gebhart/patrepeval huggingface dataset:
Big Data Processing: Scalability with Extreme Single-Node Performance (2017)

Contemporary frameworks for data analytics, such as Hadoop, Spark, and Flink seek to allow applications to scale performance flexibly by adding hardware nodes. However, we find that when the computation on each individual node is optimized, peripheral activities such as creating data partitions, messaging and synchronizing between nodes diminish the speedup obtainable from adding more hardware. We analyze workloads which distribute operations on correlated data-such as joins and aggregation found in SQL, text similarity searches, and image disparity computations. After optimizing computation on efficient, custom processors, we discover challenges in scaling the applications to hundreds of nodes on a high-bandwidth network. We then describe techniques to overcome these challenges towards prototyping a 512-node system which is able to execute SQL queries offloaded from a commercial database, and outperform SQL-on-hadoop and traditional parallel RDBMS executions by 173x and 7x respectively.
INTERACTIVE GRAPHICAL EXPLORATION OF MULTIDIMENSIONAL NONLINEAR DYNAMICAL SYSTEMS (1992)

This paper discusses the application of an inherently three-dimensional graphical representation tool, isosurfaces, as a means to interactively explore and visualize the attractors of a nonlinear dynamical system with a fifteen-dimensional parameter space. A program has been written which allows the scientist to interactively select and visualize three-dimensional sub-spaces of the fifteen-dimensional parameter space. The dynamical system used to illustrate these concepts is a discrete-time, nonlinear, three-nation Richardson model with economic constraints. This dynamical system, which models the shifting alliances of nations in an arms race, maps an initial point in the unit cube to another point in the unit cube after multiple iterations of the model functions. Using an isosurface function on the resulting volumetric data set, surfaces indicating the changing alliances of nations are generated and rendered.
Adaptive frequency prior for frequency selective reconstruction of images from non-regular subsampling (2016)

Image signals typically are defined on a rectangular two-dimensional grid. However, there exist scenarios where this is not fulfilled and where the image information only is available for a non-regular subset of pixel position. For processing, transmitting or displaying such an image signal, a re-sampling to a regular grid is required. Recently, Frequency Selective Reconstruction (FSR) has been proposed as a very effective sparsity-based algorithm for solving this under-determined problem. For this, FSR iteratively generates a model of the signal in the Fourier-domain. In this context, a fixed frequency prior inspired by the optical transfer function is used for favoring low-frequency content. However, this fixed prior is often too strict and may lead to a reduced reconstruction quality. To resolve this weakness, this paper proposes an adaptive frequency prior which takes the local density of the available samples into account. The proposed adaptive prior allows for a very high reconstruction quality, yielding gains of up to 0.6 dB PSNR over the fixed prior, independently of the density of the available samples. Compared to other state-of-the-art algorithms, visually noticeable gains of several dB are possible.
High-Stability Bi-Layer Films Incorporated with Liposomes @Anthocyanin/Carrageenan/Agar for Shrimp Freshness Monitoring (2023)

High-stability bi-layer films were prepared by incorporating anthocyanin-loaded liposomes into carrageenan and agar (A-CBAL) for non-destructive shrimp freshness monitoring. The encapsulation efficiency of the anthocyanin-loaded liposomes increased from 36.06% to 46.99% with an increasing ratio of lecithin. The water vapor transmission (WVP) of the A-CBAL films, with a value of 2.32 × 10<sup>-7</sup> g · m<sup>-1</sup> · h<sup>-1</sup> · pa<sup>-1</sup>, was lower than that of the film with free anthocyanins (A-CBA). The exudation rate of the A-CBA film reached 100% at pH 7 and pH 9 after 50 min, while the A-CBAL films slowed down to a value lower than 45%. The encapsulation of anthocyanins slightly decreased the ammonia sensitivity. Finally, the bi-layer films with liposomes successfully monitored shrimp freshness with visible color changes to the naked eye. These results indicated that films with anthocyanin-loaded liposomes have potential applications in high-humidity environments.
Better lime purification of sugar beet juice obtained by low temperature aqueous extraction assisted by pulsed electric field (2011)

Purification of the sugar beet juices obtained by novel low temperature extraction (at 30 °C) assisted by pulsed electric field (PEF) and conventional high temperature extraction (at 70 °C) was done by the method of lime-carbon dioxide treatment. The total concentration of lime used for the purification was varied from 6 to 15 kg of CaO/m3 of the juice. Filtration properties of the juices of first carbonation, as well as purity and coloration of the final thin juices, were compared. It was observed that purification of the juice extracted at 30 °C results in faster filtration of the juice of first carbonation and lower coloration of the final thin juice as compared to the juice obtained by means of purification of the juice extracted at 70 °C. It suggests that the quantity of CaO required for the efficient juice purification may be decreased from 15 kg/m3 (for the juice extracted at 70 °C without PEF treatment) to approx. 8 kg/m3 (for the juice obtained by PEF-assisted extraction at 30 °C).
Synergistic Action of Nitric Oxide Release from Murine Macrophages Caused by Group B Streptococcal Cell Wall and β‐Hemolysin/Cytolysin (2002)

Group B streptococcus (GBS) is the leading cause of sepsis in neonates. Nitric oxide (NO) release plays a role in the hypotension that characterizes septic shock. It has been shown that GBS beta-hemolysin/cytolysin (beta-h/c) stimulates the transcription of inducible NO synthase (iNOS) in murine macrophages via intracellular pathways similar to those that mediate lipopolysaccharide-induced iNOS activation. Here, it is demonstrated that the GBS cell wall and beta-h/c act synergistically to induce iNOS in interferon (IFN)-gamma-primed [corrected] RAW 264.7 murine macrophages. In nonprimed macrophages, combined activation by the GBS cell wall plus beta-h/c is necessary to induce an NO response, which indicates that both virulence factors cooperate to substitute for the priming signal typically provided by IFN-gamma [corrected].
Aspergillus lentulus sp. nov., a New Sibling Species of A. fumigatus (2005)

In a prior study, we identified seven clinical isolates of an Aspergillus sp. that were slow to sporulate in multiple media and demonstrated decreased in vitro susceptibilities to multiple antifungals, including amphotericin B, itraconazole, voriconazole, and caspofungin. These isolates were initially considered to be variants of Aspergillus fumigatus because of differences in mitochondrial cytochrome b sequences and unique randomly amplified polymorphic DNA PCR patterns (S. A. Balajee, M. Weaver, A. Imhof, J. Gribskov, and K. A. Marr, Antimicrob. Agents Chemother. 48: 1197-1203, 2004). The present study was performed to clarify the taxonomic status of these organisms by phylogenetic analyses based on multilocus sequence typing of five genes (the beta-tubulin gene, the rodlet A gene, the salt-responsive gene, the mitochondrial cytochrome b gene, and the internal transcribed spacer regions). Results revealed that four of the seven variant isolates clustered together in a clade very distant from A. fumigatus and distinct from other members of the A. fumigatus group. This new clade, consisting of four members, was monophyletic with strong bootstrap support when the protein-encoding regions were analyzed, indicating a new species status under the phylogenetic species concept. Phenotype studies revealed that the variant isolate has smaller conidial heads with diminutive vesicles compared to A. fumigatus and is not able to survive at 48 degrees C. Our findings suggest the presence of a previously unrecognized, potentially drug-resistant Aspergillus species that we designate A. lentulus.
Electrical Stimulation of the Retina to Produce Artificial Vision (2016)

Retinal prostheses aim to restore vision to blind individuals suffering from retinal diseases such as retinitis pigmentosa and age-related macular degeneration. These devices function by electrically stimulating surviving retinal neurons, whose activation is interpreted by the brain as a visual percept. Many prostheses are currently under development. They are categorized as epiretinal, subretinal, and suprachoroidal prostheses on the basis of the placement of the stimulating microelectrode array. Each can activate ganglion cells through direct or indirect stimulation. The response of retinal neurons to these modes of stimulation are discussed in detail and are placed in context of the visual percept they are likely to evoke. This article further reviews challenges faced by retinal prosthesis and discusses potential solutions to address them.
Towards physical layout of assembly lines (1999)

info:eu-repo/semantics/published
In vitro rapid inactivation of SARS-CoV-2 by visible light photocatalysis using boron-doped bismuth oxybromide (2021)

Abstract Inactivation of SARS-CoV-2 in wastewater and on surfaces is critical to prevent the fecal-oral and fomite transmission, respectively. We hypothesized that visible light active photocatalysts could dramatically enhance the rate or extent of virus inactivation and enable the use of visible light rather than shorter wavelength ultraviolet light. A novel visible light active photocatalyst, boron-doped bismuth oxybromide (B-BiOBr), was synthesized and tested for its SARS-CoV-2 inactivation towards Vero E6 cell lines in dark and under irradiation at 426 nm by a light emitting diode (LED) in water. SARS-CoV-2 inactivation in the presence of B-BiOBr (0.8 g/L) under LED irradiation reached 5.32-log in 5 min, which was 400 to 10,000 times higher than those achieved with conventional photocatalysts of tungsten or titanium oxide nanomaterials, respectively. Even without LED irradiation, B-BiOBr inactivated 3.32-log of SARS-CoV-2 in the dark due to the ability of bismuth ions interfering with the SARS-CoV-2 helicase function. LED irradiation at 426 nm alone, without the photocatalyst, contributed to 10% of the observed inactivation and was attributed to production of reactive oxygen species due to blue-light photoexcitation of molecules in the culture media, which opens further modes of action to engineer disinfection strategies. The visible light active B-BiOBr photocatalyst, with its rapid SARS-CoV-2 inactivation in the presence and absence of light, holds tremendous opportunities to build a healthy environment by preventing the fecal-oral and fomite transmission of emerging pathogens.
Efficient Nonlinear Frequency Conversion with Maximal Atomic Coherence (1996)

We demonstrate efficient nonlinear frequency conversion in atomic Pb vapor under conditions where the linear susceptibility and the effective nonlinear susceptibility are of the same order. This is accomplished by using electromagnetically induced transparency to prepare a near-maximal atomic coherence on a Raman transition. This strongly driven transition is used to convert an intense laser beam from 425 to 293 nm with an efficiency of $\ensuremath{\sim}40%$.
Degradation of Components of the Lpt Transenvelope Machinery Reveals LPS-Dependent Lpt Complex Stability in Escherichia coli (2021)

Lipopolysaccharide (LPS) is a peculiar component of the outer membrane (OM) of many Gram-negative bacteria that renders these bacteria highly impermeable to many toxic molecules, including antibiotics. LPS is assembled at the OM by a dedicated intermembrane transport system, the Lpt (LPS transport) machinery, composed of seven essential proteins located in the inner membrane (IM) (LptB<sub>2</sub>CFG), periplasm (LptA), and OM (LptDE). Defects in LPS transport compromise LPS insertion and assembly at the OM and result in an overall modification of the cell envelope and its permeability barrier properties. LptA is a key component of the Lpt machine. It connects the IM and OM sub-complexes by interacting with the IM protein LptC and the OM protein LptD, thus enabling the LPS transport across the periplasm. Defects in Lpt system assembly result in LptA degradation whose stability can be considered a marker of an improperly assembled Lpt system. Indeed, LptA recruitment by its IM and OM docking sites requires correct maturation of the LptB<sub>2</sub>CFG and LptDE sub-complexes, respectively. These quality control checkpoints are crucial to avoid LPS mistargeting. To further dissect the requirements for the complete Lpt transenvelope bridge assembly, we explored the importance of LPS presence by blocking its synthesis using an inhibitor compound. Here, we found that the interruption of LPS synthesis results in the degradation of both LptA and LptD, suggesting that, in the absence of the LPS substrate, the stability of the Lpt complex is compromised. Under these conditions, DegP, a major chaperone-protease in <i>Escherichia coli</i>, is responsible for LptD but not LptA degradation. Importantly, LptD and LptA stability is not affected by stressors disturbing the integrity of LPS or peptidoglycan layers, further supporting the notion that the LPS substrate is fundamental to keeping the Lpt transenvelope complex assembled and that LptA and LptD play a major role in the stability of the Lpt system.
Three-Way Cell-Based Screening of Antistress Compounds: Identification, Validation, and Relevance to Old-Age-Related Pathologies (2023)

A variety of environmental stress stimuli have been linked to poor quality of life, tissue dysfunctions, and ailments including metabolic disorders, cognitive impairment, and accelerated aging. Oxidative, metal, and hypoxia stresses are largely associated with these phenotypes. Whereas drug development and disease therapeutics have advanced remarkably in last 3 decades, there are still limited options for stress management. Because the latter can effectively decrease the disease burden, we performed cell-based screening of antistress compounds by recruiting 3 chemical models of oxidative (paraquat), metal (cadmium nitrate), or hypoxia (cobalt chloride) stresses. The screening of 70 compounds for their ability to offer protection against oxidative, metal, and hypoxia stresses resulted in the selection of 5 compounds: Withaferin-A (Wi-A), methoxy Withaferin-A (mWi-A), Withanone (Wi-N), triethylene glycol (TEG), and Ashwagandha (Withania somnifera) leaf M2-DMSO extract (M2DM). Molecular assays revealed that whereas stress caused increase in (a) apoptosis, (b) reactive oxygen species accumulation coupled with mitochondrial depolarization, (c) DNA double-strand breaks, and (d) protein aggregation, low nontoxic doses of the selected compounds caused considerable protection. Furthermore, Wi-N, TEG, and their mixture-treated normal human fibroblasts (at young, mature, and senescent stages representing progressively increasing accumulation of stress) showed increase in proliferation. Taken together, these results suggested 3-way (oxidative, metal, and hypoxia) antistress potential of Wi-N and TEG that may be useful for management of environmental and old-age-related pathologies.
Grazing pressure on coral reefs decreases across a wide depth gradient in the Gulf of Aqaba, Red Sea (2009)

Algae are an essential component of healthy coral reefs and serve as the base of the food chain and as a living habitat for numerous organisms. Herbivorous fish play an important role in coral reef ecology by mediating competition between fast-growing algae and relatively slow-growing corals. However, because of diving-related difficulties, the importance of herbivory in deep mesophotic coral reefs (30 to 150 m) remains largely unknown. We examined the relationship between herbivores and algae along a depth gradient down to 65 m, and evaluated grazing pressure along the depth gradient. We visually assessed the abundance of herbivorous fish along the depth gradient and estimated fish biomass. We measured in situ turf algae growth rates and performed experimental assessments of grazing pressure using settlement plates and bioassays. We discovered that, while both algal growth and fish density decrease with depth, the decrease in grazing pressure is steeper, with a consumption of < 20% of turf-algae production at 65 m versus 40 to 60% at depths of 5 to 20 m. Concomitantly, a decrease in fish biomass and density along the depth gradient reduced potential grazing pressure on macroalgae. Our findings suggest a less important role for herbivorous fish in maintaining algal-free substrate for coral recruitment and growth in deep zones compared with the shallow reef.
Lysosome Targeting Chimeras (LYTACs) That Engage a Liver-Specific Asialoglycoprotein Receptor for Targeted Protein Degradation (2020)

&lt;p&gt;Selective protein degradation platforms have afforded new development opportunities for therapeutics and tools for biological inquiry. The first lysosome targeting chimeras (LYTACs) targeted extracellular and membrane proteins for degradation by bridging a target protein to an endogenous lysosome targeting receptor, the cation-independent mannose-6-phosphate receptor (CI-M6PR). Here we developed LYTACs that engage the asialoglycoprotein receptor (ASGPR), a liver-specific lysosomal targeting receptor, to degrade membrane proteins in a tissue-specific manner. We conjugated antibody-based binders targeting cell-surface proteins to a tri-GalNAc motif that engages ASGPR. The resulting LYTACs directed lysosome trafficking of the bound targets and subsequent degradation. Degradation mediated by an EGFR-targeted GalNAc-LYTAC resulted in significant functional effects on the downstream kinase signaling of EGFR compared to canonical inhibition with a monoclonal antibody. Furthermore, we demonstrated that a small target binder, a 3.4 kDa peptide, can be linked to a single tri-GalNAc ligand to degrade integrins and significantly reduce cell proliferation. Site-specific chemical conjugation of one or two tri-GalNAc ligands to antibody scaffolds improved the pharmacokinetic profile of GalNAc-LYTACs &lt;i&gt;in vivo&lt;/i&gt; compared to non-specific chemical conjugation. GalNAc-LYTACs represent an exciting new paradigm for cell-type restricted degradation of proteins.&lt;/p&gt;
Compositional Rate Transient Analysis in Liquid Rich Shale Reservoirs (2016)

Abstract Conventional rate transient analysis (RTA) is based on the solution of single-phase diffusivity equation, derived from mass balance with an assumption that fluid and rock compressibility are small and constant. The conventional technique also provides accurate practical results for gas and black oil reservoirs in engineering applications because (1) the mass balance is conducted at standard conditions of pressure and temperature, and (2) it is assumed that the gas and oil composition remains the same at standard conditions—thus, the viability of volume balance technique. On the other hand, for reservoirs with highly composition-dependent fluids, the invariance of composition at standard conditions is not accurate. For example, oils produced from liquid-rich shale reservoirs exhibit large variation in produced oil and associated gas composition with production time. In this paper we address these issues and present a compositional model for liquid-rich unconventional reservoirs using an improved compositional volume balance technique. Specifically, we reduce the component flow equations to a single pressure equation using partial molar volumes as weighting factors. This pressure equation is the unique feature of this paper and is used to analyze pressure and rate transient tests (RTA) to determine various flow regimes and reservoir properties in liquid-rich shale reservoirs. In addition, the model is an excellent tool to forecast long-term production. The diagnostic models we have generated include: (1) a numerical model of flow for a well that has been stimulated by multi-stage hydraulic factures, and (2) an analytical composition-dependent model for the rate transient analysis (RTA) of light oils. The numerical model is a 2-D, three-phase, dual-porosity simulator, which uses compositional volume balance method. The algorithm decouples the hydrocarbon and aqueous phases in the matrix and fracture which reveals the clarity of underlying mass transport concepts and ease of coding. Because of the explicit nature of the phase saturation calculations, we introduce a molar mass balance correction term to minimize the material balance errors of the computation. Furthermore, we validated our partial molar volume algorithm against published experimental data of Wu and Ehrlich (1973) and with the CMG GEM compositional simulator. Finally, unsteady state permeability measurements of several unconventional shale reservoirs were performed. These measurements show that tighter core with abundant micro and nano fractures exhibit a more stress dependent matrix permeability characteristics.
Formation of Long-Lived Color Centers for Broadband Visible Light Emission in Low-Dimensional Layered Perovskites (2017)

We investigate the origin of the broadband visible emission in layered hybrid lead-halide perovskites and its connection with structural and photophysical properties. We study ⟨001⟩ oriented thin films of hexylammonium (HA) lead iodide, (C<sub>6</sub>H<sub>16</sub>N)<sub>2</sub>PbI<sub>4</sub>, and dodecylammonium (DA) lead iodide, (C<sub>12</sub>H<sub>28</sub>N)<sub>2</sub>PbI<sub>4</sub>, by combining first-principles simulations with time-resolved photoluminescence, steady-state absorption and X-ray diffraction measurements on cooling from 300 to 4 K. Ultrafast transient absorption and photoluminescence measurements are used to track the formation and recombination of emissive states. In addition to the excitonic photoluminescence near the absorption edge, we find a red-shifted, broadband (full-width at half-maximum of about 0.4 eV), emission band below 200 K, similar to emission from ⟨110⟩ oriented bromide 2D perovskites at room temperature. The lifetime of this sub-band-gap emission exceeds that of the excitonic transition by orders of magnitude. We use X-ray diffraction measurements to study the changes in crystal lattice with temperature. We report changes in the octahedral tilt and lattice spacing in both materials, together with a phase change around 200 K in DA<sub>2</sub>PbI<sub>4</sub>. DFT simulations of the HA<sub>2</sub>PbI<sub>4</sub> crystal structure indicate that the low-energy emission is due to interstitial iodide and related Frenkel defects. Our results demonstrate that white-light emission is not limited to ⟨110⟩ oriented bromide 2D perovskites but a general property of this class of system, and highlight the importance of defect control for the formation of low-energy emissive sites, which can provide a pathway to design tailored white-light emitters.