gebhart/patrepeval huggingface dataset:
Key interactions with deazariboflavin cofactor for light-driven energy transfer in Xenopus (6–4) photolyase (2021)

Photolyases are flavoenzymes responsible for light-driven repair of carcinogenic crosslinks formed in DNA by UV exposure. They possess two non-covalently bound chromophores: flavin adenine dinucleotide (FAD) as a catalytic center and an auxiliary antenna chromophore that harvests photons and transfers solar energy to the catalytic center. Although the energy transfer reaction has been characterized by time-resolved spectroscopy, it is strikingly important to understand how well natural biological systems organize the chromophores for the efficient energy transfer. Here, we comprehensively characterized the binding of 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF) to Xenopus (6-4) photolyase. In silico simulations indicated that a hydrophobic amino acid residue located at the entrance of the binding site dominates translocation of a loop upon binding of 8-HDF, and a mutation of this residue caused dysfunction of the efficient energy transfer in the DNA repair reaction. Mutational analyses of the protein combined with modification of the chromophore suggested that Coulombic interactions between positively charged residues in the protein and the phenoxide moiety in 8-HDF play a key role in accommodation of 8-HDF in the proper direction. This study provides a clear evidence that Xenopus (6-4) photolyase can utilize 8-HDF as the light-harvesting chromophore. The obtained new insights into binding of the natural antenna molecule will be helpful for the development of artificial light-harvesting chromophores and future characterization of the energy transfer in (6-4) photolyase by spectroscopic studies.
Age as a risk factor in colonoscopy: fact versus fiction. (1988)

Age has been assumed to be an independent risk factor in patients undergoing colonoscopy. However, this has never been specifically studied. We evaluated 302 patients 65 yr old or older, to determine the incidence of complications. We found that the risk is comparable to that of the heterogeneous patient population previously reported, except for a slightly increased incidence of delayed bleeding subsequent to polypectomy. In addition, the presence of cardiac, pulmonary, liver, or kidney disease was not found to be associated with an increased incidence of complications. Neither was there an increased risk of complications in patients undergoing colonoscopy, who had previously undergone abdominal or pelvic surgery. In summary, older patients experience the same risks as younger patients, except for post-polypectomy delayed bleeding, which may be related to atherosclerosis of the blood vessels, and appears to be more common in elderly patients.
Accumulative density (2005)

In this paper we study a notion of density for subsets of R<sup>2</sup> called accumulative density, which is similar to the density for sequences in the unit disc developed by Seip. Along the way we derive some new properties of Beurling density. Finally, we prove that the accumulative density and the Beurling density coincide.
Large-area visually augmented navigation for autonomous underwater vehicles (2005)

Submitted to the Joint Program in Applied Ocean Science & Engineering in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2005
Evidence for circulatory benefits of resveratrol in humans (2013)

Impairments of endothelial function, which can be assessed noninvasively by flow-mediated dilation (FMD) of the brachial artery, contribute to the development of cardiovascular disease. Associations between FMD and cognition suggest a vascular component in the loss of cognitive function. Certain vasoactive nutrients that have been shown to improve FMD may also have the potential to enhance cerebral perfusion and cognition. Preclinical studies show that trans-resveratrol can enhance nitric oxide bioavailability, thereby increasing endothelium-dependent vasodilation. We have now shown that acute administration of resveratrol elicits dose-dependent increases of FMD with greater potency than other vasoactive nutrients and that this benefit is sustained following regular consumption. We describe the potential implications of this vasodilator benefit of resveratrol and its role in enhancing cerebrovascular and cognitive functions.
La gouverrnance, un nouveau paradigme étatique ? (2003)

International audience
A virally inactivated platelet‐derived growth factor/vascular endothelial growth factor concentrate fractionated from human platelets (2010)

Human PC can be fractionated into a purified, virally inactivated PDGF and VEGF concentrate, opening perspectives for the development of a new range of blood products for clinical use and cell therapy procedures.
An effective blind watermark algorithm based on DCT (2008)

Using the information hiding technology is to be more and more important in the multimedia network transmission, but what is used in the commercial image copyright protection mainly is the digital watermark technology. Realizing the digital watermark can use the digital watermark technology based on picturepsilas transform, which does DCT transform to the picture. It converts the host image block to the matrix, selects the partial frequency component from the transformed matrix DCT coefficient, converts the watermark to the matrix, then embeds the watermark in the host image, which obtain watermark image by IDCT transform. Extracting the watermark use the reverse process of embedding watermark.
Using MACS to Identify Peaks from ChIP‐Seq Data (2011)

Model-based Analysis of ChIP-Seq (MACS) is a command-line tool designed by X. Shirley Liu and colleagues to analyze data generated by ChIP-Seq experiments in eukaryotes, especially mammals. MACS can be used to identify transcription factor binding sites and histone modification-enriched regions if the ChIP-Seq data, with or without control samples, are given. This unit describes two basic protocols that provide detailed information on how to use MACS to identify either the binding sites of a transcription factor or the enriched regions of a histone modification with broad peaks. Furthermore, the basic ideas for the MACS algorithm and its appropriate usage are discussed.
Hyperthermia-triggered release of hypoxic cell radiosensitizers from temperature-sensitive liposomes improves radiotherapy efficacy in vitro (2019)

Hypoxia is a characteristic feature of solid tumors and an important cause of resistance to radiotherapy. Hypoxic cell radiosensitizers have been shown to increase radiotherapy efficacy, but dose-limiting side effects prevent their widespread use in the clinic. We propose the encapsulation of hypoxic cell radiosensitizers in temperature-sensitive liposomes (TSL) to target the radiosensitizers specifically to tumors and to avoid unwanted accumulation in healthy tissues. The main objective of the present study is to develop and characterize TSL loaded with the radiosensitizer pimonidazole (PMZ) and to evaluate the in vitro efficacy of free PMZ and PMZ encapsulated in TSL in combination with hyperthermia and radiotherapy. PMZ was actively loaded into TSL at different drug/lipid ratios, and the physicochemical characteristics and the stability of the resulting TSL-PMZ were evaluated. PMZ release was determined at 37 °C and 42 °C in HEPES buffer saline and fetal bovine serum. The concentration-dependent radiosensitizing effect of PMZ was investigated by exposing FaDu cells to different PMZ concentrations under hypoxic conditions followed by exposure to ionizing irradiation. The efficacy of TSL-PMZ in combination with hyperthermia and radiotherapy was determined in vitro, assessing cell survival and DNA damage by means of the clonogenic assay and histone H2AX phosphorylation, respectively. All TSL-PMZ formulations showed high encapsulation efficiencies and were stable for 30 d upon storage at 4 °C and 20 °C. Fast PMZ release was observed at 42 °C, regardless of the drug/lipid ratio. Increasing the PMZ concentration significantly enhanced the effect of ionizing irradiation. Pre-heated TSL-PMZ in combination with radiotherapy caused a 14.3-fold increase in cell death as compared to radiotherapy treatment alone. In conclusion, our results indicate that TSL-PMZ in combination with hyperthermia can assist in improving the efficacy of radiotherapy under hypoxic conditions.
Synthesis of the CDE ring system of the ginkgolides (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of the CDE ring system of the ginkgolidesEdwin B. Villhauer and Robert C. AndersonCite this: J. Org. Chem. 1987, 52, 7, 1186–1189Publication Date (Print):April 1, 1987Publication History Published online1 May 2002Published inissue 1 April 1987https://doi.org/10.1021/jo00383a002RIGHTS & PERMISSIONSArticle Views277Altmetric-Citations15LEARN 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 InReddit PDF (625 KB) Get e-Alerts Get e-Alerts
HHT based on the LS-SVM and its application in the voltage flicker and harmonic detection of microgrid (2011)

Microgrid contains many distributed resources (DR), such as photovoltaic, wind power, and these DR which have the characteristics of random, volatility and intermittent, will cause voltage fluctuation and flicker, therefore, harmonic pollution will be produced from power electronic devices in DR. Hilbert-Huang Transform (HHT) can distill these disturbing signals automatically and time-frequency spectrum can be obtained. However, in the application of this method there are serious end effects that mixed mode phenomenon will appear, affecting the detecting results. In order to suppress the end effects, a novel HHT based on Least Squares Support Vector Machine (LS-SVM) is applied to analyze voltage flicker and harmonic in microgrid. The results show that the improved HHT method is effective to control the end effects and the time, frequency and amplitude of disturbing signal will be detected quickly and effectively.
Leveraging the Graph Structure of Neural Network Training Dynamics (2022)

Understanding the training dynamics of deep neural networks (DNNs) is important as it can lead to improved training efficiency and task performance. Recent works have demonstrated that representing the wirings of neurons in feedforward DNNs as graphs is an effective strategy for understanding how architectural choices can affect performance. However, these approaches fail to model training dynamics since a single, static graph cannot capture how DNNs change over the course of training. Thus, in this work, we propose a compact, expressive temporal graph framework that effectively captures the dynamics of many workhorse architectures in computer vision. Specifically, our framework extracts an informative summary of graph properties (e.g., degree, eigenvector centrality) over a sequence of DNN graphs obtained during training. We demonstrate that the proposed framework captures useful dynamics by accurately predicting trained, task performance when using a summary over early training epochs (<5) across four different architectures and two image datasets. Moreover, by using a novel, highly-scalable DNN graph representation, we further demonstrate that the proposed framework captures generalizable dynamics as summaries extracted from smaller-width networks are effective when evaluated on larger widths.
Effect of frequency difference on sensitivity of beats perception (2011)

Two vibrations with slightly different frequencies induce the beats phenomenon. In tactile perception, when two pins of different frequencies stimulate the fingertips, an individual perceives a beats caused by a summation stimulus of the two vibrations. The present study demonstrates experimentally that humans can perceive another vibration based on the beats phenomenon when two tactile stimuli with slightly different frequencies are stimulated on the finger pad with a small contactor in different locations at the same time. Moreover, we examined the amplitude of the detection threshold to be able to perceive beats phenomenon on the index finger with 5 carrier frequency (63.1, 100, 158.5, 251.2, and 398.1 Hz) and 4 beats frequency (2.5, 3.98, 6.31, and 10 Hz) when two stimuli 1 mm distance apart are vibrated at a slightly different frequency. From the experiments, it is concluded that the amplitude threshold to be able to perceive beats decreases as the standard frequency increases under 398 Hz. Furthermore, from comparing the absolute detection threshold and beats detection threshold, as the carrier frequency increases, the required amplitude at two pins for the detection of beats decreases compared to absolute vibration.
The Reproducibility of Global Electrical Heterogeneity ECG Measurements (2018)

Reproducibility of a 10-second automated GEH ECG measurements was substantial, and precision was perfect.
Theory of Half-Metallic Ferrimagnetism in Double Perovskites (2011)

Double perovskites such as Sr(2)FeMoO(6) are rare examples of materials with half-metallic ground states and a ferrimagnetic T(c) above room temperature. We present a comprehensive theory of the temperature and disorder dependence of their magnetic properties by deriving and validating a new effective spin Hamiltonian for these materials, amenable to large-scale three-dimensional simulations. We show how disorder, ubiquitous in these materials, affects T(c), the magnetization, and the conduction electron polarization. We conclude with a novel proposal to enhance T(c) without sacrificing polarization.
Identification of RF Power Amplifier Memory Effect Origins using Third-Order Intermodulation Distortion Amplitude and Phase Asymmetry (2006)

This paper describes a technique to determine the physical origins of memory effects in RF power amplifiers using amplitude and phase asymmetries of two-tone third order intermodulation distortion (IMD) products measured over a range of power levels and frequency spacing. Determining the origins of the memory effects is done by extracting the portion of the IMD product in each sideband that contributes to the asymmetry, and comparing these on a statistical basis to the responses of simple equivalent circuit models that represent thermal self-heating, and bias voltage feedback. A 90W, singled-ended GaN pHEMT PA stage is compared to a 650W push-pull combined Si LDMOS PA at 2.14 GHz. It is shown that the GaN PA memory effects are dominated by bias feedback (which is later improved), and that the LDMOS PA memory effects are dominated by thermal self-heating. These results are further quantified by comparing memory ratios
Role of the .alpha.C Domains of Fibrin in Clot Formation (1994)

The role of the carboxyl-terminal portion of the alpha chains of fibrin (alpha C domains) in clot formation was investigated by transmission and scanning electron microscopy and turbidity studies of clots made from preparations of molecules missing one or both of these domains. Highly purified and entirely clottable preparations of bovine fragment X monomer, one containing primarily molecules missing a single alpha C domain (fragment X1) and the other consisting of molecules missing both alpha C domains (fragment X2), were used for these experiments. These preparations were characterized by various methods, including the complete determination of the amino- and carboxyl-termini of all peptides and fragments. These preparations formed clots on dilution to neutral pH. In all cases, clots observed by either scanning or transmission electron microscopy were made up of a branched network of fibers, similar to those formed by thrombin treatment of intact fibrinogen, suggesting that the alpha C domains are not necessary for protofibril and fiber formation or branching. However, both the fiber and clot structure varied with the different fractions, indicating that the alpha C domains do participate in polymerization. The rate of assembly, as indicated by the lag period and maximum rate of turbidity increase, as well as the final turbidity, was decreased with removal of the alpha C domains, suggesting that they accelerate polymerization. preparations of isolated alpha C fragment added to fibrin monomer have striking effects on the turbidity curves, showing a decrease in the rate of polymerization in a dose-dependent manner but not complete inhibition. Electron microscopy of fibrin monomer desA molecules at neutral pH showed that most of the alpha C domains, like those in fibrinogen, remain associated with the central region. Thus, it appears that normally with thrombin cleavage of fibrinogen the effects of the interactions of alpha C domains observed here will be most significant for lateral aggregation.
High Temperature Enthalpy, Heat Capacity, Heat of Fusion, and Melting Point of Zirconium Tetrafluoride. (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHigh Temperature Enthalpy, Heat Capacity, Heat of Fusion, and Melting Point of Zirconium Tetrafluoride.R. A McDonald, G. C. Sinke, and D. R. StullCite this: J. Chem. Eng. Data 1962, 7, 1, 83Publication Date (Print):January 1, 1962Publication History Published online1 May 2002Published inissue 1 January 1962https://pubs.acs.org/doi/10.1021/je60012a026https://doi.org/10.1021/je60012a026research-articleACS PublicationsRequest reuse permissionsArticle Views272Altmetric-Citations11LEARN 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
n-3 Oil sources for use in aquaculture – alternatives to the unsustainable harvest of wild fish (2008)

The present review examines renewable sources of oils with n-3 long-chain (> or = C20) PUFA (n-3 LC-PUFA) as alternatives to oil from wild-caught fish in aquafeeds. Due to the increased demand for and price of wild-caught marine sources of n-3 LC-PUFA-rich oil, their effective and sustainable replacement in aquafeeds is an industry priority, especially because dietary n-3 LC-PUFA from eating fish are known to have health benefits in human beings. The benefits and challenges involved in changing dietary oil in aquaculture are highlighted and four major potential sources of n-3 LC-PUFA for aquafeeds, other than fish oil, are compared. These sources of oil, which contain n-3 LC-PUFA, specifically EPA (20:5n-3) and DHA (22:6n-3) or precursors to these key essential fatty acids, are: (1) other marine sources of oil; (2) vegetable oils that contain biosynthetic precursors, such as stearidonic acid, which may be used by fish to produce n-3 LC-PUFA; (3) single-cell oil sources of n-3 LC-PUFA; (4) vegetable oils derived from oil-seed crops that have undergone genetic modification to contain n-3 LC-PUFA. The review focuses on Atlantic salmon (Salmo salar L.), because it is the main intensively cultured finfish species and it both uses and stores large amounts of oil, in particular n-3 LC-PUFA, in the flesh.
Thin-film transistors using DNA-wrapped semiconducting single-wall carbon nanotubes with selected chiralities (2015)

Selected semiconducting chiralities, , , and , of DNA-wrapped single-wall carbon nanotubes (DNA-SWCNTs) were used for thin-film transistors (TFTs). Chirality separation was carried out by ion exchange chromatography (IEX) with the ssDNA of the (TAT)4 sequence. An on/off ratio of 3.8 × 106 with a carrier mobility of 11 cm2/(V·s) was successfully achieved in the fabricated SWCNT-TFTs. The comparison between the on/off ratios obtained before (101–102) and after IEX (104–107) indicated that the IEX separation process sufficiently improves the performance of SWCNT-TFTs because of the reducing metallic SWCNT pathways in the TFT channel.
Rapid Detection of the Severe Acute Respiratory Syndrome (SARS) Coronavirus by a Loop-Mediated Isothermal Amplification Assay (2004)

Severe acute respiratory syndrome (SARS) is a newly emerging disease that first emerged in Guangdong Province, China in November 2002 (1 ). The SARS coronavirus (SARS-CoV) was found to be the etiology of the disease (2-4 ). Subsequent surveillance studies have indicated that this virus is of animal origin and have suggested that the source of the disease is still circulating in this geographic region (5 ). Indeed, the potential risk of reemergence of SARS is further highlighted by a recent confirmed SARS case in January 2004 (6 ). Therefore, the establishment of a rapid SARS diagnostic method is a high priority for control of the disease.
ChemInform Abstract: Stable Vinylnitroxyl Radicals, Pyrroline Derivatives. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Wireless security analysis (2009)

Our research focuses on the wireless security vulnerabilities that exist in 802.11. We specifically analyze the surrounding area of Purdue University as a sample to estimate the overall wireless security posture in and around major cities within the United States. Some common wireless attacks will be demonstrated during the session.
Substrate-Determined Shape of Free Surface Profiles in Spin-Cast Polymer Blend Films (2003)

Sectional views of thin films of symmetric polystyrene/polyisoprene (PS/PI) blends spin-cast from toluene (C6H5CH3) onto CH3- and COOH-terminated self-assembled monolayers (CH3−SAM and COOH−SAM) show concave- (sharp-edged) and convex-shaped (round) protrusions, respectively, while other morphology features are identical. A 3-dimensional phase domain arrangement was determined with spectroscopic techniques (profiling and mapping mode of dynamic secondary ion mass spectrometry, dSIMS, and X-ray photoelectron spectroscopy). Surface topography was examined with atomic force microscopy and monitored, during the dSIMS analysis, with secondary electrons. In addition, solvent evaporation from PS, PI, and PS/PI layers cast on CH3−SAM and COOH−SAM was determined. The collected data were used to put forward a model of morphology formation and to elucidate the role of evaporation speed dependent on substrate chemistry in this process, demonstrated here for the first time.