gebhart/patrepeval huggingface dataset:
Dendritic Cells Require STAT-1 Phosphorylated at Its Transactivating Domain for the Induction of Peptide-Specific CTL (2009)

Phosphorylation of transcription factor STAT-1 on Y701 regulates subcellular localization whereas phosphorylation of the transactivating domain at S727 enhances transcriptional activity. In this study, we investigate the impact of STAT-1 and the importance of transactivating domain phosphorylation on the induction of peptide-specific CTL in presence of the TLR9-dependent immune adjuvant IC31. STAT-1 deficiency completely abolished CTL induction upon immunization, which was strongly reduced in animals carrying the mutation of the S727 phospho-acceptor site. A comparable reduction of CTL was found in mice lacking the type I IFN (IFN-I) receptor, whereas IFN-gamma-deficient mice behaved like wild-type controls. This finding suggests that S727-phosphorylated STAT-1 supports IFN-I-dependent induction of CTL. In adoptive transfer experiments, IFN-I- and S727-phosphorylated STAT-1 were critical for the activation and function of dendritic cells. Mice with a T cell-specific IFN-I receptor ablation did not show impaired CTL responses. Unlike the situation observed for CTL development S727-phosphorylated STAT-1 restrained proliferation of naive CD8(+) T cells both in vitro and following transfer into Rag-deficient mice. In summary, our data reveal a dual role of S727-phosphorylated STAT-1 for dendritic cell maturation as a prerequisite for the induction of CTL activity and for T cell autonomous control of activation-induced or homeostatic proliferation.
Improved Surface Velocity and Trajectory Estimates in the Gulf of Mexico from Blended Satellite Altimetry and Drifter Data (2015)

Abstract This study investigates the results of blending altimetry-based surface currents in the Gulf of Mexico with available drifter observations. Here, subsets of trajectories obtained from the near-simultaneous deployment of about 300 Coastal Ocean Dynamics Experiment (CODE) surface drifters provide both input and control data. The fidelity of surface velocity fields are measured in the Lagrangian frame by a skill score that compares the separation between observed and hindcast trajectories to the observed absolute dispersion. Trajectories estimated from altimetry-based velocities provide satisfactory average results (skill score &gt; 0.4) in large (~100 km) open-ocean structures. However, the distribution of skill score values within these structures is quite variable. In the DeSoto Canyon and on the shelf where smaller-scale structures are present, the overall altimeter skill score is typically reduced to less than 0.2. After 3 days, the dataset-averaged distance between hindcast and drifter trajectories, , is about 45 km—only slightly less than the average dispersion of the observations, km. Blending information from a subset of drifters via a variational method leads to significant improvements in all dynamical regimes. Skill scores typically increase to 0.8 with reduced to less than half of . Blending available drifter information with altimetry data restores velocity field variability at scales not directly sampled by the altimeter and introduces ageostrophic components that cannot be described by simple Ekman superposition. The proposed method provides a means to improve the fidelity of near-real-time synoptic estimates of ocean surface velocity fields by combining altimetric data with modest numbers of in situ drifter observations.
Three-Dimensional Solution Structure of the Cyanide Adduct of a Variant of Saccharomyces cerevisiae Iso-1-cytochrome c Containing the Met80Ala Mutation. Identification of Ligand-Residue Interactions in the Distal Heme Cavity (1995)

The 1H NMR spectrum of the the cyanide adduct of a triply mutated Saccharomyces cerevisiae iso-1-cytochrome c (His39Gln/Met80Ala/Cys102Ser) in the oxidized form has been assigned through 1D NOE and 2D COSY, TOCSY, NOESY, and NOE-NOESY experiments; 562 protons out of a total of 683 have been assigned. The solution structure, the first of a paramagnetic heme protein, was determined using 1426 meaningful NOE constraints out of a total of 1842 measured NOEs. The RMSD values at the stage of restrained energy minimization of 17 structures obtained from distance geometry calculations are 0.68 +/- 0.11 and 1.32 +/- 0.14 A for the backbone and all heavy atoms, respectively. The quality, in terms of RMSD, of the present structure is the same as that obtained for the solution structure of the diamagnetic horse heart ferrocytochrome c [Qi, P. X., et al. (1994) Biochemistry 33, 6408-6419]. The secondary structure elements and the overall folding in the variant are observed to be the same as those of the wild-type protein for which the X-ray structure is available. However, the replacement of the methionine axial ligand with an alanine residue creates a ligand-binding "distal cavity". The properties of the distal cavity seen in this solution structure are compared to those of other heme proteins.
Estimation of Stress in the Inner Framework Structure of a Single Heaving Buoy Wave Energy Converter (2012)

This paper details a method for strain measurements in the inner framework structure of the single heaving buoy wave energy converter (WEC). This type of the WEC consists of a linear direct drive generator placed on the seafloor and connected to the floating buoy through the connection line. The study focuses on estimation of stress in the inner framework structure of the WEC using strain measurements in the material. Stress in ocean structures is as important as maximum stress. The offshore experiment took place at the Lysekil research site a few kilometers from the Swedish west coast. Stresses had the maximum value when the translator hit an end stop. Interesting observations were made: compressive stress occurred in the framework crossbar at a sea state of 1.32-m waves, but both compressive and tensile stresses occurred at a sea state of 3.2-m waves. A computational procedure employs good results. Error estimation is calculated and represented. This work is a step that may influence future design of wave energy devices in terms of the material aspect, survivability in a hard wave climate, and cost-effective renewable energies.
Individual Seawater Ions’ Impact on the Rheology of Crosslinked Polymers in the Presence of a Chelating Agent (2023)

Seawater (SW) has the potential to replace freshwater in hydraulic fracturing operations, which promotes sustainability. In this study, we investigated the influence of SW ions individually on a crosslinked polymer solution containing a chelating agent. The tested salts include calcium chloride, magnesium chloride, sodium chloride, and sodium sulfate. First, the concentrations of the delayed zirconium crosslinker, which is used to crosslink the carboxymethyl hydroxypropyl (CMHPG) polymer, and high-pH GLDA were optimized. The testing parameters for the crosslinker and chelating agent optimization experiments were a 70 °C temperature, a 500 psi pressure, and a 100 1/s shear rate. However, the temperature was raised to 120 °C representing harsh reservoir conditions. Results showed that sulfate had a significant effect on the rheology of the crosslinked CMHPG polymer. Unlike DI water, the viscosity of SW and individual ions increased when the crosslinker concentration was increased. In addition, the solution stability of magnesium chloride and DI water was improved. Adding a chelating agent at a low concentration improved the solution stability of magnesium chloride and DI water. These findings are critical for comprehending the rheology of produced water and SW-based fracturing fluids.
Supplementary Table 1 from GDC-0941, a Novel Class I Selective PI3K Inhibitor, Enhances the Efficacy of Docetaxel in Human Breast Cancer Models by Increasing Cell Death <i>In Vitro</i> and <i>In Vivo</i> (2023)

&lt;p&gt;XLS file, 36KB, Summary of Breast Cancer Cell Growth Inhibition and Bliss Sums After Treatment with GDC-0941, Docetaxel (DTX) or the Combination of Both Drugs.&lt;/p&gt;
Competitive Fitness of Influenza B Viruses with Neuraminidase Inhibitor-Resistant Substitutions in a Coinfection Model of the Human Airway Epithelium (2015)

Influenza B viruses are important human respiratory pathogens contributing to a significant portion of seasonal influenza virus infections worldwide. The development of resistance to a single class of available antivirals, the neuraminidase (NA) inhibitors (NAIs), is a public health concern. Amino acid substitutions in the NA glycoprotein of influenza B virus not only can confer antiviral resistance but also can alter viral fitness. Here we used normal human bronchial epithelial (NHBE) cells, a model of the human upper respiratory tract, to examine the replicative capacities and fitness of NAI-resistant influenza B viruses. We show that virus with an E119A NA substitution can replicate efficiently in NHBE cells in the presence of oseltamivir or zanamivir and that virus with the H274Y NA substitution has a relative fitness greater than that of the wild-type NAI-susceptible virus. This study is the first to use NHBE cells to determine the fitness of NAI-resistant influenza B viruses.
Periodontal Treatment Improves Prostate Symptoms and Lowers Serum PSA in Men with High PSA and Chronic Periodontitis (2015)

was to assess whether non-surgical periodontal treatment has an effect on prostate symptom score and serum PSA and levels of proinflammatory cytokines, viz., IL-1 and CRP in men with elevated serum PSA and chronic periodontitis.
Session Security Envelope (2017)

This memo specifies the details of the Session Security Envelope
(SSE). SSE is a session protocol aiming to guarantee confidentiality,
integrity and authentication completely independently by the
underlying context, namely network and transport layers. A single
session using the SEE protocol can include a single transport session
or multiple transport sessions. This mean that SSE can survive the
break-down in network and transport layers or to attacks carried
against them. SSE is also applicable in networks lacking in classic
inter-networking and transport protocols SSE relies on modern AEAD
block cipher modes of operations, a class of block cipher modes which
allows, at the same time, to authenticate the message while encrypting
a part of it.
Ruthenium Catalyzed Synthesis of Cross-Conjugated Polymers and Related Hyperbranched Materials. Copoly(arylene/1,1-vinylene)s (1998)

Dihydridocarbonyltris(triphenylphosphine)ruthenium catalyzed copolymerization of acetophenone and 1,4-bis((trimethylsilyl)ethynyl)benzene yields a linear copolymercopoly[2-acetyl-1,3- phenylene/α,α‘-bis((trimethylsilyl)methylene)-1,4-xylenylene]. This reaction involves regioselective catalytic addition of the ortho C−H bonds of acetophenone across the C−C triple bonds of 1,4-bis((trimethylsilyl)ethynyl)benzene such that the hydrogen becomes bonded to the carbon which bears the trimethylsilyl group. A similar ruthenium catalyzed reaction between 1,4-bis((trimethylsilyl)ethynyl)benzene and 2-methylacetophenone has been used to prepare α,α‘-1,4-bis-[β-(trimethylsilyl)-2-acetyl-3-methylstyrenyl]benzene, a monomeric compound which possesses the same type of chromophore as the linear polymer. Analogous ruthenium catalyzed reaction of 4-((trimethylsilyl)ethynyl)acetophenone yields a hyperbranched material. All three of these cross-conjugated unsaturated materials have regularly alternating arylene and 1,1-vinylene units. These materials have been characterized by 1H, 13C, and 29Si NMR and by IR, UV, and fluorescence spectroscopy. Polymer properties have been measured by GPC, DSC, and TGA.
Crystal-polarity dependence of Ti/Al contacts to freestanding n-GaN substrate (2001)

The effect of crystal polarity on the electrical properties of Ti/Al contacts to n-GaN substrate has been investigated. The Ti/Al contacts prepared on Ga-face n-GaN substrate became ohmic with a contact resistivity of 2×10−5 Ω cm2 after annealing at temperatures higher than 600 °C for 30 s. On the contrary, the contacts on N-face n-GaN substrate exhibited nonlinear current–voltage curve and high Schottky barrier heights over 1 eV were measured at the same annealing conditions. These results could be explained by opposite piezoelectric-field at GaN/AlN heterostructure resulted from different polarity of the GaN substrate.
Synthesis of crosslinked poly(styrene‐co‐sodium styrenesulfonate) latexes (1994)

Abstract Latexes of 100 nm diameter were synthesized by emulsifier‐free copolymerization of styrene, sodium styrenesulfonate, and 1–5 wt% divinylbenzene using persulfate initiator at 91°C. A shot growth method was used to incorporate a high density of sulfonate groups. Coefficients of variation of particle size were 0.04–0.08 without resort to seed growth polymerization. Redox initiation at 40–50°C produced larger, more polydisperse, and less colloidally stable crosslinked latexes. © 1994 John Wiley &amp; Sons, Inc.
Report on the Second International Workshop on Self-Managing Database Systems (SMDB 2007) (2007)

Information management systems are growing rapidly in scale and complexity, \nwhile skilled database administrators\nare becoming rarer and more expensive. Increasingly, the total cost of \nownership of information management systems is dominated by the cost of people, \nrather than hardware or software costs. This economic dynamic dictates that \ninformation systems of the future be more automated and simpler to use, with \nmost administration tasks transparent to the user. Autonomic, or self-managing, \nsystems are a promising approach to achieving the goal of systems that are \nincreasingly automated and easier to use. The aim of the workshop was to \nprovide a forum for researchers from both industry and academia to present and \ndiscuss ideas related to self-managing database systems. SMDB 2007 was the \nfirst event organized by the new {IEEE Computer Society Data Engineering\nWorkgroup on Self-Managing Database Systems} (http ://db.uwaterloo.ca/tcde−\nsmdb/). The workgroup, which was founded in October 2005, is intended to foster \nresearch aimed at enabling information management systems to manage themselves \nseamlessly, thereby reducing the cost of deployment and administration.
Temperature- and doping-concentration-dependent characteristics of junctionless gate-all-around polycrystalline-silicon thin-film transistors (2017)

The temperature effects of both gate-all-around polycrystalline silicon nanowire (GAA poly-Si NW) junctionless (JL) and inversion mode (IM) transistor devices at various temperatures (77–410 K) were investigated. The electrical characteristics of these devices, such as subthreshold swing (SS), threshold voltage (Vth), and drain-induced barrier lowering (DIBL), were also characterized and compared in this study. Moreover, JL devices with different doping concentrations at various temperatures were also discussed. Both Vth and Ion showed significant doping concentration dependences for JL devices with doping concentrations of 1 × 1019 and 5 × 1019 cm−3. However, the electrical characteristics of JL devices showed less thermal sensitivity when the doping concentration reached 1020 cm−3.
Data from Cyclooxygenase-2 Inhibition Suppresses α<sub>v</sub>β<sub>6</sub> Integrin–Dependent Oral Squamous Carcinoma Invasion (2023)

&lt;div&gt;Abstract&lt;p&gt;Worldwide oral squamous cell carcinoma (OSCC) represents about 5.5% of all malignancies, with ∼30,000 new cases each year in the United States. The integrin α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt; and the enzyme cyclooxygenase-2 (COX-2) are implicated in OSCC progression and have been suggested as possible therapeutic targets. Each protein also is reported to identify dysplasias at high risk of malignant transformation, and current clinical trials are testing the efficacy of nonsteroidal anti-inflammatory drugs (NSAID) at preventing OSCC development. Given the probable increased expression of α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt; and COX-2 in OSCC and the inhibition of several integrins by NSAIDs, we investigated whether NSAIDs affected α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;-dependent cell functions. We found that expression of both α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt; and COX-2 was significantly higher in OSCC compared with oral epithelial dysplasias. Neither protein preferentially identified those dysplastic lesions that became malignant. Using OSCC cell lines, modified to express varying levels of α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;, we assessed the effect of COX-2 inhibition on cell invasion. We found that the COX-2 inhibitor NS398 inhibited specifically α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;-dependent, but not α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;-independent, OSCC invasion &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;, and this effect was modulated through prostaglandin E&lt;sub&gt;2&lt;/sub&gt; (PGE&lt;sub&gt;2&lt;/sub&gt;)–dependent activation of Rac-1. Transient expression of constitutively active Rac-1, or addition of the COX-2 metabolite PGE&lt;sub&gt;2&lt;/sub&gt;, prevented the anti-invasive effect of NS398. Conversely, RNA interference down-regulation of Rac-1 inhibited α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt;-dependent invasion. These findings suggest that COX-2 and α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt; interact in promoting OSCC invasion. This is a novel mechanism that, given the ubiquity of α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;6&lt;/sub&gt; expression by head and neck cancers, raises the possibility that NSAIDs could protect against OSCC invasion. (Cancer Res 2006; 66(22): 10833-42)&lt;/p&gt;&lt;/div&gt;
Analysis of Die Edge Bond Pads in Hybrid Bonded Multi-Die Stacks (2022)

The Direct Bond Interconnect (DBI <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> ) Ultra technology is a die-to-wafer (D2W) or die-to-die (D2D) hybrid bonding technology that offers high density Cu-Cu interconnect modules using low processing temperatures. Advances in wafer-to-wafer hybrid bonding technology enabled high volume production of backside-illuminated CMOS images sensors [1] several years ago. Continued development of the supply chain and technology enabled manufacturing of D2W hybrid bonded performance compute modules, for example CPU L3 SRAM [2], [3]. The DBI Ultra D2W technology offers a die-on-tape process that meets the needs of high throughput assembly. The value of the DBI technology can be realized across a wide range of devices and form factors including 2.5 and 3D IC stacking. To proliferate this technology in the industry, it is necessary to define design guidelines and understand the influence of processing and layout interactions.Hybrid bond pad performance is studied as a function of the proximity to the die edge for single die and multi-die stack configurations. The test structures for multi-die stacking analysis are 8 mm x 12 mm die that contain TSVs on a 35 μm pitch which connect to a 15 μm direct bond pad. The direct bond pad array areas include a die center array with 9,480 direct bond interconnects and edge arrays that contain 315 links per column of interconnect. The eight outermost columns of the DBI pad array extend to 80 μm from the die edge.Die stacks ranging from 1-8 die are bonded with the DBI Ultra process at room temperature, followed by an anneal at 250°C. The bond interface is characterized with C-mode scanning acoustic microscopy (CSAM) and the interconnect quality is measured through electrical resistance and cross-sectional scanning electron microscopy (SEM). Die bonding configurations include face to face (DBI pad to DBI pad) and face to back (DBI pad to TSV). The electrical test yield and link resistance are presented as a function of distance from the die edge. Additionally, a set of 5-die stacks is subjected to JEDEC standard temperature cycling and high temperature storage tests for comparison between the edge array bond pads and die center array pads. In all design cases, the resistance data showed little dependence on the distance from the die edge beyond 80 μm indicating a minimal width of the peripheral keep-out-zone, which maximizes the area for active DBI pads.
Recommendations for OCT Angiography Reporting in Retinal Vascular Disease (2022)

This study provides international consensus recommendations for reporting OCTA findings in retinal vascular disease, which may help to improve the interpretability and description in clinic and clinical trials. Further validation in these settings is warranted and ongoing. Efforts are continuing to address unresolved questions.
Current insights into ocular graft-versus-host disease (2010)

This review summarizes current data on ocular GVHD and focuses on novel treatment options for this severe ocular disorder. More data on the impact of ocular GVHD and the development of therapeutic and preventive measures are needed.
Understanding performance of I/O intensive containerized applications for NVMe SSDs (2016)

Our cloud-based IT world is founded on hyper-visors and containers. Containers are becoming an important cornerstone, which is increasingly used day-by-day. Among different available frameworks, docker has become one of the major adoptees to use containerized platform in data centers and enterprise servers, due to its ease of deploying and scaling. Further more, the performance benefits of a lightweight container platform can be leveraged even more with a fast back-end storage like high performance SSDs. However, increase in number of simultaneously operating docker containers may not guarantee an aggregated performance improvement due to saturation. Thus, understanding performance bottleneck in a multi-tenancy docker environment is critically important to maintain application level fairness and perform better resource management. In this paper, we characterize the performance of persistent storage option (through data volume) for I/O intensive, dockerized applications. Our work investigates the impact on performance with increasing number of simultaneous docker containers in different workload environments. We provide, first of its kind study of I/O intensive containerized applications operating with NVMe SSDs. We show that 1) a six times better application throughput can be obtained, just by wise selection of number of containerized instances compared to single instance; and 2) for multiple application containers running simultaneously, an application throughput may degrade upto 50% compared to a stand-alone applications throughput, if good choice of application and workload is not made. We then propose novel design guidelines for an optimal and fair operation of both homogeneous and heterogeneous environments mixed with different applications and workloads.
The Case for Reexamining Integrated File System Design (2000)

Research in integrated file systems---file systems that support different types of data and applications with diverse performance requirements---has stagnated since the commercial failure of video-on-demand systems in the 1990s. However, the past two years have seen an acceleration in the development and deployment of several new technologies aimed at web-based multimedia applications. These technologies have opened up a fertile research ground for new file system optimizations and rekindled interest in integrated file systems. In this paper, we describe some of these technology trends, examine their implications on file system design, and present a sampling of the new research problems that arise due to these technological changes. Based on these observations, we argue for a renewed effort in designing next-generation integrated file systems.