gebhart/patrepeval huggingface dataset:
FAK PROTAC Inhibits Ovarian Tumor Growth and Metastasis by Disrupting Kinase Dependent and Independent Pathways (2022)

Focal adhesion kinase (FAK) is highly expressed in a variety of human cancers and is a target for cancer therapy. Since FAK kinase inhibitors only block the kinase activity of FAK, they are not highly effective in clinical trials. FAK also functions as a scaffold protein in a kinase-independent pathway. To effectively target FAK, it is required to block both FAK kinase-dependent and FAK-independent pathways. Thus, we tested a new generation drug FAK PROTAC for ovarian cancer therapy, which blocks both kinase and scaffold activity. We tested the efficacy of FAK PROTAC and its parent kinase inhibitor (VS-6063) in ovarian cancer cell lines <i>in vitro</i> by performing cell functional assays including cell proliferation, migration, invasion. We also tested <i>in vivo</i> activity in orthotopic ovarian cancer mouse models. In addition, we assessed whether FAK PROTAC disrupts kinase-dependent and kinase-independent pathways. We demonstrated that FAK PROTAC is highly effective as compared to its parent FAK kinase inhibitor VS-6063 in inhibiting cell proliferation, survival, migration, and invasion. FAK PROTAC not only inhibits the FAK kinase activity but also FAK scaffold function by disrupting the interaction between FAK and its interaction protein ASAP1. We further showed that FAK PROTAC effectively inhibits ovarian tumor growth and metastasis. Taken together, FAK PROTAC inhibits both FAK kinase activity and its scaffold protein activity by disrupting the interaction between FAK and ASAP1 and is highly effective in inhibiting ovarian tumor growth and metastasis.
Spin-multiplet energies from time-dependent density functional theory (1996)

Starting from a formally exact density-functional representation of the frequency-dependent linear density response and exploiting the fact that the latter has poles at the true excitation energies, we develop a density-functional method for the calculation of excitation energies. Simple additive corrections to the Kohn-Sham single-particle transition energies are derived whose actual computation only requires the ordinary static Kohn-Sham orbitals and the corresponding eigenvalues. Numerical results are presented for spin-singlet and triplet energies. © 1996 John Wiley & Sons, Inc.
Vision-Based Goal-Conditioned Policies for Underwater Navigation in the\n Presence of Obstacles (2020)

We present Nav2Goal, a data-efficient and end-to-end learning method for\ngoal-conditioned visual navigation. Our technique is used to train a navigation\npolicy that enables a robot to navigate close to sparse geographic waypoints\nprovided by a user without any prior map, all while avoiding obstacles and\nchoosing paths that cover user-informed regions of interest. Our approach is\nbased on recent advances in conditional imitation learning. General-purpose,\nsafe and informative actions are demonstrated by a human expert. The learned\npolicy is subsequently extended to be goal-conditioned by training with\nhindsight relabelling, guided by the robot's relative localization system,\nwhich requires no additional manual annotation. We deployed our method on an\nunderwater vehicle in the open ocean to collect scientifically relevant data of\ncoral reefs, which allowed our robot to operate safely and autonomously, even\nat very close proximity to the coral. Our field deployments have demonstrated\nover a kilometer of autonomous visual navigation, where the robot reaches on\nthe order of 40 waypoints, while collecting scientifically relevant data. This\nis done while travelling within 0.5 m altitude from sensitive corals and\nexhibiting significant learned agility to overcome turbulent ocean conditions\nand to actively avoid collisions.\n
Unextendible maximally entangled bases (2011)

We introduce the notion of the unextendible maximally entangled basis (UMEB), a set of orthonormal maximally entangled states in ${\mathbb{C}}^{d}\ensuremath{\bigotimes}{\mathbb{C}}^{d}$ consisting of fewer than ${d}^{2}$ vectors which have no additional maximally entangled vectors orthogonal to all of them. We prove that UMEBs do not exist for $d=2$ and give explicit constructions for a six-member UMEB with $d=3$ and a 12-member UMEB with $d=4$.
Environmentally-compatible alkyd paints stabilized by wood hemicelluloses (2019)

Wood biorefining currently involves large-scale industrial processes where a notable portion of raw materials, namely hemicelluloses and lignin, are either lost with the process water, degraded, or burnt for energy. Value added utilization of polymeric hemicelluloses is challenging due to their intermediate molar mass and the presence of other wood components, such as phenolic residues or wood extractives. Oil-in-water (O/W) emulsions represent a diverse and abundant class of applications in which the natural properties of wood hemicelluloses are beneficial. In the current work, we present highly promising new technical alkyd paint emulsion systems stabilized with hardwood glucuronoxylans (GX) and softwood galactoglucomannans (GGM). Samples from three isolation methods and their further fractionation by ethanol precipitation were systematically compared with regard to hemicellulose composition, interfacial activity, and functionality in emulsions. Emulsification of alkyd resins was successful with both GX and GGM obtained by various biorefining strategies. The highest emulsion stability over storage was achieved using crude non-purified GX and GGM fractions, and was correlated with the presence of phenolic compounds and extractives, interfacial activity, and small droplet size. Hardwood GX and softwood GGM are envisioned as natural emulsifiers of alkyd O/W emulsions, which are examples of diverse and abundantly-used technical dispersions. This study can be utilized as a guideline for targeted extraction of hemicelluloses with desired functionality, and as a protocol for developing environmentally-compatible industrial dispersions.
Intrinsically electrically conducting poly(metal tetrathiooxalates) (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIntrinsically electrically conducting poly(metal tetrathiooxalates)John R. Reynolds, James C. W. Chien, and C. Peter LillyaCite this: Macromolecules 1987, 20, 6, 1184–1191Publication Date (Print):June 1, 1987Publication History Published online1 May 2002Published inissue 1 June 1987https://doi.org/10.1021/ma00172a003RIGHTS & PERMISSIONSArticle Views362Altmetric-Citations48LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
Variable tuning in LCL compensated contactless power transfer pickups (2009)

This paper analyses the effects of tuning deviation in the resonant tank of an LCL Inductive Power Transfer (IPT) pickup. It also proposes a method of active tuning which maintains unity power factor at the input to the pickup. By varying the second inductor in the LCL network, variations in the tuning capacitor can be compensated which also acts to increase the output power to the load after the retuning action. The power increase is limited by the available control action and component rating. A self tuning pickup has been built using a saturable inductor to vary the impedance of the tuning components. The pickup successfully maintains unity input power factor when the tuning was deliberately deviated.
Can a single function for χ account for block copolymer and homopolymer blend phase behavior? (1998)

Most theoretical treatments of polymer–polymer phase behavior assume that homopolymer mixtures and block copolymer melts are controlled by a common segment–segment interaction parameter knows as χ. This publication describes the results of small-angle neutron scattering (SANS) experiments conducted as a function of temperature and composition from homogeneous mixtures of poly(ethylene) (PE) and poly(ethylenepropylene) (PEP) of equal molecular weight. Analysis of these SANS measurements based on the random phase approximation indicates that χPE/PEP is independent of composition and linear in T−1. The associated symmetric phase diagram calculated with Flory–Huggins theory contains a stability curve that is consistent with the divergence in single phase susceptibility obtained by SANS. This function χPE/PEP(T) is compared with functions for χPE–PEP(T) associated with the homologous PE–PEP diblock copolymers, extracted both from the temperature dependence of the disordered state scattering structure factor, and from the N dependence of the order–disorder transition (ODT) temperature TODT, where N is the degree-of-polymerization. Analysis of these data using mean-field and fluctuation theories leads to four distinct expressions for χPE–PEP(T), none of which is consistent with χPE/PEP(T). We attribute this disparity to the effects of polarization and stretching of diblock molecules in the vicinity of the ODT. A simple model calculation that corrects the prediction for (χN)ODT based on the experimentally determined shift in the SANS peak location corroborates this deduction. We conclude that current theories cannot account for block copolymer and homopolymer phase behavior based on a single function for χ, and suggest that this deficiency may be rectified with a more sophisticated block copolymer theory that properly accounts for chain stretching.
Screening of Lactic Acid Bacteria Having the Ability to Produce Reuterin (2002)

ロイテリンは,Lactobacillus reuteri によって生産される低分子量の抗菌性物質で,各種の細菌,酵母,かび類の増殖を阻害することが報告されている。本報では,サイレージ発酵への応用を目的に,ロイテリン様物質(RLC)を生産する乳酸菌を検索するとともに,生産されたRLCの抗菌スペクトルの諸性質と分離・精製および同定について検討した。保存乳酸菌148株の培養菌体をグリセリン溶液と接触させる静置培養法により,6株のRLCを有する乳酸菌を選抜した。このうち,Lactobacillus coryniformis 394が最も高い生産性を示し,上記培養時に0.5%CaCO3を添加し,25℃,12時間嫌気的に保持することにより最大生産値が得られた。RLC画分をHPLCおよびTLCにより精製し,H-NMRとC-NMRにより検討した結果,本画分中の抗菌性物質はロイテリン(β-ヒドロキシプロピオンアルデヒド)であると同定された。一方,ロイテリンを含むこの培養上清液は,殺菌作用を有しサイレージ発酵に有用な乳酸菌類を除く種々の細菌類,酵母およびかびの増殖を強く阻害することから,サイレージ発酵への応用の可能性が示唆された。
Supplementary Table 9 from Cancer-Associated Fibroblasts Promote Aggressive Gastric Cancer Phenotypes via Heat Shock Factor 1–Mediated Secretion of Extracellular Vesicles (2023)

&lt;p&gt;List of antibodies used in the study&lt;/p&gt;
Bayesian and maximum likelihood estimation of genetic maps (2005)

There has recently been increased interest in the use of Markov Chain Monte Carlo (MCMC)-based Bayesian methods for estimating genetic maps. The advantage of these methods is that they can deal accurately with missing data and genotyping errors. Here we present an extension of the previous methods that makes the Bayesian method applicable to large data sets. We present an extensive simulation study examining the statistical properties of the method and comparing it with the likelihood method implemented in Mapmaker. We show that the Maximum A Posteriori (MAP) estimator of the genetic distances, corresponding to the maximum likelihood estimator, performs better than estimators based on the posterior expectation. We also show that while the performance is similar between Mapmaker and the MCMC-based method in the absence of genotyping errors, the MCMC-based method has a distinct advantage in the presence of genotyping errors. A similar advantage of the Bayesian method was not observed for missing data. We also re-analyse a recently published set of data from the eggplant and show that the use of the MCMC-based method leads to smaller estimates of genetic distances.
Front Cover: Comparative Performance of PETase as a Function of Reaction Conditions, Substrate Properties, and Product Accumulation (ChemSusChem 1/2022) (2021)

The Front Cover shows the application of poly(ethylene terephthalate) (PET) hydrolase enzymes on post-consumer waste plastic, towards the development of an enzymatic PET recycling strategy. More information can be found in the Full Paper by E. Erickson et al.
Deconvolution of the epigenetic age discloses distinct inter-personal variability in epigenetic aging patterns (2021)

Background The epigenetic age can now be extrapolated from one of several epigenetic clocks, which are based on age-related changes in DNA methylation levels at specific multiple CpG sites. Accelerated aging, calculated from the discrepancy between the chronological age and the epigenetic age, has shown to predict morbidity and mortality rate. We assumed that deconvolution of epigenetic age to its components could shed light on the diversity of epigenetic, and by inference, on inter-individual variability in the causes of biological aging. Results Using the Horvath original epigenetic clock, we identified several CpG sites linked to distinct genes that quantitatively explain much of the interpersonal variability in epigenetic aging, with CpG sites related to secretagogin and malin being the most variable. We show that equal epigenetic age in different subjects can result from variable contribution size of the same CpG sites to the total epigenetic age. In a healthy cohort, the most variable CpG sites are responsible for accelerated and decelerated epigenetic aging, relative to chronological age. Conclusions Of the 353 CpG sites that form the basis for the Horvath epigenetic age, we have found the CpG sites that are responsible for accelerated and decelerated epigenetic aging in healthy subjects. However, the relative contribution of each site to aging varies between individuals, leading to variable personal aging patterns. Our findings pave the way to form personalized aging cards allowing the identification of specific genes related to CpG sites, as aging markers, and perhaps treatment of these targets in order to hinder undesirable age drifting.
Development of Potential Orphan Drug Therapy of Intravesical Liposomal Tacrolimus for Hemorrhagic Cystitis Due to Increased Local Drug Exposure (2012)

Single dose pharmacokinetics revealed that bladder instillation of liposome encapsulated tacrolimus significantly decreased systemic exposure to instilled tacrolimus as well as vehicle related toxicity. Intravesical liposomal tacrolimus may be a promising approach as an orphan drug indication for hemorrhagic cystitis.
A Diffusion Model to Explain Mixing of Flowing Miscible Fluids in Porous Media (1957)

Published in Petroleum Transactions, AIME, Volume 210, 1957, pages 345–349. Abstract This paper presents a mathematical analysis of the fluid mixing which occurs during flow through porous media. The analysis is based on the well-known diffusion equation with mass transfer term. It is pointed out that the use of this equation is justified by a single general assumption which does not specify any particular mechanism for the mixing process. Formulas are given for tracer fluid concentrations for two different boundary and initial conditions. Calculated numerical values compare closely with some published results of experiments in which no viscosity or density difference existed between displaced and displacing fluids. Introduction A phenomenological theory of the mixing and diffusion process is presented for the flow in a porous medium of two miscible liquids of equal viscosity and density. This is based on the classical diffusion equation which has been used to explain such processes as Brownian motion and heat conduction. More recently, this same differential equation has been derived (in a manner analogous to the work in this paper) for the problem of heat transfer during fluid flow in porous media. The purpose of this paper is to show that the available experimental evidence justifies the use of this simple diffusion equation. The recent data of Koch and Slobod and of von Rosenberg are used to test this diffusion model by comparing concentration curve shapes and calculating "effective diffusion coefficients". The same differential equation for miscible displacement, as well as some experimental confirmation, has been published in Japan by K. Yuhara, and recently in this country by Day. Yuhara arrives at his conclusions through analogy with turbulent diffusion, describing the microscopic velocities in terms of "eddy motion" although unlike the ordinary eddies of hydraulics. Day proceeds directly from Scheidegger's concept of the dispersion of velocities. After a very clear description of Scheidegger's theory, he applies it to calculate the motion first of a drop and then of a thin layer of brine into a bed of sand. For the latter case, Day derives and solves the same differential equation as Eq. 1.
Vibration Centers for Planar Motion (1996)

Abstract A novel analysis is presented for the planar free vibration of an elastically suspended rigid body. Vibration centers describe the modes shapes and are shown to be constrained to regions specified by the center-of-elasticity, center-of-mass, and stiffness principal directions. Responses are classified by the number of pure translational modes and conditions for existence are given. Numerical examples illustrate the results.
Comparative evaluation of linear-rotary actuator topologies for highly dynamic applications (2017)

A Linear-Rotary Actuator (LiRA) is an electrical machine whose mover can move linearly and rotate as a direct drive (without mechanical transmissions/gearboxes). Such actuators are successfully used in various applications such as pick-and-place machines that mount components on Printed Circuit Boards (PCBs), servo actuation of gearboxes, and in robot arms and/or end effectors. In order to design a compact LiRA with high dynamics, two different LiRA topologies are compared in this paper. A fair comparison is obtained by fixing the outer dimensions of the examined LiRA topologies (diameter and length). Electrical loading of the machines is determined using a simple thermal model, and an optimization based on finite element analysis is carried out. Performance criteria, such as circumferential and axial accelerations as well as maximum axial forces of all analyzed machines are compared. Moreover, metrics like total machine mass and volume of the used permanent magnets are included in the evaluation.
Comparison of Lund'07 vehicular channel measurements with the IEEE 802.11p channel model (2008)

This paper presents a very preliminary comparison between the IEEE 802.11p channel model parameters with parameters evaluated from new high speed measurements in Lund, Sweden. Following interesting differences as well as similarities are observed: The measured maximum excess delay is about one fifth of the one proposed in the IEEE 802.11p model. The amplitude distribution for each tap can be approximated as Ricean distribution, with a very high Rice factor for the first tap and small Rice factors for later taps. Similar to the IEEE 802.11p model we observe a strong line of sight path near to the Doppler frequency of zero and weaker paths at Doppler frequencies about twice the measurement vehicle’s speed. As a key result we show that the average delay-Doppler spectra, which is one part of the tap delay model, does not reflect the time variant behavior of the radio channel.
Inspection of laser-seam welds in automobile manufacturing (2005)

Recent developments in infrared camera technology, testing methods and data processing algorithms have brought significant progress for high resolution spatial and temporal analysis of thermal radiation. Together with industry standard automation technology and specific infrared image data processing it became possible to non destructively inspect laser welded seams and other types of joints using heat flux analysis subsequent to active thermal excitation. High thermal diffusion coefficients of the usually metallic samples under test make the availability of high-speed infrared cameras as a key hardware component indispensable. Since high-speed infrared cameras with frame rates of at least 500 Hz have become available for commercial applications, non-destructive testing systems with a new class of performance were designed, manufactured, and implemented at industrial sites. Heat flux analysis as a new and robust method of non-destructive testing has been implemented for various types of equipment, ranging from off-line tools for laboratory use to automated robot based systems enabling fast and operator-free in-line inspection. Depending on environment, implementation surroundings, and geometry of objects to be inspected, different types of pulsed or continuous operating heat sources (e.g. flash light, laser, ...) are selected. Due to its outstanding industrial relevance some examples of non-destructive testing of laser welded seams in automobile manufacturing are shown.
Communicating Our Science to Our Customers: The Vital Role of Passionate Public Advocacy (2016)

As scientists, we are comfortable communicating our work to our peers. However, communicating with equal passion to those outside our field is something we as a community often shy away from. This reticence has often been exploited by those wishing to present their own view of the science we practice. Herein, we urge the scientific community to actively re-engage with the general public, openly and creatively sharing our endeavors beyond these pages, in order to reconnect with the <i>real</i> consumers of the work we produce.
Sparse Multiple Kernel Learning for Signal Processing Applications (2009)

In many signal processing applications, grouping of features during model development and the selection of a small number of relevant groups can be useful to improve the interpretability of the learned parameters. While a lot of work based on linear models has been reported to solve this problem, in the last few years, multiple kernel learning has come up as a candidate to solve this problem in nonlinear models. Since all of the multiple kernel learning algorithms to date use convex primal problem formulations, the kernel weights selected by these algorithms are not strictly the sparsest possible solution. The main reason for using a convex primal formulation is that efficient implementations of kernel-based methods invariably rely on solving the dual problem. This work proposes the use of an additional log-based concave penalty term in the primal problem to induce sparsity in terms of groups of parameters. A generalized iterative learning algorithm, which can be used with a linear combination of this concave penalty term with other penalty terms, is given for model parameter estimation in the primal space. It is then shown that a natural extension of the method to nonlinear models using the "kernel trick" results in a new algorithm, called Sparse Multiple Kernel Learning (SMKL), which generalizes group-feature selection to kernel selection. SMKL is capable of exploiting existing efficient single kernel algorithms while providing a sparser solution in terms of the number of kernels used as compared to the existing multiple kernel learning framework. A number of signal processing examples based on the use of mass spectra for cancer detection, hyperspectral imagery for land cover classification, and NIR spectra from wheat, fescue grass, and diesel are given to highlight the ability of SMKL to achieve a very high accuracy with a very few kernels.