gebhart/patrepeval huggingface dataset:
Detection and characterization of carbon contamination on EUV multilayer mirrors (2009)

In this paper, we detect and characterize the carbon contamination layers that are formed during the illumination of extreme ultraviolet (EUV) multilayer mirrors. The EUV induced carbon layers were characterized ex situ using spectroscopic ellipsometry (SE) and laser generated surface acoustic waves (LG-SAW). We show that both LG-SAW and SE are very sensitive for measuring carbon layers, even in the presence of the highly heterogeneous structure of the multilayer. SE has better overall sensitivity, with a detection limit of 0.2 nm, while LG-SAW has an estimated detection limit of 2 nm. In addition, SE reveals that the optical properties of the EUV induced carbon contamination layer are consistent with the presence of a hydrogenated, polymeric like carbon. On the other hand, LG-SAW reveals that the EUV induced carbon contamination layer has a low Young's modulus (<100 GPa), which means that the layer is mechanically soft. We compare the limits of detection and quantification of the two techniques and discuss their prospective for monitoring carbon contamination build up on EUV optics.
Anterior Cruciate Ligament Reconstruction With LARS Artificial Ligament: A Multicenter Study With 3‐ to 5‐Year Follow‐up (2010)

Level IV, therapeutic case series.
Effect of gaseous permeability of overcoat layer on KrF chemically amplified positive resists (1996)

The process of removing an overcoat (OC) on the tert-butoxycarbonyl (t-BOC) type chemically amplified positive resists has been studied, and it has been found that in the case of removing the OC after postexposure bake (PEB), or at development, the decrease in the dissolution rate at the exposed region results in the formation of the surface insoluble layer and scum. This reduction in the rate became larger with increasing the OC thickness and the t-BOC ratio in the resist, and it was shown by Fourier transform infrared spectra that the t-BOC group disappeared and a small amount of tert-butoxy moiety appeared in the fully exposed region. When the OC layer remained on the resist film during PEB, isobutene generated by the deprotection of t-BOC was prevented from permeating out of the resist film and then recombined with the OH group in the base polymer. Therefore, it was found and verified that by using the acidic OC material which exhibits a high permeability for gases, the resist performance was improved.
Posttranslational Modifications of Tau - Role in Human Tauopathies and Modeling in Transgenic Animals (2004)

Alzheimer's disease (AD) is characterized histopathologically by beta-amyloid-containing plaques, neurofibrillary tangles (NFT), reduced synaptic density, and neuronal loss in selected brain areas. Plaques consist of aggregates of a small peptide termed Abeta which is derived by proteolysis of the larger amyloid precursor protein APP, whereas NFT are composed of hyperphosphorylated forms of the microtubule-associated protein tau. Tau pathology in the presence of scant or no beta-amyloid plaques characterizes additional neurodegenerative disorders collectively called tauopathies. In the course of plaque and NFT formation, the major proteinaceous components of these lesions undergo post-translational modifications. In the case of tau, these include phosphorylation of mainly serine and threonine, but also tyrosine residues. In addition, tau is subject to ubiquitination, nitration, truncation, prolyl isomerization, association with heparan sulfate proteoglycan, glycosylation, glycation and modification by advanced glycation end-products (AGEs). This review aims to provide insight into the complexity of tau modifications in human tauopathies such as AD and frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17). Selected aspects of the post-translational modification of tau have been reproduced in transgenic animal models. Most of this work has been done in mice, but insight has also been gained from studies in the sea lamprey, the nematode C. elegans and Drosophila. Attempts have been made to link specific post-translational modifications with tau aggregation and nerve cell dysfunction.
Caspase-9 Activation by the Apoptosome Is Not Required for Fas-mediated Apoptosis in Type II Jurkat Cells (2009)

Activation of executioner caspases during receptor-mediated apoptosis in type II cells requires the engagement of the mitochondrial apoptotic pathway. Although it is well established that recruitment of mitochondria in this context involves the cleavage of Bid to truncated Bid (tBid), the precise post-mitochondrial signaling responsible for executioner caspase activation is controversial. Here, we used distinct clones of type II Jurkat T-lymphocytes in which the mitochondrial apoptotic pathway had been inhibited to investigate the molecular requirements necessary for Fas-induced apoptosis. Cells overexpressing either Bcl-2 or Bcl-x(L) were protected from apoptosis induced by agonistic anti-Fas antibody. By comparison, Apaf-1-deficient Jurkat cells were sensitive to anti-Fas, exhibiting Bid cleavage, Bak activation, the release of cytochrome c and Smac, and activation of executioner caspase-3. Inhibiting downstream caspase activation with the pharmacological inhibitor Z-DEVD-fmk or by expressing the BIR1/BIR2 domains of X-linked inhibitor of apoptosis protein (XIAP) decreased all anti-Fas-induced apoptotic changes. Additionally, pretreatment of Bcl-x(L)-overexpressing cells with a Smac mimetic sensitized these cells to Fas-induced apoptosis. Combined, our findings strongly suggest that Fas-mediated activation of executioner caspases and induction of apoptosis do not depend on apoptosome-mediated caspase-9 activation in prototypical type II cells.
Plane-wave-based electron tunneling through Au nanojunctions: Numerical calculations (2010)

Electron tunneling across a nanojunction is an important topic relevant to scanning tunnel microscope imaging, nanoconductance measurements, and nanoelectronic devices. To understand such tunneling phenomena, one needs to comprehend the electron-state coupling between the metal electrode and the vacuum, the dependence of such coupling on the shape of the electrode tip, and the dependence of the tunneling currents on the electrode-electrode distance. Due to the experimental difficulty to determine the exact atomic structure of the electrode tip, theoretical simulation can play an important role on such studies. This requires high-fidelity quantum-transport calculations for the tunneling system. However, most of the current quantum-transport calculations are performed using atom-centered localized basis sets, which cannot adequately describe the wave function in the vacuum region. In this work, we present tunneling-conductance calculations obtained using the transport calculation method introduced by Wang [Phys. Rev. B 72, 045417 (2005)] and Garcia-Lekue and Wang [Phys. Rev. B 74, 245404 (2006)]. Since this method employs a plane-wave basis set, it provides variational description for the electron wave functions in all real space. We will present results for the tunneling-current dependence on the electrode-electrode distance, the electrode wave functions in the vacuum region depending on the electrode shape, and electron state couplings between the vacuum and the electrode.
Structure of the human steroidogenic acute regulatory (StAR) protein gene: StAR stimulates mitochondrial cholesterol 27-hydroxylase (1995)

Steroidogenic acute regulatory protein (StAR) plays a key role in steroid hormone synthesis by enhancing the metabolism of cholesterol into pregnenolone. We determined the organization of the StAR structural gene, mapped to 8p11.2. The gene spans 8 kb and consists of seven exons interrupted by six introns. The 1.3 kb of DNA upstream from the transcription start site directed expression of a luciferase reporter gene in mouse Y-1 adrenal cortical tumor cells but not in BeWo choriocarcinoma cells. Reporter gene expression in the Y-1 cells was increased more than 2-fold by 8-Br-cAMP, indicating that the 1.3 kb DNA fragment contains sequences that confer tissue-specific expression and cAMP regulation. The sequence of a related StAR pseudogene, mapped to chromosome 13, lacks introns and has an insertion, numerous substitutions, and deletions. Expression of StAR in COS-1 cells cotransfected with cholesterol 27-hydroxylase (P450c27) and adrenodoxin resulted in a 6-fold increase in formation of 3 beta-hydroxy-5-cholestenoic acid, demonstrating that StAR's actions are not specific to steroidogenesis but extend to other mitochondrial cholesterol-metabolizing enzymes.
Evidence that aggregation of mouse sperm receptors by ZP3 triggers the acrosome reaction. (1989)

In the mouse, considerable evidence indicates that initial sperm binding to the zona pellucida (ZP) is mediated by ZP3. In addition, this same glycoprotein is also responsible for inducing the acrosome reaction (AR). Whereas the O-linked oligosaccharides of ZP3 appear to mediate sperm-ZP binding, the portion of ZP3 bearing AR activity has not been defined. To try to understand the bifunctional role of ZP3 (binding and AR inducing activities), we have examined the hypothesis that ZP3 aggregates sperm receptor molecules. By analogy with findings in a variety of other extracellular signal transducing systems, including receptors for growth factors and insulin, this aggregation event could initiate the cascade resulting in the AR. To test this hypothesis, we have generated monospecific polyclonal antibodies against ZP2 and against ZP3, and examined the effects of these probes on capacitated sperm incubated in the absence or presence of various ZP protein preparations. For some experiments, we have used proteolytic fragments of ZP3, a preparation known to retain specific binding, but not AR-inducing, activity. We show here that capacitated mouse sperm, incubated with ZP glycopeptides, displayed ARs when incubated subsequently with anti-ZP3 IgG; ARs did not occur when parallel sperm samples were incubated with anti-ZP2 IgG or with anti-ZP3 Fab fragments. When capacitated sperm were treated successively, with (a) ZP3 glycopeptides, (b) anti-ZP3 Fab fragments, and (c) goat anti-rabbit IgG, ARs occurred in the majority of sperm. An alternative approach to examine this hypothesis used ZP proteins obtained from tubal eggs treated previously with bioactive phorbol diester (12-O-tetradecanoyl phorbol-13-acetate [TPA]). This preparation arrests capacitated sperm in an intermediate state of the AR. We demonstrate here that these sperm can be induced to undergo a complete AR by subsequent treatment with anti-ZP3 IgG. Together, these findings are consistent with the hypothesis under examination, and suggest that the aggregation of sperm molecules recognized by ZP3 glycopeptides or by TPA-treated ZP is sufficient to trigger the events that occur during acrosomal exocytosis.
COP1, the negative regulator of ETV1, influences prognosis in triple-negative breast cancer (2015)

COP1 might be a tumor suppressor by negative regulating ETV1 in patients with TNBCs. COP1 and ETV1 are a pair of independent predictors of prognosis for TNBC cases. Thus, targeting them might be a potential strategy for personalized TNBC treatment.
Sull'origine dell'ermeneutica del sé (2012)

Trentadue anni dopo l'invito da parte del comitato americano Howison Lectures vengono pubblicate le due conferenze sul tema Truth and Subjectivity inedite in Italia e in Europa, risalenti all'ottobre e novembre del 1980. Il nucleo del libro e rappresentato dalla traduzione delle due conferenze pronunciate da Michel Foucault in inglese, nell'autunno del 1980 a Berkeley e al Dartmouth College, rimaste fino a oggi inedite sia in italiano sia in francese. In queste conferenze vengono esplorate le origini della moderna ermeneutica del soggetto, introducendo il tema delle di e studiando in particolare due di queste tecniche - l'esame di se e la confessione - prima nel mondo antico e in seguito nel Cristianesimo dei primi secoli. Foucault inaugura cosi un'indagine genealogica del soggetto moderno, o meglio, quella genealogia dei rapporti tra soggettivita e verita che occupera buona parte del suo lavoro negli anni compresi tra il 1980 e il 1984. In quegli anni e, a partire da queste conferenze, forse per la prima volta in modo cosi chiaro, il filosofo individua in una di noi stessi: la principale posta in gioco etico-politica del nostro tempo. Infatti come si legge nella prefazione al volume - bisognerebbe sbarazzarsi delle tecnologie costruite nel corso dei secoli, aprendo cosi lo spazio a una di noi stessi. Una conclusione che, d'altronde, richiama cio che Foucault aveva gia detto all'inizio della prima conferenza, alludendo a una fondamentale dimensione politica - quindi critica - connessa al suo progetto di una genealogia del se occidentale: un'analisi che si riferisce a cio che siamo disposti ad accettare nel nostro mondo; ad accettare, rifiutare e cambiare sia in noi stessi, sia nella nostra situazione (...) si tratta di cercare un altro tipo di filosofia critica: che ricerchi le condizioni e le indefinite possibilita per trasformare noi stessi. Il volume comprende un'introduzione e un apparato critico, che situano queste due conferenze nel percorso biografico e filosofico di Foucault e una postfazione di Arnold I. Davidson, che mette in luce gli elementi di attualita presenti nella riflessione foucaultiana.
A non-invasive method for focusing ultrasound through the human skull (2002)

A technique for focusing ultrasound through the human skull is described and verified. The approach is based on a layered wavevector-frequency domain model, which propagates ultrasound from a hemisphere-shaped transducer through the skull using input from CT scans of the head. The algorithm calculates the driving phase of each transducer element in order to maximize the signal at the intended focus. This approach is tested on ten ex vivo human skulls using a 0.74 MHz, 320-element array. A stereotaxic reference frame is affixed to the skulls in order to provide accurate registration between the CT images and the transducer. The focal quality is assessed with a hydrophone placed inside the skull. In each trial the phase correction algorithm successfully restored the focus inside the skull at a location within 1 mm from the intended focal point. The results demonstrate the feasibility of using the method for completely non-invasive ultrasound brain surgery and therapy.
Subgenomic RNA sequence of human astrovirus supports classification of Astroviridae as a new family of RNA viruses (1993)

We report the sequence of the subgenomic RNA of human astrovirus serotype 2. This 2,484-nucleotide RNA contains a single open reading frame, which encodes a protein with a predicted molecular mass of 88 kDa. We propose that this protein is the 90-kDa capsid precursor observed in infected cells. The deduced protein sequence does not contain conserved amino acid patterns reported for the capsid proteins of picornaviruses or caliciviruses, consistent with the classification of astroviruses as a new family of RNA viruses, designated Astroviridae.
Inactivation of viruses with photoactive compounds. (1992)

The transmission of human immunodeficiency virus (HIV-1) and other enveloped virus by blood transfusion is a major concern. Photosensitive dyes such as hematoporphyrin derivative (HPD), dihematoporphyrin ether (DHE), benzoporphyrin derivatives (BPD), extended ring porphyrins, sapphyrins and texaphyrins, and various cyanines were used with viral cultures to test the feasibility of using those light-excitable dyes to kill virus. A photodynamic flow cell was used to irradiate viral suspensions or viral infected cells in culture media or in whole blood. Herpes virus (HSV-1) was used to screen compounds. Effective compounds were subsequently tested for their ability to kill HIV-1, CMV, and SIV in culture medium and in blood and proved to effectively kill free virus and infected cells at significant viremias. Irradiation was achieved with a filtered xenon light source and/or tunable dye laser. Concentrations of dyes at 10 times viral kill dose were irradiated in blood which was tested for damage to erythrocytes (RBC), platelets, and blood proteins. No damage to RBC, complement factors, and immunoglobulins was evident immediately after photodynamic treatment. Platelet condition is minimally modified with time. Photodynamic treatment of blood appears to be a feasible means of eradicating virus and some protozoans from blood.
Targeted immune interventions for type 1 diabetes (2014)

Advances in our fundamental understanding of how the human diabetes immune response is activated and regulated coupled with lessons that have been learnt from the most recent era of completed trials are guiding us toward the development of more effective, multipronged therapies to ablate diabetes autoimmunity, restore immune tolerance, preserve β cells, and, ultimately, improve the lives of patients with T1D.
Prognostic Implications of Abnormalities in Renal Function in Patients With Acute Coronary Syndromes (2002)

Patients presenting with ACS frequently have abnormal RF. Abnormal RF is a marker of adverse baseline clinical characteristics and is independently associated with increased risk of death and death/MI.
Ocular α 2 -Receptor Subclasses and Antiglaucoma Efficacy (1994)

An overview of the ocular hypotensive actions of some alpha 2-agonists with imidazoline structures is presented. These agents inhibit isoproterenol-stimulated adenylate cyclase (AC) activity in ciliary process membrane through a Na+ and GTP-dependent mechanism. Receptor binding studies with the alpha 2-agonist radioligand [125I] p-iodoclonidine ([125I]PIC) in rabbit ciliary body membranes indicate that the alpha 2-receptor subtype is alpha 2A. Gpp(NH)p and NaCl dose-dependently decreased the number of [125I]PIC binding sites by shifting the receptor-G protein complexes from the high affinity state to the low affinity state for agonist binding. This is consistent with the observations that inhibition of AC was Na+ and GTP dependent. The NaCl and Gpp(NH)p effects on binding appeared to be through different mechanisms. The alpha 2-receptor in ciliary process thus appears to be an alpha 2A-receptor that is negatively coupled to the AC-cAMP generating system.
The Boosting Effect of Exploratory Behaviors (2010)

Active object exploration is one of the hallmarks of human and animal intelligence. Research in psychology has shown that the use of multiple exploratory behaviors is crucial for learning about objects. Inspired by such research, recent work in robotics has demonstrated that by performing multiple exploratory behaviors a robot can dramatically improve its object recognition rate. But what is the cause of this improvement? To answer this question, this paper examines the conditions under which combining information from multiple behaviors and sensory modalities leads to better object recognition results. Two different problems are considered: interactive object recognition using auditory and proprioceptive feedback, and surface texture recognition using tactile and proprioceptive feedback. Analysis of the results shows that metrics designed to estimate classifier model diversity can explain the improvement in recognition accuracy. This finding establishes, for the first time, an important link between empirical studies of exploratory behaviors in robotics and theoretical results on boosting in machine learning.
Rapid and Sustained Reductions in Current Suicidal Ideation Following Repeated Doses of Intravenous Ketamine (2016)

ClinicalTrials.gov identifier: NCT01582945.
Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection (2015)

CRISPR-Cas9 systems provide a platform for high efficiency genome editing that are enabling innovative applications of mammalian cell engineering. However, the delivery of Cas9 and synthesis of guide RNA (gRNA) remain as steps that can limit overall efficiency and ease of use. Here we describe methods for rapid synthesis of gRNA and for delivery of Cas9 protein/gRNA ribonucleoprotein complexes (Cas9 RNPs) into a variety of mammalian cells through liposome-mediated transfection or electroporation. Using these methods, we report nuclease-mediated indel rates of up to 94% in Jurkat T cells and 87% in induced pluripotent stem cells (iPSC) for a single target. When we used this approach for multigene targeting in Jurkat cells we found that two-locus and three-locus indels were achieved in approximately 93% and 65% of the resulting isolated cell lines, respectively. Further, we found that the off-target cleavage rate is reduced using Cas9 protein when compared to plasmid DNA transfection. Taken together, we present a streamlined cell engineering workflow that enables gRNA design to analysis of edited cells in as little as four days and results in highly efficient genome modulation in hard-to-transfect cells. The reagent preparation and delivery to cells is amenable to high throughput, multiplexed genome-wide cell engineering.
Therapeutic potential of targeting protein for Xklp2 silencing for pancreatic cancer (2015)

The targeting protein for Xklp2 (TPX2) is a microtubule- and, cell cycle-associated protein who's overexpression has been reported in various malignancies. In this study, we verified the overexpression of TPX2 in both surgically resected specimens of pancreatic cancer and multiple pancreatic cancer cell lines. Subsequently, we found that TPX2 siRNA effectively suppressed the proliferation of pancreatic cancer cells in culture, and the direct injection of TPX2 siRNA into subcutaneously implanted pancreatic cancer cells in nude mice revealed antiproliferative effects. These results implied a therapeutic potential of TPX2 siRNA in pancreatic cancer. Among 56 angiogenesis-related factors examined using angiogenesis arrays, the average protein levels of insulin-like growth factor-binding protein-3 (IGFBP-3) were significantly higher in TPX2 siRNA-treated tumors than in the Control siRNA-treated tumors. Moreover, we demonstrated that CD34-positive microvessels were significantly reduced in tumors treated with TPX2 siRNA compared to tumors that treated with Control siRNA. The attenuated expression of CD34 in TPX2 siRNA-treated tumors coincided with the overexpression of IGFBP-3. These results indicated that TPX2 has an impact on tumor angiogenesis in pancreatic cancer. The results also implied that the antiangiogenic effect observed in TPX2 siRNA-treated pancreatic cancer cells may be partly explained by the upregulation of IGFBP-3.
Chebyshev Approximation for Nonrecursive Digital Filters with Linear Phase (1972)

An efficient procedure for the design of finite-length impulse response filters with linear phase is presented. The algorithm obtains the optimum Chebyshev approximation on separate intervals corresponding to passbands and/or stopbands, and is capable of designing very long filters. This approach allows the exact specification of arbitrary band-edge frequencies as opposed to previous algorithms which could not directly control pass- and stopband locations and could only obtain <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(N - 1)/2</tex> different band-edge locations for a length <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</tex> low-pass filter, for fixed <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\delta_{1}</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\delta_{2}</tex> . As an aid in practical application of the algorithm, several graphs are included to show relations among the parameters of filter length, transition width, band-edge frequencies, passband ripple, and stopband attenuation.