gebhart/patrepeval huggingface dataset:
Comparative expression profiling in primary and immortalized endothelial cells: changes in gene expression in response to hydroxy methylglutaryl-coenzyme A reductase inhibition (2006)

Immortalized cell lines offer significant logistical advantages over primary cells when used for in-vitro studies. Immortalized cells may, however, exhibit important differences relative to their primary cell counterparts. In this study, microarrays were used to make a genome-wide comparison between primary human umbilical vein endothelial cells (HUVECs) and EA.hy926, an immortalized HUVEC cell line, in their baseline properties and in their response to inhibition of the mevalonate pathway with an inhibitor of hydroxy methylglutaryl-coenzyme A reductase (statin). HUVECs and EA.hy926 were incubated with control medium, atorvastatin, mevalonate, or a combination of atorvastatin and mevalonate for 24 h. Gene expression profiles were obtained in duplicates using Affymetrix Human Genome U133A 2.0 arrays (Santa Clara, California, USA). Probe-sets were selected according to the following criteria: a twofold or greater increase/decrease in atorvastatin-treated cells compared with untreated cells; a twofold or greater reversal of the effect of atorvastatin by combined treatment with atorvastatin and mevalonate; no significant change in gene expression in cells treated with mevalonate alone compared with untreated cells. Most genes that were expressed by untreated HUVECs, were also expressed by untreated EA.hy926 cells. EA.hy926 cells, however, constitutively expressed a large number of additional genes, many of which were related to cell cycle control and apoptosis. Atorvastatin induced differential expression (> or = twofold) of 103 genes in HUVECs (10 up, 93 down) and 466 genes in EA.hy926 cells (198 up, 268 down). Applying the above selection criteria, thrombomodulin and tissue plasminogen activator were up-regulated in both cell types, whereas, connective tissue growth factor, thrombospondin-1, and cysteine-rich angiogenic inducer 61 were down-regulated. In conclusion, EA.hy926 cells retain most of the characteristics of endothelial cells under baseline conditions as well as after treatment with atorvastatin. It is necessary, however, to carefully select and validate changes in genes that are the focus of studies when using EA.hy926 cells. While this cell line is highly useful in studies on some genes, including genes encoding molecules involved in regulating thrombohemorrhagic homeostasis, they appear to be less suited for studies focused on other genes, particularly those involved in the regulation of cell proliferation and apoptosis.
Power-efficient Scheduling of Periodic Real-time Tasks on Lightly Loaded Multicore Processors (2012)

본 논문에서는 작업 개수보다 프로세싱 코어 개수가 많은 저부하 멀티코어 프로세서에 적합한 실시간 작업용 저전력 스케쥴링 기법을 제안하였다. 제시된 기법을 시스템상에 존재하는 모든 프로세싱 코어들을 사용하지 않고, 주어진 작업들의 전체 계산량을 고려하여 일부의 프로세싱 코어들만을 사용하고 나머지 사용하지 않는 코어들의 전원을 소등하여 전력소모량을 줄였다. 또한 휴리스틱 기법을 사용하여 주어진 작업들을 프로세싱 코어들에게 빠르게 배치하였다. 마지막을 각각의 프로세싱 코어는 배치된 작업들의 데드라인 모두 만족하면서 전력소모량을 최소화하도록 프로세싱 코어에 적용되는 최적의 클락 주파수를 선택하여 사용하였다. 제시된 스케쥴링 기법과 기존의 프로세싱 코어들을 최대한 많이 사용하는 방법을 비교하는 실험에서, 제시된 기법이 기존 방법의 전력소모량을 최대 78%까지 감소시킴을 확인하였다. In this paper, we propose a power-efficient scheduling scheme for lightly loaded multicore processors which contain more processing cores than running tasks. The proposed scheme activates a portion of available cores and inactivates the other unused cores in order to save power consumption. The tasks are assigned to the activated cores based on a heuristic mechanism for fast task assignment. Each activated core executes its assigned tasks with the optimal clock frequency which minimizes the power consumption of the tasks while meeting their deadlines. Evaluation shows that the proposed scheme saves up to 78% power consumption of the previous method which activates as many processing cores as possible for the execution of the given tasks.
Investigating Slurry Transport Beneath a Wafer during Chemical Mechanical Polishing Processes (2000)

In order to better understand the role of the fluid behavior in chemical mechanical planarization, we measured slurry transport beneath a glass wafer. We quantified the slurry transport using residence time distribution techniques and two measures of slurry transport efficiency, defined as the percentage of new slurry beneath a wafer. Slurry transport efficiency depended on platen speed, flow rate, and the conditioning method. We found that the average fluid residence times under the wafer decreased roughly linearly with platen speed. A threefold increase in platen speed decreased slurry mean residence time by a factor of 3.5. Changing the flow rate from 20 to 50 mL/min decreased the slurry mean residence times by 80%. In situ conditioning generally increased the slurry mean residence times and the amount of slurry mixing. In situ conditioning also decreased gradients in the slurry composition across the wafer. Pad topography had a large effect on the slurry gradients that developed across the wafer. Finally, we found that the slurry mixing history can be accurately modeled using a simple continuous function. © 2000 The Electrochemical Society. All rights reserved.
The Physical Properties of the Cyanophenylcyclohexyl Ethanes (PECH) (1983)

Abstract The physical properties of a new homologous series of stable, low-melting nematic materials, the cyanophenylcyclohexyl ethanes (PECH) are reported and compared with those of other stable, nematic materials. A broad range mixture is reported with a low viscosity, medium birefringence and large positive dielectric anisotropy. This mixture shows a high order parameter which increases the contrast of displays using dissolved pleochroic dyes. A comparison is also made between the structural isomers of PECH and PCH which questions the validity of molecular theories of elastic constants.
Dynamic Compilation of C++ Template Code (2003)

Generic programming using the C++ template facility has been a successful method for creating high‐performance, yet general algorithms for scientific computing and visualization. However, adding template code tends to require more template code in surrounding structures and algorithms to maintain generality. Compiling all possible expansions of these templates can lead to massive template bloat. Furthermore, compile‐time binding of templates requires that all possible permutations be known at compile time, limiting the runtime extensibility of the generic code. We present a method for deferring the compilation of these templates until an exact type is needed. This dynamic compilation mechanism will produce the minimum amount of compiled code needed for a particular application, while maintaining the generality and performance that templates innately provide. Through a small amount of supporting code within each templated class, the proper templated code can be generated at runtime without modifying the compiler. We describe the implementation of this goal within the SCIRun dataflow system. SCIRun is freely available online for research purposes.
The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally (2013)

Despite the importance of maintaining redox homeostasis for cellular viability, how cells control redox balance globally is poorly understood. Here we provide new mechanistic insight into how the balance between reduced and oxidized electron carriers is regulated at the level of gene expression by mapping the regulon of the response regulator ArcA from Escherichia coli, which responds to the quinone/quinol redox couple via its membrane-bound sensor kinase, ArcB. Our genome-wide analysis reveals that ArcA reprograms metabolism under anaerobic conditions such that carbon oxidation pathways that recycle redox carriers via respiration are transcriptionally repressed by ArcA. We propose that this strategy favors use of catabolic pathways that recycle redox carriers via fermentation akin to lactate production in mammalian cells. Unexpectedly, bioinformatic analysis of the sequences bound by ArcA in ChIP-seq revealed that most ArcA binding sites contain additional direct repeat elements beyond the two required for binding an ArcA dimer. DNase I footprinting assays suggest that non-canonical arrangements of cis-regulatory modules dictate both the length and concentration-sensitive occupancy of DNA sites. We propose that this plasticity in ArcA binding site architecture provides both an efficient means of encoding binding sites for ArcA, σ(70)-RNAP and perhaps other transcription factors within the same narrow sequence space and an effective mechanism for global control of carbon metabolism to maintain redox homeostasis.
Structural analysis of sign bridge structures and luminaire supports (2004)

The Wisconsin Department of Transportation has experienced failures of a high-mast luminaire (HML) support structure and a full-span overhead sign support structure. Furthermore, cracking has been found in many sign support structures composed of welded round hollow structural shapes (HSS). The purpose of the research conducted was to provide fatigue life estimates for these structures, which could then shed light onto the causes of the cracking found and the failures experienced. The analytical and experimental effort conducted was also used to establish rational inspection intervals for these structures and recommend changes (as required) to the procedures for design of high-mast luminaire and full-span sign support structures targeted to improve in-service performance.
Xylanase: A promising enzyme (2016)

Xylanase is a naturally occurring enzyme found in microbes and fungi. Xylanase belonging to pentosanases, a class of enzyme which breaks down cell wall matrix of plants breaks down xylan into xylose. Thus this property of xylanase makes it important at commercial level. Recently, xylanases are being produced by the help of genetically modified organisms (bacteria and fungus). Xylanases also find its application in various industries. These include textile and paper industry, beverage industry, bakery industry, pharmaceuticals industry, biofuel production. In this review we are tried to highlight the importance of xylanase at commercial level.
<scp>I</scp>srael the Grammarian (2017)

A survey of the life and works of Israel the Grammarian, a tenth‐century Breton scholar at the court of Æthelstan king of the English.
Plant Defense Stimulation by Natural Isolates of <i>Bacillus</i> Depends on Efficient Surfactin Production (2013)

Some plant-associated Bacillus strains produce induced systemic resistance (ISR) in the host, which contributes to their protective effect against phytopathogens. Little is known about the variety of elicitors responsible for ISR that are produced by Bacillus strains. Working with a particular strain, we have previously identified the surfactin lipopeptide as a main compound stimulating plant immune-related responses. However, with the perspective of developing Bacillus strains as biocontrol agents, it is important to establish whether a central role of surfactin is generally true for isolates belonging to the B. subtilis/amyloliquefaciens complex. To that end, we set up a comparative study involving a range of natural strains. Their secretomes were first tested for triggering early defense events in cultured tobacco cells. Six isolates with contrasting activities were further evaluated for ISR in plants, based both on macroscopic disease reduction and on stimulation of the oxylipin pathway as defense mechanism. A strong correlation was found between defense-inducing activity and the amount of surfactin produced by the isolates. These results support the idea of a widespread role for surfactin as a nonvolatile elicitor formed by B. subtilis/amyloliquefaciens, and screening for strong surfactin producers among strains naturally secreting multiple antibiotics could be an efficient approach to select good candidates as biopesticides.
Proteome Organization in a Genome-Reduced Bacterium (2009)

The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating organisms. To study the basic principles of bacterial proteome organization, we used tandem affinity purification-mass spectrometry (TAP-MS) in a proteome-wide screen. The analysis revealed 62 homomultimeric and 116 heteromultimeric soluble protein complexes, of which the majority are novel. About a third of the heteromultimeric complexes show higher levels of proteome organization, including assembly into larger, multiprotein complex entities, suggesting sequential steps in biological processes, and extensive sharing of components, implying protein multifunctionality. Incorporation of structural models for 484 proteins, single-particle electron microscopy, and cellular electron tomograms provided supporting structural details for this proteome organization. The data set provides a blueprint of the minimal cellular machinery required for life.
Stress birefringent, space-variant wave plates for vortex illumination (2006)

We describe the use of stress birefringence in the creation of vortex illumination. A trifold symmetric stress pattern will provide an annular region that exhibits polarization vortices when illuminated with linearly polarized light and scalar vortices when illuminated with circularly polarized light. A finite element plane-stress model is used to analyze the space-variant anisotropy.
Supply Chain Risk Management: An Agent-Based Simulation to Study the Impact of Retail Stockouts (2013)

In today's highly dynamic and competitive environment, companies are under the pressure to improve their supply chain strategy in order to be more responsive to customer demand. However, supply chains are susceptible to unanticipated events that make responsive supply chain management a challenging task. One such disruption event is a product stockout at the retailer. In this paper, we investigate retail stockouts through the development of an agent-based simulation model in order to develop a better understanding of the effect of different stockout lengths for different products (with different consumer response profiles to stockouts) on both the retailer and the manufacturer of the product. We consider the change of market share as a measure of resilience for both the manufacturer and the retailer to examine the impact of the stockout. Insights are developed for manufacturers and retailers in responding to the stockout disruption.
TGF-beta1 reduces Wilms' tumor suppressor gene expression in podocytes (2011)

TGF-beta1 reduces WT1 expression in cultured human podocytes and podocytes in mice before overt glomerulosclerosis begins. The effects are at least partially Smad4 dependent. Our findings identify a novel pathway linking TGF-beta1 to podocyte injury and FSGS. The WT1 reduction may be a useful marker for early podocyte injury.
Understanding Body-Fixed Sensor Output From Projectile Flight Experiments (2003)

Abstract : Accurate measurement of in-flight kinematics significantly contributes to the development of experimental projectiles and rockets and to diagnostics for existing munitions and weapons systems. Ground-based instruments such as radar and cameras provide useful measurements but are often limited to portions of a trajectory and/or have limited resolution. On-board sensor systems fixed to a projectile body combined with a telemetry system can provide high resolution continuous data throughout a projectile's entire trajectory. However, there is a twofold difficulty in correctly interpreting and employing data from body-fixed sensors. First, sensor responses many times are affected by stimuli other than those which a sensor is intended to quantify, e.g., an angular rate sensor may be affected by any g forces to which it is subjected. Second, sensor systems often, of necessity, make measurements in a body-fixed coordinate system, and the quantities whose values are desired are best described in another coordinate system. This report treats issues affecting the output of the body-fixed sensors used by the U.S. Army Research Laboratory's Weapons and Materials Research Directorate (Advanced Munitions Concepts Branch) in flight tests of military ordnance and provides the mathematics necessary to transform body-fixed measurements to earth-fixed parameters.
FACILE SYNTHESIS OF 2-METHYLENE-4-BUTYROLACTONES (1986)

Abstract 2-Methylene-4-butyrolactones were conveniently synthesized by treatment of an aldehyde with 2-carboethoxyallyl(-ic) bromide and metallic tin (and aluminum) in good yields. Protolichesterinic acid was synthesized by employing the method.
Fast T<sub>2</sub> relaxometry with an accelerated multi‐echo spin‐echo sequence (2010)

A new method has been developed to reduce the number of phase-encoding steps in a multi-echo spin-echo imaging sequence allowing fast T(2) mapping without loss of spatial resolution. In the proposed approach, the k-space data at each echo time were undersampled and a reconstruction algorithm that exploited the temporal correlation of the MR signal in k-space was used to reconstruct alias-free images. A specific application of this algorithm with multiple-receiver acquisition, offering an alternative to existing parallel imaging methods, has also been introduced. The fast T(2) mapping method has been validated in human brain T(2) measurements in a group of nine volunteers with acceleration factors up to 3.4. The results demonstrated that the proposed method exhibited excellent linear correlation with the regular T(2) mapping with full sampling and achieved better image reconstruction and T(2) mapping with respect to SNR and reconstruction artifacts than the selected reference acceleration techniques. The new method has also been applied for quantitative tracking of injected magnetically labeled breast cancer cells in the rat brain with acceleration factors of 1.8 and 3.0. The proposed technique can provide an effective approach for accelerated T(2) quantification, especially for experiments with single-channel coil when parallel imaging is not applicable.
Mapping of sequences with 2-fold symmetry on the simian virus 40 genome: a photochemical crosslinking approach. (1977)

Sequences with 2-fold axes of symmetry have been detected and mapped on the simian virus 40 (SV40) genome by their ability to form hairpin turns in single-stranded SV40 DNA. Supercoiled SV40 DNA (SV40 I) was digested with restriction enzymes EcoRI and HpaII. The resulting linear DNA molecules with lengths of the complete SV40 genome were then denatured and photochemically reacted with 4,5',8-trimethylpsoralen (trioxsalen) at 16.0 +/- 0.5 degrees and different ionic strengths. Secondary structures on the single-stranded SV40 DNA were crosslinked and their positions analyzed by electron microscopy. There were no observable hairpin turns on the denatured SV40 DNA when it was photoreacted in 1 mM Tris-HCl/0.1 mM EDTA at pH 7.0. In 20 mM NaCl, one specific hairpin turn was detected at 0.17 +/- 0.02 map units on the map of EcoRI-digested SV40 DNA, where the 3' ends of early 19S mRNA, late 19S mRNA, and 16S mRNA of SV40 have been mapped. In 30 mM NaCl there are five more major hairpin turns besides the most stable one. The centers of four of these specific hairpin turns were mapped at 0.26 +/- 0.02, 0.68 +/- 0.03, 0.84 +/- 0.02, and 0.94 +/- 0.01 units on the map of EcoRI-digested SV40. The fifth one is at or near the unique EcoRI cleavage site on SV40 DNA. The possible functions of these sequences are discussed in terms of the nature of the promoter sites, the replication origin, the processing of RNA precursors, and regulation at the translational level.
Real-time estimation of horizontal gaze angle by saccade integration using in-ear electrooculography (2018)

The manuscript proposes and evaluates a real-time algorithm for estimating eye gaze angle based solely on single-channel electrooculography (EOG), which can be obtained directly from the ear canal using conductive ear moulds. In contrast to conventional high-pass filtering, we used an algorithm that calculates absolute eye gaze angle via statistical analysis of detected saccades. The estimated eye positions of the new algorithm were still noisy. However, the performance in terms of Pearson product-moment correlation coefficients was significantly better than the conventional approach in some instances. The results suggest that in-ear EOG signals captured with conductive ear moulds could serve as a basis for light-weight and portable horizontal eye gaze angle estimation suitable for a broad range of applications. For instance, for hearing aids to steer the directivity of microphones in the direction of the user's eye gaze.
Magnetically retrievable catalysts for organic synthesis (2012)

The use of magnetic nanoparticles (MNPs) as a catalyst support in organic synthesis is summarized. The recovery of expensive catalysts after catalytic reaction and reusing them without losing their activity is an essential feature in the sustainable process development. The aim of this article is to highlight the progress in the synthesis and catalytic applications of magnetic catalysts in organic synthesis. The heterogenization of the catalyst using magnetic nanoparticles allows it to be recovered and reused using an external magnet.
Interplay among Etsrp/ER71, Scl, and Alk8 signaling controls endothelial and myeloid cell formation (2008)

Vascular endothelial and myeloid cells have been proposed to originate from a common precursor cell, the hemangioblast. The mechanism of endothelial and myeloid cell specification and differentiation is poorly understood. We have previously described the endothelial-specific zebrafish Ets1-related protein (Etsrp), which was both necessary and sufficient to initiate vasculogenesis in the zebrafish embryos. Here we identify human Etv2/ER71 and mouse ER71 proteins as functional orthologs of Etsrp. Overexpression of mouse ER71 and Etsrp caused strong expansion of hemangioblast and vascular endothelial lineages in a zebrafish embryo. In addition, we show that etsrp is also required for the formation of myeloid but not erythroid cells. In the absence of etsrp function, the number of granulocytes and macrophages is greatly reduced. Etsrp overexpression causes expansion of both myeloid and vascular endothelial lineages. Analysis of mosaic embryos indicates that etsrp functions cell autonomously in inducing myeloid lineage. We further demonstrate that the choice of endothelial versus myeloid fate depends on a combinatorial effect of etsrp, scl, and alk8 genes.
Optical scanning image sensor (1988)

Abstract As an image input device such as a facsimile and an image scanner, various image sensors have been studied. This paper describes an optical scanning contact image sensor as a form of contact image sensor. In the optical scanning type, the dots of the LED array used as a light source are activated one by one and a text is illuminated via a rod lens. The reflected light is converted to electrical signals by one photo‐detector. This system has the advantage of an extremely small power consumption. In the present trial fabrication, an a‐Si photodetector (with a pin structure) with one long element of 128 × 0.5 mm and reading width of the text 122 mm is employed. As a result, the power consumption of the present image sensor is 0.25 W (power supply voltage of 5 V) including the illumination.