gebhart/patrepeval huggingface dataset:
Sensitive and real-time determination of H2O2 release from intact peroxisomes (2002)

Peroxisomes are essential and ubiquitous cell organelles having a key role in mammalian lipid and oxygen metabolism. The presence of flavine oxidases makes them an important intracellular source of H(2)O(2): an obligate product of peroxisomal redox reactions and a key reactive oxygen species. Peroxisomes proliferate in response to external signals triggered by peroxisome-proliferator-activated receptor signalling pathways. Peroxisome-derived oxidative stress as a consequence of this proliferation is increasingly recognized to participate in pathologies ranging from carcinogenesis in rodents to alcoholic and non-alcoholic steatosis hepatitis in humans. To date, no sensitive approach exists to record H(2)O(2) turnover of peroxisomes in real time. Here, we introduce a sensitive chemiluminescence method that allows the monitoring of H(2)O(2) generation and degradation in real time in suspensions of intact peroxisomes. Importantly, removal, as well as release of, H(2)O(2) can be assessed at nanomolar, non-toxic concentrations in the same sample. Owing to the kinetic properties of catalase and oxidases, H(2)O(2) forms fast steady-state concentrations in the presence of various peroxisomal substrates. Substrate screening suggests that urate, glycolate and activated fatty acids are the most important sources for H(2)O(2) in rodents. Kinetic studies imply further that peroxisomes contribute significantly to the beta-oxidation of medium-chain fatty acids, in addition to their essential role in the breakdown of long and very long ones. These observations establish a direct quantitative release of H(2)O(2) from intact peroxisomes. The experimental approach offers new possibilities for functionally studying H(2)O(2) metabolism, substrate transport and turnover in peroxisomes of eukaryotic cells.
Advanced Fluid Characterization of Pauto Complex, Colombia (2010)

Abstract This paper presents a detailed fluid characterization study for a group of compartmentalized gas condensate &amp; volatile oil reservoirs making up the Pauto Complex. Fluid oil-gas ratios range from 30 to 350 bbl/MMscf, producing from depths of 12,000–16,000 ft, with estimated IGIP&amp;gt;1 Tcf and significant oil/condensate resources. A single equation of state (EOS) was developed to describe the complex phase and volumetric behaviour of eight reservoir fluids undergoing depletion. The EOS also describes accurately the vaporization of retrograde condensate from one of the richer reservoir fluids when contacted by a leaner hydrocarbon gas. Years of experience in this thrust-belt basin have consistently demonstrated that the quality of fluids samples, PVT test design, lab-data QC, EOS tuning, and fluid initialization are essential to understand the hydrocarbon systems, reservoir compartmentalization, and recovery mechanisms. We show how integration of fluid characterization assists in the evaluation of depletion versus gas-injection strategies, development decisions, and ongoing reservoir management. The methodology used in this study has general application to PVT data acquisition and developing fluid characterizations exhibiting complex phase behaviour. We also provide standardized methods to QC the thermodynamic consistency of an EOS model, particularly when binary interaction parameters (BIPs) are used extensively. A single EOS model was developed successfully for describing the phase and volumetric behaviour of a wide range of fluids undergoing depletion and vaporization. This was achieved by modifying heavy-component properties, but more importantly, modifying BIPs extensively; these BIP modifications were possible only because considerable equilibrium compositional data was available. We believe this paper is significant as a proven case history. With the PVT data provided in our paper, the same problem can be used to test other fluid characterization methodologies and serve as a complex phase behaviour benchmark.
Proceedings of the 32nd Annual ACM Symposium on User Interface Software and Technology (2019)

We present StackMold, a DIY molding technique to prototype multi-material and multi-colored objects with embedded electronics. The key concept of our approach is a novel multi-stage mold buildup in which casting operations are interleaved with the assembly of the mold to form independent compartments for casting different materials. To build multi-stage molds, we contribute novel algorithms that computationally design and optimize the mold and casting procedure. By default, the multi-stage mold is fabricated in slices using a laser cutter. For regions that require more surface detail, a high-fidelity 3D-printed mold subsection can be incorporated. StackMold is an integrated end-to-end system, supporting all stages of the process: it provides a UI to specify material and detail regions of a 3D~object; it generates fabrication files for the molds; and it produces a step-by-step casting instruction manual.
U-shaped nano-apertures for enhanced optical transmission and resolution (2011)

The subject of light transmission through optically thin metal films perforated with arrays of subwavelength nanoholes has recently attracted significant attention. In this work, we present experimental and calculated results on optical transmission/reflection of the U-shaped nanoapertures for enhanced optical transmission and resolution. We propose different structure designs in order to prove the effect of geometry on resonance and enhanced fields. Theoretical calculations of transmission/reflection spectra and field distributions of U-shaped nano-apertures are performed by using 3-dimensional finite-difference time-domain method. The results of these numerical calculations show that transmission through the apertures is indeed concentrated in the gap region. Added to theoretical calculations we also performed a liftoff free plasmonic device fabrication technique based on positive resist electron beam lithography and reactive ion etching in order to fabricate U-shaped nanostructures. After transferring nanopattern on 80 nm thick suspended SiNx membrane using EBL followed by dry etching, a directional metal deposition processes is used to deposit 5 nm thick Ti and 30 nm thick Au layers. Theoretical calculations are supported with experimental results to prove the tunability of resonances with the geometry at the mid-infrared wavelengths which could be used for infrared detection of biomolecules.
Sustainable Thermal Energy Batteries from Fully Bio‐Based Transparent Wood (2023)

The sustainable development of functional energy-saving building materials is important for reducing thermal energy consumption and promoting natural indoor lighting. Phase-change materials embedded in wood-based materials are candidates for thermal energy storage. However, the renewable resource content is usually insufficient, the energy storage and mechanical properties are poor, and the sustainability aspect is unexplored. Here a novel fully bio-based transparent wood (TW) biocomposite for thermal energy storage, combining excellent heat storage properties, tunable optical transmittance, and mechanical performance is introduced. A bio-based matrix based on a synthesized limonene acrylate monomer and renewable 1-dodecanol is impregnated and in situ polymerized within mesoporous wood substrates. The TW demonstrates high latent heat (89 J g<sup>-1</sup> ) exceeding commercial gypsum panels, combined with thermo-responsive optical transmittance (up to 86%) and mechanical strength up to 86 MPa. The life cycle assessment shows that the bio-based TW has a 39% lower environmental impact than transparent polycarbonate panels. The bio-based TW holds great potential as scalable and sustainable transparent heat storage solution.
Optical Emission Detector Based on Plasma Discharge Generation at the Tip of a Multimaterial Fiber (2020)

Experimental development of a compact optical emission detector based on the assembly of a polymer-metal and a standard silica fiber is presented in this paper. This device is exploited in a proof-of-principle experiment for gas detection application by means of plasma spectroscopy in the visible-Near Infrared spectral region. A multimode fiber (MMF) is associated with a functional hollow dual-electrodes elongated structure fabricated by the direct preform-to-fiber homothetic co-drawing. A potential of 1.5 kV is applied between the two electrodes embedded inside the composite cladding, which generates an atmospheric pressure dc glow discharge at the tip of the fiber bundle. The emitted light is then collected by the MMF for optical diagnostics. Probing of different atmospheres is presented at the end of this study.
Nanostructured delivery systems with improved leishmanicidal activity: a critical review (2017)

Leishmaniasis is a vector-borne zoonotic disease caused by protozoan parasites of the genus <i>Leishmania</i>, which are responsible for numerous clinical manifestations, such as cutaneous, visceral, and mucocutaneous leishmaniasis, depending on the site of infection for particular species. These complexities threaten 350 million people in 98 countries worldwide. Amastigotes living within macrophage phagolysosomes are the principal target of antileishmanial treatment, but these are not an easy target as drugs must overcome major structural barriers. Furthermore, limitations on current therapy are related to efficacy, toxicity, and cost, as well as the length of treatment, which can increase parasitic resistance. Nanotechnology has emerged as an attractive alternative as conventional drugs delivered by nanosized carriers have improved bioavailability and reduced toxicity, together with other characteristics that help to relieve the burden of this disease. The significance of using colloidal carriers loaded with active agents derives from the physiological uptake route of intravenous administered nanosystems (the phagocyte system). Nanosystems are thus able to promote a high drug concentration in intracellular mononuclear phagocyte system (MPS)-infected cells. Moreover, the versatility of nanometric drug delivery systems for the deliberate transport of a range of molecules plays a pivotal role in the design of therapeutic strategies against leishmaniasis. This review discusses studies on nanocarriers that have greatly contributed to improving the efficacy of antileishmaniasis drugs, presenting a critical review and some suggestions for improving drug delivery.
ChemInform Abstract: Synthesis of Aza Macrocycles from Polycyclic 5‐Aminoisoxazoline Precursors. (1991)

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.
Editorial: Engineering the Microbial Platform for the Production of Biologics and Small-Molecule Medicines (2019)

EDITORIAL article Front. Microbiol., 09 October 2019Sec. Microbial Physiology and Metabolism Volume 10 - 2019 | https://doi.org/10.3389/fmicb.2019.02307
Identification of Direct Target Engagement Biomarkers for Kinase-Targeted Therapeutics (2011)

Pharmacodynamic (PD) biomarkers are an increasingly valuable tool for decision-making and prioritization of lead compounds during preclinical and clinical studies as they link drug-target inhibition in cells with biological activity. They are of particular importance for novel, first-in-class mechanisms, where the ability of a targeted therapeutic to impact disease outcome is often unknown. By definition, proximal PD biomarkers aim to measure the interaction of a drug with its biological target. For kinase drug discovery, protein substrate phosphorylation sites represent candidate PD biomarkers. However, substrate phosphorylation is often controlled by input from multiple converging pathways complicating assessment of how potently a small molecule drug hits its target based on substrate phoshorylation measurements alone. Here, we report the use of quantitative, differential mass-spectrometry to identify and monitor novel drug-regulated phosphorylation sites on target kinases. Autophosphorylation sites constitute clinically validated biomarkers for select protein tyrosine kinase inhibitors. The present study extends this principle to phosphorylation sites in serine/threonine kinases looking beyond the T-loop autophosphorylation site. Specifically, for the 3'-phosphoinositide-dependent protein kinase 1 (PDK1), two phospho-residues p-PDK1(Ser410) and p-PDK1(Thr513) are modulated by small-molecule PDK1 inhibitors, and their degree of dephosphorylation correlates with inhibitor potency. We note that classical, ATP-competitive PDK1 inhibitors do not modulate PDK1 T-loop phosphorylation (p-PDK1(Ser241)), highlighting the value of an unbiased approach to identify drug target-regulated phosphorylation sites as these are complementary to pathway PD biomarkers. Finally, we extend our analysis to another protein Ser/Thr kinase, highlighting a broader utility of our approach for identification of kinase drug-target engagement biomarkers.
Electronic surface and heterostructure: band offsets in ternary wurtzite and zincblende III-nitrides (2021)

The band structures of wurtzite and zincblende III-nitrides are aligned by the electron affinities and the band gaps calculated using a unified hybrid density-functional theory. Based on the Anderson’s electron-affinity rule, the conduction (and valence) band offsets of 1.60 (1.15), 2.47 (0.30), and 4.07 (1.45) eV have been extracted for wurtzite GaN/InN, AlN/GaN, and AlN/InN interfaces, where the conduction (and valence) band offsets of 1.85 (0.89), 1.32 (0.43), and 3.17 (1.32) eV have been procured for zincblende GaN/InN, AlN/GaN, and AlN/InN interfaces, respectively. The valence band edges of both wurtzite and zincblende ternary III-nitrides could be linearly interpolated because the dominant anion compositions at the valence band maximum have a weak dependence on the cation mole fractions. Contrarily, the large bowings on the conduction band edges are attributed to the cation-like nature. Both wurtzite and zincblende AlGaN behaves differently from InGaN and AlInN because (1) the conduction band edges at &Gamma;-valley are composed of anion orbitals, which account for the linear relationship between the conduction band edges and the cation mole fractions, and (2) the conduction band edges of zincblende Al<sub>x</sub>Ga<sub>1-x</sub>N shift from &Gamma;- to X-valley when x &gt; 0.65, which results in an anion-to- cation transition and leads to a large conduction-band-edge bowing.
Structure from failure (2007)

We investigate the problem of learning the dependencies among servers in large networks based on failure patterns in their up-time behaviour. We model up-times in terms of exponential distributions whose inverse lifetime parameters lmay vary with the state of other servers. Based on a conjugate Gamma prior over inverse lifetimes we identify the most likely network con guration given that any node has at most one parent. The method can be viewed as a special case of learning a continuous time Bayesian network. Our approach enables us to easily incorporate existing expert prior knowledge. Furthermore our method enjoys advantages over a stateof-the-art rule-based approach. We validate the approach on synthetic data and apply it to ve year data for a set of over 500 servers at a server farm of a major Microsoft web site. 1.
Pion and thermal photon spectra as a possible signal for a phase transition (1995)

We calculate thermal photon and neutral pion spectra in ultrarelativistic heavy-ion collisions in the framework of three-fluid hydrodynamics. Both spectra are quite sensitive to the equation of state used. In particular, within our model, recent data for S+Au at 200A GeV can only be understood if a scenario with a phase transition (possibly to a quark-gluon plasma) is assumed. Results for Au+Au at 11A GeV and Pb+Pb at 160A GeV are also presented.
Vincristine, dexamethasone and epratuzumab for older relapsed/refractory CD22+ B-acute lymphoblastic leukemia patients: a phase II study (2014)

After treatment
Pumping effect in an axially vibrating choke nozzle. Flow pattern and pumping principle. (1990)

The purpose of the present paper is to clarify the pumping effect obtained by a vibrating choke nozzle in a stationary liquid and to investigate the possibility of practical applications. The relation of liquid rise height to the vibration conditions was investigated experimentally. By the liquid velocity measurement, pressure measurement and the flow visualization, the flow mechanism was made clear and a suitable geometrical form for the vibrating choke nozzle was determined. It has been suggested that there is a good possibility of realizing practical transportation machinery by utilizing the pumping effect.
Acetylcholine Suppresses Ventricular Arrhythmias and Improves Conduction and Connexin‐43 Properties During Myocardial Ischemia in Isolated Rabbit Hearts (2015)

ACh may suppress VT/VF by preventing loss of Gj and improving CV in IBZ during acute MI.
Development of MEMS microbolometer detector for THz applications (2010)

INO has been actively working on extending its microbolometer technology to THz applications. Several techniques have been developed recently to improve the performance of the microbolometer. This article will present these techniques and discuss some potential applications of INO THz microbolometer.
LIQUID JET IMPINGEMENT (1995)

Liquid jet impingement is appealing because the liquid supply arrangement is relatively simple and low thermal resistances can be routinely achieved. When operated at high velocity, jets can remove fluxes several times that at the surface of the sun. This article reviews heat transfer and flow phenomena during unsubmerged liquid jet impingement and provides correlations for calculating the heat transfer coefficients. Convective transport without phase change is covered in detail. Results for the stagnation zone are given first, followed by those for the regions downstream. Both axisymmetric and planar jets are considered. The splattering that accompanies turbulent jet impingement is described, and other aspects of liquid jet impingement cooling are surveyed briefly.
Role of the Third Mobile Phase Solvent in Bonded Phase Chromatography (1983)

Journal Article Role of the Third Mobile Phase Solvent in Bonded Phase Chromatography Get access D.D. Blevins, D.D. Blevins Department of Chemistry, University of Arizona, Tuscon, Arizona 85721 Search for other works by this author on: Oxford Academic PubMed Google Scholar M.F. Burke, M.F. Burke ** Department of Chemistry, University of Arizona, Tuscon, Arizona 85721 **Author to whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar V.J. Hruby V.J. Hruby Department of Chemistry, University of Arizona, Tuscon, Arizona 85721 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Chromatographic Science, Volume 21, Issue 11, November 1983, Pages 490–494, https://doi.org/10.1093/chromsci/21.11.490 Published: 01 November 1983 Article history Received: 25 March 1983 Published: 01 November 1983
Engrailed homeoprotein acts as a signaling molecule in the developing fly (2011)

Homeodomain transcription factors classically exert their morphogenetic activities through the cell-autonomous regulation of developmental programs. In vertebrates, several homeoproteins have also been shown to have direct non-cell-autonomous activities in the developing nervous system. We present the first in vivo evidence for homeoprotein signaling in Drosophila. Focusing on wing development as a model, we first demonstrate that the homeoprotein Engrailed (En) is secreted. Using single-chain anti-En antibodies expressed under the control of a variety of promoters, we delineate the wing territories in which secreted En acts. We show that En is a short-range signaling molecule that participates in anterior crossvein development, interacting with the Dpp signaling pathway. This report thus suggests that direct signaling with homeoproteins is an evolutionarily conserved phenomenon that is not restricted to neural tissues and involves interactions with bona fide signal transduction pathways.
Pulmonary Delivery of Butyrylcholinesterase as a Model Protein to the Lung (2016)

Pulmonary delivery has great potential for delivering biologics to the lung if the challenges of maintaining activity, stability, and ideal aerosol characteristics can be overcome. To study the interactions of a biologic in the lung, we chose butyrylcholinesterase (BuChE) as our model enzyme, which has application for use as a bioscavenger protecting against organophosphate exposure or for use with pseudocholinesterase deficient patients. In mice, orotracheal administration of free BuChE resulted in 72 h detection in the lungs and 48 h in the broncheoalveolar lavage fluid (BALF). Free BuChE administered to the lung of all mouse backgrounds (Nude, C57BL/6, and BALB/c) showed evidence of an acute cytokine (IL-6, TNF-α, MIP2, and KC) and cellular immune response that subsided within 48 h, indicating relatively safe administration of this non-native biologic. We then developed a formulation of BuChE using Particle Replication in Non-Wetting Templates (PRINT). Aerosol characterization demonstrated biologically active BuChE 1 μm cylindrical particles with a mass median aerodynamic diameter of 2.77 μm, indicative of promising airway deposition via dry powder inhalers (DPI). Furthermore, particulate BuChE delivered via dry powder insufflation showed residence time of 48 h in the lungs and BALF. The in vivo residence time, immune response, and safety of particulate BuChE delivered via a pulmonary route, along with the cascade impaction distribution of dry powder PRINT BuChE, showed promise in the ability to deliver active enzymes with ideal deposition characteristics. These findings provide evidence for the feasibility of optimizing the use of BuChE in the clinic; PRINT BuChE particles can be readily formulated for use in DPIs, providing a convenient and effective treatment option.
Mitogen-Activated Protein Kinase-Activated Kinase RSK2 Plays a Role in Innate Immune Responses to Influenza Virus Infection (2009)

Viral infections induce signaling pathways in mammalian cells that stimulate innate immune responses and affect cellular processes, such as apoptosis, mitosis, and differentiation. Here, we report that the ribosomal protein S6 kinase alpha 3 (RSK2), which is activated through the "classical" mitogen-activated protein kinase pathway, plays a role in innate immune responses to influenza virus infection. RSK2 functions in the regulation of cell growth and differentiation but was not known to play a role in the cellular antiviral response. We have found that knockdown of RSK2 enhanced viral polymerase activity and growth of influenza viruses. Influenza virus infection stimulates NK-kappaB- and beta interferon-dependent promoters. This stimulation was reduced in RSK2 knockdown cells, suggesting that RSK2 executes its effect through innate immune response pathways. Furthermore, RSK2 knockdown suppressed influenza virus-induced phosphorylation of the double-stranded RNA-activated protein kinase PKR, a known antiviral protein. These findings establish a role for RSK2 in the cellular antiviral response.