gebhart/patrepeval huggingface dataset:
A proteomics analysis of CK2β(−/−) C2C12 cells provides novel insights into the biological functions of the non‐catalytic β subunit (2019)

The acronym CK2 (derived from the misnomer 'casein kinase-2') denotes a pleiotropic acidophilic protein kinase implicated in a plethora of cellular functions, whose abnormally high expression correlates with malignancy. CK2 holoenzyme is composed of two catalytic (α and/or α') and two noncatalytic β-subunits. The β-subunits are not responsible for either activation or inactivation of the catalytic ones. Hence, to gain additional information about the roles of the individual CK2 subunits, we have generated C2C12 myoblasts entirely devoid either of both catalytic subunits, or of the β-subunit. Here, we show that while CK2α/α'<sup>(-/-)</sup> cells grow similarly to wild-type cells, the growth of CK2β<sup>(-/-)</sup> cells is severely impaired, consistent with the hypothesis that not all cellular functions of the β-subunit are mediated by CK2 holoenzyme. To get a deeper insight into the functional implications of the β-subunit, a quantitative proteomics study of CK2β<sup>(-/-)</sup> cells was performed, leading to the identification and quantification of more than 1200 proteins. Of these, 187 showed a significantly altered expression (fold change ≥ 1.5 or ≤ -1.5) as compared to wild-type cells. A functional analysis of these proteins discloses the implication of CK2β in many processes, for example, cell cycle, proliferation, transport, metabolic processes, etc., and in some of which the catalytic subunits of CK2 do not seem to play a relevant role. On the other hand, the pool of ecto-CK2 is not apparently affected by the lack of the β-subunit. Collectively, our data corroborate the concept that the cellular functions of the β-subunit of CK2 are partially independent of CK2 holoenzyme.
Real-time aberration correction using phase diversity on the IBM SP2 parallel computer (1996)

Optical aberrations are characterized by orthogonal basis functions composed of discretized Zernike polynomials. The coefficients associated with each Zemike polynomial can be measured using a Phase Diversity wave front sensing technique. Nonlinear optimization techniques are utilized to calculate the Zernike coefficients in a serial manner. Even though this traditional method is attractive, it is computationally a very formidable task to calculate several Zernike coefficients for a given system. Hence the method is not applicable in a real time image reconstruction scheme. In this paper we first show that each Zemike coefficient can be calculated independently in a parallel fashion from each other. Our method uses nonlinear optimization of a single variable only. We use a modified Gonsalves error metric function involving only a single unknown aberration coefficient. Next, we describe an implementation of the algorithm on the IBM SP2 parallel computer. We used the PVM software for parallelizing the computational tasks across the processors in a master/slave fashion. We will show that the computation can be performed in an efficient manner using this strategy. 

Key Words: optical aberration; Zernike polynomials; Zernike coefficients; phase diversity; parallel computation
Modelling the drainage evolution of a river–shelf system forced by Quaternary glacio‐eustasy (2002)

ABSTRACT The Quaternary glaciations had a profound impact on the geomorphology and stratigraphy of passive continental margins. The challenge is to resolve the contributions of the main forcing controls relative sea‐level change and sediment flux. The key to answer this question is to understand the interaction between the marine and terrestrial environments, where river dynamics play an essential role. A comprehensible three‐dimensional numerical model is presented in order to investigate quantitatively the behaviour of river–shelf sedimentary systems under glacio‐eustatic conditions. Distinctive features observed in the model results include river avulsion, delta‐lobe switching, incision and knickpoint migration. An important event in the development of the modelled river–shelf system is the establishment of a direct and inextricable link between the drainage basin and the depocentre on the shelf edge, thereby bypassing the exposed shelf. This is termed as ‘drainage connection’. In the model, the timing of drainage connection occurs over a broad interval when the model run is repeated many times with small differences in the initial topography, reflecting the sensitivity of the system to its initial state. It demonstrates the inherent variability in the evolution of a sedimentary system as a consequence of non‐linear behaviour. A statistical approach to modelling is suggested in order to deal with this problem.
Pumping Effect in an Axially Vibrating Choke Nozzle. Pump Performance. (1995)

A newly developed pumping system is presented. The pumping effect was experimentally obtained using a vibrating choke nozzle in a stationary liquid. The relation-ship between pump performance and the input vibration conditions was investigated. By the flow visualization of inflow and outflow bubbles, the flow mechanism in the actual pump operation was investigated. It has been confirmed that this pumping effect can be utilized in actual pump machinery.
Pulsed Sonoelectrochemical Synthesis of Cadmium Selenide Nanoparticles (1999)

Powders of CdSe nanoparticles were prepared by a pulsed sonoelectrochemical technique. The crystal size could be varied from X-ray amorphous up to 9 nm (sphalerite phase) by controlling the various electrodeposition and sonic parameters. The mechanisms for the effects of the various parameters on particle size are discussed. Optical properties of the powders were measured by diffuse reflection spectroscopy and the measured increase in band gap due to size quantization correlated with particle size.
Fundamentals of configuration methodology: aligning customer requirements into design philosophy (2016)

The objective of this paper is to introduce a methodological approach with the view to elaborate the concept of configuration process applicable to develop customised product. This preliminary configuration process will lead to offer true customer value and achieve superior competitive advantage. In this research, an information and communication technology-based configuration system is presented that might contribute to reduce product development lead time and faster sales-delivery process. It is believed that the illustrated configuration framework will bridge the gap between the manufacturers and customers to develop customer-satisfied product variants that consequently fulfil business target in terms of earning more revenues. The configuration framework as outlines in this research contributes to both product design and manufacturing perspectives and supports manufacturing firms for achieving product customisation strategy in upstream and downstream of developmental phases. The proposed framework is also validated by implementing the concept within a case company's demo configuration system. This paper is concluded after defining the research limitations and identifying future research potentials.
Anisotropic Nanoparticle Complementarity in DNA-Mediated Co-crystallization* (2020)

Whether two species will co-crystallize depends on the chemical, physical and structural complementarity of the interacting components. Here, by using DNA as a surface ligand, we selectively 616co-crystallize mixtures of two different anisotropic nanoparticles and systematically investigate the effects of nanoparticle size and shape complementarity on the resultant crystal symmetry, microstrain, and effective “DNA bond” length and strength. We then use these results to understand a more complicated system where both size and shape complementarity change, and where one nanoparticle can participate in multiple types of directional interactions. Our findings offer improved control of nonspherical nanoparticles as building blocks for the assembly of sophisticated macroscopic materials, and provide a framework to understand complementarity and directional interactions in DNA-mediated nanoparticle crystallization.
A fourth level of regulation of PEP synthetase in Escherichia coli; implications of ADP-dependent inactivation (2011)

In Escherichia coli, phosphoenolpyruvate synthetase (PEPS) catalyzes the conversion of pyruvate to phosphoenolpyruvate (PEP). The enzyme is regulated at four levels: it is regulated at the level of transcription by the carbon source available for growth, by regulation of mRNA stability, by metabolic intermediates, and, by a recently discovered phosphorylation/ dephosphorylation mechanism. This manuscript reviews our current understanding of the four levels of regulation of the peps gene and its gene product and reports on recent advances made in our understanding of the post-translational regulation of the protein. A model is proposed that summarizes the control of pyruvate metabolism in E. coli (and other bacterial species possessing PEP synthetase or pyruvate, orthophosphate dikinase); whether pyruvate is used for the generation of ATP or whether pyruvate is converted to PEP for use in gluconeogenesis, aromatic amino acid synthesis and other anabolic pathways. Finally, we provide some suggestions regarding the use of PEPS in the biotechnology industry based on our understanding of the regulation of the enzyme.
Neue Technik zur variablen Spritzmitteldosierung (2015)

Am Institut für Agrartechnik Potsdam-Bornim (ATB) wurde ein Sensor zur Pflanzenmasseerfassung entwickelt, ein weiterer Sensor zur Unkrauterkennung befindet sich in Erbrobung. Beide ensoren erfassen während der Fahrt kleinräumige Heterogenitäten und ermöglichen durch unmittelbare Signalverarbeitung die Anpassung der Spritzmittelmenge von Fungiziden und Herbiziden in Echtzeit. Der hierführ erforderliche breite Regelbereich kann durch eine neue Düsentechnik realisiert werden. Im Beitrag wird auf das Bus-System zur Informationsübertragung und das Kennlinienfeld des VarioSelect Düsensystems eingegangen.
Statistical Analysis and Process Variation-Aware Routing and Skew Assignment for FPGAs (2008)

With constant scaling of process technologies, chip design is becoming increasingly difficult due to process variations. The FPGA community has only recently started focusing on the effects of variations. In this work we present a statistical analysis to compare the effects of variations on designs mapped to FPGAs and ASICs. We also present CAD and architecture techniques to mitigate the impact of variations. First we present a variation-aware router that optimizes statistical criticality. We then propose a modification to the clock network to deliver programmable skews to different flip-flops. Finally, we combine the two techniques and the result is a 9x reduction in yield loss that translates to a 12% improvement in timing yield. When the desired timing yield is set to 99%, our combined statistical routing and skew assignment technique results in a delay improvement of about 10% over a purely deterministic approach.
FEM-Simulation and Experimental Realization of Low-Cost Electrowetting Actuators for a Flexible Microfluidic Pixel (2017)

We investigate and characterize three different fabrication methods facilitating low-cost electrowetting-on-dielectric (EWOD) structures. EWOD allows setting fluid droplets in motion by electrically altering the surface tension equilibrium at the triple contact line. We present a fabrication method for flexible EWOD structures by screen printing a transparent and conducting poly (3, 4-ethylenedioxythiophene) polystyrene sulfonate (PDOT:PSS) polymer on polyethylene terephthalate (PET) foil. As a demonstrator for applications, i.e., a flexible microfluidic EWOD display cell is simulated using FEM and characterized in terms of feasibility and response speed for various pixel scaling. The accordingly fabricated microfluidic pixel serves as a basis cell for a bendable and flexible EWOD cell multigrid, where all pixels are directly addressable.
Novel UAS Propeller Design Part 2: Design Hub and Tip Angle of Attack Sensitivity of UAS Propellers Designed for Minimum Induced Drag (2022)

Abstract Increased interest in eVTOL (electronic vertical take-off and landing) vehicles is growing. These vehicles will become urban air taxis and delivery vehicles, reducing the time involved for moving people and goods in the cities. There is also growth in the small Unmanned Aircraft System (sUAS). The propulsion system for both vehicles use an electric motor with propellers. These vehicles need propellers which are more efficient and have reduced noise generation if they are to coexist in either an urban environment or be used on ISR missions. Previous studies show that a propeller designed for minimum induced drag using a 50% “hub” break with a “tip” break of 90% leading to zero tip thrust loading results in a propeller that is both quieter and more aerodynamically efficient. This design incorporates a constant angle of attack (AOA) from the hub to an r/R of 50% where the section propeller thrust loading then dropped to an AOA with zero lift at an r/R of 90%. AOA sensitivity of both the hub and the tip are studied. Using a hub AOA lower than the value for Cl/Cd max can result in an mechanical power reduction of 6.4% compared to a commercial propeller. A slightly less negative tip AOA than zero lift will also lead to the lowest mechanical power required. However, if a lower sound pressure level is desired, then, for the lower hub angles of attack, a tip angle of attack slightly more negative than zero lift should be used, resulting in up to a 7.8% reduction in SPL. As seen in the data, there exists a tradeoff with between lower aerodynamic power and lower SPL using various combinations of hub and tip angles of attack.
Imaging of melanin distribution using multiphoton autofluorescence decay curves (2009)

Our study confirms that FLIM can non-invasively provide data of the melanin distribution with almost the same quality as the conventional Fontana-Masson staining method, and demonstrates that FLIM is useful for in vivo observation of melanin granules in human skin.
Combined Analysis of Plasma Amphiregulin and Heregulin Predicts Response to Cetuximab in Metastatic Colorectal Cancer (2015)

A subgroup of CRC patients with high amphiregulin and low heregulin respond to cetuximab therapy better than other patients.
ChemInform Abstract: Key Study on the Potential of Hydrazine Bisborane for Solid‐ and Liquid‐State Chemical Hydrogen Storage. (2015)

Abstract The title compound, N 2 H 4 (BH 3 ) 2 , is prepared from a mixture of freshly ground [N 2 H 5 ][HSO 4 ] and NaBH 4 in THF (Ar‐filled glovebox, round‐bottom flask, 40 °C, 42—90 h, 87% yield).
Effects of oxygen and nutrients limitation on ajmalicine production and related enzyme activities in high density cultures of Catharanthus roseus (1994)

Oxygen and nutrient limitation was investigated in order to identify the origin of a lower specific ajmalicine production in Catharanthus roseus cultures at high cell densities in an induction medium. The effect of oxygen limitation was explored by comparing two identically aerated and agitated high cell density bioreactor cultures with dissolved oxygen (DO) concentration of 15% and 85% of air saturation, with respect to alkaloid formation and related enzymes activities. Oxygen had an evident effect on ajmalicine production: in the high DO cultures production was more than 5 times higher than in the low DO cultures. The difference in ajmalicine production between high and low DO could not be explained by the enzyme activity profiles. Moreover, the productivity in the high density culture could not restored to the level of a low density culture (at a high DO) by increasing the DO alone. The effect of nutrient limitation was studied with response surface methodology in shake flask cultures. Nutrient limitation could not be demonstrated to be responsible for the productivity loss. Alkaloid and enzyme measurements in the shake flask cultures supported previous findings that the tryptamine pathway may regulate alkaloid production, provided that the terpenoid pathway is sufficiently active. (c) 1994 John Wiley & Sons, Inc.
[Dental pain and cardiac pain]. (1990)

Some aching troubles encountered in heart disease can affect the jaw and patients can visit a dentist for this reason. The severity of this affection needs a quick diagnostic for preserving the patient's life.
Electrostatics and the Lab on a Chip (2004)

At the heart of the laboratory on a chip are chemical or biochemical probes designed to detect specific molecules or reaction products. For these probes to perform their function, a microfluidic plumbing is needed to accept samples, then manipulate, dispense, and distribute tiny liquid volumes on the chip. The most promising mechanisms for handling such small quantities of liquid -- from microliters down to tens of picoliters -- are all electrostatic, e.g., electrocapillarity, electroconvection, electrophores is, electro-osmosis, and dielectrophoresis. Despite years of study of these effects, the body of existing work is an imperfect guide to their effective exploitation in microfluidic applications. Attempts to harness electrostatic forces in structures <100 microns in size often encounter unanticipated behavior. Such surprises can be attributed to dramatic changes in the relative influences of the various competitive forces (e.g., viscous shear, surface wetting, and capillarity). In this paper, some of the more promising avenues of research on electric-fiel dmediated microfluidics are examined. To explicate why and when electrostatic forces can be advantageous in the lab on a chip, Trimmer’s bracket notation is invoked to perform an investigation of the scaling laws for microfluidic systems. The methodology facilitates examination of the effects of device size on throughput, processing time, temperature rise, and other important measures of system performance.
Unification of compressed imaging techniques in the microwave range and deconvolution strategy (2015)

International audience
Nonintegrating Foamy Virus Vectors (2010)

Foamy viruses (FVs), or spumaviruses, are integrating retroviruses that have been developed as vectors. Here we generated nonintegrating foamy virus (NIFV) vectors by introducing point mutations into the highly conserved DD35E catalytic core motif of the foamy virus integrase sequence. NIFV vectors produced high-titer stocks, transduced dividing cells, and did not integrate. Cells infected with NIFV vectors contained episomal vector genomes that consisted of linear, 1-long-terminal-repeat (1-LTR), and 2-LTR circular DNAs. These episomes expressed transgenes, were stable, and became progressively diluted in the dividing cell population. 1-LTR circles but not 2-LTR circles were found in all vector stocks prior to infection. Residual integration of NIFV vectors occurred at a frequency 4 logs lower than that of integrase-proficient FV vectors. Cre recombinase expressed from a NIFV vector mediated excision of both an integrated, floxed FV vector and a gene-targeted neo expression cassette, demonstrating the utility of these episomal vectors. The broad host range and large packaging capacity of NIFV vectors should make them useful for a variety of applications requiring transient gene expression.
Genetic, Physical, and Informatics Resources for Maize. On the Road to an Integrated Map (2002)

Maize ( Zea mays ) is among the most important crop plants in the world. For any crop plant, an integrated genetic and physical map serves as the foundation for numerous studies, especially those aimed at improving the agronomic characteristics of the plant. Once a phenotypically defined locus
SAM: A Semantic-Aware Multi-tiered Source De-duplication Framework for Cloud Backup (2010)

Existing de-duplication solutions in cloud backup environment either obtain high compression ratios at the cost of heavy de-duplication overheads in terms of increased latency and reduced throughput, or maintain small de-duplication overheads at the cost of low compression ratios causing high data transmission costs, which results in a large backup window. In this paper, we present SAM, a Semantic-Aware Multitiered source de-duplication framework that first combines the global file-level de-duplication and local chunk-level deduplication, and further exploits file semantics in each stage in the framework, to obtain an optimal tradeoff between the deduplication efficiency and de-duplication overhead and finally achieve a shorter backup window than existing approaches. Our experimental results with real world datasets show that SAM not only has a higher de-duplication efficiency/overhead ratio than existing solutions, but also shortens the backup window by an average of 38.7%.
Improved Algorithms for Two Energy-Optimal Routing Problems in Ad-Hoc Wireless Networks (2016)

We study two problems of assigning transmission power to the nodes of ad hoc wireless networks to minimize total power consumption while satisfying certain connectivity constraints. The first problem requires to establish k node-disjoint paths from a given source to a given destination. Our new algorithm works for the most general cost model, and returns an optimal solution in time O(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) (where n is the number of nodes), improving the running time over the previously published algorithm by a factor of k. The second problem assumes that the power requirement between any two nodes is symmetric, and that there are exactly two possible power levels, one of which is negligible. A source is given and all the nodes in the network must be reachable from the source (unidirectional links allowed for broadcast). We obtain a (4 + ln n)-approximation algorithm, while the best published approximation ratio is 2 (1+ln(n-1)). It was also known that no approximation ratio better than O(ln n) is possible unless P = NP.
Free Convex Algebraic Geometry (2013)

This chapter is a tutorial on techniques and results in free convex algebraic geometry and free real algebraic geometry (RAG). The term free refers to the central role played by algebras of noncommutative polynomials R in free (freely noncommuting) variables x=(x_1,...,x_g). The subject pertains to problems where the unknowns are matrices or Hilbert space operators as arise in linear systems engineering and quantum information theory. The subject of free RAG flows in two branches. One, free positivity and inequalities is an analog of classical real algebraic geometry, a theory of polynomial inequalities embodied in algebraic formulas called Positivstellensätze; often free Positivstellensätze have cleaner statements than their commutative counterparts. Free convexity, the second branch of free RAG, arose in an effort to unify a torrent of ad hoc optimization techniques which came on the linear systems engineering scene in the mid 1990's. Mathematically, much as in the commutative case, free convexity is connected with free positivity through the second derivative: A free polynomial is convex if and only if its Hessian is positive. However, free convexity is a very restrictive condition, for example, free convex polynomials have degree 2 or less. This article describes for a beginner techniques involving free convexity. As such it also serves as a point of entry into the larger field of free real algebraic geometry.
Electrochemistry and <i>In Situ</i> EPR Spectroelectrochemistry of Poly(3,4-ethylenedithiothiophene) (2013)

Polymer films of poly(3,4-ethylenedithiothiophene) obtained by electrochemical oxidative polymerisation of the corresponding monomer have been investigated. p-Doping process of the polymer was characterized by in situ EPR spectroelectrochemisty. Compared to its close relative – PEDOT, the polymer features two distinct voltammetric peaks. The results of our studies indicate that both represent faradaic processes and that each manifests generation of charge carriers in the polymer.