gebhart/patrepeval huggingface dataset:
Data from Merkel Cell Polyomavirus-Specific CD8<sup>+</sup> and CD4<sup>+</sup> T-cell Responses Identified in Merkel Cell Carcinomas and Blood (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Merkel cell polyomavirus (MCPyV) is prevalent in the general population, integrates into most Merkel cell carcinomas (MCC), and encodes oncoproteins required for MCC tumor growth. We sought to characterize T-cell responses directed against viral proteins that drive this cancer as a step toward immunotherapy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Intracellular cytokine cytometry, IFN-γ enzyme-linked immunospot (ELISPOT) assay, and a novel HLA-A*2402–restricted MCPyV tetramer were used to identify and characterize T-cell responses against MCPyV oncoproteins in tumors and blood of MCC patients and control subjects.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We isolated virus-reactive CD8 or CD4 T cells from MCPyV-positive MCC tumors (2 of 6) but not from virus-negative tumors (0 of 4). MCPyV-specific T-cell responses were also detected in the blood of MCC patients (14 of 27) and control subjects (5 of 13). These T cells recognized a broad range of peptides derived from capsid proteins (2 epitopes) and oncoproteins (24 epitopes). HLA-A*2402–restricted MCPyV oncoprotein processing and presentation by mammalian cells led to CD8-mediated cytotoxicity. Virus-specific CD8 T cells were markedly enriched among tumor infiltrating lymphocytes as compared with blood, implying intact T-cell trafficking into the tumor. Although tetramer-positive CD8 T cells were detected in the blood of 2 of 5 HLA-matched MCC patients, these cells failed to produce IFN-γ when challenged &lt;i&gt;ex vivo&lt;/i&gt; with peptide.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our findings suggest that MCC tumors often develop despite the presence of T cells specific for MCPyV T-Ag oncoproteins. The identified epitopes may be candidates for peptide-specific vaccines and tumor- or virus-specific adoptive immunotherapies to overcome immune evasion mechanisms in MCC patients. &lt;i&gt;Clin Cancer Res; 17(21); 6671–80. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Type I Interferons Ameliorate Zinc Intoxication of Candida glabrata by Macrophages and Promote Fungal Immune Evasion (2020)

Host and fungal pathogens compete for metal ion acquisition during infectious processes, but molecular mechanisms remain largely unknown. Here, we show that type I interferons (IFNs-I) dysregulate zinc homeostasis in macrophages, which employ metallothionein-mediated zinc intoxication of pathogens as fungicidal response. However, Candida glabrata can escape immune surveillance by sequestering zinc into vacuoles. Interestingly, zinc-loading is inhibited by IFNs-I, because a Janus kinase 1 (JAK1)-dependent suppression of zinc homeostasis affects zinc distribution in macrophages as well as generation of reactive oxygen species (ROS). In addition, systemic fungal infections elicit IFN-I responses that suppress splenic zinc homeostasis, thereby altering macrophage zinc pools that otherwise exert fungicidal actions. Thus, IFN-I signaling inadvertently increases fungal fitness both in vitro and in vivo during fungal infections. Our data reveal an as yet unrecognized role for zinc intoxication in antifungal immunity and suggest that interfering with host zinc homeostasis may offer therapeutic options to treat invasive fungal infections.
Membrane dynamics of dividing cells imaged by lattice light-sheet microscopy (2016)

Membrane remodeling is an essential part of transferring components to and from the cell surface and membrane-bound organelles and for changes in cell shape, which are particularly critical during cell division. Earlier analyses, based on classical optical live-cell imaging and mostly restricted by technical necessity to the attached bottom surface, showed persistent formation of endocytic clathrin pits and vesicles during mitosis. Taking advantage of the resolution, speed, and noninvasive illumination of the newly developed lattice light-sheet fluorescence microscope, we reexamined their assembly dynamics over the entire cell surface and found that clathrin pits form at a lower rate during late mitosis. Full-cell imaging measurements of cell surface area and volume throughout the cell cycle of single cells in culture and in zebrafish embryos showed that the total surface increased rapidly during the transition from telophase to cytokinesis, whereas cell volume increased slightly in metaphase and was relatively constant during cytokinesis. These applications demonstrate the advantage of lattice light-sheet microscopy and enable a new standard for imaging membrane dynamics in single cells and multicellular assemblies.
Effect of thermally expandable particle additives on the mechanical and reversibility performance of adhesive joints (2021)

This paper provides an experimental investigation of the effect of Thermally Expandable Particle (TEP) adhesive additive on the mechanical and reversibility performance of epoxy-bonded load single lap joints (SLJs). Joint substrates are made of aluminum 6061 and woven carbon fiber reinforced plastic 0/90/0 substrates. TEP additive is used for modifying the structural epoxy adhesive used in this study. An electrically charged RF coil is placed around the joint bond area; generated electromagnetic field would heat the aluminum substrate which would in turn heat the modified adhesive. Very large volumetric expansion of the hollow spherical Thermally Expandable Particles (TEPs) would significantly reduce adhesive strength and lead to joint debonding under a minimal load of 100 N. Various weight concentrations of the TEP in the range of 5% to 25% with particulate size from 6 to 16 µm are used for investigating the effect on joint static and fatigue strength as well as the reversibility performance. Measured time to achieve full debonding of the joint (under charged RF coil), is used for assessing the reversibility performance.
Overcoming Repetition: Robotic Fabrication Processes at a Large Scale (2013)

In the context of the Future Cities Laboratory (FCL) of ETH Zurich, the Professorship for Architecture and Digital Fabrication of Fabio Gramazio and Matthias Kohler has set up a robotic laboratory to investigate the potentials of non-standard robotic fabrication for high rise constructions in Singapore. The high degree of industrialisation of this dominant building typology implies standardisation, simplification and repetition and accounts for the increasing monotony evident in many Asian metropolises. The aim of this research on material systems for robotic construction is to develop a new and competitive construction method that makes full use of the malleable potential of concrete as a building material. A novel, spatial, robotic “weaving” method of a tensile active material that simultaneously acts as the form defining mould, folds two separate aspects of concrete -reinforcement and formwork-into one single robotic fabrication process (see Figure 1). This in-situ process could permit the fabrication of structurally differentiated, spatially articulated and material efficient buildings.
Company Profile: Sequenom, Inc. (2012)

There is broad acceptance in both the research and clinical communities that the age of personalized medicine is rapidly approaching. Numerous examples of biomarkers (and tests based on those biomarkers) have been shown to be relevant to clinically important phenotypes. Sequenom, Inc. is at the forefront of this molecular medicine revolution. The company provides genetic analysis instrumentation and reagents to the clinical and research communities. These products are being used for clinical validation of relevant biomarkers as well as for development of diagnostic tests based on those biomarkers.
Room Temperature Photoluminescence from 4H-SiC Epilayers: Non-Destructive Estimation of In-Grown Stacking Fault Density (2012)

Room temperature photoluminescence was obtained by UV excitation of homoepitaxially grown 4H-SiC thin films. A broad band emission from boron deep levels centered at 517nm was observed along with the band-edge emission of 4H-SiC at 391 nm. The wavelength of the excitation was varied and the change in the relative intensity of the two emission peaks was observed. The variation of the relative intensity was correlated with the in-grown stacking fault density in the epilayer. A physical model was developed to explain the correlation in terms of carrier diffusion length. For epilayers with very high density of in-grown stacking faults, a sharp emission was observed at 480nm.
Cross-linked Composite Gel Polymer Electrolyte using Mesoporous Methacrylate-Functionalized SiO2 Nanoparticles for Lithium-Ion Polymer Batteries (2016)

Liquid electrolytes composed of lithium salt in a mixture of organic solvents have been widely used for lithium-ion batteries. However, the high flammability of the organic solvents can lead to thermal runaway and explosions if the system is accidentally subjected to a short circuit or experiences local overheating. In this work, a cross-linked composite gel polymer electrolyte was prepared and applied to lithium-ion polymer cells as a safer and more reliable electrolyte. Mesoporous SiO2 nanoparticles containing reactive methacrylate groups as cross-linking sites were synthesized and dispersed into the fibrous polyacrylonitrile membrane. They directly reacted with gel electrolyte precursors containing tri(ethylene glycol) diacrylate, resulting in the formation of a cross-linked composite gel polymer electrolyte with high ionic conductivity and favorable interfacial characteristics. The mesoporous SiO2 particles also served as HF scavengers to reduce the HF content in the electrolyte at high temperature. As a result, the cycling performance of the lithium-ion polymer cells with cross-linked composite gel polymer electrolytes employing methacrylate-functionalized mesoporous SiO2 nanoparticles was remarkably improved at elevated temperatures.
Modulation of Pharmacologically Relevant Properties of Piperidine Derivatives by Functional Groups in an Equatorial or Axial β‐Position to the Amino Group (2019)

Thirteen epimeric pairs of 5-substituted N-piperonyl-3-phenylpiperidine derivatives were synthesized in order to explore the stereospecific modulation of basicity, lipophilicity, aqueous solubility, and membrane permeation by functional groups in equatorial or axial positions beta to the amine unit. While this comprehensive data set provides enhanced insight into multiple factors that affect basicity and lipophilicity, it fills an important knowledge gap, providing a frame of reference for the property-based design of bioactive compounds. Impacts on amine basicity are very pronounced for the β-equatorial functional groups and parallel basicity-lowering effects known for acyclic amine derivatives. For β-axial functional groups, the basicity-lowering effects are generally decreased, with the nitrile group as the only exception. Basicity and lipophilicity modulations observed for β-axial functional groups are quite diverse and rationalized in terms of intramolecular hydrogen bonding, dipolar interactions, and special solvation effects. Aqueous solubility and (artificial) membrane permeability are discussed with reference to lipophilicity.
Novel Metal–Organic Framework (MOF) Based Composite Material for the Sequestration of U(VI) and Th(IV) Metal Ions from Aqueous Environment (2017)

The combination of magnetic nanoparticles and metal-organic frameworks (MOFs) has demonstrated their prospective for pollutant sequestration. In this work, a magnetic metal-organic framework nanocomposite (Fe<sub>3</sub>O<sub>4</sub>@AMCA-MIL53(Al) was prepared and used for the removal of U(VI) and Th(IV) metal ions from aqueous environment. Fe<sub>3</sub>O<sub>4</sub>@AMCA-MIL53(Al) nanocomposite was characterized by TGA, FTIR, SEM-EDX, XRD, HRTEM, BET, VSM (vibrating sample magnetometry), and XPS analyses. A batch technique was applied for the removal of the aforesaid metal ions using Fe<sub>3</sub>O<sub>4</sub>@AMCA-MIL53(Al) at different operating parameters. The isotherm and kinetic data were accurately described by the Langmuir and pseudo-second-order models. The adsorption capacity was calculated to be 227.3 and 285.7 mg/g for U(VI) and Th(IV), respectively, by fitting the equilibrium data to the Langmuir model. The kinetic studies demonstrated that the equilibrium time was 90 min for each metal ion. Various thermodynamic parameters were evaluated which indicated the endothermic and spontaneous nature of adsorption. The collected outcomes showed that Fe<sub>3</sub>O<sub>4</sub>@AMCA-MIL53(Al) was a good material for the exclusion of these metal ions from aqueous medium. The adsorbed metals were easily recovered by desorption in 0.01 M HCl. The excellent adsorption capacity and the response to the magnetic field made this novel material an auspicious candidate for environmental remediation technologies.
CCDC 785672: Experimental Crystal Structure Determination (2010)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
"Tcl cures 98.3% of all known simulation configuration problems"claims astonished researcher! (1994)

We build detailed event-driven simulations of I/O systems as a way to earn a living, and use them to explore storage system architectures. Our major tool (the TickerTAIP simulator) is a large kit of parts that can be configured, combined, replicated, and connected in innumerable ways.Tcl lets us retain our sanity: it makes configuring the simulator a breeze compared to our prior techniques. In this paper we describe the general approach we adopted, and a few of the tricks and idioms we had to develop to make it work. Our approach and techniques should be useful to anybody using Tcl as a control language for a set of underlying objects. • Disk: the object that ties together a Link (for the bus speed), a DMAengine, a DiskMechanism, a request scheduler and a Cache. Each of these objects can usually be configured further: for example, a Link takes a bandwidth and overhead, a Cache has a size and an allocation granularity. Indeed, the configuration data for Disks and DiskMechanisms are so complex that they are objects in their own right. When we began, we wrote C++ code to control the configuration, using a wealth of command-line flags to select various design alternatives. This rapidly got out of hand: for example, in our current set of simulations for a new storage subsystem we are running about thirty different experiments, each of which compares a set of policy choices (each of which can sometimes have multiple parameter values) against a baseline. Somewhere around the time we were running out of letters of the alphabet for our command-line interface, we happened across Tcl [Ousterhout94]. The result of that fortuitous event is the subject of this paper.
Inhibition of Experimental Abdominal Aortic Aneurysm in the Rat by Use of Decoy Oligodeoxynucleotides Suppressing Activity of Nuclear Factor κB and ets Transcription Factors (2003)

We demonstrated that inhibition of the progression of AAA was achieved by a novel strategy with chimeric decoy ODN used against NF-kappaB and ets in rat model. NF-kappaB and ets are considered to play an important role in the pathogenesis of AAA.
Abstract LB333: Cytokine affinity tuning using the AlphaSeq platform to generate targeted immuno-oncology therapeutics (2023)

Abstract Here, we demonstrate a novel approach for generating affinity detuned cytokines that can be fused to antibodies for selective immune cell activation to improve anti-tumor responses and mitigate systemic toxicity. Although cytokine therapies have demonstrated curative effects in some cancer patients, clinical use remains limited with current toxicity profiles accompanying systemic administration. Next generation cytokine approaches include conditional signaling focused to sites of interest, including the tumor microenvironment or specific immune cell populations. In this presentation, we share a novel approach for generating detuned cytokine therapeutic candidates using the AlphaSeq platform, which involves the repurposing of yeast agglutination and mating to quantitatively measure protein-protein interactions at a library-on-library scale. We show, for the first time, how AlphaSeq can be used to measure interactions between cytokines and their receptors as well as generate engineered cytokines with a broad range of affinities. A saturated mutational library was created for a cytokine of interest and subsequently screened against a second library consisting of axis receptor chains, their species orthologs and off-target receptors. Cytokine variants with lower affinity than parental were recombinantly expressed as Fc fusion proteins to orthogonally measure affinity with biolayer interferometry and characterize potency with an in vitro human PBMC phosflow assay. Finally, detuned cytokine candidates were fused to antibodies recognizing surface antigens of interest to demonstrate cell population-specific signaling. Our results show the AlphaSeq platform can accurately quantitate thousands of cytokine variant affinities simultaneously against multiple relevant receptors which translates to signaling potency in primary human cells. When engineered as antibody fusion proteins, candidate immunocytokines are identified that only induce signaling in intended cell populations. AlphaSeq’s rapid, comprehensive affinity determination can be utilized to develop a portfolio of clinically relevant therapeutic immunocytokines. Citation Format: Ryan Swanson, Davis Goodnight, Jeff Adamo, Kyle Minch, Emily Engelhart, Randolph Lopez, David Younger. Cytokine affinity tuning using the AlphaSeq platform to generate targeted immuno-oncology therapeutics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB333.
Mechanism of the First Lithiation/Delithiation Process in the Anode Material CoFeOPO4@C for Li-Ion Batteries (2018)

A cobalt iron oxyphosphate CoFeOPO4@C (abbreviated as CFP@C) anode was prepared via a solid-state route, and its electrochemical performance was investigated vs Li+/Li over a wide voltage range of 0.01–3.0 V at different current rates C/n (n = 20, 10, 5, 2, and 1). This anode material is able to intercalate more than six lithium ions into the structure at the C/10 current rate, delivering a specific capacity of 748.23 mAh g–1, which is much higher than the theoretical capacity (593.7 mAh g–1) calculated when the insertion of a five lithium ions is considered. A reversible capacity of 200 mAhg–1 was maintained after 30 cycles. Raman spectroscopy confirmed the incorporation of carbon layers into the CoFeOPO4@C composite. Scanning electronic microscopy revealed that CFP@C particles have an angular-flake shape with particle sizes ranging between 1 and 5 μm. In situ X-ray absorption spectroscopy of Fe and Co at the K-edge showed that both transition metals are active during the whole discharge and charge. In operando high-energy X-ray diffraction revealed that this material undergoes a gradual evolution of the structure with lower crystallinity after the first discharge. Correlating electrochemical performance to the structural and electronic features indicated that the cycling mechanism of the CFP@C anode material exhibits a combination of intercalation and conversion processes.
Thermal atomic layer etching of crystalline GaN using sequential exposures of XeF2 and BCl3 (2019)

Gallium nitride (GaN) is a wide-bandgap semiconductor that is useful for optoelectronics and high speed and high power electronics. Fabrication of GaN devices requires etching for many processing steps. Gas phase thermal atomic-layer-controlled etching is desirable for damage-free isotropic etching. In this letter, the thermal atomic layer etching (ALE) of crystalline GaN was demonstrated using sequential exposures of XeF2 and BCl3. GaN ALE was achieved with an etch rate of 0.55 Å/cycle at 195 °C using XeF2 exposures for 20 s at 40 mTorr and BCl3 exposures for 0.5 s at 50 mTorr. At the same reactant exposures, GaN etch rates varied with temperature from 0.18 Å/cycle at 170 °C to 0.72 Å/cycle at 300 °C. The GaN etch rates increased slowly with increasing XeF2 exposure. In addition, the GaN etch rate was self-limiting with respect to both increasing BCl3 pressures and BCl3 exposure times. This self-limiting behavior for BCl3 is consistent with a ligand-exchange mechanism for GaN ALE. Alternative fluorination reactants were also investigated including HF, SF4, and NF3 plasma. Sequential exposures of NF3 plasma and BCl3 yielded GaN etch rates of 2.5–2.9 Å/cycle at 250 °C. In contrast, the HF and SF4 fluorination reactants could not etch crystalline GaN.
Highly Monodisperse Bismuth Nanoparticles and Their Three-Dimensional Superlattices (2010)

A simple and reproducible synthesis of highly monodisperse and ligand-protected bismuth nanoparticles (Bi NPs) is reported. The size of the single-crystalline and spherically shaped NPs is controlled between 11 and 22 nm mainly by the reaction temperature. The high uniformity of the NPs allows their self-assembly into long-range-ordered two- and three-dimensional superstructures.
ChemInform Abstract: Chlorination of 3,4,5‐Trichloropyridazin‐6‐one and Synthesis of 3,4,5‐Trichloro‐1‐(4,5,6‐trichloropyridazin‐3‐yl)pyridazin‐6‐one. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Shear force sensor using a cantilever with liquid-embedded hinges (2012)

We propose a shear force sensor using standing piezoresistive cantilevers with liquid-embedded hinges. The hinges of the cantilevers are positioned in elastomer compartments filled with liquid, while the tip and the root of them are buried in the elastomer shell of the compartments. This design allows most of the cantilever body to freely deform when the compartment shell is deformed with shear forces. Consequently, the stress concentration that is often found in conventional design of such type of sensor is effectively eliminated. The sensor therefore endures larger loading. We measured the relationship between the displacement of the tip of the cantilevers and their change in resistivity, and calculated the sensitivity of the sensors. We confirmed that the proposed design improved the measurement force range of such piezoresistive-cantilever-based force sensors.