gebhart/patrepeval huggingface dataset:
Co-occurrence and ranking of entities based on semantic annotation (2008)

This paper presents an extension of the KIM semantic annotation and search platform called CORE: Co-Occurrence and Ranking of Entities. It enables popularity timeline analysis and a novel faceted search interface. The idea and its advantages to the traditional keyword search are explained along with the environment, technical description and use case scenarios. The essence of the approach is a specific indexing, performed on the basis of semantic annotation of text with respect to named entities and key-phrases forming a reduced-dimension feature space. This allows for a sort of semantic search through adaptation of standard probabilistic IR models where documents are also considered contexts.
Visualizing a hierarchy of performance models for software systems (1993)

Abstract Definition of a software process to be analyzed is normally top‐down. Analysis starts with a rough description and evolves into finer granularity as more performance and functional requirements become available. This process involves different performance models at each stage. The relationship between these models forms a hierarchy of performance models. Performance parameters propagate bottom‐up and the analysis of these models is very complex, so that it is essential to develop computer aided performance evaluation (CAPE) tools to support the evaluation process. In this work, we developed a graphical interface for CAPE environments called the GRAphical Performance Evaluation (GRAPE) system. GRAPE supports the structural design of five different performance models: queueing, state, computation structure, data flow and statistical models. These models can be used to design parallel/distributed real‐time software systems at different levels of granularity. GRAPE is the front‐end tool for a CAPE environment that will allow the user to integrate the relationships between different performance metrics at different levels of analysis. These metrics propagate between the modeling hierarchy to arrive at a final quantitative or symbolic measure of its performance.
Response of canine soft tissue sarcomas to radiation or radiation plus hyperthermia: a randomized phase II study (1992)

Sixty-four dogs with spontaneous soft tissue sarcomas without evidence of metastases were stratified by tumour volume and randomized to receive graded doses of radiotherapy (XRT) alone or radiotherapy plus hyperthermia (HT). An improvement in duration of local control was achieved with the addition of hyperthermia as compared with XRT alone (Wilcoxon, p = 0·040; log rank, p = 0·064). Overall frequency of late complications was not different for the two treatment arms when comparing across equivalent XRT dose groups. Frequency of distant metastases after therapy completion was not significantly different for the two treatment arms at 1 year (7·4% for XRT versus 20% for HT plus XRT) or 2 years (11·5% for XRT versus 25% for HT plus XRT) post therapy. These results suggest that a therapeutic gain was achieved for this group of tumour-bearing animals. Uni- and multivariate analyses were performed to examine the potential for various factors to influence treatment outcome. Patient related variables included tumour stage, histologic subtype and grade and tumour site. Treatment related variables included total radiation dose and 15 descriptors of temperature distributions achieved during hyperthermia. When considering patient related factors, tumour histology, grade and location were important predictors of time to minimum volume, but only tumour location influenced time to tumour regrowth. When considering treatment related factors, radiation dose was not significantly correlated with time to minimum volume or time to local regrowth, but it was correlated with probability for late normal tissue damage in the XRT alone group (p = 0·005). For the hyperthermia treatments, 13 of 15 tumour temperature distribution descriptors were correlated with time to minimum volume, but none were correlated with time to local regrowth. These results suggest that caution should be used in interpreting the value of temperature distribution descriptors in predicting for long-term local control after hyperthermia and radiotherapy, based on analysis of short-term responses.
Macrocyclic Envelope Glycoprotein Antagonists that Irreversibly Inactivate HIV-1 <i>before</i> Host Cell Encounter (2015)

We derived macrocyclic HIV-1 antagonists as a new class of peptidomimetic drug leads. Cyclic peptide triazoles (cPTs) retained the gp120 inhibitory and virus-inactivating signature of parent PTs, arguing that cyclization locked an active conformation. The six-residue cPT 9 (AAR029b) exhibited submicromolar antiviral potencies in inhibiting cell infection and triggering gp120 shedding that causes irreversible virion inactivation. Importantly, cPTs were stable to trypsin and chymotrypsin compared to substantial susceptibility of corresponding linear PTs.
Immunolocalization of cytokines in the nasal mucosa of normal and perennial rhinitic subjects. The mast cell as a source of IL-4, IL-5, and IL-6 in human allergic mucosal inflammation. (1993)

Allergic mucosal inflammation is characterized by the presence of cell infiltration, predominantly with IgE-sensitized mast cells and activated eosinophils, and appears to be regulated by the local production and release of several cytokines, particularly IL-4 and IL-5. Although attention has focused on the Th2 subpopulation of CD4+ T lymphocytes as an important source of these cytokines, human mast cells have been shown to both store and secrete IL-4 and TNF-alpha. To investigate the expression of cytokines relevant to allergic inflammation and to identify their cellular localization within the nasal mucosa, we have undertaken specific immunohistochemical staining of thin sections of inferior turbinate biopsies from patients with perennial allergic rhinitis and, for comparison, from nonatopic healthy volunteers. The cytokines investigated were IL-4, IL-5, IL-6, and IL-8. In both the normal and rhinitic biopsies numerous cells immunoreactive for IL-4, IL-5, and IL-6 were seen. Staining of adjacent 2-microns sections for CD3, mast cell tryptase, and eosinophil cationic protein revealed that 90% of the IL-4 immunoreactive cells were mast cells, with biopsies from rhinitic subjects containing significantly more IL-4+ cells than biopsies from normal controls (p = 0.02), especially when assessed with the anti-IL-4 mAb 3H4. Mast cells also accounted for > 90% of IL-6 and > 50% of IL-5 immunoreactive cells. IL-5 immunoreactivity was also localized to eosinophils, whereas IL-8 localized predominantly to the nasal epithelium in both groups. No cytokines were found in association with T lymphocytes. These findings indicate that the mast cell is an important source of preformed cytokines and as such may contribute to the chronicity of the mucosal inflammation that characterizes allergic rhinitis.
Single-step, multiple retroviral transduction of human T cells (2002)

Background Retroviral transduction of human peripheral blood T cells has considerable potential in the development of gene therapy strategies for immunological disorders. New vectors and experimental procedures have been developed for efficient transduction of several genes into human T cells. Methods Bicistronic retroviral vectors encoding distinct cell markers were used for the simultaneous multiple transduction of a human T-cell line (MT-2), as well as of human peripheral blood T cells from normal donors. Transduction efficiencies were evaluated by flow cytometry and double- and triple-transduced cells were isolated by fluorescence cell sorting. Results Four new bicistronic retroviral vectors were developed that express different gene markers under the control of the internal ribosome entry site (IRES) of the encephalomyocarditis virus. These markers are, respectively, enhanced green fluorescent protein (EGFP), β-galactosidase, and truncated versions of human nerve growth factor receptor (ΔNGFR) and human growth hormone receptor (ΔGHR). A single 1 h spinoculation infection, performed in the presence of polybrene and using transiently produced amphotropic retroviral particles, was sufficient to obtain transduction efficiencies consistently greater than 50% on human peripheral blood T lymphocytes which had been previously stimulated for 3 days with immobilized anti-CD3. The transient production of viral particles encoding EGFP, ΔNGFR, and ΔGHR markers in the same viral supernatant has allowed up to three different genes to be introduced simultaneously into human T cells. Conclusions This study describes new experimental conditions for efficient single-step multiple transduction of human primary T lymphocytes. The procedure could be of interest for the development of gene therapy approaches. Copyright © 2002 John Wiley & Sons, Ltd.
Switch-induced error voltage on a switched capacitor (1984)

A concise analytical expression for switch-induced error voltage on a switched capacitor is derived from the distributed MOSFET model. The result can be interpreted in terms of a simple lumped equivalent circuit. With this expression the dependence is investigated of the error voltage on process parameters and on switch turnoff rate, source resistance, and other circuit parameters. These results can be used to quickly predict the error voltage. The analytical expression is in close agreement with computer simulations and experiments.
Application of Computational Fluid Dynamics Techniques to Blood Pumps (1996)

Present-day computational fluid dynamics (CFD) techniques can be used to analyze the behavior of fluid flow in a variety of pumps. CFD can be a powerful tool during the design stage for rapid virtual prototyping of different designs, analyzing performance parameters, and making design improvements. Computational flow solutions provide information such as the location and size of stagnation zones and the local shear rate. These parameters can be correlated to the extent of hemolysis and thrombus formation and are critical to the success of a blood pump. CFD-ACE, an advanced commercial CFD code developed by CFD Research Corporation, has been applied to fluid flows in rotary machines, such as axial flow pumps and inducers. Preprocessing and postprocessing tools for efficient grid generation and advanced graphical flow visualization are integrated seamlessly with CFD-ACE. The code has structured multiblock grid capability, non-Newtonian fluid treatment, a variety of turbulence models, and an Eulerian-Lagrangian particle tracking model. CFD-ACE has been used successfully to study the flow characteristics in an axial flow blood pump. An unstructured flow solver that greatly automates the process of grid generation and speeds up the flow simulation is under development.
Pyro (2003)

In this article we describe a programming framework called Pyro, which provides a set of abstractions that allows students to write platform-independent robot programs. This project is unique because of its focus on the pedagogical implications of teaching mobile robotics via a top-down approach. We describe the background of the project, its novel abstractions, its library of objects, and the many learning modules that have been created from which curricula for different types of courses can be drawn. Finally, we explore Pyro from the students' perspective in a case study.
Numerical Simulation of Mixing Enhancement in a Hot Supersonic Jet (1996)

Experimental observations show that the presence of small tabs on the edge of a hot, compressible jet exiting into a slower moving, colder ambient flow can increase the rate of spreading of the jet. This suggests that the rate of mixing of the jet and the ambient fluid is also increased. In order to elucidate the physical mechanism responsible for the increased spreading rate a set of calculations were carried out within the framework of the compressible three dimensional Navier-Stokes equations. A series of grid re#nements were made to assess the accuracy of the results. We first simulated the flow without the tabs, obtaining reasonable agreement with experimental measurements of the velocity. We then simulated the flow, without tabs, over a range of values of the convective Mach number in order to determine the dependence of the mixing on this parameter. Simulations with modeled tabs were also carried out. In these calculations the effect of the tabs on the flow was modeled by pairs of counter rotating vortices. The results of these calculations indeed show that the presence of the tabs increase the spreading rate of the jet. The basic physical mechanism responsible for the enhanced spreading rate is discussed and qualitative comparisons with flow visualizations are made.
Simulation of materials processing : theory, methods and applications : Proceedings of the Fifth International Conference on Numerical Methods in Industrial Forming Processes - NUMIFORM '95, Ithaca, New York, USA, 18-21 June 1995 (1995)

Numerical simulation has emerged as a powerful tool in the design and analysis of industrial forming processes. The major difficulties of complex three-dimensional workpiece geometries and ill-defined material properties during processing are being addressed with rapidly improving efficacy. The NUMIFORM conference held at three-year intervals, offer a well-recognized forum for practitioners from both academia and industry to exchange knowledge on new developments. This volume consists of papers presented at the 5th conference and reflect the state-of-art of quantitatively addressing critical issues in the industrial processes of metals, polymers and other materials. Topics: Keynote lectures; Invited lectures; Material behaviour; Simulation methods and large scale computation; Metals: General topics; Rolling of metals; Polymer: General topics; Polymer injection molding and casting of metals.
[Glycinebetaine applied through roots protects the photosynthetic apparatus of tobacco seedlings under water stress]. (2006)

Two tobacco (Nicotiana tabacum L.) cultivars (DHJ5210 and ZY100) with different drought tolerance were used to study the photosynthetic response to different water stress and the effects of glycinebetaine applied through roots on photosynthetic capacity. The physiological mechanisms of the improvement of tobacco photosynthesis by glycinebetaine applied through roots were analyzed. The results indicated that photosynthetic apparatus of tobacco leaves were more brittle and damaged by water stress, accompanied by negative changes of RWC (Fig. 2), chlorophyll content (Fig. 3), PSII photochemistry efficiency (Fig. 4), activity of Hill reaction (Fig. 5) and ATPase (Fig. 6), and the damage was more serious to ZY100 (drought sensitive cultivar) than DHJ5210 (drought resistant cultivar) under the same stress condition. Glycinebetaine applied through roots could be absorbed by tobacco roots and then accumulated in leaves (Fig. 1), which alleviated the decrease in photosynthetic variables of two cultivars and the improvement was more significant on ZY100 than DHJ5210. The positive function of glycinebetaine might be involved in its protective effect on antioxidant enzymes (Fig. 8), chloroplast protein and thylakoid membrane (Fig. 7).
Punched-Card Controlled Aircraft Navigation Computer (1953)

This paper presents the theory and a description of a course-line navigation computer for use with the presently available vhf omnirange navigation system or with the proposed complete omnirange-dme navigation system. A position fix may be obtained with the equipment by triangulation using line of bearing information from two omniranges. A further computation then produces course and distance indications with respect to an arbitrary ground point as selected by the pilot. Alternatively, position-fix information derived from an oange-dme ground station may be used as input data for course-line computation. The punched-card reference-data system and pictorial course display instrumentation associated with the computer are described.
Studies on the specificity of Candida rugosa lipase catalyzed esterification reactions in organic media (2006)

In this study, the feasibility of the synthesis of various flavor esters catalyzed by a commercial lipase from Candida rugosa was investigated and the process parameters were optimized. Lipase from C. rugosa successfully catalyzed the synthesis of 19 esters. The highest yields, of more than 90 % after 20 h, were observed in the synthesis of short-chain esters, pentyl propanoate, isopentyl butanoate, and butyl butanoate. Increasing the number of carbon atoms of both substrates above 8 caused a significant decrease of the initial reaction rates and the final yields. The enzyme showed surprisingly low affinity towards pentanoic acid and hexanoic acid, compared with the higher homologues, octanoic acid and decanoic acid. In addition to the number of carbon atoms, the structure of the substrates had a significant influence on the enzyme activity. Namely, the activity of the enzyme towards isopropanol was significantly lower compared with n-propanol. Additionally, cis-9-octadecenoic acid was a better substrate than octadecanoic acid, its saturated analogue.
An Efficient Single-Anchor Localization Method Using Ultra-Wide Bandwidth Systems (2019)

Ultra-wideband technology has the merits of high temporal resolution and stability, and it has been widely used for high-accuracy localization and tracking. However, most ultra-wideband localization systems need multiple anchors for trilateration, which results in high system cost, large messages overhead, and insufficient extraction of information. In this paper, we propose a single-anchor localization (SAL) mehtod that achieves high-accuracy multi-agent localization with high efficiency. In the proposed method, the anchor broadcasts the first two messages and then each agent responds one message to the anchor (quasi-)simultaneously. Based on the received message with superpositioned agent responses, the time-of-flight and angle-of-arrival information from all agents to the anchor can be extracted altogether. We implement the localization system in two indoor environments, and show that the proposed method can achieve decimeter-level accuracy for multiple agents using three messages. Our method provides design guidelines for high-accuracy and high-efficiency multi-agent localization systems.
<i>XPD</i> and <i>XRCC1</i> Genetic Polymorphisms Are Prognostic Factors in Advanced Non—Small-Cell Lung Cancer Patients Treated With Platinum Chemotherapy (2004)

Genetic polymorphisms in XPD and XRCC1 may be important prognostic factors in platinum-treated patients with advanced NSCLC.
Gut microbiome and depression: what we know and what we need to know (2018)

Gut microbiome diversity has been strongly associated with mood-relating behaviours, including major depressive disorder (MDD). This association stems from the recently characterised bi-directional communication system between the gut and the brain, mediated by neuroimmune, neuroendocrine and sensory neural pathways. While the link between gut microbiome and depression is well supported by research, a major question needing to be addressed is the causality in the connection between the two, which will support the understanding of the role that the gut microbiota play in depression. In this article, we address this question by examining a theoretical 'chronology', reviewing the evidence supporting two possible sequences of events. First, we discuss that alterations in the gut microbiota populations of specific species might contribute to depression, and secondly, that depressive states might induce modification of specific gut microbiota species and eventually contribute to more severe depression. The feasibility of both sequences is supported by pre-clinical trials. For instance, research in rodents has shown an onset of depressive behaviour following faecal transplantations from patients with MDD. On the other hand, mental induction of stress and depressive behaviour in rodents resulted in reduced gut microbiota richness and diversity. Synthesis of these chronology dynamics raises important research directions to further understand the role that gut microbiota play in mood-relating behaviours, which holds substantial potential clinical outcomes for persons who experience MDD or related depressive disorders.
Lidocaine Oxidation by Electrogenerated Reactive Oxygen Species in the Light of Oxidative Drug Metabolism (2010)

The study of oxidative drug metabolism by Cytochrome P450s (P450) is important in the earlier stages of drug development. For this purpose, automated analytical techniques are needed for fast and accurate estimation of oxidative drug metabolism. Previous studies have shown that electrochemistry in combination with mass spectrometry is a versatile analytical technique to generate drug metabolites that result from direct electron transfer. Here we show that electrochemical generation of reactive oxygen species (ROS), a process reminiscent of the catalytic cycle of P450, extends the applicability of electrochemistry in drug metabolism research. Oxidation products of lidocaine from one and two-compartment electrochemical cells, operated under various conditions were analyzed by LC-MS and metabolite structures were elucidated by collision-induced (LC-MS/MS), and thermally induced (APCI) fragmentation. Direct oxidation of lidocaine at the anode resulted in N-dealkylation, whereas reaction with H(2)O(2), generated at the cathode, produced the N-oxide, both known in vivo lidocaine metabolites. Catalytic activation of hydrogen peroxide, using the Fenton reaction, resulted in benzylic and aromatic hydroxylations thus covering all of the known in vivo phase-I metabolites of lidocaine. This study extends the applicability of electrochemistry combined with mass spectrometry as a valuable technique in assessing oxidative drug metabolism related to P450.
Replication-Competent Bacterial Artificial Chromosomes of Marek's Disease Virus: Novel Tools for Generation of Molecularly Defined Herpesvirus Vaccines (2003)

Marek's disease (MD), a highly infectious disease caused by an oncogenic herpesvirus, is one of the few herpesvirus diseases against which live attenuated vaccines are used as the main strategy for control. We have constructed bacterial artificial chromosomes (BACs) of the CVI988 (Rispens) strain of the virus, the most widely used and effective vaccine against MD. Viruses derived from the BAC clones were stable after in vitro and in vivo passages and showed characteristics and growth kinetics similar to those of the parental virus. Molecular analysis of the individual BAC clones showed differences in the structure of the meq gene, indicating that the commercial vaccine contains virus populations with distinct genomic structures. We also demonstrate that, contrary to the published data, the sequence of the L-meq of the BAC clone did not show any frameshift. Virus stocks derived from one of the BAC clones (clone 10) induced 100 percent protection against infection by the virulent strain RB1B, indicating that BAC-derived viruses could be used with efficacies similar to those of the parental CVI988 vaccines. As a DNA vaccine, this BAC clone was also able to induce protection in 6 of 20 birds. Isolation of CVI988 virus from all of these six birds suggested that immunity against challenge was probably dependent on the reconstitution of the virus in vivo and that such viruses are also as immunogenic as the in vitro-grown BAC-derived or parental vaccine viruses. Although the reasons for the induction of protection only in a proportion of birds (33.3%) that received the DNA vaccine are not clear, this is most likely to be related to the suboptimal method of DNA delivery. The construction of the CVI988 BAC is a major step towards understanding the superior immunogenic features of CVI988 and provides the opportunity to exploit the power of BAC technology for generation of novel molecularly defined vaccines.