gebhart/patrepeval huggingface dataset:
Speed and Reliability of Nanomagnetic Logic Technology (2014)

Nanomagnetic logic is an energy efficient computing architecture that relies on the dipole field coupling of neighboring magnets to transmit and process binary information. In this architecture, nanomagnet chains act as local interconnects. To assess the merits of this technology, the speed and reliability of magnetic signal transmission along these chains must be experimentally determined. In this work, time-resolved pump-probe x-ray photo-emission electron microscopy is used to observe magnetic signal transmission along a chain of nanomagnets. We resolve successive error-free switching events in a single nanomagnet chain at speeds on the order of 100 ps per nanomagnet, consistent with predictions based on micromagnetic modeling. Errors which disrupt transmission are also observed. We discuss the nature of these errors, and approaches for achieving reliable operation.
Intelligent manager of scientific knowledge based in Gamification (Gicci-Game) (2015)

Here's where we consider appropriate to set up a smart manager to apply scientific knowledge gamification techniques in order to manage information and provide a mechanism to create, store and access it.
Sur la reduction par les hydrures complexes de benzyl-3 camphres (1972)

Benzyl-3 camphors have been prepared and the stereochemistry of their reduction by complex hydrides is reported; the corresponding benzyl-3 borneols have also been prepared and characterized.
Salt Intake, Oxidative Stress, and Renal Expression of NADPH Oxidase and Superoxide Dismutase (2003)

The hypothesis that a high salt (HS) intake increases oxidative stress was investigated and was related to renal cortical expression of NAD(P)H oxidase and superoxide dismutase (SOD). 8-Isoprostane PGF(2alpha) and malonyldialdehyde were measured in groups (n = 6 to 8) of conscious rats during low-salt, normal-salt, or HS diets. NADPH- and NADH-stimulated superoxide anion (O(2)(.-)) generation was assessed by chemiluminescence, and expression of NAD(P)H oxidase and SOD were assessed with real-time PCR. Excretion of 8-isoprostane and malonyldialdehyde increased incrementally two- to threefold with salt intake (P < 0.001), whereas prostaglandin E(2) was unchanged. Renal cortical NADH- and NADPH-stimulable O(2)(.-) generation increased (P < 0.05) 30 to 40% with salt intake. Compared with low-salt diet, HS significantly (P < 0.005) increased renal cortical mRNA expression of gp91(phox) and p47(phox) and decreased expression of intracellular CuZn (IC)-SOD and mitochondrial (Mn)-SOD. Despite suppression of the renin-angiotensin system, salt loading enhances oxidative stress. This is accompanied by increased renal cortical NADH and NADPH oxidase activity and increased expression of gp91(phox) and p47(phox) and decreased IC- and Mn-SOD. Thus, salt intake enhances generation of O(2)(.-) accompanied by enhanced renal expression and activity of NAD(P)H oxidase with diminished renal expression of IC- and Mn-SOD.
Visco-Elastic Properties of Nematic-MoS2Nanotubes Mixtures (2005)

ABSTRACT We investigated experimentally the viscoelastic properties of MoS2 nanotubes mixed with liquid crystal 8CB in the nematic phase. The MoS2 nanotubes were dispersed with ultra-sound in ethanol and then mixed with liquid crystal; then the ethanol was evaporated. Dynamic light scattering (DLS) was used to measure the viscoelastic coefficients of the mixture in its nematic phase from the SmA-N up to the N-I phase transition. The relaxation time τ of orientational fluctuations depends on the concentration of dispersed MoS2 nanotubes in liquid crystal, temperature and orientation of the director. By measuring the dependence of τ as a function of the scattering wave vector q, the ratio K 1/η1 and K 3/η3 were obtained (K i - Frank elastic constants, η i - effective viscosities). Comparison of the obtained results with the values of K i /η i of pure 8CB liquid crystal shows that the ratios K 1/η1 and K 3/η3 decrease with increasing concentration of the MoS2 nanotubes.
Tryptophanyl fluorescence heterogeneity of apomyoglobins. Correlation with the presence of two distinct structural domains (1981)

The individual fluorescence of the two tryptophan residues (Trp-7 and Trp-14) of mammalian apomyoglobins has been resolved by comparing the fluorescence properties of these proteins to those of bluefin tuna apomyoglobin, which contains only Trp-14. The two tryptophan residues have been found to have different emission maxima, i.e., 321 for Trp-14 and 333 for Trp-7. The fluorescence of Trp-14 depends on the protonation of a sterically related histidyl residue in the pH range between 8.3 and 5.6, where no conformational change was detected. This residue has been identified as His-119. At pH 8.3 the quantum yield of Trp-7 is lower than that of Trp-14. An increase of the fluorescence intensity of Trp-7 occurs when the heme binding site of apomyoglobin is destroyed by acid or a low concentration of guanidine hydrochloride. An independent unfolding of the N-terminal district of the apomyoglobin molecular occurs on increasing the guanidine concentration. The two distinct structural transitions have been discussed in terms of two domains of tertiary structure.
Integrating extracellular vesicle and circulating cell-free DNA analysis on a single plasma aliquot from breast cancer patients improves the detection of HER2 positivity (2023)

Abstract Background Multi-analyte liquid biopsies represents an emerging opportunity for non-invasive cancer assessment. We developed ONCE (ONe Aliquot for Circulating Elements), a novel multi-analytes liquid biopsy approach for the isolation of extracellular vesicles (EVs) and cell-free DNA (cfDNA) from a single aliquot of blood. Methods We assessed ONCE performance to classify HER2-positive early-stage breast cancer (BrCa) patients by combining RNA and DNA signals on n=64 healthy donors (HD) and non–metastatic BrCa patients. Specifically, we investigated EVs-derived RNA (EV-RNA) and cfDNA by next-generation sequencing (NGS) and by digital droplet PCR (ddPCR). Additionally, we utilized imaging flow cytometry to evaluate EVs as potential carriers of the HER2 protein. Results Western blot analysis and immunocapture assay revealed that EVs-enriched proteins were detected at similar levels among the HER2+ and HER2- subtypes. Sequencing of cfDNA and EV-RNA from HER2- and HER2+ patients demonstrated concordance with in situ molecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity in ERBB2/ HER2 detection compared to single nucleic acid components. Multi-analyte liquid biopsy prediction performance was comparable to tissue-based sequencing results from TCGA. Also, we observed HER2 protein on the surface of EVs isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EVs as companion analyte to cfDNA. Conclusions This data confirms the relevance of combining cfDNA and EV-RNA analytes for cancer assessment and supports the ONCE approach as a valuable tool for multi-analytes liquid biopsies’ clinical implementation.
New Electrodes for Chronopotentiometry in Thin Layers of Solution. (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew Electrodes for Chronopotentiometry in Thin Layers of Solution.A. T. Hubbard and F. C. AnsonCite this: Anal. Chem. 1964, 36, 4, 723–726Publication Date (Print):April 1, 1964Publication History Published online1 May 2002Published inissue 1 April 1964https://pubs.acs.org/doi/10.1021/ac60210a008https://doi.org/10.1021/ac60210a008research-articleACS PublicationsRequest reuse permissionsArticle Views264Altmetric-Citations94LEARN 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
Thermal-aware TSV Repair for Electromigration in 3D ICs (2016)

Electromigration (EM) occurrence on through-silicon-vias (TSVs) is a major reliability concern for Three-Dimensional Integrated-Circuits (3D ICs), and EM can severely reduce the mean-time-to-failure (MTTF). In this work, a novel fault tolerant technique is proposed to increase the MTTF of the functional TSV network through the assignment of spare TSVs to EM-vulnerable functional TSVs. The objective is to meet the target MTTF with minimum spare TSVs and minimal impact on the circuit timing. By considering the impact of temperature variation, the proposed technique provides a more robust repair solution for EM-induced TSV defects with minimum delay overhead, compared to previous thermal-unaware methods.
A Bioelectrochemical Method for the Quantitative Description of the Hofmeister Effect of Ionic Liquids in Aqueous Solution (2012)

It is imperative to establish a simple, efficient, and practical method to investigate the Hofmeister effect of ionic liquids (ILs) on the behavior of proteins (enzymes). In this study, the effects of the cations and anions of different ILs in aqueous media on the structural stability of horseradish peroxidase (HRP), a model oxidoreductase, were systematically investigated using electrochemical methods. It is found that without ILs no direct electron transfer current signals of HRP appear at bare glassy carbon electrode (GCE) in phosphate buffer (pH 7.0) even after incubation and accumulation at a negative potential. In the presence of ILs, however, a current signal occurs at GCE, depending on the structure of the IL and its concentration. A linear relationship between the peak currents and the scan rates demonstrates that the direct electron transfer is a surface-confined thin-layer electrochemical process. The redox signal at GCE is from the heme of HRP. An IL has a perturbing effect on the HRP structure. The anodic peak current of HRP at GCE, the catalytic activity of HRP, and the secondary structure of HRP are well correlated. Different cations or anions at varied concentrations have different effects on the structural stability of HRP, resulting in different current signals at GCE. Thus, the anodic peak current of HRP at GCE can be used as an indicator to quantitatively characterize the effect of ILs on the structural stability of HRP. The present Hofmeister series for cations and anions is in good agreement with that reported elsewhere. To our knowledge, this is a first attempt to establish a simple and practical electrochemical method to correlate Hofmeister effects with characteristics of ions and solvents. The present investigation not only deepens our understanding of the complex electrochemical behavior of proteins in ILs media but also offers a practical guidance to designing "green" and biocompatible ILs for protein (enzyme) separation, purification, and enzymatic catalysis and conversion.
Model-based estimation of the frequency tuning of the inner-hair-cell stereocilia from neural tuning curves (2017)

This study proposes that the frequency tuning of the inner-hair-cell (IHC) stereocilia in the intact organ of Corti can be derived from the responses of the auditory fibers (AFs) using computational tools. The frequency-dependent relationship between the AF threshold and the amplitude of the stereocilia vibration is estimated using a model of the IHC-mediated mechanical to neural transduction. Depending on the response properties of the considered AF, the amplitude of stereocilia deflection required to drive the simulated AF above threshold is 1.4 to 9.2 dB smaller at low frequencies (≤500 Hz) than at high frequencies (≥4 kHz). The estimated frequency-dependent relationship between ciliary deflection and neural threshold is employed to derive constant-stereocilia-deflection contours from previously published AF recordings from the chinchilla cochlea. This analysis shows that the transduction process partially accounts for the observed differences between the tuning of the basilar membrane and that of the AFs.
Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity (2009)

Summary The genome of Desulfovibrio vulgaris strain DePue, a sulfate‐reducing Deltaproteobacterium isolated from heavy metal‐impacted lake sediment, was completely sequenced and compared with the type strain D. vulgaris Hildenborough. The two genomes share a high degree of relatedness and synteny, but harbour distinct prophage and signatures of past phage encounters. In addition to a highly variable phage contribution, the genome of strain DePue contains a cluster of open‐reading frames not found in strain Hildenborough coding for the production and export of a capsule exopolysaccharide, possibly of relevance to heavy metal resistance. Comparative whole‐genome microarray analysis on four additional D. vulgaris strains established greater interstrain variation within regions associated with phage insertion and exopolysaccharide biosynthesis.
Comparative genomic hybridization and transcriptome analysis with a pan‐genome microarray reveal distinctions between JP2 and non‐JP2 genotypes of Aggregatibacter actinomycetemcomitans (2012)

It was postulated that the highly virulent JP2 genotype of Aggregatibacter actinomycetemcomitans may possess a constellation of distinct virulence determinants not found in non-JP2 genotypes. This study compared the genome content and the transcriptome of the serotype b JP2 genotype and the closely related serotype b non-JP2 genotype of A. actinomycetemcomitans. A custom-designed pan-genomic microarray of A. actinomycetemcomitans was constructed and validated against a panel of 11 sequenced reference strains. The microarray was subsequently used for comparative genomic hybridization of serotype b strains of JP2 (six strains) and non-JP2 (six strains) genotypes, and for transcriptome analysis of strains of JP2 (three strains) and non-JP2 (two strains). Two JP2-specific and two non-JP2-specific genomic islands were identified. In one instance, distinct genomic islands were found to be inserted into the same locus among strains of different genotypes. Transcriptome analysis identified five operons, including the leukotoxin operon, to have at least two genes with an expression ratio of 2 or greater between genotypes. Two of the differentially expressed operons were members of the membrane-bound nitrate reductase system (nap operon) and the Tol-Pal system of gram-negative bacterial species. This study is the first to demonstrate the differences in the full genome content and gene expression between A. actinomycetemcomitans strains of JP2 and non-JP2 genotypes. The information is essential for designing hypothesis-driven experiments to examine the pathogenic mechanisms of A. actinomycetemcomitans.
Automated Cell Tracking and Analysis in Phase-Contrast Videos (iTrack4U): Development of Java Software Based on Combined Mean-Shift Processes (2013)

Cell migration is a key biological process with a role in both physiological and pathological conditions. Locomotion of cells during embryonic development is essential for their correct positioning in the organism; immune cells have to migrate and circulate in response to injury. Failure of cells to migrate or an inappropriate acquisition of migratory capacities can result in severe defects such as altered pigmentation, skull and limb abnormalities during development, and defective wound repair, immunosuppression or tumor dissemination. The ability to accurately analyze and quantify cell migration is important for our understanding of development, homeostasis and disease. In vitro cell tracking experiments, using primary or established cell cultures, are often used to study migration as cells can quickly and easily be genetically or chemically manipulated. Images of the cells are acquired at regular time intervals over several hours using microscopes equipped with CCD camera. The locations (x,y,t) of each cell on the recorded sequence of frames then need to be tracked. Manual computer-assisted tracking is the traditional method for analyzing the migratory behavior of cells. However, this processing is extremely tedious and time-consuming. Most existing tracking algorithms require experience in programming languages that are unfamiliar to most biologists. We therefore developed an automated cell tracking program, written in Java, which uses a mean-shift algorithm and ImageJ as a library. iTrack4U is a user-friendly software. Compared to manual tracking, it saves considerable amount of time to generate and analyze the variables characterizing cell migration, since they are automatically computed with iTrack4U. Another major interest of iTrack4U is the standardization and the lack of inter-experimenter differences. Finally, iTrack4U is adapted for phase contrast and fluorescent cells.
Substrates for neural metabolism of xenobiotics in adult and developing brain. (1994)

Cellular heterogeneity and structural complexity of the nervous system, coupled with regional and cellular differences in the metabolic capabilities of neurons, glia and other non-neuronal elements, may underlie the selective cellular involvement following exposure to neurotoxicants. Determination of the role of biotransformation of xenobiotics in neural pathoclisis requires an understanding of the cellular distribution of both phase I and phase II enzyme systems in the brain. While ependyma, choroid plexus and endothelial linings of blood vessels throughout the nervous system appear to contain appreciable amounts of several isoforms of cytochrome P450 (CYP450), glia and neurons tend to be highly specific in which forms of CYP450 they express. Regional and cellular heterogeneity similarly characterize the distribution of glutathione (GSH) and the conjugating enzyme glutathione S-transferase (GST) in the brain. While all cells of the embryonic nervous system express high levels of GSH and pi-GST (with lesser amounts of alpha- and mu-class), by adulthood neurons and non-neuronal cells differ in the distribution of GSH and isoforms of GST. Neurons (except the dorsal root ganglia and the cerebellar granule cells) become GSH-negative but contain alpha-, mu-, and pi-GST. Glia, ependyma, choroid plexus and neurovascular cells are rich in GSH and variously express GSTs. The differences found in the cellular distribution of GSH and GSTs may contribute to changes in the vulnerability of the nervous system to neurotoxicants at different ages. A comprehensive understanding of the neurotoxicological and pharmacological consequences of the cellular heterogeneity in the localization the CYP450s and glutathione S-transferases pre- and postnatally will require systematic study of the distribution, substrate specificity, and inducibility of the various isoforms of these enzyme systems.
Urinary uranium and kidney function parameters in professional assistance workers in the Epidemiological Study Air Disaster in Amsterdam (ESADA) (2007)

Occupational exposure to the air disaster in Amsterdam was neither significantly associated with higher uranium concentrations, nor with disturbed kidney function parameters. In this large cohort of professional assistance workers, urinary uranium concentrations were in the low range compared with previously published reference populations. No indications of nephrotoxicity were found at urinary uranium concentrations around 2 ng/g creatinine.
Optical layer survivability: a services perspective (2000)

This article provides a perspective on optical layer protection and restoration based on the services offered by carriers using the optical layer. This is different from other viewpoints that provide a taxonomy of protection techniques in a more abstract fashion for the purposes of standardization. The latter viewpoints are mostly based on the classification adopted in the SONET/SDH standards. In contrast, taking a services-based view provides a way to distinguish between protection schemes based on implementation costs and the associated services enabled by the protection scheme.
Supramolecular Self-Assembly and Radical Kinetics in Conducting Self-Replicating Nanowires (2014)

By using a combination of experimental and theoretical tools, we elucidate unique physical characteristics of supramolecular triarylamine nanowires (STANWs), their packed structure, as well as the entire kinetics of the associated radical-controlled supramolecular polymerization process. AFM, small-angle X-ray scattering, and all-atomic computer modeling reveal the two-columnar "snowflake" internal structure of the fibers involving the π-stacking of triarylamines with alternating handedness. The polymerization process and the kinetics of triarylammonium radicals formation and decay are studied by UV-vis spectroscopy, nuclear magnetic resonance and electronic paramagnetic resonance. We fully describe these experimental data with theoretical models demonstrating that the supramolecular self-assembly starts by the production of radicals that are required for nucleation of double-columnar fibrils followed by their growth in double-strand filaments. We also elucidate nontrivial kinetics of this self-assembly process revealing sigmoid time dependency and complex self-replicating behavior. The hierarchical approach and other ideas proposed here provide a general tool to study kinetics in a large number of self-assembling fibrillar systems.
Prominent roles of the NorR and Fur regulators in the Escherichia coli transcriptional response to reactive nitrogen species (2004)

We examined the genomewide transcriptional responses of Escherichia coli treated with nitrosylated glutathione or the nitric oxide (NO)-generator acidified sodium nitrite (NaNO(2)) during aerobic growth. These assays showed that NorR, a homolog of NO-responsive transcription factors in Ralstonia eutrophus, and Fur, the global repressor of ferric ion uptake, are major regulators of the response to reactive nitrogen species. In contrast, SoxR and OxyR, regulators of the E. coli defenses against superoxide-generating compounds and hydrogen peroxide, respectively, have minor roles. Moreover, additional regulators of the E. coli response to reactive nitrogen species remain to be identified because several of the induced genes were regulated normally in norR, fur, soxRS, and oxyR mutant strains. We propose that the E. coli transcriptional response to reactive nitrogen species is a composite response mediated by the modification of multiple transcription factors containing iron or redox-active cysteines, some specifically designed to sense NO and its derivatives and others that are collaterally activated by the reactive nitrogen species.