gebhart/patrepeval huggingface dataset:
Total Synthesis and Stereochemistry of Pinnatoxins B and C (2006)

[Structure: see text] Pinnatoxins B and C were synthesized from diols (34R)-3b and (34S)-3a, respectively, in a stereochemically controlled manner. Through extensive analysis of the 1H NMR spectra of synthetic PnTXs B and C, the diagnostic NMR signals were first identified to differentiate (34S)- and (34R)-diastereomers and then used to establish the C34 configuration of natural PnTXs B and C as 34S and 34R, respectively.
Induction of a CD8 T cell intrinsic DNA damage and repair response is associated with clinical response to PD-1 blockade in uterine cancer (2022)

Abstract Despite the success of immune checkpoint blockade (ICB), many patients fail to achieve durable clinical benefit, and the underlying immunological mechanisms remain poorly understood. Here, we investigated immune reinvigoration by ICB in advanced or recurrent hypermutated or microsatellite instability-high, mismatch repair deficient (MSI-H/MMRd) uterine cancer patients treated with anti-PD-1 (nivolumab). CD8 T cells underwent rapid pharmacodynamic proliferation 2-4 weeks after initiating PD-1 blockade. This immunological response, however, did not correlate with clinical response. We hypothesized that the T cell-intrinsic response to proliferative and genotoxic stress might contribute to the disparity between immunological and clinical response. We developed a high-dimensional single cell cytometric platform to simultaneously analyze T cell differentiation with changes in DNA damage and repair (DDR) pathways. This DDR-Immune platform revealed T cell subset-specific patterns of DDR, and distinct DDR pathways induced by different types of DNA damage. Applying this platform to MSI-H/MMRd or hypermutated uterine cancer patients revealed a signature of DDR exemplified by rapid increase in phosphorylated-ATM (pATM) intrinsic to CD8 T cells proliferating in response to PD-1 blockade that distinguished clinical responders and non-responders. ATM regulated transcriptional circuits in T cells were associated with better clinical response to PD-1 blockade. These findings highlight a previously unrecognized role for CD8 T cell-intrinsic DDR as a potential determinant of immune fitness and clinical outcome of PD-1 blockade therapy. STATEMENT OF SIGNIFICANCE Using high-dimensional immune and DNA damage response (DDR) profiling in T cell subsets we identified distinct signatures in anti-PD-1 treated MSI-H/hypermutated uterine cancer patients associated with clinical response versus non-response. Thus, T cell-intrinsic DDR is a potential determinant of immune responsiveness and clinical outcome to PD-1 blockade therapy in cancer.
Content-based analysis and indexing for speech, sound and multimedia (2000)

Overview of Ellis's work on applying information retrieval to multimedia content, particularly sound mixtures that are broken up into objects using computational auditory scene analysis.
Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility (2010)

Single-domain allostery has been postulated to occur through intramolecular pathways of signaling within a protein structure. We had previously investigated these pathways by introducing a local thermal perturbation and analyzed the anisotropic propagation of structural changes throughout the protein. Here, we develop an improved approach, the Rotamerically Induced Perturbation (RIP), that identifies strong couplings between residues by analyzing the pathways of heat-flow resulting from thermal excitation of rotameric rotations at individual residues. To explore the nature of these couplings, we calculate the complete coupling maps of 5 different PDZ domains. Although the PDZ domain is a well conserved structural fold that serves as a scaffold in many protein-protein complexes, different PDZ domains display unique patterns of conformational flexibility in response to ligand binding: some show a significant shift in a set of alpha-helices, while others do not. Analysis of the coupling maps suggests a simple relationship between the computed couplings and observed conformational flexibility. In domains where the alpha-helices are rigid, we find couplings of the alpha-helices to the body of the protein, whereas in domains having ligand-responsive alpha-helices, no couplings are found. This leads to a model where the alpha-helices are intrinsically dynamic but can be damped if sidechains interact at key tertiary contacts. These tertiary contacts correlate to high covariation contacts as identified by the statistical coupling analysis method. As these dynamic modules are exploited by various allosteric mechanisms, these tertiary contacts have been conserved by evolution.
Chiral hybrid materials based on pyrrolidine building units to perform asymmetric Michael additions with high stereocontrol (2018)

A new chiral mesoporous hybrid material was synthesized based on pyrrolidine units included in a siliceous framework, HybPyr, and integrated into the organic-inorganic structure, from a specific bis-silylated precursor. A fluoride sol-gel methodology under soft synthesis conditions and in the absence of sophisticated structural directing agents allowed the generation of a mesoporous architecture with a homogeneous distribution of active chiral moieties along the network. The hybrid material was studied by means of different characterization techniques (TGA, NMR and IR spectroscopy, chemical and elemental analyses, TEM, and textural measurements), verifying the stability and integrity of the asymmetric active sites in the solid. The hybrid material, HybPyr, is an excellent asymmetric heterogeneous and recyclable catalyst for enantioselective Michael addition of linear aldehydes to β-nitrostyrene derivatives with high stereocontrol of the reaction products.
Geometry-Based Clustering Characteristics for Outdoor Measurements at 28–30 GHz (2022)

This letter presents an analysis of channel characteristics for an outdoor scenario at the frequency band of 28–30 GHz. A geometry-based clustering algorithm is proposed to group the measured multipath components (MPCs) from the interaction points on the surrounding walls or objects according to ray-tracing three-dimensional (3-D) simulations, giving results that are more physically interpretable than the traditional clustering algorithms. The cluster-level characteristics at 15 positions along a predefined route covering both line-of-sight (LoS) and non-LoS (NLoS) scenarios are investigated. Moreover, power contributions of MPCs with multiple bounces (up to seven bounces in NLoS scenario) from the interaction objects are also investigated.
Successive interference cancellation using stage dependent decision functions (2004)

In this paper, we introduce the concept of stage-dependent decision functions. The latter exploit the improvement of the soft-decisions' reliability with increasing number of stages to take more hard-decisions and thus cancels more noise from stage to stage. We prove that if the stage-dependent thresholds can be optimized at each stage then the nonlinear SIC can approach the single user bound. Simulation results show significant BER improvement compared to the SIC using stage-independent decision functions.
Synthesis and reactions of simple 3(2H)-furanones (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and reactions of simple 3(2H)-furanonesAmos B. Smith III, Patricia A. Levenberg, Paula J. Jerris, Robert M. Scarborough Jr., and Peter M. WovkulichCite this: J. Am. Chem. Soc. 1981, 103, 6, 1501–1513Publication Date (Print):March 1, 1981Publication History Published online1 May 2002Published inissue 1 March 1981https://pubs.acs.org/doi/10.1021/ja00396a034https://doi.org/10.1021/ja00396a034research-articleACS PublicationsRequest reuse permissionsArticle Views1650Altmetric-Citations120LEARN 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
Large Schottky barriers and memory operation for Ni/p-GaN contacts (1999)

Pancreas disease (PD) is an economically important viral disease in Norwegian aquaculture, with 75 to 89 annual outbreaks from 2009 to 2011. To hinder further spread of disease from an initial endemic area on the west coast of Norway, measures for surveillance and control are in place, and the disease is notifiable on a national level. Since 2008, the Norwegian coastline has been divided into 2 administrative zones separated by a production-free area of 10 nautical miles at approximately 63°N. At the same time, a vaccination program involving most marine salmonid farms was initiated by the industry, using a vaccine against PD that was made commercially available in 2007. The effects of the vaccine in the field have been questioned, since the annual number of PD outbreaks has not decreased as expected. However, other production parameters can be used for evaluation of vaccine effect, and in this study the effects of vaccination on cumulative mortality, growth rate, feed conversion factor and number of discarded fish were analyzed using data collected from fish cohorts with and without PD put to sea between spring 2007 and spring 2009. The results show that vaccination against PD has a positive effect in reducing the number of outbreaks, and decreasing cumulative mortality and the number of fish discarded at slaughter.
Early donepezil monotherapy or combination with metoprolol significantly prevents subsequent chronic heart failure in rats with reperfused myocardial infarction (2022)

Despite the presence of clinical guidelines recommending that β-blocker treatment be initiated early after reperfused myocardial infarction (RMI), acute myocardial infarction remains a leading cause of chronic heart failure (CHF). In this study, we compared the effects of donepezil, metoprolol, and their combination on the progression of cardiac remodeling in rats with RMI. The animals were randomly assigned to untreated (UT), donepezil-treated (DT), metoprolol-treated (MT), and a combination of donepezil and metoprolol (DMT) groups. On day 8 after surgery, compared to the UT, the DT and DMT significantly improved myocardial salvage, owing to the suppression of macrophage infiltration and apoptosis. After the 10-week treatment, the DT and DMT exhibited decreased heart rate, reduced myocardial infarct size, attenuated cardiac dysfunction, and decreased plasma levels of brain natriuretic peptide and catecholamine, thereby preventing subsequent CHF. These results suggest that donepezil monotherapy or combined therapy with β-blocker may be an alternative pharmacotherapy post-RMI.
Intelligent Physical Layer Security Approach for V2X Communication (2019)

Intelligent transportation systems (ITS) with advanced sensing and computing technologies are expected to support a whole new set of services including pedestrian and vehicular safety, internet access for vehicles, and eventually, driverless cars. Wireless communication is a major driving factor behind ITS, enabling reliable communication between vehicles, infrastructure, pedestrians and network, generally referred to as vehicle to everything (V2X) communication. However, the broadcast nature of wireless communication renders it prone to jamming, eavesdropping and spoofing attacks which can adversely affect ITS. Keeping in view this issue, we suggest the use of an intelligent security framework for V2X communication security, referred to as intelligent V2X security (IV2XS), to provide a reliable and robust solution capable of adapting to different conditions, scenarios and user requirements. We also identify the conditions that impact the security and describe the open challenges in achieving a realistic IV2XS system.
Electron beam lithography writing strategies for low loss, high confinement silicon optical waveguides (2011)

The authors present a robust process for fabricating passive silicon photonic components by direct-write electron beam lithography (EBL). Using waveguide transmission loss as a metric, we study the impact of EBL writing parameters on waveguide performance and writing time. As expected, write strategies that reduce sidewall roughness improve waveguide loss and yield. In particular, averaging techniques such as overlap or field shift writing reduce loss, however, the biggest improvement comes from writing using the smaller field-size option of our EBL system. The authors quantify the improvement for each variation and option, along with the tradeoff in writing time.
Rapid and sensitive detection of neuron specific enolase with a polydopamine coated plasmonic chip utilizing a rear-side coupling method (2017)

A rapid and sensitive detection of a cancer marker, neuron specific enolase (NSE), is demonstrated by using a disposable silver plasmonic chip functionalized with a mussel-inspired polydopamine (PDA) coating. A plasmonic chip consisting of a diffraction grating coated with a silver thin film is used for the excitation of propagating surface plasmon resonance through a rear-side grating coupling method. Simple and quick bio-functionalization of the sensor surface is performed by PDA coating which requires 20 min for deposition, and allows direct attachment of the capture antibody without using any coupling agents. A fluorescence based sandwich immunoassay is used for the detection of NSE by utilizing surface plasmon enhanced fluorescence (SPF) spectroscopy. The developed biosensor scheme provides approximately linear sensor responses for the sample containing NSE with the concentration around the clinically important value (12 ng mL<sup>-1</sup>) in both buffer and diluted human serum (25 vol% to a buffer solution). The detection limit for NSE is 0.5 ng mL<sup>-1</sup> (11 pM) and 1.4 ng mL<sup>-1</sup> (30 pM) in a buffer solution and diluted human serum, respectively. The presented biosensor scheme requires a small amount of the sample down to 10 μL in human serum and a short incubation time (15 min) of the sample solution containing NSE, enabling less invasive and rapid detection of NSE. This is the first example of the sensitive sandwich immunoassay demonstrated by using a plasmonic chip for the measurement of the sample dissolved in a complex medium with a rear side coupling method, which progresses the universal use of the SPF biosensors with a disposable plasmonic chip.
An Experimental Cognitive Radio for First Responders (2008)

Small form factor (SFF) software defined radio (SDR) platform is used to implement an experimental cognitive radio for first responders. The system was demonstrated in the 2007 Software Defined Radio technical conference and product exhibition, and is selected for presentation in the demonstrations and experimentation track in the IEEE DySPAN 2008. Different processing tasks are divided between a TI c64x+ DSP and a Xilinx Virtex IV FPGA while an ARM9 core is used to host Greenhills operating system. To tackle the complexity of development, we used progressive simulation based design. Starting from pure simulation of the system, we substitute the models with real modules step by step to build a fully functional modem. To develop the network of the cognitive radio modems, we deploy the available real modems with simulated primary and secondary users in a central simulation. Three real nodes are presented in our demonstration which perform channel sensing and data transmission.
HOLDeR: a layered system for vision-guided robotics (2002)

HOLDeR (Hierarchical, Object-centered, Learning Dextrous Robotics) is a new approach to the problem of object-centered task execution. It balances stored object knowledge with flexibility to produce a system that is capable of manipulating a wide variety of known and unknown objects. HOLDeR utilizes a layered approach to sensory-motor coordination that enables a robot to use as much object-specific data as possible, given time and computational constraints. The architecture also incorporates learning to allow the system to adapt to new objects and new classes of objects that it encounters. HOLDeR is based upon a modification of an active deformable model technique called dynamic pressure snakes. The techniques can be adapted to a variety of robotic tasks.
Creation of a novel inverted charge density wave state (2022)

Charge density wave (CDW) order is an emergent quantum phase that is characterized by periodic lattice distortion and charge density modulation, often present near superconducting transitions. Here, we uncover a novel inverted CDW state by using a femtosecond laser to coherently reverse the star-of-David lattice distortion in 1<i>T</i>-TaSe<sub>2</sub>. We track the signature of this novel CDW state using time- and angle-resolved photoemission spectroscopy and the time-dependent density functional theory to validate that it is associated with a unique lattice and charge arrangement never before realized. The dynamic electronic structure further reveals its novel properties that are characterized by an increased density of states near the Fermi level, high metallicity, and altered electron-phonon couplings. Our results demonstrate how ultrafast lasers can be used to create unique states in materials by manipulating charge-lattice orders and couplings.
Clinical outcomes of the Dynesys dynamic neutralization system: 1-year preliminary results (2007)

The early clinical outcomes of treatment with Dynesys are promising, with lessening of pain and disability found at follow-up review. Dynesys may be preferable to fusion for surgical treatment of degenerative spondylolisthesis and stenosis because it decreases back and leg pain while avoiding the relatively greater tissue destruction and the morbidity of donor site problems encountered in fusion. However, long-term follow-up care is still recommended.
Mutual injection-locking properties of monolithically-integrated surface-emitting multiple-quantum-well distributed feedback lasers (1990)

The mutual injection-locking properties of a coupled pair of multiple-quantum-well distributed-feedback lasers with grating output couplers were investigated experimentally and theoretically. When the mutual injection locking occurred, the output of one laser decreased while that of the other increased. The locking curve was asymmetric, and a stable and an unstable locking region existed. From the theoretical analysis, it was found that the phase delay with which the electric field emitted from each laser to the other laser significantly influences the locking characteristics. The increase and decrease of the locked output power are caused by the phase delay. It is also shown that the laser which receives the larger optical injection behaves like a slave laser and the laser which has less optical injection behaves like a master laser, and the shape of the locking curve is determined by the balance between the alpha parameter and the thermal resistance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Quantum mechanical calculations on the Ar++N2 charge transfer reaction (1989)

Calculations of cross sections for the charge transfer reaction Ar+(2P3/2)+N2(v=0, j) →Ar+N+2(v′=1, j′) are reported for thermal collision energies. A three-dimensional quantum-mechanical method is used in which separate rotational close-coupling calculations are performed for the Ar++N2(v=0)→Ar+N+2(v′=0) and Ar++N2(v=1) →Ar+N+2 (v′=1) channels, and the cross sections for the v=0→v′=1 channel are computed using a coupled channel-distorted wave Born approximation. Potential energy surfaces and couplings are taken from ab initio data. The predicted rotational product distributions for N+2 (v′=1, j′) agree fairly well with those measured in a molecular beam laser-induced fluorescence experiment.
Catalyst-Exsolving Anode-Supported Solid Oxide Fuel Cell (2021)

Exsolution is the process in which cations that make up the lattice of a mixed ionic/electronic conductor (MIEC) are reduced to metals and migrate to the surface of the host ceramic. These materials have become quite attractive for solid oxide fuel cells (SOFCs) because they can facilitate oxygen and electron transport through their bulk and act as electrocatalysts on the surface of SOFC anodes. Also, because of the nature of the exsolution process, the highly dispersed nano-catalysts have strong particle-host interactions which have shown resistance to common SOFC failure mechanisms such as agglomeration and coking. However, the practical application of such materials has not been well studied since most research focuses on the electrolyte-supported cells, which offer a quick method for screening electrochemical activity but the large ohmic resistance makes this cell unrealistic for real energy conversion devices, especially at lower temperatures. Here, we use a scalable ceramic processing technique to fabricate a ceramic-anode-supported SOFC that exsolves nano-catalysts for low temperature operation (600°C). SrFe 0.2 Ni 0.4 Mo 0.4 O 3- δ (SFNM) is used as the anode material due to its high conductivity and exsolution ability. By shifting the mechanically supporting layer from the electrolyte to this anode, we are able to drastically reduce the overall ohmic resistance of the cell. Additionally, we avoid extra processing steps for conventional catalyst deposition by taking advantage of the in-situ catalyst exsolution. During the exsolution process, we show that our cell performance increases over time, up to a peak power density of 300 mW/cm 2 at 600°C with H 2 fuel. Further, we discuss two major challenges facing exsolution-anode-supported SOFCs along the way and we show our efforts to identify and address the root causes of these problems.