gebhart/patrepeval huggingface dataset:
LAPS : A General Framework for Modeling Alias Management Using Access Permission Sets (2012)

This thesis presents a general model of access control. It uses a simple notion of an access permission token, which gives permission to reference an associated object. Sets of permission tokens are used to model the maximum reach of an object, and reasoning about access to groups of objects. Links between sets are used to model propagation. Restricting access to an object is important for example when dealing with aliasing, multiple references to a single object. Aliasing is ubiquitous in object-oriented programming, and while practical and even necessary for many purposes, it is also a common source of errors. Since an aliased object may change at any time without notice to the other holders of references to that object, one can generally not guarantee that the state observed through a reference will be the same the next time it is observed. Many techniques for alias control, such as uniqueness and ownership types, have been proposed and implemented to limit and prevent the problems potentially caused by aliasing. However, they are often formulated in very specific settings, making formal comparison between different techniques difficult. This thesis presents a general framework that allows several common alias management policies to be implemented using the same mechanisms, allowing for easy comparison and unification of existing systems, as well as reasoning about new systems. The framework is formally implemented as LAPS, a small object-oriented language that uses access permission sets to express the aliasing policies of a program. Alias management concepts from several existing languages are translated into LAPS, showing how it can be used as a common platform for reasoning about access control properties of different systems.
High Throughput Screening for Small Molecule Enhancers of the Interferon Signaling Pathway to Drive Next-Generation Antiviral Drug Discovery (2012)

Most of current strategies for antiviral therapeutics target the virus specifically and directly, but an alternative approach to drug discovery might be to enhance the immune response to a broad range of viruses. Based on clinical observation in humans and successful genetic strategies in experimental models, we reasoned that an improved interferon (IFN) signaling system might better protect against viral infection. Here we aimed to identify small molecular weight compounds that might mimic this beneficial effect and improve antiviral defense. Accordingly, we developed a cell-based high-throughput screening (HTS) assay to identify small molecules that enhance the IFN signaling pathway components. The assay is based on a phenotypic screen for increased IFN-stimulated response element (ISRE) activity in a fully automated and robust format (Z'>0.7). Application of this assay system to a library of 2240 compounds (including 2160 already approved or approvable drugs) led to the identification of 64 compounds with significant ISRE activity. From these, we chose the anthracycline antibiotic, idarubicin, for further validation and mechanism based on activity in the sub-µM range. We found that idarubicin action to increase ISRE activity was manifest by other members of this drug class and was independent of cytotoxic or topoisomerase inhibitory effects as well as endogenous IFN signaling or production. We also observed that this compound conferred a consequent increase in IFN-stimulated gene (ISG) expression and a significant antiviral effect using a similar dose-range in a cell-culture system inoculated with encephalomyocarditis virus (EMCV). The antiviral effect was also found at compound concentrations below the ones observed for cytotoxicity. Taken together, our results provide proof of concept for using activators of components of the IFN signaling pathway to improve IFN efficacy and antiviral immune defense as well as a validated HTS approach to identify small molecules that might achieve this therapeutic benefit.
Oxygen Flask Method for the Assay of Tritium-,Carbon-14-, and Sulfur-35-Labeled Compounds. (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxygen Flask Method for the Assay of Tritium-,Carbon-14-, and Sulfur-35-Labeled Compounds.H. E. DobbsCite this: Anal. Chem. 1963, 35, 7, 783–786Publication Date (Print):June 1, 1963Publication History Published online1 May 2002Published inissue 1 June 1963https://pubs.acs.org/doi/10.1021/ac60200a007https://doi.org/10.1021/ac60200a007research-articleACS PublicationsRequest reuse permissionsArticle Views61Altmetric-Citations83LEARN 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
A Computer Vision Pipeline for Automated Determination of Cardiac Structure and Function and Detection of Disease by Two-Dimensional Echocardiography (2017)

Automated cardiac image interpretation has the potential to transform clinical practice in multiple ways including enabling low-cost serial assessment of cardiac function in the primary care and rural setting. We hypothesized that advances in computer vision could enable building a fully automated, scalable analysis pipeline for echocardiogram (echo) interpretation. Our approach entailed: 1) preprocessing; 2) convolutional neural networks (CNN) for view identification, image segmentation, and phasing of the cardiac cycle; 3) quantification of chamber volumes and left ventricular mass; 4) particle tracking to compute longitudinal strain; and 5) targeted disease detection. CNNs accurately identified views (e.g. 99% for apical 4-chamber) and segmented individual cardiac chambers. Cardiac structure measurements agreed with study report values (e.g. mean absolute deviations (MAD) of 7.7 mL/kg/m2 for left ventricular diastolic volume index, 2918 studies). We computed automated ejection fraction and longitudinal strain measurements (within 2 cohorts), which agreed with commercial software-derived values [for ejection fraction, MAD=5.3%, N=3101 studies; for strain, MAD=1.5% (n=197) and 1.6% (n=110)], and demonstrated applicability to serial monitoring of breast cancer patients for trastuzumab cardiotoxicity. Overall, we found that, compared to manual measurements, automated measurements had superior performance across seven internal consistency metrics with an average increase in the Spearman correlation coefficient of 0.05 (p=0.02). Finally, we developed disease detection algorithms for hypertrophic cardiomyopathy and cardiac amyloidosis, with C-statistics of 0.93 and 0.84, respectively. Our pipeline lays the groundwork for using automated interpretation to support point-of-care handheld cardiac ultrasound and large-scale analysis of the millions of echos archived within healthcare systems.
Gallbladder disease in pregnancy. (1985)

Cholecystitis should be considered in the evaluation of any pregnant woman with abdominal complaints. Acute cholecystitis can mimic many other intra-abdominal problems, both obstetric and nonobstetric. Most patients respond to conservative management, with minimal increase in maternal or fetal morbidity and mortality. A few will not respond to therapy or will have severe complications requiring more aggressive management, including surgery.
Design considerations and initial physical layer performance results for a space time coded OFDM 4G cellular network (2003)

The exponential growth of cellular radio, WLANs and the Internet sets the context for a discussion on the, role and objectives of 4G. In this paper OFDM is proposed as a leading candidate for a 4G cellular communications standard. The key design considerations and link parameters for a 4G OFDM system are identified and initial physical layer performance results are presented for a number of transmission modes and channel scenarios. Additionally, space-time techniques are considered as a means of enhancing the performance of the coded OFDM system.
Changes in skin levels of two neutotrophins (glial cell line derived neurotrophic factor and neurotrophin-3) cause alterations in cutaneous neuron responses to mechanical stimuli. (2008)

Neurotrophins are important for the development and maintenance of both high and low threshold mechanoreceptors (HTMRs and LTMRs). In this series of studies, the effects of constitutive overexpression of two different neurotrophins, neurotrophin-3 (NT-3) and glial cell line derived neurotrohic factor (GDNF), were examined. Previous studies indicated that both of them may be implicated in the normal development of mouse dorsal root ganglion (DRG) neurons. Neurons from mice transgenically altered to overexpress NT-3 or GDNF (NT-3-OE or GDNF-OE mice) in the skin were examined using several physiological, immunohistochemical and molecular techniques. Ex vivo skin/ nerve/DRG/spinal cord and skin/ nerve preparations were used to determine the response characteristics of the cutaneous neurons; immunohistochemistry was used to examine the biochemical phenotype of DRG cells and the skin; RT-PCR was used to examine the levels of candidate ion channels in skin and DRG that may correlate with changes in physiological responses. In GDNF-OE mice, I-isolectin B4 (IB4)-immunopositive C-HTMRs (nociceptors), a large percentage of which are sensitive to GDNF, had significantly lower mechanical thresholds than wildtype (WT) neurons. Heat thresholds for the same cells were not different. Mechanical sensitivity changes in GDNF-OE mice were correlated with significant increases in acid sensing ion channels 2a (ASIC2a) and 2b (ASIC2b) and transient receptor potential channel A1 (TRPA1), all of which are putative mechanosensitive ion channels. Overexpression of NT-3 affected the responses of A-LTMRs and A-HTMRs, but had no effect on C-HTMRs. Slowly adapting type 1 (SA1) LTMRs and A-HTMRs had increased mechanical sensitivity compared to WT. Mechanical sensitivity was correlated with significant increases in acid-sensing ion channels ASIC1 and ASIC3. This data indicates that both neurotrophins play roles in determining mechanical thresholds of cutaneous HTMRs and LTMRs and that sensitivity changes involve the ASIC family of putative mechanoreceptive ion channels.
Preservation of Functioning Rabbit Hearts In Vitro (1968)

SHORT-TERM preservation of organs in a functional state is essential to allow adequate time for surgeons to match the tissues of the donor and the recipient. Most of the current research in organ preservation utilizes low temperatures with or without hyperbaric oxygen. Most organs sustain irreversible damage at 4C after five to seven hours.<sup>1,2</sup>Canine hearts for example will function after storage at 4C for seven hours. If, however, the hearts are left at 4C for over seven hours, they may regain rhythmicity on reimplantation but cannot take the circulatory load.<sup>1</sup> The present study is particularly concerned with electrolytes and nutrients in the media used to perfuse mammalian organs stored in vitro. Various tissue culture media have been devised in the past few years to support the growth of living cells for many generations in vitro.<sup>3</sup>We utilized one of these media and after
In vivo time-resolved autofluorescence measurements on human skin (2006)

In this paper we present preliminary results obtained from fluorescence lifetime measurements on human skin using time-correlated single photon counting (TCSPC) techniques. Human skin was exposed to light from a pulsed LED of 700 ps pulse width at a wavelength of 375 nm and fluorescence decays were recorded at four different emission wavelengths (442, 460, 478 and 496 nm) using a photomultiplier tube (PMT) coupled to a monochromator. Measurements were carried out on the left and right palms of subjects recruited for the study after obtaining consent using a UCLA IRB approved consent form. The subjects recruited consisted of 18 males and 17 females with different skin complexions and ages ranging from 10 to 70 years. In addition, a set of experiments were also performed on various locations including the palm, the arm and the cheek of a Caucasian subject. The fluorescence decays thus obtained were fit to a three-exponential decay model in all cases and were approximately 0.4, 2.7 and 9.4 ns, respectively. The variations in these lifetimes with location, gender, skin complexion and age are studied. It is speculated that the shorter lifetimes correspond to free and bound NADH while the longer lifetime is due to AGE crosslinks.
Internet of Things Patterns for Devices (2017)

\n Devices are an important part of the Internet of Things. They\n collect data from their environment with sensors and, based on this\n data, also act on their environment by using actuators. Many use\n cases require them to support characteristics such as being cheap,\n light, small, mobile, energy efficient, or autonomously powered.\n This creates constraints for available energy sources and leads to\n different kinds of operating modes. Based on existing terminology\n and additional examples, we describe these energy constraints and\n the operation modes in the form of Patterns. These Patterns are\n interconnected with other Patterns to form an Internet of Things\n Pattern Language that enables practitioners to find and navigate\n through proven solutions for their problems at hand.\n
Aberrant overexpression and function of the miR-17-92 cluster in <i>MLL</i> -rearranged acute leukemia (2010)

MicroRNA (miRNA)-17-92 cluster (miR-17-92), containing seven individual miRNAs, is frequently amplified and overexpressed in lymphomas and various solid tumors. We have found that it is also frequently amplified and the miRNAs are aberrantly overexpressed in mixed lineage leukemia (MLL)-rearranged acute leukemias. Furthermore, we show that MLL fusions exhibit a much stronger direct binding to the locus of this miRNA cluster than does wild-type MLL; these changes are associated with elevated levels of histone H3 acetylation and H3K4 trimethylation and an up-regulation of these miRNAs. We further observe that forced expression of this miRNA cluster increases proliferation and inhibits apoptosis of human cells. More importantly, we show that this miRNA cluster can significantly increase colony-forming capacity of normal mouse bone marrow progenitor cells alone and, particularly, in cooperation with MLL fusions. Finally, through combinatorial analysis of miRNA and mRNA arrays of mouse bone marrow progenitor cells transfected with this miRNA cluster and/or MLL fusion gene, we identified 363 potential miR-17-92 target genes that exhibited a significant inverse correlation of expression with the miRNAs. Remarkably, these potential target genes are significantly enriched (P < 0.01; >2-fold) in cell differentiation, hematopoiesis, cell cycle, and apoptosis. Taken together, our studies suggest that overexpression of miR-17-92 cluster in MLL-rearranged leukemias is likely attributed to both DNA copy number amplification and direct up-regulation by MLL fusions, and that the miRNAs in this cluster may play an essential role in the development of MLL-associated leukemias through inhibiting cell differentiation and apoptosis, while promoting cell proliferation, by regulating relevant target genes.
Normal Exophthalmometry Measurements in a United States Pediatric Population (2012)

Exophthalmometric measurements vary with age among the pediatric population. Reference data are presented for each age group in a U.S. cohort.
AMPA receptor antibodies in limbic encephalitis alter synaptic receptor location (2009)

Antibodies to GluR1/2 associate with LE that is often paraneoplastic, treatment responsive, and has a tendency to relapse. Our findings support an antibody-mediated pathogenesis in which patients' antibodies alter the synaptic localization and number of AMPARs.
β-Hairpin Peptide That Targets Vascular Endothelial Growth Factor (VEGF) Receptors (2011)

VEGF receptors have been the target of intense research aimed to develop molecules able to inhibit or stimulate angiogenesis. Based on the x-ray structure of the complex placental growth factor-VEGF receptor 1(D2), we designed a VEGF receptor-binding peptide reproducing the placental growth factor β-hairpin region Gln(87)-Val(100) that is involved in receptor recognition. A conformational analysis showed that the designed peptide adopts the expected fold in pure water. Moreover, a combination of NMR interaction analysis and cell binding studies were used to demonstrate that the peptide targets VEGF receptors. The VEGF receptor 1(D2)-interacting residues were characterized at the molecular level, and they correspond to the residues recognizing the placental growth factor sequence Gln(87)-Val(100). Finally, the peptide biological activity was characterized in vitro and in vivo, and it showed a VEGF-like behavior. Indeed, the peptide activated VEGF-dependent intracellular pathways, induced endothelial cell proliferation and rescue from apoptosis, and promoted angiogenesis in vivo. This compound is one of the few peptides known with proangiogenic activity, which makes it a candidate for the development of a novel peptide-based drug for medical applications in therapeutic angiogenesis.
Design and implementation of flash based NVDIMM (2014)

Flash based NVDIMM memory is a practical nonvolatile memory technology that can be used to replace DRAM based computer main memory. It is cost effective and readily available than other types of emerging non-volatile memories. NVDIMM memory can be inserted into off-the-shelf computer boards and requires very minimum system modifications. It fits as an ideal transitional memory technology towards the generic storage class memory (SCM) technology in the future. In this paper, we describe the design of Flash based NVDIMM module and its controller architecture. The module layout, design trade offs and implementing results are discussed. Flash based NVDIMM use commodity DRAM memory during normal operations, it backups data from DRAM to Flash during power surge event. NVDIMM requires ultra-capacitors to provide energy during power transitions. The size of ultra-capacitor required for this task is dependent on the module's power consumption as well as data backup speed. We implemented NVDIMM controller design in FPGA. The module can backup 4 gigabyte data in 13 seconds. We also created two types of non-volatile RAMDISK by configuring the NVDIMM controller with DIMM or PCI-E as main interface. Test measurements shown their IOPS performance are much higher than that of hard disk drive.
Single-Pulse and multiple-pulse femtosecond spectroscopy of ferroelectric materials (1995)

Ultrafast-time-resolved spectroscopy of ferroelectric materials and phase transitions is discussed. Impulsive stimulated Raman scattering (ISRS) experiments on optic phonon modes, including soft modes, are reviewed and new data on anharmonic phonon responses in PbTiO3 are presented. Multiple-pulse ISRS excitation of lattice vibrations is also reviewed. The prospects for driving large-amplitude vibrational responses and inducing ultrafast switching between different domain orientations or different phases are discussed. The need for theoretical guidance of these efforts is emphasized.
Swarm Creativity: Competitive Advantage through Collaborative Innovation Networks (2006)

"Swarm Creativity introduces a powerful new concept - Collaborative Innovation Networks, or COINs. Its aim is to make the concept of COINs as ubiquitous among business managers as any other methodology to enhance quality and competitive advantage. The difference, though, is that COINs are nothing like other methodologies. A COIN is a cyberteam of self-motivated people with a collective vision, enabled by technology to collaborate in achieving a common goal - an innovation - by sharing ideas, information, and work. It is no exaggeration to state that COINs are the most productive engines of innovation ever."--BOOK JACKET.
Sudden Death of Citrus in Brazil: A Graft-Transmissible Bud Union Disease (2004)

Citrus Sudden Death (CSD), a new, graft-transmissible disease of sweet orange and mandarin trees grafted on Rangpur lime rootstock, was first seen in 1999 in Brazil, where it is present in the southern Triângulo Mineiro and northwestern São Paulo State. The disease is a serious threat to the citrus industry, as 85% of 200 million sweet orange trees in the State of São Paulo are grafted on Rangpur lime. After showing general decline symptoms, affected trees suddenly collapse and die, in a manner similar to trees grafted on sour orange rootstock when affected by tristeza decline caused by infection with Citrus tristeza virus (CTV). In tristeza-affected trees, the sour orange bark near the bud union undergoes profound anatomical changes. Light and electron microscopic studies showed very similar changes in the Rangpur lime bark below the bud union of CSD-affected trees: size reduction of phloem cells, collapse and necrosis of sieve tubes, overproduction and degradation of phloem, accumulation of nonfunctioning phloem (NFP), and invasion of the cortex by old NFP. In both diseases, the sweet orange bark near the bud union was also affected by necrosis of sieve tubes, and the phloem parenchyma contained characteristic "chromatic" cells. In CSD-affected trees, these cells were seen not only in the sweet orange phloem, but also in the Rangpur lime phloem. Recent observations indicated that CSD affected not only citrus trees grafted on Rangpur lime but also those on Volkamer lemon, with anatomical symptoms similar to those seen in Rangpur lime bark. Trees on alternative rootstocks, such as Cleopatra mandarin and Swingle citrumelo, showed no symptoms of CSD. CSD-affected trees did recover when they were inarched with seedlings of these rootstocks, but not when inarched with Rangpur lime seedlings. These results indicate that CSD is a bud union disease. In addition, the bark of inarched Rangpur lime and Volkamer lemon seedlings showed, near the approach-graft union, the same anatomical alterations as the bud union bark from the Rangpur lime rootstock in CSD-affected trees. The dsRNA patterns from CSD-affected trees and unaffected trees were similar and indicative of CTV. CSD-affected trees did not react by immunoprinting-ELISA using monoclonal antibodies against 11 viruses. No evidence supported the involvement of viroids in CSD. The potential involvement of CTV and other viruses in CSD is discussed.
Template‐Directed Synthesis in 3′‐ and 5′‐Direction with Reversible Termination (2012)

Extending both ways: A method for DNA-templated synthesis on solid support is described. Controlled, stepwise chain extension was demonstrated both in the direction favored by nature (3′-extension; see scheme) and in the direction typical for conventional DNA synthesizers (5′-extension).