gebhart/patrepeval huggingface dataset:
Trichodimerol (BMS-182123) inhibits lipopolysaccharide-induced eicosanoid secretion in THP-1 human monocytic cells (1996)

The fungal metabolite trichodimerol (BMS-182123) has demonstrated inhibition of lipopolysaccharide (LPS)-stimulated tumor necrosis factor-alpha (TNF-alpha) secretion in various in vitro macrophage models (human and murine) including primary and tumor cell lines. When challenged with LPS, differentiated THP-1 monocytic cells secrete elevated levels of the cyclooxygenase products prostaglandin E2 (PGE2), thromboxane B2, and prostaglandin F2alpha (PGF2alpha). Studies directed at elucidating the mechanism of action of BMS-182123 as a TNF-alpha inhibitor revealed that the compound has a profound inhibitory effect on prostanoid secretion in response to LPS challenge. The key enzymes in prostaglandin synthesis are the constitutive cyclooxygenase, prostaglandin H synthase-1 (PGHS-1), and the mitogen-induced cyclooxygenase (PGHS-2), which is induced upon LPS stimulation in THP-1 cells. BMS-182123 did not inhibit the cyclooxygenase activity of PGHS-1 in an in vitro assay, suggesting that inhibition is due to a blockade in synthesis of cyclooxygenase enzyme. Western blot analysis of microsomal pellets from THP-1 cells stimulated with LPS (with or without BMS-182123 pretreatment) provided convincing evidence that the inhibition of prostaglandin synthesis is a result of suppressed synthesis of PGHS-2 enzyme. Northern blot analysis of THP-1 RNA demonstrated that BMS-182123 inhibits the induction of PGHS-2 at the level of transcription.
Efficient deep models for monocular road segmentation (2016)

This paper addresses the problem of road scene segmentation in conventional RGB images by exploiting recent advances in semantic segmentation via convolutional neural networks (CNNs). Segmentation networks are very large and do not currently run at interactive frame rates. To make this technique applicable to robotics we propose several architecture refinements that provide the best trade-off between segmentation quality and runtime. This is achieved by a new mapping between classes and filters at the expansion side of the network. The network is trained end-to-end and yields precise road/lane predictions at the original input resolution in roughly 50ms. Compared to the state of the art, the network achieves top accuracies on the KITTI dataset for road and lane segmentation while providing a 20× speed-up. We demonstrate that the improved efficiency is not due to the road segmentation task. Also on segmentation datasets with larger scene complexity, the accuracy does not suffer from the large speed-up.
Propylene Polymerization with rac‐SiMe2(2‐Me‐4‐PhInd)2ZrMe2/MAO: Polymer Characterization and Kinetic Models (2003)

Abstract Poly(propylene)s were prepared with metallocene catalyst rac ‐SiMe 2 (2‐Me‐4‐PhInd) 2 ZrMe 2 /MAO ( rac ‐dimethylsilylbis(2‐methyl‐4‐phenylindenyl)dimethylzirconium/methylaluminoxane) in heptane solution at temperatures from 50 to 80 °C with varying concentrations of monomer, hydrogen, triisobutylaluminium (TIBA) and MAO. Polymer molar mass depended on the monomer, MAO, TIBA, and hydrogen concentrations and on polymerization temperature. The isotacticity was very high ( mmmm &gt; 95%), and only a slight decrease was detected at high temperatures. Regio selectivity was also high; the total amount of 2,1‐ and 3,1‐insertions was less than 0.4 mol‐%. Lowering the monomer concentration and raising the temperature increased the amount of 3,1 defects over the amount of 2,1 defects. End‐group analysis by 13 C NMR spectroscopy revealed isobutyl and allyl end‐groups. Chain transfer to aluminium and β ‐CH 3 elimination were concluded to be the dominating chain‐termination mechanisms. The importance of β ‐CH 3 elimination increased with temperature. Hydrogen addition changed both the initiation and termination mechanisms as indicated by the presence of propyl, butyl and 2,3‐dimethylbutyl end‐groups. According to modeling studies, the molar mass follows a first‐order relationship with propylene and hydrogen concentrations, and a half‐order relationship with MAO concentration. Arrhenius‐type activation energy coefficients were 125 kJ · mol −1 for β ‐CH 3 elimination, 66 kJ · mol −1 for chain transfer to aluminium, and 53 kJ · mol −1 for chain transfer to hydrogen. A value of 45 kJ · mol −1 was used for the propagation. magnified image
The Generation and Characterization of LMP2-Specific CTLs for Use as Adoptive Transfer From Patients With Relapsed EBV-Positive Hodgkin Disease (2004)

Cellular adoptive immunotherapy for virus-associated malignant disease is an attractive strategy, since viral antigens provide targets for specific T lymphocytes. In Epstein-Barr virus (EBV)-positive Hodgkin disease (HD), a limited number of EBV-encoded antigens such as the latent membrane antigens (LMP) 1 and 2 are expressed on the malignant Reed-Sternberg cells. The authors aimed to generate cytotoxic T lymphocytes (CTLs) from patients with relapsed HD by specifically targeting LMP2A. Patients with relapsed HD have highly immunosuppressive tumors and have been heavily pretreated with cytotoxic agents. As a result, monocytes and lymphocytes are numerically reduced and functionally impaired. Approaches using dendritic cells (DCs) as the sole antigen-presenting cell to expand LMP2-specific CTL lines in vitro have proved impractical. The authors now show how small amounts of patient peripheral blood can be used to produce DCs expressing LMP2 after Ad5F35 transduction, and how an initial reactivation of LMP2-specific CTLs can be followed by stimulation with lymphoblastoid cell lines overexpressing LMP2 from the same vector. Large numbers of LMP2-specific cytotoxic lymphocytes are produced that contain both CD4+ and CD8+ T cells (favoring long-term persistence in vivo) and recognize multiple LMP2 epitopes (minimizing the risk of tumor antigen loss variants). This approach is being used in a current clinical trial.
Coumarin-4-ylmethoxycarbonyls as Phototriggers for Alcohols and Phenols (2003)

Caged compounds can be used to regulate the spatial and temporal dynamics of signaling molecules in live cells. Photochemical properties of coumarin-4-ylmethoxy carbonates (1a-d) are investigated to construct caged compounds of hydroxy-containing molecules. All the compounds possess desired properties as phototriggers for alcohols and phenols. The 6-bromo-7-hydroxycoumarin-4-ylmethoxycarbonyl (Bhcmoc) group has the highest photochemical efficiency and is applied to make caged compounds of 1,2-dioctanoylglycerol (diC(8)), Tyr-OMe, and adenosine. [reaction: see text]
Identification of a Specific Domain Responsible for JNK2α2 Autophosphorylation (2005)

c-Jun N-terminal kinases (JNKs) are a group of mitogen-activated protein kinase family members that are important in regulating cell growth, proliferation, and apoptosis. Activation of the JNK pathway has been implicated in the formation of several human tumors. We have previously demonstrated that a 55-kDa JNK isoform is constitutively activated in 86% of human brain tumors and more recently demonstrated that this isoform is either JNK2alpha2 or JNK2beta2. Importantly, we have also found that among the 10 known JNK isoforms, the JNK2 isoforms are unique in their ability to autophosphorylate in vitro and in vivo. This does not require the participation of any upstream kinases and also leads to substrate kinase activity in vitro and in vivo. To clarify the mechanism of JNK2alpha2 autoactivation, we have generated a series of chimeric cDNAs joining portions of JNK1alpha2, which does not have detectable autophosphorylation activity, with portions of JNK2alpha2, which has the strongest autophosphorylation activity. Through in vivo and in vitro kinase assays, we were able to define a domain ranging from amino acids 218 to 226 within JNK2alpha2 that is required for its autophosphorylation. Mutation of JNK2alpha2 to its counterpart of JNK1alpha2 in this region abrogated the autophosphorylation activity and c-Jun substrate kinase activity in vivo and in vitro. Notably, switching of JNK1alpha2 to JNK2alpha2 at this 9-amino acid site enabled JNK1alpha2 to gain the autophosphorylation activity in vivo and in vitro. We also found two other functional sites that participate in JNK2alpha2 activity. One site ranging from amino acids 363 to 382 of JNK2alpha2 is required for efficient c-Jun binding in vitro, and a site ranging from amino acids 383 to 424 enhances autophosphorylation intensity, although it is not required for triggering the autophosphorylation in vitro. These findings have uncovered the regions required for JNK2alpha2 autophosphorylation, and this information could be used as potential targets to block JNK2alpha2 activation.
Synthesis and properties of polydimethylsiloxane‐containing block copolymers via living radical polymerization (2001)

Abstract Polydimethylsiloxane (PDMS) block copolymers were synthesized by using PDMS macroinitiators with copper‐mediated living radical polymerization. Diamino PDMS led to initiators that gave ABA block copolymers, but there was low initiator efficiency and molecular weights are somewhat uncontrolled. The use of mono‐ and difunctional carbinol–hydroxyl functional initiators led to AB and ABA block copolymers with narrow polydispersity indices (PDIs) and controlled number‐average molecular weights ( M n 's). Polymerization with methyl methacrylate (MMA) and 2‐dimethylaminoethyl methacrylate (DMAEMA) was discovered with a range of molecular weights produced. Polymerizations proceeded with excellent first‐order kinetics indicative of living polymerization. ABA block copolymers with MMA were prepared with between 28 and 84 wt % poly(methyl methacrylate) with M n 's between 7.6 and 35 K (PDI &lt;1.30), which show thermal transitions characteristic of block copolymers. ABA block copolymers with DMAEMA led to amphiphilic block copolymers with M n 's between 9.5 and 45.7 K (PDIs of 1.25–1.70), which formed aggregates in solution with a critical micelle concentration of 0.1 g dm −3 as determined by pyrene fluorimetry experiments. Monocarbinol functional PDMS gave AB block copolymers with both MMA and DMAEMA. © 2001 John Wiley &amp; Sons, Inc. J Polym Sci A: Polym Chem 39: 1833–1842, 2001
Genetic Epidemiology of Asthma (1997)

Asthma is an increasingly common disease in the developed world (1-3). In the United States, the second National Health and Nutrition Examination Survey (NHANES II) (1976-1980) estimates of asthma prevalence (4) were 6.9 percent for whites and 9.2 percent for blacks. Most current definitions of asthma (5) characterize it as a (rapidly or slowly) reversible narrowing of the conducting airways of the lungs, usually associated with evidence of airway wall inflammation and eosinophilia (6, 7). Acute and delayed bronchoconstriction can be precipitated by inhalation by the asthmatic individual of a number of agents, such as ozone, cold dry air, proteins (mainly enzymes), or low molecular weight chemicals, and presents clinically as development (and resolution) of dyspnea, wheezing, and cough. Asthma is clinically heterogenous, but the bulk of cases tend to be characterized by childhood onset, markers of allergic hypersensitiveness such as wheezing and bronchoconstriction following inhalation of antigen (allergen), and elevated levels of total serum immunoglobulin E. There may be remission of symptoms for up to 20 years after childhood, so that earlier mild episodes may be forgotten by the individual, though not by the parent (8, 9). Most genetic studies have concentrated on this type of asthma (i.e., allergic or extrinsic asthma). However, a few studies have attempted to determine if different genes might be acting in the 20 percent of asthmatics who do not exhibit any signs of allergy (i.e., nonallergic or intrinsic asthma).
A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array (2005)

One of the biggest problems facing microarray experiments is the difficulty of translating results into other microarray formats or comparing microarray results to other biochemical methods. We believe that this is largely the result of poor gene identification. We re-identified the probesets on the Affymetrix U133 plus 2.0 GeneChip array. This identification was based on the sequence of the probes and the sequence of the human genome. Using the BLAST program, we matched probes with documented and postulated human transcripts. This resulted in the redefinition of approximately 37% of the probes on the U133 plus 2.0 array. This updated identification specifically points out where the identification is complicated by cross-hybridization from splice variants or closely related genes. More than 5000 probesets detect multiple transcripts and therefore the exact protein affected cannot be readily concluded from the performance of one probeset alone. This makes naming difficult and impacts any downstream analysis such as associating gene ontologies, mapping affected pathways or simply validating expression changes. We have now automated the sequence-based identification and can more appropriately annotate any array where the sequence on each spot is known.
Properties of monoclonal antibodies specific for determinants of a protein antigen, myoglobin. (1980)

Monoclonal hybridoma antibodies specific for the protein antigen sperm whale myoglobin were produced using hyperimmune spleen cells from mice with the genetic trait of high responsiveness to myoglobin. Antibodies from the several clones tested were found to produce linear Scatchard plots, as predicted for homogeneous antibodies, and to possess high affinities for the immunogen (KA congruent to 10(9) M-1). None of the monoclonal antibodies tested reacted with either fragment (1-55) or fragment (132-153) of sperm whale myoglobin. Competitive binding assays using human and horse myoglobins suggested that several of these monoclonal antibodies, which can readily distinguish these myoglobins, recognize different antigenic determinants on the myoglobin molecule. Studies using additional myoglobin sequence variants as competitors should be able to more closely define these antigenic determinants.
Plasmon resonances on gold nanowires directly drawn in a step-index fiber (2010)

We report the successful production of high-quality gold wires, with diameters down to 260nm, by direct fiber drawing from a gold-filled fused-silica cane. The stack-and-draw technique makes it straightforward to incorporate a conventional step-index core, adjacent to the gold wire, in the cane. In the drawn fiber, strong coupling of light from the glass core to SPP resonances on the gold wire is observed at specific well-defined wavelengths. Such embedded wires have many potential applications, for example, as nanoscale electrodes, in nonlinear optical plasmonics, and as near-field scanning optical microscope tips.
Fabrication and Alignment of Wires in Two Dimensions (1998)

Arrays of high-aspect ratio “wires”, assembled from organically functionalized silver nanocrystals, were found to form spontaneously at the air/water interface. For all cases, the wires were 1 particle high, although the width of the wires could be controlled from 20 to 300 nm with a given set of wires characterized by a narrow (15−25%) distribution of widths. The interwire separation distance, as well as the alignment of the wires, could be controlled via compression of the wires using the Langmuir technique. The wires were found to maintain their structure and alignment up to interwire separation distances of less than 10 nm.
Anabolic Action of Parathyroid Hormone Is Skeletal Site Specific at the Tissue and Cellular Levels in Mice (2002)

The cellular and molecular events triggering the anabolic response of the skeleton to exogenous parathyroid hormone (PTH) are not well understood. Despite the numerous bone mass studies in rats, few data are available for mice. Therefore, we treated 10-week-old female intact C57BL/6J mice with human PTH(1-34) delivered subcutaneously at a dose of 40 microg/kg per day 5 days a week for 3 weeks and 7 weeks. Bone mineral density (BMD) of total bone, femur, tibia, and lumbar vertebrae was measured weekly by PIXImus. Bone turnover was examined by histomorphometry, and gene expression of bone formation and resorption markers and osteoclastogenesis regulators in the excised femur and tibia was assessed by reverse-transcription polymerase chain reaction (RT-PCR) at 3 weeks and 7 weeks. The PTH-stimulated increase in BMD was more prominent in the tibia and femur than in the lumbar vertebrae, with an anabolic effect detected within 1-2 weeks and BMD continuing to increase. The appearance of a detectable PTH-stimulated increase in BMD was slower in the lumbar vertebrae where the increase was only significant after 7 weeks of treatment. Histomorphometric analysis of the proximal tibia at both 3 weeks and 7 weeks indicated significant time-dependent increases in trabecular area, trabecular number, trabecular and cortical widths, and osteoblast and osteoid perimeters. In the lumbar vertebrae, these stimulatory effects of PTH on trabecular area, trabecular number, and cortical width were smaller and not detected until 7 weeks. PTH-stimulated increases in bone turnover were evident by increased gene expression of osteocalcin (OC), tartrate-resistant acid phosphatase (TRAP), and receptor of activator nuclear factor kappaB (NF-kappaB) ligand (RANKL) in the tibia and femur. No significant difference in gene expression was observed between the two long bone sites. In conclusion, PTH exerts an anabolic action at the tissue and cellular levels in intact mice and the magnitude and temporal pattern of this anabolic action, as assessed by densitometry and histomorphometry, are skeletal site specific.
Vertebrate Endoderm Development (1999)

Endoderm, one of the three principal germ layers, contributes to all organs of the alimentary tract. For simplicity, this review divides formation of endodermal organs into four fundamental steps: (a) formation of endoderm during gastrulation, (b) morphogenesis of a gut tube from a sheet of cells, (c) budding of organ domains from the tube, and (d) differentiation of organ-specific cell types within the growing buds. We discuss possible mechanisms that regulate how undifferentiated endoderm becomes specified into a myriad of cell types that populate the respiratory and gastrointestinal tracts.
Induction of Interleukin 2 Messenger RNA Inhibited by Cyclosporin A (1984)

Cyclosporin A blocked production of the lymphokine interleukin 2 by activated T lymphocytes. In a human and a murine cell line this inhibition reflected an absence of interleukin 2 messenger RNA. Under conditions in which these cells are normally stimulated to secrete high levels of interleukin 2, they failed to do so in the presence of cyclosporin A. In both cell lines this failure was accompanied by an absence of interleukin 2 messenger accumulation.
Polymerase chain reaction analyses identify two distinct classes of Borrelia burgdorferi (1991)

We sequenced homologous chromosomal loci from several North American and European isolates of the Lyme disease spirochete Borrelia burgdorferi, as well as from the relapsing fever spirochete Borrelia hermsii. Inter- and intraspecies sequence comparisons permitted the design of B. burgdorferi-specific polymerase chain reaction primers that detected all strains tested (n = 31) from diverse geographical and biological origins. Polymerase chain reaction "typing" with other unique sets of primers subdivided B. burgdorferi isolates into two groups: all North American isolates and a few European isolates made up one group, while the majority of the European and Asian isolates made up the second group. This classification may have a clinical correlate reflected in differences between "typical" Lyme borreliosis in North America and Europe.
An adamantane derivative (N-N'(1-adamantil)-ethylene diamine dibromide) induced automaticity in the ventricular myocardium of the frog. (1981)

The effect of an adamantane derivative (N-N'(1-adamantil)-ethylene diamine dibromid; AED) on the transmembrane potentials and contractile activity of isolated electrically driven frog ventricular strips were studied. The effect of AED on the 42K efflux in ventricular muscle rings was also investigated. AED at a concentration of 10(-3) M markedly reduced the rate of depolarization and prolonged the duration of action potential. The resting potential was shifted to less negative potential ranges and pacemaker-like action potentials appeared within 10 minutes of exposure to drug. AED was found to exert an enhancing effect on the contractile force of the frog ventricular muscle. The slow Ca2+-channel blocked D-600 was able to abolish completely the AED-induced automaticity, while the beta-adrenoceptor blocker pindolol failed to prevent this action. The pacemaker activity was reduced by increasing external K+ concentration. AED markedly reduced the 42K efflux in ventricular muscle rings. In conclusion, the AED was shown to be able to induce automaticity by decreasing the outward movement of potassium ions and by depolarizing the cell membrane.
Enrichment of omega-3 fatty acids in suckling pigs by maternal dietary fish oil supplementation (1993)

This study was designed to determine whether substituting menhaden fish oil (FO) for lard (LA) in a practical sow diet was a suitable method for enriching newborn pigs with omega-3 polyunsaturated fatty acids (n-3 PUFA). On d 107 of gestation, 18 crossbred sows were randomly allotted to one of three experimental diets, in which FO was substituted for LA at 0, 3.5, and 7% of the diet. On d 1, 7, 14, and 21 after farrowing samples of milk and serum from the sows and pig serum were collected for fatty acid analysis. The content of n-3 PUFA in the serum of sows fed FO increased six-fold over that in serum of LA-fed sows P < .0001). Feeding FO decreased the levels of arachidonic acid in maternal serum by approximately 50% (P < .0001). Similar changes were reflected in the fatty acid profiles of sow's milk. Pig serum n-3 PUFA levels were elevated over 5- and 10-fold within 24 h of birth in those litters born to sows fed 3.5 and 7% fish oil, respectively. Eicosapentaenoic acid levels in pig serum increased linearly (P < .01) during the first 2 wk postnatally in pigs suckling FO-feds sows and accounted for as much as 12% of the total fatty acids present on d 21. In conclusion, we have demonstrated that feeding FO to sows during late gestation and lactation enriches the newborn pig with n-3 PUFA.
SVGPU: real time 3D rendering to vector graphics formats (2016)

We focus on the real-time realistic rendering of a 3-D scene to a 2-D vector image. There are several application domains which could benefit substantially from the compact and resolution independent intermediate format that vector graphics provides. In particular, cloud streaming services, which transmit large amounts of video data and notoriously suffer from low resolution and/or high latency. In addition, display resolutions are growing rapidly, exacerbating the issue. Raster images for large displays prove a significant bottleneck when being transported over communication networks. However the alternative of sending a full 3D scene worth of geometry is even more prohibitive. We implement a real time rendering pipeline that utilizes analytic visibility algorithms on the GPU to output a vector graphics representation of a 3D scene. Our system SVGPU (Scalable Vector on the GPU) is fast and efficient on modern hardware, and simple in design. As such we are making a much needed step towards enabling the benefits of vector graphics representations to be reaped by the real time community.