gebhart/patrepeval huggingface dataset:
AJAX Crawl: Making AJAX Applications Searchable (2009)

Current search engines such as Google and Yahoo! are prevalent for searching the Web. Search on dynamic client-side Web pages is, however, either inexistent or far from perfect, and not addressed by existing work, for example on Deep Web. This is a real impediment since AJAX and Rich Internet Applications are already very common in the Web. AJAX applications are composed of states which can be seen by the user, but not by the search engine, and changed by the user using client-side events. Current search engines either ignore AJAX applications or produce false negatives. The reason is that crawling client-side code is a difficult problem that cannot be solved naively by invoking user events. The challenges are: lack of caching, duplicate states detection, very granular events, reducing the number of AJAX calls and infinite event invocation. This paper sets the stage for this new search challenge and proposes a solution: it shows how an AJAX Web application can be crawled in the granularity of the application states. A model of AJAX Web sites is presented. An AJAX Crawler and optimizations for caching and duplicate elimination are defined, and finally, the gain in search result quality and corresponding performance price are evaluated on YouTube, a real AJAX application.
Soft Spherical Tensegrity Robot Design Using Rod-Centered Actuation and Control (2017)

This paper presents the design, analysis, and testing of a fully actuated modular spherical tensegrity robot for co-robotic and space exploration applications. Robots built from tensegrity structures (composed of pure tensile and compression elements) have many potential benefits including high robustness through redundancy, many degrees-of-freedom in movement and flexible design. However, to take full advantage of these properties, a significant fraction of the tensile elements should be active, leading to a potential increase in complexity, messy cable, and power routing systems and increased design difficulty. Here, we describe an elegant solution to a fully actuated tensegrity robot: The TT-3 (version 3) tensegrity robot, developed at UC Berkeley, in collaboration with NASA Ames, is a lightweight, low cost, modular, and rapidly prototyped spherical tensegrity robot. This robot is based on a ball-shaped six-bar tensegrity structure and features a unique modular rod-centered distributed actuation and control architecture. This paper presents the novel mechanism design, architecture, and simulations of TT-3, an untethered, fully actuated cable-driven six-bar spherical tensegrity robot. Furthermore, this paper discusses the controls and preliminary testing performed to observe the system's behavior and performance and is evaluated against previous models of tensegrity robots developed at UC Berkeley and elsewhere.
p210BCR/ABL, p190BCR/ABL, and TEL/ABL activate similar signal transduction pathways in hematopoietic cell lines. (1996)

The Philadelphia chromosome translocation generates a chimeric oncogene, BCR/ABL which causes chronic myelogenous leukemia. Two different fusion proteins can be produced, p190BCR/ABL and p210BCR/ABL, depending on the location of the breakpoint in BCR. Although the ABL tyrosine kinase activity of the resulting oncoprotein is essential for transformation, the exact functional contribution of BCR to transformation is unclear. A novel oncogene containing ABL is formed by the (9;12) translocation which fuses part of the ets-family member TEL to c-ABL in patients with acute leukemia. In an effort to compare the biological effects of various ABL oncogenes, we transformed two different factor-dependent murine hematopoietic cell lines with cDNA's encoding p210BCR/ABL, p190BCR/ABL, or TEL/ABL. Transfection of each of the three activated ABL oncogenes resulted in rapid emergence of growth factor-independence, and 2-4 sublines from each cell line with each oncogene were further studied. Each oncogene induced an increase in the tyrosine phosphorylation of cellular proteins and autophosphorylation of the oncoprotein itself. Overall, the pattern of increased tyrosine phosphorylation was similar in the cell lines, suggesting that many of the major substrates were identical. We specifically examined a series of proteins known to be p210BCR/ABL substrates, including rasGAP, Shc, SH-PTP2, SH-PTP1, CRK-L, CBL, paxillin, and STATs, and found that each were also tyrosine phosphorylated in response to p190BCR/ABL and TEL/ABL. These results suggest that the function of BCR can be largely replaced by the unrelated protein TEL with regards to transformation of murine hematopoietic cell lines to factor-independence, and support the hypothesis that a major contribution of both fusion partners is to activate the ABL tyrosine kinase.
Amyloid β‐protein (Aβ)1–40 protects neurons from damage induced by Aβ1–42 in culture and in rat brain (2003)

Previously, we found that amyloid beta-protein (Abeta)1-42 exhibits neurotoxicity, while Abeta1-40 serves as an antioxidant molecule by quenching metal ions and inhibiting metal-mediated oxygen radical generation. Here, we show another neuroprotective action of nonamyloidogenic Abeta1-40 against Abeta1-42-induced neurotoxicity in culture and in vivo. Neuronal death was induced by Abeta1-42 at concentrations higher than 2 microm, which was prevented by concurrent treatment with Abeta1-40 in a dose-dependent manner. However, metal chelators did not prevent Abeta1-42-induced neuronal death. Circular dichroism spectroscopy showed that Abeta1-40 inhibited the beta-sheet transformation of Abeta1-42. Thioflavin-T assay and electron microscopy analysis revealed that Abeta1-40 inhibited the fibril formation of Abeta1-42. In contrast, Abeta1-16, Abeta25-35, and Abeta40-1 did not inhibit the fibril formation of Abeta1-42 nor prevent Abeta1-42-induced neuronal death. Abeta1-42 injection into the rat entorhinal cortex (EC) caused the hyperphosphorylation of tau on both sides of EC and hippocampus and increased the number of glial fibrillary acidic protein (GFAP)-positive astrocytes in the ipsilateral EC, which were prevented by the concurrent injection of Abeta1-40. These results indicate that Abeta1-40 protects neurons from Abeta1-42-induced neuronal damage in vitro and in vivo, not by sequestrating metals, but by inhibiting the beta-sheet transformation and fibril formation of Abeta1-42. Our data suggest a mechanism by which elevated Abeta1-42/Abeta1-40 ratio accelerates the development of Alzheimer's disease (AD) in familial AD.
3D printing facilitated scaffold-free tissue unit fabrication (2014)

Tissue spheroids hold great potential in tissue engineering as building blocks to assemble into functional tissues. To date, agarose molds have been extensively used to facilitate fusion process of tissue spheroids. As a molding material, agarose typically requires low temperature plates for gelation and/or heated dispenser units. Here, we proposed and developed an alginate-based, direct 3D mold-printing technology: 3D printing microdroplets of alginate solution into biocompatible, bio-inert alginate hydrogel molds for the fabrication of scaffold-free tissue engineering constructs. Specifically, we developed a 3D printing technology to deposit microdroplets of alginate solution on calcium containing substrates in a layer-by-layer fashion to prepare ring-shaped 3D hydrogel molds. Tissue spheroids composed of 50% endothelial cells and 50% smooth muscle cells were robotically placed into the 3D printed alginate molds using a 3D printer, and were found to rapidly fuse into toroid-shaped tissue units. Histological and immunofluorescence analysis indicated that the cells secreted collagen type I playing a critical role in promoting cell-cell adhesion, tissue formation and maturation.
Metal-Mediated Inhibition of <i>Escherichia </i><i>c</i><i>oli</i> Methionine Aminopeptidase:  Structure−Activity Relationships and Development of a Novel Scoring Function for Metal−Ligand Interactions (2005)

We report the discovery of thiabendazole as a potent inhibitor (K(i) = 0.4 microM) of Escherichia coli methionine aminopeptidase (ecMetAP) and the synthesis and pharmacological evaluation of thiabendazole congeners with activity in the upper nanomolar range. Elucidation of the X-ray structure of ecMetAP in complex with thiabendazole and an unrelated inhibitor that was independently described by another group showed that that both compounds bind to an additional Co(II) ion at the entrance of the active site. This unexpected finding explains the inactivity of the compounds under in vivo conditions. It also allows us to discuss the structure-activity relationships of this series of compounds in a meaningful way, based upon docking runs with an auxiliary metal ion. We describe a new scoring function for the evaluation of metal-mediated inhibitor binding that, unlike the previously used scoring function implemented in the docking program, allows us to distinguish between active and inactive compounds. Finally, conclusions for the structure-based design of in vivo-active inhibitors of ecMetAP are drawn.
Real-time method for fitting time-resolved reflectance and transmittance measurements with a Monte Carlo model (1998)

An efficient method is proposed for the evaluation of theabsorption and the transport scattering coefficients from atime-resolved reflectance or transmittance distribution. Theprocedure is based on a library of Monte Carlo simulations and is fastenough to be used in a nonlinear fitting algorithm. Tests performedagainst both Monte Carlo simulations and experimental measurements ontissue phantoms show that the results are significantly better thanthose obtained by fitting the data with the diffusion approximation, especially for low values of the scattering coefficient. The methodrequires an a priori assumption on the value of theanisotropy factor g. Nonetheless, the transportscattering coefficient is rather independent of the exact knowledge ofthe g value within the range 0.7 < g < 0.9.
Uterine Insulin-Like Growth Factor-1: Regulation of Expression and Its Role in Estrogen-Induced Uterine Proliferation* (1990)

THE response of the uterus to estrogen is a complexphenomenon involving numerous biochemical events (1). The most dramatic outcome of estrogenization of the immature uterus is the proliferation of various cell types. It is customary to divide the response of the uterus to estrogen into two major temporal phases. In the early phase, within the first 4 h after estrogen administration, there is an increase in uterine wet weight (2), glucose metabolism (3), histamine depletion (4), and RNA polymerase activity (5). One of the early events that is likely to be important in the proliferative response of the uterus to estrogen is activation of protooncogenes which encode nuclear regulatory proteins (6–8) and the enhanced expression of growth factors and their receptors (9) and cAMP-independent protein kinase (10). The intermediate and late phase (4–48 h after estrogen) responses include increases in protein and RNA synthesis and an increase in uterine dry weight and DNA content (11, 12).
A High-Performance Digital-Input Class-D Amplifier with Direct Battery Connection in a 90nm Digital CMOS Process (2008)

The class-D amplifier system presented in this paper is a second-order architecture that operates on a digital PWM input and eliminates the use of an external carrier signal. It consists of two identical audio channels and a common section consisting of a PLL and a reference system. Each channel has a digital interpolation filter followed by a digital DeltaSigma modulator, PWM generator and two second-order analog loops.
Surface Film Formation on a Graphite Negative Electrode in Lithium-Ion Batteries:  Atomic Force Microscopy Study on the Effects of Film-Forming Additives in Propylene Carbonate Solutions (2001)

In situ electrochemical atomic force microscopy (AFM) observation of the basal plane of highly oriented pyrolytic graphite (HOPG) was performed during cyclic voltammetry in 1 M LiClO4/propylene carbonate (PC) containing 3 wt % vinylene carbonate (VC), fluoroethylene carbonate (FEC), and ethylene sulfite (ES) in order to clarify the roles of these additives in the formation of a protective surface film on a graphite negative electrode in lithium-ion batteries. Particle-like precipitates appeared on the HOPG surface at the potentials 1.35, 1.15, and 1.05 V versus Li+/Li in PC + VC, PC + FEC, and PC + ES, respectively, and covered the whole surface at lower potentials. No evidence for cointercalation of solvent molecules was observed in the presence of each additive. It was concluded that the layer of the precipitates functions as a protective surface film, which suppresses cointercalation of PC molecules as well as direct solvent decomposition on the surface of the graphite negative electrode.
Effect of Antioxidant Intake on Sperm Chromatin Stability in Healthy Nonsmoking Men (2005)

Oxidative stress is detrimental to sperm function and a significant factor in the etiology of male infertility. This report examines the association between dietary and supplementary intake of the antioxidants vitamin C, vitamin E, and beta-carotene and sperm chromatin integrity. Eighty-seven healthy male volunteers donated semen samples, completed food-frequency questionnaires, and provided information about their sociodemographic characteristics, medical and reproductive histories, and lifestyle habits. Sperm chromatin integrity was measured using the DNA fragmentation index (DFI) and related parameters, obtained from the sperm chromatin structure assay (SCSA). SCSA measures the susceptibility of sperm DNA to acid-induced denaturation in situ. After adjusting for age and duration of abstinence, there was no dose-response association between any DFI outcome and any antioxidant intake measure. Non-dose-related associations were found between beta-carotene intake and both the standard deviation of DFI (SD DFI) and the percent of immature sperm. Participants with moderate, but not high, beta-carotene intake had an increase in SD DFI compared with participants with low intake (adjusted means 206.7 and 180.5, respectively; P = .03), as well as an increase in the percentage of immature sperm (adjusted means 6.9% and 5.0%, respectively; P = .04). If antioxidant intake in the range studied is indeed beneficial for fertility in healthy men, it does not appear to be mediated through the integrity of sperm chromatin. The results of this study do not preclude possible beneficial effects of high antioxidant intake on sperm chromatin integrity for men with fertility problems.
Bactericidal Antibiotics and Oxidative Stress: A Radical Proposal (2007)

A recent publication suggests that many antibiotics exert their bactericidal effects via the production of hydroxyl radicals, regardless of their molecular targets. This proposal represents an abrupt departure from conventional models, and it will attract further experimental tests.
New insights into mechanisms of atrial fibrillation (2010)

Although atrial fibrillation (AF) is the most common cardiac arrhythmia in clinical practice, precise mechanisms that lead to the onset and persistence of AF have not completely been elucidated. Over the last decade, outstanding progress has been made in understanding the complex pathophysiology of AF. The key role of ectopic foci in pulmonary veins as a trigger of AF has been recognized. Furthermore, structural remodeling was identified as the main mechanism for AF persistence, confirming predominant role of atrial fibrosis. Systemic inflammatory state, oxidative stress injury, autonomic balance and neurohormonal activation were discerned as important modifiers that affect AF susceptibility. This new understanding of AF pathophysiology has led to the emergence of novel therapies. Ablative interventions, renin-angiotensin system blockade, modulation of oxidative stress and targeting tissue fibrosis represent new approaches in tackling AF. This review aims to provide a brief summary of novel insights into AF mechanisms and consequent therapeutic strategies.
Dendritic field size and morphology of midget and parasol ganglion cells of the human retina. (1992)

The visual system of the macaque monkey has provided a useful model for understanding the neural basis of human vision, yet, there are few detailed comparisons of neural populations other than photoreceptors for the two species. Using intracellular staining in an in vitro preparation of the isolated and intact human retina, we have characterized the relationship of dendritic field size to retinal eccentricity for the two major ganglion cell classes, the midget and the parasol cells. We report three findings. (i) The difference in dendritic field diameter between the parasol and midget cells increases from a ratio of approximately 3:1 in the retinal periphery to approximately 10:1 at 3 degrees eccentricity, suggesting that human midget cells may outnumber parasol cells by as much as 30:1 in the central retina. (ii) The dendritic fields of human ON-center parasol and midget cells are 30-50% larger in diameter than their OFF-center counterparts, suggesting a distinct asymmetry in the human ON-OFF visual pathways. (iii) The dendritic fields of parasol cells, but not midget cells, are larger in humans than in macaques. The difference increases from approximately 20% in the retinal periphery to approximately 90% at 5 degrees eccentricity. This result predicts that the human parasol cells should show a lower resolving ability and an increased sensitivity to luminance contrast than their equivalents in the macaque.
Ultrasound-Induced Blood-Brain Barrier Opening (2012)

Over 4 million U.S. men and women suffer from Alzheimer's disease; 1 million from Parkinson's disease; 350,000 from multiple sclerosis (MS); and 20,000 from amyotrophic lateral sclerosis (ALS). Worldwide, these four diseases account for more than 20 million patients. In addition, aging greatly increases the risk of neurodegenerative disease. Although great progress has been made in recent years toward understanding of these diseases, few effective treatments and no cures are currently available. This is mainly due to the impermeability of the blood-brain barrier (BBB) that allows only 5% of the 7000 small-molecule drugs available to treat only a tiny fraction of these diseases. On the other hand, safe and localized opening of the BBB has been proven to present a significant challenge. Of the methods used for BBB disruption shown to be effective, Focused Ultrasound (FUS), in conjunction with microbubbles, is the only technique that can induce localized BBB opening noninvasively and regionally. FUS may thus have a huge impact in trans-BBB brain drug delivery. The primary objective in this paper is to elucidate the interactions between ultrasound, microbubbles and the local microenvironment during BBB opening with FUS, which are responsible for inducing the BBB disruption. The mechanism of the BBB opening in vivo is monitored through the MRI and passive cavitation detection (PCD), and the safety of BBB disruption is assessed using H&E histology at distinct pressures, pulse lengths and microbubble diameters. It is hereby shown that the BBB can be disrupted safely and transiently under specific acoustic pressures (under 0.45 MPa) and microbubble (diameter under 8 μm) conditions.
Metal–Organic Framework Nodes Support Single-Site Magnesium–Alkyl Catalysts for Hydroboration and Hydroamination Reactions (2016)

Here we present the first example of a single-site main group catalyst stabilized by a metal-organic framework (MOF) for organic transformations. The straightforward metalation of the secondary building units of a Zr-MOF with Me2Mg affords a highly active and reusable solid catalyst for hydroboration of carbonyls and imines and for hydroamination of aminopentenes. Impressively, the Mg-functionalized MOF displayed very high turnover numbers of up to 8.4 × 10(4) for ketone hydroboration and could be reused more than 10 times. MOFs can thus be used to develop novel main group solid catalysts for sustainable chemical synthesis.
The optical near field and analytical chemistry (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe optical near field and analytical chemistryAaron Lewis and Klony LiebermanCite this: Anal. Chem. 1991, 63, 11, 625A–638APublication Date (Print):June 1, 1991Publication History Published online30 May 2012Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/ac00011a726https://doi.org/10.1021/ac00011a726research-articleACS PublicationsRequest reuse permissionsArticle Views26Altmetric-Citations23LEARN 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
Confocal three dimensional tracking of a single nanoparticle with concurrent spectroscopic readouts (2006)

We present an apparatus that noninvasively tracks a moving nanoparticle in three dimensions while providing concurrent sequential spectroscopic measurements. The design, based on confocal microscopy, uses a near-infrared laser and a dark-field condenser for illumination of a gold nanoparticle. By monitoring the scattered light from the nanoparticle and using a piezoelectric stage, the system was able to continuously bring the diffusive particle in a glycerol/water solution back to the focal volume with spatial resolution and response time of less than 210nm and a millisecond, respectively.
Phenol-containing antagonists of the CXCR2 receptor (2008)

Background: ELR+ chemokines interact with the CXCR2 receptor on neutrophils and other immune cells to induce chemotaxis. This event plays a key role in a large number of autoimmune diseases and thus antagonists of the CXCR2 receptor have garnered considerable interest in the pharmaceutical industry during the past decade and a half. Objective: The objective of the article is to review recent developments in the patent literature related to the phenol-containing antagonists. Method: Although many other chemotypes have emerged since the first disclosure of phenol-containing antagonists, this compound class is by far the most successful, having yielded all but one of the clinical candidates reported so far, and thus the scope of this review is limited just this antagonist type. Conclusion: During the past few years, phenol-containing CXCR2 antagonists have evolved from promising leads to clinical candidates, and structural diversity within the class has been expanded. Lead compounds have now entered patient studies and will be of great importance not just for this compound class, but also for the therapeutic viability of CXCR2 antagonists in general.