gebhart/patrepeval huggingface dataset:
Intron requirement for expression of the human purine nucleoside phosphorylase gene (1992)

Abbreviated purine nucleoside phosphorylase (PNP) genes were engineered to determine the effect of introns on human PNP gene expression. PNP minigenes containing the first intron (complete or shortened from 2.9 kb down to 855 bp), the first two introns or all five PNP introns resulted in substantial human PNP isozyme expression after transient transfection of murine NIH 3T3 cells. Low level human PNP activity was observed after transfection with a PNP minigene containing the last three introns. An intronless PNP minigene construct containing the PNP cDNA fused to genomic flanking sequences resulted in undetectable human PNP activity. Heterogeneous, stable NIH 3T3 transfectants of intron-containing PNP minigenes (verified by Southern analysis), expressed high levels of PNP activity and contained appropriately processed 1.7 kb message visualized by northern analysis. Stable transfectants of the intronless PNP minigene (40-45 copies per haploid genome) contained no detectable human PNP isozyme or mRNA. Insertion of the 855 bp shortened intron 1 sequence in either orientation upstream or downstream of a chimeric PNP promoter-bacterial chloramphenicol acetyltransferase (CAT) gene resulted in a several-fold increase in CAT expression in comparison with the parental PNP-CAT construct. We conclude that human PNP gene expression at the mRNA and protein level is dependent on the presence of intronic sequences and that the level of PNP expression varies directly with the number of introns included. The disproportionately greatest effect of intron 1 can be explained by the presence of an enhancer-like element retained in the shortened 855 bp intron 1 sequence.
Evaluation of regulatory potential and conservation scores for detecting <i>cis</i> -regulatory modules in aligned mammalian genome sequences (2005)

Techniques of comparative genomics are being used to identify candidate functional DNA sequences, and objective evaluations are needed to assess their effectiveness. Different analytical methods score distinctive features of whole-genome alignments among human, mouse, and rat to predict functional regions. We evaluated three of these methods for their ability to identify the positions of known regulatory regions in the well-studied HBB gene complex. Two methods, multispecies conserved sequences and phastCons, quantify levels of conservation to estimate a likelihood that aligned DNA sequences are under purifying selection. A third function, regulatory potential (RP), measures the similarity of patterns in the alignments to those in known regulatory regions. The methods can correctly identify 50%-60% of noncoding positions in the HBB gene complex as regulatory or nonregulatory, with RP performing better than do other methods. When evaluated by the ability to discriminate genomic intervals, RP reaches a sensitivity of 0.78 and a true discovery rate of approximately 0.6. The performance is better on other reference sets; both phastCons and RP scores can capture almost all regulatory elements in those sets along with approximately 7% of the human genome.
Property extraction in well-founded property sets (1975)

To carry out significant program optimization, it is necessary to know what properties hold at each program unit. Frequently the properties of interest form a partially ordered set with a minimum condition (i.e., well-founded). When this occurs, it is possible to directly compute the properties that can be attached to program units and, optionally, to expand the program text to obtain a strong assignment of properties. Techniques are presented for property computation in iterative and recursive programs. Application to a variety of property sets is discussed.
A gene signature of loss of oestrogen receptor (ER) function and oxidative stress links ER-positive breast tumours with an absent progesterone receptor and a poor prognosis (2008)

Prognostic gene signatures like the wound and hypoxia signature differ by assumptions of cellular growth. Although gene signatures show little overlap, they also track within the group of luminal breast tumours those with a high proliferation and poor prognosis. Oxidative stress is another assumption of cellular growth. It affects several pathological conditions through its influence on the regulation of protein kinases and signal transduction pathways. A comprehensive set of 62 core genes from cultured oestrogen- and oestrogen receptor-deprived epithelial breast cancer cells is responsive to three forms of oxidative stress. Evidence is presented that oxidative stress involves the development of an aggressive subset of primary oestrogen receptor-positive breast tumours.
Timber harvest and drought interact to impact oak seedling growth and survival in the Central Hardwood Forest (2016)

Abstract Oak ( Quercus ) is a dominant component of the overstory in the Central Hardwood Forest region, but is currently failing to regenerate throughout much of its range. Loss of oak as a canopy dominant species would be devastating to the numerous species of wildlife that rely on acorns as a food resource. Intolerance to shade, competitive interactions, and herbivory (especially by deer) all contribute to oak regeneration failure by suppressing oak seedling growth and reducing survival. Timber harvest is one way to create light conditions favorable for shade‐intolerant oak seedlings, but other biotic factors, especially competition and herbivory, continue to play a role in oak seedling growth and survival following harvest. We experimentally planted oak seedlings in several timber harvesting treatments and under varying conditions of herbivory and interspecific competition to assess the relative importance of these drivers of early oak life history and their interaction with timber harvest. Overall, seedling survival over the 4‐yr study was negatively related to competition but not herbivory, and growth was negatively related to herbivory but not competition. Herbivore pressure was generally mild across the study area. Abiotic factors also played an important role: Severe drought during the first two growing seasons (2011–2012) had a negative effect on both growth and survival, especially for seedlings in harvest openings and on southwestern‐facing slopes (sites that should normally favor shade‐intolerant oak). Meanwhile, a partial harvesting technique (shelterwood harvest) increased available light for oak regeneration while appearing to buffer against the effects of the drought. More extreme weather conditions, brought on by climate change, will likely present challenges for forest managers seeking to regenerate oak via timber harvest. Phased harvesting systems like shelterwoods, in addition to their other advantages, may mitigate the impacts of drought while still encouraging oak seedling growth.
Tests to monitor quality of deep‐frying fats and oils (2004)

Abstract There are dozens of tests an oil chemist has at his disposal for evaluating fresh and used frying oils. These include chemical tests, instrumental methods, physical methods and rapid tests. Not all are applicable to use when evaluating oils used for deep‐fat frying. Rather than run the gamut of all the tests available to the oil chemist or quality control technician, this presentation will focus on the different rapid tests that have been developed for the marketplace. These include physical tests, tests that measure physical parameters of the oil, and chemical tests. Tests may be quite simple or complex. The presenter will provide an overview on the different rapid test methods, but will emphasize that it is up to the researcher or the processor to evaluate for themselves whether the technology is something that they can use in their own operations.
Hardware/software selected cycle solution (2002)

For many system designs where hardware and software are co-dependent, there often exists a design bottleneck where most of the hardware design has to be completed and fabricated before meaningful software verification can begin. In some sectors of electronic design where competitive markets require that the design cycle has to be completed quickly-mobile phone handsets and image decoders, for instance-having the software ready and substantially debugged as soon as the hardware is ready can give a significant competitive advantage. This paper describes a methodology that allows practical hardware/software co-simulation to achieve meaningful software verification early in the design cycle. The technique allows software development and testing to be more concurrent with the hardware development by using simulated models of the hardware design to interact with the software programs. A high level of performance is achieved by using the simulated description on selected target processor cycles only. Only the important bus cycles are simulated in the hardware simulator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ergebnisse und Probleme der <i>O</i>‐Glykosidsynthese (1974)

Abstract Die Synthese von biologisch wichtigen Naturstoffen mit mehr oder minder kompliziertem Kohlenhydratanteil wirft erhebliche Probleme auf. Im vorliegenden Fortschrittsbericht wird über neuere Entwicklungen bei der Knüpfung der O ‐Glykosidbindung — ausgehend von 1‐Halogenzuckern und von 1,2‐Zuckerorthoestern — berichtet. Dabei wird versucht, aufgrund reaktions‐mechanistischer Überlegungen vor allem den stereochemischen Ablauf von Glykosylierungsreaktionen besser zu verstehen. Die Untersuchung der Silbersalzabhängigkeit der Koenigs‐Knorr‐Synthese führte zu präparativen Verbesserungen des Verfahrens und zu neuen Vorstellungen über den Reaktionsablauf. Eine wesentliche Bereicherung der präparativen Möglichkeiten zur Synthese von trans ‐Glykosiden war die Einführung von 1,2‐Zuckerorthoestern als Glykosylierungskomponente. Sehr bemerkenswerte Fortschritte sind vor allem auch bei der Synthese von cis ‐Glykosiden, u. a. durch Ausnutzung von neuartigen Nachbargruppeneffekten, zu verzeichnen.
LSTM-Based Intrusion Detection System for In-Vehicle Can Bus Communications (2020)

The modern automobile is a complex piece of technology that uses the Controller Area Network (CAN) bus system as a central system for managing the communication between the electronic control units (ECUs). Despite its central importance, the CAN bus system does not support authentication and authorization mechanisms, i.e., CAN messages are broadcast without basic security features. As a result, it is easy for attackers to launch attacks at the CAN bus network system. Attackers can compromise the CAN bus system in several ways including Denial of Service (DoS), Fuzzing and Spoofing attacks. It is imperative to devise methodologies to protect modern cars against the aforementioned attacks. In this paper, we propose a Long Short-Term Memory (LSTM)-based Intrusion Detection System (IDS) to detect and mitigate the CAN bus network attacks. We generate our own dataset by first extracting attack-free data from our experimental car and by injecting attacks into the latter and collecting the dataset. We use the dataset for testing and training our model. With our selected hyper-parameter values, our results demonstrate that our classifier is efficient in detecting the CAN bus network attacks, we achieved an overall detection accuracy of 99.995%. We also compare the proposed LSTM method with the Survival Analysis for automobile IDS dataset which is developed by the Hacking and Countermeasure Research Lab, Korea. Our proposed LSTM model achieves a higher detection rate than the Survival Analysis method.
Determination of prescription dose for Cs‐131 permanent implants using the BED formalism including resensitization correction (2014)

Inclusion of an allowance for resensitization led to significant dose corrections for Cs-131 permanent implants, and should be applied to prescription dose calculation. The adjustment of the Cs-131 prescription doses with resensitization correction for gynecological permanent implants was consistent with clinical experience and observations. However, the Cs-131 prescription doses converted from other implant doses can be further adjusted based on new experimental results, clinical observations, and clinical outcomes.
Evidence for functional redundancy of class IA PI3K isoforms in insulin signalling (2007)

Recent genetic knock-in and pharmacological approaches have suggested that, of class IA PI3Ks (phosphatidylinositol 3-kinases), it is the p110alpha isoform (PIK3CA) that plays the predominant role in insulin signalling. We have used isoform-selective inhibitors of class IA PI3K to dissect further the roles of individual p110 isoforms in insulin signalling. These include a p110alpha-specific inhibitor (PIK-75), a p110alpha-selective inhibitor (PI-103), a p110beta-specific inhibitor (TGX-221) and a p110delta-specific inhibitor (IC87114). Although we find that p110alpha is necessary for insulin-stimulated phosphorylation of PKB (protein kinase B) in several cell lines, we find that this is not the case in HepG2 hepatoma cells. Inhibition of p110beta or p110delta alone was also not sufficient to block insulin signalling to PKB in these cells, but, when added in combination with p110alpha inhibitors, they are able to significantly attenuate insulin signalling. Surprisingly, in J774.2 macrophage cells, insulin signalling to PKB was inhibited to a similar extent by inhibitors of p110alpha, p110beta or p110delta. These results provide evidence that p110beta and p110delta can play a role in insulin signalling and also provide the first evidence that there can be functional redundancy between p110 isoforms. Further, our results indicate that the degree of functional redundancy is linked to the relative levels of expression of each isoform in the target cells.
<i>N</i>-Tosyl-(<i>S</i><sub>a</sub>)-binam-<scp>l</scp>-prolinamide as Highly Efficient Bifunctional Organocatalyst for the General Enantioselective Solvent-Free Aldol Reaction (2008)

N-Tosyl-(Sa)-binam-L-prolinamide (5 mol%) and benzoic acid (1 mol%) were used as catalysts in the enantioselective direct aldol reaction between different ketones and aldehydes under solvent-free conditions in the presence or absence of water. Under this reaction conditions it was possible to reduce the amount of required ketone to 2 equiv to give the corresponding aldol products with high yields, regio-, diastereo- and enantioselectivities. The aldol reaction between aldehydes or the intramolecular aldol reaction can be also performed with excellent results.
Functional role of J domain of cysteine string protein in Ca<sup>2+</sup>-dependent secretion from acinar cells (2009)

The heat shock protein 70 family members Hsc70 and Hsp70 are known to play a protective role against the onset of experimental pancreatitis, yet their molecular function in acini is unclear. Cysteine string protein (CSP-alpha) is a zymogen granule (ZG) membrane protein characterized by an NH(2)-terminal "J domain" and a central palmitoylated string of cysteine residues. The J domain functions as a cochaperone by modulating the activity of Hsc70/Hsp70 family members. A role for CSP-alpha in regulating digestive enzyme exocytosis from pancreas was investigated by introducing CSP-alpha truncations into isolated acini following their permeabilization with Perfringolysin O. Incubation of acini with CSP-alpha(1-82), containing the J domain, significantly augmented Ca(2+)-stimulated amylase secretion. Effects of CSP-alpha(1-82) were concentration dependent, with a maximum 80% increase occurring at 200 microg/ml of protein. Although CSP-alpha(1-82) had no effects on basal secretion measured in the presence of < or =10 nM free Ca(2+), it did significantly augment GTP-gammaS-induced secretion under basal Ca(2+) conditions by approximately 25%. Mutation of the J domain to abolish its cochaperone activity failed to augment Ca(2+)-stimulated secretion, implicating the CSP-alpha/Hsc70 cochaperone system as a regulatory component of the secretory pathway. CSP-alpha physically associates with vesicle-associated membrane protein 8 (VAMP 8) on ZGs, and the CSP-alpha-VAMP 8 interaction was dependent on amino acids 83-112 of CSP-alpha. Immunofluorescence analysis of acinar lobules or purified ZGs confirmed the CSP-alpha colocalization with VAMP 8. These data establish a role for CSP-alpha in regulating digestive enzyme secretion and suggest that CSP-alpha and Hsc70 modulate specific soluble N-ethylmaleimide-sensitive attachment receptor interactions necessary for exocytosis.
Calculating Relative Clock Drifts Using IEEE 802.11 Beacons (2009)

This paper proposes an approach to calculate the relative clock drift occurring between two communicating nodes in an WLAN system using IEEE 802.11 beacon frames. The IEEE 802.11 beacon frames contain a timestamp field that tells the time at which the packet was sent from the transmitting node. If a IEEE 802.11 packet is received, the WLAN card stores a timestamp that precisely depicts the time at which the packet was received. Using these timestamps, we developed an algorithm that calculates the relative clock drift between two nodes and conducted many experimental measurements using off-the-shelf WLAN cards showing the clock drifts under different circumstances. Knowing the relative clock drifts is important for two-way time-of-arrival (TOA) location tracking.
Paroxysmal slow cortical activity in Alzheimer’s disease and epilepsy is associated with blood-brain barrier dysfunction (2019)

Transient EEG slowing events are shared by patients and models of Alzheimer’s and epilepsy and are associated with blood-brain barrier dysfunction.
Design and Performance of a Resistor Multiplexing Readout Circuit for a SiPM Detector (2013)

A silicon photomultiplier (SiPM)-based positron emission tomography (PET) detector was developed using a resistor network charge division multiplexing circuit for detector readout. The detector consists of a lutetium-yttrium oxy-orthosilicate (LYSO) scintillation crystal array, an SiPM array detector (SPMArray 4, SensL Inc., Cork, Ireland) and the resistor multiplexing network implemented in a through-hole package to facilitate changing of resistor values. For purposes of optimizing the readout circuit, the LYSO array used was a 4 4 crystal array with crystal size mm on a pitch of 3.37 mm, matched to the SiPM pixel size. Flood image, energy resolution, photopeak amplitude, timing resolution, and signal time-pickoff measurements were performed using standard NIM electronics. The resistor network values were optimized through an iterative process. The performance of the detector was evaluated over a range of temperatures from 23°C to 60°C by heating the detector. The ability of the detector to resolve crystals smaller than the SiPM pixel pitch was evaluated using a dual-layer LYSO array with crystals of 1.67-mm pitch. The optimal resistor network values were found to be 100 Ω along the rows connecting the SiPM pixels and 56 Ω for the columns. For these resistor value settings, the average energy resolution for the central four crystals in the array at 23.5°C was 13.3% ± 0.3% and degraded to 16.3% ± 0.3% at 60°C. The photopeak amplitude decreased by 2%/°C, and the timing resolution degraded from 3.43 ± 0.22 ns to 4.64 ± 0.25 ns for a 350-750-keV energy window over this temperature range. The signal time-pick-off point shifted earlier by 2.7 ns as the temperature increased, an effect likely due to changes in the signal shape with temperature. The detector was able to resolve all 113 crystals in the dual-layer LYSO array. These results demonstrate that the resistor multiplexing readout circuit functions well for reading out SiPM array based detectors, which use scintillator crystal arrays much smaller than the SiPM pixel pitch. The reduced number of output signals achieved through this signal multiplexing greatly reduces the number of signal cables required. In addition, the ability of this detector to function over a wide range of temperatures offers significant flexibility in defining the system operating temperature set point.
Limb Movements Classification Using Wearable Wireless Transceivers (2011)

A feasibility study, where small wireless transceivers are used to classify some typical limb movements used in physical therapy processes is presented. Wearable wireless low-cost commercial transceivers operating at 2.4 GHz are supposed to be widely deployed in indoor settings and on people's bodies in tomorrow's pervasive computing environments. The key idea of this work is to exploit their presence by collecting the received signal strength measured between those worn by a person. The measurements are used to classify a set of kinesiotherapy activities. The collected data are classified by using both support vector machine and K-nearest neighbor methods, in order to recognise the different activities.
Effect of 2-(3,4-dichlorophenoxy)triethylamine on tomato Lycopersicon esculentum cv. UCD-82 (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of 2-(3,4-dichlorophenoxy)triethylamine on tomato Lycopersicon esculentum cv. UCD-82Wan Jean Hsu and Henry YokoyamaCite this: J. Agric. Food Chem. 1991, 39, 1, 96–98Publication Date (Print):January 1, 1991Publication History Published online1 May 2002Published inissue 1 January 1991https://doi.org/10.1021/jf00001a018RIGHTS & PERMISSIONSArticle Views48Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (375 KB) Get e-Alerts Get e-Alerts
On-chip modulation of evanescent illumination and live-cell imaging with polymer waveguides (2011)

Imaging of live cells was carried out using evanescent-wave excitation on a polymer waveguide chip. Integrated waveguide-based interferometric light modulators were fabricated in order to demonstrate on-chip control of excitation light, e.g., for time-lapse fluorescence microscopy. When combined with a sensitive high-resolution imaging system, the integrated waveguide-excitation platform provides an ideal method of near-surface studies of live cells, where photobleaching and/or phototoxicity effects are of critical concern.
Stabilization of Small, Pyrophoric Iron Particles by Surface Polymerization (1970)

Pyrophoric iron powders, produced by the reduction of , have been stabilized with respect to air oxidation by a method of surface polymerization which results in the formation of a plastic film around the particles. The polymer‐coated iron was subjected to various heat treatments in air and to test its resistance to oxidation. The iron was highly resistant to oxidation as long as the decomposition temperature of the polymer was not exceeded (between 140° and 180°C). Therefore, this method of stabilization holds promise in overcoming a major problem in the use of fine particles of magnetic metals and alloys for permanent magnets and magnetic recording applications.