gebhart/patrepeval huggingface dataset:
An Improved Cell-Penetrating, Caspase-Activatable, Near-Infrared Fluorescent Peptide for Apoptosis Imaging (2009)

Apoptosis is required for normal cellular homeostasis, and deregulation of the apoptotic process is implicated in various diseases. Previously, we developed a cell-penetrating near-infrared fluorescence (NIRF) probe based on an activatable strategy to detect apoptosis-associated caspase activity in vivo. This probe consisted of a cell-penetrating Tat peptide conjugated to an effector recognition sequence (DEVD) that was flanked by a fluorophore-quencher pair (Alexa Fluor 647 and QSY 21). Once exposed to effector caspases, the recognition sequence was cleaved, resulting in separation of the fluorophore-quencher pair and signal generation. Herein, we present biochemical analysis of a second generation probe, KcapQ, with a modified cell-penetrating peptide sequence (KKKRKV). This modification resulted in a probe that was more sensitive to effector caspase enzymes, displayed an unexpectedly higher quenching efficiency between the fluorophore-quencher pair, and was potentially less toxic to cells. Assays using recombinant caspase enzymes revealed that the probe was specific for effector caspases (caspase 3 > 7 > 6). Analysis of apoptosis in HeLa cells treated with doxorubicin showed probe activation specific to apoptotic cells. In a rat model of retinal neuronal excitotoxicity, intravitreal injection of N-methyl-d-aspartate (NMDA) induced apoptosis of retinal ganglion cells (RGCs). Eyecup and retinal flat-mount images of NMDA-pretreated animals injected intravitreally with KcapQ using a clinically applicable protocol showed specific and widely distributed cell-associated fluorescence signals compared to untreated control animals. Fluorescence microscopy images of vertical retinal sections from NMDA-pretreated animals confirmed that activated probe was predominantly localized to RGCs and colocalized with TUNEL labeling. Thus, KcapQ represents an improved effector caspase-activatable NIRF probe for enhanced noninvasive analysis of apoptosis in whole cells and live animals.
Cervical cytology biobanking: quality of DNA from archival cervical Pap-stained smears (2008)

The study indicates that commercial DNA isolation techniques are suitable for PCR amplification of DNA isolated from archival smears, yielding amplicons up to 400 base pairs. Proteinase K digestion is not suitable to obtain amplifiable DNA from fixed and stained Pap-stained smears.
Distributed deep learning on edge-devices: Feasibility via adaptive compression (2017)

A large portion of data mining and analytic services use modern machine learning techniques, such as deep learning. The state-of-the-art results by deep learning come at the price of an intensive use of computing resources. The leading frameworks (e.g., TensorFlow) are executed on GPUs or on high-end servers in datacenters. On the other end, there is a proliferation of personal devices with possibly free CPU cycles; this can enable services to run in users' homes, embedding machine learning operations. In this paper, we ask the following question: Is distributed deep learning computation on WAN connected devices feasible, in spite of the traffic caused by learning tasks? We show that such a setup rises some important challenges, most notably the ingress traffic that the servers hosting the up-to-date model have to sustain. In order to reduce this stress, we propose AdaComp, a novel algorithm for compressing worker updates to the model on the server. Applicable to stochastic gradient descent based approaches, it combines efficient gradient selection and learning rate modulation. We then experiment and measure the impact of compression, device heterogeneity and reliability on the accuracy of learned models, with an emulator platform that embeds TensorFlow into Linux containers. We report a reduction of the total amount of data sent by workers to the server by two order of magnitude (e.g., 191-fold reduction for a convolutional network on the MNIST dataset), when compared to a standard asynchronous stochastic gradient descent, while preserving model accuracy.
New Strategies for Isolation of Low Abundance Viral and Host cDNAs: Application to Cloning of the Hepatitis E Virus and Analysis of Tissue-Specific Transcription (1992)

The ability to clone viruses molecularly has led to dramatic advances in our understanding of this diverse group of agents at the molecular level. These insights are critical to the development of experimental strategies for the containment and control of the various viral pathogens that cause hepatitis in man. Knowledge of the genes and gene products have, for example, assisted in the design of expression systems that have been useful for the cell-free expression and production of viral constituents in the development of a subunit (recombinant) vaccine for HBV. Of particular advantage to the experimenter would be the ability to clone the virus directly from the infectious source without the need to resort to biologic amplification systems that require costly investments of money and manpower. This would obviate the need for the time-intensive development of a tissue culture propagation or the expensive cost of developing an animal model. The methods described here have applications to the discovery and isolation of low abundance transcripts from host (cellular) genes. These host encoded products may have important roles in virus replication and certainly by themselves constitute a growing area of study. The direct selection protocol has already proven its value in the isolation of novel (previously undescribed) gene sequences from complex cellular sources. The application of these methodologies should, at the single cell level, aid in the delineation of those important host-encoded gene products that are critical for the efficient in vitro propagation of hepatotropic viruses. The identification of these low abundance cellular genes will elucidate the biologic interplay between host and obligate intracellular parasite (virus) and potentially lead to the development of new strategies for virus control that take into consideration the role of the cell as host.
Inactivation of class A .beta.-lactamases by clavulanic acid: the role of arginine-244 in a proposed nonconcerted sequence of events (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInactivation of class A .beta.-lactamases by clavulanic acid: the role of arginine-244 in a proposed nonconcerted sequence of eventsUzma Imtiaz, Eric Billings, James R. Knox, Elias K. Manavathu, Stephen A. Lerner, and Shahriar MobasheryCite this: J. Am. Chem. Soc. 1993, 115, 11, 4435–4442Publication Date (Print):June 1, 1993Publication History Published online1 May 2002Published inissue 1 June 1993https://pubs.acs.org/doi/10.1021/ja00064a003https://doi.org/10.1021/ja00064a003research-articleACS PublicationsRequest reuse permissionsArticle Views543Altmetric-Citations122LEARN 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
Light Harvesting at Oblique Incidence Decoupled from Transmission in Organic Solar Cells Exhibiting 9.8% Efficiency and 50% Visible Light Transparency (2020)

Abstract For many years, it has been recognized that potential organic photovoltaic cells must be integrated into elements requiring high transparency. In most of such elements, sunlight is likely to be incident at large angles. Here it is demonstrated that light transmission can be largely decoupled from harvesting by optically tailoring an infrared shifted nonfullerene acceptor based organic cell architecture. A 9.67% power conversion efficiency at 50° incidence is achieved together with an average visual transmission above 50% at normal incidence. The deconstruction of a 1D nanophotonic structure is implemented to conclude that just two λ/4 thick layers are essential to reach, for a wide incidence angle range, a higher than 50% efficiency increase relative to the standard configuration reference. In an outdoor measurement of vertically positioned 50% visible transparent cells, it is demonstrated that 9.80% of sunlight energy can be converted into electricity during the course of 1 day.
REVIEWS (1980)

REVIEWS Get access Hilary of Poitiers: a Study in Theological Method. By G. M. Newlands. Pp. ix+216. (European University Studies, Series XXIII, Theology, Vol. 108.) Berne: Peter Lang, 1978. N.p. MAURICE WILES MAURICE WILES Search for other works by this author on: Oxford Academic Google Scholar The Journal of Theological Studies, Volume XXXI, Issue 1, April 1980, Pages 208–209, https://doi.org/10.1093/jts/XXXI.1.208 Published: 01 April 1980
Coating Fine Nickel Particles with Al <sub>2</sub> O <sub>3</sub> Utilizing an Atomic Layer Deposition‐Fluidized Bed Reactor (ALD–FBR) (2004)

An atomic layer deposition–fluidized bed reactor (ALD–FBR) method has been developed to deposit ultrathin and conformal coatings on fine particles. Experiments of Al 2 O 3 deposition on 150‐μm‐diameter nickel particles were conducted. The fluidized bed was constructed to operate under vacuum, and the fluidizing gas used was nitrogen. Trimethylaluminum and water were used as dosing reagents. The reactions were conducted at 450 K. Successful deposition of alumina films, with thickness controllable at the nanometer level, was observed based on transmission electron microscopy imaging, inductively coupled plasma atomic emission spectrometry, X‐ray photoemission spectroscopy, particle‐size distributions, and wavelength‐dispersive spectrometry imaging.
Optimal selection of measurement configurations for robot calibration using simulated annealing (2002)

Measuring robot positions and orientations is a crucial step in a robot calibration process. Off-line optimal selection of measurement configurations can significantly improve the accuracy of kinematic identification. Since the dimension of the parameter space is very large and the cost function is highly nonlinear, this selection process could be well beyond the capacity of today's computers if a global optimal solution is sought by an exhaustive search. On the other hand, gradient-based algorithms are often trapped into local minima. A simulated annealing (SA) approach is adopted in this paper to obtain optimal or near optimal measurement configurations for robot calibration. Simulated annealing is capable of overcoming local minimum points. It is also very convenient for the inclusion of joint travel limits. The SA algorithm is costly computationally; however, since optimal configuration selection can be performed off-line, this may not be a serious problem. To accelerate the convergence rate, a suitable cooling schedule is devised. Practical implementation considerations are discussed. Experimental results are presented to demonstrate the feasibility of the proposed approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A comparative study of the antitumor effectiveness of E. coli and Erwinia asparaginases. (1976)

The relative antineoplastic effectiveness of E. coli and Erwinia asparaginases was tested against lymphoid leukemias EARAD-1 and L5178Y/CA55. E. coli and Erwinia asparaginases had similar clearance rates from plasma in mice, and at a dose of 250 IU/kg body weight both enzymes lowered plasma asparagine to undetectable levels. Nevertheless, the dosage of Erwinia asparaginase needed to cause similar prolongation of median survival time in leukemic mice was at least twice that of E. coli asparaginase. The factors which may be responsible for the more potent therapeutic effectiveness of the E. coli asparaginase are discussed.
Gene expression profiling of connective tissue growth factor (CTGF) stimulated primary human tenon fibroblasts reveals an inflammatory and wound healing response in vitro. (2011)

This study specifies the important role of hCTGF for primary tenon fibroblast function. The RNA expression profile yields new insights into the relevance of hCTGF in influencing biologic processes like wound healing, inflammation, proliferation, and extracellular matrix remodelling in vitro via transcriptional regulation of specific genes. The results suggest that CTGF potentially acts as a modulating factor in inflammatory and wound healing response in fibroblasts of the human eye.
Design optimization of a boost power factor correction converter using genetic algorithms (2003)

This paper presents a software tool for designing a low-cost boost power factor correction front-end converter with an input electromagnetic interference filter. A genetic algorithm based discrete optimizer is used to obtain the design. A detailed and experimentally validated model of the system, including second order effects, is considered. A graphical user interface for managing the design specifications and system component databases, controlling and monitoring the optimization process, and analyzing the performance of the top designs found by the optimizer is also described. The results of a design study for a 1.15 kW unit are presented to demonstrate the usefulness of the software tool.
Use of Chromogenic Substrate S-2251 for Determination of Plasminogen Activator in Rat Ovaries (1981)

A simple specific and reproducible method for determination of plasminogen activator activity in rat ovaries has been developed by using the chromogenic substrate S-2251. The two steps of enzymatic reactions, i.e. activation of plasminogen and subsequent hydrolysis of the substrate was performed in one step incubation. A linear relationship was observed between the amount of chromogen produced and activator activity in the range of the optical density form 0.05 to 1.20 for 30 min's incubation. Endogenous activity of non-specific proteases, plasmin or plasmin inhibitors which might be contained in rat ovaries turned out not to interfere with the specificity of a standardized assay procedure. Reproducibility was firmly established with coefficient of variation not exceeding 10%. Using this method, a marked increase followed by a drastic decrease in the activator activity was shown with rat ovaries around the time of ovulation after the injection of human chorionic gonadotropin.
<i>In vivo</i> studies on the roles of Tic110, Tic40 and Hsp93 during chloroplast protein import (2004)

A multisubunit translocon of the inner envelope membrane, termed Tic, mediates the late stages of protein import into chloroplasts. Membrane proteins, Tic110 and Tic40, and a stromal chaperone, Hsp93, have been proposed to function together within the Tic complex. In Arabidopsis, single genes, atTIC110 and atTIC40, encode the Tic proteins, and two homologous genes, atHSP93-V and atHSP93-III, encode Hsp93. These four genes exhibited relatively uniform patterns of expression, suggesting important roles for plastid biogenesis throughout development and in all tissues. To investigate the roles played by these proteins in vivo, we conducted a comparative study of T-DNA knockout mutants for each Tic gene, and for the most abundantly expressed Hsp93 gene, atHSP93-V. In the homozygous state, the tic110 mutation caused embryo lethality, implying an essential role for atTic110 during plastid biogenesis. Homozygous tic110 embryos exhibited retarded growth, developmental arrest at the globular stage and a 'raspberry-like' embryo-proper phenotype. Heterozygous tic110 plants, and plants homozygous for the tic40 and hsp93-V mutations, exhibited chlorosis, aberrant chloroplast biogenesis, and inefficient chloroplast-import of both photosynthetic and non-photosynthetic preproteins. Non-additive interactions amongst the mutations occurred in double mutants, suggesting that the three components may cooperate during chloroplast protein import.
The Physics of Three Dimensional Radiation Therapy (1993)

The Physics of Three Dimensional Radiation Therapy presents a broad study of the use of three-dimensional techniques in radiation therapy. These techniques are used to specify the target volume precisely and deliver radiation with precision to minimize damage to surrounding healthy tissue. The book discusses multimodality computed tomography, complex treatment planning software, advanced collimation techniques, proton radiotherapy, megavoltage imaging, and stereotactic radiosurgery. A review of the literature, numerous questions, and many illustrations make this book suitable for teaching a course.The themes covered in this book are developed and expanded in Webb's The Physics of Conformal Radiotherapy and the two may be used together or in successive semesters for teaching purposes.
Back signaling by the Nrg-1 intracellular domain (2003)

Transmembrane isoforms of neuregulin-1 (Nrg-1), ligands for erbB receptors, include an extracellular domain with an EGF-like sequence and a highly conserved intracellular domain (ICD) of unknown function. In this paper, we demonstrate that transmembrane isoforms of Nrg-1 are bidirectional signaling molecules in neurons. The stimuli for Nrg-1 back signaling include binding of erbB receptor dimers to the extracellular domain of Nrg-1 and neuronal depolarization. These stimuli elicit proteolytic release and translocation of the ICD of Nrg-1 to the nucleus. Once in the nucleus, the Nrg-1 ICD represses expression of several regulators of apoptosis, resulting in decreased neuronal cell death in vitro. Thus, regulated proteolytic processing of Nrg-1 results in retrograde signaling that appears to mediate contact and activity-dependent survival of Nrg-1-expressing neurons.
Publisher's Note (1994)

Murray Yanowitch has announced that he will retire this year from the editorship of Problems of Economic Transition, in order to devote more time to an intensive program of research. Among those projects is a major study of the human resource and institutional dimensions of Russia's transformation, which is being conducted in Moscow under the sponsorship of Hofstra University's Center for the Study of Labor and Democracy.
Serum bile acids in primary biliary cirrhosis: Effect of ursodeoxycholic acid therapy (1993)

Serum bile acid levels and distributions were studied every 6 mo in patients with primary biliary cirrhosis who were randomly assigned to receive ursodeoxycholic acid (13 to 15 mg/kg/day) (n = 73) or a placebo (n = 73) over a 2-yr period. In the ursodeoxycholic acid group, ursodeoxycholic acid was the predominant serum bile acid at 6 mo and throughout the 2-yr treatment period. The total concentration of endogenous bile acids decreased with a reduction in cholic acid (in the ursodeoxycholic acid group and the placebo group, respectively [mean +/- S.E.]: 13.0 +/- 2.2 and 12.6 +/- 2.5 mumol/L at entry vs. 3.5 +/- 0.6 and 9.0 +/- 2.2 mumol/L at 2 yr; p < 0.002), chenodeoxycholic acid (in the ursodeoxycholic acid group and the placebo group, respectively: 12.1 +/- 1.7 and 12.7 +/- 2.3 mumol/L at entry vs. 5.8 +/- 0.8 and 10.7 +/- 2.2 mumol/L at 2 yr; p < 0.02) and 3 beta-hydroxy-delta 5-cholenoic acid. The concentration of deoxycholic acid did not change, whereas that of lithocholic acid increased significantly (in the ursodeoxycholic acid group and the placebo group, respectively: 0.63 +/- 0.06 and 0.81 +/- 0.12 mumol/L at entry vs. 1.26 +/- 0.12 and 0.90 +/- 0.15 mumol/L at 2 yr; p < 0.001). These changes were independent of the histological stage of the disease. Thus during ursodeoxycholic acid administration the liver was exposed to a lower level of endogenous bile acids and to an increased concentration of ursodeoxycholic acid.(ABSTRACT TRUNCATED AT 250 WORDS)
Performance of the IBIS Compton mode (2004)

The IBIS instrument launched on board the ESA INTEGRAL observatory on October 2002 is a coded mask telescope composed by two position sensitive detection planes, one with 16384 Cadmium Telluride pixels (ISGRI) and the other with 4096 Caesium Iodide pixels (PICsIT). Events detected in coincidence in the two detector layers are flagged as generated by Compton scattered photons and can be then processed and filtered using the Compton kinematic equations. The analysis of these data is, however, quite complex, mainly due to the presence of a great number of fake events generated by random coincidences between uncorrelated ISGRI and PICsIT events; if this component is not subtracted with great accuracy, false source detections can be produced. In this work, we present the performance (spectral and imaging) obtainable from the IBIS Compton data, by analyzing ground calibration acquisitions. We also analyze the IBIS Compton flight data relative to the Crab observation, to determine its scientific capabilities.
Total variation regulated EM algorithm (2002)

An iterative Bayesian reconstruction algorithm based on the total variation (TV) norm constraint is proposed. The motivation for using TV regularization is that it is extremely effective for recovering edges of images. The TV norm minimization, introduced in 1992 was shown to be effective for restoring blurred images with a Gaussian noise model and was demonstrated to be effective for noise suppression and edge preservation. The images were diffused according to a set of nonlinear anisotropic diffusion partial differential equations, which suffered from computational difficulties. This paper extends the TV norm minimization constraint to the field of SPECT image reconstruction with a Poisson noise model. The regularization norm is included in the ML-EM (maximum likelihood expectation maximization) algorithm. The partial differential equation approach is not utilized here. Reconstructions of computer simulations and patient data show that the proposed algorithm has the capacity to smooth the noise and maintain sharp edges without introducing over/under shoots and ripples around the edges.