gebhart/patrepeval huggingface dataset:
AP-1 and C/EBP transcription factors contribute tomda-7 gene promoter activity during human melanoma differentiation (2000)

Treatment of human melanoma cells with a combination of recombinant fibroblast interferon (IFN-beta) and the protein kinase C (PKC) activator mezerein (MEZ) causes a rapid and irreversible suppression in growth and terminal cell differentiation. Temporal subtraction hybridization combined with random clone selection, reverse Northern hybridization, high throughput microchip cDNA array screening, and serial cDNA library arrays permit the identification and cloning of genes that are differentially expressed during proliferative arrest and terminal differentiation in human melanoma cells. A specific melanoma differentiation associated (mda) gene, mda-7, exhibits reduced expression as a function of melanoma progression from melanocyte to metastatic melanoma. In contrast, treatment of metastatic melanoma cells with IFN-beta + MEZ results in expression of mda-7 mRNA and protein. To evaluate the mechanism underlying the differential expression of mda-7 as a function of melanoma progression and induction of growth arrest and differentiation in human melanoma cells the promoter region of this gene has been isolated from a human placental genomic library and characterized. Sequence analysis by GCG identifies multiple recognition sites for the AP-1 and C/EBP transcription factors. Employing a heterologous mda-7 luciferase gene reporter system, we demonstrate that ectopic expression of either AP-1/cJun or C/EBP can significantly enhance expression of the mda-7 promoter in melanoma cells. In contrast, a dominant negative mutant of cJun, TAM67, is devoid of promoter-enhancing ability. Western blot analyses reveals that cJun and the C/EBP family member C/EBP-beta are physiologically relevant transcription factors whose expression corresponds with mda-7 mRNA expression. Electrophoretic mobility shift assays (EMSA) performed using nuclear protein extracts from terminally differentiated human melanoma cells document binding to regions of the mda-7 promoter that correspond to consensus binding sites for AP-1 and C/EBP. These results provide further mechanistic insights into the regulation of the mda-7 gene during induction of terminal cell differentiation in human melanoma cells.
An object-oriented framework for modelling control policies in a supply chain (2009)

In this paper, a framework for an object-oriented Supply Chain (SC) environment is proposed. This framework is based on object-oriented methodology, which allows the building of complex simulation models by combining some basic or primitive objects. This proposed framework provides several advantages over existing SC systems. First of all, this system incorporates the independent decision-making at each SC node by modelling each node as an autonomous entity. In the proposed framework, independent SC nodes are connected to each other by mutual relationships. These relationships are determined using the relevant control policies of each node. These relationships may change during execution of the simulation model in accordance with the control policies. The proposed framework is generic enough to incorporate both the manufacturing and nonmanufacturing type of nodes. In this framework, the SC system is studied in terms of five entity flows: material, information, money, resource and decision. Another major contribution of this framework is the provision of a number of control policies for major SC decisions such as source selection, inventory management, transportation and production planning. This framework is also capable of modelling, simulating and analysing nondeterministic SC systems where one or more of the uncontrollable variables are stochastic. In addition, this framework can also be used for improving the performance of SCs by suggesting the optimal control policies.
Quality Control Platform for the Standardization of a Regenerative Medicine Product (2022)

Adipose tissue is an attractive source of stem cells due to its wide availability. They contribute to the stromal vascular fraction (SVF), which is composed of pre-adipocytes, tissue-progenitors, and pericytes, among others. Because its direct use in medical applications is increasing worldwide, new quality control systems are required. We investigated the ability of the Non-Equilibrium Earth Gravity Assisted Dynamic Fractionation (NEEGA-DF) method to analyze and separate cells based solely on their physical characteristics, resulting in a fingerprint of the biological sample. Adipose tissue was enzymatically digested, and the SVF was analyzed by NEEGA-DF. Based on the fractogram (the UV signal of eluting cells versus time of analysis) the collection time was set to sort alive cells. The collected cells (F-SVF) were analyzed for their phenotype, immunomodulation ability, and differentiation potential. The SVF profile showed reproducibility, and the alive cells were collected. The F-SVF showed intact adhesion phenotype, proliferation, and differentiation potential. The methodology allowed enrichment of the mesenchymal component with a higher expression of mesenchymal markers and depletion of debris, RBCs, and an extracellular matrix still present in the digestive product. Moreover, cells eluting in the last minutes showed higher circularity and lower area, proving the principles of enrichment of a more homogenous cell population with better characteristics. We proved the NEEGA-DF method is a "gentle" cell sorter that purifies primary cells obtained by enzymatic digestion and does not alter any stem cell function.
Radical-Initiated Functionalization of Methane and Ethane in Fuming Sulfuric Acid (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTRadical-Initiated Functionalization of Methane and Ethane in Fuming Sulfuric AcidNaomi Basickes, Terrence E. Hogan, and Ayusman SenView Author Information Department of Chemistry The Pennsylvania State University University Park, Pennsylvania 16802 Cite this: J. Am. Chem. Soc. 1996, 118, 51, 13111–13112Publication Date (Web):December 25, 1996Publication History Received16 September 1996Published online25 December 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja9632365https://doi.org/10.1021/ja9632365rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views1308Altmetric-Citations113LEARN 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:Chemical reactions,Functionalization,Hydrocarbons,Ions,Sulfuric acid Get e-Alerts
Topological wave insulators: a review (2020)

Originally discovered in condensed matter systems, topological insulators (TIs) have been ubiquitously extended to various fields of classical wave physics including photonics, phononics, acoustics, mechanics, and microwaves. In the bulk, like any other insulator, electronic TIs exhibit an excessively high resistance to the flow of mobile charges, prohibiting metallic conduction. On their surface, however, they support one-way conductive states with inherent protection against certain types of disorder and defects, defying the common physical wisdom of electronic transport in presence of impurities. When transposed to classical waves, TIs open a wealth of exciting engineering-oriented applications, such as robust routing, lasing, signal processing, switching, etc., with unprecedented robustness against various classes of defects. In this article, we first review the basic concept of topological order applied to classical waves, starting from the simple one-dimensional example of the Su–Schrieffer–Heeger (SSH) model. We then move on to two-dimensional wave TIs, discussing classical wave analogues of Chern, quantum Hall, spin-Hall, Valley-Hall, and Floquet TIs. Finally, we review the most recent developments in the field, including Weyl and nodal semimetals, higher-order topological insulators, and self-induced non-linear topological states.
Sequence-based structural signatures of genome evolution. (2001)

Among the multitude of methods available for the study of origin and evolution of various life forms on Earth, the phylogenetic approach, i.e. the delineation of natural genetic relatedness amongst different groups of organisms, has been of particular interest to evolutionary biologists. An approach towards analysing phylogeny is the comparison of genome sequences of extant organisms by a variety of computational techniques. These studies rely mostly on the similarity or dissimilarity in global character of the genome in terms of sequence, without any consideration to its structure. In this work, we report a potentially new methodology towards elucidation of molecular phylogeny. The approach considers a structural parameter of the genome, namely its flexibility, and uses it to compare the small subunit ribosomal ribonucleic acid (SSU rRNA) gene from a cross-section of species. We find that the flexibility pattern of the genome is strikingly similar in organisms that are closer in evolutionary distance than the ones that are separated. This method of comparison thus might be utilised in constructing phylogenetic trees from flexibility patterns derived from nucleotide sequence.
Estimation and adaptive observation of environmental plumes (2011)

The estimation and forecasting environmental plume movement based on information from mobile sensors recently received renewed attention due to the Gulf coast oil and Icelandic ash problems, and remains of sustained interest today in homeland security settings (plant explosions, dirty bombs, etc.). The present work refines and tests the scientific algorithms at the heart of this problem. In particular, we combine the Ensemble Kalman Filter (EnKF), which provides a computationally feasible low-rank approximation of the un certainty of the estimate, with our recently developed Dynamic Adaptive Observation (DAO) algorithm for optimizing feasible sensor vehicle trajectories that minimize forecast uncertainty. A numerical experiment is performed which applies this combined EnKF/DAO algorithm to determine waypoints along optimized feasible sensor vehicle trajectories that improve the forecast of an environmental plume represented by a passive scalar convectively driven in a 2D fluid flow.
Shock wave formation in droplet impact on a rigid surface: lateral liquid motion and multiple wave structure in the contact line region (2003)

The early phase of high-speed liquid droplet impact on a rigid wall is characterized by compressibility effects through the creation of a shock wave attached to the contact area periphery. Initially, the area of compressed liquid is assumed to be bounded by the shock envelope, which propagates both laterally and upwardly into the bulk of the liquid. In this paper, an analytical model accounting for the lateral liquid motion in the compressed area is developed and compared to the axisymmetric numerical solution of the inviscid (Euler) flow equations. It is shown that the often employed assumption that the compressed area is separated from the liquid bulk by a single shock wave attached to the contact line breaks down and results in an anomaly. This anomaly emerges prior to the time when the shock wave departs from the contact line, initiating lateral liquid jetting. In order to remove this anomaly, the analytical model presented in this paper proposes the transition from a single to a multiple wave structure in the contact line region, prior to jetting eruption. The occurrence of this more complex multiple wave structure is also supported by the numerical results.
Nonlinear Polarizabilities of Symmetric and Non-symmetric Polyene and Cyanine-Like Organic Molecules (1992)

There is considerable interest in understanding the origin of the molecular nonlinear polarizabilities. Recently, the important role of bond alternation (difference in the carbon-carbon double bond and single bond lengths) in influencing the second order polarizability, β, of asymmetric conjugated dyes has been pointed out.[1] It was suggested that there is an optimal degree of alternation needed to maximize β. The connection between bond-alternation and the electronic, optical and chemical properties of conjugated molecules has also been recognized previously.[2] These studies as well as the results of prior experimental studies[3] have led us to investigate the affect of bond alternation on the third-order polarizability, γ. One aim of the present work is to gain insight into the differences between the magnitude and signs of γ for simple polyenes and cyanines. For moderate length to long polyenes, nonresonant electronic γ is positive, whereas for comparable cyanines γ is negative.
ZUMA: a platform for smart-home environments - the case for infrastructure (2006)

A wide range of disconnected communication networks is emerging in the home. Each has different functions and implementation architectures. The user experience as well as the overall functionality would be vastly enhanced if these networks could collaborate in a seamless fashion. Collaboration is challenging because it requires disparate devices and components to interoperate in a user friendly, scalable and upgradeable fashion. We conjecture that such cooperation might be most efficiently assured using a supporting infrastructure. The universal contents router (UCR) is introduced as an infrastructural component. The UCR moves the burden of connectivity away from the end devices to the system core. The paper spells out ZUMA, or functions that a UCR should support, discusses UCR architecture and presents a first-order prototype. (10 pages)
A fully integrated dual‐band low‐noise amplifier for bluetooth and wireless LAN applications (2004)

Abstract A fully integrated dual‐band low‐noise amplifier (LNA) implemented in a standard 0.18‐μm 1P6M CMOS process is presented in this paper. The LNA draws 12‐mA current from a 1.5‐V voltage supply and achieves power gains of 25 and 10 dB, and noise figures of 3.6 and 4 dB at 2.4 and 5.6 GHz respectively. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 297–301, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20121
Cobalt and iron oxides dispersed onto activated carbons: The size effect (2015)

The effect the nature of activated carbons prepared from natural renewable resources has on the metal particle size in cobalt- and iron-containing systems that can be used as catalysts in Fischer-Tropsch synthesis (FTS) is studied. The highest dispersity is observed for the Co3O4-WS (wood sawdust) system. The average particle size is 9.5 nm.
Guaranteed Trajectory Tracking under Learned Dynamics with Contraction Metrics and Disturbance Estimation (2021)

This paper presents an approach to trajectory-centric learning control based on contraction metrics and disturbance estimation for nonlinear systems subject to matched uncertainties. The approach uses deep neural networks to learn uncertain dynamics while still providing guarantees of transient tracking performance throughout the learning phase. Within the proposed approach, a disturbance estimation law is adopted to estimate the pointwise value of the uncertainty, with pre-computable estimation error bounds (EEBs). The learned dynamics, the estimated disturbances, and the EEBs are then incorporated in a robust Riemann energy condition to compute the control law that guarantees exponential convergence of actual trajectories to desired ones throughout the learning phase, even when the learned model is poor. On the other hand, with improved accuracy, the learned model can help improve the robustness of the tracking controller, e.g., against input delays, and can be incorporated to plan better trajectories with improved performance, e.g., lower energy consumption and shorter travel time.The proposed framework is validated on a planar quadrotor example.
Oral 15-Hydroxyeicosatetraenoic Acid Induces Pulmonary Hypertension in Mice by Triggering T Cell–Dependent Endothelial Cell Apoptosis (2020)

Pulmonary arterial hypertension (PAH) is a fatal disease characterized by increased mean pulmonary arterial pressure. Elevated plasma and lung concentrations of oxidized lipids, including 15-hydroxyeicosatetraenoic acid (15-HETE), have been demonstrated in patients with PAH and animal models. We previously demonstrated that feeding mice with 15-HETE is sufficient to induce pulmonary hypertension, but the mechanisms remain unknown. RNA sequencing data from the mouse lungs on 15-HETE diet revealed significant activation of pathways involved in both antigen processing and presentation and T cell-mediated cytotoxicity. Analysis of human microarray from patients with PAH also identified activation of identical pathways compared with controls. We show that in both 15-HETE-fed mice and patients with PAH, expression of the immunoproteasome subunit 5 is significantly increased, which was concomitant with an increase in the number of CD8/CD69 (cluster of differentiation 8 / cluster of differentiation 69) double-positive cells, as well as pulmonary arterial endothelial cell apoptosis in mice. Human pulmonary arterial endothelial cells cultured with 15-HETE were more prone to apoptosis when exposed to CD8 cells. Cultured intestinal epithelial cells secreted more oxidized lipids in response to 15-HETE, which is consistent with accumulation of circulating oxidized lipids in 15-HETE-fed mice. Administration of an apoA-I (apolipoprotein A-I) mimetic peptide, Tg6F (transgenic 6F), which is known to prevent accumulation of circulating oxidized lipids, not only inhibited pulmonary arterial endothelial cell apoptosis but also prevented and rescued 15-HETE-induced pulmonary hypertension in mice. In conclusion, our results suggest that (1) 15-HETE diet induces pulmonary hypertension by a mechanism that involves oxidized lipid-mediated T cell-dependent pulmonary arterial endothelial cell apoptosis and (2) Tg6F administration may be a novel therapy for treating PAH.
Trisubstituted Pyridinylimidazoles as Potent Inhibitors of the Clinically Resistant L858R/T790M/C797S EGFR Mutant: Targeting of Both Hydrophobic Regions and the Phosphate Binding Site (2017)

Inhibition of the epidermal growth factor receptor represents one of the most promising strategies in the treatment of lung cancer. Acquired resistance compromises the clinical efficacy of EGFR inhibitors during long-term treatment. The recently discovered EGFR-C797S mutation causes resistance against third-generation EGFR inhibitors. Here we present a rational approach based on extending the inhibition profile of a p38 MAP kinase inhibitor toward mutant EGFR inhibition. We used a privileged scaffold with proven cellular potency as well as in vivo efficacy and low toxicity. Guided by molecular modeling, we synthesized and studied the structure-activity relationship of 40 compounds against clinically relevant EGFR mutants. We successfully improved the cellular EGFR inhibition down to the low nanomolar range with covalently binding inhibitors against a gefitinib resistant T790M mutant cell line. We identified additional noncovalent interactions, which allowed us to develop metabolically stable inhibitors with high activities against the osimertinib resistant L858R/T790M/C797S mutant.
Displacement amplified synthetic jets (2014)

Synthetic ynthetic jet actuators are attractive devices for active flow control because, in contrast to many other actuators, they do not require a pressurized air source. Instead, they cyclically ingest and expel air from the external flow that is being controlled. To accomplish this, a piston or diaphragm is used compress and expand the volume of the actuator cavity. Various approaches to compress and expand the volume of the cavity have been explored including: speaker drivers,1 mechanical pistons2 and piezoelectric diaphragms.
Thyronamines Are Substrates for Human Liver Sulfotransferases (2007)

Sulfotransferases (SULTs) catalyze the sulfation of many endogenous compounds that include monoamine neurotransmitters, such as dopamine (DA), and thyroid hormones (iodothyronines). Decarboxylation of iodothyronines results in formation of thyronamines. In the mouse, thyronamines act rapidly in a nongenomic fashion to initiate hypothermia and decrease cardiac output and heart rate. These effects are attenuated after 1-4 h, and metabolism of thyronamines via sulfation may be a mechanism for termination of thyronamine action. We carried out this study to test thyronamine (T0AM), 3-iodothyronamine (T1AM), 3,5-diiodothyronamine (T2AM), and 3,5,3'-triiodothyronamine (T3AM) as substrates for human liver and cDNA-expressed SULT activities. We characterized several biochemical properties of SULTs using the thyronamines that acted as substrates for SULT activities in a human liver high-speed supernatant pool (n=3). T1AM led to the highest SULT activity. Activities with T0AM and T3AM were 10-fold lower, and there was no detectable activity with T2AM. Thyronamines were then tested as substrates with eight cDNA-expressed SULTs (1A1, 1A2, 1A3, 1C2, 1E1, 2A1, 2B1a, and 2B1b). Expressed SULT1A3 had the greatest activity with T0AM, T1AM, and T3AM, whereas SULT1A1 showed similar activity only with T3AM. Expressed SULT1E1 had low activity with each substrate. T1AM, the most active thyronamine pharmacologically, was associated with the greatest SULT activity of the thyronamines tested in the liver pool and in both the expressed SULT1A3 and SULT1E1 preparations. Our results support the conclusion that sulfation contributes to the metabolism of thyronamines in human liver and that SULT activities may regulate the physiological effects of endogenous thyronamines.
The Effect of Private Information and Monitoring on the Role of Accounting Quality in Investment Decisions* (2010)

We investigate how private information and monitoring affect the role of accounting quality in reducing the investment-cash flow sensitivity. We argue that access to private information and direct restrictions on investments are likely to affect the extent to which accounting quality reduces financing constraints. Our results suggest that for financially constrained firms, banks' access to private information decreases the value of accounting quality. We further find that, for both financially constrained and unconstrained firms, covenants directly restricting capital expenditures also mitigate the importance of accounting quality. Our results suggest that when information asymmetry problems are likely to be the largest, accounting quality is most important. However, the importance of accounting quality is mitigated if outside capital suppliers have access to private information and is eliminated if they impose contractual restrictions on investment. We also provide evidence that banks' access to private information reduces the cash flow sensitivity of cash and mitigates the importance of accounting quality in reducing this sensitivity. This additional evidence suggests that our investment-cash flow sensitivity results are not driven by measurement error of the investment opportunity set.