gebhart/patrepeval huggingface dataset:
Cleavage of 14-3-3ε by the enteroviral 3C protease dampens RIG-I mediated antiviral signaling (2022)

Abstract Viruses have evolved diverse strategies to evade the host innate immune response and promote infection. The RIG-I-like-receptors RIG-I and MDA5 (RLRs) are antiviral factors that sense viral RNA and signal downstream via mitochondrial antiviral-signaling protein (MAVS) to activate type I interferon (IFN) expression. 14-3-3ε is a key component of the RIG-I translocon complex that interacts with MAVS at the mitochondrial membrane; however, the exact role of 14-3-3ε in this pathway is not well understood. In this study, we demonstrate that 14-3-3ε is a direct substrate of both the poliovirus and coxsackievirus B3 (CVB3) 3C proteases (3C pro ), and that it is cleaved at Q236↓G237, resulting in the generation of N- and C-terminal fragments of 27.0 and 2.1 kDa, respectively. Expression of the N-terminal cleavage fragment in cells reduces IFNB mRNA production during poly(I:C) stimulation, thus suggesting an antagonistic effect in the presence of the endogenous 14-3-3ε protein. The N-terminal 14-3-3ε fragment does not interact with RIG-I in co-immunoprecipitation assays, nor can it facilitate RIG-I translocation to the mitochondria. Probing the intrinsically disordered C-terminal region identifies key residues responsible for RIG-I signaling. Finally, overexpression of the N-terminal fragment promotes CVB3 infection and influenza A virus (H1N1) RNA production and reduces IFNB mRNA production during infection. The strategic enterovirus 3C pro -mediated cleavage of 14-3-3ε antagonizes RIG-I signaling by disrupting critical interactions within the RIG-I translocon complex, thus contributing to evasion of the host antiviral response. Author Summary Host antiviral factors work to sense virus infection through various mechanisms, including a complex signaling pathway known as the RIG-I like receptor (RLR) pathway. This pathway drives the production of antiviral molecules known as interferons, which are necessary to establish an antiviral state in the cellular environment. Key to this antiviral signaling pathway is the small chaperone protein 14-3-3ε, which facilitates the delivery of a viral sensor protein, RIG-I, to the mitochondria. In this study, we show that the enteroviral 3C protease cleaves 14-3-3ε during infection, rendering it incapable of facilitating this antiviral response. We also find that the cleavage fragment inhibits RIG-I signaling and promotes virus infection. Our findings reveal a novel viral strategy that restricts the antiviral host response and provides insights into the mechanisms underlying 14-3-3ε function in RIG-I antiviral signaling.
A mechanistic investigation of subharmonic response from polymer-shelled microbubbles in response to high-frequency ultrasound (2012)

Polymer-shelled ultrasound contrast agents (UCAs) can undergo a “compression only” behavior leading to shell rupture and nonlinear response of the released gas bubbles when excited below 10 MHz. This study investigated if polymer-shelled UCAs exhibited a similar behavior when excited at frequencies above 10 MHz. Four varieties of polylactide-shelled UCAs, each with a distinct shell-thickness-to-radius ratio (STRR), were employed; the STRRs were 7.5, 40, 65, and 100 nm/μm. Two experiments were performed: one examined the compression-induced rupture of UCA shells by subjecting them to static overpressure, and the other investigated subharmonic components in the backscattered signal produced by individual UCAs sonicated with 20-MHz tone bursts. The four UCAs exhibited distinctly different compression-induced rupture thresholds that were linearly related to their STRR, but were uncorrelated with UCA size. The subharmonic response of the UCAs increased with increasing STRR. Thus, the UCAs with larger STRRs were more resilient to rupture, but they produced significantly greater subharmonic activity. The results of this two-part study indicated that the polymer-shelled UCAs may not adhere to the rupture-based mechanism of subharmonic generation when excited at 20 MHz.
User Behavior and Change (2014)

Though the impact of file-sharing of copyrighted content has been discussed for over a decade, only in the past few years have countries begun to adopt legislation to criminalize this behavior. These laws impose penalties ranging from warnings and monetary fines to disconnecting Internet service. While their supporters are quick to point out trends showing the efficacy of these laws at reducing use of file-sharing sites, their analyses rely on brief snapshots of activity that cannot reveal long- and short-term trends.
A novel CDMA multiuser interference cancellation receiver with reference symbol aided estimation of channel parameters (1996)

A novel multistage successive interference cancellation scheme is proposed which operates on the reverse code-division multiple-access (CDMA) link using binary phase shift keying (BPSK) modulation, coherent detection and reference symbols to obtain channel estimates. The results of a single cell multiuser investigation demonstrate increased traffic capacity. However, this increase is initially very moderate due to corruption of the channel estimates by interference from symbols not yet demodulated and cancelled. A modification in the transmitted signal structure addressing this problem is proposed. The results of a single cell analysis of the modified cancellation scheme demonstrate that the system's traffic capacity reaches approximately 80% of that of a multistage successive interference cancelling receiver operating with the perfect knowledge of channel parameters. A subsequent multicell investigation shows that for a hexagonal cell geometry with a path loss exponent of four and without any forward error correction (FEC) coding or cell sectorization, the system capacity compares very favorably with that of the IS-95 system, which employs powerful error control coding. Capacities with other path loss exponents and cell geometries are also investigated. The results show a substantial traffic capacity increase over that of a comparable receiver without interference cancellation.
Divide and conquer: an efficient solution to highly multimoded photonic lanterns from multicore fibres (2017)

Photonic lanterns typically allow for single-mode action in a multimode fibre. Since their invention over a decade ago for applications in astrophotonics, they have found important uses in diverse fields of applied science. To date, large aperture highly-mulitmoded to single-mode lanterns have been difficult as fabrication techniques are not practical for mass replication. Here as a proof of concept, we demonstrate three different devices based on multicore fibre photonic lanterns with: 100µm core diameters; NAs = 0.16 and 0.15; and requiring 259 single-mode core system, specifically 7 multicore fibres each with 37 cores, instead of 259 individual single-mode fibres. The average insertion loss excluding coupling efficiencies is only 0.4dB (>91% transmission). This concept has numerous advantages, in particular, (i) it is a direct scaleable solution, (ii) eases imprinting of photonic functions, e.g. fibre Bragg gratings; and (iii) new approach for large-area optical fibre slicers for future large-aperture telescopes.
Optimum Operating Condition for Co-Gasification - A Thermodynamic Study (2018)

Background: Gasification is a popular process for producing syngas from solid fuels. The focus has nowadays shifted to co-gasification using a mixed feed of coal and biomass. An optimum gasifier operating condition (OGOC) is an extremely important process parameter for gasification system. &lt;/P&gt;&lt;P&gt; Method: A thermodynamic analysis was done to calculate this condition for co-gasifier operation. The relative product gas generation trends in co-gasification were compared with the single feed coal gasification in this study. &lt;/P&gt;&lt;P&gt; Conclusion: An OGOC of 618°C with CO2 feed of 0.6475 moles and H2O feed of 1.3525 moles was found to be the best condition for co-gasifier operation producing 1.6429 moles of syngas (of syngas ratio 1.5905) and 54.96% H2O conversion with the gasifier product gas containing over 61% syngas. Such OGOC can be found for gasification systems ensuring the advantages of thermoneutral operation as well as 100% carbon conversion.
Combined Addition of Alkenyl and Allenic Anions to Squarate Esters. Direct Competition between Six-Ring and Eight-Ring Electrocyclization of 1,2,4,6,8-Cumulenic Pentaenes (1997)

The sequential addition of 1 equiv each of a lithioallene and an alkenyllithium to diisopropyl squarate has been studied. The product compositions resulting from the ensuing reaction cascades were not at all comparable to those resulting from the reverse mode of nucleophile addition. These results require that different intermediates intervene. When the alkenyl anion is the lead reagent, the lithioallene enters predominantly trans and two sequential electrocyclic steps ensue. Initial introduction of methoxyallene causes the second nucleophile to enter preferably from the cis direction, presumably because of oxygen coordination to lithium. The proximal orientation of the unsaturated moieties leads to operation of the dianionic oxy-Cope rearrangement. The second electrocyclic event that transpires following formation of the trans dialkoxide is not of the customary 8pi conrotatory type. Rather, a 6pi disrotatory process occurs exclusively. This "allene effect" is shown to originate from strain, orbital alignment, and conjugative factors operating at the transition state.
Regulating VEGF signaling in platelet concentrates via specific VEGF sequestering (2016)

Platelets contain an abundance of growth factors that mimic the composition of the wound healing milieu, and platelet-derived VEGF in particular can negatively influence wound healing if unregulated. Here, we sought to capture and regulate the activity of VEGF factor from human platelets using poly(ethylene glycol) microspheres. In this communication, we demonstrate that platelet freeze/thaw produced significantly higher levels of Vascular Endothelial Growth Factor (VEGF) than either calcium chloride treatment, protease activated receptor 1 activating peptide (PAR1AP) treatment, or thrombin treatment. PEG microspheres containing a VEGF-binding peptide (VBP), derived from VEGFR2, sequestered VEGF from platelet concentrate, prepared via freeze/thaw, and reduced the bioactivity of platelet concentrate in HUVEC culture, which suggests that VBP microspheres sequestered and reduced the activity of VEGF from patient-derived platelets. Here, we demonstrate the ability of VEGF sequestering microspheres to regulate the activity of VEGF derived from a growth factor-rich autologous human blood product.
Colloidal synthesis of rare earth-based nanoparticles (2015)

Colloidal nanocrystals (NCs) are free-standing nano-sized objects, coordinated by a layer of organic amphiphilic molecules which allows their dispersion in solvents, making easy the manipulation. The organic molecules play a central role in all the synthesis steps by controlling the NC surface during the growth, allowing to obtain a fine control over the size and the shape of NCs. In addition, organic ligands prevent the occurrence of aggregation phenomena. Luminescent NCs, presenting intense emission in the visible and NIR region of the spectra, are of great interest for application in several fields, as optoelectronics and bio-imaging. On the other hand, rare-earth elements, generally in form of trivalent cation, emit sharp-fluorescence peaks which allow their application in bio-imaging and therapeutics. Here, we focused on the synthesis of Gd-based NCs by the “thermal decomposition of organometallic precursor in hot coordinating solvents” using exclusively natural products for each synthetic phase, with the exception for the organometallic NC precursor. In particular, seed oil was used as high-boiling and coordinating solvent and ethanol was used as non-solvent in purification processes. The optical properties of synthesized NCs were monitored by UV-vis absorption and photoluminescence spectroscopy during the NC growth. The morphology of NCs has been monitored by SEM microscopy. Experimental measurement highlighted the formation of Gd-based NCs, 30-40 nm in diameter, characterized by a strong absorption in the UV region of the spectrum and an intense photoluminescence in the green.
P3‐048: Arginine metabolism and higher‐order polyamines impact tau aggregation, microtubule assembly, and autophagy in models of tauopathies (2015)

Currently no disease modifying agents exist on the market for Alzheimer's disease (AD). One major hallmark includes tau neuropathology and associates with several neurodegenerative diseases collectively known as tauopathies. Strategies aimed at reducing tau burden include increasing clearance, targeting kinases, posttranslational modifications, reducing aggregation, and modifying inflammation. Arginine metabolism acts as a substrate and critical branch-point, which dictates several outcomes: nitric oxide generation from nitric oxide synthases (NOS) or polyamine production from arginase (Arg1). Several reports show that nitration of tau impacts tau metabolism and increases aggregation, thus biasing one or more pathways may dictate tau fate. Depletion of arginine may also lead to increased autophagy through amino acid sensing. Utilizing gene therapy (adeno-associated virus), cellular, animal models of tauopathy (rTg4510 and PS19 mice), and recombinant protein experiments we tested each of these potential mechanisms: 1) decrease tau nitration (shifting arginine metabolism away from the NOS pathway); 2) arginine depletion (and activation of autophagy); and 3) polyamine production. We find dysregulation of the polyamine pathway in tau transgenic mice. Our data indicates that Arg1 overexpression in mouse models of tauopathy reduces the many aspects of the tau phenotype including reduced phospho-tau and nitrated tau, reduced tangle pathology, reduced atrophy, reduced high molecular weight tau, reduced markers of inflammation, reduced inhibitors of autophagy, and reduced protein kinase activation. We find similar outcomes in cell lines overexpressing tau with parallel Arg1 manipulations. Importantly, we identified that higher-order polyamines at physiological concentrations directly block tau aggregation and facilitate tubulin polymerization but acetylated forms fail to mimic this affect. These data suggest arginine metabolism and the polyamine pathway as therapeutic targets that may arrest or slow the progression of the tau pathology in models of tauopathies.
基于Web of Science对土壤重金属污染修复研究的计量分析 (2018)

为了解国内外土壤重金属污染修复技术的最新研究进展、研究热点及发展趋势，通过Web of ScienceTM核心合集数据库，利用Web of Science（简称WOS）数据库自带的分析工具、HistCite引文图谱分析软件、VOSviewer可视化分析软件和Origin 9.1作图软件，从发文量TOP10的国家（地区）、高产作者、来源期刊、重要研究机构、研究方向热点等方面对21世纪以来（2000—2016年间）发表的有关土壤重金属污染修复研究文献进行计量分析。结果表明：该领域研究中国发文量第一，但均篇被引次数较低；高产作者主要来自美国和中国，前三名分别为美国作者Ma L Q、比利时作者Vangronsveld J和中国作者Zhou Q X（周启星）；重要研究机构前三名为中国科学院、浙江大学和美国佛罗里达大学；主要期刊有Environmental Science & Technology、Journal of Hazardous Materials、Chemosphere和Environmental Pollution等；主要研究热点是植物修复技术以及生物修复、固化/稳定化修复技术；主要研究的土壤重金属对象是镉（Cd）、铅（Pb）、铜（Cu）、锌（Zn）、类重金属砷（As）等；研究主要涉及的学科是环境科学、生态学、工程学、农学和水资源学等。本文对该领域初学者了解该领域研究方向、发展趋势和研究热点具有指导意义。
What's in a Name? (2017)

Nomenclature is important—it codifies terms on which members of a guild mutually concur, so as to understand one another better instead of rambling along in imprecise babble. In this issue, Jeffrey Flier and Joseph Loscalzo have thoughtfully applied this principle to how certain sectors of our profession are labeled. They have been resourceful in their analysis and balanced in their recommendations. Names and terms do mean something, usually for the better. But sometimes, they need interpretation. When I first heard about “translational research” many years ago, I was excited, because having worked on RNA and gene expression, I thought it meant that more NIH dollars would be flowing to the ribosome and related fields. Alas. I had two encounters with nomenclature in my first days as an independent investigator. Shortly after publication of one of the first papers from my laboratory, I received a letter (an actual letter, in an envelope, with a stamp) from one Waldo E. Cohn at Oak Ridge National Laboratory, telling me that “SDS” was an unacceptable term for the detergent I had put into my electrophoretic gels. (For more than you've ever wanted to know about the advent of SDS gel electrophoresis, see ref. 1.) Dr. Cohn said that he was in charge of biochemical nomenclature and told me it had to be written as “NaDodSO4.” Having been an undergraduate student of chemistry, where its elegant nomenclature was one of the things that had turned me on, I thought this term was totally nuts from every angle, chemistry or etymology. A couple of years later, a copyeditor at Academic Press told me that I could not use the term “dry ice” in an article but that I had to say “solid CO2.” I retorted that some of my colleagues might not even know that solid CO2 meant dry ice, but I lost the battle and again needed the publication. (It also occurred to me on that occasion, for the first time, that had life used its chemical sibling silicon instead of carbon, we would be sitting on dry ice on the beach with lungs that could handle sand. I give that copyeditor credit for this idea.) Nomenclature issues are not the same as ambiguity or mispronunciation, the latter as when an innocent student says that he has inhibited DNA transcription with the antibiotic “actomyosin,” or simple grammatical errors (2), such as when one says that he has changed “the media” on one plate of cells. And at a deeper level, nomenclature and definition often feud. A “stem cell” can be defined in several ways, and each way of thinking about such cells has subtle nuances of differentiation (no pun intended). So, I say that thinking about nomenclature and being careful are important, and thus, thank Flier and Loscalzo. What they present is one way to avoid having the biomedical profession descend into “alt-terms,” with the resulting danger of being taken as “alt-facts,” for how we name our scientific corridors.
The mechanism of ranolazine action to reduce ischemia-induced diastolic dysfunction (2006)

Ischaemia of myocardium is associated with increases in the late sodium current (INa), intracellular sodium and calcium concentrations, calcium overload, and impairment of contractile relaxation (i.e. increased diastolic wall tension). An increase in diastolic wall tension compresses the vasculature and reduces nutritive blood flow, creating a positive feedback system that further impairs myocardial oxygenation and contractile function. Ranolazine reduces the late INa and, is expected to decrease sodium entry into ischaemic myocardial cells. As a consequence, ranolazine is proposed to reduce calcium uptake indirectly via the sodium/calcium exchanger and to preserve ionic homeostasis and reverse ischaemia-induced contractile dysfunction.
Ultrasonography system of implant in bones for orthopedic surgery (2004)

This paper describes an ultrasonography system of implant in bones aided by fuzzy logic. Although conventional X-ray CT method call visualize the implant in the CT table, it has serious disadvantage of X-ray exposure. Therefore, we require the system which can he used the orthopedic surgery with no X-ray exposure. This paper solves the problem in an intramedullary nail by our ultrasonic device and fuzzy logic techniques. We localize the distal transverse screw hole in the nail under surgeries for femur fracture. Their screw hole positions are identified by calculating two fuzzy degrees of intensity and the variance. As the result, our experimental result shows that our system can identify their screw hole positions within error of 2.5 mm.
&lt;title&gt;Novel spatial light modulators for active and adaptive optics&lt;/title&gt; (2000)

We present here results of laboratory and field experiments using two novel active optic elements, a membrane mirror, and a dual frequency nematic liquid crystal. These devices have the advantage of low cost, low power consumption, and compact size. Possible applications of the devices are astronomical adaptive optics, laser beam control, laser cavity mode control, and real time holography.
CTIM-10. REPRODUCIBILITY OF CLINICAL TRIALS USING CMV-TARGETED DENDRITIC CELL VACCINES IN PATIENTS WITH GLIOBLASTOMA (2021)

Abstract INTRODUCTION Vaccination with dendritic cells (DCs) fares poorly in primary and recurrent glioblastoma (GBM). Moreover, GBM vaccine trials are often underpowered due to limited sample size. METHODS To address these limitations, we conducted three sequential clinical trials utilizing Cytomegalovirus (CMV)-specific DC vaccines in patients with primary GBM. Autologous DCs were generated and electroporated with mRNA encoding for the CMV protein pp65. Serial vaccination was given throughout adjuvant temozolomide cycles, and 111Indium radiolabeling was implemented to assess migration efficiency of DC vaccines. Patients were followed for median overall survival (mOS) and OS. RESULTS Our initial study was the phase II ATTAC study (NCT00639639; total n=12) with 6 patients randomized to vaccine site preconditioning with tetanus-diphtheria (Td) toxoid. This led to an expanded cohort trial (ATTAC-GM; NCT00639639) of 11 patients receiving CMV DC vaccines containing granulocyte-macrophage colony-stimulating factor (GM-CSF). Follow-up data from ATTAC and ATTAC-GM revealed 5-year OS rates of 33.3% (mOS 38.3 months; CI95 17.5-undefined) and 36.4% (mOS 37.7 months; CI95 18.2-109.1), respectively. ATTAC additionally revealed a significant increase in DC migration to draining lymph nodes following Td preconditioning (P=0.049). Increased DC migration was associated with OS (Cox proportional hazards model, HR=0.820, P=0.023). Td-mediated increased migration has been recapitulated in our larger confirmatory trial ELEVATE (NCT02366728) of 43 patients randomized to preconditioning (Wilcoxon rank sum, Td n=24, unpulsed DC n=19; 24h, P=0.031 and 48h, P=0.0195). In ELEVATE, median follow-up of 42.2 months revealed significantly longer OS in patients randomized to Td (P=0.026). The 3-year OS for Td-treated patients in ELEVATE was 34% (CI95 19-63%) compared to 6% given unpulsed DCs (CI95 1-42%). CONCLUSION We report reproducibility of our findings across three sequential clinical trials using CMV pp65 DCs. Despite their small numbers, these successive trials demonstrate consistent survival outcomes, thus supporting the efficacy of CMV DC vaccine therapy in GBM.
Additional file 1: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing (2016)

Control dataset sample identification, protocol information, and RNA sequencing stats. Experimental group, protocol information and RNA sequencing statistics for each sample used in primary analyses. Alignment statistics were based on STAR alignment to hg19 and were with respect to reads retained after trimming for primer or poly-A sequences [21]. (XLS 62 kb)
Metal-Loaded TE/TM Polarization Splitter Consisting of Embedded Waveguides With Slightly Different Core Widths (2006)

A TE/TM polarization splitter, in which the metal-loaded core is slightly widened, is analyzed using the beam-propagation method. An extinction ratio of &gt; 25 dB is obtained at a wavelength of 1.55 µm.