gebhart/patrepeval huggingface dataset:
TGFβ controls alveolar type 1 epithelial cell plasticity and alveolar matrisome gene transcription (2023)

Premature birth disrupts normal lung development and places infants at risk for bronchopulmonary dysplasia (BPD), a disease increasing in incidence which disrupts lung health throughout the lifespan. The TGFβ superfamily has been implicated in BPD pathogenesis, however, what cell lineage it impacts remains unclear. We show that <i>Tgfbr2</i> is critical for AT1 cell fate maintenance and function. Loss of <i>Tgfbr2</i> in AT1 cells during late lung development leads to AT1-AT2 cell reprogramming and altered pulmonary architecture, which persists into adulthood. Restriction of fetal lung stretch and associated AT1 cell spreading through a model of oligohydramnios enhances AT1-AT2 reprogramming. Transcriptomic and proteomic analysis reveal the necessity of <i>Tgfbr2</i> expression in AT1 cells for extracellular matrix production. Moreover, TGFβ signaling regulates integrin transcription to alter AT1 cell morphology, which further impacts ECM expression through changes in mechanotransduction. These data reveal the cell intrinsic necessity of TGFβ signaling in maintaining AT1 cell fate and reveal this cell lineage as a major orchestrator of the alveolar matrisome.
Ebola virus disease candidate vaccines under evaluation in clinical trials (2016)

Filoviruses are the etiological agents of two human illnesses: Ebola virus disease and Marburg virus disease. Until 2013, medical countermeasure development against these afflictions was limited to only a few research institutes worldwide as both infections were considered exotic due to very low case numbers. Together with the high case-fatality rate of both diseases, evaluation of any candidate countermeasure in properly controlled clinical trials seemed impossible. However, in 2013, Ebola virus was identified as the etiological agent of a large disease outbreak in Western Africa including almost 30,000 infections and more than 11,000 deaths, including case exportations to Europe and North America. These large case numbers resulted in medical countermeasure development against Ebola virus disease becoming a global public-health priority. This review summarizes the status quo of candidate vaccines against Ebola virus disease, with a focus on those that are currently under evaluation in clinical trials.
Playful and multi-sensory fieldwork: seeing, hearing and touching New York (2015)

Geographical fieldwork is being reinvigorated through pedagogical and methodological innovations. Yet, while there are many good ideas in circulation, there is less evidence of where these ideas are taking us: what students are getting out of them, and what significance they may have for the discipline. These questions are explored through case studies involving playful and multi-sensory fieldwork: collecting sounds, urban climbing, finding "accidental art" and getting lost. Students tend enjoy this approach to fieldwork, which inspires them to learn actively and creatively, fosters the acquisition of new skills and explores the broader possibilities of playful and multi-sensory geographies.
The human β-globin locus control region confers an early embryonic erythroid-specific expression pattern to a basic promoter driving the bacterial lacZ gene (1996)

The beta-globin locus control region (LCR) is contained on a 20 kb DNA fragment and is characterized by the presence of five DNaseI hypersensitive sites in erythroid cells, termed 5'HS1-5. A fully active 6.5 kb version of the LCR, called the muLCR, has been described. Expression of the beta-like globin genes is absolutely dependent on the presence of the LCR. The developmental expression pattern of the genes in the cluster is achieved through competition of the promoters for the activating function of the LCR. Transgenic mice experiments suggest that subtle changes in the transcription factor environment lead to the successive silencing of the embryonic epsilon-globin and fetal gamma-globin promoters, resulting in the almost exclusive transcription of the beta-globin gene in adult erythropoiesis. In this paper, we have asked the question whether the LCR and its individual hypersensitive sites 5'HS1-4 can activate a basic promoter in the absence of any other globin sequences. We have employed a minimal promoter derived from the mouse Hsp68 gene driving the bacterial beta-galactosidase (lacZ) gene. The results show that the muLCR and 5'HS3 direct erythroid-specific, embryonic expression of this construct, while 5'HS1, 5'HS2 and 5'HS4 are inactive at any stage of development. Expression of the muLCR and 5'HS3 transgenes is repressed during fetal stages of development. The transgenes are in an inactive chromatin conformation and the lacZ gene is not transcribed, as shown by in situ hybridization. These data are compatible with the hypothesis that the LCR requires the presence of an active promoter to adopt an open chromatin conformation and with models proposing progressive heterochromatization during embryogenesis. The results suggest that the presence of a beta-globin gene is required for LCR function as conditions become more stringent during development.
Fuel Economy and CO<sub>2</sub> Emissions of Ethanol-Gasoline Blends in a Turbocharged DI Engine (2013)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Engine dynamometer testing was performed comparing E10, E20, and E30 splash-blended fuels in a Ford 3.5L EcoBoost direct injection (DI) turbocharged engine. The engine was tested with compression ratios (CRs) of 10.0:1 (current production) and 11.9:1. In this engine, E20 (96 RON) fuel at 11.9:1 CR gave very similar knock performance to E10 (91 RON) fuel at 10:1 CR. Similarly, E30 (101 RON) fuel at 11.9:1 CR resulted in knock-limited performance equivalent to E20 at 10:1 CR, indicating that E30 could have been run at even higher CR with acceptable knock behavior.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;The data was used in a vehicle simulation of a 3.5L EcoBoost pickup truck, which showed that the E20 (96 RON) fuel at 11.9:1 CR offers 5% improvement in U.S. EPA Metro-Highway (M/H) and US06 Highway cycle tank-to-wheels CO₂ emissions over the E10 fuel, with comparable volumetric fuel economy (miles per gallon) and range before refueling. The results also indicated that the E30 (101 RON) fuel at 11.9:1 CR provides improvements in CO₂ emissions of 5% on the EPA M/H cycle and 7.5% on the US06 Highway cycle, while volumetric fuel economy was 3% lower on the M/H cycle and approximately equal on the US06 Highway cycle, compared to the baseline E10 fuel at 10:1 CR.&lt;/div&gt;&lt;/div&gt;
Studies of chain conformational kinetics in poly(di-n-alkylsilanes) by spectroscopic methods. 1. Poly(di-n-hexylsilane), poly(di-n-heptylsilane), and poly(di-n-octylsilane) (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies of chain conformational kinetics in poly(di-n-alkylsilanes) by spectroscopic methods. 1. Poly(di-n-hexylsilane), poly(di-n-heptylsilane), and poly(di-n-octylsilane)J. F. Rabolt, D. Hofer, R. D. Miller, and G. N. FickesCite this: Macromolecules 1986, 19, 3, 611–616Publication Date (Print):March 1, 1986Publication History Published online1 May 2002Published inissue 1 March 1986https://pubs.acs.org/doi/10.1021/ma00157a021https://doi.org/10.1021/ma00157a021research-articleACS PublicationsRequest reuse permissionsArticle Views227Altmetric-Citations159LEARN 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
AlGaN/GaN HEMT With a Transparent Gate Electrode (2009)

AlGaN/GaN high-electron-mobility transistors (HEMTs) with indium tin oxide (ITO) transparent gate electrodes have been fabricated. The transparent gate electrodes enable the investigation of photon, electron, and phonon behaviors in active regions in HEMTs using optical characterizations such as electroluminescence, photoluminescence, and Raman spectroscopy technologies. Leakage current, on/off ratio, and transparency have been compared for transistors using Ni/Au/Ni, ITO, and Ni/ITO stacks as gate electrodes. Compared to the Ni/Au/Ni gate transistor, the ITO gate device shows a comparable current gain cutoff frequency ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> ) but a much lower power gain cutoff frequency ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> ) due to the low conductivity of ITO.
A G-Rich Sequence within the c-kit Oncogene Promoter Forms a Parallel G-Quadruplex Having Asymmetric G-Tetrad Dynamics (2009)

Guanine-rich DNA sequences with the ability to form quadruplex structures are enriched in the promoter regions of protein-coding genes, particularly those of proto-oncogenes. G-quadruplexes are structurally polymorphic and their folding topologies can depend on the sample conditions. We report here on a structural study using solution state NMR spectroscopy of a second G-quadruplex-forming motif (c-kit2) that has been recently identified in the promoter region of the c-kit oncogene. In the presence of potassium ions, c-kit2 exists as an ensemble of structures that share the same parallel-stranded propeller-type conformations. Subtle differences in structural dynamics have been identified using hydrogen-deuterium exchange experiments by NMR spectroscopy, suggesting the coexistence of at least two structurally similar but dynamically distinct substates, which undergo slow interconversion on the NMR timescale.
Metal atom–guided conformational analysis of single polynuclear coordination molecules (2021)

Microscopic observation of single molecules is a rapidly expanding field in chemistry and differs from conventional characterization techniques that require a large number of molecules. One of such form of single-molecule microscopy is high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), which is especially suitable for coordination compounds because of its atomic number-dependent contrast. However, to date, single-molecule observations using HAADF-STEM has limited to simple planar molecules. In the present study, we demonstrate a direct structural investigation of nonplanar dendronized polynuclear Ir complexes with subnanometer resolution using Ir as an atomic label. Decreasing the electron dose to the dendrimer complexes is critical for the single-molecule observation. A comparison with simulated STEM images of conformational isomers is performed to determine the most plausible conformation. Our results enlarge the potential of electron microscopic observation to realize structural analysis of coordination macromolecules, which has been impossible with conventional methods.
Model-based optical proximity correction for immersion lithography-based flat optics platform (2023)

We introduce well-developed optical proximity correction (OPC) techniques to the metasurface-based flat optics manufacturing process. Flat optics, formed by subwavelength scale nanostructure pillar (nanopillar) array, so called metasurface, has become promising substitutes for conventional bulky optical components. For its manufacturing, photolithography is preferable rather than the electron beam lithography (EBL) technique because of its time and cost effectiveness for mass manufacturing. However, the required feature size and pitch of the metasurface for the visible light is approaching the process limit of the ArF immersion lithography. It results in critical dimension (CD) errors due to optical proximity effect and could result in efficiency degradation of the flat optics. In the semiconductor manufacturing industry, OPC based on process modelling and numerical computation has been developed for the last few decades to control the CD on the wafer. Here, a machine learning (ML) model is constructed to avoid the time consumption of the conventional OPC method without losing the accuracy. Various pitches of flat optics metalens, from 465 nm to 160 nm, has been studied for the implementation of the ML OPC. The root mean square (RMS) CD errors &lt; 1 nm and the CD accuracies &lt; 6 nm can be achieved. The CD error percentages over the pillar diameters &lt; 6 % is observed and the improvement of CD error and CD accuracy compared to rule based OPC in small pitches of metalens is demonstrated.
Comprehensive genomic and immunological characterization of Chinese non-small cell lung cancer patients (2019)

Deep understanding of the genomic and immunological differences between Chinese and Western lung cancer patients is of great importance for target therapy selection and development for Chinese patients. Here we report an extensive molecular and immune profiling study of 245 Chinese patients with non-small cell lung cancer. Tumor-infiltrating lymphocyte estimated using immune cell signatures is found to be significantly higher in adenocarcinoma (ADC, 72.5%) compared with squamous cell carcinoma (SQCC, 54.4%). The correlation of genomic alterations with immune signatures reveals that low immune infiltration was associated with EGFR mutations in ADC samples, PI3K and/or WNT pathway activation in SQCC. While KRAS mutations are found to be significantly associated with T cell infiltration in ADC samples. The SQCC patients with high antigen presentation machinery and cytotoxic T cell signature scores are found to have a prolonged overall survival time.
Phase dependent structural perturbation of a robust multicomponent assembled icosahedral array (2018)

We report on the assembly of three-fold axially compressed icosahedral arrays of the bowl shaped p-sulfonatocalix[4]arene molecules in the solid-state, intricately bound to dipicolinate and yttrium(iii) ions, with the compression reflected in Hirshfeld surface analyses. Solution studies show dissolution of the icosahedra intact, but with a geometrical rearrangement to regular icosahedra.
Functional testing provides unique insights into the pathomechanics of femoroacetabular impingement and an objective basis for evaluating treatment outcome (2013)

Femoroacetabular impingement (FAI) has been recognized as a significant clinical problem. While hip reshaping surgery for treating FAI has had positive clinical outcomes, there remains a need for objective functional outcomes of FAI treatment. We tested the hypothesis that during walking and stair climbing significant changes in hip kinematics would occur following hip reshaping surgery that indicate restoration of normal function post-operatively. Hip and pelvic kinematics were collected for 17 FAI patients pre- and 1 year post-operatively and compared to 17 healthy matched controls. Prior to surgery, FAI patients had significantly reduced hip internal rotation and hip sagittal plane range of motion during walking (p = 0.01, p < 0.001, respectively) and stair climbing (p = 0.01, p < 0.001, respectively) as compared with controls. Post-operatively, these motions were restored to normal during walking (p = 0.70, p = 0.46, respectively), but remained significantly reduced in the FAI patients during stair climbing (p = 0.03, p < 0.001, respectively). These results have important implications for understanding the functional pathomechanics of FAI and providing an objective basis for evaluating treatment outcome. The stair climbing results indicate that problems still exist in the hip joint for activities requiring higher ranges of hip motion and suggest a basis for exploring future improvements for the treatment of FAI.
Design and Simulational Verification for a Stretchable Optical Waveguide Sensor Featuring a Semi-Divided Core Cross Section (2022)

Stretchable optical waveguides provide viable sensing solutions for soft robots. So far, basic single layer or core-cladding waveguides have been developed using various manufacturing methods. Extending their structure to increase sensing functionality has been mostly unexplored. This study investigates a waveguide design featuring a semi-divided core cross section guiding the light from one light source to two light outputs. With optical ray tracing simulations using COMSOL, we verify the design’s two main working principles that enable two-degree-of-freedom sensing in various strain modes.
CELLULOSE NANOCOMPOSITES WITH DUCTILE MECHANICAL BEHAVIOR (2015)

Ductility mechanisms in biocomposites based on cellulose nano fibers (CNF) are discussed.Preparation is as follows: porous CNF networks are formed, and impregnated by unsaturated polyester or epoxy.
An AC active filter for use at capacitor commutated HVDC converters (2003)

Summary form only given, as follows. This paper discusses the application of an AC side active power filter in HVDC schemes involving capacitor commutated converters. A suitable topology and control algorithm is selected to achieve the necessary objective of filtering the lower order characteristic harmonics. The dependence of the filter's rating on parameters such as the extent of de-tuning of its passive elements is investigated. The performance of this filter in a capacitor commutated converter application is evaluated using an electromagnetic transient simulation program.
Abstract B161: Chemoproteomic profiling for target identification using chloroalkane derivatized compounds (2015)

Abstract Chemoproteomic technologies enable the quantitative and qualitative profiling of small molecule protein interactions. Here we report a new approach utilizing a chloroalkane (CA) capture tag which can be chemically attached to small molecules to enable the isolation of their respective protein targets through selective capture onto an immobilized HaloTag protein. We have combined our chemoproteomics workflow with multiplexed chemical labeling methods to enable the analysis of dose dependent target engagement studies in a single LC-MS/MS experiment. Here we demonstrate this workflow using BIRB796-CA, a modified kinase inhibitor. Target enrichment experiments were performed by incubating HEK293 cells with the BIRB-CA. Cells were then lysed and the BIRB-CA, together with the bound targets, was rapidly captured onto immobilized HaloTag protein. Unmodified compound was used to competitively elute putative interacting proteins. To study dose dependent effects on the protein interaction profile, cells were incubated with multiple mixtures of BIRB and BIRB-CA at varying relative concentrations. The eluted proteins were processed using SDS-PAGE and in-gel digestion. Digested material was labeled with Tandem Mass Tags (TMT) 10plex reagents and analyzed using nanoscale LC-MS/MS coupled with a Q Exactive mass spectrometer (Thermo). Protein identification was performed with MaxQuant (MaxQuant.org) and data validation and visualization was performed using Perseus (Perseus-framework.org). We tested this chemoproteomics workflow using the interaction of MAP kinases (MAPK) with BIRB796, an allosteric kinase inhibitor. Treatment of LPS simulated THP-1 cells with BIRB796 and BIRB-CA revealed minimal impact of the CA modification on the inhibition of TNFα secretion. The interaction of BIRB-CA with known BIRB targets MAPK13, MAPK12, MAPK9 and MAPK14 has been confirmed using label free quantitative proteomic profiling. We have optimized the TMT labeling method for minimal losses and sample processing steps. We are applying the TMT method to BIRB-CA and control pull downs and extending this workflow to include the BIRB/BIRB-CA titration samples. Here we will use post-acquisition data processing of the BIRB/BIRB-CA titration pull down data to assess compound binding characteristics with the inferred extension to compounds with unknown binding specificities. Citation Format: Michael Ford, Richard Jones, Ravi Amunugama, Danette Daniels, Rachel Ohana, Sergiy Levin, Thomas Kirkland, Marjeta Urh, Keith Wood. Chemoproteomic profiling for target identification using chloroalkane derivatized compounds. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B161.
An unusual Fischer indole synthesis with 4-keto acids: an indole incorporating the terminal hydrazine nitrogen (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn unusual Fischer indole synthesis with 4-keto acids: an indole incorporating the terminal hydrazine nitrogenRobin S. Eichen Conn, Alan W. Douglas, Sandor Karady, Edward G. Corley, Alfred V. Lovell, and Ichiro ShinkaiCite this: J. Org. Chem. 1990, 55, 9, 2908–2913Publication Date (Print):April 1, 1990Publication History Published online1 May 2002Published inissue 1 April 1990https://pubs.acs.org/doi/10.1021/jo00296a063https://doi.org/10.1021/jo00296a063research-articleACS PublicationsRequest reuse permissionsArticle Views994Altmetric-Citations18LEARN 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
Hepatomegaly in transgenic mice expressing an oncogenic form of beta-catenin. (2001)

Inappropriate activation of the Wnt/beta-catenin signaling, resulting mainly from activating mutations of the beta-catenin gene, has been implicated recently in the development of hepatocellular carcinoma (HCC). We have generated transgenic mice expressing an oncogenic form of beta-catenin in their hepatocytes to analyze the effect of deregulated beta-catenin signaling on liver homeostasis. These mice rapidly developed hepatomegaly soon after birth, with livers three to four times heavier than those of nontransgenic littermates. The liver cell hyperplasia resulted from increased cell proliferation without any compensatory apoptosis. Although the genes encoding c-myc and cyclin D1 are potential targets of the beta-catenin signaling pathway, neither of them was overexpressed in the hyperplastic livers of beta-catenin transgenic mice. Thus, the key target genes of the beta-catenin signaling pathway in the liver remain to be identified.