gebhart/patrepeval huggingface dataset:
Villin Enhances Hepatocyte Growth Factor-induced Actin Cytoskeleton Remodeling in Epithelial Cells (2003)

Villin is an actin-binding protein localized to intestinal and kidney brush borders. In vitro, villin has been demonstrated to bundle and sever F-actin in a calcium-dependent manner. Although villin is not necessary for the bundling of F-actin in vivo, it is important for the reorganization of the actin cytoskeleton elicited by stress during both physiological and pathological conditions ( Ferrary et al., 1999 ). These data suggest that villin may be involved in actin cytoskeleton remodeling necessary for many processes requiring cellular plasticity. Here, we study the role of villin in hepatocyte growth factor (HGF)-induced epithelial cell motility and morphogenesis. For this purpose, we used primary cultures of enterocytes derived from wild-type and villin knock-out mice and Madin-Darby canine kidney cells, expressing villin in an inducible manner. In vitro, we show that epithelial cell lysates from villin-expressing cells induced dramatic, calcium-dependent severing of actin filaments. In cell culture, we found that villin-expressing cells exhibit enhanced cell motility and morphogenesis upon HGF stimulation. In addition, we show that the ability of villin to potentiate HGF-induced actin reorganization occurs through the HGF-activated phospholipase Cγ signaling pathway. Collectively, these data demonstrate that villin acts as a regulator of HGF-induced actin dynamics.
Bluues server: electrostatic properties of wild-type and mutated protein structures (2012)

The Bluues server, examples and extensive help files are available for non-commercial use at URL: http://protein.bio.unipd.it/bluues/.
Stoichiometry of Ta–N Film and Its Application for Diffusion Barrier in the Al<sub>3</sub>Ta/Ta–N/Si Contact System (1990)

In order to obtain a stable contact structure applicable to Si–LSI thin film technology, we have produced the contact structure of Al 3 Ta/Ta–N/Si by interposing the Ta–N film as a diffusion barrier between Al 3 Ta film and Si substrate. The contact structure was heat-treated at various temperatures in vacuum, and the behavior of mass transport across the interfaces of both Al 3 Ta/Ta–N and Ta–N/Si caused by the heating process was examined by Auger depth analysis. Also, on the basis of X-ray diffraction and XPS analysis, the barrier properties of the Ta–N film were examined with respect to the crystalline state and the chemical bonding state of the film. It is revealed that the thermal stability of this contact structure is closely related to the stoichiometry of the Ta–N film used as a diffusion barrier.
A Gradient-Based Inverse Lithography Technology for Double-Dipole Lithography (2009)

Resolution enhancement techniques (RETs) have become indispensable for the sub-wavelength optical lithography. Inverse lithography technology (ILT) is one kind of RETs, which attempts to consider the mask synthesis as an inverse problem and compute the optimum mask by using the entire area of the design pattern with a rigorous mathematical approach. Doubledipole lithography (DDL) uses two orthogonal dipole illuminations and one or two masks to print the desired wafer pattern. The main challenge of using such an IC-manufacturing technique remains how to properly synthesize the proper mask pattern for the arbitrarily given target pattern. This paper presents a gradient-based ILT approach addressing the problem above, called DDL-ILT. This method has been demonstrated by synthesizing various kinds of masks for printing 45-nm critical dimension (CD) features. Images with good fidelity have been achieved.
An Automated Synoptic Typing Procedure to Predict Freezing Rain: An Application to Ottawa, Ontario, Canada (2004)

Freezing rain is a major weather hazard that can compromise human safety, significantly disrupt transportation, and damage and disrupt built infrastructure such as telecommunication towers and electrical transmission and distribution lines. In this study, an automated synoptic typing and logistic regression analysis were applied together to predict freezing rain events. The synoptic typing was developed using principal components analysis, an average linkage clustering procedure, and discriminant function analysis to classify the weather types most likely to be associated with freezing rain events for the city of Ottawa, Ontario, Canada. Meteorological data used in the analysis included hourly surface observations from the Ottawa International Airport and six atmospheric levels of 6-hourly NCEP-NCAR upper-air reanalysis weather variables for the winter months (Nov-Apr) of 1958/59-2000/01. The data were divided into two parts: a developmental dataset (1958/59-1990/91) for construction (development) of the model and an independent or validation dataset (1991/90-2000/01) for validation of the model. The procedure was able to successfully identify weather types that were most highly correlated with freezing rain events at Ottawa.
High-quality transparent conductive indium oxide films prepared by thermal evaporation (1980)

Highly transparent (over 90% transmission in the visible range) and highly conductive (resistivity ≃2×10−4 Ω cm) indium oxide (undoped) films have been produced by thermal evaporation from an In+In2O3 source in a vacuum chamber containing low pressures of O2. These properties are comparable or superior to the best tin-doped indium oxide films ever reported, and excellent reproducibility has been achieved. Hall effect measurements have revealed that the observed low resistivity is primarily a result of the excellent electron mobility (≃70 cm2/V sec), although the electron concentration is also rather high (⩾4×1020/cm3). X-ray diffraction measurements show distinctly polycrystalline In2O3 structure with a lattice constant ranging from 10.07 to 10.11 Å. Electrolytic electroreflectance spectra exhibit at least four critical transitions, from which we have determined the direct and indirect optical band gaps (≃3.56 and 2.69 eV, respectively). Burstein shifts due to the population of electrons in the conduction band are also observed. These and other results along with a discussion of the processing details are reported.
Activation of pS2 gene transcription is a primary response to estrogen in the human breast cancer cell line MCF-7. (1984)

We have shown previously that an increase in the level of accumulated pS2 mRNA is first detectable in MCF-7 cells after 3 hr of estradiol treatment. Using in vitro nuclear run-on transcription with nuclei prepared from MCF-7 cells grown in the presence of estradiol or in estradiol-stripped medium, we demonstrate here that expression of the pS2 gene is controlled by estrogen at the transcriptional level. Induction of transcription is a very early event that is already apparent within 15 min after addition of estradiol to the culture medium. In addition, pretreatment of the cells with the protein synthesis inhibitor cycloheximide does not prevent induction of pS2 gene transcription, indicating that it corresponds to a primary effect of estrogen. The pS2 gene in MCF-7 cells represents a unique example of a human gene whose transcription is directly controlled by estrogen.
Cloning and Sequencing of Two <i>Ceriporiopsis subvermispora</i> Bicupin Oxalate Oxidase Allelic Isoforms: Implications for the Reaction Specificity of Oxalate Oxidases and Decarboxylases (2005)

Oxalate oxidase is thought to be involved in the production of hydrogen peroxide for lignin degradation by the dikaryotic white rot fungus Ceriporiopsis subvermispora. This enzyme was purified, and after digestion with trypsin, peptide fragments of the enzyme were sequenced using quadrupole time-of-flight mass spectrometry. Starting with degenerate primers based on the peptide sequences, two genes encoding isoforms of the enzyme were cloned, sequenced, and shown to be allelic. Both genes contained 14 introns. The sequences of the isoforms revealed that they were both bicupins that unexpectedly shared the greatest similarity to microbial bicupin oxalate decarboxylases rather than monocupin plant oxalate oxidases (also known as germins). We have shown that both fungal isoforms, one of which was heterologously expressed in Escherichia coli, are indeed oxalate oxidases that possess < or =0.2% oxalate decarboxylase activity and that the organism is capable of rapidly degrading exogenously supplied oxalate. They are therefore the first bicupin oxalate oxidases to have been described. Heterologous expression of active enzyme was dependent on the addition of manganese salts to the growth medium. Molecular modeling provides new and independent evidence for the identity of the catalytic site and the key amino acid involved in defining the reaction specificities of oxalate oxidases and oxalate decarboxylases.
Multiple melting in segmented polyurethane block copolymers (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMultiple melting in segmented polyurethane block copolymersJeffrey T. Koberstein and Adam F. GalambosCite this: Macromolecules 1992, 25, 21, 5618–5624Publication Date (Print):October 1, 1992Publication History Published online1 May 2002Published inissue 1 October 1992https://pubs.acs.org/doi/10.1021/ma00047a010https://doi.org/10.1021/ma00047a010research-articleACS PublicationsRequest reuse permissionsArticle Views1148Altmetric-Citations161LEARN 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
Dwarfism, impaired skin development, skeletal muscle atrophy, delayed bone development, and impeded adipogenesis in mice lacking Akt1 and Akt2 (2003)

To elucidate the functions of the serine/threonine kinase Akt/PKB in vivo, we generated mice lacking both akt1 and akt2 genes. Akt1/Akt2 double-knockout (DKO) mice exhibit severe growth deficiency and die shortly after birth. These mice display impaired skin development because of a proliferation defect, severe skeletal muscle atrophy because of a marked decrease in individual muscle cell size, and impaired bone development. These defects are strikingly similar to the phenotypes of IGF-1 receptor-deficient mice and suggest that Akt may serve as the most critical downstream effector of the IGF-1 receptor during development. In addition, Akt1/Akt2 DKO mice display impeded adipogenesis. Specifically, Akt1 and Akt2 are required for the induced expression of PPARgamma, the master regulator of adipogenesis, establishing a new essential role for Akt in adipocyte differentiation. Overall, the combined deletion of Akt1 and Akt2 establishes in vivo roles for Akt in cell proliferation, growth, and differentiation. These functions of Akt were uncovered despite the observed lower level of Akt activity mediated by Akt3 in Akt1/Akt2 DKO cells, suggesting that a critical threshold level of Akt activity is required to maintain normal cell proliferation, growth, and differentiation.
Electrical aspects of aerosol formation and control (1968)

Abstract The particles or droplets of an aerosol are usually charged or can be induced to acquire charge. This makes possible their manipulation by electric and, to some extent, by magnetic fields, not only when they are already fully grown, but also during the process of their formation or disappearance. In this manner their size, number, trajectories, form and site of deposition can be varied within wide limits. These principles have been applied in some cases and are obviously potentially applicable to a great many more. My own researches are concerned with the physics of combustion processes, where such methods can be used to act on dispersions of fuel, solid products or intermediates, but extrapolations to other fields readily suggest themselves.
RObust Header Compression Version 2 (ROHCv2): Profiles for RTP, UDP, IP, ESP and UDP-Lite (2008)

This document specifies an Internet standards track protocol for the Internet community, and requests discussion and suggestions for improvements.
Substrate-induced band gap in graphene on hexagonal boron nitride:<i>Ab initio</i>density functional calculations (2007)

We determine the electronic structure of a graphene sheet on top of a lattice-matched hexagonal boron nitride $(h\text{\ensuremath{-}}\mathrm{B}\mathrm{N})$ substrate using ab initio density functional calculations. The most stable configuration has one carbon atom on top of a boron atom, and the other centered above a BN ring. The resulting inequivalence of the two carbon sites leads to the opening of a gap of $53\phantom{\rule{0.3em}{0ex}}\mathrm{meV}$ at the Dirac points of graphene and to finite masses for the Dirac fermions. Alternative orientations of the graphene sheet on the BN substrate generate similar band gaps and masses. The band gap induced by the BN surface can greatly improve room temperature pinch-off characteristics of graphene-based field effect transistors.
Tenascin is differentially expressed in endometrium and endometriosis (1999)

Endometriosis is characterized by the presence of functional endometrial tissue outside the uterine cavity, most commonly on the ovary and peritoneum. The aetiology of endometriosis is not understood, although the adhesion of endometrial cells to the extracellular matrix (ECM) would be expected to play a central role in its pathogenesis. The expression of ECM molecules in endometrium and in endometriosis has been investigated using immunohistochemistry and western blotting techniques. The ECM components collagen IV, laminin, vitronectin, and fibronectin had a similar pattern of expression throughout the menstrual cycle in endometrium and endometriosis. Expression of tenascin was elevated in the stroma of the functionalis region of the endometrium during the proliferative stage of the menstrual cycle and in endometriosis. Tenascin expression in endometriosis was not modulated according to the stage of the menstrual cycle. It is concluded that expression of tenascin is strictly regulated in endometrium and may be important in endometrial regeneration and in the pathogenesis of endometriosis.
In vitro Lipid Binding Assay (2013)

This is a protocol to examine in vitro protein-lipid binding using membrane strips coated with various lipids. It has been successfully used to study in vitro interaction between lipids and C. elegans proteins.
An eXtensible Web Modeling Framework (1999)

This document presents the eXtensible Web Modeling Framework (XWMF) which is based on the Resource Description Framework (RDF) [5, 10]. Both frameworks use metadata to describe properties of web resources. Our proposed framework applies the same (meta-) data model to reason about web site data, and to specify the structure and content of a web site and making statements about the elements of a web site. A formal model defining the various properties can lead to a consistent structure and easier maintenance. The formal model of the XWMF results in machine-understandable and interoperable content- and meta-data of a web site. The data model is capable to structure information from small units such as elements or single web pages (for authoring-in-the-small) to large structures such as web sites (for authoring-in-the-large). The formal model of XWMF can lead to the development of better software tools supplying web site development and maintenance.
miR-320 Regulates Glucose-Induced Gene Expression in Diabetes (2012)

miRNAs play an important role in several biological processes. Here, we investigated miR-320 in glucose-induced augmented production of vasoactive factors and extracellular matrix (ECM) proteins. High glucose exposure decreased the expression of microRNA 320 (miR-320) but increased the expression of endothelin 1 (ET-1), vascular endothelial growth factor (VEGF), and fibronectin (FN) in human umbilical vein endothelial cells (HUVECs). Transfection of miR-320 mimics restored ET-1, VEGF and FN mRNA, and protein expression in HUVECs treated with high glucose. Furthermore, miR-320 mimic transfection reduced glucose-induced augmented production of ERK1/2. Data from this study indicates that miR-320 negatively regulates expression of ET-1, VEGF, and FN through ERK 1/2. Identification of such novel glucose-induced mechanism regulating gene expression may offer a new strategy for the treatment of diabetic complications.
Facial Expression Recognition for In-the-wild Videos (2020)

In this paper, we propose a method for facial expression recognition for in-the-wild videos. Our method combines Deep Residual Network (ResNet) and Bidirectional Recurrent Neutral Network with Long-Short-Term Memory Unit (BLSTM). This method won the 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> place in the seven basic expression classification track of Affective Behavior Analysis in-the-wild Competition held in conjunction with the IEEE International Conference on Automatic Face and Gesture Recognition (FG) 2020, achieving 66.9% accuracy and 40.8% final metric on the test set. We also visualize the learned attention maps and analyze the importance of different regions in facial expression recognition.
Transverse diaphragms and unbonded CFRP post-tensioning in box-beam bridges (2010)

This paper presents the effects of the number of transverse diaphragms and the level of transverse posttensioning forces using unbonded carbon-fiber-reinforced-polymer (CFRP) strands on the behavior of side-by-side box-beam bridges. An experimental program, consisting of load- and strain-distribution tests, was conducted on a half-scale, 30-deg-skew, side-by-side box-beam bridge model. The bridge model was tested under 3 different phases: uncracked deck slab, cracked deck slab, and replaced beam. An ultimate-load test was conducted to evaluate the response of the unbonded transverse posttensioning arrangement up to failure of the bridge model. The experimental results show that increasing the level of transverse posttensioning forces generally improved the flexural behavior of the bridge model. Furthermore, the different arrangements of the transverse posttensioning forces had insignificant influence on the transverse strains developed in the region between the diaphragms. From the results of the ultimate-load test, it was evident that the unbonded transverse posttensioning arrangement coupled with the deck slab uniformly distributed the applied eccentric load in the transverse direction until complete flexural failure of the bridge model occurred.
Improved Approach of Seed Point Selection in RPCCL Algorithm for Aerial Remote Sensing Hyper-spectral Data Clustering with Data Dimensionality Reduction (2007)

The existing RPCCL (rival penalization controlled competitive learning) algorithm has provide an attractive way to perform data clustering. However its performance is sensitive to the selection of the initial cluster center. In this paper, we further investigate the RPCCL and present an improved approach of seed point selection which chooses non-neighbor data points of the greatest local density as seed points. We compare the performance of the RPCCL clustering with the selecting seed points and with the random seed points in red tide and oil spill aerial remote sensing hyper-spectral data (ARSHD) image. The experiments have produced the promising results. Additionally, because of the redundancy of high dimensions in the oil spill hyper-spectral data, a dimensionality reduction method is also described.
Human Cytomegalovirus Inhibits Major Histocompatibility Complex Class II Expression By Disruption of the Jak/Stat Pathway (1998)

Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus that is able to persist for decades in its host. HCMV has evolved protean countermeasures for anti-HCMV cellular immunity that facilitate establishment of persistence. Recently it has been shown that HCMV inhibits interferon gamma (IFN-gamma)-stimulated MHC class II expression, but the mechanism for this effect is unknown. IFN-gamma signal transduction (Jak/Stat pathway) and class II transactivator (CIITA) are required components for IFN-gamma-stimulated MHC class II expression. In this study, we demonstrate that both a clinical isolate and a laboratory strain of HCMV inhibit inducible MHC class II expression at the cell surface and at RNA level in human endothelial cells and fibroblasts. Moreover, reverse transcriptase polymerase chain reaction and Northern blot analyses demonstrate that neither CIITA nor interferon regulatory factor 1 are upregulated in infected cells. Electrophoretic mobility shift assays reveal a defect in IFN-gamma signal transduction, which was shown by immunoprecipitation to be associated with a striking decrease in Janus kinase 1 (Jak1) levels. Proteasome inhibitor studies with carboxybenzyl-leucyl-leucyl-leucine vinyl sulfone suggest an HCMV-associated enhancement of Jak1 protein degradation. This is the first report of a mechanism for the HCMV-mediated disruption of inducible MHC class II expression and a direct virus-associated alteration in Janus kinase levels. These findings are yet another example of the diverse mechanisms by which HCMV avoids immunosurveillance and establishes persistence.
Spectrally resolved passive acoustic imaging (2020)

Ultrasound in combination with circulating microbubble contrast agents has emerged as a promising modality for therapy and imaging of brain diseases. Despite progress, the need for spatio-temporal mapping and control of the cerebrovascular microbubble dynamics necessitates the development of fast and spectrally resolved trans-skull imaging methods. In this talk, we will present our recent efforts towards establishing such methods. First, we will introduce a general methodology using the angular spectrum (AS) approach in a heterogeneous medium, which is based on a numerical marching scheme to approximate the full implicit solution, and reveal its functionality for trans-skull passive acoustic imaging (70% source localization error reduction from 2.89 ± 1.76 mm to 0.68 ± 52 mm). Then, we will demonstrate the ability of AS in combination with a nonlinear state controller that uses specific frequency bands of the microbubble acoustic emissions (harmonic, ultra-harmonic, etc.) to attain stable cavitation activity for tens of seconds. Finally, we will present our progress towards adapting the AS method for rapid visualization of vessel structures with diameters of a few hundreds of microns. The superior image quality and computation efficiency (&gt;100-fold faster from time-domain delay-and-sum methods) of AS offers unique opportunities for spectrally resolved passive acoustic imaging and image guided therapy of human disease.
Book reviews (2010)

Click to increase image sizeClick to decrease image size Notes 1. Available: http://www.un.org/millenniumgoals/maternal.shtml (accessed 4 June 2010). 2. Available:http://www.who.int/reproductivehealth/publications/general/RHR_04_8/en/index.html (accessed 4 June 2010). 3. Available: http://unmillenniumproject.org/resources/quickwins.htm (accessed 4 June 2010).