gebhart/patrepeval huggingface dataset:
145 CHARACTERIZATION OF THE PROTEIN ARGININE METHYLTRANSFERASE-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE-NITRIC OXIDE AXIS DURING PORCINE EMBRYO DEVELOPMENT (2011)

Transcriptional deep sequencing analysis by Bauer et al. (2010) revealed a significant increase in expression of the arginine transporter SLC7A1 in in vitro–cultured porcine blastocysts compared with those cultured in vivo and this was corrected through supplemental arginine. This indicates an important role for arginine during porcine embryo development. Arginine is the precursor for nitric oxide (NO) production and previous work in mice and cattle has shown decreased development when embryos were cultured with a nitric oxide synthase (NOS) inhibitor. The NOS activity is inhibited by monomethylarginine (MMA) and asymmetric dimethylarginine (ADMA) that are released during degradation of proteins methylated by protein arginine methyltransferases (PRMT). The enzyme dimethylarginine dimethylaminohydrolase (DDAH) is responsible for degrading MMA and ADMA in the cell. Therefore, the goal of this study was to investigate whether this PRMT-DDAH-NO axis exists in pre-implantation porcine embryos. To this end, expression of PRMT1, PRMT3, PRMT5, DDAH1 and endothelial NOS (NOS3) was analysed at different stages of embryonic development using real-time quantitative RT-PCR. In addition, the effect of supplemental arginine (1.69 mM) on the expression of the aforementioned genes was investigated. Production of NO in porcine embryos was also visualised using 4-amino-5-methylamino-2,7-difluorofluorescein diacetate (DAF-FM-DA). In vitro–fertilized porcine embryos were collected at the 4-cell and blastocyst stages. The RNA was isolated from pools of 18 to 20 embryos and cDNA, was synthesised using Superscript III (Invitrogen, Carlsbad, CA, USA). Real-time PCR analysis was performed and the mean fold change in gene expression from the reference gene YWHAG was analysed by t-test after a log transformation. Expression of PRMT3 and PRMT5 was significantly higher (P &amp;lt; 0.05) in blastocysts versus 4-cell embryos. Expression of PRMT1, however, was higher in 4-cell embryos (P &amp;lt; 0.05). The expression of DDAH1 was detected in 4-cell embryos, but DDAH1 became undetectable by the blastocyst stage. Previous microarray analysis in our laboratory by Whitworth et al. (2005 Biol. Reprod.72(6), 1437–1451) also revealed a significant up-regulation of DDAH2 expression at the 4-cell stage versus blastocysts. Expression of NOS3 was undetectable in the 4-cell and blastocyst; however, NO was detected in 4-cell and blastocyst stage embryos by using DAF-FM-DA. This suggests that a different NOS may be acting in the porcine embryo. Addition of arginine did not have a significant effect on expression of the analysed genes. These results suggest that PRMT-DDAH regulated NO production may play a role during porcine embryo development. Understanding the PRMT-DDAH-NO axis and its regulation during embryonic development will further our ability to tailor in vitro culture so that it more appropriately mimics that of an in vivo environment. Funding was provided by NIH U42 RR18877.
Introduction (2007)

The information overload is a well-known phenomenon of the information age, since due to the progress in computer power and storage capacity over the last decades, data is produced at an incredible rate, and our ability to collect and store these data is increasing at a faster rate than our ability to analyze it. But, the analysis of these massive, typically messy and inconsistent, volumes of data is crucial in many application domains. For decision makers, analysts or emergency response teams it is an essential task to rapidly extract relevant information from the flood of data.
Electrified Drive-Unit Parametric Mechanical-Loss Model Development and Calibration (2019)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;As the automotive industry vies to meet progressively more stringent global CO2 regulations in a cost-effective manner, electrified drive system cost and losses must be reduced. To this end, a parametric Drive Unit (DU) mechanical-loss model was developed to aid in the design and development of electrified propulsion systems, where the total propulsion system cost and DU losses can be directly linked (e.g., Hybrid Electric Vehicle (HEV) motor/inverter/engine content, or Battery Electric Vehicle (BEV) battery size).&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Many DUs for electrified propulsion systems are relatively “simple” drive systems, consisting of gears, bearings, shafts, lip seals, and an electric motor(s), but without clutches, high-pressure lube systems, or chains/belts as found in conventional automatic transmissions. The DU loss model described in this paper studies these simple DUs, with the mechanical losses dissected into 10 loss components.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Analysis was conducted at the vehicle level to assess the relative loss contributions of the DU, motors, engine, etc. for the entire vehicle propulsion system to show the DU loss contribution to the total system. The DU loss model was used to deconstruct the total DU mechanical loss into subcomponents of Speed-Dependent (SD) and Load-Dependent (LD) losses. For each loss component, standard loss model equations were modified, or new equations were created, and calibrated based on loss data/trends of component-level bench tests, supplier data, and/or DU-level tests. Particular emphasis was placed on the LD components of the gear and bearing losses, as a function of load, speed and temperature, as they can represent a large portion of the total DU loss. DU-level tests were conducted at various positive and negative (regenerative braking) loads, speeds, fluid types, temperatures, and sump-fill levels to aid the development of the model. The model calibration methodology is described, where the calibrations of some of the individual component models were iterated, so that a universal set of loss model calibrations produced loss results that closely matched the test DU losses at the various operating conditions.&lt;/div&gt;&lt;/div&gt;
SK2 Channels Are Neuroprotective for Ischemia-Induced Neuronal Cell Death (2011)

In mouse hippocampal CA1 pyramidal neurons, the activity of synaptic small-conductance Ca(2+)-activated K(+) channels type 2 (SK2 channels) provides a negative feedback on N-methyl-D-aspartate receptors (NMDARs), reestablishing Mg(2+) block that reduces Ca(2+) influx. The well-established role of NMDARs in ischemia-induced excitotoxicity led us to test the neuroprotective effect of modulating SK2 channel activity following cerebral ischemia induced by cardiac arrest and cardiopulmonary resuscitation (CA/CPR). Administration of the SK channel positive modulator, 1-ethyl-benzimidazolinone (1-EBIO), significantly reduced CA1 neuron cell death and improved CA/CPR-induced cognitive outcome. Electrophysiological recordings showed that CA/CPR-induced ischemia caused delayed and sustained reduction of synaptic SK channel activity, and immunoelectron microscopy showed that this is associated with internalization of synaptic SK2 channels, which was prevented by 1-EBIO treatment. These results suggest that increasing SK2 channel activity, or preventing ischemia-induced loss of synaptic SK2 channels, are promising and novel approaches to neuroprotection following cerebral ischemia.
SU-FF-J-12: Computed 4D Patient Models for Motion Compensation in Radiotherapy (2005)

Purpose: We designed a system that can track tumors moving due to respiratory motion, allowing more specific and effective irradiation of the tumor. Method and Materials: First two CT scans are taken during maximal inhalation and exhalation. Then several synthetic intermediate scans are computed by using morphing methods, yielding a 3D motion picture. Before treatment x-ray images are taken periodically and compared to the 4D model. After registration of the x-ray with the model we know the best matching stack and therefore tumor position and respiratory state. Thus we acquire correlation from respiratory state to tumor position. Due to a registration time of 10 seconds for each stack, we only get intermittent information about the target location. The target may already have moved. Therefore we use an infrared tracking system, with emitters attached to significant positions of the patient's body, to report information on the current state of respiration in real-time. The information of the sensor is correlated to the target location computed by the comparison between the live shot and the model. Results: To create the model we use a thin-plate spline-based method. 47 corresponding control points were manually selected for deforming a lung. To evaluate the results transversal snap shots were compared with the model, yielding the corresponding respiratory state. We also tested the 2D/4D registration process by generating two mutually orthogonal DRRs, which we matched afterwards to the model. The best match was the stack containing the DRRs, furthermore the neighboring stacks led to the next best results. Conclusion: We have shown that it is possible to determine the respiratory state by matching a synthetic x-ray to a generated 4D model of an internal organ. Next steps will be to improve our method of generating the model and to test the registration with real x-rays.
High-efficiency expression gene cloning by flow cytometry. (1996)

Our goal was to develop a convenient and widely applicable procedure for gene cloning based on flow cytometry. To this purpose, we have developed an efficient protocol for DNA transfection and selection of rare transfectants. Transfection by calcium phosphate co-precipitation was extensively investigated. The use of specific batches of calcium chloride, of carrier DNA purified in guanidinium thiocyanate, and of plasmid DNA banded in cesium chloride proved crucial for high efficiency of transfection. Several tissue culture parameters were also found critical. With the optimized procedure we can transfect almost 100% of the COS-7 cells with cDNA encoding cell surface antigens or green fluorescent protein. Moreover, we routinely obtain high average levels of expression. Efficient cell sorting in flow cytometry was achieved by subtracting the cell autofluorescence background, by displacing stained cells in the red dimension, and by combining fluorescein-conjugated primary and secondary antibodies. Efficient recovery of the transfected DNA constructs was obtained from 2500-3000 cells directly sorted in Hirt lysis buffer. Using the above protocol we have cloned by expression the gene encoding Trop-2, a cell surface glycoprotein expressed by human carcinomas.
Content adaptation for visual impairment in MPEG-21 (2004)

In this paper, we propose content adaptation for visual impairments in MPEG-21. The proposed content adaptation aims to give enhanced visual accessibility to users with visual impairment in MPEG-21. In this paper, we consider two major visual impairments: low vision impairment and color vision deficiency. The proposed method includes description for the visual impairments and content adaptation technique based on it. We have developed a symptom-based description of visual impairment characteristics for users with visual impairment in the context of MPEG-21 digital item adaptation (DIA). To verify usefulness of the proposed method, we performed some experiments with the content adaptation based on the description in MPEG-21. The experiment results showed that the proposed method is effective content adaptation for user with visual impairment and gives enhanced visual accessibility to them.
Supplemental Table S2-3 from The BET Bromodomain Inhibitor OTX015 Affects Pathogenetic Pathways in Preclinical B-cell Tumor Models and Synergizes with Targeted Drugs (2023)

&lt;p&gt;Supplemental Table S2-3. Supplemental Table S2: List of genes affected by OTX015 in DLBCL cell lines exposed to OTX015. Supplemental Table S3: gene-sets affected by OTX015 in DLBCL cell lines exposed to OTX015.&lt;/p&gt;
PI3K Inhibition Activates SGK1 via a Feedback Loop to Promote Chromatin-Based Regulation of ER-Dependent Gene Expression (2019)

The PI3K pathway integrates extracellular stimuli to phosphorylate effectors such as AKT and serum-and-glucocorticoid-regulated kinase (SGK1). We have previously reported that the PI3K pathway regulates estrogen receptor (ER)-dependent transcription in breast cancer through the phosphorylation of the lysine methyltransferase KMT2D by AKT. Here, we show that PI3Kα inhibition, via a negative-feedback loop, activates SGK1 to promote chromatin-based regulation of ER-dependent transcription. PI3K/AKT inhibitors activate ER, which promotes SGK1 transcription through direct binding to its promoter. Elevated SGK1, in turn, phosphorylates KMT2D, suppressing its function, leading to a loss of methylation of lysine 4 on histone H3 (H3K4) and a repressive chromatin state at ER loci to attenuate ER activity. Thus, SGK1 regulates the chromatin landscape and ER-dependent transcription via the direct phosphorylation of KMT2D. These findings reveal an ER-SGK1-KMT2D signaling circuit aimed to attenuate ER response through a role for SGK1 to program chromatin and ER transcriptional output.
Optical memory effect in GaN epitaxial films (1997)

We report on memory effects in the optical properties of GaN and AlN epitaxial-films grown by atmospheric pressure metal organic chemical vapor deposition. After exposing selected areas of particular samples with He–Cd laser light (3.8 eV), we observed a persistent and marked decrease in the near band edge photoluminescence (PL) intensity emitted from these areas. This effect has been observed in epitaxial films that typically have a pyramidlike hillock surface. This ability to modulate PL emission intensity at individual points in these materials can be exploited as a method for optical data storage. A means of erasing information stored using this effect has also been investigated using lower energy (∼2 eV).
Enabling Introduction of Stereoscopic (3D) Video: Formats and Compression Standards (2007)

After the introduction of HDTV, the next expected milestone is stereoscopic (3D) TV. This paper gives a summary of the new MPEG-C part 3 standard, capable of compressing the 2D+Z format, and shows how it can be used to serve the Is generation of 3DTVs. Furthermore it gives directions on how this standard could be extended to serve also the generations beyond.
Heterogeneous Reactions on Salts (2003)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHeterogeneous Reactions on SaltsMichel J. RossiView Author Information Laboratoire de Pollution Atmosphérique et Sol (LPAS), Institut des Sciences et Techniques de l'Environnement (ISTE), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland Cite this: Chem. Rev. 2003, 103, 12, 4823–4882Publication Date (Web):November 18, 2003Publication History Received3 February 2003Published online18 November 2003Published inissue 1 December 2003https://pubs.acs.org/doi/10.1021/cr020507nhttps://doi.org/10.1021/cr020507nresearch-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views2006Altmetric-Citations175LEARN 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 SUBJECTS:Aerosols,Anions,Chemical reactions,Salts,Solution chemistry Get e-Alerts
Contrasting Metabolic Profiles of TGFβ2 and TNFα in the Induction of Retinal Epithelial‐Mesenchymal Transition (EMT) (2022)

Epithelial‐mesenchymal‐transition (EMT) is a process whereby epithelial cells transdifferentiate into matrix‐producing mesenchymal cells. EMT of retinal pigment epithelial cells (RPE) plays a crucial role in severe ocular pathologies including retinal fibrosis. Emerging evidence implicates metabolic and mitochondrial dysfunction as key drivers of EMT. Both transforming growth factor‐beta 2 (TGFβ2) and tumor necrosis factor‐alpha (TNFα) have the capacity to induce EMT in RPE; however, little is known about their impact on mitochondrial metabolism. We hypothesized that TGFβ2 and TNFα should share similar metabolic effects, i.e. repressed mitochondrial function and enhanced glycolysis, to support EMT of RPE. Matured human primary RPE (H‐RPE) were treated with TGFβ2 or TNFα (both at 10 ng/ml) for up to 5 days for Seahorse metabolic assays (Mito and Glycolytic Stress Tests), qPCR and untargeted metabolomics analysis (West Coast Metabolomics Center) analyzed using MetaboAnalyst. Both TGFβ2 and TNFα induced the upregulation of mesenchymal genes (fibronectin and matrix metalloproteinase‐2) in H‐RPE. While TNFα significantly upregulated inflammatory genes (IL‐6, IL‐8, IL‐1β, MCP‐1), no changes were evident in TGFβ2‐treated cells. Metabolically, TGFβ2 induced the “Warburg effect” in H‐RPE with enhanced glycolysis and a suppression of oxidative phosphorylation capacity. Surprisingly, TNFα showed the opposite effect with enhanced oxidative phosphorylation (higher basal levels of oxygen consumption and maximal respiration) and reduced glycolysis and glycolytic capacity. Metabolomics profiling showed distinct metabolomics signatures associated with TGFβ2‐ and TNFα‐treated primary RPE cells. Of the 188 metabolites tested, 7 metabolites were significantly changed in TGFβ2‐treated cells and 26 in TNFα‐treated cells. Enrichment analysis depicted altered glutathione metabolism, proline metabolism, aminoacyl‐tRNA synthesis, nicotinamide metabolism, pentose phosphate pathway and arachidonic acid metabolism in TNFα‐treated cells whereas TGFβ2‐treated cells showed perturbations in the biosynthesis of fatty acids, tryptophan metabolism, linoleic acid metabolism and arachidonic acid metabolism. The divergent bioenergetic rewiring governing TGFβ2 and TNFα in their induction of EMT may be linked to their differential effect on inflammation. Elucidating the contributions of TGFβ2 and TNFα and their mechanistic differences will enable the development of more effective drug targets for combating retinal fibrosis.
Predictive Model for Macular Hole Closure Speed: Insights From Intraoperative Optical Coherence Tomography (2019)

This study provides unique insights into the potential role of iOCT imaging in predicting retinal tissue behavior during MH repair.
Data from IND-Enabling Studies for a Clinical Trial to Genetically Program a Persistent Cancer-Targeted Immune System (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;To improve persistence of adoptively transferred T-cell receptor (TCR)–engineered T cells and durable clinical responses, we designed a clinical trial to transplant genetically-modified hematopoietic stem cells (HSCs) together with adoptive cell transfer of T cells both engineered to express an NY-ESO-1 TCR. Here, we report the preclinical studies performed to enable an investigational new drug (IND) application.&lt;/p&gt;Experimental Design:&lt;p&gt;HSCs transduced with a lentiviral vector expressing NY-ESO-1 TCR and the PET reporter/suicide gene HSV1-sr39TK and T cells transduced with a retroviral vector expressing NY-ESO-1 TCR were coadministered to myelodepleted HLA-A2/K&lt;sup&gt;b&lt;/sup&gt; mice within a formal Good Laboratory Practice (GLP)–compliant study to demonstrate safety, persistence, and HSC differentiation into all blood lineages. Non-GLP experiments included assessment of transgene immunogenicity and &lt;i&gt;in vitro&lt;/i&gt; viral insertion safety studies. Furthermore, Good Manufacturing Practice (GMP)–compliant cell production qualification runs were performed to establish the manufacturing protocols for clinical use.&lt;/p&gt;Results:&lt;p&gt;TCR genetically modified and &lt;i&gt;ex vivo&lt;/i&gt;–cultured HSCs differentiated into all blood subsets &lt;i&gt;in vivo&lt;/i&gt; after HSC transplantation, and coadministration of TCR-transduced T cells did not result in increased toxicity. The expression of NY-ESO-1 TCR and sr39TK transgenes did not have a detrimental effect on gene-modified HSC's differentiation to all blood cell lineages. There was no evidence of genotoxicity induced by the lentiviral vector. GMP batches of clinical-grade transgenic cells produced during qualification runs had adequate stability and functionality.&lt;/p&gt;Conclusions:&lt;p&gt;Coadministration of HSCs and T cells expressing an NY-ESO-1 TCR is safe in preclinical models. The results presented in this article led to the FDA approval of IND 17471.&lt;/p&gt;&lt;/div&gt;
Effects of stearic acid coated talc, CaCO3, and mixed talc/CaCO3 particles on the rheological properties of polypropylene compounds (2004)

Abstract The effect of the stearic acid coated fillers and their geometry on the shear/dynamic viscosity and complex viscosity has been investigated using polypropylene (PP) compounds filled with stearic acid uncoated and coated talc, calcite, and mixed talc/calcite particles. The viscosity was measured over a wide range of shear rates (10 −8 to 10 3 ) using a capillary, cone‐plate and sandwich rheometer. Overall, the rheological properties of the compounds exhibited different behavior upon different filler systems, stearic acid involvement, shear stress or strain, and frequencies due to stearic acid involvement. This implies that the stearic acid lowers the interfacial force between the filler surface and the resin matrix, followed by a favorable processing. In addition, at very low shear stresses, the viscosity of talc(un) compounds was higher than calcite(un) ones; at very high shear stresses, on the other hand, talc compounds became lower than calcite(un) compounds. This is interpreted as due to the different geometry between talc and calcite. The yield value as a function of shear stress was observed for all filler systems and exhibited lower than that obtained from the extrapolation. Furthermore, the Cox–Merz relation between the complex and shear viscosity for both the stearic acid uncoated and coated compounds is found not valid. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 2105–2113, 2004
Extracting reliable electronic properties from transmission spectra of indium tin oxide thin films and nanocrystal films by careful application of the Drude theory (2012)

Analysis of the transmittance and reflectance of transparent conducting oxide thin films and nanocrystal films can be accurately modeled using the Drude free electron theory to extract electrical transport properties if enough care is taken. However, several fits starting from different initial guesses are needed before confidence in the extracted Drude parameters can be obtained. Film thickness, optical carrier concentration, and optical carrier mobility can be reliably derived when using either a fully empirical or semiempirical model for the ionized impurity scattering. The results are in good agreement with those based on more arduous spectroscopic ellipsometry measurements. Furthermore, fitting the reflectance along with the transmittance reduces the uncertainty, but does not significantly affect the values of the extracted parameters.