gebhart/patrepeval huggingface dataset:
Deep Neural Network Inverse Design of Integrated Photonic Power Splitters (2019)

Predicting physical response of an artificially structured material is of particular interest for scientific and engineering applications. Here we use deep learning to predict optical response of artificially engineered nanophotonic devices. In addition to predicting forward approximation of transmission response for any given topology, this approach allows us to inversely approximate designs for a targeted optical response. Our Deep Neural Network (DNN) could design compact (2.6 × 2.6 μm<sup>2</sup>) silicon-on-insulator (SOI)-based 1 × 2 power splitters with various target splitting ratios in a fraction of a second. This model is trained to minimize the reflection (to smaller than ~ -20 dB) while achieving maximum transmission efficiency above 90% and target splitting specifications. This approach paves the way for rapid design of integrated photonic components relying on complex nanostructures.
Toll-like receptor expression reveals CpG DNA as a unique microbial stimulus for plasmacytoid dendritic cells which synergizes with CD40 ligand to induce high amounts of IL-12 (2001)

Human plasmacytoid dendritic cells (DC) (PDC, CD123+) and myeloid DC (MDC, CD11c+) may be able to discriminate between distinct classes of microbial molecules based on a different pattern of Toll-like receptor (TLR) expression. TLR1-TLR9 were examined in purified PDC and MDC. TLR9, which is critically involved in the recognition of CpG motifs in mice, was present in PDC but not in MDC. TLR4, which is required for the response to LPS, was selectively expressed on MDC. Consistent with TLR expression, PDC were susceptible to stimulation by CpG oligodeoxynucleotide (ODN) but not by LPS, while MDC responded to LPS but not to CpG ODN. In PDC, CpG ODN supported survival, activation (CD80, CD86, CD40, MHC class II), chemokine production (IL-8, IP-10) and maturation (CD83). CD40 ligand (CD40L) and CpG ODN synergized to activate PDC and to stimulate the production of IFN-alpha and IL-12 including bioactive IL-12 p70. Previous incubation of PDC with IL-3 decreased the amount of CpG-induced IFN-alpha and shifted the cytokine response in favor of IL-12. CpG ODN-activated PDC showed an increased ability to stimulate proliferation of naive allogeneic CD4 T cells, butTh1 polarization of developing T cells required simultaneous activation of PDC by CD40 ligation and CpG ODN. CpG ODN-stimulated PDC expressed CCR7, which mediates homing to lymph nodes. In conclusion, our studies reveal that IL-12 p70 production by PDC is under strict control of two signals, an adequate exogenous microbial stimulus such as CpG ODN, and CD40L provided endogenously by activated T cells. Thus, CpG ODN acts as an enhancer of T cell help, while T cell-controlled restriction to foreign antigens is maintained.
IDENTIFYING NONPOLAR TRANSBILAYER HELICES IN AMINO ACID SEQUENCES OF MEMBRANE PROTEINS (1986)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More
New Cementing Technologies Successfully Solved the Problems in Shallow Gas, Low Temperature and Easy Leakage Formations (2010)

Abstract The buried depths of reservoirs in North Buzachi oilfield range between 400~500m, but Its geologic structure is very complex due to the existence of shallow gas and aqueous layer within 20~160m and a HP gas layer at 300m(1.30–1.50 g/cm3). In addition, the reservoir is easy to leak for its high permeability and low fracture gradient (1.6g/cm3), and the ground temperature is −40□ in winter. All these factors bring great challenges for the cementing jobs here and often result in poor cementing quality such as shallow water &amp; gas channeling from wellheads and serious leakage in reservoirs. 72 out of the 97 wells cemented during 1974~2000 were abandoned due to poor cementing jobs. Gas and water channeling were found from 15 wellheads that were cemented from 2003 to 2004. This paper focuses on how we develop a new cementing technology to improve the cementing quality in this oilfield. Based on the High Packing Theory, we developed the High Performance Low Temperature No-waiting &amp; Low Density Cementing ™ technology(NLDC) whose slurry density can as low as 1.20g/cm3, which includes high performance cementing additives, superfine active mineral materials, Super-low temperature accelerator, and Anti-migration additive, etc. This technology are characterized by good anti-channeling &amp; Anti-leakage &amp; early strength development ability under the temperature 20~30□. Up to now, more than 300 wells have been cemented successfully with this technology, 97% of which are with excellent bonding quality. Those problems which have puzzled the North Buzachi for long have been radically solved, such as bad isolation, annular migration, shallow gas and water blowing off from wellheads and leakage during cementing. This NLDC cementing technology has been widely applied in North Buzachi oilfield for 5 years and also a good solution to shallow gas &amp; water cementing and low pressure-easy-leakage formation cementing.
Internal Composition versus the Mechanical Properties of Polyelectrolyte Multilayer Films: The Influence of Chemical Cross-Linking (2009)

Different types of polyelectrolyte multilayer films composed of poly(L-lysine)/hyaluronan (PLL/HA), chitosan/hyaluronan (CHI/HA) and poly(allylamine hydrochloride)/poly(L-glutamic acid) (PAH/PGA) have been investigated for their internal composition, including water content, ion pairing, and ability to be covalently cross-linked, as well as for their mechanical properties. Film buildup under physiological conditions was monitored by the quartz crystal microbalance with dissipation monitoring (QCM-D) and attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), which allows unambiguous quantification of the different groups present in the polyelectrolytes. (PAH/PGA) films emerged as the most dense films with the lowest hydration (29%) and the highest COO(-) molar density. In addition, PAH is greatly in excess in these films (3 PAH monomers per PGA monomer). The formation of amide bonds during film cross-linking using the water-soluble carbodiimide EDC was also investigated. All of the films could be cross-linked in a tunable manner, but PAH/PGA exhibited the highest absolute number of amide bonds created, approximately 7 times more than for (PLL/HA) and (CHI/HA) films. The Young's modulus E of the films measured by AFM nanoindentation was shown to vary over 1 to 2 orders of magnitude for the different systems. Interestingly, a linear relationship between E and the density of the covalent cross-links created was observed for (PLL/HA) and (CHI/HA) films whereas (PGA/PAH) films exhibited biphasic behavior. The mean distance between covalent cross-links was estimated to be approximately 11 nm for (PLL/HA) and (CHI/HA) films and only approximately 6 nm for (PAH/PGA) films for the maximum EDC concentration tested (100 mg/mL).
Treatment of active Crohn's disease with onercept (recombinant human soluble p55 tumour necrosis factor receptor): results of a randomized, open‐label, pilot study (2003)

Neutralizing the activity of tumour necrosis factor-alpha with its soluble p55 receptor may be valuable in the treatment of patients with Crohn's disease. Larger placebo-controlled trials are indicated.
All-Photonic Molecular Half-Adder (2006)

One molecule acts as both an AND and an XOR Boolean logic gate that share the same two photonic inputs. The molecule comprises a half-adder, adding two binary digits with only light as inputs and outputs, and consists of three covalently linked photochromic moieties, a spiropyran and two quinoline-derived dihydroindolizines. The AND function is based on the absorption properties of the molecule, whereas the XOR function is based on an off-on-off response of the fluorescence to the inputs that results from interchromophore excited-state quenching interactions. The half-adder is simple to operate and can be cycled many times.
Catalytic asymmetric epoxidation and kinetic resolution: modified procedures including in situ derivatization (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalytic asymmetric epoxidation and kinetic resolution: modified procedures including in situ derivatizationYun Gao, Janice M. Klunder, Robert M. Hanson, Hiroko Masamune, Soo Y. Ko, and K. Barry SharplessCite this: J. Am. Chem. Soc. 1987, 109, 19, 5765–5780Publication Date (Print):September 1, 1987Publication History Published online1 May 2002Published inissue 1 September 1987https://pubs.acs.org/doi/10.1021/ja00253a032https://doi.org/10.1021/ja00253a032research-articleACS PublicationsRequest reuse permissionsArticle Views17663Altmetric-Citations1735LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Indole-3-carbinol Inhibits CDK6 Expression in Human MCF-7 Breast Cancer Cells by Disrupting Sp1 Transcription Factor Interactions with a Composite Element in the CDK6 Gene Promoter (2001)

Indole-3-carbinol (I3C), a compound naturally occurring in Brassica vegetables, can induce a G(1) cell cycle arrest of human MCF-7 breast cancer cells that is accompanied by the selective inhibition of cyclin-dependent kinase 6 (CDK6) expression. Reverse transcriptase-polymerase chain reaction analysis of CDK6 mRNA decay rates revealed that I3C had no effect on CDK6 transcript stability. We report the first identification and functional characterization of the CDK6 promoter in order to determine whether I3C inhibits CDK6 transcription. In MCF-7 cells stably transfected with CDK6 promoter-linked luciferase reporter plasmids, I3C inhibited CDK6 promoter activity in an I3C-specific response that was not a consequence of the growth-arrested state of the cells. Deletion analysis revealed a 167-base pair I3C-responsive region of the CDK6 promoter between -805 and -638. Site-specific mutations within this region revealed that both Sp1 and Ets-like sites, which are spaced 5 base pairs apart, were necessary for I3C responsiveness in the context of the CDK6 promoter. Electrophoretic mobility shift analysis of protein-DNA complexes formed with nuclear proteins isolated from I3C-treated and -untreated cells, in combination with supershift assays using Sp1 antibodies, demonstrated that the Sp1-binding site in the CDK6 promoter forms a specific I3C-responsive DNA-protein complex that contains the Sp1 transcription factor. Taken together, our results suggest that I3C down-regulates CDK6 transcription by targeting Sp1 at a composite DNA site in the CDK6 promoter.
Colloidal lithography and current fabrication techniques producing in-plane nanotopography for biological applications (2006)

Substrate topography plays a vital role in cell and tissue structure and function in situ, where nanometric features, for example, the detail on single collagen fibrils, influence cell behaviour and resultant tissue formation. In vitro investigations demonstrate that nanotopography can be used to control cell reactions to a material surface, indicating its potential application in tissue engineering and implant fabrication. Developments in the catalyst, optical, medical and electronics industries have resulted in the production of nanopatterned surfaces using a variety of methods. The general protocols for nanomanufacturing require high resolution and low cost for fabricating devices. With respect to biological investigations, nanotopographies should occur across a large surface area (ensuring repeatability of experiments and patterning of implant surfaces), be reproducible (allowing for consistency in experiments), and preferably, accessible (limiting the requirement for specialist equipment). Colloidal lithography techniques fit these criteria, where nanoparticles can be utilized in combination with a functionalized substrate to produce in-plane nanotopographies. Subsequent lithographic processing of colloidal substrates utilizing, for example, reactive ion etching allows the production of modified colloidal-derived nanotopographies. In addition to two-dimensional in-plane nanofabrication, functionalized structures can be dip coated in colloidal sols, imparting nanotopographical cues to cells within a three-dimensional environment.
Simulation of germination of pioneer species along an experimental drought gradient. (2006)

The germination of ten plant species from the Iberian Peninsula was assessed along a water deficit gradient between -0. 1652 (moist) and -0.4988 MPa (dry) of osmotic potential, created by addition of increasing concentrations of polyethylene glycol (PEG 6000) to distilled water in which plants were grown hydroponically. The level and rate of germination of Daucus carota and Thapsia villosa significantly decreased with decreasing psi. Seeds of Dactylis glomerata and Dittrichia viscosa had positive germination responses to low osmotic potentials; germination of Epilobium hirsutum was not affected by osmotic potential. Germination of Medicago arabica, Cynosurus cristatus, Cistus ladanifer and Cistus albidus, was no favored by the addition of polyethylene glycol (PEG). Germination of Foeniculum vulgare and Thapsia villosa was inhibited by PEG.
A Deep Learning Approach to Data-driven Parameterizations for Statistical Parametric Speech Synthesis (2014)

Nearly all Statistical Parametric Speech Synthesizers today use Mel Cepstral coefficients as the vocal tract parameterization of the speech signal. Mel Cepstral coefficients were never intended to work in a parametric speech synthesis framework, but as yet, there has been little success in creating a better parameterization that is more suited to synthesis. In this paper, we use deep learning algorithms to investigate a data-driven parameterization technique that is designed for the specific requirements of synthesis. We create an invertible, low-dimensional, noise-robust encoding of the Mel Log Spectrum by training a tapered Stacked Denoising Autoencoder (SDA). This SDA is then unwrapped and used as the initialization for a Multi-Layer Perceptron (MLP). The MLP is fine-tuned by training it to reconstruct the input at the output layer. This MLP is then split down the middle to form encoding and decoding networks. These networks produce a parameterization of the Mel Log Spectrum that is intended to better fulfill the requirements of synthesis. Results are reported for experiments conducted using this resulting parameterization with the ClusterGen speech synthesizer.
Tunable Electronic Coupling and Driving Force in Structurally Well-Defined Tetracene Dimers for Molecular Singlet Fission: A Computational Exploration Using Density Functional Theory (2013)

Singlet fission (SF), a process by which two excited states are formed in a chromophoric system following the absorption of a single photon, has the potential to increase the theoretical efficiency of solar energy conversion devices beyond the single-junction Shockley-Quiesser limit. Although SF is observed with high yield in the solid state of certain molecules, linearly linked dimers based on these same constituents exhibit small yields in part due to small interchromophore electronic coupling. Previous work from our group demonstrated enhancement of SF yield in polycrystalline tetracene (Tc) via excitation of intermolecular motions, which increased direct overlap of monomer π-systems. In this current work, a series of norbornyl-bridged bistetracene (BT) dimers are investigated using DFT and the ability to control SF thermodynamics along with important interchromophore electronic coupling parameters via bridging geometry is shown. Although the electronic coupling of a series of C2v-symmetric dimers (BT1-BT3) that differ in norbornyl bridge length is larger than in previously studied Tc dimers, a key nonhorizontal electron-transfer (ET) matrix element used in determining the SF rate is zero due to symmetry. In these systems, SF may be expected but electronic excitation will require coupling to vibrational modes that break symmetry. Singly bridged dimer isomers BT1-trans and BT1-cis, which break the C2v symmetry of BT1 by exploiting attachment of the norbornyl bridge at the 1,2 instead of the 2,3 Tc positions, are expected to be significantly more favorable for SF due to an exoergic driving force, increased electronic coupling, a lower charge-transfer-state energy (particularly in the case of BT1-cis), and nonhorizontal ET matrix elements that are nonzero.
Phosphatidylinositol 3-Kinase/Akt Stimulates Androgen Pathway through GSK3β Inhibition and Nuclear β-Catenin Accumulation (2002)

PI3K/Akt plays a critical role in prostate cancer cell growth and survival. Recent studies have shown that the effect of PI3K/Akt in prostate cells is mediated through androgen signaling. The PI3K inhibitor, LY294002, and a tumor suppressor, PTEN, negatively regulate the PI3K/Akt pathway and repress AR activity. However, the molecular mechanisms whereby PI3K/Akt and PTEN regulate the androgen pathway are currently unclear. Here, we demonstrate that blocking the PI3K/Akt pathway reduces the expression of an endogenous AR target gene. Moreover, we show that the repression of AR activity by LY294002 is mediated through phosphorylation and inactivation of GSK3beta, a downstream substrate of PI3K/Akt, which results in the nuclear accumulation of beta-catenin. Given the recent evidence that beta-catenin acts as a coactivator of AR, our findings suggest a novel mechanism by which PI3K/Akt modulates androgen signaling. In a PTEN-null prostate cancer cell line, we show that PTEN expression reduces beta-catenin-mediated augmentation of AR transactivation. Using the mutants of beta-catenin, we further demonstrate that the repressive effect of PTEN is mediated by a GSK3beta-regulated degradation of beta-catenin. Our results delineate a novel link among the PI3K, wnt, and androgen pathways and provide fresh insights into the mechanisms of prostate tumor development and progression.
Cloning of the Amino-terminal and 5′-Flanking Region of the Human MUC5AC Mucin Gene and Transcriptional Up-regulation by Bacterial Exoproducts (1998)

To obtain gene regulatory sequence for the mucin gene <i>MUC5AC</i>, we have isolated the <i>MUC5AC</i> amino terminus cDNA and 5′-flanking region. This was possible through the use of rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR) in which the 5′ sequence of the human gastric mucin cDNA HGM-1 (1) was used to design the first <i>MUC5AC</i>-specific primer. Primers for subsequent rounds of RACE were designed from the 5′-ends of amplified RACE products. After five rounds of RACE-PCR, we could no longer generate upstream extensions of the cDNA and hypothesized that we had reached the 5′-end. Primer extension and RNase protection analysis confirmed this. Combined nucleotide sequence for the RACE-PCR products was 3.3 kb with an open reading frame encoding 1100 amino acids. A putative translation start site was found at nucleotide +48. This was followed by a 45 nucleotide putative signal sequence. This amino-terminal sequence contains no tandem repeats but is >60% similar to the amino-terminal nucleotide sequence of <i>MUC2</i>. The positions of cysteine residues in this <i>MUC2</i>-similar region are almost 100% conserved between the two genes. Northern analysis showed expression of cognate RNA in the stomach and airway but not muscle and esophagus. This pattern was the same as that obtained using previously reported 3′-<i>MUC5AC</i>sequences. We have cloned approximately 4 kb of genomic DNA upstream of the transcription start site and have sequenced 1366 nucleotides containing a TATA box, a CACCC box, and putative binding sites for NFκB and Sp 1. Within 4 kb of the transcription start site are elements mediating transcriptional up-regulation in response to bacterial exoproducts.
Small cantilevers for force spectroscopy of single molecules (1999)

We have used a simple process to fabricate small rectangular cantilevers out of silicon nitride. They have lengths of 9–50 μm, widths of 3–5 μm, and thicknesses of 86 and 102 nm. We have added metallic reflector pads to some of the cantilever ends to maximize reflectivity while minimizing sensitivity to temperature changes. We have characterized small cantilevers through their thermal spectra and show that they can measure smaller forces than larger cantilevers with the same spring constant because they have lower coefficients of viscous damping. Finally, we show that small cantilevers can be used for experiments requiring large measurement bandwidths, and have used them to unfold single titin molecules over an order of magnitude faster than previously reported with conventional cantilevers.
(CN)-chelate, N,N'-bridged dimeric palladium complexes derived from hydrazones PhC(R):NN'HPh. X-ray structure of [Pd(o-C6H4C(R):NNPh)L]2 [R = Me, L = P(OMe)3] (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT(CN)-chelate, N,N'-bridged dimeric palladium complexes derived from hydrazones PhC(R):NN'HPh. X-ray structure of [Pd(o-C6H4C(R):NNPh)L]2 [R = Me, L = P(OMe)3]Pablo Espinet, Gabriel Garcia, Francisco J. Herrero, Yves Jeannin, and Michele Philoche-LevisallesCite this: Inorg. Chem. 1989, 28, 23, 4207–4211Publication Date (Print):November 1, 1989Publication History Published online1 May 2002Published inissue 1 November 1989https://doi.org/10.1021/ic00322a007RIGHTS & PERMISSIONSArticle Views122Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (547 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts