gebhart/patrepeval huggingface dataset:
Standardizing DEVS Model Representation (2018)

This chapter focuses on various methods for standardizing Discrete EVent system Specification (DEVS) model representations, which is necessary to enable platform-independent DEVS models to interoperate with each other. The concept relies on defining a generic representation that other tools can use to understand how a model is created, which allows sharing of existing models. The DEVSML is a novel way of writing DEVS models in Extensible Markup Language. DEVSML is built on JAVAML. The chapter presents an overview and the software architecture of DEVS/Service oriented architecture (SOA) and its implementation using web standards. It shows how the DEVS/SOA framework is able to integrate several DEVS and non-DEVS models. The behavior of a DEVS model is limited to atomic components; that is, the body of the transition and output functions as well as the time advance function.
RNAi-mediated downregulation of urokinase plasminogen activator and its receptor in human meningioma cells inhibits tumor invasion and growth (2006)

In recent years, RNA interference (RNAi) has emerged as an effective method to target specific genes for silencing. Several groups are actively exploring the use of small interfering RNA (siRNA) for therapeutic applications to treat cancer. Our previous studies have demonstrated the inhibition of various proteases, including serine proteases, cysteine proteases and matrix metalloproteases, via RNA interference (RNAi) in gliomas. Similar to gliomas, malignant meningiomas also exhibit elevated protease levels in comparison to normal brain and benign meningiomas. Here, we used siRNA to simultaneously target urokinase plasminogen activator (uPA) and its receptor, uPAR. A human CMV promoter-driven mammalian expression vector (pU2) was used to produce hairpin double-stranded RNA (hp RNA) to target uPA and uPAR. As determined by Western blotting and fibrin zymography, pU2 effectively inhibited uPAR protein levels and uPA enzymatic activity in meningioma cells (IOMM-Lee). In vitro studies (Matrigel invasion and spheroid migration) revealed reduced meningioma cell invasion and migration. Intratumoral injections of the plasmid vector expressing siRNA for uPA and uPAR resulted in regression of pre-established, subcutaneous tumors in mice. In addition, in vivo studies of mice injected with pU2-transfected meningioma cells revealed inhibition of intracranial tumor formation. These findings suggest that siRNA can be used as a potent and specific therapeutic tool for the treatment of malignant meningiomas in humans.
Kinetic studies of biological interactions by affinity chromatography (2009)

The rates at which biological interactions occur can provide important information on the mechanism and behavior of such processes in living systems. This paper will discuss how affinity chromatography can be used as a tool to examine the kinetics of biological interactions. This approach, referred to here as biointeraction chromatography, uses a column with an immobilized binding agent to examine the association or dissociation of this agent with other compounds. The use of HPLC-based affinity columns in kinetic studies has received particular attention in recent years. Advantages of using HPLC with affinity chromatography for this purpose include the ability to reuse the same ligand within a column for a large number of experiments, and the good precision and accuracy of this approach. A number of techniques are available for kinetic studies through the use of affinity columns and biointeraction chromatography. These approaches include plate height measurements, peak profiling, peak fitting, split-peak measurements, and peak decay analysis. The general principles for each of these methods are discussed in this paper and some recent applications of these techniques are presented. The advantages and potential limitations of each approach are also considered.
Delayed Luminescence of Biophotons from Plant Leaves (2004)

Delayed luminescence of plant leaves was imaged by a 2-D cooled charge-coupled device. We report the delayed luminescence imaging of normal/injured leaves picked ami the leaves intact. The luminescent intensity was lower in leaf veins, scars and edge cut. The intensity of delayed luminescence from intact leaves was higher than that of picked leaves. These results indirectly support the argument that the delayed luminescence of a photosynthetic system is closely related to the electron transfer process of PSII in the thylakoid membrane.
Laser Impact on Marine Planktonic Diatoms: An Experimental Study Using a Flow Cytometry System (2003)

A flow cytometry system was used to evaluate the impact of pulsed laser irradiations from an Nd:YAG laser on two marine coastal water diatoms, Chaetoceros gracilis and Skeletonema costatum. Three flow speeds, i.e. 9, 18 and 27 ml min-1 and three laser fluences, i.e. 0.025, 0.05 and 0.1 J cm-2 pulse-1 were tested during this study. The reduction in cell density and chlorophyll a (chl a) concentrations were monitored by reference to non-irradiated samples as controls. Upon irradiation, the cell density and the chl a concentrations became reduced significantly compared to the control (one way ANOVA p < 0.001 for the cell density in both the species and p < 0.05 for chl a concentrations in both species). A maximum mortality of 0.77 log10 (about 83%) for C. gracilis and 0.68 log10 (about 78%) for S. costatum was observed at 9 ml min-1 flow speed and 0.1 J cm-2 laser fluence. The maximum reduction observed in the chl a concentration was about 26% (control 0.413 and sample 0.306 mg ml-1) for C. gracilis and 27% (control 0.222 and sample 0.16 mg ml-1) for S. costatum, when the flow rate was 9 ml min-1 and the fluence 0.1 J cm-2. In general, mortality increased with an increase in the laser fluence. The results thus show if the cooling water is laser-irradiated to mitigate biofouling, this could result in significant damage to the planktonic flora of the flowing seawater system, which in turn might reduce algal biofilm formation on industrially important structures. The reduction in the chl a concentration showed that the laser irradiations also could result in a significant reduction in the primary productivity of the cooling water.
Single Image Reflection Removal via Attention Model and SN-GAN (2020)

Single image reflection removal is of great practical importance for various computer vision tasks. Most non-learning methods try to solve this problem through the model-optimization scheme, which fails to produce promising results due to the shortage of suitable priors to model the difference between the reflection layer and the transmission layer. This paper presents an improved generative adversarial network to resolve this problem. First, we suggest that reflection removal is not only a channel-wise separation problem, but also a spatial variational occlusion removal task, which is sensitive to both spatial and channel-wise features. To this end, we integrate the CBAM module into the generator to enhance both spatial and channel-wise feature representation. Second, we consider the reflection layer as a spatial mask with space-relevant reflection intensity information, which can be used to elevate the performance of the discriminator. We then design a novel SNGAN structure with utilize the predicted reflection as a guidance to achieve better adversarial supervision. Specifically, our new generative network has an encoder-decoder structure with skip-connections, where the attention enhancement block is integrated into each skip-connection of the encoder-decoder subnet, and followed by an eight-layer fully convolutional subnet. Furthermore, the SNGAN loss is combined with L2 pixel loss and L1 VGG19 perceptual loss for training. The experimental results with benchmark datasets indicate that our method outperforms several state-of-the-art networks.
Novel Object Recognition for Studying Memory in Mice (2014)

Memory tests are important indexes of the brain functions for rodents behavior assay. Many memory tasks require external forces (e.g. electric shocks) or intrinsic forces (e.g. hunger and thirsty) to trigger the responses. Under those conditions, rodents are under stresses, such as pain, tired, malnutrition or dehydration, which potentially affect the natural neural responses. Novel object recognition is a non-force driving and spontaneous memory test. It is derived from curiosity but easy to be interfered with manipulation factors. In addition to stepwise procedure, the protocol described here emphasizes how to reduce the noise in the novel object recognition., 记忆测试是啮齿动物行为测定的大脑功能的重要指标。 许多记忆任务需要外力（例如电击）或内在力（例如饥饿和渴望）来触发响应。 在这些条件下，啮齿动物处于压力下，例如疼痛，疲劳，营养不良或脱水，这可能影响自然神经反应。 新物体识别是一种非力驱动和自发记忆测试。 它源于好奇心，但容易受到操纵因素的干扰。 除了逐步过程，这里描述的协议强调如何减少新物体识别中的噪声。
Proteomic Analysis of Pancreatic Ductal Adenocarcinoma Cells Reveals Metabolic Alterations (2011)

In this present work, we characterized the proteomes of pancreatic ductal adenocarcinoma (PDAC) cells and normal pancreatic duct cells by mass spectrometry using LTQ-Orbitrap, and identified more than 1200 proteins from each sample. On the basis of spectra count label-free quantification approach, we identified a large number of differentially expressed metabolic enzymes and proteins involved in cytoskeleton, cell adhesion, transport, transcription, translation, and cell proliferation as well. The data demonstrated that metabolic pathways were altered in PDAC, consistent with Warburg effect. Our analysis provides a potentially comprehensive picture of metabolism in PDAC, which may serve as the basis of new diagnostic and treatment of PDAC.
Nitrogen adduction by three coordinate group 10 organometallic cations: platinum is favoured over nickel and palladium (2011)

Previous studies have shown that highly reactive product ions formed by collision-induced dissociation (CID) of precursor ions generated via electrospray can readily react with residual solvent or drying gases, especially in ion trap mass spectrometers. Here we report on the rapid addition of nitrogen to the coordinatively unsaturated organoplatinum cation, [(phen)Pt(CH(3))](+) (phen=1,10-phenanthroline) formed via decarboxylation of the acetate complex [(phen)Pt(O(2) CCH(3))](+). This contrasts with the related coordinatively unsaturated group 10 cations: addition of nitrogen to [(phen)Pd(CH(3))](+) occurs at longer reaction times, whereas addition of nitrogen to [(phen)Ni(CH(3))](+) is virtually non-existent. To better understand these reactions, density functional theory (DFT) calculations were carried out at the B3LYP/SDD6-31+G(d) level of theory to determine the N(2)-binding energies of [(phen)M(CH(3))](+). [(phen)Pt(CH(3))](+) has a higher binding energy to N(2) (1.06 eV) than either [(phen)Ni(CH(3))](+) (0.61 eV) or [(phen)Pd(CH(3))](+) (0.66 eV), consistent with the experimental ease of addition of nitrogen to the coordinatively unsaturated organometallic complexes, [(phen)M(CH(3))](+). Finally, [(phen)M(CH(3))](+) are reactive to other background gases, forming [(phen)M(O(2))](.+) (for M=Ni) in reactions with oxygen and undergoing water addition (for M=Ni, Pd and Pt) and water addition/CH(4) elimination reactions to yield [(phen)M(OH)](+) (for M=Ni and Pt).
G PROTEIN βγ SUBUNITS (1997)

Guanine nucleotide binding (G) proteins relay extracellular signals encoded in light, small molecules, peptides, and proteins to activate or inhibit intracellular enzymes and ion channels. The larger G proteins, made up of G alpha beta gamma heterotrimers, dissociate into G alpha and G beta gamma subunits that separately activate intracellular effector molecules. Only recently has the G beta gamma subunit been recognized as a signal transduction molecule in its own right; G beta gamma is now known to directly regulate as many different protein targets as the G alpha subunit. Recent X-ray crystallography of G alpha, G beta gamma, and G alpha beta gamma subunits will guide the investigation of structure-function relationships.
Improved performance compressed sensing based pulse Doppler radar (2013)

In this paper, we present improved performance compressed sensing (CS) based pulse Doppler radar. CS is an emerging sampling technique which uses very few number of samples to reconstruct original signal. Improvement in performance is achieved using Orthogonal Matching Pursuit (OMP) method with Fourier dictionary at low signal to noise ratio (SNR). OMP is an iterative and fast reconstruction method while Fourier dictionary is used to transform the original signal from time domain to Fourier domain. A significant reduction of sampling frequency by a factor of 360 is achieved at SNR as low as 10 dB, while preserving essential signal information. Low signal reconstruction error leads to good detection performance using Generalized Likelihood Ratio Test (GLRT), a detector based on ratio of probabilities of detection and false alarm. Simulation results demonstrate usefulness of the ideas presented.
The 1,2,4-Trimesityl 1,4-Diketones and Related Compounds, Including the Stereoisomeric Mono and Dienols1 (1940)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe 1,2,4-Trimesityl 1,4-Diketones and Related Compounds, Including the Stereoisomeric Mono and Dienols1Robert E. Lutz and Charles J. KiblerCite this: J. Am. Chem. Soc. 1940, 62, 2, 360–372Publication Date (Print):February 1, 1940Publication History Published online1 May 2002Published inissue 1 February 1940https://pubs.acs.org/doi/10.1021/ja01859a039https://doi.org/10.1021/ja01859a039research-articleACS PublicationsRequest reuse permissionsArticle Views54Altmetric-Citations5LEARN 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
Glucose control in diabetes during home confinement for the first pandemic wave of COVID-19: a meta-analysis of observational studies (2021)

Lockdown showed no significant detrimental effect on HbA1c in either T1DM or T2DM. Conversely, home confinement led to a reduction in mean glucose and glucose variability in T1DM, although with a high heterogeneity of results.
Correction: Aberrant DNA Methylation of Matrix Remodeling and Cell Adhesion Related Genes in Pterygium (2011)

Background: Pterygium is a common ocular surface disease characterized by abnormal epithelial and fibrovascular proliferation, invasion, and matrix remodeling. This lesion, which migrates from the periphery to the center of the cornea, impairs vision and causes considerable irritation. The mechanism of pterygium formation remains ambiguous, and current treatment is solely surgical excision, with a significant risk of recurrence after surgery. Here, we investigate the role of methylation in DNA sequences that regulate matrix remodeling and cell adhesion in pterygium formation.
Efficient Closed-Loop Schemes for MIMO WLAN (2005)

The existing wireless local area network (WLAN) systems defined by the IEEE 802.11a standard are single-input single-output (SISO) orthogonal frequency-division multiplexing (OFDM) based systems and can support data rates up to 54 Mbps. We consider deploying two transmit and two receive antennas in a WLAN system and double the maximum data rate to 108 Mbps. Applying our recent multiple-input multiple-output (MIMO) transceiver designs, including the geometric mean decomposition (GMD) and the uniform channel decomposition (UCD) schemes, we propose a simple and efficient closed-loop MIMO-OFDM design for much improved performance compared to its open-loop counterpart. The extra cost is to feed back unitary precoders, which can be made very moderate with careful precoder quantization.
Report on the 25th Australasian Document Computing Symposium (ADCS 2021) (2022)

The 25th Australasian Document Computing Symposium (ADCS 2021) took place as a virtual seminar series from December 2021 through to February 2022, co-hosted by the University of Melbourne and RMIT University, and held in cooperation with ACM SIGIR. Five sessions were dedicated to presenting and discussing nine accepted research papers, book-ended by opening and closing keynotes. The virtual nature of ADCS 2021, coupled with free registration, attracted a broader audience than usual, with 110 registrants from 16 countries including those outside of Australia and New Zealand. Date: 9 December, 2021 -- 24 February, 2022. Website: http://adcs-conference.org/2021.
RAS Mutations Affect Tumor Necrosis Factor–Induced Apoptosis in Colon Carcinoma Cells via ERK-Modulatory Negative and Positive Feedback Circuits Along with Non-ERK Pathway Effects (2009)

More than 40% of colon cancers have a mutation in K-RAS or N-RAS, GTPases that operate as central hubs for multiple key signaling pathways within the cell. Utilizing an isogenic panel of colon carcinoma cells with K-RAS or N-RAS variations, we observed differences in tumor necrosis factor-α (TNFα)–induced apoptosis. When the dynamics of phosphorylated ERK response to TNFα were examined, K-RAS mutant cells showed lower activation whereas N-RAS mutant cells exhibited prolonged duration. These divergent trends were partially explained by differential induction of two ERK-modulatory circuits: negative feedback mediated by dual-specificity phosphatase 5 and positive feedback by autocrine transforming growth factor-α. Moreover, in the various RAS mutant colon carcinoma lines, the transforming growth factor-α autocrine loop differentially elicited a further downstream chemokine (CXCL1/CXCL8) autocrine loop, with the two loops having opposite effects on apoptosis. Although the apoptotic responses of the RAS mutant panel to TNFα treatment showed significant dependence on the respective phosphorylated ERK dynamics, successful prediction across the various cell lines required contextual information concerning additional pathways including IKK and p38. A quantitative computational model based on weighted linear combinations of these pathway activities successfully predicted not only the spectrum of cell death responses but also the corresponding chemokine production responses. Our findings indicate that diverse RAS mutations yield differential cell behavioral responses to inflammatory cytokine exposure by means of (a) differential effects on ERK activity via multiple feedback circuit mechanisms, and (b) differential effects on other key signaling pathways contextually modulating ERK-related dependence.
Synthesis and Characterization of Composite Nucleic Acids Containing 2‵,5‵-Oligoriboadenylate Linked to Antisense DNA (1996)

Composite nucleic acids, known as 2-5A antisense chimeras, cause the 2-5A-dependent ribonuclease (RNase L) to catalyze the specific cleavage of RNA in cell free systems and in intact cells. Such 2-5A antisense chimeras are 5'-monophosphorylated, 2,'5'-linked oligoadenylates covalently attached to antisense 3',5'-oligodeoxyribonucleotides by means of a linker containing two residues of 1,4-butanediol phosphate. Here we report a fully automated synthesis of 2-5A antisense chimeras on a solid support using phosphoramidite methodology with specific coupling time modifications and their subsequent purification by reverse-phase ion-pair and anion exchange HPLC. Purified 2-5A antisense chimeras were characterized by [1H]NMR and [31P]NMR, MALDIMS, and capillary gel electrophoresis. The synthetic 2',5'-linked oligoadenylate showed no phosphodiester isomerization to 3',5' during or after synthesis. In addition, we have developed facile methodologies to characterize the chimeras using digestion with various hydrolytic enzymes including snake venom phosphodiesterase I and nuclease P1. Finally, Maxam-Gilbert chemical sequencing protocols have been developed to confirm the entire sequence of these chimeric oligonucleotides.
Relativistic free electrons in an intense laser field: Experimental observations of optically-induced deflection of an ultrashort electron beam (2005)

We present experimental evidence of the deflection of electrons via the transfer of longitudinal momentum from an intense laser beam. The electrons are in the form of a narrow divergence beam created through self-modulated laser-wakefield acceleration with energies up to 6 MeV and an expected temporal duration of about 1 ps. A second laser pulse intersects the electron beam at an angle of 135&deg; causing part of the beam to be deflected. The deflection is detected by using the scintillating plastic LANEX that provides spatial information of the electron beam. By taking column-wise and row-wise summations of the signal from the LANEX we examine how the beam profile changes with a change in the delay between the electron pulse and the secondary laser pulse. By using a set of metrics, we show how the beam is deflected and distorted. By measuring the time elapsed through the change in the electron beam, an estimate of the electron beam duration is given as less than 2 picoseconds. Inside of the 2 ps window, we show that different periods of deflection based on electron beam temperature can be explained by the laser sampling portions of the electron beam with different temperatures. It is also demonstrated in both theory and experiment that this process has no dependence on the polarization direction of the laser field. This physical process can be altered by changing the angle of incidence and laser intensity to examine deflection of different ranges of electron energies. This provides an important tool for the temporal measurement of ultrafast electron beams that can provide electron energy information.