gebhart/patrepeval huggingface dataset:
The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire (2020)

Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR-encoding genes. The availability of the hexaploid wheat (<i>Triticum aestivum</i>) cultivar Chinese Spring reference genome allows a detailed study of its NLR complement. However, low <i>NLR</i> expression and high intrafamily sequence homology hinder their accurate annotation. Here, we developed NLR-Annotator, a software tool for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. We applied our tool to wheat and combined it with a transcript-validated subset of genes from the reference gene annotation to characterize the structure, phylogeny, and expression profile of the <i>NLR</i> gene family. We detected 3,400 full-length NLR loci, of which 1,560 were confirmed as expressed genes with intact open reading frames. NLRs with integrated domains mostly group in specific subclades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains, suggesting a paired helper function. Most <i>NLRs</i> (88%) display low basal expression (in the lower 10 percentile of transcripts). In young leaves subjected to biotic stress, we found up-regulation of 266 of the <i>NLRs</i> To illustrate the utility of our tool for the positional cloning of resistance genes, we estimated the number of <i>NLR</i> genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease-resistant varieties.
Toughening mechanisms of nanoparticle-modified epoxy polymers (2008)

An epoxy resin, cured with an anhydride, has been modified by the addition of silica nanoparticles. The particles were introduced via a sol-gel technique which gave a very well-dispersed phase of nanosilica particles which were about 20 nm in diameter. Atomic force and electron microscopies showed that the nanoparticles were well-dispersed throughout the epoxy matrix. The glass transition temperature was unchanged by the addition of the nanoparticles, but both the modulus and toughness were increased. The measured modulus was compared to theoretical models, and good agreement was found. The fracture energy increased from 100 J/m2 for the unmodified epoxy polymer to 460 J/m2 for the epoxy polymer with 13 vol% of nanosilica. The fracture surfaces were inspected using scanning electron and atomic force microscopies, and the results were compared to various toughening mechanisms proposed in the literature. The toughening mechanisms of crack pinning, crack deflection and immobilised polymer were discounted. The microscopy showed evidence of debonding of the nanoparticles and subsequent plastic void growth. A theoretical model of plastic void growth was used to confirm that this mechanism was indeed most likely to be responsible for the increased toughness that was observed due to the presence of the nanoparticles.
Sustainability through massively integrated computing: Are we ready to break the energy efficiency wall for single-chip platforms? (2011)

While traditional cluster computers are more constrained by power and cooling costs for solving extreme-scale (or exascale) problems, the continuing progress and integration levels in silicon technologies make possible complete end-user systems on a single chip. This massive level of integration makes modern multicore chips all pervasive in domains ranging from climate forecasting and astronomical data analysis, to consumer electronics, smart phones, and biological applications. Consequently, designing multicore chips for exascale computing while using the embedded systems design principles looks like a promising alternative to traditional cluster-based solutions. This paper aims to present an overview of new, far-reaching design methodologies and run-time optimization techniques that can help breaking the energy efficiency wall in massively integrated single-chip computing platforms.
Roadmap on Deep Learning for Microscopy (2023)

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.
Sustainable Electrocatalytic Architectures Enable Rechargeable Zinc–Air Batteries with Low Voltage Hysteresis (2020)

Rechargeable zinc–air batteries require air cathodes that support efficient electrocatalysis of both oxygen reduction and oxygen evolution. Electrocatalysts synthesized from abundant, low-cost elements with low-risk supply chains, such as the oxides and hydroxides of manganese, iron, and nickel, are necessary to enable large-scale adoption of zinc–air technology. However, such materials often underperform their cobalt-containing counterparts when required to act as bifunctional catalysts. Using two distinct sustainable electrocatalysts—α-MnO2 for oxygen reduction and Ni2FeOx for oxygen evolution—expressed as ultraporous nanoarchitectures (aerogels) and combining the respective particles in simple powder-composite cathodes, we achieve competitive performance to cobalt-based electrocatalysts. Performance characteristics are verified by pairing these cathodes with zinc (Zn) sponge anodes in Zn–air coin-cells and cycling at a technologically relevant current density (10 mA cm–2) to areal energies of 18–36 mW h cm–2 (areal capacities of 15–30 mA h cm–2). With a composite cathode comprising a 1:1 weight-to-weight mixture of α-MnO2 and Ni2FeOx aerogels, the cell cycles at a low voltage hysteresis of 700 mV, which is among the most efficient reported under similar operational conditions. A Zn–air cell, using this down-selected cathode, delivered more than 1 A h cm–2 of total capacity over 200 h of cycling before capacity fade occurred. The air cathode reported here is a stepping-stone to enable sustainable, rechargeable, and energy-dense Zn–air batteries.
Synthesis and polymerization of 2,15-diaza-1,16-dioxo[16]paracyclophane (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and polymerization of 2,15-diaza-1,16-dioxo[16]paracyclophaneJ. H. Glans and M. K. AkkapeddiCite this: Macromolecules 1992, 25, 20, 5526–5527Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/ma00046a062https://doi.org/10.1021/ma00046a062research-articleACS PublicationsRequest reuse permissionsArticle Views75Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Stimulus-Responsive Light Coupling and Modulation with Nanofiber Waveguide Junctions (2012)

We report a systematic study of light coupling at junctions of overlapping SnO(2) nanofiber waveguides (WGs) as a function of gap separation and guided wavelength. The junctions were assembled on silica substrates using micromanipulation techniques and the gap separation was controlled by depositing thin self-assembled polyelectrolyte coatings at the fiber junctions. We demonstrate that the coupling efficiency is strongly dependent on the gap separation, showing strong fluctuations (0.1 dB/nm) in the power transfer when the separation between nanofibers changes by as little as 2 nm. Experimental results correlate well with numerical simulations using three-dimensional finite-difference time-domain techniques. To demonstrate the feasibility of using coupled nanofiber WGs to modulate light, we encased the junctions in an environment-responsive matrix and exposed the junctions to gaseous vapor. The nanofiber junctions show an ~95% (or ~80%) modulation of the guided 450 nm (or 510 nm) light upon interaction with the gaseous molecules. The results reveal a unique nanofiber-based sensing scheme that does not require a change in the refractive index to detect stimuli, suggesting these structures could play important roles in localized sensing devices including force-based measurements or novel chemically induced light modulators.
Moderate Deviations of a Random Riccati Equation (2012)

The paper characterizes the invariant filtering measures resulting from Kalman filtering with intermittent observations in which the observation arrival is modeled as a Bernoulli process with packet arrival probability γ̅. Our prior work showed that, for γ̅ >; 0 , the sequence of random conditional error covariance matrices converges weakly to a unique invariant distribution μ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">γ̅</sup> . This paper shows that, as γ̅ approaches one, the family {μ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">γ̅</sup> } <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">γ̅ &gt;; 0</sub> satisfies a moderate deviations principle with good rate function I (·): (1) as γ̅ ↑ 1 , the family {μ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">γ̅</sup> } converges weakly to the Dirac measure δ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P*</sub> concentrated on the fixed point of the associated discrete time Riccati operator; (2) the probability of a rare event (an event bounded away from P*) under μ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">γ̅</sup> decays to zero as a power law of (1-γ̅) as γ̅↑ 1; and, (3) the best power law decay exponent is obtained by solving a deterministic variational problem involving the rate function I (·). For specific scenarios, the paper develops computationally tractable methods that lead to efficient estimates of rare event probabilities under μ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">γ̅</sup> .
Market User Interface Design [Extended Abstract] ⋆ (2012)

Electronic markets are becoming more and more pervasive but a remaining challenge is to develop user interfaces (UIs) to promote efficient market outcomes. This can be a challenge in markets with a large number of choices, yet traditional economic models do not consider that humans have cognitive costs,
Hyperspectral optical fiber refractive index measurement spanning 2.5 octaves (2013)

Optical fiber refractive index profiles were measured across a 2.5 octave wavelength range (from 375 nm to 2100 nm) using a single phase-shifting interferometer. This spectral range is more than a factor of 2 larger than previously reported multi-wavelength interferometers, and includes the pump and amplification bands of Er-doped, Yb-doped, Er:Yb-doped, and Tm-doped fibers. The apparatus can measure the material dispersion in a spatially-resolved manner that permits more accurate prediction of the fiber’s waveguide properties. The measurement wavelength can be tailored to optimize the beneficial or deleterious effects of material dispersion, optical resolution, and interferometric phase ambiguities.
A Search Engine for Discovery of Scientific Challenges and Directions (2021)

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/
Meta-Analysis Comparing WatchmanTM and Amplatzer Devices for Stroke Prevention in Atrial Fibrillation (2020)

<b>Background:</b> For patients with atrial fibrillation who are at high risk for bleeding or who cannot tolerate oral anticoagulation, left atrial appendage (LAA) closure represents an alternative therapy for reducing risk for thromboembolic events. <b>Objectives:</b> To compare the efficacy and safety of the Amplatzer and Watchman<sup>TM</sup> LAA closure devices. <b>Methods:</b> A meta-analysis was performed of studies comparing the safety and efficacy outcomes of the two devices. The Newcastle-Ottawa Scale was used to appraise study quality. <b>Results:</b> Six studies encompassing 614 patients were included in the meta-analysis. Overall event rates were low for both devices. No significant differences between the devices were found in safety outcomes (i.e., pericardial effusion, cardiac tamponade, device embolization, air embolism, and vascular complications) or in the rates of all-cause mortality, cardiac death, stroke/transient ischemic attack, or device-related thrombosis. The total bleeding rate was significantly lower in the Watchman<sup>TM</sup> group (Log OR = -0.90; 95% CI = -1.76 to -0.04; <i>p</i> = 0.04), yet no significant differences was found when the bleeding rate was categorized into major and minor bleeding. Total peridevice leakage rate and insignificant peridevice leakage rate were significantly higher in the Watchman<sup>TM</sup> group (Log OR = 1.32; 95% CI = 0.76 to 1.87; <i>p</i> < 0.01 and Log OR = 1.11; 95% CI = 0.50 to 1.72; <i>p</i> < 0.01, respectively). However, significant peridevice leakages were similar in both the devices. <b>Conclusions:</b> The LAA closure devices had low complication rates and low event rates. Efficacy and safety were similar between the systems, except for a higher percentage of insignificant peridevice leakages in the Watchman<sup>TM</sup> group. A randomized controlled trial comparing both devices is underway, which may provide more insight on the safety and efficacy outcomes comparison of the devices.
IONIZED SERUM CALCIUM LEVELS DURING ACUTE RENAL FAILURE: INTERMITTENT HEMODIALYSIS VS. CONTINUOUS HEMODIAFILTRATION (2002)

Abnormal serum ionized calcium concentrations are frequent in ARF patients before and during renal replacement. Once dialytic therapy is applied, CVVHDF is more likely to lower serum calcium concentrations, while IHD is more likely to induce hypercalcemia. Appreciation of these different biochemical effects may assist clinicians in adjusting dialytic therapy in selected patients.
The Placebo Response in Adult ADHD as Objectively Assessed by the TOVA Continuous Performance Test (2020)

<b>Objective:</b> We compared the placebo response (PR) as measured by the Test of Variables of Attention (TOVA) and the Conners' Adult ADHD Rating Scale (CAARS) scores. <b>Method:</b> A retrospective data analysis from a double-blind placebo-controlled study of metadoxine-ER in adults with ADHD. An additional database was used for comparison to TOVA response after methylphenidate challenge (TOVA-MPH-R). <b>Results:</b> PR was highest when calculated from the TOVA-Attention Composite Score (ACS). The PR showed significantly fewer variables improving concomitantly compared with MPH-R. The most prominent correlation between the CAARS-PR and the TOVA-PR was in the Omissions score (<i>p</i> = .032), which was age-dependent (<i>b</i> = .0007, <i>p</i> <.001). <b>Discussion:</b> TOVA-PR has an index-specific profile compared with CAARS-PR and TOVA-MPH-R. The partial correlation of TOVA-PR with CAARS-PR suggests that a composite score of TOVA specific indices and CAARS could have a synergic impact to improve the reliability of the response assessment in adult ADHD.
Adsorption and Desorption of SOxon Diesel Oxidation Catalysts (2009)

The deactivation of NO oxidation by SO2 was studied with the use of commercial diesel oxidation catalysts (DOC) and Pt/Al2O3 as reference material, coated on cordierite monolith. Despite their slightly different elemental compositions, the NO conversion rates of the fresh commercial catalysts were very similar. The maximum NO conversion was 38% at 350 °C, and above this temperature conversion started to be limited by the thermodynamics of the reaction. The rates of NO conversion strongly decreased with the start of SO2 dosing. For analysis of SO2 conversion and uptake, SO2 and SO3/H2SO4 were determined separately in the gas phase by absorption and titration. Under typical exhaust gas conditions (1 ppm SO2, 250 °C), the catalysts functioned as sulfur traps and stored a large part of the emitted SO2. The SOx storage was divided into two phases: a fast saturation of the catalyst surface with sulfuric acid, which hampered NO conversion, and a slow, long-lasting sulfation of the washcoat. The storage capacities of the oxidation catalysts reached their maxima at 250 °C due to the temperature dependency of sulfur adsorption and desorption. Adsorbed sulfuric acid desorbed between 350 and 400 °C, whereas more stable compounds, such as aluminum sulfate, were decomposed at higher temperatures. Deactivated catalysts could be completely regenerated within a few minutes at temperatures above 350 °C. However, repeated or lengthier thermal treatments resulted in a reduced sulfur storage capacity and irreversible activity losses for NO oxidation due to a reduction of the active surface by sintering.
Impact of surgeon and surgical team on outcomes in immediate implant based breast reconstruction (IBR) (2014)

Gfrerer, Lisa MD; Mattos, David BA; Mastroianni, Melissa MD; Ricci, Joseph A. MD; Weng, Christina BS; Winograd, Jon; Cetrulo, Curtis L. Jr. MD, FACS; Austen, William G. Jr. MD; Liao, Eric C. MD, PhD Author Information
Effects of Alcohol-A Preliminary to Study to Detect Intoxication- (2008)

Physiological parameters were obtained before and after alcohol drinking with subjective drunkenness, mood scores and task performances from nineteen male graduate students. Blood was sampled to measure Blood Alcohol Content (BAC) every 30 minute after drinking and Breath Alcohol Content (BrAC) was also measured. Heart rate increase and HF component of heart rate variability decrease were observed as shown in the responses induced by mental stress. However, a different pattern was shown in Tissue Blood Flow comparing with the responses induced by mental stress and physical stimulus. A reaction tine in a multiple task environment increased after drinking while a simple reaction time was not affected by drinking.
Proceedings of the Eleventh European Conference on Computer Systems (2016)

Welcome to EuroSys 2016, held at Imperial College London, UK! This year's program includes 38 wonderful papers that cover a wide range of topics, including multicore systems and concurrency, distributed machine learning, studies of familiar operating system abstractions, heterogeneous and non-volatile memory systems, data center networking, novel techniques for energy and power optimization, and experiences from production systems.
Quantitative and qualitative effects of experimental radioimmunotherapy on tumor vascular permeability (1995)

Localization of radiolabeled antibodies in the perivascular space of tumors resulted in morphological changes in blood vessel structure and physiological changes in tumor vessel function. Vessel diameter decreased by day 14 and was associated with a significant decline in vascular volume (VV). Upon recovery of VV, the basement membrane surrounding the endothelium had thickened. Tumor vascular permeability (VP) decreased within 7 days of treatment and remained suppressed throughout the 42-day observation period of our study. The decline in VP, which could be visualized by fluorescent microscopy of FITC-dextran extravasation, was dose-related and could be quantified at doses as low as 800 cGy. The radioantibody-induced 50-80% decline in tumor VP was observed in 3 human colonic xenografts (GW-39, LSI74T and MOSER). Decreases in VP have been observed for proteins ranging in size from 20 to 150 kDa. Similar effects on VP were noted when low protein doses (10-30 micrograms), which resulted in heterogeneous antibody distribution, were used or with high protein doses (400-750 micrograms), which resulted in more uniform penetration of antibody. If 188Re or 90Y, radiometals with higher beta-energy and longer path lengths, were substituted for 131I, a similar decrease in VP was observed. The radioimmunotherapy (RAIT)-induced decrease in tumor VP resulted in a 90% decline in accretion of a second dose of radioantibody. The 10% of the second dose that was taken up by the tumor targeted many already non-viable tumor regions and some, but not all, viable tumor cell clusters.
Quantitative measurement of cavitation activity during red blood cell lysis and sonoporation (2000)

Ultrasound contrast agents have proven to be an effective agent for producing cavitation-associated bioeffects. A comparative analysis of the strength and duration of cavitation activity and the lifetime of nucleation sites during red blood cell (RBC) lysis and sonoporation was performed. The RBCs were treated with 1.1-MHz tone-burst ultrasound in the presence of contrast agents and analyzed for hemoglobin release and the uptake of FITC-dextran (MW= 4 kD). Pulse durations ranged from 100 to 10&amp;lt;th&amp;gt;000 ms and the total number of bursts for each pulse duration was selected to ensure a constant exposure. The extent and duration of cavitation activity during treatment was monitored using a passive cavitation detection system. The collected cavitation-activity data was analyzed quantitatively and correlated with the percent of hemolysis and the ratio of fluorescent cells to total cells treated.