gebhart/patrepeval huggingface dataset:
Long‐term tracing of adenoviral expression in rat and rabbit using luciferase imaging (2005)

Luciferase expression after adenoviral gene delivery can persist for longer than 6 months, even in immunocompetent animals. Live imaging of luciferase expression can be performed not only in small animals, but also in larger animals such as rabbits.
Web-based automated black-box testing framework for component based robot software (2012)

Reliability of component based robot software depends on the quality of each component because any defective components will have a ripple effect on systems built with them. Thus, testing of unit component, composite component and component based robot software is critical for checking the correctness of the software functionality. This paper proposes Web-based automated black-box testing framework for component based robot software. The proposed framework provides automated testing service, testing for different robot platform and distributed test environment, and sharing test resources. We have implemented the proposed framework and evaluated it on the component based front guidance application to output a guidance statement by sensing front obstacles, and control robot wheels by sensing a back user.
Integrated nanofabrication with the scanning electron microscope and scanning tunneling microscope (1993)

The combination of electron beam lithography using the scanning electron microscope (SEM) and direct nanofabrication with the scanning tunneling microscope (STM) has been used to fabricate a nanometer size link between two prefabricated nanometer size wires. The wires were fabricated by electron beam lithography using a high resolution SEM. This sample was then transferred to a combined SEM and STM instrument which is used to locate the wires, position them beneath the STM tip, and fabricate the link using the technique of tip bias pulsing with the STM.
Apo‐Hsp90 coexists in two open conformational states in solution (2008)

The present study shows, for the first time, the structure of the entire eukaryotic apo-Hsp90, along with its intrinsic flexibility. Although large structural rearrangements, leading to partial closure of the Hsp90 dimer, were previously attributed to the binding of nucleotides, our results reveal that they are in fact mainly due to the intrinsic flexibility of Hsp90 dimer. Taking into account the preponderant role of the dynamic nature of the structure of Hsp90, we reconsider the Hsp90 ATPase cycle.
Near-real-time satellite image processing: metacomputing in CC++ (1996)

Metacomputing combines heterogeneous system elements in a seamless computing service. In this case study, we introduce the elements of metacomputing and describe an application for cloud detection and visualization of infrared and visible-light satellite images. The application processes the satellite images by using Compositional C++ (CC++)-a simple, yet powerful extension of C++-and its runtime system, Nexus, to integrate specialized resources, high-speed networks, parallel and distributed computing, and stereoscopic visualization in virtual reality (VR) displays.
An enhanced approach to determine a small forward node set based on multipoint relays (2003)

Multipoint relays (MPR) (A. Qayyum et al., 2002) provide a localized and optimized way of determining a small forward node set for broadcasting messages in an ad hoc network. Using 2-hop neighborhood information, each node determines a small set of forward neighbors to relay messages. Selected forward nodes form a connected dominating set (CDS) to ensure full coverage. Recently, Adjih, Jacquet, and Viennot [Ref. 1] proposed a novel localized algorithm to construct a small forward node set based on MPR. In this paper, we provide a further extension to generate a smaller forward node set without additional cost. The effectiveness of our approach is confirmed through a simulation study.
How to draw a directed graph (2003)

Several recent tools for visualizing software and information engineering problems have used directed graphs as a basic model. Thus considerable interest has arisen in algorithms for drawing directed graphs so that they are easy to understand and remember. The paper defines three aesthetic criteria for drawings of directed graphs, and discusses a general method for obtaining drawings according to these criteria. Several recent algorithms to draw directed graphs are instances of this general method. The aesthetic criteria can be viewed as goals of optimization problems. Each step of the general method aims to achieve one of the criteria by solving these optimization problems. The authors discuss the current state of knowledge of each of these problems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA (2010)

Cren7, a newly found chromatin protein, is highly conserved in the Crenarchaeota. The protein shows higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils in vitro and is associated with genomic DNA in vivo. Here we report the crystal structures of the Cren7 protein from Sulfolobus solfataricus in complex with two DNA sequences. Cren7 binds in the minor groove of DNA and causes a single-step sharp kink in DNA (∼53°) through the intercalation of the hydrophobic side chain of Leu28. Loop β3-β4 of Cren7 undergoes a significant conformational change upon binding of the protein to DNA, suggesting its critical role in the stabilization of the protein–DNA complex. The roles of DNA-contacting amino acid residues in stabilizing the Cren7–DNA interaction were examined by mutational analysis. Structural comparison of Cren7-DNA complexes with Sac7d-DNA complexes reveals significant differences between the two proteins in DNA binding surface, suggesting that Cren7 and Sul7d serve distinct functions in chromosomal organization.
Composition Planning for Networked Appliances (2009)

Today, the networked appliances are evolving toward service-enabled networked appliances by service oriented computing. They can be advertising the functionality of devices in the terms of services that can be offer to the network. The user and other networked appliances would become possible to creating a new virtual appliance by composite those services. In this paper, we present the service score calculated mechanism for planner process which use to select the best service for composition in our framework.Today, the networked appliances are evolving toward service-enabled networked appliances by service oriented computing. They can be advertising the functionality of devices in the terms of services that can be offer to the network. The user and other networked appliances would become possible to creating a new virtual appliance by composite those services. In this paper, we present the service score calculated mechanism for planner process which use to select the best service for composition in our framework.
MPLS-based QoS interworking among wide area subsystems (2005)

This paper deals with a novel protocol architecture to interconnect autonomous systems (ASes), together with guaranteeing the QoS provision. The adoption of the MPLS protocol allows defining an effective way to face the heterogeneity due to the interconnection of ASes implementing different QoS technologies. In this view, the problem regarding the management of the traffic flows that cross the boundaries of the ASes reveals to be a hot topic of research and will be deeply investigated in the paper.
CAGE, a novel cancer/testis antigen gene, promotes cell motility by activation ERK and p38 MAPK and downregulating ROS. (2006)

We previously identified a novel cancer/testis antigen gene CAGE by screening cDNA expression libraries of human testis and gastric cancer cell lines with sera of gastric cancer patients. CAGE is expressed in many cancers and cancer cell lines, but not in normal tissues apart from the testis. In the present study, we investigated its role in the motility of cells of two human cancer cell lines: HeLa and the human hepatic cancer cell line, SNU387. Induction of CAGE by tetracycline or transient transfection enhanced the migration and invasiveness of HeLa cells, but not the adhesiveness of either cell line. Overexpression of CAGE led to activation of ERK and p38 MAPK but not Akt, and inhibition of ERK by PD98059 or p38 MAPK by SB203580 counteracted the CAGE-promoted increase in motility in both cell lines. Overexpression of CAGE also resulted in a reduction of ROS and an increase of ROS scavenging, associated with induction of catalase activity. Inhibition of ERK and p38 MAPK increased ROS levels in cells transfected with CAGE, suggesting that ROS reduce the motility of both cell lines. Inhibition of ERK and p38 MAPK reduced the induction of catalase activity resulting from overexpression of CAGE, and inhibition of catalase reduced CAGE-promoted motility. We conclude that CAGE enhances the motility of cancer cells by activating ERK and p38 MAPK, inducing catalase activity, and reducing ROS levels.
Relation between Renal Dysfunction and Cardiovascular Outcomes after Myocardial Infarction (2004)

Even mild renal disease, as assessed by the estimated GFR, should be considered a major risk factor for cardiovascular complications after a myocardial infarction.
The Plasminogen (Fibrinolytic) System (1999)

Introduction The plasminogen (fibrinolytic) system (Fig. 1) comprises an inactive proenzyme, plasminogen, that can be converted to the active enzyme, plasmin. Plasmin degrades fibrin and activates matrix metalloproteinases (MMPs) that, in turn, degrade the extracellular matrix (ECM).1-3 Two physiological plasminogen activators (PAs) have been identified: tissue-type PA (t-PA) and urokinase-type PA (u-PA), which binds to a cellular u-PA receptor (u-PAR). Inhibition of the plasminogen/MMP system occurs at the level of the PA, by specific PA inhibitors (PAIs), at the level of plasmin, primarily by α2-antiplasmin, or at the level of MMPs, by tissue inhibitors of MMPs (TIMPs). The dual roles of the plasminogen system are presently well established. The t-PA-mediated pathway is primarily involved in fibrin homeostasis, and the u-PA-mediated pathway is primarily involved in phenomena, such as cell migration and tissue remodeling. Consequently, the terminology “fibrinolytic system” has become inadequate and, therefore, will be replaced by “plasminogen system” in the present review. In 1980, the state of knowledge concerning the plasminogen system was summarized.4 At that time, most of the components of the system (except the PAIs) were identified and biochemically characterized (except t-PA), but thrombolytic therapy was still in its infancy. The pathophysiologic role of the plasminogen system was deduced indirectly from correlations between levels of its components and clinical disease states, whereas its role in vascular biology, matrix remodeling, tumor growth and dissemination, wound healing, and infection was largely unknown. The last 20 years have witnessed a rapidly progressing elucidation of the biochemistry, (patho)physiology, and therapeutic applications of the plasminogen system. This development has been catalyzed by the emergence of powerful molecular biological technologies, including recombinant DNA techniques for the expression of heterologous proteins and targeted gene manipulation in vivo for the elucidation of the (patho)physiological role of their translation products. The aim of the present review is to summarize the main developments in the plasminogen field since the 1980s. This account will be incomplete, since references to much significant work were omitted due to space limitations. To alleviate this shortcoming, reference is made primarily to review articles, in which more details and citations to original work can be found.
Cyclooxygenase-2 Inhibition Augments the Hepatic Antitumor Effect of Oral Salmonella Typhimurium in a Model of Mouse Metastatic Colon Cancer (2002)

Oral cyclooxygenase-2 inhibitor appeared to act synergistically with S. typhimurium to reduce tumor burden. This combination therapy may have clinical application in the treatment or prevention of hepatic metastases associated with colorectal cancer.
An Enantioselective β‐Lactam Synthesis Starting from <scp>L</scp>‐<i>(S)</i>‐Glyceraldehyde Acetonide (1983)

Abstract Complete diastereoselectivity is observed during the cyclocondensation of activated glycine derivatives with aldimines derived from L ‐ (S) ‐glyceraldehyde acetonide. 3,4‐ cis ‐β‐lactams are isolated in high optical and chemical yields. They are converted into key intermediates used in the syntheses of various mono‐ and bicyclic β‐lactam antibiotics. A mechanism is suggested to explain this remarkable diastereoselectivity.
Load prediction models in web-based systems (2006)

Run-time management of modern Web-based services requires the integration of several algorithms and mechanisms for job dispatching, load sharing, admission control, overload detection. All these algorithms should take decisions on the basis of present and/or future load conditions of the system resources. In particular, we address the issue of predicting future resource loads under real-time constraints in the context of Internet-based systems. In this situation, it is extremely difficult to deduce a representative view of a system resource from collected raw measures that show very large variability even at different time scales. For this reason, we propose a two-step approach that first aims to get a representative view of the load trend from measured raw data, and then applies a load prediction algorithm to load trends. This approach is suitable to support different decision systems even for highly variable contexts and is characterized by a computational complexity that is compatible to run-time decisions. The proposed models are applied to a multi-tier Web-based system, but the results can be extended to other Internet-based contexts where the systems are characterized by similar workloads and resource behaviors.
Asynchronous replication timing of imprinted loci is independent of DNA methylation, but consistent with differential subnuclear localization (2003)

Genomic imprinting in mammals marks the two parental alleles resulting in differential gene expression. Imprinted loci are characterized by distinct epigenetic modifications such as differential DNA methylation and asynchronous replication timing. To determine the role of DNA methylation in replication timing of imprinted loci, we analyzed replication timing in Dnmt1- and Dnmt3L-deficient embryonic stem (ES) cells, which lack differential DNA methylation and imprinted gene expression. Asynchronous replication is maintained in these ES cells, indicating that asynchronous replication is parent-specific without the requirement for differential DNA methylation. Imprinting centers are required for regional control of imprinted gene expression. Analysis of replication fork movement and three-dimensional RNA and DNA fluorescent in situ hybridization (FISH) analysis of the Igf2-H19 locus in various cell types indicate that the Igf2-H19 imprinting center differentially regulates replication timing of nearby replicons and subnuclear localization. Based on these observations, we suggest a model in which cis elements containing nonmethylation imprints are responsible for the movement of parental imprinted loci to distinct nuclear compartments with different replication characteristics resulting in asynchronous replication timing.
Interferons: their role in clinical practice. (1995)

Interferons are accepted therapy for a number of conditions. Their range of therapeutic uses will undoubtedly increase as further knowledge is obtained.
Powder sampling and particle size measurement (1997)

Volume 1: Permeametry and gas diffusion. Surface area determination by gas adsorption. Determination of pore size distribution by gas adsorption. Pore size determination by mercury porosimetry. Other methods for determining surface area. Volume 2: Powder sampling. Data presentation and interpretation. Particle size by image analysis. Particle size analysis by sieving. Fluid classification. Interaction between fluids and particles. Sedimentation theory. Sedimentation methods of particle size measurement. Stream scanning methods of particle size measurement. Field scanning methods of particle size measurement. Industrial applications of particle size measurement. Appendix: Manufacturers and suppliers. Author index. Subject index.
Sequential pattern discovery for Intrusion Detection System (2010)

Intrusion Detection System (IDS) is the key technology to ensure the security of dynamic systems. We employ a sequential pattern mining approach to discover significant system call sequences to prevent malicious attacks. To reduce the computing time of generating meaningful rules, we design a weighted suffix tree structure to detect intrusive events on the fly. The experimental results show our method can substantially enhance the accuracy and efficiency of IDS.
Solution Structure and Dynamics of the Plasminogen Kringle 2−AMCHA Complex:  3<sub>1</sub>-Helix in Homologous Domains<sup>,</sup> (1999)

The kringle 2 (K2) module of human plasminogen (Pgn) binds L-lysine and analogous zwitterionic compounds, such as the antifibronolytic agent trans-(aminomethyl)cyclohexanecarboxylic acid (AMCHA). Far-UV CD and NMR spectra reveal little conformational change in K2 upon ligand binding. However, retarded (1)H-(2)H isotope exchange kinetics induced by AMCHA indicate stabilization of the K2 conformation by the ligand. Assessment of secondary structure content from CD spectra yields approximately 26% beta-STRAND, approximately 13% beta-TURN, approximately 15% 3(1)-HELIX, and approximately 6% 3(10)-HELIX. The NMR solution conformation of the K2 domain complexed to AMCHA has been determined [heavy atom rmsd = 0.49 +/- 0.09A (BACKBONE) AND 1.02+/- 0.08 (ALL)]. The K2 molecule has overall dimensions of approximately 34.5A times approximately 33.4A times approximately 22.7A . Analogous with the polypeptide outline of homologous domains, K2 contains three short antiparallel beta-sheets (paired strands 15-16/20-21, 24-25/48-49, and 62-64/72-74) and four defined beta-turns (residues 6-9, 16-19, 53-56, AND 67-70). Consistent with the CD analysis, albeit novel in the context of kringle folding, the NMR structure reveals an unpaired beta-strand structured by residues 30-32, a turn of 3(10)-helix compromising residues 38-41, and a 3(1)-helix for residues 21-24 and 74-79. We also identify alignable 3(1)-helices in previously reported homologous kringle structures. Rather high order parameter S(2) values (<S(2)>= approximately 0.85 +/- 0.04) characterize the K2 backbone dynamics. The lowest flexibility is observed for the two inner loop segments of residues 51-63 AND 63-75 (<S(2)>= approximately 0.86-0.87 +/- 0.03). Overhauser connectivities reveal close hydrophobic contacts of the ligand ring with side chains of Tyr(36), Trp(62), Phe(64), Trp(72), AND Leu(74). In most K2 structures, the N atom of AMCHA places itself approximately 3.9 and 4.4A from the anionic groups of Glu(57) and Asp(55), respectively, while its carboxylate group, H-bonded to the Tyr(36) side chain OH(eta), ion-pairs the Arg(71) guanidinium group. Consistent with the preference of K2 for binding 5-aminopentanoic acid over 6-aminohexanoic acid, the positions of the ionic centers within the K2 binding site approach each other approximately 1A closer relative to what is observed in lysine binding sites of homologous Pgn modules.
Human chorionic gonadotropin (1976)

Human chorionic gonadotropin (hCG) is a glycoprotein hormone that is synthesised by the syncytiotrophoblast cells of the placenta. The hormone is homologous in structure with human luteinising hormone (hLH) and shares with hLH similar qualitative biological actions on the ovary and the testis (Bishop, Nureddin and Ryan, 1976). Whereas the major function of hLH in women is to act synergistically with FSH to produce ovulation and initiate development of the corpus luteum, the function that hCG appears to serve is to convey a hormonal stimulus from the implanted, fertilised ovum to the corpus luteum which calls forth an augmented production of steroid hormones. Its action in the first few days after fertilisation stimulates secretion of oestrogen and progestins by the corpus luteum to prevent the decline in luteal function that normally occurs in an infertile menstrual cycle (Ross et al., 1970; Vande Wiele et al., 1970). hCG is bound at the same receptors as hLH in the ovary (Kammerman et al., 1972; Gospodarowicz, 1973) and the testis (Catt and Dufau, 1973).
Upconverting Tm3+ doped Ba–Y–Yb–F thin film waveguides for visible and ultraviolet light sources (1995)

We report the results of Tm3+ doped Ba–Y–Yb–F thin film planar waveguides in glassy form, which produced red, green, blue, and ultraviolet upconverted luminescence when pumped by infrared radiation at λ=960 nm. The films of nominal composition BaYYbF8 doped with 1% Tm have been deposited with both thermal and e-beam evaporation techniques on substrates of fused silica, Si, and GaAs. Planar waveguiding was demonstrated for the films deposited on fused silica. Optimal deposition conditions with respect to the ability of the films to produce upconverted luminescence and low propagation loss are discussed.
<title>An analysis of methods of atmospheric gas concentration retrieving from diode laser measurements</title> (2004)

Atmospheric gas tunable diode laser (TDL) monitoring scheme is sensitive, local, real-time and portable. The traditional spectrophotometric methods have more performances for gas analysing, but are slow in response in high spectral resolution scheme and depend on influences by different gas species. Local measurements of small atmospheric gas components concentration (CH<sub>4</sub>, CO, etc.) with diode-laser spectrometers are widely used in various of science and technical applications. An inverse task is usuallu solved by the correlation method (using all the measurement wavelengths) or other methods (for example, the method of fitting of the recorded spectrum under modelling). Each of these approaches has restrictions on retrieving connected with the features of measurement methods used in practice. This report, the results of the different inverse methods for retrieving the methane concentration from the data of a diode-laser spectrometer working in the NIR spectral range are analyzed. The methane diode-laser detector has a reference cell (with the known methane concentration) and a cross-flow cell (atmospheric air) as shown in Fig.1. The program of control and data processing of measurements is written with help of LabView software.