gebhart/patrepeval huggingface dataset:
BET Bromodomain Proteins Regulate Transcriptional Reprogramming in Genetic Dilated Cardiomyopathy (2020)

ABSTRACT The bromodomain and extraterminal (BET) family of epigenetic reader proteins are key regulators of pathologic gene expression in the heart. Using mice carrying a human mutation in phospholamban (PLN R9C ) that develop progressive dilated cardiomyopathy (DCM), we previously identified the activation of inflammatory gene networks as a key early driver of DCM. We reasoned that BETs control this inflammatory process, representing a key node in the progression of genetic DCM. Using a chemical genetic strategy, PLN R9C or age-matched wild type mice were treated longitudinally with the BET inhibitor JQ1 or vehicle. JQ1 abrogated DCM, reduced cardiac fibrosis, and prolonged survival in PLN R9C mice by inhibiting inflammatory gene network expression at all disease stages. Cardiac fibroblast proliferation was also substantially reduced by JQ1. Interestingly, JQ1 had profound effects on pathologic gene network expression in cardiac fibroblasts, while having little effect on transcription in cardiomyocytes. Using co-immunoprecipitation, we identified BRD4 as a direct and essential regulator of NFκB-mediated inflammatory gene transcription in cardiac fibroblasts. In this this model of chronic, heritable DCM, BETs activate inflammatory gene networks in cardiac fibroblasts via an NFκB-dependent mechanism, marking them as critical effectors of pathologic gene expression.
Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature (2006)

X-ray crystallography has revealed two similar alpha/beta domains of the aspartate racemase from the hyperthermophilic archaeon, Pyrococcus horikoshii OT3. The active site is located in the cleft between the two domains where two cysteine residues face each other. This arrangement allows the substrate to enter the cleft and enables the two cysteine residues to act synergistically. However, the distance between their thiolates was estimated to be 9.6 angstroms, which is beyond the distance for cooperative action of them. We examined the molecular mechanism for the racemization reaction of this hyperthermophilic aspartate racemase by mutational analyses and molecular dynamics simulations. The mutational analyses revealed that Arg48 and Lys164 were essential for catalysis in addition to the putative catalytic cysteine residues. The molecular dynamics simulations revealed that the distance between the two active gamma-sulfur atoms of cysteine residues oscillate to periodically become shorter than the predicted cooperative distance at high temperature. In addition, the conformation of Tyr160, which is located at the entrance of the cleft and inhibits the entry of a substrate, changes periodically to open the entrance at 375 K. The opening of the gate is likely to be induced by the motion of the adjacent amino acid, Lys164. The entrance of an aspartate molecule was observed by molecular dynamics (MD) simulations driven by the force of the electrostatic interaction with Arg48, Lys164, and also Asp47. These results provide insights into the roles of amino acid residues at the catalytic site and also the activation mechanism of a hyperthermophilic aspartate racemase at high temperature.
Response to Letter Regarding Article, “The Effect of Selective Heart Rate Slowing in Heart Failure With Preserved Ejection Fraction” (2016)

We thank de Dios for their comments related to the differences in outcomes noted between our observations and previously published work exploring the role of ivabradine in patients with heart failure with preserved ejection fraction (HFpEF).
Noise and signal properties in PSF-based fully 3D PET image reconstruction: an experimental evaluation (2010)

The addition of accurate system modeling in PET image reconstruction results in images with distinct noise texture and characteristics. In particular, the incorporation of point spread functions (PSF) into the system model has been shown to visually reduce image noise, but the noise properties have not been thoroughly studied. This work offers a systematic evaluation of noise and signal properties in different combinations of reconstruction methods and parameters. We evaluate two fully 3D PET reconstruction algorithms: (1) OSEM with exact scanner line of response modeled (OSEM+LOR), (2) OSEM with line of response and a measured point spread function incorporated (OSEM+LOR+PSF), in combination with the effects of four post-reconstruction filtering parameters and 1-10 iterations, representing a range of clinically acceptable settings. We used a modified NEMA image quality (IQ) phantom, which was filled with 68Ge and consisted of six hot spheres of different sizes with a target/background ratio of 4:1. The phantom was scanned 50 times in 3D mode on a clinical system to provide independent noise realizations. Data were reconstructed with OSEM+LOR and OSEM+LOR+PSF using different reconstruction parameters, and our implementations of the algorithms match the vendor's product algorithms. With access to multiple realizations, background noise characteristics were quantified with four metrics. Image roughness and the standard deviation image measured the pixel-to-pixel variation; background variability and ensemble noise quantified the region-to-region variation. Image roughness is the image noise perceived when viewing an individual image. At matched iterations, the addition of PSF leads to images with less noise defined as image roughness (reduced by 35% for unfiltered data) and as the standard deviation image, while it has no effect on background variability or ensemble noise. In terms of signal to noise performance, PSF-based reconstruction has a 7% improvement in contrast recovery at matched ensemble noise levels and 20% improvement of quantitation SNR in unfiltered data. In addition, the relations between different metrics are studied. A linear correlation is observed between background variability and ensemble noise for all different combinations of reconstruction methods and parameters, suggesting that background variability is a reasonable surrogate for ensemble noise when multiple realizations of scans are not available.
Supplementary document for Manipulation of quantum dot emission with semiconductor metasurfaces exhibiting magnetic quadrupole resonances - 5013425.pdf (2021)

Supporting Information
Autologous Hematopoietic Cell Transplantation for Systemic Light Chain (AL‐) Amyloidosis (2009)

This chapter contains sections titled: Introduction Epidemiology Pathogenesis Diagnosing AL-amyloidosis Clinical presentations Prognosis Therapy Conclusion References
<title>Wavelet interpolation networks for hierarchical approximation</title> (1999)

In this paper, we motivate and describe a scattered data interpolation scheme based on a hierarchical wavelet subfamily selection process named allocation. This interpolation method applies in any dimension, where it compares well to regularization techniques, especially in terms of stability, of adaptivity and of sparsity of the learned function representation. Adaptive convergence theorems are stated, and their proofs are outlined. We also describe a variant of this approach that can be incremental, and thus works as an online learning process.
35Gb/s Ultralow-Voltage Three-Terminal Si-Ge Avalanche Photodiode (2019)

We demonstrate a 35Gb/s three-terminal waveguide silicon-germanium avalanche photodiode using a lateral interdigitated multiplication region. A breakdown voltage of −6V, a bandwidth of 18.9GHz, and a multiplication gain of 15 are achieved.
On the accuracy of point correspondence methods in three-dimensional measurement systems using fringe projection (2013)

Different concepts of correspondence findings in contactless optical three-dimensional (3-D) measurement systems using fringe projection are analyzed concerning the accuracy of the 3-D point calculation. These concepts are different concerning the kind of performance of the triangulation procedure in order to calculate the resulting 3-D points and the use of geometric constraints versus second projection sequence. Triangulation may be alternatively performed between camera pixels and the phase origin of the projection, between one camera pixel in the prior camera and the image of the corresponding measured phase value in the second camera, or between the image points of certain raster phase values in the two observation cameras. Additionally, triangulation procedures can be distinguished concerning the use of two perpendicular projection directions of the fringes versus the use of geometric constraints, i.e., epipolar geometry instead of the second projection direction. Advantages and disadvantages of the different techniques are discussed. In addition, a theoretical analysis of the application of synthetic data has been simulated as well as experiments performed on real measurement data. Both simulations and real data experiments confirm the theoretical assumptions concerning the magnitudes of the random errors occurring in 3-D point determination.
Six-Coordinate Trigonal-Prismatic Complexes1 (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSix-Coordinate Trigonal-Prismatic Complexes1Edward I. Stiefel and Harry B. GrayCite this: J. Am. Chem. Soc. 1965, 87, 17, 4012–4013Publication Date (Print):September 1, 1965Publication History Published online1 May 2002Published inissue 1 September 1965https://pubs.acs.org/doi/10.1021/ja01095a061https://doi.org/10.1021/ja01095a061research-articleACS PublicationsRequest reuse permissionsArticle Views148Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Proceedings of the 2016 ACM Workshop on Multimedia for Personal Health and Health Care (2016)

We are delighted to welcome you to the First International Workshop on Multimedia for Personal Health and Health Care, held on October 16, 2016 in conjunction with ACM Multimedia in Amsterdam. Multimedia and health is a new and developing field and has become an integral part of the tools and systems that are providing solutions to today's societal challenges such as personal health and health care. This workshop is addressing the different aspects of multimedia in personal health. The special characteristic of the workshop is the joining of a challenging and highly application domain and multimedia research. The workshop is of a very interdisciplinary nature which is reflected by its faceted topics of interest which are also covered by the different expertise of the organizers. With this workshop we aim to give the topics a clear home where the domain expertise meets with multimedia research questions. The program of the workshop is offering a wonderful spectrum of ongoing international work in the field of multimedia in health and health care. The program of the workshop offers a set of full and short papers as well as an exciting and interactive demonstration session. We are looking forward to an exciting discussion in this new area.
Cross-Validated Bagged Prediction of Survival (2006)

In this article, we show how to apply our previously proposed Deletion/Substitution/Addition algorithm in the context of right-censoring for the prediction of survival. Furthermore, we introduce how to incorporate bagging into the algorithm to obtain a cross-validated bagged estimator. The method is used for predicting the survival time of patients with diffuse large B-cell lymphoma based on gene expression variables.
Demo (2015)

Glimpse is a continuous, real-time object recognition system for camera-equipped mobile devices. Glimpse captures full-motion video, locates objects of interest, recognizes and labels them, and tracks them from frame to frame for the user. Because the algorithms for object recognition entail significant computation, Glimpse runs them on server machines. To achieve high accuracy, Glimpse uses an active cache of video frames on the mobile device. A subset of the frames in the active cache are used to track objects on the mobile, using (stale) hints about objects that arrive from the server from time to time. To reduce network bandwidth usage, Glimpse computes trigger frames to send to the server for recognizing and labeling.
Cleanability Improvement of Cotton Fabrics Through Their Topographical Changes Due to the Conditioning with Cellulase Enzyme (2011)

Abstract In this study, topographical changes of woven cotton fabrics conditioned with a cellulase enzyme during several wash–dry cycles are systematically studied. A recent study of cellulase enzyme effect on cellulose films has proven that this substance selectively attacks amorphous regions of cellulose, consisting of small hills in a matrix of flat crystalline regions. In another study, topographical changes caused by cotton treatment with cellulase by conditioning while washing were analysed on three different length scales in order to interpret their cooperation on water and oil absorption mechanisms and, hence, on the cleanability of cotton fabrics stained with liquid–solid, liquid and solid soils. In the present study, we emphasise the micro‐topographical changes resulting from several wash–dry cycles by the application of mathematical methods to quantify the changes of yarn micro‐surfaces. As a result, we present a conceptual model that describes how the topographical effect of washing and conditioning by cellulase enzyme improves the cleanability of woven plain cotton fabrics.
Transferrin Non-Viral Gene Therapy for Treatment of Retinal Degeneration (2020)

Dysregulation of iron metabolism is observed in animal models of retinitis pigmentosa (RP) and in patients with age-related macular degeneration (AMD), possibly contributing to oxidative damage of the retina. Transferrin (TF), an endogenous iron chelator, was proposed as a therapeutic candidate. Here, the efficacy of TF non-viral gene therapy based on the electrotransfection of pEYS611, a plasmid encoding human TF, into the ciliary muscle was evaluated in several rat models of retinal degeneration. pEYS611 administration allowed for the sustained intraocular production of TF for at least 3 and 6 months in rats and rabbits, respectively. In the photo-oxidative damage model, pEYS611 protected both retinal structure and function more efficiently than carnosic acid, a natural antioxidant, reduced microglial infiltration in the outer retina and preserved the integrity of the outer retinal barrier. pEYS611 also protected photoreceptors from N-methyl-N-nitrosourea-induced apoptosis. Finally, pEYS611 delayed structural and functional degeneration in the RCS rat model of RP while malondialdehyde (MDA) ocular content, a biomarker of oxidative stress, was decreased. The neuroprotective benefits of TF non-viral gene delivery in retinal degenerative disease models further validates iron overload as a therapeutic target and supports the continued development of pEY611 for treatment of RP and dry AMD.
What Is Governed? Comparing Governance Modes in Large Metropolis (2012)

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Comparative Study of Flat and Round Collectors Using a Validated 1D Fluid Probe Model (2006)

Abstract In the literature two different types of Gundestrup‐like probe designs are proposed: design with flat and with round collectors. In this paper we study the influence of different collector shapes of Gundestrup‐like probes on the accuracy of the measurement of the parallel and perpendicular flows. A one dimensional fluid probe model is used for deducing both Mach numbers of the unperturbed flow from the probe data. An analytical expression relates the plasma flow to the measured ion saturation currents collected at the upstream and downstream collecting surfaces of the probe. For flat collectors, the analytical model is validated by comparing it to a two dimensional quasi‐neutral Particle In Cell (PIC) simulation code. An extension of the theoretical model then allows us to study round collectors. We performed an accuracy study which showed that systematic errors are introduced when round collectors are employed for determination of the perpendicular flow which is systematically overestimated. The error can reach more than 70% when the perpendicular flow increases and when the angle of the collecting surface with respect to the magnetic field ( θ → 0)is small. The correct analytical expression is applied to experimental data from Gundestrup probe measurements with round collectors on the CASTOR tokamak. The analysis shows that for these measurements the error introduced by using the expression for flat collectors remains negligible, supporting our former use of the model for flat collectors. A new advanced Gundestrup‐like probe design and the motivation for the choice of flat collectors are presented. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
NMR Structure Determination of a Novel Conotoxin, [Pro 7,13] αA-Conotoxin PIVA, (1997)

A high-resolution solution conformation of a novel conotoxin, [Pro 7,13] alpha A-conotoxin PIVA, GCCGSYPNAACHPCSCKDROSYCGQ-NH2, has been determined by two-dimensional 1H NMR methods and distance geometry calculations. The total of 324 NOE-derived interproton distance restraints including 33 long-range NOE restraints as well as 11 phi and 7 chi 1 torsion angle restraints was used for computation of structures. Back-calculation from the experimental NOE spectrum has provided 49 new NOE restraints and yielded the final R-factors of Ra = 0.641 and Rb = 0.157. The final RMSD values are 0.90 and 1.16 A for the backbone and the heavy atoms, respectively. The C-terminal half of the molecule involving the residues 12-24 is extremely well-defined with a backbone RMSD value of 0.56 A, whereas the N-terminal 3-11 disulfide loop is relatively flexible, possessing a backbone RMSD value of 1.09 A. The [Pro 7,13] alpha A-conotoxin PIVA does not contain any significant secondary structure although the 21S-24G nearly completes one turn of a 3(10) helix. The overall protein fold is largely maintained by the three disulfide bridges of 2-16, 3-11, and 14-23. The presence of the three disulfide bridges imposes geometric constraints that force the molecule to form six continuous bends involving the following residues: 3C-5S, 7P-10A, 12H-14C, 15S-17K, 17K-19R, and 21S-25Q. The overall shape of the [Pro 7,13] alpha A-conotoxin PIVA can be described as an "iron". Residues 15S-19R form a loop that protrudes out of the "bottom plate" formed by the rest of the protein and constitute the handle of the iron. The N-terminal tip of the molecule is relatively immobile due to attractive electrostatic interactions between the gamma-hydroxyl group of 20 Hyp and the phenolic hydroxyl group of 22Y. The flexible 3-11 disulfide loop consists mostly of hydrophobic residues, while the best-defined 14-23 disulfide loop contains the highly charged hydrophilic 15S-19R "handle" domain exposed to the exterior of the protein. Binding to nicotinic acetylcholine receptor can be mediated through two different types of interactions: one involving the aromatic hydrophobic residues such as 6Y and 12H and the other involving the positively charged hydrophilic side chain of the 19R. The side chain of the 19R in the [Pro 7, 13] alpha A-conotoxin PIVA and that of the 9R of the alpha-conotoxin G1, and also the side chains of the 12H and 6Y in the former and those of 10H and 11Y in the latter can be aligned to point to the same direction when the corresponding backbone atoms are superimposed to an RMSD value of 2.5 A.
Online Recovery of Temporally Correlated Sparse Signals Using Multiple Measurement Vectors (2014)

This work addresses the problem of sequential recovery of temporally correlated sparse vectors with common support from noisy under-determined linear measurements. The Kalman sparse Bayesian learning (SBL) algorithm is an efficient tool for solving the problem when the temporal correlation is modeled using a first order autoregressive model. However, this method processes the input data in a batch mode, which results in high latency. We propose two online SBL algorithms which operate on the observations in a serial fashion. They are sequential expectation maximization (EM) schemes, implemented using fixed lag smoothing and sawtooth lag smoothing. The online algorithms require significantly lower computational and memory resources compared to their offline counterparts. Also, estimates of the sparse vectors become available after a fixed delay from the time observations arrive. Using Monte Carlo simulations, we illustrate that the mean square error and support recovery performance of the proposed algorithms is very close to the offline Kalman SBL algorithm.
An Improved Synthesis of BrettPhos‐ and RockPhos‐Type Biarylphosphine Ligands (2012)

Improved processes for the preparation of biphenyl-based phosphine ligands <i>t</i>-BuBrettPhos, RockPhos, and BrettPhos are presented. The new methods, featuring the use of Grignard reagents and catalytic amounts of copper, are superior to the previous methods, which require the use of <i>t</i>-butyllithium and stoichiometric amounts of copper. Specifically, the use of less dangerous reagents provides a safer process, while the use of catalytic amounts of copper allows for the isolation of pure products in high yield. These improvements are particularly significant for the large scale preparation of these ligands.
ChemInform Abstract: CRYSTAL STRUCTURES OF TWO TITANIUM TARTRATE ASYMMETRIC EPOXIDATION CATALYSTS (1985)

Abstract Die Molekül‐ und Kristallstrukturen der beidendimeren Ti‐Komplexe (I) (RG C222 " Z=4) und (II) (RG P2" Z=2) werden röntgenanalytisch ermittelt.
Painless squeaking following cervical disc replacement: A case report (2015)

The aetiology of this painless squeaking has been elusive and is likely to be multifactorial. However we hypothesise that the audible squeak associated with the prestige LP disc maybe related to specific design characteristics and needs further evaluation.