gebhart/patrepeval huggingface dataset:
Differential regulation of adherens junction dynamics during apical–basal polarization (2012)

Adherens junctions (AJs) in epithelial cells are constantly turning over to modulate adhesion properties under various physiological and developmental contexts, but how such AJ dynamics are regulated during the apical–basal polarization of primary epithelia remains unclear. Here, we used new and genetically validated GFP markers of Drosophila E-cadherin (DE-cadherin, hereafter referred to as DE-Cad) and β-catenin (Armadillo, Arm) to quantitatively assay the in vivo dynamics of biosynthetic turnover and membrane redistribution by fluorescence recovery after photobleaching (FRAP) assays. Our data showed that membrane DE-Cad and Arm in AJs of polarizing epithelial cells had much faster biosynthetic turnover than in polarized cells. Fast biosynthetic turnover of membrane DE-Cad is independent of actin- and dynamin-based trafficking, but is microtubule-dependent. Furthermore, Arm in AJs of polarizing cells showed a faster and diffusion-based membrane redistribution that was both quantitatively and qualitatively different from the slower and exchange-based DE-Cad membrane distribution, indicating that the association of Arm with DE-Cad is more dynamic in polarizing cells, and only becomes stable in polarized epithelial cells. Consistently, biochemical assays showed that the binding of Arm to DE-Cad is weaker in polarizing cells than in polarized cells. Our data revealed that the molecular interaction between DE-Cad and Arm is modulated during apical–basal polarization, suggesting a new mechanism that might be crucial for establishing apical–basal polarity through regulating the AJ dynamics.
Electrical characterization of MOCVD grown epitaxial and polycrystalline PLT thin films (2002)

Ferroelectric thin films with high charge storage density, low leakage current density and extremely high dielectric constant hold a very special promise for non-volatile memory applications. In this paper we report on the electrical properties of PLT (lanthanum modified lead titanate) thin films exhibiting varying degrees of epitaxy or texture. The films were deposited on sapphire substrates using the metal organic vapor deposition method (MOCVD). The dielectric properties of these films were measured as a function of frequency, AC voltage and DC bias voltage as well as temperature. Leakage current characteristics and hysteresis behavior are also reported. Epitaxial films are found to have a dielectric constant around 900 and almost no frequency dispersion, while polycrystalline films showed a large frequency dispersion with dielectric constants ranging from 4000 at low frequencies to 1100 at the highest frequencies. Epitaxial films had correspondingly lower dissipation factors and lower leakage currents and much narrower hysteresis loops than the polycrystalline films which make them more suitable for DRAM memories.
Cardiac Imaging for Assessment of Left Ventricular Thrombus (2009)

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Phase transformations in sputtered thin films of Tix(Ni, Cu)1−xII: Displacive transformations (1997)

Abstract Part I of this series described diffusional transformations in sputtered films of Ti x (NiCu)1−x containing about 5 at.% Cu. The as-deposited amorphous films supported substantial supersaturation either of Ti or of Ni + Cu at 300 K. Subsequent isothermal annealing produced fine oriented precipitates which altered the matrix chemistry and often exerted long-range stress fields arising from coherency strains. These phenomena will be shown in part II to influence strongly the subsequent displacive transformation behaviour. In Ti47.4Ni46.5Cu6.1 films, precipitates of (NiCu)2 Ti2 resulted in B2←R and R←B19′ transformations. Extensive precipitation of Ti2(Ni, Cu) in Ti51.0Ni44.4Cu4.6 films led to formation of an orthorhombic martensite, with preferred [010]B19‖[011]B2 and (202)B19‖(211)B2 orientation relationships, prior to transformation to a monoclinic phase that formed along alternating {322}B2 and {112}B2 steps. Even in films with compositions near stoichiometry. small quantities of transgranular Ti40Ni56.5Cu3.5 and Ti2(NiCu) precipitates significantly influenced transformation sequences, temperatures and details of martensite crystallography.
The mammalian purine salvage pathway as an exploitable route for cerebral bioenergetic support after brain injury (2022)

Purine-based molecules play ancient, fundamental, and evolutionarily-conserved roles across life on Earth, ranging from DNA and RNA, to the universal energy currency, ATP. In mammals, the two primary routes for the synthesis of the adenine nucleotides ATP, ADP and AMP, and, as a consequence, the major bioactive metabolite adenosine, are the de novo purine biosynthesis (DNPB) pathway, and the purine salvage pathway (PSP). Of the two, the PSP dominates in both the mammalian brain and heart. This is because the PSP utilizes the breakdown products of ATP, occasioned by the high energy demands of these organs, to rapidly regenerate adenine nucleotides. This resynthesis route, while efficient and energetically favourable, leaves these organs vulnerable to loss of salvageable metabolites, with the potential for protracted depletion of the means to synthesize ATP, and the ability to deploy neuro- and cardioprotective adenosine. Having previously shown that hippocampal cellular ATP and adenosine release can be increased by supplying substrates for the PSP (d-ribose and adenine), we now explore the expression of DNPB and PSP enzymes in hippocampal neurons and astrocytes based on available transcriptomic data. We find that key enzymes of the PSP are expressed at higher levels than those in the DNPB pathway, and that PSP enzymes are expressed at higher levels in neurons than in astrocytes. These data reflect the importance of the PSP in the mammalian brain and imply that pharmacological targeting of the PSP may be particularly beneficial to neurons at times of metabolic stress. This article is part of the Special Issue on 'Purinergic Signaling: 50 years'.
ChemInform Abstract: Enzyme Catalyzed Reactions. Part 24. A Convenient Synthesis of (S)‐2‐ Azidonitriles, (S)‐2‐Aminonitriles and (S)‐1,2‐Diamines. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Au22Ir3(PET)18: An Unusual Alloy Cluster through Intercluster Reaction (2017)

An intercluster reaction between Au<sub>25</sub>(PET)<sub>18</sub> and Ir<sub>9</sub>(PET)<sub>6</sub> producing the alloy cluster, Au<sub>22</sub>Ir<sub>3</sub>(PET)<sub>18</sub> exclusively, is demonstrated where the ligand PET is 2-phenylethanethiol. Typical reactions of this kind between Au<sub>25</sub>(PET)<sub>18</sub> and Ag<sub>25</sub>(SR)<sub>18</sub>, and other clusters reported previously, produce mixed cluster products. The cluster composition was confirmed by detailed high-resolution electrospray ionization mass spectrometry (ESI MS) and other spectroscopic techniques. This is the first example of Ir metal incorporation in a monolayer-protected noble metal cluster. The formation of a single product was confirmed by thin layer chromatography (TLC). Density functional theory (DFT) calculations suggest that the most favorable geometry of the Au<sub>22</sub>Ir<sub>3</sub>(PET)<sub>18</sub> cluster is one wherein the three Ir atoms are arranged triangularly with one Ir atom at the icosahedral core and the other two on the icosahedral shell. Significant contraction of the metal core was observed due to strong Ir-Ir interactions.
Neuroprotective role of retinal SIRT3 against acute photo-stress (2017)

SIRT3 is a key regulator of mitochondrial reactive oxygen species as well as mitochondrial function. The retina is one of the highest energy-demanding tissues, in which the regulation of reactive oxygen species is critical to prevent retinal neurodegeneration. Although previous reports have demonstrated that SIRT3 is highly expressed in the retina and important in neuroprotection, function of SIRT3 in regulating reactive oxygen species in the retina is largely unknown. In this study, we investigated the role of retinal SIRT3 in a light-induced retinal degeneration model using SIRT3 knockout mice. We demonstrate that SIRT3 deficiency causes acute reactive oxygen species accumulation and endoplasmic reticulum stress in the retina after the light exposure, which leads to increased photoreceptor death, retinal thinning, and decreased retinal function. Using a photoreceptor-derived cell line, we revealed that reactive oxygen species were the upstream initiators of endoplasmic reticulum stress. Under SIRT3 knockdown condition, we demonstrated that decreased superoxide dismutase 2 activity led to elevated intracellular reactive oxygen species. These studies have helped to elucidate the critical role of SIRT3 in photoreceptor neuronal survival, and suggest that SIRT3 might be a therapeutic target for oxidative stress-induced retinal disorders.
Configurable Flow Models for FPGA Particle Graphics Engines (2008)

We describe the implementation of a hardware-accelerated particle graphics engine on a reconfigurable computer. The engine incorporates a configurable flow model that enables the simulation of complex spatially-dependent particle graphics effects. The FPGA particle engine was designed using the Mitrion-C high-level language, and did not require detailed hardware design. The engine was implemented on a SGI Altix 350 with four Xilinx Virtex-4 LX200 FPGAs. The engine achieves speedups of 35 to 58 times over a 1.5 GHz Itanium 2 CPU when using one and four FPGAs respectively.
Genome-Wide Analyses of Nkx2-1 Binding to Transcriptional Target Genes Uncover Novel Regulatory Patterns Conserved in Lung Development and Tumors (2012)

The homeodomain transcription factor Nkx2-1 is essential for normal lung development and homeostasis. In lung tumors, it is considered a lineage survival oncogene and prognostic factor depending on its expression levels. The target genes directly bound by Nkx2-1, that could be the primary effectors of its functions in the different cellular contexts where it is expressed, are mostly unknown. In embryonic day 11.5 (E11.5) mouse lung, epithelial cells expressing Nkx2-1 are predominantly expanding, and in E19.5 prenatal lungs, Nkx2-1-expressing cells are predominantly differentiating in preparation for birth. To evaluate Nkx2-1 regulated networks in these two cell contexts, we analyzed genome-wide binding of Nkx2-1 to DNA regulatory regions by chromatin immunoprecipitation followed by tiling array analysis, and intersected these data to expression data sets. We further determined expression patterns of Nkx2-1 developmental target genes in human lung tumors and correlated their expression levels to that of endogenous NKX2-1. In these studies we uncovered differential Nkx2-1 regulated networks in early and late lung development, and a direct function of Nkx2-1 in regulation of the cell cycle by controlling the expression of proliferation-related genes. New targets, validated in Nkx2-1 shRNA transduced cell lines, include E2f3, Cyclin B1, Cyclin B2, and c-Met. Expression levels of Nkx2-1 direct target genes identified in mouse development significantly correlate or anti-correlate to the levels of endogenous NKX2-1 in a dosage-dependent manner in multiple human lung tumor expression data sets, supporting alternative roles for Nkx2-1 as a transcriptional activator or repressor, and direct regulator of cell cycle progression in development and tumors.
Association of Escherichia coli ribosomes with the inner membrane requires the signal recognition particle receptor but is independent of the signal recognition particle (2000)

In mammalian cells, as well as Escherichia coli, ribosomes translating membrane proteins interact cotranslationally with translocons in the membrane, and this interaction is essential for proper insertion of nascent polypeptides into the membrane. Both the signal recognition particle (SRP) and its receptor (SR) are required for functional association of ribosomes translating integral membrane proteins with the translocon. Herein, we confirm that membrane targeting of E. coli ribosomes requires the prokaryotic SRalpha homolog FtsY in vivo. Surprisingly, however, depletion of the E. coli SRP54 homolog (Ffh) has no significant effect on binding of ribosomes to the membrane, although Ffh depletion is detrimental to growth. These and other observations suggest that, in E. coli, SRP may operate downstream of SR-mediated targeting of ribosomes to the plasma membrane.
Long-Range Order in Nanocrystal Assemblies Determines Charge Transport of Films (2017)

Self-assembly of semiconductor nanocrystals (NCs) into two-dimensional patterns or three-dimensional (2-3D) superstructures has emerged as a promising low-cost route to generate thin-film transistors and solar cells with superior charge transport because of enhanced electronic coupling between the NCs. Here, we show that lead sulfide (PbS) NCs solids featuring either short-range (disordered glassy solids, GSs) or long-range (superlattices, SLs) packing order are obtained solely by controlling deposition conditions of colloidal solution of NCs. In this study, we demonstrate the use of the evaporation-driven self-assembly method results in PbS NC SL structures that are observed over an area of 1 mm × 100 μm, with long-range translational order of up to 100 nm. A number of ordered domains appear to have nucleated simultaneously and grown together over the whole area, imparting a polycrystalline texture to the 3D SL films. By contrast, a conventional, optimized spin-coating deposition method results in PbS NC glassy films with no translational symmetry and much shorter-range packing order in agreement with state-of-the-art reports. Further, we investigate the electronic properties of both SL and GS films, using a field-effect transistor configuration as a test platform. The long-range ordering of the PbS NCs into SLs leads to semiconducting NC-based solids, the mobility (μ) of which is 3 orders of magnitude higher than that of the disordered GSs. Moreover, although spin-cast GSs of PbS NCs have weak ambipolar behavior with limited gate tunability, SLs of PbS NCs show a clear p-type behavior with significantly higher conductivities.
Wake up and smell the coffee (2008)

Evaluation methodology underpins all innovation in experimental computer science. It requires relevant workloads, appropriate experimental design, and rigorous analysis. Unfortunately, methodology is not keeping pace with the changes in our field. The rise of managed languages such as Java, C#, and Ruby in the past decade and the imminent rise of commodity multicore architectures for the next decade pose new methodological challenges that are not yet widely understood. This paper explores the consequences of our collective inattention to methodology on innovation, makes recommendations for addressing this problem in one domain, and provides guidelines for other domains. We describe benchmark suite design, experimental design, and analysis for evaluating Java applications. For example, we introduce new criteria for measuring and selecting diverse applications for a benchmark suite. We show that the complexity and nondeterminism of the Java runtime system make experimental design a first-order consideration, and we recommend mechanisms for addressing complexity and nondeterminism. Drawing on these results, we suggest how to adapt methodology more broadly. To continue to deliver innovations, our field needs to significantly increase participation in and funding for developing sound methodological foundations.
The role of physisorption in the cryogenic etching process of silicon (2019)

Abstract The growth mechanism of the passivation layer in the cryogenic process used for silicon deep etching is explored experimentally in an inductively coupled plasma reactor. In particular, the role of SiF 4 etching by-products on the SiO x F y layer deposition is investigated. The deposition of a SiO x F y layer using SiF 4 and O 2 gases is studied by in situ ellipsometric spectroscopy in different experimental configurations to devise the deposition mechanism: SiF 4 /O 2 plasma mixture, alternation of SiF 4 plasma and O 2 plasma steps and alternation of SiF 4 flow without plasma and O 2 plasma steps. The refractive index and the thickness of the deposited layer are measured for different substrate temperatures, from −125 °C to 20 °C. Although some of the passivation layer is removed during the wafer warm up, a residual amount remains at the surface. The deposited SiO x F y layer forms more efficiently at low temperature with an optimal temperature of −100 °C in our experimental conditions. The passivation layer was etched by a SF 6 plasma without bias versus the deposition temperature, to evaluate its resistance to plasma etching steps. The passivation layer was analyzed by ex situ EDX and XPS. We investigated the role of SiF 4 low temperature physisorption in the formation of the passivation layer on the sidewalls of the features that are being etched, which are not submitted to ion bombardment. It is shown that physisorption of SiF x species play an important role because their residence time at the surface is longer, thus increasing the probability of reaction with oxygen.
Simulation of Induction Heating Prior to Hot Working and Coating (2010)

Abstract The most popular metal hot working processes for which induction heating is applied are forging, forming, extrusion, and rolling. This article focuses on estimation techniques to determine basic induction heating process parameters, including coil power, length of heating line, and frequency selection. It discusses three modes of heat transfer: conduction, convection, and radiation, in induction heating. The article describes the factors affected by a distortion of the magnetic field at the coil end through a schematic illustration of distribution of three magnetic force components experienced by the turns of the coil. It concludes with information on some case studies of numerical simulation.
Microfabrication, Characterization, and Application of Carbon Nanotube Templated Thin Layer Chromatography Plates, and Functionalization of Porous Graphitic Carbon (2012)

The cyclic adenosine monophosphate-protein kinase A (cAMP-PKA) signalling pathway is evolutionarily conserved in eukaryotes and plays a crucial role in defending against external environmental challenges, which can modulate the cellular response to external stimuli. Arthrobotrys oligospora is a typical nematode-trapping fungus that specializes in adhesive networks to kill nematodes. To elucidate the biological roles of the cAMP-PKA signalling pathway, we characterized the orthologous adenylate cyclase AoAcy, a regulatory subunit (AoPkaR), and two catalytic subunits (AoPkaC1 and AoPkaC2) of PKA in A. oligospora by gene disruption, transcriptome, and metabolome analyses. Deletion of Aoacy significantly reduced the levels of cAMP and arthrobotrisins. Results revealed that Aoacy, AopkaR, and AopkaC1 were involved in hyphal growth, trap morphogenesis, sporulation, stress resistance, and autophagy. In addition, Aoacy and AopkaC1 were involved in the regulation of mitochondrial morphology, thereby affecting energy metabolism, whereas AopkaC2 affected sporulation, nuclei, and autophagy. Multi-omics results showed that the cAMP-PKA signalling pathway regulated multiple metabolic and cellular processes. Collectively, these data highlight the indispensable role of cAMP-PKA signalling pathway in the growth, development, and pathogenicity of A. oligospora, and provide insights into the regulatory mechanisms of signalling pathways in sporulation, trap formation, and lifestyle transition.
Quantum Kernels for Real-World Predictions Based on Electronic Health Records (2022)

Research on near-term quantum machine learning has explored how classical machine learning algorithms endowed with access to quantum kernels (similarity measures) can outperform their purely classical counterparts. Although theoretical work has shown provable advantage on synthetic data sets, no work done to date has studied empirically whether quantum advantage is attainable and with what data. In this paper, we report the first systematic investigation of empirical quantum advantage (EQA) in healthcare and life sciences and propose an end-to-end framework to study EQA. We selected electronic health records (EHRs) data subsets and created a configuration space of 5-20 features and 200-300 training samples. For each configuration coordinate, we trained classical support vector machine (SVM) models based on radial basis function (RBF) kernels and quantum models with custom kernels using an IBM quantum computer, making this one of the largest quantum machine learning experiments to date. We empirically identified regimes where quantum kernels could provide advantage and introduced a terrain ruggedness index, a metric to help quantitatively estimate how the accuracy of a given model will perform. The generalizable framework introduced here represents a key step towards a priori identification of data sets where quantum advantage could exist.
Conductive Semiconductor Interfaces Fabricated by Room Temperature Covalent Wafer Bonding (2016)

Low temperature direct bonding in the range of maximum 400°C opened an entirely new applications field as it allowed for the direct bonding of wafers with metallization (e.g CMOS) while maintaining a high alignment accuracy as well as bonding of thermally mismatched materials. Despite the clear benefits of the low temperature direct bonding process, the requirements of some categories of applications in terms of allowing for room temperature covalent bonding or oxide-free, electrically conductive interfaces fabrication cannot be fulfilled. A new technology was developed to address these types of applications: EVG ® 580 Combond ® . This paper reports on fabrication of oxide-free, electrically conductive Si-Si and Si-GaAs bonded interfaces based on the newly developed technology. Experimental results on bonding quality and electrical performance of the bonded interfaces are presented.
Resource Allocation in a Breeding Program for Phosphorus Concentration in Maize Grain (2004)

When beef cattle ( Bos taurus ) are fed grain of maize ( Zea mays L.) in which the concentration of phosphorus (P) exceeds the animal's need for this element, the excess P is excreted in the feces. Spreading this manure on cropland increases the potential for P pollution of surface waters by run‐off. Experiments were undertaken to determine the relative magnitudes of genotypic and nongenotypic variances of P concentration in maize grain (P‐Gr) to assess the ability to select maize genotypes in which this trait more closely matches the dietary need of beef cattle. Genetic variability was found in a population developed from a cross of Illinois High Protein (IHP) × Illinois Low Protein (ILP). Because of few low P‐Gr segregates, the IHP × ILP population was not considered a good breeding source for this trait. Nongenetic sources of variance were significant but small compared with genotypic variances. Broad‐sense heritability ( H ) for P‐Gr among S 1 family means in the IHP × ILP population was estimated at 0.82. This high value suggested that this trait would respond to selection. A comparison of mean values of S 1 families selected on the basis of performance in 2000 or in 2001 alone to those selected on the basis of 2‐yr data suggested that the loss in efficiency resulting from selecting on 1‐yr data would be only approximately 5%.