gebhart/patrepeval huggingface dataset:
Applying dynamical systems techniques to real ocean drifters (2022)

Abstract. This paper presents the first comprehensive comparison of several different dynamical-systems-based measures of stirring and Lagrangian coherence, computed from real ocean drifters. Seven commonly used methods (finite-time Lyapunov exponent (FTLE), trajectory path length, trajectory correlation dimension, trajectory encounter volume, Lagrangian-averaged vorticity deviation, dilation, and spectral clustering) were applied to 144 surface drifters in the Gulf of Mexico in order to map out the dominant Lagrangian coherent structures. Among the detected structures were regions of hyperbolic nature resembling stable manifolds from classical examples, divergent and convergent zones, and groups of drifters that moved more coherently and stayed closer together than the rest of the drifters. Many methods highlighted the same structures, but there were differences too. Overall, five out of seven methods provided useful information about the geometry of transport within the domain spanned by the drifters, whereas the path length and correlation dimension methods were less useful than others.
Driver Monitoring (2017)

Driver inattention is a major cause of traffic accidents and fatalities worldwide. This has spawned considerable interest and research toward using computer vision and other forms of sensing technologies to proactively monitor driver behavior and provide appropriate feedback and intervention to enhance safety and comfort. This chapter presents an overview of in-vehicle driver monitoring technologies with a focus on visual sensing, analysis, and feedback. Driver behavior can be inferred both directly from inward driver-facing cameras and indirectly from outward scene-facing sensors. Since the latter is covered elsewhere in the text, the chapter emphasizes the former and describes methodologies for acquiring footage of driver-facing video, techniques to efficiently detect the face and eyes, algorithms for gaze direction and head pose estimation, facial expression monitoring techniques, and fusion of multimodal data acquired by heterogeneous sensors. A broad survey of the state of the art is complemented with a detailed treatment of a few selected topics.
Stereoselective Synthesis of the Di-Spirooxindole Analogs Based Oxindole and Cyclohexanone Moieties as Potential Anticancer Agents (2021)

A new series of di-spirooxindole analogs, engrafted with oxindole and cyclohexanone moieties, were synthesized. Initially, azomethine ylides were generated via reaction of the substituted isatins <b>3a-f</b> (isatin, <b>3a</b>, 6-chloroisatin, <b>3b</b>, 5-fluoroisatin, <b>3c</b>, 5-nitroisatin, <b>3d</b>, 5-methoxyisatin, <b>3e</b>, and 5-methylisatin, <b>3f</b>, and (2<i>S</i>)-octahydro-1<i>H</i>-indole-2-carboxylic acid <b>2</b>, in situ azomethine ylides reacted with the cyclohexanone based-chalcone <b>1a-f</b> to afford the target di-spirooxindole compounds <b>4a-n</b>. This one-pot method provided diverse structurally complex molecules, with biologically relevant spirocycles in a good yields. All synthesized di-spirooxindole analogs, engrafted with oxindole and cyclohexanone moieties, were evaluated for their anticancer activity against four cancer cell lines, including prostate PC3, cervical HeLa, and breast (MCF-7, and MDA-MB231) cancer cell lines. The cytotoxicity of these di-spirooxindole analogs was also examined against human fibroblast BJ cell lines, and they appeared to be non-cytotoxic. Compound <b>4b</b> was identified as the most active member of this series against prostate cancer cell line PC3 (IC<sub>50</sub> = 3.7 ± 1.0 µM). The cyclohexanone engrafted di-spirooxindole analogs <b>4a</b> and <b>4l</b> (IC<sub>50</sub> = 7.1 ± 0.2, and 7.2 ± 0.5 µM, respectively) were active against HeLa cancer cells, whereas NO<sub>2</sub> substituted isatin ring and <i>meta</i>-fluoro-substituted (2<i>E</i>,6<i>E</i>)-2,6-dibenzylidenecyclohexanone containing <b>4i</b> (IC<sub>50</sub> = 7.63 ± 0.08 µM) appeared to be a promising agent against the triple negative breast cancer MDA-MB231 cell line. To explore the plausible mechanism of anticancer activity of di-spirooxindole analogs, molecular docking studies were investigated which suggested that spirooxindole analogs potentially inhibit the activity of MDM2.
Finding patches in a heterogeneous aquatic environment: pH‐taxis by the dispersal stage of choanoflagellates (2017)

Abstract Microbial eukaryotes that feed on bacteria are critical links in aquatic food webs. We used the choanoflagellate Salpingoeca rosetta , whose life history includes fast‐ and slow‐swimming unicellular forms and multicellular colonies, to study performance of these different forms at finding and accumulating in patches of prey. Video microscopy of behavior in microfluidic experiments showed that only unicellular fast swimmers exhibited taxis into patches of attractant. Of the chemical cues tested, only pH affected behavior: fast swimmers moved toward patches of water that had pH in the range of 6–7 from water with higher or lower pH. Since bacteria can lower the pH of the water in their vicinity, we suggest that seeking regions with a moderately more acidic pH than average seawater helps the fast‐swimming dispersal stage of choanoflagellates find particles or surfaces rich in prey.
Human Radiation Dose Assessment of the ACP Experimentation (2004)

The Advanced spent fuel Conditioning Process(ACP) is under development for the effective management of spent fuels which have been generated in nuclear plants. The ACP needs a hot cell where most of the operations will be performed. To give priority to environmental safety, radiation dose evaluation for the radioactive nuclides was preliminarily performed with the basic concept design report, the meteorological data and the recent site specific data. According to the production and release rate of the nuclides, dose evaluations for residents around the facility were performed. Evaluation results compared with the regulation limits presented a very good safety level, but the elimination efficiency for several important nuclides has to be highly maintained.
Erratum: Triplets Contribute to Both an Increase and Loss in Fluorescent Yield in Organic Light Emitting Diodes [Phys. Rev. Lett.108, 267404 (2012)] (2014)

Received 21 October 2014DOI:https://doi.org/10.1103/PhysRevLett.113.189903© 2014 American Physical Society
Genomics of Plants and Fungi (2003)

Fungi: aspergillus, Michael J. Anderson, Jayne L. Brookman, and David W. Denning developmental processes in filamentous fungi, Reinhard Fischer and Ursula Kuesi multiple GATA transcription factors control distinct regulatory circuits and cellularactivities in neurospora, George A. Marzluf molecular genetics of metabolite production by industrial filamentous fungi, Christian P. Kubicek acquiring a new viewpoint - tools for functional genomics in the filamentous fungi, Todd M. DeZwaan, Keith D.Allen, Matthew M. Tanzer, Kiichi Adachi, Lakshman Ramamurthy, Sanjoy Mahanty, and Lisbeth Hamer. Plants: functional and comparative genomics of cyanobacteria, Bradley Postier and Robert L. Burnap genomic analysis of arabidopsis gene expression inresponse to a systemic fungicide, Huey-Wen Chuang, Tzung-Fu Hsieh, Manuel Duval, and Terry L. Thomas identification of T-DNA insertions in arabidopsis genes, Laszlo Szabados and Csaba Koncz genomic approaches for studying gene families in plants, CathalWilson, Balazs Melikant, and Erwin Heberle-Bros industrialization of plant gene function discovery, Douglas Boyes, Robert Ascenzi, Rao Mulpuri, Susanne Kjemtrup, Andreas Kloti, and Keith R. Davis functional genomics of plant abiotic stress tolerance,John C. Cushman. Bioinformatics: using workflow to build an information management system for a geographically distributed genome sequencing initiative, David Hall, John Miller, Jonathan Arnold, Krys Kochut, Amit Sheth, and Michael Weise.
A Virus-Like Particle Vaccine Elicits Broad Neutralizing Antibody Responses in Humans to All Chikungunya Virus Genotypes (2016)

Chikungunya virus (CHIKV) is an alphavirus that has emerged as a global health burden. There are 3 CHIKV genotypes: Asian, West African, and Eastern/Central/South African. No licensed CHIKV vaccine is available, and whether the antibody response elicited by one genotype can neutralize heterologous genotypes is unclear. We assessed neutralizing antibody (NAb) responses of volunteers in a phase 1 study of a CHIKV vaccine against 9 viral strains representing all 3 genotypes. Minimal differences in vaccine-elicited NAb responses were observed among genotypes, suggesting that vaccination with a single CHIKV strain can elicit cross-protective NAbs against all 3 genotypes.
Optimizing iterative algorithms for distributed memory machines (1992)

Scientific and engineering computations, although numerically intensive, are typically regular both in terms of the control flow patterns and the employed data structures. Such computations often involve iterative applications of numerical algorithms to all (or the majority of) the parts of the data structures, a characteristic very suitable for massively parallel processing. Algorithms that employ such iterative applications are referred to here as iterative algorithms. Among the existing parallel architectures, distributed memory machines support the highest degree of scalability and hence they are deemed to be the most promising candidates for massively parallel processing. This dissertation focuses on optimization of iterative algorithms designed for execution on distributed memory machines.
Suitable alignment of various arrays in an iterative algorithm reduces interprocessor communication costs, which are often very expensive in a distributed memory machine. Data alignment determines the relative shifts among the index domains of the various data structures in a computation that minimize the communication cost. We show that finding such data alignment is closely related to the problem of finding the closest vector in an integer lattice. We establish the complexity of this problem and provide algorithms for its exact solution. We also present a polynomial-time algorithm for approximate solution and discuss its performance.
In iterative algorithms, wavefront of computation can often be formed to (1) define the hyperplanes of simultaneous execution of the index points, and (2) partition the index domains and allocate the partitions to the processors. The problem is to find a wavefront that maximizes the overall speed of computation. We describe algorithms for finding such wavefront and discuss related issues.
Finally, we formalize the problem of determining the optimal loop-structure and minimizing the memory requirement of the computation at each processor. The optimal loop structure allows the compiler to form minimum window(s) on the dimension(s) of the various arrays in a computation. We provide an efficient algorithm for determining the optimal window sizes for a given loop structure. We also establish the complexity of the problem of finding the best loop structure and provide exact and heuristic algorithms to obtain one.
The role of iodide in the formation of lithium hydroxide in lithium–oxygen batteries (2017)

Iodide ions promote deprotonation of water; in consequence LiOH/LiOH·H<sub>2</sub>O is formed as a final discharge product.
Near Surface Noise Characterization With Multicomponent Measurements (2007)

Near Surface Noise Characterization With Multicomponent Measurements Ed Kragh (Schlumberger Cambridge Research (SCR)) and Everhard Muyzert (Schlumberger Cambridge Research (SCR)) SUMMARY____________________________________________________________ On land the effect of the near-surface is the major cause of poor seismic data quality. Surface noise heterogeneity causing scattering statics coupling variations wavefield attenuation and anisotropy all degrade the quality of the wavefield recorded at the surface. To further improve the quality of land seismic data one approach is to gain a fundamental understanding of the wave propagation in the near-surface. As an example a consistent observation which requires explaining is the amount of cross-line energy recorded
Efficient and Specific Internal Cleavage of a Retroviral Palindromic DNA Sequence by Tetrameric HIV-1 Integrase (2007)

Our findings suggest that the restriction-like cleavage of palindromic sequences may be a general physiological activity of retroviral INs and that IN tetramerisation is strongly favoured by DNA symmetry, either at the target site for the concerted integration or when the DNA contains the 2-LTR junction in the case of the palindromic internal cleavage.
Synthesis and Isolation of Antiaromatic Expanded Azacoronene via Intramolecular Vilsmeier-Type Reaction (2019)

An antiaromatic cation of the expanded hexapyrrolohexaazacoronene (HPHAC) <b>1</b><sup><b>+</b></sup> was synthesized by a Vilsmeier-type reaction of the partially unfused HPHAC <b>2</b>. X-ray diffraction analysis revealed the formation of a seven-membered ring with a methyne linkage between the pyrrole moieties. Although <b>1</b><sup><b>+</b></sup> is a monocation, upfield shifts of the peripheral ethyl protons were clearly observed in the <sup>1</sup>H NMR spectra, indicating 24π antiaromaticity. Global antiaromaticity was also supported by nucleus-independent chemical shift and anisotropy of the induced current density calculations. Cation <b>1</b><sup><b>+</b></sup> displayed two reversible oxidations and one irreversible reduction in the cyclic voltammetry measurements. Treatment of <b>1</b><sup><b>+</b></sup> with NOSbF<sub>6</sub> gave aromatic trication <b>1</b><sup><b>3+</b></sup> with 22π-electron conjugation.
The Effect of Predictability on Subjective Duration (2007)

Events can sometimes appear longer or shorter in duration than other events of equal length. For example, in a repeated presentation of auditory or visual stimuli, an unexpected object of equivalent duration appears to last longer. Illusions of duration distortion beg an important question of time representation: when durations dilate or contract, does time in general slow down or speed up during that moment? In other words, what entailments do duration distortions have with respect to other timing judgments? We here show that when a sound or visual flicker is presented in conjunction with an unexpected visual stimulus, neither the pitch of the sound nor the frequency of the flicker is affected by the apparent duration dilation. This demonstrates that subjective time in general is not slowed; instead, duration judgments can be manipulated with no concurrent impact on other temporal judgments. Like spatial vision, time perception appears to be underpinned by a collaboration of separate neural mechanisms that usually work in concert but are separable. We further show that the duration dilation of an unexpected stimulus is not enhanced by increasing its saliency, suggesting that the effect is more closely related to prediction violation than enhanced attention. Finally, duration distortions induced by violations of progressive number sequences implicate the involvement of high-level predictability, suggesting the involvement of areas higher than primary visual cortex. We suggest that duration distortions can be understood in terms of repetition suppression, in which neural responses to repeated stimuli are diminished.
The Effect of Neutron Source Distribution on Subcriticality Measurement of Pressurized Water Reactors Using the Modified Neutron Source Multiplication Method (2003)

A modified neutron source multiplication method has been investigated for application to subcriticality measurement in commercial Pressurized Water Reactors (PWRs). This method is based on the extraction of the fundamental mode from measured neutron signals and corrections for spatial effects. In commercial reactors, mainly two types of neutron sources are expected, one from burnt fuels and the other from in-core fixed neutron sources. To calculate the extraction and spatial correction factors, the fixed source problem was solved by the Finite Difference Method (FDM) to explicitly deal with spatial intensities of neutron sources. Sensitivity analysis was carried out to investigate how the accuracy of estimated subcriticality depends on approximation levels of neutron source distributions. It was found that both of the neutron sources should be taken into account. For a pin rod type of the in-core fixed neutron source, a node-wise distribution for which the localized source intensity is averaged over the radial direction in the relevant nodes is applicable, since it can estimate the subcriticality with almost the same accuracy as in the case with a rigid spatial treatment. This ensures that nodal calculations can be used in the evaluation of correction factors instead of burdensome FDM calculations.
Interactive display system having a digital micromirror imaging device (2023)

A display system includes a waveguide optical panel having an inlet face and an opposite outlet face. A projector cooperates with a digital imaging device, e.g. a digital micromirror imaging device, for projecting an image through the panel for display on the outlet face. The imaging device includes an array of mirrors tiltable between opposite display and divert positions. The display positions reflect an image light beam from the projector through the panel for display on the outlet face. The divert positions divert the image light beam away from the panel, and are additionally used for reflecting a probe light beam through the panel toward the outlet face. Covering a spot on the panel, e.g. with a finger, reflects the probe light beam back through the panel toward the inlet face for detection thereat and providing interactive capability.
Infraorbital Nerve: A Road Map to the Pterygopalatine Fossa, Cavernous Sinus, and Skull Base in Endoscopic Transmaxillary Approaches (2015)

Introduction: Endoscopic transmaxillary approaches are becoming more commonly performed for pathology of the anterolateral skull base, including the cavernous sinus, pterygopalatine fossa, and infratemporal fossa. This is an anatomically complex region which contains branches of the trigeminal nerve, external carotid artery, and is in close proximity to the internal carotid artery. Intraoperatively, we have found the infraorbital nerve (ION) located within the roof maxillary sinus to be an easily identifiable landmark that leads to the skull base. In this study, we sought to study the anatomy of the ION and describe its relationship to other neurovascular structures encountered in endoscopic transmaxillary approaches.
Systematic high-level address code transformations for piece-wise linear indexing: illustration on a medical imaging algorithm (2002)

Exploring data transfer and storage issues is crucial to efficiently map data intensive applications (e.g., multimedia) onto programmable processors. Code transformations are used to minimise main memory bus load and hence also power and system performance, However this typically incurs a considerable arithmetic overhead in the addressing and local control. For instance, memory optimising in-place and data-layout transformations add costly module and integer division operations to the initial addressing code. In this paper, we show how the cycle overhead can be almost completely removed. This is done according to a systematic methodology which is a combination of an algebraic transformation exploration approach for the (non)linear arithmetic on top of an efficient transformation technique for reducing the piece-wise linear indexing to linear pointer arithmetic. The approach is illustrated on a real-life medical application, using a variety of programmable processor architectures. Total gains in cycle count ranging between a factor 5 and 25 are obtained compared to conventional compilers.
The Bioengineered Cardiac Left Ventricle (2017)

Left ventricle and aortic valve underdevelopment are presentations in the congenital cardiac condition hypoplastic left heart syndrome (HLHS); current clinical treatments involve right ventricle refunctionalization. Cardiac organoid models provide simplified open chambers engineered into a flow loop, to ameliorate ventricle-type function. Complete bioengineered ventricle development presents a significant advancement in cardiac organoids. This study provides the foundation for bioengineered complete ventricle (BECV) fabrication. Bioengineered trileaflet valve (BETV) molds and chitosan scaffolds were developed to emulate human neonate aortic valve geometry. Bioengineered complete ventricle were fabricated by fitting BETV into a bioengineered open ventricle (BEOV); the chamber was cellularized using a two-stage cellularization strategy, and BETV were passively seeded with rat neonatal cardiac fibroblasts and perfusion cultured for 3 days. Average pressure generated ranged from 0.06 to 0.12 mm Hg; average biopotential output was 1.02 mV. Histologic assessment displayed syncytial-type cardiomyocyte aggregates at the BECV chamber surface; BETV displayed randomly oriented, diffusely distributed cardiac fibroblasts. The fabrication of this novel BECV may aid in developing a functional engineered left ventricle for clinical application in HLHS.
Antibody-Dependent Enhancement of SARS-CoV-2 Infection Is Mediated by the IgG Receptors FcγRIIA and FcγRIIIA but Does Not Contribute to Aberrant Cytokine Production by Macrophages (2021)

The coronavirus disease 2019 (COVID-19) pandemic has raised concerns about the detrimental effects of antibodies. Antibody-dependent enhancement (ADE) of infection is one of the biggest concerns in terms of not only the antibody reaction to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) upon reinfection with the virus but also the reaction to COVID-19 vaccines. In this study, we evaluated ADE of infection by using COVID-19 convalescent-phase plasma and BHK cells expressing human Fcγ receptors (FcγRs). We found that FcγRIIA and FcγRIIIA mediated modest ADE of infection against SARS-CoV-2. Although ADE of infection was observed in monocyte-derived macrophages infected with SARS-CoV-2, including its variants, proinflammatory cytokine/chemokine expression was not upregulated in macrophages. SARS-CoV-2 infection thus produces antibodies that elicit ADE of infection, but these antibodies do not contribute to excess cytokine production by macrophages. <b>IMPORTANCE</b> Viruses infect cells mainly via specific receptors at the cell surface. Antibody-dependent enhancement (ADE) of infection is an alternative mechanism of infection for viruses to infect immune cells that is mediated by antibodies and IgG receptors (FcγRs). Because ADE of infection contributes to the pathogenesis of some viruses, such as dengue virus and feline coronavirus, it is important to evaluate the precise mechanism of ADE and its contribution to the pathogenesis of SARS-CoV-2. Here, using convalescent-phase plasma from COVID-19 patients, we found that two types of FcγRs, FcγRIIA and FcγRIIIA, mediate ADE of SARS-CoV-2 infection. Although ADE of infection was observed for SARS-CoV-2 and its recent variants, proinflammatory cytokine production in monocyte-derived macrophages was not upregulated. These observations suggest that SARS-CoV-2 infection produces antibodies that elicit ADE of infection, but these antibodies may not be involved in aberrant cytokine release by macrophages during SARS-CoV-2 infection.