gebhart/patrepeval huggingface dataset:
Origins, genetic organization and transcription of a family of non‐autonomous helitron elements in maize (2005)

Helitron transposable elements carrying gene fragments were recently discovered in maize. These elements are frequently specific to certain maize lineages. Here we report evidence supporting the involvement of helitrons in the rapid evolution of the maize genome, in particular in the multiplication of related genic fragments across the genome. We describe a family of four closely related, non-autonomous maize helitrons and their insertion sites at four non-allelic genetic loci across the maize genome: two specific to the B73 inbred, and two to the Mo17 inbred. We propose the phylogeny of this helitron family and provide an approximate timeline of their genomic insertions. One of these elements, the Mo17-specific helitron on chromosome 1 (bin 1.07), is transcriptionally active, probably as a result of insertion in the vicinity of a promoter. Significantly, it produces an alternatively spliced and chimeric transcript joining together genic segments of different chromosomal origin contained within the helitron. This transcript potentially encodes up to four open reading frames. During the course of evolution, transcribed helitrons containing multiple gene fragments may occasionally give rise to new genes with novel biochemical functions by a combinatorial assembly of exons. Thus helitrons not only constantly reshape the genomic organization of maize and profoundly affect its genetic diversity, but also may be involved in the evolution of gene function.
Multiple Binding Sites on the Pyrin Domain of ASC Protein Allow Self-association and Interaction with NLRP3 Protein (2012)

A key process underlying an innate immune response to pathogens or cellular stress is activation of members of the NOD-like receptor family, such as NLRP3, to assemble caspase-1-activating inflammasome complexes. Activated caspase-1 processes proinflammatory cytokines into active forms that mediate inflammation. Activation of the NLRP3 inflammasome is also associated with common diseases including cardiovascular disease, diabetes, chronic kidney disease, and Alzheimer disease. However, the molecular details of NLRP3 inflammasome assembly are not established. The adaptor protein ASC plays a key role in inflammasome assembly. It is composed of an N-terminal pyrin domain (PYD) and a C-terminal caspase recruitment domain, which are protein interaction domains of the death fold superfamily. ASC interacts with NLRP3 via a homotypic PYD interaction and recruits procaspase-1 via a homotypic caspase recruitment domain interaction. Here we demonstrate that ASC PYD contains two distinct binding sites important for self-association and interaction with NLRP3 and the modulatory protein POP1. Modeling of the homodimeric ASC PYD complex formed via an asymmetric interaction using both sites resembles a type I interaction found in other death fold domain complexes. This interaction mode also permits assembly of ASC PYDs into filaments. Furthermore, a type I binding mode is likely conserved in interactions with NLRP3 and POP1, because residues critical for interaction of ASC PYD are conserved in these PYDs. We also demonstrate that ASC PYD can simultaneously self-associate and interact with NLRP3, rationalizing the model whereby ASC self-association upon recruitment to NLRP3 promotes clustering and activation of procaspase-1.
Comparing the T and $\pi$ Equivalent Circuits for the Calculation of Transformer Inrush Currents (2012)

The most commonly used equivalent circuit for transformers is the traditional (Steinmetz) <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</i> -equivalent proposed toward the end of the 19th century. This model has two leakage impedance branches and one magnetizing branch. The <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</i> model properly represents the terminal behavior of the transformer for most low-frequency operating conditions. Another model derived from the principle of duality between magnetic and electric circuits exists, the π equivalent circuit, which has two magnetizing branches and one leakage branch. This paper shows that while the two equivalent circuits provide the same accuracy in steady state, better accuracy for the calculation of inrush currents is obtained with the π -equivalent circuit. Laboratory tests performed on three transformers with different characteristics demonstrate that inrush current simulations with the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</i> equivalent circuit can have errors up to 73%, while the π equivalent estimates the measurements in every case within a few percent.
Synergistic antibacterial activity of chitosan–silver nanocomposites on<i>Staphylococcus aureus</i> (2011)

The approach of combining different mechanisms of antibacterial action by designing hybrid nanomaterials provides a new paradigm in the fight against resistant bacteria. Here, we present a new method for the synthesis of silver nanoparticles enveloped in the biopolymer chitosan. The method aims at the production of bionanocomposites with enhanced antibacterial properties. We find that chitosan and silver nanoparticles act synergistically against two strains of Gram-positive Staphylococcus aureus (S. aureus). As a result the bionanocomposites exhibit higher antibacterial activity than any component acting alone. The minimum inhibitory (MIC) and minimum bactericidal (MBC) concentrations of the chitosan-silver nanoparticles synthesized at 0 °C were found to be lower than those reported for other types of silver nanoparticles. Atomic force microscopy (AFM) revealed dramatic changes in morphology of S. aureus cells due to disruption of bacterial cell wall integrity after incubation with chitosan-silver nanoparticles. Finally, we demonstrate that silver nanoparticles can be used not only as antibacterial agents but also as excellent plasmonic substrates to identify bacteria and monitor the induced biochemical changes in the bacterial cell wall via surface enhanced Raman scattering (SERS) spectroscopy.
Electro-optic sampling measurements of high-speed InP integrated circuits (1987)

Multigigahertz waveforms in an InGaAs/InP metal-insulator-semiconductor field-effect transistor inverter circuit have been measured noninvasively using the electro-optic sampling technique with pulses from a gain-switched InGaAsP laser. Propagation delays as low as 15 ps in a single inverter stage have been measured.
Switchable pulses generation in passively Q-switchedmultilongitudinal-mode microchip laser (2006)

Periodical switching laser pulses with nanosecond pulse width and several kilowatts peak power from wide-separated multilongitudinal-mode oscillation were observed experimentally in laser-diode pumped passively Q-switched Yb:YAG microchip laser with Cr 4+ :YAG as saturable absorber. Pulses from different longitudinal modes oscillate alternatively. Periodical pulses oscillation dynamics induced by spatial hole burning effect and mode competition was investigated numerically by the evolution of the inversion population of different modes and the bleaching and recovery of the inversion population of the saturable absorber. The numerical simulations of switchable periodical pulsation of multilongitudinal-mode passively Q-switched Yb:YAG/Cr 4+ :YAG microchip lasers are in good agreement with experimental results and confirmed that such pulsations are an intrinsic property in passively Q-switched Yb:YAG/Cr 4+ :YAG microchip lasers.
A review on various temperature-indication methods for Li-ion batteries (2019)

The working principle of Li-ion batteries is explained.
Stereospecificity in the reductive coupling of 4-pyridinecarboxaldehyde (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereospecificity in the reductive coupling of 4-pyridinecarboxaldehydeJames F. Rusling and Petr ZumanCite this: J. Org. Chem. 1981, 46, 9, 1906–1909Publication Date (Print):April 1, 1981Publication History Published online1 May 2002Published inissue 1 April 1981https://pubs.acs.org/doi/10.1021/jo00322a032https://doi.org/10.1021/jo00322a032research-articleACS PublicationsRequest reuse permissionsArticle Views127Altmetric-Citations16LEARN 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
A reliable fail-safe system (1998)

The paper describes a fault tolerant system that is based on two replicas of a self checking module and on an error masking interface. The main contributions of this work rely on the fail safe/strongly fail safe design of the error masking interface, and on the analysis of the competitiveness of this fault tolerant scheme with respect to its reliability.
Surface chemical patterning for long‐term single‐cell culture (2011)

Surface chemical patterning of polystyrene (PS) dishes for long-term single-cell culture was accomplished by oxygen plasma treatment through the windows of a polydimethylsiloxane membrane mask that produced hydrophilic areas of different shapes and sizes, followed by overnight incubation with either Pluronic F108 solution or a mixture of Pluronic F108 solution and fibronectin. Selective cell attachment on pattern areas of PS dishes was investigated in light of cell seeding experiments and X-ray photoelectron spectroscopy measurements. Activation of the hydrophilic areas of patterned PS surfaces by serum proteins in the culture medium was conducive to cell attachment on the pattern areas of dishes incubated with only Pluronic solution. Preferential adsorption of fibronectin on hydrophilic pattern areas enhanced selective cell attachment on patterned dishes incubated with a mixture of Pluronic solution and fibronectin. Cell-culture experiments demonstrated an effect of surface patterning on both cell and nucleus shape and confirmed the long-term (>2 weeks) stability of the produced single-cell patterns in serum medium.
APPLICATION OF NUCLEAR SPECTROSCOPY LOGS TO THE DERIVATION OF FORMATION MATRIX DENSITY (2000)

Formation matrix properties, such as matrix density, can be estimated from the elemental concentrations available from modern, openhole, nuclear spectroscopy logging techniques. Although this estimation is similar to that of mineral-based interpretation frequently practiced today, it can preempt the a priori selection of minerals by solving for matrix properties directly from the elements. This simple approach greatly enhances the ability to perform wellsite interpretations in both simple and complex formations. The interpretation for the matrix density is derived from a comprehensive database containing hundreds of core samples analyzed for both mineralogy and chemistry. The chemical analysis includes not only the major elements, but also the minor and trace elements that significantly influence wireline log responses. These data are used to forward model the matrix which is then solved as a linear combination of four elements (silicon, calcium, iron, sulfur) that are measured by prompt neutron capture spectroscopy. Comparisons are shown between measured and derived matrix density along with statistical measures of goodness of fit. Although in many cases the errors could be reduced by local optimization, the overall agreement is quite good.
Light trapping and optical losses in microcrystalline Si and micromorph solar cells (2003)

We have developed the 3-dimensional optical model for thin film silicon solar cells (amorphous, microcrystalline, single or multijunction) with nanorough surfaces/interfaces. For these cells the external quantum efficiency, short circuit current, total reflectance and all absorption losses can be computed taking into account roughness, angular distribution of scattered light, thicknesses and experimentally determined optical constants of all layers. The model gives very good agreement with the experimentally determined data for micro-crystalline silicon and micromorph (amorphous-microcrystalline silicon tandem) solar cells. Based on the analysis of optical losses and possible improvements in the materials properties, a roadmap for over 15% stable efficiency of micromorph solar cell has been suggested.
A mitigation model for TCP SYN flooding with IP spoofing (2011)

DDoS attack is considered to be a major threat among security problems in today's Internet. These kinds of attack are potentially severe. They bring down business of company drastically. DDoS attack can easily exhaust the computing and communication resources of its victim within a short period of time. There are attacks exploiting some vulnerability or implementation bug in the software implementation of a service, to bring the server down. Some attacks will use all the available resources at the target machine. This paper deals on attacks that consume all the bandwidth available to the victim machine. While concentrating on the bandwidth attack the TCP SYN flood is the more prominent attack. TCP/IP protocol suite is the most widely used protocol suite for data communication. The TCP SYN flood works by exhausting the TCP connection queue of the host and thus denying legitimate connection requests. There are various methods used to detect and prevent this attack, one of which is to block the packet based on SYN flag count from the same IP address. This kind of prevention methods becomes unsuitable when the attackers use the Spoofed IP address. For the prevention of this kind of attacks, the TCP specific probing is used in the proposed scheme where the client is requested to change the windows size/ cause packet retransmission while sending the ACK in the three way hand shake. This is very useful to find the Spoofed IP Packets/TCP SYN flood and preventing them.
New Virus Fingered in Malaysian Epidemic (1999)

Scientists have unmasked a killer responsible for the deaths of at least 95 people in Malaysia in the last 6 months, most of them pig farm workers. The culprit, named the Nipah virus for the small town from whence the strain was first identified, is a previously unknown virus that replicates in pigs and seems to be easily transmitted to humans. It is closely related to another notorious agent, the Hendra virus, which surfaced in Australia in 1994 and killed two people and more than a dozen horses. But the new virus spreads much more rapidly, making it “an emerging virus of grave concern,” says John Mackenzie, head of the department of microbiology and parasitology at the University of Queensland in Brisbane, Australia.
Glidobactins D, E, F, G and H; Minor components of the antitumor antibiotic glidobactin. (1988)

Sultamicillin (SBTPC) is a combination drug of sulbactam (SBT) and ampicillin (ABPC) in an ester bonding at 1:1 ratio. SBT, a new semisynthetic beta-lactamase inhibitor restores and extends the spectrum of ABPC against resistant strains of bacteria. SBTPC granules were administered to 26 pediatric patients with infections, and clinical efficacies were studied in 23 patients. The clinical efficacy rate was 95.7% and the drug was evaluated to be highly effective for the treatment of infectious diseases in the pediatric field. SBTPC was safe and well tolerated.
First Synthesis of Poly(ethene-<i>c</i><i>o</i>-1,3-butadiene) with Neodymocene Catalysts (2000)

International audience
Sequencing of proteins extracted from stones. (1994)

Proteins from urinary tract and gallbladder stones were extracted and characterized to determine the composition of the matrix and possibly unravel the role of the organic phase in stone formation. Proteins from crushed stones were extracted by electrodialysis and concentrated in the Amicon centricon cartridge or by lyophilization after dialysis against distilled water. Aliquots were first analyzed by isoelectric focusing in gel and if suitable subjected to two-dimensional (2D) electrophoresis. The most promising spots were harvested and the N-terminal amino acids sequenced, thus providing maximum information with minimum expenditure of material. The 2D separations and amino acid sequences of several protein extracts demonstrated similarities and differences in composition and achieved the identification or demonstration of previously and recently detected polypeptides.
Nonlinear, Non-Stationary Analysis of Interarea Oscillations via Hilbert Spectral Analysis (2006)

Hilbert spectral analysis (HSA) is used to characterize the time evolution of non-stationary power system oscillations following large perturbations. Using an analytical procedure based on the Hilbert-Huang Technique (HHT), data from transient stability simulations are decomposed into a finite number of time-varying oscillating components that can be associated with different time scales. Hilbert analysis is then utilized to characterize the time evolution of critical components giving rise to the observed oscillations. The objectives of this study are to obtain information of a quantitative nature on nonlinear processes in power system oscillatory phenomena and assess the applicability of the developed procedures to track the evolving dynamics of critical system modes. A six-area, 377-machine power system is analyzed to examine the onset of nonlinear, non-stationary behavior. Examples of the developed procedures to detect and quantify the strength of nonlinear interaction in power system behavior and to estimate the distribution of the non-stationarity are provided
Pro-inflammatory Cytokine GM-CSF Improves Learning/Memory and Brain Pathology in Dp16 Down Syndrome Mice and Improves Learning/Memory in Wild-Type Mice (2021)

Abstract Down syndrome (DS) is characterized by chronic neuroinflammation, peripheral inflammation, astrogliosis, imbalanced excitatory/inhibitory neuronal function, and cognitive deficits in both humans and mouse models. Suppression of inflammation has been proposed as a therapeutic approach to treating DS co-morbidities, including intellectual disability (DS/ID). Conversely, we discovered previously that treatment with the pro-inflammatory cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) improved cognition and reduced biomarkers of brain pathology in humans with Alzheimer’s disease (AD), another inflammatory disorder, and in a mouse model of AD. To investigate the effects of GM-CSF treatment on DS/ID, we assessed behavior and brain pathology in 12-14 month-old DS mice (Dp[16]1Yey) and their wild-type (WT) littermates, neither of which develop amyloid, and found that GM-CSF treatment improved performance in the radial arm water maze in both Dp16 and WT mice compared to placebo. Dp16 mice also showed abnormal astrocyte morphology and aggregation and fewer calretinin-positive interneurons, both of which were improved by GM-CSF treatment. These findings suggest that stimulating and/or modulating inflammation and the innate immune system with GM-CSF treatment may enhance cognition in both people with DS/ID and in the typical aging population.
Results of analyzing VLSI interconnect structures by a methodology based on mixed frequency-time domain (2002)

The results of the analysis, from a digital point of view, of some interconnection structures in GaAs integrated circuits are presented. These results are given in graphical format, as engineering charts, to assist designers, and with a polynomial fitting useful for timing analysis. In addition to computing timing parameters such as propagation time and signed slopes (waveforms), the methodology also provides estimations of noise and crosstalk levels.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Lifetime evaluation model for Wireless Sensor Networks based on mote redundancy (2012)

Wireless Sensor Networks are able to sense large amount of physical environments with low energy consumption. In order to achieve that, the battery-powered wireless motes have to optimize the usage of their batteries to make them last longer. However, these motes must keep doing the main purpose for which they were deployed, that is, sampling the environment. These requirements provide a research framework in which many authors have been studying in the last years. They have stated several different descriptions of sensor network lifetime. Some definitions measure the time when the first network mote stops working (due to the lack of battery energy). Other definitions keep track of the time spent until a certain amount of motes fail. In these cases, the network lifetime is independent of the sampled environment and does not take into account redundancy and fault tolerance. Using a new innovative concept of network lifetime, a new battery-powered WSN lifetime model based in data redundacy and hardware redundacy is proposed. With this model, energy consumption can be minimized, and therefore, a reduction in the change of batteries is obtained. The proposed method also provides a new metric which determines when a network stops being useful.
Human Polynucleotide Kinase Participates in Repair of DNA Double-Strand Breaks by Nonhomologous End Joining but not Homologous Recombination (2007)

Human polynucleotide kinase (hPNK) is a bifunctional enzyme possessing a 5'-DNA kinase activity and a 3'-phosphatase activity. Studies based on cell extracts and purified proteins have indicated that hPNK can act on single-strand breaks and double-strand breaks (DSB) to restore the termini to the chemical form required for further action by DNA repair polymerases and ligases (i.e., 5'-phosphate and 3'-hydroxyl termini). These studies have revealed that hPNK can bind to XRCC4, and as a result, hPNK has been implicated as a participant in the nonhomologous end joining (NHEJ) pathway for DSB repair. We sought to confirm the role of hPNK in NHEJ in the cellular setting using a genetic approach. hPNK was stably down-regulated by RNA interference expression in M059K glioblastoma cells, which are NHEJ positive, and M059J cells, which are NHEJ deficient due to a lack of DNA-PK catalytic subunit (DNA-PKcs). Whereas depletion of hPNK significantly sensitized M059K cells to ionizing radiation, no additional sensitization was conferred to M059J cells, clearly implying that hPNK operates in the same DNA repair pathway as DNA-PKcs. On the other hand, depletion of hPNK did not increase the level of sister chromatid exchanges, indicating that hPNK is not involved in the homologous recombination DSB repair pathway. We also provide evidence that the action of hPNK in the repair of camptothecin-induced topoisomerase 1 "dead-end" complexes is independent of DNA-PKcs and that hPNK is not involved in the nucleotide excision repair pathway.