gebhart/patrepeval huggingface dataset:
Maize WRKY Transcription Factor ZmWRKY106 Confers Drought and Heat Tolerance in Transgenic Plants (2018)

WRKY transcription factors constitute one of the largest transcription factor families in plants, and play crucial roles in plant growth and development, defense regulation and stress responses. However, knowledge about this family in maize is limited. In the present study, we identified a drought-induced WRKY gene, <i>ZmWRKY106</i>, based on the maize drought <i>de novo</i> transcriptome sequencing data. ZmWRKY106 was identified as part of the WRKYII group, and a phylogenetic tree analysis showed that ZmWRKY106 was closer to OsWRKY13. The subcellular localization of ZmWRKY106 was only observed in the nucleus. The promoter region of <i>ZmWRKY106</i> included the C-repeat/dehydration responsive element (DRE), low-temperature responsive element (LTR), MBS, and TCA-elements, which possibly participate in drought, cold, and salicylic acid (SA) stress responses. The expression of <i>ZmWRKY106</i> was induced significantly by drought, high temperature, and exogenous abscisic acid (ABA), but was weakly induced by salt. Overexpression of <i>ZmWRKY106</i> improved the tolerance to drought and heat in transgenic <i>Arabidopsis</i> by regulating stress-related genes through the ABA-signaling pathway, and the reactive oxygen species (ROS) content in transgenic lines was reduced by enhancing the activities of superoxide dismutase (SOD), peroxide dismutase (POD), and catalase (CAT) under drought stress. This suggested that <i>ZmWRKY106</i> was involved in multiple abiotic stress response pathways and acted as a positive factor under drought and heat stress.
deLiver'in Regeneration: Injury Response and Development (2010)

Liver regeneration has traditionally been investigated in mammalian models. Recent technological developments in mouse genetics have greatly enhanced the resolving power of these studies. In addition, the zebrafish system has emerged as a complementary genetic system to study liver regeneration. One of the most promising attributes of the zebrafish system is its amenability to large-scale screens including genetic and chemical screens. Also, as our understanding of liver development is becoming more detailed, it is important to evaluate the commonalities and differences between organ development and regeneration.
Invariant Extended Kalman Filter design for a magnetometer-plus-GPS aided inertial navigation system (2011)

We introduce a magnetometer-plus-GPS aided inertial navigation system for a helicopter UAV. A nonlinear observer is required to estimate the navigation states, typically an Extended Kalman Filter (EKF). A novel approach is the invariant observer, a constructive design method applicable to systems possessing symmetries. We review the theory and design an invariant observer for our example. Using an invariant observer guarantees a simplified form of the nonlinear estimation error dynamics. These are stabilized using an adaptation of the Invariant EKF, a systematic approach to compute the gains of an invariant observer. The resulting design is successfully implemented and validated in experiment and shows an improvement in performance over a conventional EKF.
Principles for high-quality, high-value testing (2012)

A survey of doctors working in two large NHS hospitals identified over 120 laboratory tests, imaging investigations and investigational procedures that they considered not to be overused. A common suggestion in this survey was that more training was required. And, this prompted the development of a list of core principles for high-quality, high-value testing. The list can be used as a framework for training and as a reference source. The core principles are: (1) Base testing practices on the best available evidence. (2) Apply the evidence on test performance with careful judgement. (3) Test efficiently. (4) Consider the value (and affordability) of a test before requesting it. (5) Be aware of the downsides and drivers of overdiagnosis. (6) Confront uncertainties. (7) Be patient-centred in your approach. (8) Consider ethical issues. (9) Be aware of normal cognitive limitations and biases when testing. (10) Follow the 'knowledge journey' when teaching and learning these core principles.
Analytical Approaches for Determining Chemical Oxygen Demand in Water Bodies: A Review (2017)

Chemical oxygen demand (COD) is a critical analytical parameter for water quality assessment. COD represents the degree of organic pollution in water bodies. However, the standard analytical methods for COD are time-consuming and possess low oxidation efficiency, chloride interference, and severe secondary pollution. Works performed during the last two decades have resulted in several technologies, including modified standard methods (e.g., microwave-assisted method) and new technologies or methods (e.g., electro- and photo-oxidative methods based on advanced oxidation processes) that are less time-consuming, environment friendly, and more reliable. This review is devoted in analyzing the technical features of the principal methods described in the literature to compare their performances (i.e., measuring window, reliability, and robustness) and identify the advantages and disadvantages of each method.
Polymorphic proteins encoded within BZLF1 of defective and standard Epstein-Barr viruses disrupt latency (1987)

These experiments identify an Epstein-Barr virus-encoded gene product, called ZEBRA (BamHI fragment Z Epstein-Barr replication activator) protein, which activates a switch between the latent and replicative life cycle of the virus. Our previous work had shown that the 2.7-kilobase-pair WZhet piece of rearranged Epstein-Barr virus DNA from a defective virus activated replication when introduced into cells with a latent genome, but it was not clear whether a protein product was required for the phenomenon. We now use deletional, site-directed, and chimeric mutagenesis, together with gene transfer, to show that a 43-kilodalton protein, encoded in the BZLF1 open reading frame of het DNA, is responsible for this process. The rearrangement in defective DNA does not contribute to the structural gene for the protein. Similar proteins with variable electrophoretic mobility (37 to 39 kilodaltons) were encoded by BamHI Z fragments from standard, nondefective Epstein-Barr virus genomes. Plasmids expressing the ZEBRA proteins from B95-8 and HR-1 viruses were less efficient at activating replication in D98/HR-1 cells than those which contained the ZEBRA gene from the defective virus. It is not yet known whether these functional differences are due to variations in expression of the plasmids or to intrinsic differences in the activity of these polymorphic polypeptides.
DUX4 in Cells and Mice (2008)

By targeting each FSHD candidate gene to a doxycycline-inducible locus in murine C2 myoblasts, we have shown that DUX4 is uniquely toxic, that this toxicity is caused by sensitizing cells to oxidative stress, and that both Pax3 and Pax7 act as dominant inhibitors of the DUX4 phenotype. At low, non-toxic, levels of expression, DUX4 interferes with the expression of myogenic regulators and inhibits differentiation, a feature shared by DUX4c. Using a set of deletion and frameshift mutants, we show that both repression of MyoD and inhibition of differentiation require translation of the homeodomains but not the c-terminus, while toxicity requires translation of both the homeodomains and the c-terminus. Based on these results, we introduced DUX4, in the context of the terminal D4Z4 repeat, into mouse ES cells downstream of a doxycycline-inducible promoter on the X chromosome, proximal to the ubiquitously-expressed HPRT locus. We had previously tried, unsuccessfully, to generate transgenic mice carrying DUX4 and D4Z4 in various constructs by pronuclear injection (random integration) without success. Using the X-linked inducible locus, we have now derived strains carrying D4Z4/DUX4, however surprisingly, the D4Z4/DUX4 X chromosome (XD) is malespecific lethal, even without dox. Female carriers are fertile but suffer a growth disadvantage and a severe skin phenotype. Although they do not display an obvious muscular dystrophy, these are the first mice to carry phenotypically active D4Z4 sequences. We hypothesize that D4Z4 sequences interact with our basal promoter, resulting in DUX4 expression, and consequent growth defects. We interpret previous failures to generate mice carrying active D4Z4 repeats to be due to strong selection against D4Z4 integrations into open chromatin where DUX4 may be expressed. Females may be partially protected from the dominant-lethal gene by X-inactivation, an unintended consequence of our X-linked approach. We discuss these results in the context of developing an animal model for FSHD.
Hyperammonemia and Alzheimer's Disease (1989)

To the Editor: — Dr. Mendez, in his report of a case of hepatic dementia and in the course of summarizing the associated neuropathological findings in the brain, indicates the presence of spongiform changes at the corticomedullary junction and in the striatum.1 Cortical spongiform change may also be found in a small percentage of Alzheimer brains at autopsy, usually confined to entorhinal cortex, inferior temporal gyrus, and amygdala. We have previously reported on postprandial hyperammonemia that may be found in patients with Alzheimer's disease.2 Autopsy findings, including neuropathological findings, are now available on six of these patients; this has allowed us to investigate in this small sample the relationship (if any) between ammonia level, triphasic waves, and the presence of spongiform change. Our findings are summarized in the accompanying Table and indicate that in the small sample examined no relationship was found between ammonia level and presence of triphasic waves or focal spongiform change; and that no spongiform change was noted in the two patients with evidence of triphasic waves on EEC
PCR amplification of the fimA gene sequence of Salmonella typhimurium, a specific method for detection of Salmonella spp (1996)

The goal of this study was to evaluate the suitability of the fimA gene amplification by PCR as a specific method for detection of Salmonella strains. Salmonella typhimurium and other pathogenic members of the family Enterobacteriaceae produce morphologically and antigenically related, thin, aggregative, type 1 fimbriae. A single gene, fimA, encodes the major fimbrial unit. In order to obtain higher specificity, we have selected a series of primers internal to the fimA gene sequence and have developed a PCR method for detecting Salmonella strains. A collection of 376 strains of Salmonella comprising over 80 serovars, isolated from animals and humans in Canada, have been used to evaluate this PCR method. Forty non-Salmonella strains were also tested by the same procedure. Cultures were screened by inoculating a single colony of bacteria directly into a PCR mixture containing a pair of primers specific for the fimA gene. The specific PCR product is an 85-bp fragment which was visualized by polyacrylamide gel electrophoresis and ethidium bromide staining. All Salmonella strains gave positive results by the PCR. Feed and milk samples contaminated by Salmonella strains were also detected by this procedure. The detection of all Salmonella strains tested and the failure to amplify the fragment from non-Salmonella strains confirm that the fimA gene contains sequences unique to Salmonella strains and demonstrate that this gene is a suitable PCR target for detection of Salmonella strains in food samples.
Robert de Niro’s <i>Raging Bull</i>: The History of a Performance and a Performance of History (2011)

Cet article fait une utilisation des archives de Robert De Niro, récemment acquises par le Harry Ransom Center, pour fournir une analyse théorique et historique de la contribution singulière de l’acteur au film Raging Bull (Martin Scorcese, 1980). En utilisant les notes considérables de De Niro, cet article désire montrer que le travail de cheminement du comédien s’est étendu de la pré à la postproduction, ce qui est particulièrement bien démontré par la contribution significative mais non mentionnée au générique, de l’acteur au scénario. La performance de De Niro brouille les frontières des classes de l’auteur, de la « star » et du travail de collaboration et permet de faire un portrait plus nuancé du travail de réalisation d’un film. Cet article dresse le catalogue du processus, durant près de six ans, entrepris par le comédien pour jouer le rôle du boxeur Jacke LaMotta : De la phase d’écriture du scénario à sa victoire aux Oscars, en passant par l’entrainement d’un an à la boxe et par la prise de soixante livres. Enfin, en se fondant sur des données concrètes qui sont restées jusqu’à maintenant inaccessibles, en raison de la modestie et du désir du comédien de conserver sa vie privée, cet article apporte une nouvelle perspective pour considérer la contribution importante de De Niro à l’histoire américaine du jeu d’acteur.
Size-induced diffuse phase transition in the nanocrystalline ferroelectric<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">PbTiO</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math> (1995)

We report a detailed study of the size dependence of the ferroelectric transition in an ensemble of ${\mathrm{PbTiO}}_{3}$ nanoparticles produced by coprecipitation. The phase transition was monitored by dielectric measurements, variable temperature x-ray diffraction, and differential scanning calorimetry (DSC). Size effects were found to become important only below \ensuremath{\approxeq}100 nm (coherently diffracting x-ray domain size). The tetragonal distortion of the unit cell (which is related to the spontaneous polarization) decreases exponentially with size and vanishes at 7 nm. The ${\mathit{T}}_{\mathit{c}}$ decreases gradually but the transition becomes increasingly diffuse with a decrease in the size from 80 to 30 nm, below which there is no peak in the dielectric constant or the heat flow (DSC), though ferroelectric ordering probably persists down to \ensuremath{\approxeq}7 nm.
NITROGENOUS CONSTITUENTS OF BREWING MATERIALS XII. FOAM-STABILIZING SUBSTANCES IN BEER (1963)

Material of comparatively high molecular weight was recovered from whole beer by means of a previously employed modification of the Cohn method. This fraction, which contained the bulk of the foam-stabilizing capacity of the original beer, was sub-fractionated by means of gel filtration. Five distinct components were thus obtained of which one, amounting to approximately 10% of the original material, had the greatest foam-stabilizing activity. Whereas this active fraction contained, in addition to protein, some 50% carbohydrate, including all the pentose material of the original, the inactive fractions contained little or no carbohydrate. However, further fractionation led to the removal of 60% of this carbohydrate but without removal of foam-stabilizing activity. All those fractions which could produce foams either contained protein or were substantially of protein nature.
A control scheme for batching DRAM requests to improve power efficiency (2011)

This paper introduces a closed-loop control algorithm to coordinate power management of memory ranks and thereby achieve power savings beyond independent rank power management while bounding the throughput degradation.
Densification Mechanism of Yttria-Stabilized Tetragonal Zirconia Powders by Pulse Current Pressure Sintering (2010)

The influence of an applied stress (σ) on densification behaviors of a mechanically milled 3Y-TZP ceramic powder by pulse current pressure sintering (PCPS) has been investigated. The densification rate vs temperature (ρ−T) and densification rate vs relative density (ρ−ρ) curves at the constant heating rates (HR=0.1, 0.3, 1.0 and 2.0 K/s) could be described using data points (T, ρ and ρ) selected from all the results of PCPS conducted at the various electric currents in the range of 700 to 1000 A. Although the ρ values increase with increasing HR, the T and ρ values corresponding to the peaks of ρ (ρmax) show almost the constant values of 1300 K and 0.8 (at σ=90.5 MPa) respectively, irrespective of HR. By the increase of σ, moreover, the T value corresponding to ρmax shifts to the lower T side, however the ρ value corresponding to ρmax remains unchanged. Although the stress exponent (n) values, which are the gradient of the ln ρ vs ln σeff lines (σeff: effective stress), increase continuously with increasing T, but the re-estimated n values from the ln ρ vs ln (σeff−σ0) lines (σ0: threshold stress) show almost the constant value of 1.85 to 1.97. Also, the apparent activation energy (Q) estimated from the Arrhenius plot of ln (σeff−σ0) vs 1/T is 521.14±18.43 kJ/mol. The obtained n and Q values suggest that densification of the 3Y-TZP powder compacts by PCPS proceeds by grain boundary sliding affected by the threshold stress as well as the creep deformation in the middle stress region, and rate-determined by lattice diffusion of the solute Zr4+ ions.
Micro hydraulic system using slim artificial muscles for a wearable haptic glove (2008)

Over the past few decades, various haptic gloves have been developed for use in virtual environments. The actuating systems for most existing haptic gloves require lots of external auxiliary equipment. Because of this, the motion of the user is restricted by the length of the electric wires or pneumatic tubes attached to this equipment. A compact actuation system, including related equipment, is thus indispensable for a wearable haptic glove to be truly effective. To resolve the problem of hampered motion and reach, a micro hydraulic actuating system was developed in this research. It was composed of a slim, flexible artificial muscle, a compact hydraulic module for actuating the muscle, and a micro pressure sensor for measuring without flux loss. The characteristics of the muscle were investigated for their control capacity. The step and sinusoidal responses were analyzed to evaluate the performance of the micro hydraulic system. Once these analyses were completed, a lightweight and compact actuation system was built incorporating a wearable haptic glove. By virtue of the developed micro hydraulic system, the wearable haptic glove was able to operate independently of any external equipment, and movement was completely free of any restrictions from wires or tubes.
Collaborative care documentation by exception system. (1992)

Development of a workstation-based documentation system supporting collaborative care and nurse charting by exception has been underway for the last two and one-half years at Vanderbilt University Medical Center in Nashville, Tennessee. The Pathways system has undergone two major revisions and is currently implemented on three nursing units. The system supports collaborative care by providing a mechanism for entry and printing of collaborative care pathways and collection of exception data. Paper flowsheets for manual charting are generated based on the patient's collaborative pathway and individual needs. The Pathways system has significantly decreased nursing time and effort for documentation. This paper describes the development, implementation, and impact of the workstation-based documentation system.
Erythropoietic Colonies in Cultures of Human Marrow (1974)

Abstract The cell culture method originally devised by Stephenson and Axelrad for erythropoietin-dependent erythropoietic colony formation (CFU-E) by mouse cells has been adapted to human marrow. Erythropoietic colonies from human marrow contain between eight and 150 cells and reach maximum growth after 7-9 days of incubation. Progenitors of larger colonies differ from the total pool of human CFU-E in that they have a slower mean sedimentation velocity and a greater erythropoietin requirement. The assay is quantitative and was used to determine the radiation sensitivity of human erythropoietic progenitors. The parameters of the survival curve are: Do = 113 ± 7.8, n = 1.5 ± 0.15.
A Software Requirements Specification Framework for Objective Pattern Recognition: A Set-Theoretic Classification Approach (2011)

The motivation behind pattern-oriented software development is to decompose complex problems into recognizable sub-problems with predefined solutions, hence promoting both the quality of the resulting software product and the efficiency of the development process through the reuse of optimal solutions (e.g., best practices). Unfortunately, due to the opportunistic (i.e., non-systematic and subjective) element inherent in the process of recognizing conventional patterns in a problem context, the full potential of a pattern-driven problem-solving strategy has not been yet realized. In this paper, we introduce a requirements specification framework, called Problem Decomposition Scheme (PDS), which serves as a foundation to address the challenges of pattern recognition in the context of software requirements. We establish that pattern recognition can be abstracted as a set-theoretic classification problem, and formalize the properties of the resulting classification scheme. In contrast to ill-defined sub-problems in conventional development problem contexts, patterns in PDS-based specifications can be objectively recognized. To evaluate our requirements specification framework, we conducted an empirical user study of software developers performing a requirements pattern recognition task on a PDS-based requirements specification. PDS-based specifications are shown to achieve a high degree of requirements pattern recognition consistency across developers.
A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression (2014)

R loops are three-stranded nucleic acid structures that comprise nascent RNA hybridized with the DNA template, leaving the nontemplate DNA single-stranded. R loops form naturally during transcription even though their persistent formation can be a risky outcome with deleterious effects on genome integrity. On the other hand, over the last few years, an increasingly strong case has been built for R loops as potential regulators of gene expression. Therefore, understanding their function and regulation under these opposite situations is essential to fully characterize the mechanisms that control genome integrity and gene expression. Here we review recent findings about these interesting structures that highlight their opposite roles in cellular fitness.
Syntax-directed editing environments (1993)

Article Free Access Share on Syntax-directed editing environments: issues and features Authors: Amir Ali Khwaja Arizona State Univ., Tempe Arizona State Univ., TempeView Profile , Joseph E. Urban Arizona State Univ., Tempe Arizona State Univ., TempeView Profile Authors Info & Claims SAC '93: Proceedings of the 1993 ACM/SIGAPP symposium on Applied computing: states of the art and practiceMarch 1993 Pages 230–237https://doi.org/10.1145/162754.162882Published:01 March 1993Publication History 15citation596DownloadsMetricsTotal Citations15Total Downloads596Last 12 Months46Last 6 weeks8 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF