gebhart/patrepeval huggingface dataset:
Characterization of CDNF-Secreting ARPE-19 Cell Clones for Encapsulated Cell Therapy (2019)

Cerebral dopamine neurotrophic factor (CDNF) shows beneficial effects in rodent models of Parkinson's and Alzheimer's disease. The brain is a challenging target for protein therapy due to its exclusive blood-brain barrier. Hence, the therapeutic protein should be delivered directly to the brain parenchyma. Implantation of encapsulated mammalian cells that constantly secrete CDNF is a potential approach for targeted and long-term protein delivery to the brain. In this study, we generated several CDNF-secreting cell clones derived from human retinal pigment epithelial cell line ARPE-19, and studied CDNF secretion from the clones maintained as monolayers and in polymeric microcapsules. The secretion of wild type (wt) CDNF transgene was low and the majority of the produced protein remained intracellular, locating mainly to the endoplasmic reticulum (ER). The secretion of wtCDNF decreased to even lower levels when the clones were in a non-dividing state, as in the microcapsules. Both codon optimization and deletion of the putative ER-retrieval signal (four last amino acids: KTEL) improved CDNF secretion. More importantly, the secretion of KTEL-deleted CDNF remained constant in the non-dividing clones. Thus, cells expressing KTEL-deleted CDNF, in contrast to wtCDNF, can be considered for cell encapsulation applications if the KTEL-deleted CDNF is proven to be biologically active <i>in vivo</i>.
An empathizing robot, development of &#x2018;human-like emotions and augmented dynamics&#x2019; (H.E.A.D) and it's Emotion Cloud (2013)

This paper discusses the planning and development of a robotic head which empathizes with the user and reflects their emotions with concerted response. It is structured using keywords and expressions heuristics (C.H.E.E and Mood) which embrace a non-predictable and a layered and weighted approach to emotions: `Emotion Cloud', which encompasses various inputs from the user. The paper details the design of the hardware and the software for H.E.A.D.
Biological Scaffolds for Heart Valve Tissue Engineering (2007)

Tissue engineering might bear promising solutions for overcoming the limitations of biological and mechanical heart valve substitutes. The concept of heart valve tissue engineering bases on decellularized biological matrices, as removal of cellular components might reduce immunological reactions, which are thought to be responsible for accelerated valvular graft deterioration and their subsequent repopulation with autologous cells, which leads to tissue integrity and continuous remodeling. Here, we report a method for efficient removal of cells from ovine heart valve tissue (including cusp, wall, and myocardial cuff) by detergents for the generation of biological valvular scaffolds.
Differential Flatness-Based Robust Control of a Two-Wheeled Mobile Robot in the Presence of Slip (2008)

In this paper, we present two robust trajectory-tracking controllers for a differentially driven two-wheeled mobile robot using its kinematic and dynamic model in the presence of slip. The structure of the differential flatness-based controller, which is an integrated framework for planning and control, is extended in this paper to account for slip disturbances by adding a corrective control term. Simulation results for both kinematic and dynamic controllers are presented to demonstrate the effectiveness of the robust controllers. Experiments with the kinematic controller were conducted to validate the performance of the robust controller. The simulation and experimental results show that the robust controllers are very effective in the presence of slip.
The Price of Simplicity (2008)

We study revenue-maximizing pricing by a service provider in a communication network and compare revenues from simple pricing rules to the maximum revenues that are feasible. In particular, we focus on flat entry fees as the simplest pricing rule. We provide a lower bound for the ratio between the revenue from this pricing rule and maximum revenue, which we refer to as the Price of Simplicity. We characterize what types of environments lead to a low Price of Simplicity and show that in a range of environments, the loss of revenue from using simple entry fees is small. We then study the Price of Simplicity for a simple non-linear pricing (price discrimination) scheme based on the Paris Metro Pricing. The service provider creates different service classes and charges differential entry fees for these classes. We show that the gain from this type of price discrimination is small, particularly in environments in which the simple entry fee pricing leads to a low Price of Simplicity.
Dealumination of zeolite Y with SiCl4: a two-step reaction (1990)

Evidence is presented that the dealumination of zeolite Y with SiCl4 occurs in two distinguishable reaction steps; in the first step, lattice-attached ‘SiCl3’ species and the chloride salt of the charge compensating cation are formed, followed secondly by the isomorphic substitution of Al for Si and the subsequent formation of chloro–aluminium complexes.
Demonstration of a III-nitride vertical-cavity surface-emitting laser with a III-nitride tunnel junction intracavity contact (2015)

We report on a III-nitride vertical-cavity surface-emitting laser (VCSEL) with a III-nitride tunnel junction (TJ) intracavity contact. The violet nonpolar VCSEL employing the TJ is compared to an equivalent VCSEL with a tin-doped indium oxide (ITO) intracavity contact. The TJ VCSEL shows a threshold current density (Jth) of ∼3.5 kA/cm2, compared to the ITO VCSEL Jth of 8 kA/cm2. The differential efficiency of the TJ VCSEL is also observed to be significantly higher than that of the ITO VCSEL, reaching a peak power of ∼550 μW, compared to ∼80 μW for the ITO VCSEL. Both VCSELs display filamentary lasing in the current aperture, which we believe to be predominantly a result of local variations in contact resistance, which may induce local variations in refractive index and free carrier absorption. Beyond the analyses of the lasing characteristics, we discuss the molecular-beam epitaxy (MBE) regrowth of the TJ, as well as its unexpected performance based on band-diagram simulations. Furthermore, we investigate the intrinsic advantages of using a TJ intracavity contact in a VCSEL using a 1D mode profile analysis to approximate the threshold modal gain and general loss contributions in the TJ and ITO VCSEL.
Stereocontrolled Synthesis of Methyl (Methyl-5-Acetamido-4-O-Benzoyl-7-O-Benzyl-3,5-Dideoxy-α-D-Arabino-2-Heptulopyranosid)Onate, a Model Compound for Sialic Acids (1989)

Abstract Thiophenyl 2,3-dideoxy-6-O-benzyl-α-D-erythro-hex-2-enopyranoside has been converted into a sialic acid analog, by means of methoxycarbonylation at the anomeric center and a [2,3]-sigmatropic rearrangement of the allylic glycosyl sulfoxide.
Supplementary Figure 7E-F from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus (2023)

Supplementary Figure 7E-F from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus
Synthesis and catalysis of novel mono- and bis(diene) complexes of niobium and x-ray structures of binuclear [Nb(.mu.-Cl)(C5H5)(s-cis-butadiene)]2 and mononuclear Nb(C5H5)(s-cis-2,3-dimethylbutadiene)2 (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and catalysis of novel mono- and bis(diene) complexes of niobium and x-ray structures of binuclear [Nb(.mu.-Cl)(C5H5)(s-cis-butadiene)]2 and mononuclear Nb(C5H5)(s-cis-2,3-dimethylbutadiene)2Takuji. Okamoto, Hajime. Yasuda, Akira. Nakamura, Yasushi. Kai, Nobuko. Kanehisa, and Nobutami. KasaiCite this: J. Am. Chem. Soc. 1988, 110, 15, 5008–5017Publication Date (Print):July 1, 1988Publication History Published online1 May 2002Published inissue 1 July 1988https://doi.org/10.1021/ja00223a018Request reuse permissionsArticle Views370Altmetric-Citations89LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Not All Qubits Are Created Equal (2019)

Existing and near-term quantum computers are not yet large enough to support fault-tolerance. Such systems with few tens to few hundreds of qubits are termed as Noisy Intermediate Scale Quantum computers (NISQ), and these systems can provide benefits for a class of quantum algorithms. In this paper, we study the problems of Qubit-Allocation (mapping of program qubits to machine qubits) and Qubit-Movement (routing qubits from one location to another for entanglement). We observe that there can be variation in the error rates of different qubits and links, which can impact the decisions for qubit movement and qubit allocation. We analyze publicly available characterization data for the IBM-Q20 to quantify the variation and show that there is indeed significant variability in the error rates of the qubits and the links connecting them. We show that the device variability has a significant impact on the overall system reliability. To exploit the variability in error rate, we propose Variation-Aware Qubit Movement (VQM) and Variation-Aware Qubit Allocation (VQA), policies that optimize the movement and allocation of qubits to avoid the weaker qubits and links, and guide more operations towards the stronger qubits and links. Our evaluations, with a simulation-based model of IBM-Q20, show that Variation-Aware policies can improve the system reliability by up to 1.7x. We also evaluate our policies on the IBM-Q5 machine and demonstrate that our proposal significantly improves the reliability of real systems (up to 1.9X).
Lectin Pathway of Complement Activation Is Associated with Vulnerability of Atherosclerotic Plaques (2017)

Inflammatory mechanisms may be involved in atherosclerotic plaque rupture. By using a novel histology-based method to quantify plaque instability here, we assess whether lectin pathway (LP) of complement activation, a major inflammation arm, could represent an index of plaque instability. Plaques from 42 consecutive patients undergoing carotid endarterectomy were stained with hematoxylin-eosin and the lipid core, cholesterol clefts, hemorrhagic content, thickness of tunica media, and intima, including or not infiltration of cellular debris and cholesterol, were determined. The presence of ficolin-1, -2, and -3 and mannose-binding lectin (MBL), LP initiators, was assessed in the plaques by immunofluorescence and in plasma by ELISA. LP activation was assessed in plasma by functional <i>in vitro</i> assays. Patients presenting low stenosis (≤75%) had higher hemorrhagic content than those with high stenosis (>75%), indicating increased erosion. Increased hemorrhagic content and tunica media thickness, as well as decreased lipid core and infiltrated content were associated with vulnerable plaques and therefore used to establish a plaque vulnerability score that allowed to classify patients according to plaque vulnerability. Ficolins and MBL were found both in plaques' necrotic core and tunica media. Patients with vulnerable plaques showed decreased plasma levels and intraplaque deposition of ficolin-2. Symptomatic patients experiencing a transient ischemic attack had lower plasma levels of ficolin-1. We show that the LP initiators are present within the plaques and their circulating levels change in atherosclerotic patients. In particular, we show that decreased ficolin-2 levels are associated with rupture-prone vulnerable plaques, indicating its potential use as marker for cardiovascular risk assessment in atherosclerotic patients.
Ribosome rescue inhibitors clear Neisseria gonorrhoeae in vivo using a new mechanism (2020)

Abstract The trans -translation pathway for rescuing stalled ribosomes is conserved and essential in bacterial pathogens but has no mammalian homolog, making it an ideal target for new antibiotics. We previously reported the discovery of a family of acylaminooxadiazoles that selectively inhibit trans -translation, resulting in broad-spectrum antibiotic activity. Optimization of the pharmacokinetic and antibiotic properties of the acylaminooxadiazoles produced MBX-4132, which cleared multiple-drug resistant Neisseria gonorrhoeae infection in mice after a single oral dose. Cryo-EM studies of non-stop ribosomes showed that acylaminooxadiazoles bind to a unique site near the peptidyl-transfer center and significantly alter the conformation of ribosomal protein L27, suggesting a novel mechanism for specific inhibition of trans -translation by these molecules. One Sentence Summary Ribosome rescue inhibitors reveal a new conformation of the ribosome and kill drug-resistant Neisseria gonorrhoeae in vivo .
Random and linear address allocation for mobile ad hoc networks (2005)

To join an IP network and communicate with others, a node needs to be configured either manually by an administrator or automatically through a DHCP server. However, the former method is impractical for large networks, while the latter is infeasible in the case of a mobile ad hoc network due to the mobility of the nodes. This paper introduces two distributed IP address auto-configuration mechanisms for mobile ad hoc networks, namely (a) RADA (random address allocation) and (b) LiA (linear allocation). RADA is based on random IP address selection, while LiA linearly assigns new addresses by utilizing the current maximum IP address value. We have also introduced an improved version of LiA, known as LiACR (linear allocation with collision resolution), which reduces control overhead. Then, we discuss extensions of these mechanisms capable of handling network partitioning and merging. Performance evaluations of RADA, LiA and LiACR were conducted through simulation. The results related to address allocation time and control overhead are presented and compared.
A Harmonic Retrieval Framework for (1998)

Motion discontinuities arise when there are oc- clusions or multiple moving objects in the scene that is im- aged. Conventional regularization techniques use smoothness constraints but are not applicable to motion discontinuities. In this paper, we show that discontinuous (or multiple) motion estimation can be viewed as a multicomponent harmonic retrieval problem. From this viewpoint, a number of established techniques for harmonic retrieval can be applied to solve the challeng- ing problem of discontinuous (or multiple) motion. Compared with existing techniques, the resulting algorithm is not iterative, which not only implies computational efficiency but also obviates concerns regarding convergence or local minima. It also adds flexibility to spatio-temporal techniques which have suffered from lack of explicit modeling of discontinuous motion. Experimental verification of our framework on both synthetic data as well as real image data is provided.
A method for determination of pH using a T-sensor (2002)

A model-based method for the determination of constituent concentrations in flowing nano-liter volumes of liquid is presented. This method is applied to pH measurement. A T-sensor is used to bring sample fluid into contact with indicator fluid to produce low Reynolds number, co-flowing streams in a micro-channel. By diffusion, the sample stream ions are brought into contact with the indicator stream dye molecules to produce an optically detectable signal. An analytical model of the resulting dispersion process that takes into account the different physical properties of each stream and the effects of ideal buffering is used to determine the incoming sample stream pH.
Prof. James R. Wait and mining production technology-an appreciation (2000)

Prof. James R. Wait (1951, 1953, 1967) examined electromagnetic (EM) wave propagation in many situations of interest to mining production, including propagation in tunnels, propagation along extended conductors such as cables and drill stems, and propagation in coal seams. This work remains relevant, both to the mining engineer interested in the EM environment of an operating mine and to the electrical engineer interested in verifying new computational techniques and in extending the scope of EM technology in mining production. Late work in EM focussing in a geological environment is relevant to "next generation" geophysical monitoring equipment.
Measurement of the association constants through micro-Raman spectra of supersaturated lithium perchlorate droplets (2013)

High quality micro-Raman spectra of the LiClO4droplet with mass of nanogram scale were obtained at various concentrations from dilute to supersaturated state. From component band analysis of the v1-ClO4 band, four peaks at 933.3, 936.8, 942.1 and950.7 cm 1were identified and assigned to free solvated perchlorate anion, solvent-shared ion pair, contact ion pair and complex ion aggregates, respectively. As expected, the signature of free solvated ClO4 ion was observed to decrease in intensity with the increase in concentration. The intensity of the signature from solvent-shared ion pair was observed to rise with increase in concentration from 1.8 mol/kg to 5.0 mol/kg before decreasing as the concentration was further increased to 5.6mol/kg. Signatures of contact ion pair and of complex ion aggregates were shown to increase as the concentration was enhanced. Based upon the Eigen mechanism, we show that three association equilibria can be used to describe the transformations between free solvated perchlorate anion, solvent-shared ion pair, contact ion pair and complex ion aggregates. The overall association constant, K, and the stepwise association constants Ki(i = 1 to 3) in the Eigen mechanism were determined separately with values of 0.025 ± 0.003, 0.023 ± 0.002, 0.068 ± 0.033 and 0.686 ± 0.174. Based on these constants, the electronic performance can be reasonably predicted by the optimum choice of electrolyte concentrations.
Wavefront-guided spectacle lenses (2007)

A new type of spectacle lens was developed incorporating a thin layer of a novel polymer with a light-programmable refractive index. The refractive index change can be used to change the optical power of the lens. One of the applications of this new lens is the correction of high-order aberrations of the human eye. A feasibility study was conducted to determine whether such wavefront-guided high-order correcting spectacle lenses can be 1) accurately manufactured, and 2) improve vision of human subjects. The ocular wavefront of 30 subjects was measured with a Z-View<sup>TM</sup> diffractive aberrometer. A vision correcting high-order zone canceling the subjects' ocular wavefront was "programmed" directly into pairs of wavefront-guided spectacle lenses (WFGSL). The lenses could be successfully manufactured to an average Zernike rms accuracy of 81% (range 70% to 90%). Comparison was made against identical spectacles without the high-order zone. Double-masked vision tests included high and low-contrast visual acuity, and contrast sensitivity. The subject was allowed only a few minutes of adaptation time to the spectacles. While some experienced a dramatic improvement in vision, this was not observed for all subjects, in particular for subjects with small amounts of high-order aberrations. We speculate that more consistent vision improvement can be achieved by 1) determining a subject's candidacy for WFGSL based on the subject's ocular aberrations, 2) correcting only selected aberrations, 3) manufacture with higher purity and accuracy, and 4) lengthening the adaptation period before testing each lens.
Caspase-Activated Oligonucleotide Probe (2020)

Light-activated ("caged") oligonucleotides provide a strategy for modulating the activity of antisense oligos, siRNA, miRNA, aptamers, DNAzymes, and mRNA-capturing probes with high spatiotemporal resolution. However, the near-UV and visible wavelengths that promote these bond-breaking reactions poorly penetrate living tissue, which limits some biological applications. To address this issue, we describe the first example of a protease-activated oligonucleotide probe, capable of reporting on caspase-3 during cellular apoptosis. The 2'-F RNA-peptide substrate-peptide nucleic acid (PNA) hairpin structure was generated in 30% yield in a single bioconjugation step.
Query suggestions for mobile search (2008)

Entering search terms on mobile phones is a time consuming and cumbersome task. In this paper, we explore the usage patterns of query entry interfaces that display suggestions. Our primary goal is to build a usage model of query suggestions in order to provide user interface guidelines for mobile text prediction interfaces. We find that users who were asked to enter queries on a search interface with query suggestions rated their workload lower and their enjoyment higher. They also saved, on average, approximately half of the key presses compared to users who were not shown suggestions, despite no associated decrease in time to enter a query. Surprisingly, users also accepted suggestions when the process of doing so resulted in an increase in the number of total key presses.
Laxative Abuse as a Cause for Ammonium Urate Renal Calculi (1990)

Nine women with laxative abuse and predominantly ammonium urate renal calculi underwent metabolic studies to identify common chemical abnormalities and determine pathophysiology. The 24-hour urine studies demonstrated marked decreases in volume (902 cm.3), sodium (28 mEq.), citrate (116 mg.) and potassium (21 mEq.). A significant elevation in ammonium urate supersaturation was found compared to control subjects when studied by the computer model EQUIL 2. Of the patients 7 had 1 or more urine specimens positive for phenolphthalein. Gastrointestinal loss of fluid and electrolytes allowed for chronic extracellular volume depletion. Intracellular acidosis was present as judged by low urinary citrate and potassium. The fact that the ion product for ammonium urate is increased significantly compared to controls reflects the stated pathophysiological changes. Laxative abuse should be suspected whenever a woman has an ammonium urate renal calculus in sterile urine.