gebhart/patrepeval huggingface dataset:
Inhibition of p38MAPK Increases Adipogenesis From Embryonic to Adult Stages (2006)

Formation of new adipocytes from precursor cells contributes to adipose tissue expansion and obesity. In this study, we asked whether p38 mitogen-activated protein kinase (MAPK) pathway regulates normal and pathological adipogenesis. In both dietary and genetically (ob/ob) obese mice, adipose tissues displayed a marked decrease in p38MAPK activity compared with the same tissues from lean mice. Furthermore, p38MAPK activity was significantly higher in preadipocytes than in adipocytes, suggesting that p38MAPK activity decreases during adipocyte differentiation. In agreement with an inhibitory role of p38MAPK in this process, we found that in vitro inhibition of p38MAPK, with the specific inhibitor PD169316, increased the expression of adipocyte markers in several cellular models, from embryonic to adult stages. Importantly, the expression of adipocyte markers was higher in p38MAPKalpha knockout cells than in their wild-type counterparts. Phosphorylation of C/EBPbeta, which enhances its transcriptional activity, is increased after p38MAPK inhibition. Finally, either inhibition or disruption of p38MAPK increased peroxisome proliferator-activated receptor (PPAR)gamma expression and transactivation. Rescue of p38MAPK in knockout cells reduced PPARgamma activity to the low basal level of wild-type cells. We demonstrate here, by using multipronged approaches involving p38 chemical inhibitor and p38MAPKalpha knockout cells, that p38MAPK plays a negative role in adipogenesis via inhibition of C/EBPbeta and PPARgamma transcriptional activities.
Stationary echo canceling in velocity estimation by time-domain cross-correlation (1993)

The application of stationary echo canceling to ultrasonic estimation of blood velocities using time-domain cross-correlation is investigated. Expressions are derived that show the influence from the echo canceler on the signals that enter the cross-correlation estimator. It is demonstrated that the filtration results in a velocity-dependent degradation of the signal-to-noise ratio. An analytic expression is given for the degradation for a realistic pulse. The probability of correct detection at low signal-to-noise ratios is influenced by signal-to-noise ratio, transducer bandwidth, center frequency, number of samples in the range gate, and number of A-lines employed in the estimation. Quantitative results calculated by a simple simulation program are given for the variation in probability from these parameters. An index reflecting the reliability of the estimate at hand can be calculated from the actual cross-correlation estimate by a simple formula and used in rejecting poor estimates or in displaying the reliability of the velocity estimated.
Planar front-ends with polarization agile IF systems (2002)

A low-cost front-end with polarization agility has been developed. The idea is based on IF processing and eliminates the use of front-end attenuators and phase-shifters. An X-band prototype with a dual-polarized microstrip antenna has been designed and tested. The measured isolation between the horizontal and vertical channels is better than 30 dB. Tests show that the polarization agility is achieved with a simple IF processing network.
Milk protein polymorphisms in cattle (Bos indicus), mithun (Bos frontalis) and yak (Bos grunniens) breeds and their hybrids indigenous to Bhutan (2010)

In the current study, milk protein variation was examined in cattle (Bos indicus), mithun (Bos frontalis), yak (Bos grunniens) and their hybrid populations in Bhutan to estimate genetic variability, conduct genetic characterization and assess the possibility of gene flow between mithun and cattle. Isoelectric focusing of 372 milk samples from 11 populations detected four molecular types of β-lactoglobulin (A, B, E and M), five molecular types of α(S1) -casein (A, B, C, E and X) and three molecular types of k-casein (A, B and X). Mithun and yak shared alleles but were found to exhibit different allele frequencies for the proteins studied. The degree of genetic variability within populations was measured by average heterozygosity and ranged from 24-40% in cattle, 26% for yak and 33% for mithun. We also resolved the traditional mithun and cattle hybridization system via principal component analysis. Our results suggested secondary introgression of mithun genes to the village Thrabum population, and a close genetic relationship between Bhutanese indigenous cattle and Indian cattle.
Structure Motif Discovery and Mining the PDB. (2000)

. We describe an algorithm for the automatic discovery of recurring patterns in protein structures. The patterns consist of individual residues having a defined order along the protein&amp;apos;s backbone that come close together in the structure and whose spatial conformations are similar. The residues in a pattern need not be close in the protein&amp;apos;s sequence. The work described in this paper builds on an earlier reported algorithm for motif discovery. This paper describes a significant improvement of the algorithm which makes it very efficient. The improved efficiency allows us to use it for doing unsupervised learning of patterns occurring in small subsets in a large set of structures, a non-redundant subset of the PDB database of all known protein structures. 1 Introduction Structural similarities consisting of a few secondary structures or residues can define structurally or functionally important elements of the proteins. The relationships are subtle and do not always appear sig...
Maturation-dependent upregulation of growth-promoting molecules in developing cortical plate controls thalamic and cortical neurite growth (1995)

We have tested the hypothesis that maturation-dependent changes in the cortical plate affect the spatiotemporal growth patterns of developing thalamocortical and corticocortical axonal projections. Given a choice between alternating lanes of embryonic (E18-19) and neonatal (P0-1) rat cortical plate membranes, embryonic (E18-19) thalamic and cortical neurites prefer to extend on neonatal membranes. Thalamic and cortical explants do extend neurites on uniform carpets of E19 cortical plate membranes, but the outgrowth is consistently greater on uniform carpets of P1 cortical plate membranes. These experiments demonstrate a maturation-dependent enhancement in the ability of cortical plate to support neurite growth from thalamic and cortical explants. In contrast, retinal and cerebellar neurites, which do not grow into cortex in vivo, generally grew poorly on these membranes, suggesting a degree of specificity to the neurite growth response. Immunohistochemical analysis of developing cortex suggests that several extracellular matrix (ECM) and cell adhesion molecules are upregulated in cortical plate. However, immunocharacterization of membrane carpets for these same ECM and cell adhesion molecules suggests that the growth preferences of thalamic and cortical neurites in vitro are predominantly influenced by membrane-anchored, rather than ECM, molecules. Western analysis of E19 and P1 cortical plate membranes supports this conclusion, and indicates that the membrane-anchored cell adhesion molecules L1 and N-CAM are more abundant in the P1 cortical plate membrane preparation. Experiments in which cortical plate membranes were treated to remove molecules sensitive to phosphatidylinositol (PI)-specific phospholipase C demonstrate that neurite growth promoters present in E19 cortical plate membranes are predominantly PI linked, whereas those present in P1 membranes are predominantly non-PI linked. These findings indicate that the neurite growth preferences are mediated, at least in part, by an upregulation of neurite growth-promoting molecules in developing cortical plate that are not PI linked. Taken together, these findings suggest that a maturation-dependent upregulation of neurite growth-promoting molecules on cortical plate cells controls the invasion of the cortical plate by thalamocortical and corticocortical axons.
Challenges of 29nm half-pitch NAND Flash STI patterning with 193nm dry lithography and self-aligned double patterning (2008)

High NA (1.35) Immersion litho runs into the fundamental limit of printing at 40-45nm half pitch (HP). The next generation EUVL tool is known to be ready not until year 2012. Double patterning (DP) technology has been identified as the extension of optical photolithography technologies to 3xnm and 2xnm half-pitch for the low k1 regime to fill in the gap between Immersion lithography and EUVL. Self Aligned Double Patterning (SADP) Technology utilized mature process technology to reduce risk and faster time to market to support the continuation of Moore's Law of Scaling to reduce the cost/function. SADP uses spacer to do the pitch splitting bypass the conventional double patterning (e.g. Litho-Freeze-Litho-Etch (LFLE), or Litho-Etch-Litho-Etch (LELE)) overlay problem. Having a tight overlay performance is extremely critical for NAND Flash manufacturers to achieve a fast yield ramp in production. This paper describes the challenges and accomplishment of a Line-By-Spacer (LBS) SADP scheme to pattern the 29nm half-pitch NAND Flash STI application. A 193nm Dry lithography was chosen to pattern on top of the amorphous carbon (a-C) film stack. The resist pattern will be transferred on the top a-C core layer follow by spacer deposition and etch to achieve the pitch splitting. Then the spacer will be used to transfer to the bottom a-C universal hardmask. This high selectivity a-C hardmask will be used to transfer the 29nm half-pitch pattern to the STI. Good within wafer CD uniformity (CDU) &lt;2nm and line width roughness (LWR) &lt;2nm for the 29nm half-pitch NAND FLASH STI were demonstrated as the benefits using double amorphous carbon hardmask layers. The relationships among the photoresist CDs, CD trimming , as-deposited spacer film thickness, spacer width and the final STI line/core space/gap space CDs will also be discussed in this paper since patterning is combining both lithography performance with CVD and Etch process performance. Film selection for amorphous carbon and the complete DP hardmask scheme in terms of etching selectivity, optical properties and stress optimization was another key challenge to balance excellent litho alignment signal strength and straight pattern profiles without line bending effects. Etching efforts also played a very important roll to obtain pattern integrality under such a high aspect ratio (&gt; 10) case through the whole SADP process. Finally, cost analysis for 193nm dry lithography SADP will be compared to 193nm Immersion lithography SADP.
Design and synthesis of a fluorescent molecular imprinted polymer for use in an optical fibre-based cocaine sensor (2014)

Previously, we have developed chemical sensors using fibre optic-based techniques for the detection of Cocaine, utilising molecularly imprinted polymers (MIPs) containing fluorescein moieties as the signalling groups. Here, we report the computational design of a fluorophore which was incorporated into a MIP for the generation of a novel sensor that offers improved sensitivity for Cocaine with a detection range of 1-100&mu;M. High selectivity for Cocaine over a suite of known Cocaine interferants (25&mu;M) was also demonstrated by measuring changes in the intensity of fluorescence signals received from the sensor.
Quadrature Sampling of Parametric Models with Bi-fidelity Boosting (2022)

Least squares regression is a ubiquitous tool for building emulators (a.k.a. surrogate models) of problems across science and engineering for purposes such as design space exploration and uncertainty quantification. When the regression data are generated using an experimental design process (e.g., a quadrature grid) involving computationally expensive models, or when the data size is large, sketching techniques have shown promise to reduce the cost of the construction of the regression model while ensuring accuracy comparable to that of the full data. However, random sketching strategies, such as those based on leverage scores, lead to regression errors that are random and may exhibit large variability. To mitigate this issue, we present a novel boosting approach that leverages cheaper, lower-fidelity data of the problem at hand to identify the best sketch among a set of candidate sketches. This in turn specifies the sketch of the intended high-fidelity model and the associated data. We provide theoretical analyses of this bi-fidelity boosting (BFB) approach and discuss the conditions the low- and high-fidelity data must satisfy for a successful boosting. In doing so, we derive a bound on the residual norm of the BFB sketched solution relating it to its ideal, but computationally expensive, high-fidelity boosted counterpart. Empirical results on both manufactured and PDE data corroborate the theoretical analyses and illustrate the efficacy of the BFB solution in reducing the regression error, as compared to the non-boosted solution.
Structure of a new oligomer of glutaraldehyde produced by aldol condensation reaction (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure of a new oligomer of glutaraldehyde produced by aldol condensation reactionToshio Tashima, Masahiro Imai, Yoshihiro Kuroda, Shigemasa Yagi, and Terumichi NakagawaCite this: J. Org. Chem. 1991, 56, 2, 694–697Publication Date (Print):January 1, 1991Publication History Published online1 May 2002Published inissue 1 January 1991https://pubs.acs.org/doi/10.1021/jo00002a038https://doi.org/10.1021/jo00002a038research-articleACS PublicationsRequest reuse permissionsArticle Views1012Altmetric-Citations50LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Current Developments of Scanning Confocal Electron Microscopy in a Double Aberration-Corrected Transmission Electron Microscope (2012)

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Functional Changes after Recombinant Human Growth Hormone Replacement in Patients with Chronic Traumatic Brain Injury and Abnormal Growth Hormone Secretion (2016)

We explored the effects of recombinant human growth hormone (rhGH) replacement on physical and cognitive functioning in subjects with a moderate-to-severe traumatic brain injury (TBI) with abnormal growth hormone (GH) secretion. Fifteen individuals who sustained a TBI at least 12 months prior to study enrollment were identified as having abnormal GH secretion by glucagon stimulation testing (maximum GH response less than 8 ng/mL). Peak cardiorespiratory capacity, body composition, and muscle force testing were assessed at baseline and one year after rhGH replacement. Additionally, standardized neuropsychological tests that assess memory, processing speed, and cognitive flexibility, as well as self-report inventories related to depression and fatigue, were administered at baseline and 1 year after rhGH replacement. Comparison tests were performed with proper post hoc analyses. All analyses were carried out at α < 0.05. Peak O<sub>2</sub> consumption, peak oxygen pulse (estimate of cardiac stroke volume), and peak ventilation all significantly increased (p < 0.05). Maximal isometric and isokinetic force production were not altered. Skeletal muscle fatigue did not change but the perceptual rating of fatigue was reduced by ∼25% (p = 0.06). Cognitive performance did not change significantly over time, whereas self-reported symptoms related to depression and fatigue significantly improved. The observed changes suggest that rhGH replacement has a positive impact on cardiorespiratory fitness and a positive impact on perceptual fatigue in survivors of TBI with altered GH secretion.
A Dinuclear Gold(I)–Silver(I) Derivative of 2‐Cyclopentylidene‐2‐sulfanylacetic Acid and Related Complexes: Synthesis, Crystal Structures, Properties and Antitumor Activity (2011)

Abstract The dinuclear complex [AgAu(PPh 3 ) 2 cpa] (H 2 cpa = 2‐cyclopentylidene‐2‐sulfanylacetic acid) was prepared by treating the precursor [Au(PPh 3 )(Hcpa)] with Ag(PPh 3 )NO 3 . The complex was characterised by spectroscopic methods (IR; 1 H, 13 C, 31 P NMR) and mass spectrometry, and the structure was solved by a single‐crystal X‐ray diffraction study. Luminescence and theoretical studies were carried out, and the antitumor activity was studied in vitro against HeLa‐229, A2780 and A2780cis cell lines. The related gold(I)–gold(I), [(AuPPh 3 ) 2 cpa], and silver(I)–silver(I), [(AgPPh 3 ) 2 cpa], compounds were also prepared and studied in the solid state and in solution.
Viscoelastic Loss Characteristics of Cord‐Rubber Composites (1986)

Abstract Calculated and experimentally generated complex moduli of tire cord‐rubber composites are compared. Halpin‐Tsai equations in complex form are defined and used to calculate the elastic and loss components of the composite moduli. Additionally, stress‐strain relationships for bias ply composites are included. Experimental techniques consisted of prestrained cyclic tensile and torsional tests on tubular specimens. Composite properties of typical polyester and steel tire cord reinforcements were evaluated as functions of end count, cross‐ply angle, and thickness of rubber filler between plies.
A New Transmissibility Analysis Method for Detection and Location of Damage via Nonlinear Features in MDOF Structural Systems (2014)

In this paper, a new transmissibility analysis method is proposed for the detection and location of damage via nonlinear features in multidegree-of-freedom (MDOF) structural systems. The method is derived based on the transmissibility of nonlinear output frequency response functions (NOFRFs), a concept recently proposed to extend the traditional transmissibility concept to the nonlinear case. The implementation of the method is only based on measured system output responses and by evaluating and analyzing the transmissibility of these system responses at super-harmonics. This overcomes the problems with available techniques, which assume there is one damaged component with nonlinear features in the system and/or require loading on inspected structural systems is measurable. Both numerical simulation studies and experimental data analysis have been conducted to verify the effectiveness and demonstrate the potential practical applications of the new method.
A bioactive material with dual integrin-targeting ligands regulates specific endogenous cell adhesion and promotes vascularized bone regeneration in adult and fetal bone defects (2022)

Significant progress has been made in designing bone materials capable of directing endogenous cells to promote vascularized bone regeneration. However, current strategies lack regulation of the specific endogenous cell populations for vascularized bone regeneration, thus leading to adverse tissue formation and decreased regenerative efficiency. Here, we engineered a biomaterial to regulate endogenous cell adhesion and promote vascularized bone regeneration. The biomaterial works by presenting two synthetic ligands, LLP2A and LXW7, explicitly targeting integrins α4β1 and αvβ3, respectively, expressed on the surfaces of the cells related to bone formation and vascularization, such as mesenchymal stem cells (MSCs), osteoblasts, endothelial progenitor cells (EPCs), and endothelial cells (ECs). <i>In vitro,</i> the LLP2A/LXW7 modified biomaterial improved the adhesion of MSCs, osteoblasts, EPCs, and ECs via integrin α4β1 and αvβ3, respectively. In an adult rat calvarial bone defect model, the LLP2A/LXW7 modified biomaterial enhanced bone formation and vascularization by synergistically regulating endogenous cells with osteogenic and angiogenic potentials, such as DLX5<sup>+</sup> cells, osteocalcin<sup>+</sup> cells, CD34<sup>+</sup>/CD45<sup>-</sup> cells and CD31<sup>+</sup> cells. In a fetal sheep spinal bone defect model, the LLP2A/LXW7 modified biomaterial augmented bone formation and vascularization without any adverse effects. This innovative biomaterial offers an off-the-shelf, easy-to-use, and biologically safe product suitable for vascularized bone regeneration in both fetal and adult disease environments.
Abstract B01: Genome-scale shRNA screen provides insight into the role of CUL3 in adaptive mechanisms of resistance to mutant BRAF inhibition (2020)

Abstract MAPK inhibition with targeted BRAF inhibitors has revolutionized the treatment of BRAF-mutant melanoma. However, in most cases, the effects of mutant BRAF inhibition are transient, owing to the acquisition of drug resistance. To resolve mechanisms that drive resistance to mutant BRAF inhibition, we performed a genome-scale shRNA screen capable of revealing genes whose loss of function confers resistance to vemurafenib (VEM). We validated ten of our top candidates with independent lentiviral shRNA constructs. We found that knockdown of NF1 and CUL3 confers resistance to VEM. This result is consistent with previous genome-scale loss-of-function screens that have also identified NF1 and CUL3 as drivers of resistance to mutant BRAF inhibition. NF1 encodes a protein that hydrolyzes Ras-GTP. Not surprisingly, it has been shown that loss of NF1 results in increased Ras-GTP levels that lead to reactivation of MAPK in the presence of VEM. However, little is known about the mechanistic changes that underlie CUL3-mediated resistance. Here, we show that unlike the classical reactivation of MAPK that is seen with the loss of NF1, loss of CUL3 results in increased signaling through a Rac1-dependent focal-adhesion-like process that is accompanied by sustained MAPK activity in the presence of VEM. Furthermore, we show that this mechanism of resistance can be abrogated by inhibiting the Src kinase family, a nine-member protein family that critically mediates integrin signaling. In relation to other known drivers of resistance to mutant BRAF inhibition, loss of NF1 reactivates MAPK in a manner much like RAS mutations or BRAF alterations/amplification. By contrast, loss of CUL3 leads to resistance reminiscent of a reversible therapy-resistant state that lacks the key genomic alterations in MAPK signaling proteins. Citation Format: Marion Vanneste, Eliot Zhu, Charlotte Feddersen, Afshin Varzavand, Tyler Foley, Lei Zhao, Rob Piper, Christopher Stipp, Adam Dupuy, Michael Henry. Genome-scale shRNA screen provides insight into the role of CUL3 in adaptive mechanisms of resistance to mutant BRAF inhibition [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr B01.
Imaging cellular ultrastructures using expansion microscopy (U-ExM) (2018)

Determining the structure and composition of macromolecular assemblies is a major challenge in biology. Here we describe ultrastructure expansion microscopy (U-ExM), an extension of expansion microscopy that allows the visualization of preserved ultrastructures by optical microscopy. This method allows for near-native expansion of diverse structures in vitro and in cells; when combined with super-resolution microscopy, it unveiled details of ultrastructural organization, such as centriolar chirality, that could otherwise be observed only by electron microscopy.