gebhart/patrepeval huggingface dataset:
Shedding of the Mer Tyrosine Kinase Receptor Is Mediated by ADAM17 Protein through a Pathway Involving Reactive Oxygen Species, Protein Kinase Cδ, and p38 Mitogen-activated Protein Kinase (MAPK) (2011)

Mer tyrosine kinase (MerTK) is an integral membrane protein that is preferentially expressed by phagocytic cells, where it promotes efferocytosis and inhibits inflammatory signaling. Proteolytic cleavage of MerTK at an unidentified site leads to shedding of its soluble ectodomain (soluble MER; sMER), which can inhibit thrombosis in mice and efferocytosis in vitro. Herein, we show that MerTK is cleaved at proline 485 in murine macrophages. Site-directed deletion of 6 amino acids spanning proline 485 rendered MerTK resistant to proteolysis and suppression of efferocytosis by cleavage-inducing stimuli. LPS is a known inducer of MerTK cleavage, and the intracellular signaling pathways required for this action are unknown. LPS/TLR4-mediated generation of sMER required disintegrin and metalloproteinase ADAM17 and was independent of Myd88, instead requiring TRIF adaptor signaling. LPS-induced cleavage was suppressed by deficiency of NADPH oxidase 2 (Nox2) and PKCδ. The addition of the antioxidant N-acetyl cysteine inhibited PKCδ, and silencing of PKCδ inhibited MAPK p38, which was also required. In a mouse model of endotoxemia, we discovered that LPS induced plasma sMER, and this was suppressed by Adam17 deficiency. Thus, a TRIF-mediated pattern recognition receptor signaling cascade requires NADPH oxidase to activate PKCδ and then p38, culminating in ADAM17-mediated proteolysis of MerTK. These findings link innate pattern recognition receptor signaling to proteolytic inactivation of MerTK and generation of sMER and uncover targets to test how MerTK cleavage affects efferocytosis efficiency and inflammation resolution in vivo.
New Equalizer to Improve Signal-to-Noise Ratio (1999)

Signal-to-noise ratio (SNR) of an optical memory disc deteriorates as the recording density increases. The authors have coped with this problem and developed a new equalizer which can improve the SNR by boosting higher frequency components on the readout signal without increasing the inter-symbol interference (ISI). The authors measured the jitter values on a prototype disc applying the new equalizer. The disc had a capacity of 15 Gbytes, a track pitch of 0.37 µm and a minimum pit length of 0.25 µm. An optical head with a second harmonic generation (SHG) blue laser with a wavelength of 430 nm and an objective lens with a NA of 0.6 was used. As a result, it was confirmed that the new equalizer could improve not only the SNR but also the tilt margins. Furthermore, the correlation between the jitter and the bit error rate observed on a conventional equalizer was found unchanged even with the new equalizer.
Random Sampling from Pseudo-Ranked B+ Trees (1992)

In the past, two basic approaches for sampling f5-om B+ trees have been suggested: sampling from the ranked trees and acceptance/rejection sampling i?om non-ranked trees. The first approach requires the entire root-to-leaf path to be updated with each insertion and deletion. The second has no update overhead, but incurs a high rejection rate for the compressed-key B+ trees commonly used in practice. In this paper we introduce a new sampling method based on pseudo-ranked B+ trees, which are B+ trees supplemented with information loosely describing the estimated rank limits. This new method exhibits a very small rejection rate while paying only a marginal cost of the tree update overhead. We also present comparative efficiency measurements of different methods that were run on production databases and on several prototype workload simulations.
Retroactive data structures (2007)

We introduce a new data structuring paradigm in which operations can be performed on a data structure not only in the present, but also in the past. In this new paradigm, called retroactive data structures , the historical sequence of operations performed on the data structure is not fixed. The data structure allows arbitrary insertion and deletion of operations at arbitrary times, subject only to consistency requirements. We initiate the study of retroactive data structures by formally defining the model and its variants. We prove that, unlike persistence, efficient retroactivity is not always achievable. Thus, we present efficient retroactive data structures for queues, doubly ended queues, priority queues, union-find, and decomposable search structures.
Oxaloacetate acetylhydrolase gene mutants of <i> <scp>S</scp> clerotinia sclerotiorum </i> do not accumulate oxalic acid, but do produce limited lesions on host plants (2014)

The oxaloacetate acetylhydrolase (OAH, EC 3.7.1.1)-encoding gene Ss-oah1 was cloned and functionally characterized from Sclerotinia sclerotiorum. Ss-oah1 transcript accumulation mirrored oxalic acid (OA) accumulation with neutral pH induction dependent on the pH-responsive transcriptional regulator Ss-Pac1. Unlike previously characterized ultraviolet (UV)-induced oxalate-deficient mutants ('A' mutants) which retain the capacity to accumulate OA, gene deletion Δss-oah1 mutants did not accumulate OA in culture or during plant infection. This defect in OA accumulation was fully restored on reintroduction of the wild-type (WT) Ss-oah1 gene. The Δss-oah1 mutants were also deficient in compound appressorium and sclerotium development and exhibited a severe radial growth defect on medium buffered at neutral pH. On a variety of plant hosts, the Δss-oah1 mutants established very restricted lesions in which the infectious hyphae gradually lost viability. Cytological comparisons of WT and Δss-oah1 infections revealed low and no OA accumulation, respectively, in subcuticular hyphae. Both WT and mutant hyphae exhibited a transient association with viable host epidermal cells at the infection front. In summary, our experimental data establish a critical requirement for OAH activity in S. sclerotiorum OA biogenesis and pathogenesis, but also suggest that factors independent of OA contribute to the establishment of primary lesions.
Reaction intermediate analogs for enolase (1984)

A number of compounds that appear to be analogues of the aci form of the normal carbanion intermediate are good inhibitors of yeast enolase. These include (3-hydroxy-2-nitropropyl)phosphonate (I), the ionized (pK = 8.1) nitronate form of which in the presence of 5 mM Mg2+ has a Ki of 6 nM, (nitroethyl)phosphonate (III) (pK = 8.5; Ki of the nitronate in the presence of 5 mM Mg2+ = 1 microM), phosphonoacetohydroxamate (IV) (pK = 10.2; Ki with saturating Mg2+ for the ionized form = 15 pM), and (phosphonoethyl)nitrolate (VII) (Ki at 1 mM Mg2+ = 14 nM). The oxime of phosphonopyruvate (VI) has a pH-independent Ki of 75 microM. I, IV, VI, and VII are slow binding inhibitors. All of these compounds are trigonal at the position analogous to C-2 of 2-phosphonoglycerate and contain a phosphono group, but a negatively charged metal ligand at the position isosteric with the hydroxyl attached to C-3 of 2-phosphoglycerate (as in IV) appears to contribute more to binding than a nitro group isosteric with the carboxyl of 2-phosphoglycerate (I and III). These data support the carbanion mechanism for enolase and suggest that the 3-hydroxyl of 2-phosphoglycerate is directly coordinated to Mg2+ prior to being eliminated to give phosphoenolpyruvate.
Suitability of staining techniques for the detection and quantitation of nonhistone high mobility group proteins (1990)

Three different staining techniques were compared for the detection of nonhistone high mobility group (HMG) proteins after acidic urea-polyacrylamide gel electrophoresis. Silver staining after glutaraldehyde fixation provides the highest detection sensitivity. Because of the acid solubility of HMG proteins special care has to be taken concerning fixation. Staining with colloidal CBB G-250 according to Neuhoff et al. is superior in sensitivity and reliability of quantitation when compared with noncolloidal Coomassie Brilliant Blue R-250. High detection sensitivity and reproducibility of quantitation are prerequisites for studying the tissue-specific expression of HMG proteins. In the present study tissue-specific differences in the molar amounts of various HMG proteins in thymus and erythrocytes of the chicken are documented by application of the methods tested.
Silicon microneedle array for minimally invasive human health monitoring (2018)

A silicon microneedle array with integrated microfluidic channels is presented, which is designed to extract dermal interstitial fluid (ISF) for biochemical analysis. ISF is a cell-free biofluid that is known to contain many of the same constituents as blood plasma, but the scope and dynamics of biomarker similarities are known for only a few components, most notably glucose. Dermal ISF is accessible just below the outer skin layer (epidermis), which can be reached and extracted with minimal sensation and tissue trauma by using a microneedle array. The microneedle arrays presented here are being developed to extract dermal ISF for off-chip profiling of nucleic acid constituents in order to identify potential biomarkers of disease. In order to assess sample volume requirements, preliminary RNA profiling was performed with suction blister ISF. The microneedles are batch fabricated using established silicon technology (low cost), are small in size, and can be integrated with sensors for on-chip analysis. This approach portends a more rapid, less expensive, self-administered assessment of human health than is currently achievable with blood sampling, especially in non-clinical and austere settings. Ultimately, a wearable device for monitoring a person’s health in any setting is envisioned.
Enhancement of radiation therapy by ultrasonically-stimulated microbubbles in vitro: Effects of treatment scheduling on cell viability and production of ceramide (2010)

Microbubbles are used as therapeutic agents to improve drug delivery across blood vessels and cell membranes. Recently, it was shown that the application of ultrasound and microbubbles can enhance the therapeutic effect of radiotherapy using in vitro and in vivo tumour models. This phenomenon depended on ultrasound, microbubble and x-ray exposure parameters. In this study, the effect of ultrasound-microbubble (US+MB) and ionizing radiation (XRT) treatment scheduling on cell viability and production of ceramide, an apoptosis messenger, was investigated in vitro. Human prostate cancer (PC3) and KHT-C murine fibrosarcoma cells in suspension were exposed to US+MB (f=500kHz; Pneg=580kPa; PD=32μs; PRF=3kHz; insonation time 30s; and 1% v/v microbubbles (DA04, Artenga Inc.)) and XRT (3 Gy single fraction). Timing between the treatments immediately (i.e. within 15 minutes), 3 and 6 hours and their order were varied. Following treatment, cell viability was assessed using clonogenic assay. Ceramide level within cells was quantified for up to 7.5 hours following treatment using immunohistochemistry and spectrophotometry. Ultrasound and microbubbles improved the therapeutic effect of radiotherapy in KHT-C and PC3 cells; cell death increased by ~3-5 folds with the combined treatment compared to each treatment alone. Maximal KHT-C cell death (70±2%) was achieved when US+MB was followed in three hours by XRT. KHT-C cell death of 43±2% and 25±2% was achieved with US+MB and XRT treatments, respectively. The maximal PC3 cell death (83±2%) was achieved when US+MB was followed by XRT immediately (i.e. within 15 minutes). PC3 cell death of 15±4% and 48±5% was achieved with US+MB and XRT treatments, respectively. US+MB and XRT treatments increased the level of ceramide in both cell lines compared to untreated controls. A correlation was found between cell death and ceramide at 3 h following treatment for the KHT-C and PC3 cells with correlation coefficients of 0.938 and 0.706, respectively. Ultrasonically-stimulated microbubbles can enhance the therapeutic effect of radiotherapy and the timing between the treatments and their order are important in the optimization of the therapeutic effect of radiotherapy. Future work will investigate this in vivo.
Ultra-thin silicon nitride films on Si by jet vapor deposition (2002)

Ultra-thin silicon nitride films (with equivalent oxide thicknesses /spl les/4 nm) have been successfully deposited directly on silicon substrates at room temperature using jet vapor deposition technique. These ultra-thin silicon nitride films exhibit excellent C-V and I-V characteristics, high electrical breakdown strength, low leakage current, and low densities of bulk and interface traps. These properties make JVD silicon nitride a very attractive candidate to extend the scaling limit of the gate dielectric below 4 nm of equivalent oxide thickness.
Is Consensus Required for a Benign Social Order? (1995)

Abstract This chapter argues against the notion that consensus is required for a benign social order. It suggests that benign social order need not be committed to the quest for consensus and that it can be constituted along very different, irreducibly pluralistic lines. It contends that the insistence on the pursuit of general consensus in practical matters and public affairs is unrealistic and counter-productive because it deprives people of the productive stimulus of competition and the incentive of rivalry.
Cardiac‐gated parametric images from<sup>82</sup>Rb<scp>PET</scp>from dynamic frames and direct 4D reconstruction (2017)

Direct reconstruction can produce parametric images with less noise than the indirect method, opening the potential utility of gated parametric imaging for perfusion PET.
Experimental evaluation of the surface specificity of sum-frequency vibrational spectroscopy (2000)

Summary form only given. Surface vibrational spectroscopy via infrared-visible sum-frequency generation (SFG) has been developed into a powerful tool to study the structures of surfaces and interfaces. It is based on the principle that SFG is forbidden under electric-dipole approximation in a medium with inversion symmetry, but necessarily allowed at a surface or interface where the inversion symmetry is broken. However, there is always the question whether the bulk quadrupole contribution to the reflected surface SFG spectrum is indeed negligible. To answer this question, we need to measure the quadrupole bulk contribution separately. This can be done with SFG in transmission. Because of the longer-coherence length for phase matching in transmission, the quadrupole bulk contribution could dominate over the dipole-allowed surface contribution. Although the transmission measurement cannot determine all the independent tensor elements of the quadrupole nonlinear susceptibility of the bulk, it provides at least an order-of-magnitude estimate of the bulk contribution to surface SFG. We have carried out quantitative measurements and comparison of reflected and transmitted SFG spectra for a number of samples and learned whether their reflected SFG spectra are surface-dominated.
The Design of a Low Data Rate MFSK Communication System (1970)

Low data rate communications are of considerable interest for applications in which the received signal-to-noise ratio is very low. At data rates below the neighborhood of 5 bit/s, coherent communication techniques become inefficient, and noncoherent techniques such as <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</tex> -ary frequency shift keying (MFSK) become attractive. In this paper, the design of an MFSK low data rate communication system is discussed. The problems of synchronization in time and frequency are analyzed, and experimental results of successful laboratory tests of the system are presented.
Human and yeast Hsp110 chaperones exhibit functional differences (2005)

Hsp110 proteins constitute a heterogeneous family of abundant molecular chaperones, related to the Hsp70 proteins and exclusively found in the cytosol of eukaryotic organisms. Hsp110 family members are described as efficient holdases, preventing the aggregation and assisting the refolding of heat-denatured model substrates in the presence of Hsp70 chaperones and their co-chaperones. To gain more insights into the mode of action of this protein family we compared two homologues representing two subtypes of Hsp110 proteins, S. cerevisiae Sse1 and H. sapiens Apg-2, in their structural and functional properties in vitro. In contrast to previous publications both proteins exhibited intrinsic ATPase activities, which only in the case of Sse1 could be stimulated by the Hsp40 co-chaperone Sis1. Similar to Hsp70 proteins ATP binding and hydrolysis induced conformational rearrangements in both Hsp110 proteins as detected by tryptophane fluorescence. However, nucleotide induced changes in the proteolytic digestion pattern were detected only for Sse1. Sse1 and Apg-2 thus show significant differences in their biochemical properties, which may relate to differences in their functional roles in vivo.
Using An Efficient Collision Detector In The Solution Of The Find-Path Problem Of Industrial Robots (1985)

In this paper an efficient approach to collision detection is proposed. Its incorporation in two approaches for the solution of the find-path problem is also presented. Collision detector is based on representing objects by a hierarchy of bounding spheres. Features of the collision detector are that computation time depends on the proximity of the objects and that the method concentrates its efforts on the parts of objects most likely to have geometric interference as determined by collision information. The use of this representation for collision detection in two approaches for the solution of the find-path problem, namely a generate and test approach and a free space representation based approach, are presented. The paper is organized as follows. First, a review of the literature is given. Second, details of the collision detector and its incorporation in a solution for the find-path problem are presented. Third, the implementation of this approach on a LISP machine and the preliminary performance tests performed using a PUMA 560 robot are discussed. Finally, conclusions and potential extensions are outlined.
Facile microencapsulation of HDI for self-healing anticorrosion coatings (2011)

Polyurethane (PU) microcapsules containing hexamethylene diisocyanate (HDI) as core materials are facilely manufactured via interfacial polymerization reaction of commercial methylene diphenyl diisocyanate (MDI) prepolymer and 1,4-butanediol in an oil-in-water emulsion. The resultant capsules have diameters of 5–350 μm and shell thickness of 1–15 μm, both linearly related to the agitation rate in the double logarithm coordinates. The typical core fraction of microcapsules and the yield of synthesis are around 60 wt% and 70 wt%, respectively, while varying with reaction conditions. The effects of parameters including reaction duration and temperature, surfactant concentration, agitation rate, and environmental factors on the formation of microcapsules were systematically investigated and optimized. Quality assessments of each batch of microcapsules were performed using thermogravimetric analysis and scanning electron microscopy. Anticorrosion coatings mixed with synthesized microcapsules were prepared on a steel substrate. Preliminary results indicated significant corrosion retardancy happened in the self-healing coatings under an accelerated corrosion process, showing the great potential of this facile microencapsulation technique in development of catalyst-free, one-part self-healing coatings for corrosion control.
Hoxb13 Up-regulates Transglutaminase Activity and Drives Terminal Differentiation in an Epidermal Organotypic Model (2005)

Hox genes act to differentiate and pattern embryonic structures by promoting the proliferation of specific cell types. An exception is Hoxb13, which functions as a proapoptotic and antiproliferative protein during development of the caudal spinal cord and tail vertebrae and has also been implicated in adult cutaneous wound repair. The adult epidermis, which expresses several Hox genes including Hoxb13, is continually renewed in a program of growth arrest, differentiation, and a specialized form of apoptosis (cornification). Yet little is known about the function(s) of these genes in skin. Based on its role during embryogenesis, Hoxb13 is an attractive candidate to be involved in the regulation of epidermal differentiation. Here, we demonstrate that Hoxb13 overexpression in an adult organotypic epidermal model recapitulates actions of Hoxb13 reported in embryonic development. Epidermal cell proliferation is decreased, apoptosis increased, and excessive terminal differentiation observed, as characterized by enhanced transglutaminase activity and excessive cornified envelope formation. Overexpression of Hoxb13 also produces abnormal phenotypes in the epidermal tissue that resemble certain pathological features of dysplastic skin diseases. Our results suggest that Hoxb13 functions to promote epidermal differentiation, a critical process for skin regeneration and for the maintenance of normal barrier function.
Metalorganic chemical vapor deposition of aluminum from trimethylamine alane using Cu and TiN nucleation activators (1991)

High purity Al films have been deposited on TiN and in situ evaporated Cu films on Si in a cold wall low pressure metalorganic chemical vapor deposition reactor using trimethylamine alane. TiN and Cu serve as nucleation layers for Al deposition to replace the commonly used but corrosive TiCl4. Al films deposited on TiN at 250 °C exhibit highly textured (111) orientation, whereas those grown on Cu at 150–350 °C are randomly oriented with some preferential growth in the (100) direction. These films are compared with films grown on Si and SiO2 using TiCl4 activation. Cu serves the additional purpose of diffusing into the Al during deposition to improve the electromigration resistance of the films. Electrical resistivities of the Al films on TiN are 4–6 μΩ cm, roughly twice that of bulk Al. The variation of film morphology with deposition temperature, substrate, and precursor pressure is discussed.
Disinfection of Hospital Rooms Contaminated With Vancomycin-Resistant <i>Entemcocms faecium</i> (1998)

Sixteen percent of hospital room surfaces remained colonized by vancomycin-resistant enterococci (VRE) after routine terminal disinfection. Disinfection with a new "bucket method" resulted in uniformly negative cultures. Conventional cleaning took an average of 2.8 disinfections to eradicate VRE from a hospital room, while only one cleaning was required with the bucket method.
Ion Channels as Drug Targets in Central Nervous System Disorders (2013)

Ion channel targeted drugs have always been related with either the central nervous system (CNS), the peripheral nervous system, or the cardiovascular system. Within the CNS, basic indications of drugs are: sleep disorders, anxiety, epilepsy, pain, etc. However, traditional channel blockers have multiple adverse events, mainly due to low specificity of mechanism of action. Lately, novel ion channel subtypes have been discovered, which gives premises to drug discovery process led towards specific channel subtypes. An example is Na(+) channels, whose subtypes 1.3 and 1.7-1.9 are responsible for pain, and 1.1 and 1.2 - for epilepsy. Moreover, new drug candidates have been recognized. This review is focusing on ion channels subtypes, which play a significant role in current drug discovery and development process. The knowledge on channel subtypes has developed rapidly, giving new nomenclatures of ion channels. For example, Ca(2+)s channels are not any more divided to T, L, N, P/Q, and R, but they are described as Ca(v)1.1-Ca(v)3.3, with even newer nomenclature α1A-α1I and α1S. Moreover, new channels such as P2X1-P2X7, as well as TRPA1-TRPV1 have been discovered, giving premises for new types of analgesic drugs.