gebhart/patrepeval huggingface dataset:
Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants (2002)

To assess the accuracy of the molecular dynamics (MD) models of nucleic acids, a detailed comparison between MD-calculated and NMR-observed indices of the dynamical structure of DNA in solution has been carried out. The specific focus of our comparison is the oligonucleotide duplex, d(CGCGAATTCGCG)(2), for which considerable structural data have been obtained from crystallography and NMR spectroscopy. An MD model for the structure of d(CGCGAATTCGCG)(2) in solution, based on the AMBER force field, has been extended with a 14 ns trajectory. New NMR data for this sequence have been obtained in order to allow a detailed and critical comparison between the calculated and observed parameters. Observable two-dimensional (2D) nuclear Overhauser effect spectroscopy (NOESY) volumes and scalar coupling constants were back-calculated from the MD trajectory and compared with the corresponding NMR data. The comparison of these results indicate that the MD model is in generally good agreement with the NMR data, and shows closer accord with experiment than back-calculations based on the crystal structure of d(CGCGAATTCGCG)(2) or the canonical A or B forms of the sequence. The NMR parameters are not particularly sensitive to the known deficiency in the AMBER MD model, which is a tendency toward undertwisting of the double helix when the parm.94 force field is used. The MD results are also compared with a new determination of the solution structure of d(CGCGAATTCGCG)(2) using NMR dipolar coupling data.
A covalent PIN1 inhibitor selectively targets cancer cells by a dual mechanism of action (2017)

The prolyl isomerase PIN1, a critical modifier of multiple signalling pathways, is overexpressed in the majority of cancers and its activity strongly contributes to tumour initiation and progression. Inactivation of PIN1 function conversely curbs tumour growth and cancer stem cell expansion, restores chemosensitivity and blocks metastatic spread, thus providing the rationale for a therapeutic strategy based on PIN1 inhibition. Notwithstanding, potent PIN1 inhibitors are still missing from the arsenal of anti-cancer drugs. By a mechanism-based screening, we have identified a novel covalent PIN1 inhibitor, KPT-6566, able to selectively inhibit PIN1 and target it for degradation. We demonstrate that KPT-6566 covalently binds to the catalytic site of PIN1. This interaction results in the release of a quinone-mimicking drug that generates reactive oxygen species and DNA damage, inducing cell death specifically in cancer cells. Accordingly, KPT-6566 treatment impairs PIN1-dependent cancer phenotypes in vitro and growth of lung metastasis in vivo.
Enantiospecific synthesis of 2-[18F]fluoro-l-phenylalanine and 2-[18F]fluoro-l-tyrosine by isotopic exchange (2010)

2-[(18)F]Fluoro-L-phenylalanine and 2-[(18)F]fluoro-L-tyrosine have been developed as promising radiopharmaceuticals for molecular imaging using positron emission tomography (PET). However, the lack of a convenient radiosynthetic pathway has limited their practical use. In this work a new three-step nucleophilic synthesis of these compounds starting from [(18)F]fluoride is described. Corresponding precursors (1a and 1b) were (18)F-fluorinated by isotopic exchange, followed by the removal of an activating formyl group with Rh(PPh(3))(3)Cl and subsequent hydrolysis of protecting groups in acidic medium. All reactions were carried out using both conventional and microwave heating. Conventional heated reactions yielded the desired products 2-[(18)F]Fphe and 2-[(18)F]Ftyr in 43% and 49% whereas radiochemical yields of 34% and 43%, respectively, were obtained when they were heated by microwaves. Under optimized conditions the enantiomeric purity was ≥94% for both radiopharmaceuticals.
Simulation Studies of Metal–Ligand Self‐Assembly (2016)

This chapter introduces molecular dynamics (MD) simulation studies of the metal-ligand self-assembly, which begins with modeling method, as well as the methods to fill the time scale gap between the actual and the simulated systems. It considers the elements that play important roles in the self-assembly process and explains the computation methods. The chapter focuses on the parameter that controls the metal-ligand coordination interactions, i.e. the near-field relative dielectric constant er. The accelerated simulation correctly follows the self-assembly process of the real reaction systems when we properly select the simulation parameters, e.g., er. The chapter considers the 3-D extension of the 2-D-like metal-organic frameworks (MOFs). It considers that the MD simulation can also be a valuable tool to study the temperature effects in metal-ligand coordination-directed self-assembly. The chapter shows that the appropriate strength of the metal-ligand binding is definitely important in both finite supramolecular complexes and infinite polymer networks.
The Nuclear Immune Receptor RPS4 Is Required for RRS1SLH1-Dependent Constitutive Defense Activation in Arabidopsis thaliana (2014)

Plant nucleotide-binding leucine-rich repeat (NB-LRR) disease resistance (R) proteins recognize specific "avirulent" pathogen effectors and activate immune responses. NB-LRR proteins structurally and functionally resemble mammalian Nod-like receptors (NLRs). How NB-LRR and NLR proteins activate defense is poorly understood. The divergently transcribed Arabidopsis R genes, RPS4 (resistance to Pseudomonas syringae 4) and RRS1 (resistance to Ralstonia solanacearum 1), function together to confer recognition of Pseudomonas AvrRps4 and Ralstonia PopP2. RRS1 is the only known recessive NB-LRR R gene and encodes a WRKY DNA binding domain, prompting suggestions that it acts downstream of RPS4 for transcriptional activation of defense genes. We define here the early RRS1-dependent transcriptional changes upon delivery of PopP2 via Pseudomonas type III secretion. The Arabidopsis slh1 (sensitive to low humidity 1) mutant encodes an RRS1 allele (RRS1SLH1) with a single amino acid (leucine) insertion in the WRKY DNA-binding domain. Its poor growth due to constitutive defense activation is rescued at higher temperature. Transcription profiling data indicate that RRS1SLH1-mediated defense activation overlaps substantially with AvrRps4- and PopP2-regulated responses. To better understand the genetic basis of RPS4/RRS1-dependent immunity, we performed a genetic screen to identify suppressor of slh1 immunity (sushi) mutants. We show that many sushi mutants carry mutations in RPS4, suggesting that RPS4 acts downstream or in a complex with RRS1. Interestingly, several mutations were identified in a domain C-terminal to the RPS4 LRR domain. Using an Agrobacterium-mediated transient assay system, we demonstrate that the P-loop motif of RPS4 but not of RRS1SLH1 is required for RRS1SLH1 function. We also recapitulate the dominant suppression of RRS1SLH1 defense activation by wild type RRS1 and show this suppression requires an intact RRS1 P-loop. These analyses of RRS1SLH1 shed new light on mechanisms by which NB-LRR protein pairs activate defense signaling, or are held inactive in the absence of a pathogen effector.
Novel hybrid 12-pulse boost-type rectifier with controlled output voltage (2005)

Novel hybrid 12-pulse line interphase transformer (LIT) rectifier systems with integrated single-switch or two-switch boost-type output stage that ensure a constant output voltage independent of mains and load conditions are proposed for supplying actuators of future more electric aircraft. The principle of operation, the dimensioning, and the system control are discussed. The theoretical considerations are experimentally confirmed for a 10 kW laboratory prototype. Finally, the single-and the two-switch system are comparatively evaluated concerning the level of input current ripple, power factor, and overall efficiency.
Suppression of Fracture Failure of Structures by Composite Design Based on Fracture Mechanics (2005)

This paper discusses the use of fracture mechanics for the microstructure tailoring of a fiber reinforced Engineered Cementitious Composite (ECC) to achieve extreme tensile ductility at the composite scale. It demonstrates that fracture mechanics applied to control fracture phenomena at the micro and meso material scales can lead to suppression of fracture failure at the macro structural scale. Specifically, models of tunneling crack at the fiber/matrix interface and the steady state propagation of bridged flat matrix crack combine to provide insights on composite design. Interestingly, the micromechanics model indicates that low fiber/matrix interface fracture energy and low mortar matrix fracture energy are desirable for attaining high composite ductility. These concepts are verified by an expanding set of experimental data on structural elements tested to failure. The explicit suppression of commonly observed fracture mechanisms in reinforced concrete columns under reverse cyclic loading when the concrete is replaced by ECC is described. 1
ChemInform Abstract: Synthesis of Fluorinated 1,8‐Naphthyridinone Derivatives. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Demonstration of CAM and TCAM Using Phase Change Devices (2011)

We demonstrate novel designs for Content Addressable Memory (CAM) and Ternary CAM (TCAM) using Phase Change Memory (PCM) technology, which can potentially improve density and power consumption by >;5X as compared with conventional SRAM based implementations. Using Monte-Carlo simulations, we also predict the desired characteristics of PCM devices for realizing large, high performance CAM/TCAM chips.
Barley β-Glucan and Beer Foam Stability (2001)

Barley β-glucan was examined as a potential foam-enhancing or foam-stabilizing beer component. Neither foam enhancement nor foam stabilization was observed. Treating beer with β-glucanase did not alter the foam properties. β-Glucan did not concentrate in foam collected by the foam tower method from a European Pilsner-style beer with a relatively high known β-glucan content. β-Glucan molecular weight fractionation was not observed. β-Glucan did not have independent foam stability when tested in a model beer system.
Electrically Heated Catalysts for Cold-Start Emissions in Diesel Aftertreatment (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;With a tighter regulatory environment, reduction of hydrocarbon (HC) and NO&lt;sub&gt;x&lt;/sub&gt; emissions during cold-start has emerged as a major challenge for diesel engines. In the complex diesel aftertreatment system, more than 90% of engine-out NO&lt;sub&gt;x&lt;/sub&gt; is removed in the underfloor SCR. However, the combination of low temperature exhaust and heat sink over DOC delays the SCR light-off during the cold start. In fact, the first 350 seconds during the cold light-duty FTP75 cycle contribute more than 50% of the total NO&lt;sub&gt;x&lt;/sub&gt; tailpipe emission due to the low SCR temperature. For a fast SCR light-off, electrically heated catalyst (EHC) technology has been suggested to be an effective solution as a rapid warm-up strategy.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;In this work, the EHC, placed in front of DOC, utilizes both electrical power and hydrocarbon fuel. The smart energy management during the cold-start was crucial to optimize the EHC integrated aftertreatment system. With the EHC warm-up strategy, the underfloor SCR reached the operation temperature within 100 seconds and achieved more than 90% conversion between 150 and 350 seconds during the cold FTP75. Furthermore, the integrated system provides an opportunity to improve fuel economy. In summary, the EHC has been demonstrated as an enabling technology for a clean and energy efficient NO&lt;sub&gt;x&lt;/sub&gt; aftertreatment system for diesel engines.&lt;/div&gt;&lt;/div&gt;
Reflection micro-Fresnel lenses and their use in an integrated focus sensor (1989)

Blazed reflection micro-Fresnel lenses and their use in an integrated focus sensor are proposed. Theoretical analysis indicates that the optical characteristics of reflection Fresnel lenses can be improved compared with a conventional transmission micro-Fresnel lens. These reflection Fresnel lenses were fabricated using electron-beam lithography and exhibited the diffraction-limited focusing characteristics with 71% high efficiency. The focus sensor has a folded optical path and includes a beam splitter integrated with thin film components, such as a reflection elliptical Fresnel lens and a quadrant photodetector. The reflection elliptical Fresnel lens in the focus sensor exhibiting excellent astigmatic characteristics agreed with the theoretical results, and the focus error signal was detected. This sensor can be developed as the optical head of an optical disk system.
Tiller estimation method using deep neural networks (2023)

This paper describes a method based on a deep neural network (DNN) for estimating the number of tillers on a plant. A tiller is a branch on a grass plant, and the number of tillers is one of the most important determinants of yield. Traditionally, the tiller number is usually counted by hand, and so an automated approach is necessary for high-throughput phenotyping. Conventional methods use heuristic features to estimate the tiller number. Based on the successful application of DNNs in the field of computer vision, the use of DNN-based features instead of heuristic features is expected to improve the estimation accuracy. However, as DNNs generally require large volumes of data for training, it is difficult to apply them to estimation problems for which large training datasets are unavailable. In this paper, we use two strategies to overcome the problem of insufficient training data: the use of a pretrained DNN model and the use of pretext tasks for learning the feature representation. We extract features using the resulting DNNs and estimate the tiller numbers through a regression technique. We conducted experiments using side-view whole plant images taken with plan backgroud. The experimental results show that the proposed methods using a pretrained model and specific pretext tasks achieve better performance than the conventional method.
Monolithically Integrated MESFET Devices on a High-Speed Silicon Photonics Platform (2014)

We present the design and fabrication of complimentary metal-semiconductor field-effect transistors (MESFETs) monolithically integrated on a high-speed silicon photonics platform. The transistors were built in an existing silicon photonics process without any additional process steps or modifications to maintain consistent photonics performance. The MESFETs showed a threshold voltage of -1.4 and 2.0 V for NMES and PMES, respectively. The NMES transconductance was measured to be 46.4 μS/μm, and the cutoff frequency was shown to be 2.2 GHz. Transistors of this design can be simply integrated into silicon photonics platforms for on-chip feedback circuits.
<title>Simple optical computing device for chemical analysis</title> (2001)

Multivariate Optical Computing (MOC) devices have the potential of greatly simplifying as well as reducing the cost of applying the mathematics of multivariate regression to problems of chemical analysis in the real world. These devices utilize special optical interference coatings known as multivariate optical elements (MOEs) that are encoded with pre-determined spectroscopic patterns to selectively quantify a chemical species of interest in the presence of other interfering species. A T-format prototype of the first optical computing device is presented utilizing a multilayer MOE consisting of alternating layers of two metal oxide films (Nb<SUB>2</SUB>O<SUB>5</SUB> and SiO<SUB>2</SUB>) on a BK-7 glass substrate. The device was tested by using it to quantify copper uroporphyrin in a quaternary mixture consisting of uroporphyrin (freebase), tin uroporphyrin, nickel uroporphyrin, and copper uroporphyrin. A standard error of prediction (SEP) of 0.86(mu) M was obtained for copper uroporphyrin.
ACTIVE CONTROL OF AN INCOMPRESSIBLE AXISYMMETRIC JET USING FLAPS (2009)

The near field of an incompressible round jet flow was investigated for generation of streamwise vortices using active flow control. Zero mass-flux perturbations were used to excite the flow. The lip of the jet was equipped with a small flap deflected away from the stream. Effects of changing the flap deflection angle on the flow momentum, streamwise vorticity, circulation and turbulence were studied. The emphasis is being placed on mapping the development of the trailing vortices in order to quantify the mixing achieved.
Probing the structure-property relationship of regioisomeric ionic liquids with click chemistry (2011)

Understanding the structure-property relationship of ionic liquids is a key to the development of optimized materials for specific applications, such as CO2 capture, battery electrolytes, or lubricants. Using Cu(I)-catalyzed click chemistry as a synthetic platform, a library of triazolium-based ionic liquids has been accessed for the first time. These regioisomers of ionic liquids give insight into the structure property of these important materials. The effect of substituents and the effect of regioisomerization on thermal stability, CO2 solubility and inductive effects have been correlated.
Synthesis of Nanofluids (2007)

This chapter contains sections titled: General Issues of Concern Synthetic Methods: Common Issues of Concern How we Study Nanoparticles Variety in Nanomaterials Microemulsion-Based Methods for Nanofluids Solvothermal Synthesis Synthesis using Supports Using Biology Magnetic Nanofluids Inert Gas Condensation Anisotropic Nanoparticles Other Nanofluids Summary References
Ultrahigh-speed ICs for a 100 Gbps transceiver demonstrator system (2005)

We report on advances in the OptCom-project within the fields of ultra high-speed electronics and assembly technology. We highlight how we work towards our goal: a 100 Gbps transceiver demonstrator. Results of today include ICs from several generations of development. Our current best result is an IC operating at record-breaking 165 Gbps (serial bit stream). We will also outline our future activities towards more complex IC design, including electrical pseudo-random bit sequence generation and error detection at very high speed.
Compensation of Coefficient Erasures in Frame Representations (2006)

This work explores low complexity systems to compensate for coefficient erasures in frame representations of signals. Assuming linear synthesis with a pre-specified frame it is demonstrated that erasures can be compensated for even if the origin of the representation coefficients is not known. If the transmitter is aware of the erasure occurrence, the compensation is performed by projecting the erasure error to the remaining coefficients. Furthermore, it is demonstrated that the same compensation can be executed using a transmitter/receiver combination in which the transmitter is not aware of the erasure occurrence. The transmitter compensates for all the coefficients using projections, assuming an erasure will occur. The receiver undoes the compensation for the coefficients that have not been erased, thus maintaining the compensation only of the erased coefficients
NeuroXplorer 1.0: An Extensible Framework for Architectural Exploration\n with Spiking Neural Networks (2021)

Recently, both industry and academia have proposed many different\nneuromorphic architectures to execute applications that are designed with\nSpiking Neural Network (SNN). Consequently, there is a growing need for an\nextensible simulation framework that can perform architectural explorations\nwith SNNs, including both platform-based design of today's hardware, and\nhardware-software co-design and design-technology co-optimization of the\nfuture. We present NeuroXplorer, a fast and extensible framework that is based\non a generalized template for modeling a neuromorphic architecture that can be\ninfused with the specific details of a given hardware and/or technology.\nNeuroXplorer can perform both low-level cycle-accurate architectural\nsimulations and high-level analysis with data-flow abstractions. NeuroXplorer's\noptimization engine can incorporate hardware-oriented metrics such as energy,\nthroughput, and latency, as well as SNN-oriented metrics such as inter-spike\ninterval distortion and spike disorder, which directly impact SNN performance.\nWe demonstrate the architectural exploration capabilities of NeuroXplorer\nthrough case studies with many state-of-the-art machine learning models.\n
Blending chaotic attractors using the synchronization of chaos (1995)

Building a source of low-dimensional chaotic signals with specified properties poses new challenges in the study of nonlinear systems. We address this problem using two synchronized asymmetrically coupled chaotic systems. As an uncoupled oscillator, each produces chaotic signals with distinctively different properties. The chaotic signal produced by the synchronized oscillators possesses properties intermediate with respect to the two original signals. The properties of this synthesized signal can be controlled by the ratio of the coupling parameters.
Pharmacokinetic (PK) analysis of fluticasone furoate (FF), umeclidinium (UMEC) and vilanterol (VI) following triple therapy at two UMEC doses in healthy subjects (2014)

Background: FF/UMEC/VI is a novel ICS/LAMA/LABA therapy. Dual therapies of FF/VI and UMEC/VI were recently approved for treatment of moderate-severe COPD.

Objective: Comparison of systemic exposure after co-administration of FF, UMEC and VI in a single device at two UMEC doses (250mcg or 500mcg), and vs the dual therapies FF/VI and UMEC/VI (all in ELLIPTA™ dry powder inhaler).

Methods: In an open-label, single-dose, 4-way crossover study, healthy subjects (N=44) were randomised to 4 treatment sequences, each comprising 4 treatments (table) in different order. Systemic exposure of FF, UMEC and VI was assessed by PK sampling up to 24h post-dose.

Results: Estimates of total systemic exposure (AUC(0–t') and Cmax) for FF, UMEC and VI were similar between both UMEC dose combinations and across other comparisons (table). VI Cmax was slightly greater in FF/UMEC/VI vs UMEC/VI when UMEC was dosed at 250mcg, though this difference was not considered clinically relevant.

Conclusions: FF/UMEC/VI in a single inhaler, at UMEC 250mcg or 500mcg, achieved dose-proportional systemic exposure for UMEC and similar FF or VI exposure between doses. FF/UMEC/VI achieved similar exposure to dual therapies. The safety and delivered lung dose of all three agents in a single inhaler are expected to be similar to those in approved dual therapies.

Funding: GSK (200587;[NCT01894386][1])

![Figure][2] [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT01894386&atom=%2Ferj%2F44%2FSuppl_58%2FP938.atom
 [2]: pending:yes