gebhart/patrepeval huggingface dataset:
Toll-like receptor 9 trafficking and signaling for type I interferons requires PIKfyve activity (2015)

Toll-like receptors (TLRs) traffic to distinct membranes for signaling. TLR7 and TLR9 recognize viral nucleic acids in the endosomes and induce robust anti-viral program. Signaling from these TLRs bifurcate at the level of distinct endosomal compartments, namely VAMP3(+) and LAMP(+) endosomes, to mediate the induction of cytokine and type I interferon (IFN) genes, respectively. The formation of the TLR9 endosome competent for IFNs induction requires AP-3. Phosphoinositides (PIs) mark distinct subcellular membranes and control membrane trafficking. However, their role in TLR trafficking and signaling in different dendritic cell (DC) subsets remains unclear. Here, we examined the role of phosphatidylinositol 3P 5-kinase, PIKfyve, in TLR9 trafficking and signaling. We demonstrate that inhibition of PIKfyve activity preferentially blocks TLR9 signaling for type I IFN induction in FLT3L-bone marrow-derived DCs. By confocal microscopy using RAW264.7 cells, we show that trafficking of both TLR9 and CpG to the LAMP1(+) compartment was blocked by PIKfyve inhibitor treatment, whereas their trafficking to the VAMP3(+) endosome remained intact. Further, AP-3 recruitment to TLR9 endosomes was impaired by PIKfyve inhibition. These data indicate that PIKfyve provides critical PIs necessary for the formation of endosome from which TLR9 signals to induce type I IFNs.
The paxillin LD motifs (2001)

Adapter/scaffold proteins, through their multidomain structure, perform a fundamental role in facilitating signal transduction within cells. Paxillin is a focal adhesion adapter protein implicated in growth factor- as well as integrin-mediated signaling pathways. The amino-terminus of paxillin contains five leucine-rich sequences termed LD motifs. These paxillin LD motifs are highly conserved between species as well as within the paxillin superfamily. They mediate interactions with several structural and regulatory proteins important for coordinating changes in the actin cytoskeleton associated with cell motility and cell adhesion as well as in the regulation of gene expression.
A CRLH metamaterial based RF coil element for magnetic resonance imaging at 7 tesla (2009)

The possibility of using composite right/left-handed (CRLH) zeroth-order resonant antennas (ZORAs) in magnetic resonance imaging (MRI) to provide the highly uniform RF magnetic field required for high-quality MRI is explored. A series-mode metal-insulator-metal (MIM) CRLH zeroth-order resonant “coil” (ZORC) element is proposed for this purpose. This ZORC element is shown to provide a very uniform field, appropriate for sagittal or coronal MRI images, and to exhibit a favorable loaded/unloaded Q-factor ratio of around 1/2.
Non-invasively measured cardiac magnetic field maps improve the estimation of the current distribution (2002)

Comprehensive body surface potential mapping (BSPM) and magnetic field mapping (MFM) measurements have been carried out in order to improve the estimation of the current distribution generated by the human heart. Electric and magnetic fields and also the planar gradient of the magnetic field during the QRS complex were imaged as a time series of field maps. A model of the current distribution should explain the features of both BSPM and MFM. Simulated maps generated by a single dipole or a straight line source could be fitted satisfactorily to the BSPM, but not to the MFM. Electric potential and magnetic field maps simulated on the basis of a curved line source model are in good agreement to the measured maps. Also, curved structures in the gradient field maps are in accordance with the curved line source model. The good agreement of this model to simultaneously measured electric and magnetic data indicates the presence of a curvature component in the current density distribution. This is even more evident in the maps of the planar magnetic gradient field.
Surfactant apoprotein-A concentration in airway secretions for the detection of pulmonary oedema (1996)

Patients with cardiogenic pulmonary oedema expectorate foamy sputum containing surfactant, which might be expected to include surfactant apoprotein A (SP-A). SP-A is specific for lung surfactant. We have measured the SP-A concentration in airway secretions to determine whether it is useful in distinguishing pulmonary oedema from other disorders. Samples of sputum and of aspirated airway secretion were obtained from 11 patients with cardiogenic pulmonary oedema, seven patients with clinically stable congestive heart failure, five patients with adult respiratory distress syndrome (ARDS) and 20 control patients (10 intubated) with other respiratory diseases. The samples were used for the measurement of SP-A concentration by a two-site simultaneous immunoassay with monoclonal antibodies against SP-A. SP-A concentrations, measured in samples of sputum and aspirated secretions, depended on the diagnosis of the patients from which they had come. In descending order these samples came from patients with: cardiogenic pulmonary oedema (1324 +/- 197 micrograms.mL-1; n = 33); ARDS (311 +/- 47 micrograms.mL-1; n = 23); clinically stable congestive heart failure (78 +/- 10 micrograms.mL-1; n = 21); and control conditions (3.0 +/- 0.6 micrograms.mL-1; n = 30). Concentrations from disease samples did not overlap with controls. In samples from patients with cardiogenic pulmonary oedema, the SP-A concentration correlated with mean pulmonary capillary wedge pressure (PCWP) (p < 0.001; n = 39). These findings indicate that the measurement of the surfactant apoprotein A concentration in airway secretions may be useful for the detection of pulmonary oedema.
Intracutaneous Injection of Lysophosphatidylcholine Induces Skin Inflammation and Accumulation of Leukocytes (2000)

Various cell stimuli act through activation of phospholipase A2, which hydrolyses fatty acids from membrane phospholipids, resulting in the formation of fatty acids and lysophospholipids. One of the lysophospholipid classes, lysophosphatidylcholine, is a chemoattractant for monocytes and T-lymphocytes and induces the expression of adhesion molecules on cultured endothelial cells. The purpose of the present study was to determine whether lysophosphatidylcholine possesses proinflammatory properties in vivo. This was assessed clinically and histologically by intracutaneous injection of 200-800 nmol lysophosphatidylcholine in healthy volunteers. Lysophosphatidylcholine elicited a dose- and time-dependent local erythema and oedema. The erythema disappeared within 4 h, while the induration lasted for up to 48 h. HE-stained biopsies taken after 24 h showed a leukocytoclastic vasculitis in 2 of the 6 subjects. Microscopic examination of immunohistochemically stained biopsies taken 24 h after the injection showed a significant increase in the number of T-lymphocytes, monocytes and neutrophils, whereas the number of Langerhans' cells was unchanged after lysophosphatidylcholine injection. In addition, the number of intercellular cell adhesion molecule-1 and -3-positive cells was increased approximately 3-fold after injection of lysophosphatidylcholine. In conclusion, the phospholipase A2 hydrolysis product lysophosphatidylcholine can induce erythema, oedema, a mixed cellular infiltrate and the expression of adhesion molecules.
Covalent Modification of the Transcriptional Repressor Tramtrack by the Ubiquitin-Related Protein Smt3 in <i>Drosophila</i> Flies (2000)

The ubiquitin-related SUMO-1 modifier can be covalently attached to a variety of proteins. To date, four substrates have been characterized in mammalian cells: RanGAP1, IkappaBalpha, and the two nuclear body-associated PML and Sp100 proteins. SUMO-1 modification has been shown to be involved in protein localization and/or stabilization and to require the activity of specialized E1-activating and E2 Ubc9-conjugating enzymes. SUMO-1 homologues have been identified in various species and belong to the so-called Smt3 family of proteins. Here we have characterized the Drosophila homologues of mammalian SUMO-1 and Ubc9 (termed dSmt3 and dUbc9, respectively). We show that dUbc9 is the conjugating enzyme for dSmt3 and that dSmt3 can covalently modify a number of proteins in Drosophila cells in addition to the human PML substrate. The dSmt3 transcript and protein are maternally deposited in embryos, where the protein accumulates predominantly in nuclei. Similar to its human counterpart, dSmt3 protein is observed in a punctate nuclear pattern. We demonstrate that Tramtrack 69 (Ttk69), a repressor of neuronal differentiation, is a bona fide in vivo substrate for dSmt3 conjugation. Finally, we show that both the modified and unmodified forms of Ttk69 can bind to a Ttk69 binding site in vitro. Moreover, dSmt3 and Ttk69 proteins colocalize on polytene chromosomes, indicating that the dSmt3-conjugated Ttk69 species can bind at sites of Ttk69 action in vivo. Altogether, these data indicate a high conservation of the Smt3 conjugation pathway and further suggest that this mechanism may play a role in the transcriptional regulation of cell differentiation in Drosophila flies.
Structure of pre-S2 N- and O-linked glycans in surface proteins from different genotypes of hepatitis B virus (2004)

The middle-sized (M) surface proteins of hepatitis B virus (HBV) and other orthohepadnaviruses contain a conserved N-glycan in their pre-S2 domain, which is essential for the secretion of viral particles. Recently, we also found O-glycans in the pre-S2 domain of M protein from woodchuck hepatitis virus (WHV) and HBV genotype D. Since the O-glycosylation motif is not conserved in all genotypes of HBV, the glycosylation patterns of HBV genotypes A and C were analysed. Pre-S2 (glyco)peptides were released from HBV-carrier-derived HBV subviral particles by tryptic digestion, purified by reversed-phase HPLC and identified by amino acid and amino-terminal sequence analysis as well as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Pre-S2 N-glycans were characterized by anion-exchange chromatography, methylation analysis and on-target sequential exoglycosidase digestions in combination with MALDI-TOF-MS, demonstrating the presence of partially sialylated diantennary complex-type oligosaccharides in all genotypes examined. Pre-S2 O-glycans were characterized by on-target sequential exoglycosidase digestions in combination with MALDI-TOF-MS. The pre-S2 domain of M protein and, to a minor extent, of L (large) protein from HBV genotype C and D was partially O-glycosylated by Neu5Ac(alpha2-3)Gal(beta1-3)GalNAcalpha- or Gal(beta1-3)GalNAcalpha-units at Thr-37 within a conserved sequence context. Genotype A, containing no Thr at position 37 or 38, was not O-glycosylated. Analytical data further revealed that M protein is mostly amino-terminally acetylated in all examined genotypes and that the terminal methionine is partially oxidized. The findings may be relevant for the secretion and the immunogenicity of HBV.
Machine vision-based weed spot spraying: a review and where next for sugarcane? (2010)

Automated precision weed spot spraying in the sugarcane industry has potential to increase production while reducing herbicide usage. However, commercially-available technologies based on sensing of weed optical properties are typically restricted to detecting weeds on a soil background (i.e. detection of green on brown) and are not suited to detecting weeds amongst a growing crop. Machine vision and image analysis technology potentially enables leaf colour, shape and texture to achieve discrimination between vegetation species. \n\nThe National Centre for Engineering in Agriculture (NCEA) has developed a machine vision-based weed spot spraying demonstration unit to target the weed Panicum spp. (Guinea Grass) in a sugarcane crop, which requires discrimination of a green grass weed from a green grass crop. The system operated effectively at night time for mature Guinea Grass but further work is required for the system to operate under a greater range of conditions (e.g. different times of day and crop growth stages). Techniques such as multispectral imaging and shape analysis may potentially be required to achieve more robust weed identification. The implications for machine vision detection of Guinea Grass and other weed species in sugarcane crops are considered.\n
A set of lacZ mutations in Escherichia coli that allow rapid detection of specific frameshift mutations. (1990)

We have used site-directed mutagenesis to alter bases in lacZ near the region encoding essential residues in the active site of beta-galactosidase. The altered sequences generate runs of six or seven identical base pairs which create a frameshift, resulting in a Lac- phenotype. Reversion to Lac+ in each strain can occur only by a specific frameshift at these sequences. Monotonous runs of A's (or of T's on the opposite strand) and G's (or C's) have been constructed, as has an alternating -C-G- sequence. These specific frameshift indicator strains complement a set of six previously described strains which detect each of the base substitutions. We have examined a variety of mutagens and mutators for their ability to cause reversion to Lac+. Surprisingly, frameshifts are well stimulated at many of these runs by ethyl methanesulfonate, N-methyl-N'-nitro-N-nitrosoguanidine and 2-amino-purine, mutagens not widely known to induce frameshifts. A comparison of ethyl methanesulfonate, N-methyl-N'-nitro-N-nitrosoguanidine and 2-aminopurine frameshift specificity with that found with a mutH strain suggests that these mutagens partially or fully saturate or inactivate the methylation-directed mismatch repair system and allow replication errors leading to frameshifts to escape repair. This results in a form of indirect mutagenesis, which can be detected at certain sites.
Silicon-containing resist for phase-shifting masks (1991)

A novel silicon-containing chemical amplified resist has been developed for a shifter layer of phase-shifting masks. The resist is composed of an alkaline-soluble silicone polymer and onium salt as an acid generator. The base polymer has a ladder structure and contains a methyl group as a side group and ethoxy and hydroxy groups as an end group. Shifter patterns were directly fabricated on mask substrates by electron-beam exposure and development of the new resist. Improved resolution using an i-line stepper can be achieved with the phase-shifting mask having the new silicon-containing resist shifter.
A New Technique to Exploit Instruction-Level Parallelism for Reducing Microprocessor Power Consumption (2006)

A large portion of the power consumed by a high-performance out-of order microprocessor is attributed to units within the instruction window pipeline stages, from dispatch to commit. Power consumed within the window, and by the overall processor, is reduced by dynamic size adjustment of those units based on program needs. In this article, we introduce a new metric for estimating the instruction level parallelism (ILP) for a group of instructions using a simple ratio of the longest data dependence path's length to the total number of instructions in the group, hence referred to as the longest dependence path ratio (LDPR). We couple this concept with a design where units in the instruction window are divided into segments that are dynamically disabled for power savings when they are unused. The maximum number of enabled segments that a program can utilize is limited based on the amount of ILP estimated using the LDPR. We also show how measuring the LDPR is implemented by a simple extension to the dependence-check-logic at dispatch stage. Results using the LDPR show that power is saved with a minimal impact on performance, by reducing the number of available segments, not only in low ILP periods, but also over those having very high ILP. Using the Wattch power models and the MinneSPEC benchmarks, the LDPR implementation achieves an average of 36.5% of window power savings and 11% overall processor power savings, and with an average performance loss of a very modest 1.9%
Nature of the Scrapie Agent: Current Status of Facts and Hypotheses (1985)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Computing 2-D min, median, and max filters (1993)

Fast algorithms for computing min, median, max, or any other order statistic filter transforms are described. The algorithms take constant time per pixel to compute min or max filters and polylog time per pixel, in the size of the filter, to compute the median filter. A logarithmic time per pixel lower bound for the computation of the median filter is shown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Low-Load Dual-Fuel Compression Ignition (CI) Engine Operation with an On-Board Reformer and a Diesel Oxidation Catalyst: Effects on Engine Performance and Emissions (2009)

In the exhaust gas fuel-reforming method, part of the engine exhaust gas reacts with small amounts of engine fuel in a mini-reactor fitted in the exhaust gas recirculation (EGR) loop to produce gaseous fuel named reformed EGR (REGR). In this study, hot REGR (gas containing H2, CO, CH4, and CO2) was fed back to the engine inlet, so that the diesel engine in effect operated in dual fuel with inlet heating and EGR (CO2 existence). The effects of the diesel engine dual fueling with different REGR percentages on the engine performance and emissions have been examined. The study focused at low-load engine operation, where the conditions are not favorable for efficient gaseous fuel oxidation and engine combustion stability. The addition of the premixed gaseous fuel resulted in a remarkable reduction of both NOx and smoke engine emissions. Carbon monoxide and hydrogen oxidation efficiency can be improved by careful selection of REGR addition (e.g., premixed air/fuel ratio, inlet temperature, and reduced in-cylinder O2 concentration) and in-cylinder diesel injection timing. The use of Pt supported on Al2O3 as an oxidation catalyst at the engine exhaust can eliminate both CO and H2 at temperatures lower than the engine exhaust gas temperature at part loads. Preferably, in an actual engine reformer system, the uncombusted CO and H2 will be used to enhance the aftertreatment system (i.e., diesel particulate filter, NOx traps, and hydrocarbon-selective catalytic reduction of NOx) performance.
High-pressure liquid chromatographic methods for determining arabinosyladenine-5'-monophosphate, arabinosyladenine, and arabinosylhypoxanthine in plasma and urine (1985)

New high-pressure liquid chromatographic methods for determining concentrations of arabinosyladenine (Ara-A), its 5'-monophosphate (Ara-AMP), and arabinosylhypoxanthine (Ara-H) in plasma and urine are presented. A fluorescence detector is used for Ara-A and Ara-AMP, which are first converted to highly fluorescent derivatives with chloroacetaldehyde. This increases sensitivity greatly over previous methods. The sensitivities of the methods (in micrograms per milliliter) are as follows: in plasma, Ara-AMP, 0.002; Ara-A, 0.0015; and Ara-H, 0.35; and in urine, 9 times these values, respectively. Drug concentration data are also presented, which were obtained after doses of Ara-AMP were given intramuscularly to two patients treated with this drug for severe herpes zoster. One patient was given 13 mg of Ara-AMP per kg of body weight once daily, and the other was given 6.5 mg/kg twice daily. Peak Ara-AMP and Ara-A levels in plasma occurred within 1 h after the doses, and neither exceeded 2 micrograms/ml. Ara-AMP and Ara-A concentrations in plasma fell to less than 0.01 micrograms/ml in both patients by 4 to 6 h after the doses. Peak Ara-H concentrations in plasma occurred within 1 to 2 h after doses and were 21 micrograms/ml in patient 1 and 2. The highest concentration of Ara-AMP in urine was 0.09 micrograms/ml. The highest Ara-A concentration in urine was 62 micrograms/ml, and the highest Ara-H concentration in urine was 1,080 micrograms/ml. An interfering substance of unknown nature, cochromatographing with Ara-H, was encountered sporadically in urine samples. An algorithm based on differential spectrophotometry to identify and correct for this problem is described. Estimates of the renal clearances of Ara-AMP, Ara-A, and Ara-H are also given.
The Use of Tetravalent Sulfur in Molten Chloroaluminate Secondary Batteries (1980)

A new rechargeable cell Na/Na+ ion in molten is described. This cell operates at temperatures in the range of 180°–250°C and has an open‐circuit voltage of 4.2V. The discharge process involves the reduction of tetravalent sulfur to the elemental state; sulfur can be further reduced to sulfide. The preferred sodium ion conductor is β''‐alumina. High energy density values, large percent utilization of the active material, and good energy efficiency have been demonstrated. The performance of cells prepared in the discharged and charged states were found to be the same. The number of deep charge/discharge cycles has exceeded 400.
Therapy of Multidrug-Resistant and Extensively Drug-Resistant Tuberculosis (2017)

The global epidemic of multidrug-resistant tuberculosis (MDR-TB) caused by Mycobacterium tuberculosis strains resistant to at least isoniazid and rifampin was recently reported as larger than previously estimated, with at least 580,000 new cases reported in 2015. Extensively drug-resistant tuberculosis (XDR-TB), MDR-TB with additional resistance to a second-line fluoroquinolone and injectable, continues to account for nearly 10% of MDR cases globally. Cases in India, China, and the Russian Federation account for >45% of the cases of MDR-TB. Molecular testing helps identify MDR more quickly, and treatment options have expanded across the globe. Despite this, only 20% are in treatment, and treatment is challenging due to the toxicity of medications and the long duration. In 2016 the World Health Organization updated guidelines for the treatment of MDR-TB. A new short-course regimen is an option for those who qualify. Five effective drugs, including pyrazinamide (PZA) when possible, are recommended during the initial treatment phase and four drugs thereafter. Revised drug classifications include the use of linezolid and clofazimine as key second-line drugs and the option to use bedaquiline and delamanid to complete a five-drug regimen when needed due to poor medication tolerance or extensive resistance. Despite multiple drugs and long-duration treatment regimens, the outcomes for MDR and especially XDR-TB are much worse than for drug-susceptible disease. Better management of toxicity, prevention of transmission, and identification and appropriate management of infected contacts are important challenges for the future.
Compositional Reasoning in Model-Based Verification of Adaptive Embedded Systems (2008)

Formal verification of adaptive systems allows rigorously proving critical requirements. However, design-level models are in general too complex to be handled by verification tools directly. To counter this problem, we propose to reduce model complexity on design-model level in order to facilitate model-based verification. First, we transfer existing compositional reasoning techniques for foundational models used in verification tools to design-level models. Second, we develop new compositional strategies exploiting the special features of adaptive models. Based on these results, we establish a framework for modular model-based verification of adaptive systems by model checking.