gebhart/patrepeval huggingface dataset:
Abstract 3780: Activity of the BET inhibitor INCB054329 in models of lymphoma (2016)

Abstract Inhibitors of the BET family of Bromodomain proteins have been shown to be growth inhibitory across a spectrum of tumor types due to their ability to regulate expression of key survival and cell fate determining genes such as c-myc. Among the various tumor histologies, hematologic malignancies are among the most sensitive cancers to BET inhibition. INCB054329 is a novel, non-benzodiazepine, selective BET inhibitor that is undergoing Phase 1 clinical trials and that has shown encouraging in vitro and in vivo preclinical activity in several models of hematologic malignancy. In the current study, the activity of INCB054329 was evaluated in models of B cell malignancy. INCB54329 effectively inhibited the in vitro growth of a panel of cell lines representing both Hodgkin and non-Hodgkin lymphoma. Treated cells arrested primarily in G1 with sensitive lines also exhibiting dose and time-dependent apoptosis. Within a panel of double-hit lymphoma cell lines, which have activating chromosomal rearrangements in both c-myc and bcl-2, INCB054329 potently inhibited cell growth and was more effective than antagonists of BTK, bcl-2, PIM and PI3Kδ. INCB054329 also showed in vivo efficacy in models of diffuse large B-cell lymphoma (DLBCL). As a single agent, oral administration of INCB054329 inhibited tumor growth in Pfeiffer (GBC) and WILL-2 (GCB, double-hit) subcutaneous xenograft models. The in vivo combination of bendamustine with INCB054329 enhanced anti-tumor efficacy compared with either agent alone in the Pfeiffer model, and the combination was well tolerated. A rational, targeted combination strategy was evaluated involving INCB054329 and a selective, orally active PI3Kδ inhibitor, INCB050465, which is currently in clinical trials in B cell malignancies. Combining INCB054329 with PI3Kδ inhibition markedly enhanced anti-tumor efficacy, increasing the incidence of partial tumor regressions in vivo. In this model, both INCB054329 and INCB050465 treatment led to a reduction in c-Myc protein levels, suggesting a convergence between modulation of BET transcriptional regulation and the PI3Kδ pathway. These data suggest that clinical investigation of INCB054329, both as monotherapy and in combination with standard of care or novel targeted therapies, in several classes of B cell lymphoma, including high risk double hit lymphoma, is warranted. Citation Format: Matthew Stubbs, Robert Collins, Alla Volgina, Mike Liu, Margaret Favata, Mark Rupar, Xiaomng Wen, Richard Sparks, Thomas Maduskuie, Maryanne Covington, Timothy Burn, Bruce Ruggeri, Andrew P. Combs, Wenqing Yao, Reid Huber, Gregory Hollis, Peggy Scherle, Phillip CC Liu. Activity of the BET inhibitor INCB054329 in models of lymphoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3780.
A 2-GHz 1.6-mW phase-locked loop (1997)

This paper describes the design of a 2 GHz 1.6 mW phase-locked loop (PLL) fabricated in an 18 GHz 0.6 /spl mu/m BiCMOS technology. Employing cross-coupled delay elements and inductive peaking, the circuit merges the oscillator and the mixer into one stage to lower the power dissipation. An experimental prototype exhibits an r.m.s. jitter of 2.8 ps, a tracking range of 100 MHz, and a capture range of 70 MHz while operating from a 3 V supply. The phase noise in the locked condition is -115 dBc/Hz at 400 kHz offset.
Color selection with a hygromycin-resistance-based Escherichia coli-mycobacterial shuttle vector (1995)

Hygromycin-resistance (HyR)-based Escherichia coli-mycobacterial shuttle plasmids have high efficiencies of transformation and a broad mycobacterial host range. We have introduced a lacZ alpha (encoding the alpha-polypeptide fragment of beta-galactosidase (beta Gal))-multiple cloning site cassette into a HyR-based shuttle vector to generate a plasmid with nine unique cloning sites and the added feature of beta Gal color selection in appropriate E. coli host strains.
Modeling of Characteristics for Josephson Junctions Having Nonuniform Width or Josephson Current Density (1980)

Several models, both static and dynamic, for calculating the maximum dc Josephson current versus external magnetic field “characteristic” of tunnel junctions of various geometries are described. The static models have the advantage of short computation times; the dynamic models, although slower, yield additional information on circuit-switching times. The dependence of the characteristics on the junction shape is described. The accuracy of a one-dimensional approximation used in the models has been tested experimentally, and theoretically against a two-dimensional approximation. In both cases, the one-dimensional treatment yields quantitatively good agreement provided the inductance of the junction is included in the model. Junctions defined by an oxide “window” of sinusoidal shape (maximum and minimum width at the center and ends, respectively) have a characteristic in which the side lobes are almost completely suppressed. The characteristics of a wide variety of junction shapes, including interferometers having two or more junctions, have been accurately calculated, permitting the design of devices for specific purposes.
Multiattribute Decision-Making: Use of Three Scoring Methods to Compare the Performance of Imaging Techniques for Breast Cancer Detection (2000)

Multiple Attribute Decision Making (MADM) involves "making preference decisions (such as evaluation, prioritization, selection) over the available alternatives that are characterized by multiple, usually conflicting, attributes". The problems of MADM are diverse, and can be found in virtually any topic.\nIn this paper, we use three different scoring methods for evaluating the performance of different imaging techniques used to detect cancers in the female breast. The need for such a decision support system arises from the fact that each of the several techniques which helps diagnose breast cancer today, has its own specific characteristics, advantages and drawbacks. These characteristics or attributes are generally conflicting.\nThe goal is to detect as many malignant lesions in the breast as is possible, while identifying the maximum number of benign lesions. The four imaging techniques that are compared here are Magnetic Resonance Imaging (MRI), Mammography, Ultrasonography, and Nuclear Medicine.\nThe three different multiattribute scoring methods are the Simple Additive Weighting method (SAW), the Weighted Product Method (WPM), and the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS). The three methods are described in detail, and then used to rank the four imaging techniques. The results are analyzed and the validity and robustness of the methods are tested using post-evaluation analysis.
The Effect of Ketamine on Catecholamine Metabolism in the Isolated Perfused Rat Heart (1973)

The effects of ketamine infusion on the uptake and release of norepinephrine and on formation of deaminated metabolites in the isolated, perfused rat heart were studied. Hearts were removed from animals during light ether anesthesia, transferred to a modified Langendorff perfusing apparatus, and perfused with Krebs-Ringer solution containing various doses of ketamine and 200 µg/ml of DL-norepinephrine—14C. Norepinephrine uptake was determined after perfusion for 1, 2, 4, 6, and 20 minutes. At the end of each period the ketaminetreated hearts contained less DL-norepinephrine—14C per gram of heart tissue than control hearts. The reduction was proportional to the dose of ketamine. On an equal-dose basis, ketamine was approximately 80 per cent as effective as cocaine in blocking the uptake of norepinephrine. Norepinephrine release was determined after perfusing hearts for 4 minutes with perfusate containing 200 µg/ml of DL-norepinephrine—14C, then perfusing with solution containing ketamine but free of norepinephrine for 20 minutes. After 10 minutes of perfusion a decrease in myocardial DL-norepinephrine began to appear, and at 20 minutes the decrease was significant. Ketamine infusion did not alter myocardial levels of intracellular deaminated metabolites of norepinephrine, indicating that the effects of ketamine are primarily membrane-related. The results of this study suggest that the sympathomimetic-like effects of ketamine seen in both man and animals may be due to inhibition of the reuptake processes for endogenously released norepinephrine.
HPar (2013)

Parallelizing HTML parsing is challenging due to the complexities of HTML documents and the inherent dependencies in its parsing algorithm. As a result, despite numerous studies in parallel parsing, HTML parsing remains sequential today. It forms one of the final barriers for fully parallelizing browser operations to minimize the browser’s response time—an important variable for user experiences, especially on portable devices. This article provides a comprehensive analysis on the special complexities of parallel HTML parsing and presents a systematic exploration in overcoming those difficulties through specially designed speculative parallelizations. This work develops, to the best of our knowledge, the first pipelining and data-level parallel HTML parsers. The data-level parallel parser, named HPar , achieves up to 2.4× speedup on quadcore devices. This work demonstrates the feasibility of efficient, parallel HTML parsing for the first time and offers a set of novel insights for parallel HTML parsing
The permeability of the lymphocyte membrane: applying a particle size analyzer and a hybrid computer to measure rapid changes in cell volume. (1977)

In summary, this method is ten to twenty times more sensitive than the densimeter method as presently employed. This is not to say that densimeter methods may not be feasible if suitably modified. For example, modern flow systems such as those used at Los Alamos Scientific Laboratories, which measure light transmittance and scattering on an individual cell-by-cell basis, could probably be modified and adapted to summate individual pulses as the population responds to an osmotic gradient prior to entry into the analyzer. Nevertheless, with our present method, we are able to measure the permeability profile of lymphocyte populations from peripheral blood. It should be readily applicable to isolated populations from aspirated bone marrow.
XRCE's Participation at Medical Image Modality Classification and Ad-hoc Retrieval Tasks of Image CLEF2011. (2011)

The aim of this document is to describe our methods used in the Medical Image Modality Classification and Ad-hoc Image Retrieval Tasks of ImageClef 2011. The main novelty in medical image modality classification this year was, that there were more classes (18 modalities) organized in a hierarchy and for some categories only few annotated examples were available. Therefore, our strategy in image categorization was to use a semi-supervised approach. In our experiments, we investigated mono-modal (text and image) and mixed modality based classification. The image classification was based on Fisher Vectors built on SIFT-like local orientation histograms and local color statistics. For text representation we used a binarized bag-ofwords representation where each element indicated whether the term appeared in the image caption or not. In the case of multi-modal classification, we simply averaged the text and image classification scores. For the ad-hoc retrieval task, we used the image captions for text retrieval and Fisher Vectors for visual similarity and modality detection. Our text runs were based on a late fusion of dierent state of the art text experts and the Lexical Entailment model. This Lexical Entailement model used the last year articles to compute similarities between terms and rank first at the previous challenge. Concerning the submitted runs, we realized that we forgot by inadvertance 3 , to submit our best run from last year [3]. We did not submit either improvement over this run, which was proposed in [6]. Overall, this explain the medium performance of our submitted runs. In this document, we show that our system from last year and its improvements would have achieve top performance. We have not tuned the parameter of this system for this year task, we have just evaluated the runs we did not submit
An algorithm for numerical analysis of oscillator including the shifting bias of active element (1989)

The problem of numerical analysis of oscillators has been extensively studied in the literature, O.L. Chua and P.M. Lin (1975). However the proposed iterative methods which include the effect of shifting bias of the active element are not effective enough. Problems occur with computing time when stiff problems are included in the circuit, or the oscillator is DC unstable (relaxation oscillations occur) and when a high quality factor resonant circuit is simulated. In this paper an algorithm which allows one to separate the dynamical simulation process from the shifting bias of active element, is presented. This effect as a slow time phenomenon, which appears at least after one period of oscillation time, is transformed into a suitable static problem. This approach rapidly reduces computation time, can demonstrate DC relaxations and also gives more accurate information for oscillator design. >
Structure–activity relationship of cyclic pentapeptide malformins as fibrinolysis enhancers (2016)

The formation of blood clots in blood vessels causes severe ischemic diseases such as cerebral infarction and myocardial infarction. While searching for microbial products that increase fibrinolytic activity using an in vitro fibrin degradation assay, we found malformin A1, a disulfide form of cyclo(-d-Cys-d-Cys-l-Val-d-Leu-l-Ile-), as an active compound. In this study, we synthesized malformin derivatives using a solid-phase peptide synthesis method and evaluated their fibrinolytic activity and cytotoxicity. Reduction of the disulfide bond and linearization of the cyclic peptide frame decreased the pro-fibrinolytic activity. Substitution of a branched-chain amino acid with lysine resulted in loss of activity. However, protection of the amino group in the lysine derivatives by the tert-butoxycarbonyl (Boc) group rescued the inactivity. Furthermore, the phenylalanine derivatives also exhibited a similar pro-fibrinolytic effect compared to malformin A1. These results suggest that the disulfide bond, the cyclic peptide frame, and the bulky hydrophobic side chains play a crucial role in the pro-fibrinolytic activity of malformin. The effective dose of the active derivatives for the in vitro fibrin degradation showed similar ranges (1-5μM), while the order of cytotoxic potency for the active derivatives was as follows: Phe-derivatives>BocLys-derivatives>malformin A1>reduced form. These results showed no correlation between pro-fibrinolytic activity and cytotoxicity, suggesting the possibility of the synthesis for non-toxic malformin derivatives possessing the activity.
Identification and Characterization of Protease-Resistant SecA Fragments: SecA Has Two Membrane-Integral Forms (1998)

We have identified and characterized the protease-resistant SecA fragments (X. Chen, H. Xu, and P. C. Tai, J. Biol. Chem. 271:29698-29706, 1996) through immunodetection with region-specific antibodies, chemical extraction, and sequencing analysis. The 66-, 36-, and 27-kDa proteolytic fragments in the membranes all start at Met1, whereas the 48-kDa fragment starts at Glu361. The overlapping of the sequences of the 66- and 48-kDa fragments indicates that they are derived from different SecA molecules. These two fragments were generated differently in response to ATP hydrolysis and protein translocation. Furthermore, the presence of membrane is required for the generation of the 48-kDa fragment but not for that of the 66-kDa fragment. These data suggest that there are two different integral forms of SecA in the membrane: SecA(S) and SecA(M). The combination of these two forms of SecA has several membrane-interacting domains. Both forms of SecA are integrated in the membrane, since both the 48- and 66-kDa fragments could be derived from urea- or Na2CO3-washed membranes. Moreover, all fragments are resistant to extraction with a high concentration of salt or with heparin, but the membrane-specific 48-kDa SecA domain is more sensitive to Na2CO3 or urea extraction. This suggests that this domain may interact with other membrane proteins in an aqueous microenvironment and therefore may form a part of the protein-conducting channel.
Remote and direct plasma regions for low-temperature growth of carbon nanotubes on glass substrates for display applications (2011)

A novel method for growing carbon nanotubes (CNTs) on glass substrates is introduced in this study. A two-stage plasma was used to achieve low-temperature and vertically aligned CNTs. Ni deposited on indium tin oxide/glass substrate was used as the catalyst and hydrogen and acetylene were used as gas feeds. In this investigation a new technique was developed to grow vertically aligned CNTs at temperatures below 400 °C while CNT growth by plasma-enhanced chemical vapour deposition required high temperatures. Low-temperature growth of vertically aligned CNTs was suitable for the fabrication of micro-lens and self-oriented displays on glass substrates. Also, we have reported a new configuration for CNT-based display by means of controlling the refractive index of liquid crystal around the CNT by applying a proper voltage to the top and bottom array.
Cilostazol May Prevent Cerebral Vasospasm Following Subarachnoid Hemorrhage (2009)

Cilostazol is an antiplatelet aggregation inhibitor drug associated with increased cerebral blood flow and inflammation suppression. This study evaluated administration of cilostazol to prevent cerebral vasospasm following subarachnoid hemorrhage (SAH) in 50 patients treated surgically from December 2004 to November 2006. All patients, excluding those with Hunt and Kosnik grade 5 or who had undergone late surgery, were classified into two groups: 26 patients who received 200 mg/day cilostazol from postoperative day 1 to day 14 and 24 control patients. The frequency and the degree of cerebral vasospasm, occurrence of ischemic lesion, and clinical symptoms due to vasospasm were compared between the two groups. The appearance of severe vasospasm on angiography, persistent symptomatic spasm, and new cerebral infarction due to vasospasm demonstrated by neuroimaging were apparently lower in the cilostazol group than in the control group, suggesting that cilostazol may significantly suppress cerebral vasospasm following SAH.
Digital Video Watermarking in P-Frames With Controlled Video Bit-Rate Increase (2008)

Most video watermarking algorithms embed the watermark in I-frames, but refrain from embedding in P- and B-frames, which are highly compressed by motion compensation. However, P-frames appear more frequently in the compressed video and their watermarking capacity should be exploited, despite the fact that embedding the watermark in P-frames can increase the video bit rate significantly. This paper gives a detailed overview of a common approach for embedding the watermark in I-frames. This common approach is adopted to use P-frames for video watermarking. We show that by limiting the watermark to nonzero-quantized AC residuals in P-frames, the video bit-rate increase can be held to reasonable values. Since the nonzero-quantized AC residuals in P-frames correspond to nonflat areas that are in motion, temporal and texture masking are exploited at the same time. We also propose embedding the watermark in nonzero quantized AC residuals with spatial masking capacity in I-frames. Since the locations of the nonzero-quantized AC residuals is lost after decoding, we develop a watermark detection algorithm that does not depend on this knowledge. Our video watermark detection algorithm has controllable performance. We demonstrate the robustness of our proposed algorithm to several different attacks.
Biofeedback-Assisted Relaxation in Type 2 Diabetes (2005)

This study supports the use of biofeedback and relaxation in patients with type 2 diabetes for up to 3 months after treatment. Further research is necessary to determine the long-term effects of biofeedback and the effects of mood on patients' responses to treatment.
A <i>Streptococcus pneumoniae</i> pathogenicity island encoding an ABC transporter involved in iron uptake and virulence (2001)

Restricted iron availability is a major obstacle to growth and survival of pathogenic bacteria during infection. In contrast to Gram-negative pathogens, little is known about how Gram-positive pathogens obtain this essential metal. We have identified two Streptococcus pneumoniae genetic loci, pit1 and pit2, encoding homologues of ABC iron transporters that are required for iron uptake by this organism. S. pneumoniae strains containing disrupted copies of either pit1 or pit2 had decreased sensitivity to the iron-dependent antibiotic streptonigrin, and a strain containing disrupted copies of both pit1 and pit2 was unable to use haemoglobin as an iron source and had a reduced rate of iron uptake. The pit2- strain was moderately and the pit1-/pit2- strain strongly attenuated in virulence in mouse models of pulmonary and systemic infection, showing that the pit loci play a critical role during in vivo growth of S. pneumoniae. The pit2 locus is contained within a 27 kb region of chromosomal DNA that has several features of Gram-negative bacterial pathogenicity islands. This probable pathogenicity island (PPI-1) is the first to be described for S. pneumoniae, and its acquisition is likely to have played a significant role in the evolution of this important human pathogen.
Luminescent Labels for Purine Nucleobases: Electronic Properties of Guanine Bound to Rhenium(I) (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLuminescent Labels for Purine Nucleobases: Electronic Properties of Guanine Bound to Rhenium(I)Tracy A. Oriskovich, P. S. White, and H. Holden ThorpCite this: Inorg. Chem. 1995, 34, 7, 1629–1631Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/ic00111a001https://doi.org/10.1021/ic00111a001research-articleACS PublicationsRequest reuse permissionsArticle Views167Altmetric-Citations62LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts