gebhart/patrepeval huggingface dataset:
Abstract 4881: Polycomb protein EZH2 activates Wnt/β-catenin signaling to promote hepatocellular carcinoma development (2010)

Abstract Aberrant activation of the canonical Wnt pathway due to accumulation of β-catenin occurs in approximately 70% of hepatocellular carcinomas (HCCs) and contributes to their initiation, development and progression. Genetic mutations in the components of this pathway account for only a subset of HCCs with β-catenin accumulation, suggesting that an alternative mechanism for Wnt/β-catenin activation is prevailing. Enhancer of zeste homolog 2 (EZH2) is known to promote tumorigenesis by down-regulating tumor-suppressor genes; however, whether EZH2 regulates oncogenic pathways is unclear. Using chromatin immunoprecipitation microarray, we uncovered 12 Wnt/β-catenin signal antagonists whose promoters were concordantly occupied by EZH2 and repressive histone modifications in hepatocellular HCC cells. EZH2 over-expressed in 42% (75/179) of human HCCs and significantly associated with β-catenin accumulation. Concomitant inhibition of EZH2 and histone deacetylase transcriptionally activated Wnt/β-catenin signal antagonists, suppressed T-cell factor-dependent transcriptional activity and down-regulated β-catenin transcriptional targets in HCC cells. Conversely, ectopic EZH2 over-expression in nontumorigenic hepatocytes increased cellular proliferation in a β-catenin-dependent manner and promoted tumorigenicity. This study uncovers an EZH2-mediated epigenetic mechanism that leads to Wnt/β-catenin signaling dyregulation in human HCC and suggests that therapeutic interventions targeting EZH2 may confer a clinical benefit in β-catenin-driven malignancies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4881.
Downstream effectors of light- and phytochrome-dependent regulation of hypocotyl elongation in Arabidopsis thaliana (2013)

Arabidopsis, like most plants, exhibits tissue-specific, light-dependent growth responses. Cotyledon and leaf growth and the accumulation of photosynthetic pigments are promoted by light, whereas hypocotyl growth is inhibited. The identification and characterization of distinct phytochrome-dependent molecular effectors that are associated with these divergent tissue-specific, light-dependent growth responses are limited. To identify phytochrome-dependent factors that impact the photoregulation of hypocotyl length, we conducted comparative gene expression studies using Arabidopsis lines exhibiting distinct patterns of phytochrome chromophore inactivation and associated disparate hypocotyl elongation responses under far-red (FR) light. A large number of genes was misregulated in plants lacking mesophyll-specific phytochromes relative to constitutively-deficient phytochrome lines. We identified and characterized genes whose expression is impacted by light and by phyA and phyB that have roles in the photoregulation of hypocotyl length. We characterized the functions of several identified target genes by phenotyping of T-DNA mutants. Among these genes is a previously uncharacterized LHE (LIGHT-INDUCED HYPOCOTYL ELONGATION) gene, which we show impacts light- and phytochrome-mediated regulation of hypocotyl elongation under red (R) and FR illumination. We describe a new approach for identifying genes involved in light- and phytochrome-dependent, tissue-specific growth regulation and confirmed the roles of three such genes in the phytochrome-dependent photoregulation of hypocotyl length.
Cascaded discrimination of normal, abnormal, and confounder classes in histopathology: Gleason grading of prostate cancer (2012)

Use of the CAS strategy increases the PPV for a multi-category classification system over two common alternative strategies. In classification problems such as histopathology, where multiple class groups exist with varying degrees of heterogeneity, the CAS system can intelligently assign class labels to objects by performing multiple binary classifications according to domain knowledge.
Application of High Hydrostatic Pressure to Dissociate Aggregates and Refold Proteins (2009)

Non-denaturing pressures of around 2000 bar are effective for eliminating and refolding protein aggregates and may be applicable in various phases of protein manufacturing to decrease aggregate levels in products and improve process yields. Lower aggregate levels can result in reduced immunogenicity of proteins and enable the correct refolding of proteins that might not be recovered with traditional techniques. High pressure treatment can also be used to conduct selective PEGylation and protease cleavage reactions while minimizing protein aggregation. High pressure processes have been used in the food industry for over 50 years and large scale (300 L) systems are commercially available, enabling production of proteins on the kilogram scale. This review summarizes the utility of high pressure refolding to remove and refold protein aggregates, enhance therapeutic proteins, and facilitate manufacturing improvements at industrial scales.
Volume‐regulated anion channels do not contribute extracellular adenosine during the hypoxic depression of excitatory synaptic transmission in area CA1 of rat hippocampus (2000)

We investigated whether volume-regulated anion channels (VRACs) contributed to the accumulation of extracellular adenosine during hypoxia in area CA1. The rapid hypoxic depression of the fEPSP was greatly attenuated by the selective adenosine A1 receptor antagonist DPCPX (50 nM), but not affected by the VRAC blockers tamoxifen (10-30 microM) or DNDS (1 mM). Our data argue against the efflux of adenosine per se or its precursor ATP through VRACs as making a significant contribution to extracellular adenosine during the early stages of hypoxia.
Towards full-scale numerical simulations of a traveling-wave thermoacoustic Stirling heat engine (2013)

We have carried out the first three-dimensional numerical simulation of a thermoacoustic Stirling heatengine (TASHE). The goal is to lay the groundwork for full-scale, time-resolved Navier-Stokes simulations that allow for the direct description of the non-linear processes limiting the overall efficiency of such devices. The TASHE model adopted for the present study is a double-Helmholtz resonator with the engine module at one end. The latter is composed of an infinitely thin annular tube holding the heat-exchanger/regenerator (HX/REG) unit – the only component not directly resolved. All walls are modeled as adiabatic, no-slip boundaries with a local wall-normal resolution resolving the boundary layer thickness. An imposed temperature difference across the regenerator of ∆T = 200K is sufficient to initiate the thermoacoustic instability leading to the generation of acoustic energy in the system. After the application of the heat source, the acoustic fluctuations in the engine rapidly settle towards an exponentially amplified pure tone at 59.8 Hz. By tracking a fluid parcel in the regenerator it is shown how the thermoacoustic instability intensifies exclusively plane waves traveling in the direction of the imposed temperature gradient. The Lagrangian thermodynamic history of the fluid parcel resembles a Stirling heat-engine cycle, unveiling the conversion mechanisms of heat into mechanical work central to any TASHE. A well-defined acoustic network of traveling waves looping around the HX/REG unit is established and analyzed with the aid of the time-resolved data. A simple lumped-parameter model is used to investigate the linear stability properties of the initial acoustic perturbation revealing, in particular, that the acoustic energy growth is maximized at the lowest resonant frequencies of the system. Non-linear effects are detectable from the very beginning and become dynamically important only after the first two seconds of operation. It is shown that intense acoustic fluctuations in the feedback loop component drive complex system-wide streaming flow patterns responsible, in particular, for the mean advection of hot fluid away from the HX/REG (thermal leakage) in the direction of the imposed temperature gradient and around the annular tube. This unwanted effect is contained by the introduction of a second ambient heat-exchanger, commonly found in the design of real TASHEs, allowing for the establishment of a dynamical thermal equilibrium in the system. A limit cycle in fully non-linear conditions is finally obtained for an acoustic amplitude of 178 dB.
The Weyl-Heisenberg ensemble: Statistical mechanics meets time-frequency analysis (2017)

We present our recent work on the Weyl-Heisenberg ensemble and its statistical properties [4]. The WH ensemble is a class of determinantal point processes associated with the Schrödinger representation of the Heisenberg group. As a special example, WH ensembles include a multi-layer extension of the Ginibre ensemble modeling the distribution of electrons in higher Landau levels. We describe the hyperuniformity of WH ensembles, which characterizes a state of matter for which (scaled) density fluctuations diminish towards zero at the largest length scales. Our approach is based on methods from time-frequency analysis. We introduce the main results from [4] highlighting time-frequency techniques and connections to the theory of polyanalytic functions, and also present some small extensions.
Electrocaloric cooling with electrostatic actuation (2023)

A solid-state heat transporting device including a heat transporting element whose uniformity of contact with one or multiple surfaces is controllable so that various amounts of heat may be transported to and from the one or multiple surfaces. The heat transporting element uses the electrocaloric effect to absorb and release the heat and the uniformity of contact is controlled using an electrostatic effect which may change the shape of the heat transporting element. In one embodiment, the heat transporting element is an electrostatically actuated P(VDF-TrFE-CFE) polymer stack achieving a high specific cooling power of 2.8 W/g and a COP of 13 (the highest reported coefficient of performance to date) when used as a cooling device.
Preclinical Evaluation of the Novel, Orally Bioavailable Selective Inhibitor of Nuclear Export (SINE) KPT-335 in Spontaneous Canine Cancer: Results of a Phase I Study (2014)

This study provides evidence that the novel orally bioavailable XPO1 inhibitor KPT-335 is safe and exhibits activity in a relevant, spontaneous large animal model of cancer. Data from this study provides critical new information that lays the groundwork for evaluation of SINE compounds in human cancer.
Prevalence of intestinal parasites in Korea (1971)

A survey of intestinal parasites infection among Korean people has been carried out during July 1969 to December 1970. A total of 2,250 stool specimens (male 1,101, female 1,146) was collected from all the provinces and Seoul city in Korea. The specimens were examined routinely by direct fecal smear, zinc sulfate flotation and formalin-ether sedimentation techniques. The results are summarized as follows: 1. Of 2,250 specimens examined, l,803(80.l %) were positive for intestinal parasites. 2. The positive rates of intestinal helminths were 1,644(73.1 %) among 2,250; Ascaris lumbricoides 46.0 %, Trichocephalus trichiurus 46.8 percent, hookworm 6.8 %, Trichostrongylus orientalis 7.0 percent, Clonorchis sinensis 12.1 percent, Enterobius vermicularis 1.6 %, Hymenolepis nana 0.7 percent, Taenia species 0.3 %, Metagonimus yokogawai 0.04 percent, Fasciolidae 0.04 % and one case of lung fluke Paragonimu westermani. 3. The positive rstes of intestinal protozoa were 786(34.9 %); Entamoeba histolytica 6.4 %, Entamoeba coli 20.5 percent, Endolimax nana 10.0 %, Giardia lamblia 5.1 %, Trichomonas hominis 1.1 percent, Chilomastix mesnili 0.5 percent, Iodamoeba butschlii 0.6 percent, Enteromonas hominis 0.7 percent, Dientamoeba fragilis 0.1 % and one case of Isospora hominis. 4. Sexual distribution of helminths and protozoan infections showed higher rate in female than that of male, except C. sinensis, H. nana, Taenia species or G. lamblia. 5. Infections of T. trichiurus, hookworm, T. orientalis, C. sinensis, Taenia species, E. histolytica, E. coli and E. nana increased with age. Conversely, H. nana and G. lamblia infections were more predominent in younger ages.
The Orphan G Protein-coupled Receptor GPR17 Negatively Regulates Oligodendrocyte Differentiation via Gαi/o and Its Downstream Effector Molecules (2015)

Recent studies have recognized G protein-coupled receptors as important regulators of oligodendrocyte development. GPR17, in particular, is an orphan G protein-coupled receptor that has been identified as oligodendroglial maturation inhibitor because its stimulation arrests primary mouse oligodendrocytes at a less differentiated stage. However, the intracellular signaling effectors transducing its activation remain poorly understood. Here, we use Oli-neu cells, an immortalized cell line derived from primary murine oligodendrocytes, and primary rat oligodendrocyte cultures as model systems to identify molecular targets that link cell surface GPR17 to oligodendrocyte maturation blockade. We demonstrate that stimulation of GPR17 by the small molecule agonist MDL29,951 (2-carboxy-4,6-dichloro-1H-indole-3-propionic acid) decreases myelin basic protein expression levels mainly by triggering the Gαi/o signaling pathway, which in turn leads to reduced activity of the downstream cascade adenylyl cyclase-cAMP-PKA-cAMP response element-binding protein (CREB). In addition, we show that GPR17 activation also diminishes myelin basic protein abundance by lessening stimulation of the exchange protein directly activated by cAMP (EPAC), thus uncovering a previously unrecognized role for EPAC to regulate oligodendrocyte differentiation. Together, our data establish PKA and EPAC as key downstream effectors of GPR17 that inhibit oligodendrocyte maturation. We envisage that treatments augmenting PKA and/or EPAC activity represent a beneficial approach for therapeutic enhancement of remyelination in those demyelinating diseases where GPR17 is highly expressed, such as multiple sclerosis.
OSNR monitoring by deep neural networks trained with asynchronously sampled data (2016)

We demonstrate a use of deep neural networks (DNN) for OSNR monitoring with minimum prior knowledge. By using 5-layers DNN trained with 400,000 samples, the DNN successfully estimates OSNR in a 16-GBd DP-QPSK system.
Unsupervised Depth Completion with Calibrated Backprojection Layers (2021)

We propose a deep neural network architecture to infer dense depth from an image and a sparse point cloud. It is trained using a video stream and corresponding synchronized sparse point cloud, as obtained from a LIDAR or other range sensor, along with the intrinsic calibration parameters of the camera. At inference time, the calibration of the camera, which can be different than the one used for training, is fed as an input to the network along with the sparse point cloud and a single image. A Calibrated Backprojection Layer backprojects each pixel in the image to three-dimensional space using the calibration matrix and a depth feature descriptor. The resulting 3D positional encoding is concatenated with the image descriptor and the previous layer output to yield the input to the next layer of the encoder. A decoder, exploiting skip-connections, produces a dense depth map. The resulting Calibrated Backprojection Network, or KBNet, is trained without supervision by minimizing the photometric reprojection error. KBNet imputes missing depth value based on the training set, rather than on generic regularization. We test KBNet on public depth completion benchmarks, where it outperforms the state of the art by 30.5% indoor and 8.8% outdoor when the same camera is used for training and testing. When the test camera is different, the improvement reaches 62%. Code available at: https://github.com/alexklwong/calibrated-backprojection-network.
Metadata-Aware End-to-End Keyword Spotting (2020)

Published version
Gene Editing to Accelerate Crop Breeding (2022)

Recent advances in biotechnology have helped increase tissue transformation efficiency and the frequency and specificity of gene editing to an extent that introducing allelic variants directly in elite varieties has become possible. In comparison to the conventional approach of crossing an elite recipient line with an exotic donor parent to introduce the trait of interest followed by repeated backcrossing, direct introduction of major-effect allelic variants into elite varieties saves time and resources, and eliminates yield drag resulting from the residual donor genes at the end of backcrossing.
Model Studies of CBES Decomposition (FN3/BiF Chemical Laser) (1990)

Abstract : This report investigated the use of fluorine azide (FN3) as both an advanced high energy density propellant and as a fuel for an advanced high energy visible wavelength chemical laser. The proposed laser operates by producing the electronically excited NF(a) metastable species upon thermal dissociation of FN3 and utilizing subsequent energy transfer reactions to pump the BiF(A-X) laser transitions near 450 nm. The work was done in four major blocks which include: (1) Production of FN3; (2) Conversion of FN3 to NF(a); (3) Excitation of BiF(A) by NF(a); (4) Measurement of BiF(X). In the course of performing this work knowledge was gained concerning the mechanism of reaction and a number of key kinetic rate constants. Also efficient production of electronically excited species was demonstrated at densities large enough to power a high energy laser system. Finally, the BiF(X) ground state concentration was found to be consistent with a model based on population by radiative cascade from BiF(A) and removal by NF(a) at a near gas kinetic rate. These results support the development of an NF/BiF chemical laser that is operable at visable wavelengths. (TTL)
Theoretical investigation of photonic crystal waveguide splitters incorporating ultralow refractive index metallic nanowires (2005)

The present letter theoretically investigates the optical properties, and provides design guidelines for optimum performance of a photonic crystal (PC) waveguide splitter composed of ultralow refractive index metamaterials, by utilizing a rigorous analytical modeling based on the scattering matrix technique. We believe that this type of nanocomposite metallic PC waveguide can bring additional degrees of design flexibility to ultradense optical integration, because of its compact size and relatively low-loss propagation characteristics, mainly for power-splitting applications in the visible frequency spectrum.
Optical harmonic generation from semiconductor metasurfaces (Conference Presentation) (2020)

All-dielectric optical metasurfaces consist of 2D arrangements of nanoresonators and are of great importance for shaping polarization, phase and amplitude of both linear and harmonic fields. Here, we demonstrate the generation of second harmonic (SH) with zero-order diffraction from nonlinear AlGaAs metasurfaces with spatial period comparable with a pump wavelength in the near-IR. Upon normal incidence of the pump, we demonstrate paraxial SH light into the zero order. SH polarization is effectively controlled via either the meta-atom shape or the pump polarization, with potential applications for on-axis imaging and free-space communication systems.
Macromol. Chem. Phys. 21/2015 (2015)

Front Cover: The size-dependent pairing between an-isotropic multimaterial nanoparticles is demonstrated. The association is provided by the spontaneous assembly of Janus nanoparticles upon addition of a silica precursor. A face-selective silica coating on the surface of the Janus particles induces a morphology change, which then mediates the irreversible size-dependent pairing of the particles. Further details can be found in the article by D. Estupiñán, M. B. Bannwarth,* K. Landfester, and D. Crespy* on page 2070.
NFX1 Plays a Role in Human Papillomavirus Type 16 E6 Activation of NFκB Activity (2010)

High-risk human papillomavirus (HR HPV) requires differentiating epithelial cells to continue to divide in order to replicate the viral DNA. To achieve this, HPV perturbs several regulatory pathways, including cellular apoptosis and senescence signals. HPV E6 has been identified as a regulator of the NFκB signaling pathway, a pathway important in many cellular processes, as well as regulation of virus-host cell interactions. We report here that NFX1-91, an endogenously expressed transcriptional regulator of human telomerase reverse transcriptase (hTERT) that is targeted by HPV type 16 (HPV16) E6/E6-associated protein (E6AP) for degradation, is also critical for regulation of the NFκB pathway by HPV16 E6. Microarray analysis revealed induction of NFκB-responsive genes and reduction of NFκB inhibitors with knockdown of NFX1-91. Knockdown of NFX1-91 induced downregulation of p105, an NFκB inhibitor in both primary human foreskin keratinocytes (HFKs) and HCT116 cells. Chromatin immunoprecipitation assays further confirmed that NFX1-91 bound to the p105 promoter and upregulated its expression. Similarly, in HPV16 E6-positive cells, reduction of p105 expression was observed, paralleling knockdown of NFX1-91 expression. Overall, our data suggest a mechanism for HPV16 E6 activation of the NFκB pathway through NFX1-91. Also, it provides evidence that NFX1-91 can function as a dual regulator, not only a transcriptional repressor, but also a transcriptional activator, when bound to DNA.
Hexagonal faceted SiC nanopillars fabricated by inductively coupled SF6/O2 plasma method (2015)

Abstract. We demonstrate a top-down fabrication technique for nanometer scale silicon carbide (SiC) pillars by using inductively coupled SF6/O2 plasma etching. The obtained SiC nanopillars exhibit high anisotropy features (aspect ratio ~ 6.5) with high etch depth (&amp;gt;7 µm). The etch characteristics of SiC nanopillars obtained under these conditions show a high etch rate (550 nm/min) and a high selectivity (over 60 for Ni mask). We obtained hexagonal symmetry of SiC nanopillar, which might be attributed to the crystallographic structure of the SiC phase.
Silicon optical switches for ROADM applications (2014)

Silicon photonics has been applied to integrating many thermo-optical switch elements into one-chip 8 × 8 optical path switch device for CDC-ROADMs. High extinction ratio operation independently of polarization and ambient temperature has been demonstrated.