gebhart/patrepeval huggingface dataset:
Quasiliving Carbocationic Polymerization. I. Classification of Living Polymerizations in Carbocationic Systems (1982)

Abstract It has been shown that in addition to classical living polymerizations, several other polymerization systems exist that may exhibit partially living so-called quasiliving character. The single requirement for quasiliving polymerization is the absence of irreversible termination. The various possible living systems have been classified by taking into consideration the absence or reversibility of termination and the absence, reversibility, or irreversibility of chain transfer. In regard to chain transfer, both unimolecular and/or bimolecular processes have been considered. A comprehensive examination of all possibilities yielded, in addition to the classical terminationless-transferless living system, five quasiliving systems. Kinetic analysis led to equations defining these systems and to diagnostic techniques useful for the classification and characterization of the mechanism of living carbocationic polymerizations.
Surface modification of poly(l-lactic acid) with biomolecules to promote endothelialization (2010)

Rapid endothelialization is important for biodegradable blood-contacting devices not only to prevent thrombosis but also to prevent degradation debris from entering the bloodstream and causing further complications. Here the authors report a three-step surface modification method, by which biomolecules, such as gelatin and chitosan, are covalently immobilized on the surface of plasma-treated poly(L-lactic acid) (PLLA) via -COOH groups introduced by acrylic acid grafting polymerization. Surface characterization techniques, including x-ray photoelectron spectroscopy, contact angle measurement, and colorimetric methods for surface density of functional groups, proved the feasibility and stability of this surface modification method. Surface wettability was increased by biomolecules immobilization. The -COOH surface density was measured to be 4.17±0.15 μmol/cm(2), the and amount of gelatin immobilized was 4.8 μg/cm(2). Human umbilical vein endothelial cell was used during in vitro study at seeding density of 10(4) cells/cm(2). PLLA-gAA-gelatin surface was found to enhance cell adhesion, spreading, focal adhesion formation, and proliferation significantly. Chitosan-modified PLLA shows marginally improvement in cell adhesion and proliferation. Endothelialization was achieved within 7 days on both modified PLLA surfaces. In conclusion, this work demonstrates the feasibility of the surface modification method, and its ability to promote complete endothelialization for cardiovascular applications.
Activation of insulin-epidermal growth factor (EGF) receptor chimerae regulates EGF receptor binding affinity. (1992)

Cell surface tyrosine kinase receptors are subject to a rapid activation by their ligand, which is followed by secondary regulatory processes. The IHE2 cell line is a unique model system to study the regulation of EGF binding to EGF receptors after activation of the EGF receptor kinase. IHE2 cells express both a chimeric insulin-EGF receptor kinase (IER) and a kinase-deficient EGF receptor (HER K721A). We have previously reported that IER is an insulin-responsive EGF receptor tyrosine kinase that activates one or several serine/threonine kinases, which in turn phosphorylate(s) the unoccupied HER K721A. In this article we show that insulin through IER activation induces a decrease in 125I-EGF binding to IHE2 cells. Scatchard analysis indicates that, as for TPA, the effect of insulin can be accounted for by a loss of the high affinity binding of EGF to HER K721A. Since this receptor transmodulation persists in protein kinase C downregulated IHE2 cells, it is likely to be due to a mechanism independent of protein kinase C activation. Using an in vitro system of 125I-EGF binding to transmodulated IHE2 membranes, we illustrate that the inhibition of EGF binding induced by IER activation is related to the phosphorylation state of HER K721A. Further, studies with phosphatase 2A, or at a temperature (4 degrees C) where only IER is functional, strongly suggest that the loss of high affinity EGF binding is related to the serine/threonine phosphorylation of HER K721A after IER activation. Our results provide evidence for a "homologous desensitization" of EGF receptor binding after activation of the EGF receptor kinase of the IER receptor.
Process of CoPt Alloys Electrodeposition for MEMS/NEMS Applications (2009)

CoPt electrodeposited alloys present high interest for application in MEMS/NEMS, because of their interesting magnetic characteristics. Integration of CoPt films into MEMS/NEMS devices is hampered by instability of the deposition process (change of deposition current efficiency and CoPt alloy characteristics with total charge passed through electrolyte in previous runs). The deposition process of CoPt alloys from ammonium citrate electrolyte containing the diammine-dinitrito-platinum (II) complex as the source of Pt is considered in terms of its stability and reliability. Removal of ligands by thermal treatment of Pt complex allows the elimination of the total charge effect on deposition current efficiency. The role of ammonia loss during pretreatment and operation is discussed.
Emergence of feedback in artificial gene regulatory networks (2007)

In this paper, we present a model for simulating the evolution of development together with a method for the analysis of emergence of negative feedback inside the regulatory network. In order to record the development of feedback during evolution, we analyze both the static as well as the dynamic interactions between the transcription factors in the regulatory network. When perturbing the gene regulatory network using random mutations, we find that the evolved negative feedback is the main mechanism for robustness against such mutations. We argue that this robustness is the reason for the sustained emergence of negative feedback during evolution.
Effect of soft segment and clay volume fraction on rate dependent damping of polyurethane and polyurethane-clay nanocomposites (2014)

Amorphous polymers have been extensively used for energy dissipative applications due to their relatively low density and controllable rate dependent damping. In general, molecular mobility depends on the rate of applied loading and the ambient temperature, and results in a wide variety of mechanical properties. The variation in the macromolecular chain dynamics can be obtained by altering the chemical architecture and morphology of the constituent monomers. The present study is focused on finding a correlation between the chemical structure of the constituent monomer and the rate dependent viscous damping of the macromolecules. Polyurethane (PU) made up of isophorone diisocyanate (IPDI) and polycaprolactone diol (PCL) is considered to estimate the effect of soft segments (diol content) on damping property of PU. A linear viscoelastic mathematical model (based on standard-linear solid (SLS) model) is used to extract the rate dependent relaxation time constants for the materials. It is found that increasing the soft segment content in the PU does not improve damping limitlessly. Beyond a critical percentage of soft segment content, characteristic relaxation times have a significant drop. Further, the analysis is extended for PU-clay nanocomposites and a correlation between the clay volume fraction and relaxation constants is established. The study will help to choose and design PU and volume percentage of clay nanoparticle for manufacturing PU-clay nanocomposites with desired damping property.
PBX and MEIS as Non-DNA-Binding Partners in Trimeric Complexes with HOX Proteins (1999)

HOX, PBX, and MEIS transcription factors bind DNA through a homeodomain. PBX proteins bind DNA cooperatively as heterodimers with MEIS family members and also with HOX proteins from paralog groups 1 to 10. MEIS proteins cooperatively bind DNA with ABD-B class HOX proteins of groups 9 and 10. Here, we examine aspects of dimeric and higher-order interactions between these three homeodomain classes. The most significant results can be summarized as follows. (i) Most of PBX N terminal to the homeodomain is required for efficient cooperative binding with HOXD4 and HOXD9. (ii) MEIS and PBX proteins form higher-order complexes on a heterodimeric binding site. (iii) Although MEIS does not cooperatively bind DNA with ANTP class HOX proteins, it does form a trimer as a non-DNA-binding partner with DNA-bound PBX-HOXD4. (iv) The N terminus of HOXD4 negatively regulates trimer formation. (v) MEIS forms a similar trimer with DNA-bound PBX-HOXD9. (vi) A related trimer (where MEIS is a non-DNA-binding partner) is formed on a transcriptional promoter within the cell. (vii) We observe an additional trimer class involving non-DNA-bound PBX and DNA-bound MEIS-HOXD9 or MEIS-HOXD10 heterodimers that is enhanced by mutation of the PBX homeodomain. (viii) In this latter trimer, PBX is likely to contact both MEIS and HOXD9/D10. (ix) The stability of DNA binding by all trimers is enhanced relative to the heterodimers. These findings suggest novel functions for PBX and MEIS in modulating the function of DNA-bound MEIS-HOX and PBX-HOX heterodimers, respectively.
Scar Zones (2012)

Wong, Victor W. M.D.; Levi, Kemal Ph.D.; Akaishi, Satoshi M.D., Ph.D.; Schultz, Geoffrey M.D.; Dauskardt, Reinhold H. Ph.D. Author Information
Governing resilient landscapes across the source-to-sea continuum (2021)

The source-to-sea continuum links the interconnected ecosystems of the water cycle with the associated socioeconomic processes, demands and pressures. Maximizing benefits and protecting existing resources through integrated water management and governance at scale capitalizes on existing institutional and governmental asymmetries by developing an outcome-driven management that builds on existing local, national and transboundary legal frameworks to enhance connectivity. This paper presents how to action this through focusing on three areas of governance: benefit-sharing dialogues for shared visioning; a multi-stakeholder platform to increase coordination in decision-making both up- and downstream; and improved agency coordination between basins and coasts.
Using state-space models for accurate computations of transient thermal behavior of electronic packages (2014)

Under a given set of boundary conditions, thermal performance of an electronic system is generally evaluated based on its steady state response. It is a conventional practice that actual time dependent power cycles and thermal boundary conditions are time-averaged to estimate the steady state characteristics. This approach may produce accurate results provided that the time dependency of the power cycles and/or thermal boundary conditions is small. In general, time-dependent thermal analyses with actual time-dependent boundary conditions and power cycles should be performed in order to determine the steady state behavior. Whether an experimental or numerical approach is taken, accurate prediction of transient thermal behavior of complex electronic systems is time consuming. While being less overwhelming compared to the actual laboratory experiments, fully time dependent Computational Fluid Dynamics (CFD) analysis still requires large amount of CPU time. In order to prevail over this large computational cost, a number of approximate models were developed, such as Resistor-Capacitor (R-C) thermal network approaches which have produced reasonably accurate results, and therefore have been popular in determining system transient response. It is worth noting that these approaches require some rigorous curve-fitting effort followed by an optimization process and are applicable to relatively simple systems. The present study uses state-space model to determine transient and steady state thermal behavior of complex systems as accurately as possible without compromising the speed. The aforementioned technique is applied to an SOC package placed on a printed circuit board and the results are compared to those from the fully transient CFD model computations. With a dramatic reduction in the overall CPU times, the temperature histories obtained from the state-space approach agree well with the transient CFD simulations.
Evolution of a transcriptional regulator from a transmembrane nucleoporin (2016)

Nuclear pore complexes (NPCs) emerged as nuclear transport channels in eukaryotic cells ∼1.5 billion years ago. While the primary role of NPCs is to regulate nucleo-cytoplasmic transport, recent research suggests that certain NPC proteins have additionally acquired the role of affecting gene expression at the nuclear periphery and in the nucleoplasm in metazoans. Here we identify a widely expressed variant of the transmembrane nucleoporin (Nup) Pom121 (named sPom121, for "soluble Pom121") that arose by genomic rearrangement before the divergence of hominoids. sPom121 lacks the nuclear membrane-anchoring domain and thus does not localize to the NPC. Instead, sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified transcriptional regulator, at gene promoters to control transcription of its target genes in human cells. Interestingly, sPom121 transcripts appear independently in several mammalian species, suggesting convergent innovation of Nup-mediated transcription regulation during mammalian evolution. Our findings implicate alternate transcription initiation as a mechanism to increase the functional diversity of NPC components.
UNSTEADY RANS AND DETACHED EDDY SIMULATIONS OF CAVITATING FLOW OVER A HYDROFOIL (2003)

A three-dimensional, time-accurate, compressible, homogeneous multiphase Navier-Stokes method is applied to modeling developed cavitation flow over a hydrofoil at angleof-attack. The configuration and cavitation numbers considered give rise to highly unsteady cavitation structures on the suction side of the foil, characterized by large recirculating (re-entrant) flow regions. Accordingly, a time-accurate approach is forthcoming. In the present work Unsteady Reynolds Averaged Navier-Stokes (URANS) and Detached Eddy Simulation (DES) modeling are pursued with the intent of elucidating the differences that these modeling approaches have in the prediction of important engineering quantities. Twodimensional URANS simulation results are presented for cavitation numbers of 0.4 and 0.8. Though DES can only simulate the largest scales of turbulence when applied threedimensionally, “2D DES” runs were performed for the same two cases in order to provide experience and guidance with the model. A fully three-dimensional DES simulation was performed at a cavitation number of 0.8. A very rich and interesting multiphase flow field is observed in this simulation. However, despite the large CPU requirements of this calculation, the results presented are not yet statistically stationary, making a complete quantitative statistical interpretation of the data set premature. Visualizations of 3D flow structures and short time-histories of flow variables are presented. The preliminary data suggest that the intensities of turbulence fluctuations supported by the 3D solution are less than those observed in the 2D cases, a physically plausible result. A possible mechanism for this behavior is discussed.
Systematic Cell-Based Phenotyping of Missense Alleles Empowers Rare Variant Association Studies: A Case for <i>LDLR</i> and Myocardial Infarction (2016)

&lt;div&gt;&lt;p&gt;A fundamental challenge to contemporary genetics is to distinguish rare missense alleles that disrupt protein functions from the majority of alleles neutral on protein activities. High-throughput experimental tools to securely discriminate between disruptive and non-disruptive missense alleles are currently missing. Here we establish a scalable cell-based strategy to profile the biological effects and likely disease relevance of rare missense variants &lt;i&gt;in vitro&lt;/i&gt;. We apply this strategy to systematically characterize missense alleles in the low-density lipoprotein receptor (&lt;i&gt;LDLR&lt;/i&gt;) gene identified through exome sequencing of 3,235 individuals and exome-chip profiling of 39,186 individuals. Our strategy reliably identifies disruptive missense alleles, and disruptive-allele carriers have higher plasma LDL-cholesterol (LDL-C). Importantly, considering experimental data refined the risk of rare &lt;i&gt;LDLR&lt;/i&gt; allele carriers from 4.5- to 25.3-fold for high LDL-C, and from 2.1- to 20-fold for early-onset myocardial infarction. Our study generates proof-of-concept that systematic functional variant profiling may empower rare variant-association studies by orders of magnitude.&lt;/p&gt;&lt;/div&gt;
Transfer of cytokine-inducing bacterial products across hemodialyzer membranes in the presence of plasma or whole blood. (1996)

Cytokine production by peripheral blood mononuclear cells (PBMC) is a sensitive indicator of cytokine-inducing substances which may cross from contaminated dialysate into the blood compartment. The objective of this study was to compare the transfer of cytokine-inducing substances from dialysate contaminated with a culture filtrate from Pseudomonas aeruginosa across dialyzers with low (hemophan) or intermediate ultrafiltration coefficients (modified cellulose triacetate, CTA), under conditions where either 10% plasma or whole blood was circulated in the blood compartment. Eight paired experiments of in vitro dialysis were carried out at 37 degrees C using a countercurrent recirculating loop dialysis circuit with either a new CTA or hemophan dialyzer. 10% plasma in standard tissue culture medium was circulated through the blood compartment and bicarbonate dialysate was circulated in the dialysate compartment. The dialysate was challenged sequentially by log-fold dilutions (10(2), 10(3) or 10(4)) of a Ps. aeruginosa culture filtrate. Samples were drawn from the blood compartment 5 and 15 minutes after each challenge and incubated with suspensions of PBMC in the absence or presence of polymyxin B, in order to block endotoxin. After 24 h at 37 degrees C, total interleukin-1 alpha (IL-1 alpha) was measured by RIA. Although the dialysate contained potent cytokine-inducing substances, there was no significant IL-1 alpha production by PBMC incubated with the plasma mixture from the blood compartment in the majority of experiments with both dialyzers and with each of the three dilutions of the bacterial challenge. Eight experiments were also performed with CTA dialzyers using heparinized whole blood in the blood compartment. Samples of whole blood and dialysate were drawn at baseline, after one hour of dialysis with uncontaminated dialysate and 15 minutes and three hours after dialysis with dialysate contaminated with Ps. aeruginosa filtrate. There was no significant IL-1 alpha production by PBMC isolated from the whole blood 1 h after dialysis with uncontaminated dialysate, and 15 min and 2 h after adding the Ps. aeruginosa filtrate to the dialysate side. In contrast, production of IL-1 alpha by PBMC from the same donors incubated with samples from the dialysate were 263 +/- 50, 1074 +/- 306, 2333 +/- 774 and 2602 +/- 702 pg/2.5 x 10(6) PBMC, respectively at the same four time points. These data suggest that although the Ps. aeruginosa culture filtrate present in the dialysate was a potent inducer of IL-1 alpha, neither dialyzer permitted transfer of cytokine inducing substances from the dialysate into the blood compartment.
Screening of anti-mycobacterial compounds in a naturally infected zebrafish larvae model (2016)

We have demonstrated that zebrafish larvae naturally infected with bioluminescent M. marinum M can be used for the rapid screening of anti-mycobacterial compounds with readily available equipment and limited expertise. The result is an assay that can be carried out by a wide variety of laboratories for minimal cost and without high levels of zebrafish expertise.
Thermal characteristics of light-emitting diodes and their effect on passive optical networks (1997)

LED's have been demonstrated in several new passive optical networks (PON) architectures which capitalize on their wide spectral emission. We show that, due to thermal properties, LED's exhibit higher than expected output powers under RF subcarrier modulation and baseband packet modulation, leading to advantageous power budgets in PON applications.
Simultaneous measurement of pressure and temperature in a focused ultrasound field with a fiber optic hydrophone (2008)

The characterization of high intensity focused ultrasound (HIFU) fields is important for both clinical treatment planning as well as for regulation of HIFU medical devices. In previous work, we have used a 100-μm fiber optic probe hydrophone (FOPH) to measure pressure waveforms from a 2-MHz HIFU source with 42-mm aperture and 44-mm focal length. The formation of shock waves with peak positive pressure of up to 80-MPa were measured and modeled in transparent tissue-mimicking gel phantoms and boiling was achieved in milliseconds [Canney MS, et al., J. Acoust. Soc. Am., 120:3110 (2006)]. In this work, the FOPH was also used to measure temperature changes in tissue phantoms from HIFU at peak focal intensities of 5000-20,000 W/cm2. Temperature measurements were obtained by first low-pass filtering the voltage signal measured from the FOPH to remove the acoustic part of the measurement. Then, calibration of voltage to temperature was performed using results from a separate calibration experiment. Experimental measurements were compared with numerical modeling using a KZK-type model for acoustic propagation coupled with a heat transfer model. In summary, temperatures of 100°C were measured at the HIFU focus in milliseconds, in agreement with modeling [Work supported by NIH DK43881, NSBRI SMS00402, and RFBR.]
Efficiency of GaN/InGaN light-emitting diodes with interdigitated mesa geometry (2001)

GaN/InGaN light-emitting diodes (LEDs) with different mesa structures are studied. The optical emission power as well as current–voltage characteristics of different mesa patterns are measured. The results show that the optical emission of the device with interdigitated patterns is higher than devices with traditional square-shaped patterns. The leakage current is found to increase as the mesa sidewall perimeter increases. Based on the analysis, it is concluded that a surface leakage current flows across the mesa sidewall and the leakage current is directly proportional to the mesa perimeter. The implications of the results for large-area scalable LED structures are discussed.
Supplementary Table S1 and Supplementary Figures S1-S4 from Concomitant Inhibition of PI3Kβ and BRAF or MEK in PTEN-Deficient/<i>BRAF</i>-Mutant Melanoma Treatment: Preclinical Assessment of SAR260301 Oral PI3K<b>β</b>-Selective Inhibitor (2023)

&lt;p&gt;Supplementary Tables S1. Table S1 describes the inhibitory activity of SAR260301 on AKT phosphorylation (Ser473 and Thr308) in a panel of tumor cell lines with different genetic abnormalities that are reported. Supplementary Figures S1-S4. Figure S1 illustrates the selectivity of SAR260301 against VPS34 in cellular setting: Figure S1A describes the activity of SAR260301 on VPS34 kinase function in GFP-FYVE cellular assay; Figure S1B describes the activity of SAR260301 on autophagy in GFP-LC3 cellular assays. Figure S2 describes the inhibitory activity of SAR260301 on the phosphorylation of AKT downstream effectors PRAS40 and S6RP in PC3 cell line, as a function of time. Figure S3 describes the in vitro antitumor activity of SAR260301: Figure S3A describes the antiproliferative activity of SAR260301on MEF-3T3-myr p110Î² cells. Figure S3B describes the antiproliferative activity of SAR260301on PC3 cells. Figure S3C describes the activity of SAR260301on PC3 cell death. Figure S3D describes the activity of SAR260301on LnCaP cell apoptosis. Figure S4 is a scheme describing the rationale for combining inhibitors of PI3Kï�¢ and MAPK.&lt;/p&gt;