gebhart/patrepeval huggingface dataset:
HDAC11 deficiency disrupts oncogene-induced hematopoiesis in myeloproliferative neoplasms (2019)

Protein acetylation is an important contributor to cancer initiation. Histone deacetylase 6 (HDAC6) controls JAK2 translation and protein stability and has been implicated in JAK2-driven diseases best exemplified by myeloproliferative neoplasms (MPNs). By using novel classes of highly selective HDAC inhibitors and genetically deficient mouse models, we discovered that HDAC11 rather than HDAC6 is necessary for the proliferation and survival of oncogenic JAK2-driven MPN cells and patient samples. Notably, HDAC11 is variably expressed in primitive stem cells and is expressed largely upon lineage commitment. Although Hdac11is dispensable for normal homeostatic hematopoietic stem and progenitor cell differentiation based on chimeric bone marrow reconstitution, Hdac11 deficiency significantly reduced the abnormal megakaryocyte population, improved splenic architecture, reduced fibrosis, and increased survival in the MPLW515L-MPN mouse model during primary and secondary transplantation. Therefore, inhibitors of HDAC11 are an attractive therapy for treating patients with MPN. Although JAK2 inhibitor therapy provides substantial clinical benefit in MPN patients, the identification of alternative therapeutic targets is needed to reverse MPN pathogenesis and control malignant hematopoiesis. This study establishes HDAC11 as a unique type of target molecule that has therapeutic potential in MPN.
36. Spironolactone Mitigates Fibrosis and Improves Healing of Burn Wounds (2022)

Purpose: Adhesion, contracture, and the formation of disfiguring, hypertrophic scars remain some of the most recalcitrant problems in care of the burned patient. The central pathology driving fibrosis is an imbalance of extracellular matrix (ECM). The mineralocorticoid receptor (MR) is a nuclear receptor with shared ligand-activity from both its primary activator, aldosterone, and glucocorticoids and has cell specific effects on proliferation, migration, and ECM production in fibroblasts and keratinocytes. Here we demonstrate that MR-inhibition with FDA approved spironolactone enhances epithelialization healing and mitigates hypertrophic collagen deposition after burns in mice. Methods: Female athymic mice sustained bilateral 1 cm full-thickness thermal injury and were stratified into either a) vehicle, b) spironolactone, c) aldosterone, or d) aldosterone + spironolactone. Aldosterone applied via subcutaneous pump (Alzet) spironolactone delivered intraperitoneally. Mice followed photographically for 4-to-6-weeks. At sacrifice wound biopsies were collected for H&E, Trichrome, and protein. An additional subset of samples were assessed via Pentachrome staining to assess relative ratio of collagen, fibrin, and elastic fibers. Pentachrome samples were analyzed using ImageJ (RGB Hue threshold) to isolate elastin, GAG and collagen for quantification. Results: Histologic evaluation of healing wounds from burned mice demonstrated persistence of inflammation, wound edema, and immature ECM. In mice treated with spironolactone this effect if alleviated by 4-weeks post-injury concurrent with gross findings of rapid wound epithelialization. Spironolactone treatment additionally enhanced gross and histologic evidence of scar resolution and resulted in a decreased in collagen staining vs. controls. Conclusion: We found a significant early improvement in wound epithelialization with spironolactone therapy. This suggests a potentially distinct effect from the proposed ECM-modifying strategy hypothesized. More analysis is needed but this data supports that MR-inhibition may be a valuable new therapeutic in treatment of burn scars.
Online wheel speed filtering for periodic disturbance reduction: a strategy for an advanced bicycle application (2016)

Due to geometrical errors and possible misalignment of the sensors, wheel speed measurements provided by incremental encoders in road vehicles are usually affected by significant periodic noises. This paper presents an online wheel speed filtering procedure, based on a model of the sensor, aimed at processing the speed measurement to make it suitable for advanced vehicle dynamics applications. In particular, differently from low-pass and notch filtering, this strategy is reliable for the cycling cadence estimation from the wheel speed on bicycles. Experimental data are used to show the effectiveness of the proposed approach.
Delay-aware Wireless Resource Allocation and User Association in LiFi-WiFi Heterogeneous Networks (2021)

The ever-growing wireless networks demand high capacity, have strict latency requirements, and must support diverse communication services. A LiFi-WiFi heterogeneous net-work has proven to be a useful tool to satisfy the growing capacity demand. However, to leverage these co-existing, non-interfering technologies, intelligent resource management schemes have to be developed. To support diverse applications with varying delay and data rate requirements, the resource management scheme should consider the Quality of Service (QoS) while allocating wireless resources. In this work, the downlink wireless resources are allocated to users such that the average network packet delay is minimized. Users that are both capable and not capable of multi-homing are considered and a separate optimization problem is formulated for each case. These problems are then solved using a global Branch and Bound-based solver and a genetic algorithm-based Metaheuristic is also proposed. The algorithms are then evaluated with simulations and the results show that the average network packet delay is significantly lowered and each user's strict QoS requirements are satisfied even in a network with heavy traffic flow.
Epitope Mapping of M36, a Human Antibody Domain with Potent and Broad HIV-1 Inhibitory Activity (2013)

M36 is the first member of a novel class of potent HIV-1 entry inhibitors based on human engineered antibody domains (eAds). It exhibits broad inhibitory activity suggesting that its CD4-induced epitope is highly conserved. Here, we describe fine mapping of its epitope by using several approaches. First, a panel of mimotopes was affinity-selected from a random peptide library and potential m36-binding residues were computationally predicted. Second, homology modeling of m36 and molecular docking of m36 onto gp120 revealed potentially important residues in gp120-m36 interactions. Third, the predicted contact residues were verified by site-directed mutagenesis. Taken together, m36 epitope comprising three discontinuous sites including six key gp120 residues (Site C1: Thr123 and Pro124; Site C3: Glu370 and Ile371; Site C4: Met426 and Trp427) were identified. In the 3D structure of gp120, the sites C1 and C4 are located in the bridging sheet and the site C3 is within the β15-α3 excursion, which play essential roles for the receptor- and coreceptor-binding and are major targets of neutralizing antibodies. Based on these results we propose a precise localization of the m36 epitope and suggest a mechanism of its broad inhibitory activity which could help in the development of novel HIV-1 therapeutics based on eAds.
ChemInform Abstract: Regiospecific Acylations of Aromatics and Selective Reductions of Azobenzenes over Hydrated Zirconia. (1997)

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.
Abietane Diterpenoids Isolated from Torreya nucifera Disrupt Replication of Influenza Virus by Blocking the Phosphatidylinositol-3-Kinase (PI3K)-Akt and ERK Signaling Pathway (2023)

Although vaccines and antiviral drugs are available, influenza viruses continue to pose a significant threat to vulnerable populations globally. With the emergence of drug-resistant strains, there is a growing need for novel antiviral therapeutic approaches. We found that 18-hydroxyferruginol (<b>1</b>) and 18-oxoferruginol (<b>2</b>) isolated from <i>Torreya nucifera</i> exhibited strong anti-influenza activity, with 50% inhibitory concentration values of 13.6 and 18.3 μM against H1N1, 12.8 and 10.8 μM against H9N2, and 29.2 μM (only compound <b>2</b>) against H3N2 in the post-treatment assay, respectively. During the viral replication stages, the two compounds demonstrated stronger inhibition of viral RNA and protein in the late stages (12-18 h) than in the early stages (3-6 h). Moreover, both compounds inhibited PI3K-Akt signaling, which participates in viral replication during the later stages of infection. The ERK signaling pathway is also related to viral replication and was substantially inhibited by the two compounds. In particular, the inhibition of PI3K-Akt signaling by these compounds inhibited viral replication by sabotaging influenza ribonucleoprotein nucleus-to-cytoplasm export. These data indicate that compounds <b>1</b> and <b>2</b> could potentially reduce viral RNA and viral protein levels by inhibiting the PI3K-Akt signaling pathway. Our results suggest that abietane diterpenoids isolated from <i>T. nucifera</i> may be potent antiviral candidates for new influenza therapies.
Spray rendering as a modular visualization environment (1995)

article Free Access Share on Spray rendering as a modular visualization environment Authors: Alex Pang View Profile , Craig M. Wittenbrink View Profile Authors Info & Claims ACM SIGGRAPH Computer GraphicsVolume 29Issue 2May 1995 pp 33–36https://doi.org/10.1145/204362.204370Published:01 May 1995Publication History 3citation89DownloadsMetricsTotal Citations3Total Downloads89Last 12 Months4Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
RaftLib (2015)

Stream processing or data-flow programming is a compute paradigm that has been around for decades in many forms yet has failed garner the same attention as other mainstream languages and libraries (e.g., C++ or OpenMP [15]). Stream processing has great promise: the ability to safely exploit extreme levels of parallelism. There have been many implementations, both libraries and full languages. The full languages implicitly assume that the streaming paradigm cannot be fully exploited in legacy languages, while library approaches are often preferred for being integrable with the vast expanse of legacy code that exists in the wild. Libraries, however are often criticized for yielding to the shape of their respective languages. RaftLib aims to fully exploit the stream processing paradigm, enabling a full spectrum of streaming graph optimizations while providing a platform for the exploration of integrability with legacy C/C++ code. RaftLib is built as a C++ template library, enabling end users to utilize the robust C++ standard library along with RaftLib's pipeline parallel framework. RaftLib supports dynamic queue optimization, automatic parallelization, and real-time low overhead performance monitoring.
In Situ Fibril Formation of κ-Casein by External Stimuli within Multilayer Thin Films (2013)

We have developed the in situ fibrillation of κ-casein, employed as amyloid precursor, within multilayer films consisting of κ-casein and poly(acrylic acid) (PAA) prepared by the layer-by-layer (LbL) deposition. The fibrillation of κ-casein within the multilayered films is strongly dependent on the extent of intermolecular interactions between κ-casein and PAA. When films constructed initially at pH 3 were heat treated at the same pH, κ-casein did not transform into fibrils. However, when the films were subjected to heat treatment at pH 5, κ-casein was transformed into fibrils within multilayer films due to weakened intermolecular interactions between κ-casein and PAA. We also noted that the multilayer film was swollen at pH 5 by the charge imbalance within the film, which we believe gives enough mobility for κ-caseins to form fibrils with adjacent κ-caseins within the multilayer. The fibrils were found to be uniformly distributed across the entire film thickness, and the aspect ratio as well as the number density of fibrils increased as a function of incubation time. The present study reveals a strategy to realize in situ nanocomposites within LbL multilayer films simply by triggering the formation of protein fibrils by controlling the intermolecular interactions between amyloid precursors and polyelectrolytes (PEs).
Magnetic microparticle concentration and collection using a mechatronic magnetic ratcheting system (2021)

Magnetic ratcheting cytometry is a promising approach to separate magnetically-labeled cells and magnetic particles based on the quantity of magnetic material. We have previously reported on the ability of this technique to separate magnetically-labeled cells. Here, with a new chip design, containing high aspect ratio permalloy micropillar arrays, we demonstrate the ability of this technique to rapidly concentrate and collect superparamagnetic iron oxide particles. The platform consists of a mechatronic wheel used to generate and control a cycling external magnetic field that impinges on a "ratcheting chip." The ratcheting chip is created by electroplating a 2D array of high aspect ratio permalloy micropillars onto a glass slide, which is embedded in a thin polymer layer to create a planar surface above the micropillars. By varying magnetic field frequency and direction through wheel rotation rate and angle, we direct particle movement on chip. We explore the operating conditions for this system, identifying the effects of varying ratcheting frequency, along with time, on the dynamics and resulting concentration of these magnetic particles. We also demonstrate the ability of the system to rapidly direct the movement of superparamagnetic iron oxide particles of varying sizes. Using this technique, 2.8 μm, 500 nm, and 100 nm diameter superparamagnetic iron oxide particles, suspended within an aqueous fluid, were concentrated. We further define the ability of the system to concentrate 2.8 μm superparamagnetic iron oxide particles, present in a liquid suspension, into a small chip surface area footprint, achieving a 100-fold surface area concentration, and achieving a concentration factor greater than 200%. The achieved concentration factor of greater than 200% could be greatly increased by reducing the amount of liquid extracted at the chip outlet, which would increase the ability of achieving highly sensitive downstream analytical techniques. Magnetic ratcheting-based enrichment may be useful in isolating and concentrating subsets of magnetically-labeled cells for diagnostic automation.
Calcium activates glucose-6-phosphatase in intact rat hepatic microsomes (1990)

The effects of Ca2+ on the microsomal glucose-6-phosphatase activity were investigated. Evidence is provided that increases by Ca2+ in both the pyrophosphatase and the glucose-6-phosphate-hydrolysing activities are due to an increase in microsomal transport capacity of T2, the phosphate/pyrophosphate-transport protein.
Matrix Modulation: High SNR Aspects (2003)

This chapter contains sections titled: Symmetries of Information and Performance Optimizing Performance with Orthogonal Symbol Rotations Explicit Performance Optima for ABBA Improved Performance by Extending Block Comparison of Layered Schemes for Four Tx Antennas Weighted and Multimodulation Non-orthogonal Matrix Modulation Summary
High speed global shutter image sensors for professional applications (2015)

Global shutter imagers expand the use to miscellaneous applications, such as machine vision, 3D imaging, medical imaging, space etc. to eliminate motion artifacts in rolling shutter imagers. A low noise global shutter pixel requires more than one non-light sensitive memory to reduce the read noise. But larger memory area reduces the fill-factor of the pixels. Modern micro-lenses technology can compensate this fill-factor loss. Backside illumination (BSI) is another popular technique to improve the pixel fill-factor. But some pixel architecture may not reach sufficient shutter efficiency with backside illumination. Non-light sensitive memory elements make the fabrication with BSI possible. Machine vision like fast inspection system, medical imaging like 3D medical or scientific applications always ask for high frame rate global shutter image sensors. Thanks to the CMOS technology, fast Analog-to-digital converters (ADCs) can be integrated on chip. Dual correlated double sampling (CDS) on chip ADC with high interface digital data rate reduces the read noise and makes more on-chip operation control. As a result, a global shutter imager with digital interface is a very popular solution for applications with high performance and high frame rate requirements. In this paper we will review the global shutter architectures developed in CMOSIS, discuss their optimization process and compare their performances after fabrication.
28.5L: Late‐News Paper : Wearable Display Expectations: Enabling Mobile Display Experiences of the Future (2014)

Abstract Wearable devices, fueled by sensor and context‐based technologies, are capturing the imaginations of device makers. While the benefits seem limitless, their demands impose constraints on system and display design. Qualcomm® Mirasol™ displays, as evidenced by the Qualcomm® TOQ™, appropriately address these constraints versus other leading technologies and their performance and capabilities are specifically discussed.
A study on multiple degree-of-freedom force reflecting teleoperation (2004)

This article reviews the wave variable method as it applies to multi-degree-of-freedom teleoperation systems. To demonstrate the effect of wave variables on the stability of a time-delayed multidegree-of-freedom system, initial simulation results on a three-axis robot are presented. Also the multidegree-of-freedom teleoperation system model developed in the Matlab/spl copy/ environment is described. This model, used in numerical simulations, is also utilized in real-time implementation of the controller.
A Theory of Propositions (2015)

In this paper I present a new theory of propositions, according to which propositions are abstract mathematical objects: well-formed formulas together with models. I distinguish the theory from a number of existing views and explain some of its advantages  chief amongst which are the following. On this view, propositions are unified and intrinsically truth-bearing. They are mind- and language-independent and they are governed by logic. The theory of propositions is ontologically innocent. It makes room for an appropriate interface with formal semantics and it does not enforce an overly fine or overly coarse level of granularity.
A Bifunctional Role for Group IIA Secreted Phospholipase A2 in Human Rheumatoid Fibroblast-like Synoviocyte Arachidonic Acid Metabolism (2010)

Human group IIA-secreted phospholipase A(2) (sPLA(2)-IIA) is an important regulator of cytokine-mediated inflammatory responses in both in vitro and in vivo models of rheumatoid arthritis (RA). However, treatment of RA patients with sPLA(2)-IIA inhibitors shows only transient benefit. Using an activity-impaired sPLA(2)-IIA mutant protein (H48Q), we show that up-regulation of TNF-dependent PGE(2) production and cyclooxygenase-2 (COX-2) induction by exogenous sPLA(2)-IIA in RA fibroblast-like synoviocytes (FLSs) is independent of its enzyme function. Selective cytosolic phospholipase A(2)-α (cPLA(2)-α) inhibitors abrogate TNF/sPLA(2)-IIA-mediated PGE(2) production without affecting COX-2 levels, indicating arachidonic acid (AA) flux to COX-2 occurs exclusively through TNF-mediated activation of cPLA(2)-α. Nonetheless, exogenous sPLA(2)-IIA, but not H48Q, stimulates both AA mobilization from FLSs and microparticle-derived AA release that is not used for COX-2-dependent PGE(2) production. sPLA(2)-IIA-mediated AA production is inhibited by pharmacological blockade of sPLA(2)-IIA but not cPLA(2)-α. Exogenous H48Q alone, like sPLA(2)-IIA, increases COX-2 protein levels without inducing PGE(2) production. Unlike TNF, sPLA(2)-IIA alone does not rapidly mobilize NF-κB or activate phosphorylation of p38 MAPK, two key regulators of COX-2 protein expression, but does activate the ERK1/2 pathway. Thus, sPLA(2)-IIA regulates AA flux through the cPLA(2)-α/COX-2 pathway in RA FLSs by up-regulating steady state levels of these biosynthetic enzymes through an indirect mechanism, rather than direct provision of substrate to the pathway. Inhibitors that have been optimized for their potency in enzyme activity inhibition alone may not adequately block the activity-independent function of sPLA(2)-IIA.
Synthesis of Gallium Chalcogenide Cubanes and Their Use as CVD Precursors for Ga2E3 (E = S, Se) (1996)

The gallium−chalcogen heterocubanes [Cp*Ga(μ3-E)]4, E = S (1) and Se (2), and [Cp†Ga(μ3-Se)]4 (3) have been synthesized by dehalosilylation reactions between E(SiMe3)2 (E = S, Se) and RGaCl2, R = Cp* (C5Me5) and Cp† (C5Me4Et), and are characterized by elemental analyses, NMR spectroscopy, and mass spectrometry. The use of compounds 1 and 2 as single-source MOCVD precursors for the low-temperature growth of Ga2E3 films at 290−310 °C is described. The as-deposited films were amorphous; however, upon thermal annealing (500 °C) the films crystallized to the thermodynamic cubic phases, while the corresponding tellurium analog decomposed in the solid state at 220 °C forming a gallium-rich product.
Impact of patterning strategy on mask fabrication beyond 32nm (2008)

Mask specifications of the pitch splitting type double patterning for 22nm node and beyond in logic devices have been discussed. The influences of the mask CD error and the mask induced overlay error on wafer CD have been investigated in both cases of bright field and dark filed. The specification for intra-layer overlay alignment is much smaller than inter-layer one. The specification of mask CD uniformity for dark is more challenging. In order to overcome the technology gap between single patterning and double patterning, many things will have to be improved.
Frequency Entrainment of a Forced van der pol Oscillator. (1977)

Abstract : A van der Pol relaxation oscillator that is subjected to external sinusoidal forcing can exhibit stable and unstable periodic and almost periodic responses. For some forcing amplitudes it even happens that two stable subharmonics having different periods may coexist. The stable responses of such forced oscillators are investigated. By numerically computing the rotation number of stable oscillations for various values of the forcing amplitude and oscillator tuning, descriptions are obtained of regions of phase locking, successive bifurcation of stable subharmonic and almost periodic oscillations, and overlap regions where two distinct stable oscillations can coexist.
Ohmic contact on low-doping-density p-type GaN with nitrogen-annealed Mg (2021)

We have demonstrated a fabrication process for the Ohmic contact on low-doping-density p-type GaN with nitrogen-annealed Mg. An Ohmic contact with a contact resistance of 0.158 Ω cm2 is realized on p−-GaN ([Mg] = 1.3 × 1017 cm−3). The contact resistance of p-type GaN with higher Mg concentration ([Mg]=1.0 × 1019 cm−3) can also be reduced to 2.8 × 10−5 Ω cm2. A localized contact layer is realized without any etching or regrowth damage. The mechanism underlying this reduced contact resistance is studied by scanning transmission electron microscopy with energy dispersive x-ray spectroscopy and secondary ion mass spectrometry, representing a mutual diffusion of Ga and Mg atoms on the interface. Reductions in the barrier height and surface depletion width with the nitrogen-annealed Mg layer are confirmed by XPS and Hall effect measurements qualitatively.