutaneous excimer laser discectomy. For this purpose 35 human cadaveric intervetebral discs from level L1 to L5 were irradiated with a 308 nm XeCl excimer laser with a 60 nsec pulse width at 10, 20 and 30 mj/mm2. Laser light was transmitted over a 1000 microns core optical fiber. Fluorescence emitted from the irradiated tissue was transmitted back over the same fiber over a semireflective mirror to another optical fiber, coupled into a spectrograph and O-SMA optical simultaneous multichannel spectral analyzer system. The spectral lineshape of both the annulus fibrosus and the nucleus pulposus was characterized by a broadband emission between 320 nm and 616 nm with 3 peak emissions at 358, 423 and 457 nm. Relative intensities were calculated by forming two ratios of the peak intensities of the three peaks (R1 = I 423/I 358; R2 = I 423/I 457). Statistical analysis of both ratios revealed a highly significant discrimination between annulus fibrosus and nucleus pulposus (P less than 0.001). Under penetrating conditions multiple recorded spectra showed the spectral profile of subsequently ablated nucleus and annulus. The results of this study demonstrate that discrimination between annulus fibrosus and nucleus pulposus by excimer laser-induced fluorescence is feasible under laboratory conditions. Fluorescence spectroscopy could possibly be developed into a valuable guiding system for percutaneous laser discectomy.
Irradiation of Annealed Polyethylene Crystals (1964)

The amount of gel formed on irradiation of polyethylene crystals and the efficiency of gelation have been studied. Films prepared by filtering crystals from suspension with a constant pressure difference, show a decrease in gel for increasing film thickness. At constant film thickness gel increases with increasing pressure difference. Low-angle x-ray diffraction shows that lamellae are more tightly packed in films giving higher gel. When films are heated above the temperature at which their crystals were grown, characteristic changes in gel occur; the principal one is a rapid increase once crystals start to thicken. Variations in crystalline morphology are of little importance. Two other changes in gel, an initial decrease on annealing and an increase on storing at room temperature, are suggested to arise from a smoothing of fold surfaces. The results are consistent with and support the hypothesis that radiation-induced crosslinking occurs preferentially between chain-folds of adjacent lamellas, reduced gelation being due primarily to imperfect lamellar contact. Alternative explanations in terms of solvent retained in aggregates are excluded.
Focus on histone variant H2AX: To be or not to be (2010)

Phosphorylation of histone variant H2AX at serine 139, named gammaH2AX, has been widely used as a sensitive marker for DNA double-strand breaks (DSBs). gammaH2AX is required for the accumulation of many DNA damage response (DDR) proteins at DSBs. Thus it is believed to be the principal signaling protein involved in DDR and to play an important role in DNA repair. However, only mild defects in DNA damage signaling and DNA repair were observed in H2AX-deficient cells and animals. Such findings prompted us and others to explore H2AX-independent mechanisms in DNA damage response. Here, we will review recent advances in our understanding of H2AX-dependent and independent DNA damage signaling and repair pathways in mammalian cells.
The adhesive and neurite-promoting molecule p30: analysis of the amino-terminal sequence and production of antipeptide antibodies that detect p30 at the surface of neuroblastoma cells and of brain neurons. (1988)

A membrane-bound adhesive protein that promotes neurite outgrowth in brain neurons has been isolated from rat brain (Rauvala, H., and R. Pihlaskari. 1987. J. Biol. Chem. 262:16625-16635). The protein is an immunochemically distinct molecule with a subunit size of approximately 30 kD (p30). p30 is an abundant protein in perinatal rat brain, but its content decreases rapidly after birth. In the present study the amino-terminal sequence of p30 was determined by automated Edman degradations. A single amino-terminal sequence was found, which is not present in previously studied adhesive molecules. This unique sequence has a cluster of five positive charges within the first 11 amino acid residues: Gly-Lys-Gly-Asp-Pro-Lys-Lys-Pro-Arg-Gly-Lys. Antisynthetic peptide antibodies that recognize this sequence were produced in a rabbit, purified with a peptide affinity column, and shown to bind specifically to p30. The antipeptide antibodies were used, together with anti-p30 antibodies, to study the localization of p30 in brain cells and in neuroblastoma cells as follows. (a) Immunofluorescence and immunoelectron microscopy indicated that p30 is a component of neurons in mixed cultures of brain cells. The neurons and the neuroblastoma cells expressed p30 at their surface in the cell bodies and the neurites. In the neurites p30 was found especially in the adhesive distal tips of the processes. In addition the protein was detected in ribosomal particles and in intracellular membranes in a proportion of cells. (b) The antibodies immobilized on microtiter wells enhanced adhesion and neurite growth indicating that p30 is surface exposed in adhering neural cells. (c) Immunoblotting showed that p30 is extracted from suspended cells by heparin suggesting that a heparin-like structure is required for the binding of p30 to the neuronal cell surface. A model summarizing the suggested interactions of p30 in cell adhesion and neurite growth is presented.
The Membrane Proximal Cytokine Receptor Domain of the Human Interleukin-6 Receptor Is Sufficient for Ligand Binding but Not for gp130 Association (1998)

Interleukin-6 (IL-6) belongs to the family of the "fourhelix bundle" cytokines. The extracellular parts of their receptors consist of several Ig-and fibronectin type IIIlike domains. Characteristic of these receptors is a cytokine-binding module consisting of two such fibronectin domains defined by a set of four conserved cysteines and a tryptophan-serine-X-tryptophan-serine (WSXWS) sequence motif. On target cells, IL-6 binds to a specific IL-6 receptor (IL-6R), and the complex of IL-6IL-6R associates with the signal transducing protein gp130. The IL-6R consists of three extracellular domains. The NH 2terminal Ig-like domain is not needed for ligand binding and signal initiation. Here we have investigated the properties and functional role of the third membrane proximal domain. The protein can be efficiently expressed in bacteria, and the refolded domain is shown to be sufficient for IL-6 binding. When complexed with IL-6, however, it fails to associate with the gp130 protein. Since the second and the third domain together with IL-6 can bind to gp130 and induce signaling, our data demonstrate the ligand binding function of the third domain and point to an important role of the second domain in complex formation with gp130 and signaling.
Solution-Phase Preparation of a 560-Compound Library of Individual Pure Mappicine Analogues by Fluorous Mixture Synthesis (2002)

Solution-phase mixture synthesis has efficiency advantages and favorable reaction kinetics. Applications of this technique, however, have been discouraged by the difficulty in obtaining individual, pure final products by using conventional separation and identification processes. Introduced here is a new strategy for mixture synthesis that addresses the separation and identification problems. Members of a series of organic substrates are paired with a series of fluorous tags of different chain lengths. The tagged starting materials are then mixed and taken through a multistep reaction process. Fluorous chromatography is used to demix the tagged product mixtures on the basis of the fluorine content of the tags to provide the individual pure components of the mixture, which are detagged to release the final products. The utility of fluorous mixture synthesis is demonstrated by the preparation of a 560-membered library of analogues of the natural product mappicine. A seven-component mixture is carried through a four-step mixture synthesis (two one-pot and two parallel steps) to incorporate two additional points of diversity onto the tetracyclic core. Methods for analysis and purification of the intermediates are established for the quality control of the mixture synthesis.
Expression of a human hepatocyte growth factor/scatter factor cDNA in MDCK epithelial cells influences cell morphology, motility, and anchorage-independent growth (1992)

The addition of exogenous hepatocyte growth factor (HGF)/scatter factor (SF) to MDCK epithelial cells results in fibroblastic morphology and cell motility. We generated HGF/SF producing MDCK cells by transfection with an expression plasmid containing human HGF/SF cDNA. Production of HGF/SF by these cells induced a change from an epithelial to a fibroblastic morphology and increased cell motility. In addition, the HGF/SF producing cells acquired efficient anchorage-independent growth in soft agar but did not form tumors in nude mice. The morphological change and the stimulation of the anchorage-independent growth were prevented by anti-HGF/SF antibody, suggesting that the factor is secreted and then exerts its effects through cell surface receptors.
Simultaneous modelling of metabolic, genetic and product-interaction networks (2001)

The creation of cell models from annotated genome information, as well as additional data from other databases, requires both a format and medium for its distribution. Standards are described for the representation of the data in the form of Document Type Definitions (DTDs) for XML files. Separate DTDs are detailed for genetic, metabolic and gene product-interaction networks, which can be used to hold information on individual subsystems, or which may be combined to create a whole cell DTD. In the execution of this work, a fifth DTD was also created for a metabolite thesaurus, which allows incorporation of metabolite synonyms and generic nomenclature data into the models. A gene-regulation classification scheme was also created, to facilitate incorporation of gene regulatory information in an efficient manner. The work is described with particular reference to the metabolic network of Escherichia coli, which contains 808 individual enzymes. The assignment of confidence levels to these data, through the use of Gene Ontology evidence codes, is highlighted. In silico investigations may now be performed using the mathematical simulation workbench, DBsolve, which incorporates the facility to introduce data directly from XML.