gebhart/patrepeval huggingface dataset:
Routing, Code, and Spectrum Assignment, Subcarrier Spacing, and Filter Configuration in Elastic Optical Networks [Invited] (2015)

In elastic optical networks (EONs), the modulation format can be configured to guarantee the required optical reach with efficient spectrum utilization. For this reason, the literature related to EONs has treated the problem of routing and spectrum assignment together with the problem of modulation format assignment. Recently, in addition to modulation format, code adaptation has also been successfully demonstrated to provide adequate spectrum utilization given a target optical reach. This paper presents the concept of routing, code, and spectrum assignment (RCSA) for EONs. We propose the optimization of multiple transmission parameters including code, subcarrier spacing, and filters&#x2019; passband to avoid detrimental filtering effects. Measurements are carried out in an EON testbed to identify the relation between transmission parameters and the number of traversed filters and optical reach. Then, the measurements are used as inputs in simulations to test RCSA. The simulations show that code adaptation reduces blocking probability with respect to format adaptation. Another interesting result shows that the use of several possibilities for the transmission parameter setting may induce high spectrum fragmentation.
Tunable morphology and resistivity of ternary polymer composites of carbon black/low density polyethylene/ethylene‐vinyl acetate with carbon blacks having different surface properties (2021)

Abstract Medium to extra‐high voltage electrical cables typically comprise a semiconductive polymer composite layer to homogenize the electromagnetic field through the cables. The semiconductive layers usually contain a high content of carbon black (CB) for reduced electrical resistivity. In this study, we found that both the morphology and resistivity of a ternary polymer composite of CB/low density polyethylene (LDPE)/ethylene‐vinyl acetate (EVA) depend on CBs used and the order of addition. Three types of CB were investigated. CB‐A, which has the lowest surface energy and the most uniform surface energy profile, exhibits a strong affinity to LDPE and always segregates in the LDPE phase whether it is first added in the LDPE phase or the EVA phase. CB‐B and CB‐C, which have higher and less homogeneous surface energies, distribute differently with different orders of addition. We observe a significant reduction in the percolation threshold of CB‐A in the CB/LDPE/EVA composite, but not with CB‐B or CB‐C. Adding CB‐A in the LDPE phase first results in substantially lower resistivity than adding it in the EVA phase first, whereas adding CB‐B or CB‐C in the LDPE phase first results in higher resistivity than adding them in the EVA phase first.
Highly Pathogenic Avian Influenza Virus A (H7N3) in Domestic Poultry, Saskatchewan, Canada, 2007 (2009)

Epidemiologic, serologic, and molecular phylogenetic methods were used to investigate an outbreak of highly pathogenic avian influenza on a broiler breeding farm in Saskatchewan, Canada. Results, coupled with data from influenza A virus surveillance of migratory waterfowl in Canada, implicated wild birds as the most probable source of the low pathogenicity precursor virus.
Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis (2002)

Gene expression analyses based on complex hybridization measurements have increased rapidly in recent years and have given rise to a huge amount of bioinformatic tools such as image analyses and cluster analyses. However, the amount of work done to integrate and evaluate these tools and the corresponding experimental procedures is not high. Although complex hybridization experiments are based on a data production pipeline that incorporates a significant amount of error parameters, the evaluation of these parameters has not been studied yet in sufficient detail. In this paper we present simulation studies on several error parameters arising in complex hybridization experiments. A general tool was developed that allows the design of exactly defined hybridization data incorporating, for example, variations of spot shapes, spot positions and local and global background noise. The simulation environment was used to judge the influence of these parameters on subsequent data analysis, for example image analysis and the detection of differentially expressed genes. As a guide for simulating expression data real experimental data were used and model parameters were adapted to these data. Our results show how measurement error can be balanced by the analysis tools. We describe an implemented model for the simulation of DNA-array experiments. This tool was used to judge the influence of critical parameters on the subsequent image analysis and differential expression analysis. Furthermore the tool can be used to guide future experiments and to improve performance by better experimental design. Series of simulated images varying specific parameters can be downloaded from our web-site: http://www.molgen.mpg.de/~lh_bioinf/projects/simulation/biotech/
Aryl Fluorosulfate Based Inhibitors That Covalently Target the SIRT5 Lysine Deacylase** (2022)

Abstract The sirtuin enzymes are a family of lysine deacylases that regulate gene transcription and metabolism. Sirtuin 5 (SIRT5) hydrolyzes malonyl, succinyl, and glutaryl ϵ‐ N ‐carboxyacyllysine posttranslational modifications and has recently emerged as a vulnerability in certain cancers. However, chemical probes to illuminate its potential as a pharmacological target have been lacking. Here we report the harnessing of aryl fluorosulfate‐based electrophiles as an avenue to furnish covalent inhibitors that target SIRT5. Alkyne‐tagged affinity‐labeling agents recognize and capture overexpressed SIRT5 in cultured HEK293T cells and can label SIRT5 in the hearts of mice upon intravenous injection of the compound. This work demonstrates the utility of aryl fluorosulfate electrophiles for targeting of SIRT5 and suggests this as a means for the development of potential covalent drug candidates. It is our hope that these results will serve as inspiration for future studies investigating SIRT5 and general sirtuin biology in the mitochondria.
Preclinical Evaluation of the Oncolytic Vaccinia Virus TG6002 by Translational Research on Canine Breast Cancer (2020)

Oncolytic virotherapy is a promising therapeutic approach for the treatment of cancer. TG6002 is a recombinant oncolytic vaccinia virus deleted in the thymidine kinase and ribonucleotide reductase genes and armed with the suicide gene <i>FCU1</i>, which encodes a bifunctional chimeric protein that efficiently catalyzes the direct conversion of the nontoxic 5-fluorocytosine into the toxic metabolite 5-fluorouracil. In translational research, canine tumors and especially mammary cancers are relevant surrogates for human cancers and can be used as preclinical models. Here, we report that TG6002 is able to replicate in canine tumor cell lines and is oncolytic in such cells cultured in 2D or 3D as well as canine mammary tumor explants. Furthermore, intratumoral injections of TG6002 lead to inhibition of the proliferation of canine tumor cells grafted into mice. 5-fluorocytosine treatment of mice significantly improves the anti-tumoral activity of TG6002 infection, a finding that can be correlated with its conversion into 5-fluorouracil within infected fresh canine tumor biopsies. In conclusion, our study suggests that TG6002 associated with 5-fluorocytosine is a promising therapy for human and canine cancers.
Some like it, some do not: behavioral responses and central processing of olfactory–trigeminal mixture perception (2020)

Exploring the potential of eucalyptol as a masking agent for aversive odors, we found that eucalyptol masks the olfactory but not the trigeminal sensation of ammonia in a previous study. Here, we further investigate the processing of a mixture consisting of eucalyptol and ammonia, two olfactory-trigeminal stimuli. We presented the two pure odors and a mixture thereof to 33 healthy participants. The nostrils were stimulated alternately (monorhinal application). We analyzed the behavioral ratings (intensity and pleasantness) and functional brain images. First, we replicated our previous finding that, within the mixture, the eucalyptol component suppressed the olfactory intensity of the ammonia component. Second, mixture pleasantness was rated differently by participants depending on which component dominated their mixture perception. Approximately half of the volunteers rated the eucalyptol component as more intense and evaluated the mixture as pleasant (pleasant group). The other half rated the ammonia component as more intense and evaluated the mixture as unpleasant (unpleasant group). Third, these individual differences were also found in functional imaging data. Contrasting the mixture either to eucalyptol or to both single odors, neural activation was found in the unpleasant group only. Activation in the anterior insula and SII was interpreted as evidence for an attentional shift towards the potentially threatening mixture component ammonia and for trigeminal enhancement. In addition to insula and SII, further regions of the pain matrix were involved when assessing all participant responses to the mixture. Both a painful sensation and an attentional shift towards the unpleasant mixture component complicates the development of an efficient mask because a pleasant perception is an important requirement for malodor coverage.
Modeling Biological Activities of Nanoparticles (2012)

Products are increasingly incorporating nanomaterials, but we have a poor understanding of their adverse effects. To assess risk, regulatory authorities need more experimental testing of nanoparticles. Computational models play a complementary role in allowing rapid prediction of potential toxicities of new and modified nanomaterials. We generated quantitative, predictive models of cellular uptake and apoptosis induced by nanoparticles for several cell types. We illustrate the potential of computational methods to make a contribution to nanosafety.
Atomistic Modeling of Cross-linked Epoxy Polymer (2011)

Molecular Dynamics simulations are used to study crosslinking of an epoxy polymer. OPLS force field parameters are used for modeling a 2:1 stoichiometric mixture of epoxy resin and the crosslinking agent. The model has 17,928 united atoms and a static crosslinking method is utilized along with molecular minimization and molecular dynamics techniques to achieve three different crosslink densities. The crosslinked models can be used for understanding various phenomenon occurring in crosslinked epoxy resins at the atomic scale. Glass-transition temperature ranges and thermal expansion coefficients of three differently crosslinked samples are predicted using the models. These models will be used for studying aging behavior at the atomic level in epoxy materials and understanding the influence of aging on mechanical properties. Copyright © 2011 by Gregory M. Odegard.
Noninvasive and Highly Multiplexed Five-Color Tumor Imaging of Multicore Near-Infrared Resonant Surface-Enhanced Raman Nanoparticles In Vivo (2021)

In vivo multiplexed imaging aims for noninvasive monitoring of tumors with multiple channels without excision of the tissue. While most of the preclinical imaging has provided a number of multiplexing channels up to three, Raman imaging with surface-enhanced Raman scattering (SERS) nanoparticles was suggested to offer higher multiplexing capability originating from their narrow spectral width. However, in vivo multiplexed SERS imaging is still in its infancy for multichannel visualization of tumors, which require both sufficient multiplicity and high sensitivity concurrently. Here we create multispectral palettes of gold multicore-near-infrared (NIR) resonant Raman dyes-silica shell SERS (NIR-SERRS) nanoparticle oligomers and demonstrate noninvasive and five-plex SERS imaging of the nanoparticle accumulation in tumors of living mice. We perform the five-plex ratiometric imaging of tumors by varying the administered ratio of the nanoparticles, which simulates the detection of multiple biomarkers with different expression levels in the tumor environment. Furthermore, since this method does not require the excision of tumor tissues at the imaging condition, we perform noninvasive and longitudinal imaging of the five-color nanoparticles in the tumors, which is not feasible with current ex vivo multiplexed tissue analysis platforms. Our work surpasses the multiplicity limit of previous preclinical tumor imaging methods while keeping enough sensitivity for tumor-targeted in vivo imaging and could enable the noninvasive assessment of multiple biological targets within the tumor microenvironment in living subjects.
Strategic issues in sensors and smart structures (2005)

Rapid advances have been made in recent years in the development of sensor-based technologies, which greatly expand the range and effectiveness of this application to civil, mechanical, and aerospace engineering systems. This paper attempts to overview the research conducted in recent years and the state-of-the-art. Key research topics are presented, and future strategic directions are suggested. Emerging needs for engineering application in civil infrastructure and mechatronics systems, and natural and artificial disaster mitigation are described. A review of NSF's sponsored research program activities in dynamic systems, modeling, sensing and control is also given. Strategic issues in advancing sensors and smart structural technologies and their applications are discussed. Copyright © 2005 John Wiley & Sons, Ltd.
Measurement of 100 B. anthracis Ames spores within 15 minutes by SERS at the US Army Edgewood Chemical Biological Ctr. (2014)

Since the distribution of Bacillus anthracis-Ames spores through the US Postal System, there has been a persistent fear that biological warfare agents will be used by terrorists against our military abroad and our civilians at home. While there has been substantial effort since the anthrax attack of 2001 to develop analyzers to detect this and other biological warfare agents, the analyzers remain either too slow, lack sensitivity, produce high false-positive rates, or cannot be fielded. In an effort to overcome these limitations we have been developing a surface-enhanced Raman spectroscopy system. Here we describe the use of silver nanoparticles functionalized with a short peptide to selectively capture Bacillus anthracis spores and produce SER scattering. Specifically, measurements of 100 B. anthracis-Ames spores/mL in ~25 minutes performed at the US Army’s Edgewood Chemical Biological Center are presented. The measurements provide a basis for the development of systems that can detect spores collected from the air or water supplies with the potential of saving lives during a biological warfare attack.
Authors’ Reply (2021)

In their letter, Gevers and colleagues[1][1] highlight concerns that remdesivir and its metabolite, GS-441524, may carry a risk of toxicity to the renal tubular epithelium, and that risks may be more considerable for patients with predialysis CKD. We agree that the potential risks of remdesivir and
Large scale multi-robot coordination under network and geographical constraints (2009)

This paper addresses the problem of coordinating great numbers of vehicles in large geographical areas under network connective constraints. We leverage previous work on hierarchical potential fields to create advanced skills in multi-robot systems. Skills group together various field objectives to accomplish the performance requirements in response to highlevel commands. Our framework calculates trajectories that comply with priority constraints while optimizing the desired task objectives in their null spaces. We use a model-based dynamics approach that provides a direct map from field objectives to vehicle accelerations, yielding smooth and accurate trajectory generation. We develop a real-time software system that implements the proposed methods and simulates the coordinated behaviors in a 3D graphical environment. To validate the methodology, we simulate a large exploration task and demonstrate that we can effectively enforce the required constraints while optimizing the exploration goals.
Preferred Conformations of C-Glycosides. 14. Synthesis and Conformational Analysis of Carbon Analogs of the Blood Group Determinant H-Type II (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreferred Conformations of C-Glycosides. 14. Synthesis and Conformational Analysis of Carbon Analogs of the Blood Group Determinant H-Type IIAlexander Wei, Arnaud Haudrechy, Catharine Audin, Hyuk-Sang Jun, Nathalie Haudrechy-Bretel, and Yoshito KishiCite this: J. Org. Chem. 1995, 60, 7, 2160–2169Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/jo00112a040https://doi.org/10.1021/jo00112a040research-articleACS PublicationsRequest reuse permissionsArticle Views445Altmetric-Citations64LEARN 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 (3)»Supporting Information Supporting Information Get e-Alerts
27 GHz Silicon-Contacted Waveguide-Coupled Ge/Si Avalanche Photodiode (2020)

We report a silicon-contacted Ge/Si avalanche photodiode with RF gain of 11 and a bandwidth of 27 GHz at -12 V operating at 1310 nm. The device is fabricated in an established Si photonics platform without additional process complexity and contacts only on Si. Wafer-scale performance data are presented confirming the reproducibility and the manufacturability of the device. Wide open eye diagrams are demonstrated for 25, 40, and 50 Gbps data-rates. The demonstration of such avalanche photodiode shows great potential for improving optical link margins for optical transceivers operating at 400 Gb/s and beyond.
Hypoxia-Selective Antitumor Agents. 14. Synthesis and Hypoxic Cell Cytotoxicity of Regioisomers of the Hypoxia-Selective Cytotoxin 5-[N,N-Bis(2-chloroethyl)amino]-2,4-dinitrobenzamide (1996)

A series of regioisomers of the novel hypoxia-selective cytotoxin (HSC) 5-[N,N-bis(2-chloroethyl)-amino]-2,4-dinitrobenzamide (2a) have been prepared by displacement of the chloro group from methyl chlorodinitrobenzoates or the corresponding carboxamides with diethanolamine, followed by dimesylation and mesylate displacement with LiCl. The compounds fall into two classes, where the two nitro groups have either a meta or an ortho (or para) disposition to each other. The four meta derivatives had one-electron reduction potentials in the range -340 to -375 mV, similar to that of the known isomer 2a, while the other isomers had much higher values (-262 to -285 mV). The meta derivatives were much less cytotoxic to AA8 cells under aerobic conditions (IC50s from 75 to 470 microM) than were the other compounds (IC50s from 1.6 to 20 microM). However, the ratios of IC50s of the compounds in repair-proficient (AA8) and repair-deficient (UV4) cell lines varied, indicating differing contributions of DNA alkylation to aerobic toxicity between the isomers, with no clear relationship between this and nitro group disposition. The hypoxic selectivities of the (dimethylamino)ethylcarboxamide analogues for each isomer were determined by clonogenic assay against both AA8 and UV4 cells. With one exception, the meta derivatives showed excellent hypoxic selectivities (ca. 45-115-fold) against UV4 cells, while the ortho or para isomers had little selectivity (ca. 2-7-fold). A possible reason may be that the latter compounds, with higher reduction potentials, undergo rapid bioreduction even under aerobic conditions. None showed hypoxic selectivities greater than 2-3-fold against AA8 cells. The 3-[N,N-bis(2-chloroethyl)amino]-2,6-dinitrobenzamide isomer (5b), which showed the highest hypoxic selectivity for UV4 cells in this series, was active against both hypoxic and aerobic cells in KHT tumors in mice at well-tolerated doses, and showed superior in vivo activity to the previously studied 2,4-dinitro isomer 2b.
Molecular ties between the cell cycle and differentiation in embryonic stem cells (2014)

Significance The role of the cell cycle as an inhibitor of the late stages of cellular differentiation is well known, but in early embryonic development its role is mysterious. Normally, embryonic stem (ES) cells proliferate quickly during differentiation and do not differentiate simply by cell cycle slowing. In this paper, it is shown that the role of the cell cycle in terminal stages of differentiation can be adapted for and extended into ES cells. Methods aimed at inhibiting the cell cycle drive a rapid, condensed differentiation to terminally differentiated cells, demonstrating that the cell cycle is a principle rate-limiting step of differentiation throughout early and late stages. This is beneficial as well for accelerating differentiation in ES cell applications.
Imagining the American People: Strategies for Building Political Community (2003)

This study examined how the American electorate has been described by political campaigners, the mass media, and voters themselves between 1948 and 2000. Using a large (digitized) database of campaign addresses, news stories, and letters to the editor, the authors isolated 2,924 uses of the phrase, “the American people.” By examining these phrases for descriptions of the roles, actions, qualities, and circumstances of the people, and by noting their time orientation and the forces aligned against the electorate, the authors present a picture of the people as described by three different political voices. The article concludes by arguing that examining a people's self-conception provides a fresh way of understanding their most basic thoughts and values.
Compression of Zr2InC to 52GPa (2004)

Using a synchrotron-radiation source and a diamond-anvil cell, we measured the pressure dependence of the lattice parameters of a polycrystalline Zr2InC sample. Up to a pressure of 52GPa, no phase transformations were observed. As observed in Ti3SiC2 and Ti3Si0.5Ge0.5C2, the compressibility of Zr2InC along the c axis was greater than along the a axis. The bulk modulus is 127±5GPa, with a pressure derivative of 4.25±0.3; the former is in excellent agreement with our ab initio calculations (130.9GPa). The a(3.367Å) and c(15.100Å) parameters from the ab initio calculations are also slightly larger than those measured here, viz., 3.35 and 14.91Å. Surprisingly, a hysteresis was observed in the a-lattice parameters; they were higher upon unloading than loading. The reason for this hysteresis is not clear at this time.
EFFECTS OF EXPLOSIVE BRAIN DEATH ON CYTOKINE ACTIVATION OF PERIPHERAL ORGANS IN THE RAT1 (1998)

Activation of peripheral organs following explosive brain death may be caused by various interrelated events, including the effects of massive acute central injury, hypotension, and circulating factors. Almost complete suppression of these changes could be produced by biological agents. Such interventions, if reproducible in humans, could improve the quality of organs from "marginal" donors, broadening the criteria for donor acceptance.