Spectroscopic classification of AT 2017byx as a Type Ia Supernova

NASA Astrophysics Data System (ADS)

Vinko, J.; Wheeler, J. C.; Sarneczky, K.; Szakats, R.; Szalai, T.; Szekely, P.; HETDEX Collaboration

2017-05-01

During the commissioning phase of the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) survey we observed AT 2017byx (ATLAS17bla, PS17bve) at R.A.=14:17:48.36 Dec.=+52:41:54.6 with the Visible Integral-field Replicable Unit Spectrograph (VIRUS) at McDonald Observatory on 2017-04-28.2 UT. The spectrum (range between 3500 and 5500 Angstroms) indicates that AT 2017byx is a Type Ia supernova.

Design of the fiber optic support system and fiber bundle accelerated life test for VIRUS

NASA Astrophysics Data System (ADS)

Soukup, Ian M.; Beno, Joseph H.; Hayes, Richard J.; Heisler, James T.; Mock, Jason R.; Mollison, Nicholas T.; Good, John M.; Hill, Gary J.; Vattiat, Brian L.; Murphy, Jeremy D.; Anderson, Seth C.; Bauer, Svend M.; Kelz, Andreas; Roth, Martin M.; Fahrenthold, Eric P.

2010-07-01

The quantity and length of optical fibers required for the Hobby-Eberly Telescope* Dark Energy eXperiment (HETDEX) create unique fiber handling challenges. For HETDEX‡, at least 33,600 fibers will transmit light from the focal surface of the telescope to an array of spectrographs making up the Visible Integral-Field Replicable Unit Spectrograph (VIRUS). Up to 96 Integral Field Unit (IFU) bundles, each containing 448 fibers, hang suspended from the telescope's moving tracker located more than 15 meters above the VIRUS instruments. A specialized mechanical system is being developed to support fiber optic assemblies onboard the telescope. The discrete behavior of 448 fibers within a conduit is also of primary concern. A life cycle test must be conducted to study fiber behavior and measure Focal Ratio Degradation (FRD) as a function of time. This paper focuses on the technical requirements and design of the HETDEX fiber optic support system, the electro-mechanical test apparatus for accelerated life testing of optical fiber assemblies. Results generated from the test will be of great interest to designers of robotic fiber handling systems for major telescopes. There is concern that friction, localized contact, entanglement, and excessive tension will be present within each IFU conduit and contribute to FRD. The test apparatus design utilizes six linear actuators to replicate the movement of the telescope over 65,000 accelerated cycles, simulating five years of actual operation.

Replication domains are self-interacting structural chromatin units of human chromosomes

NASA Astrophysics Data System (ADS)

Arneodo, Alain

2011-03-01

In higher eukaryotes, the absence of specific sequence motifs marking the origins of replication has been a serious hindrance to the understanding of the mechanisms that regulate the initiation and the maintenance of the replication program in different cell types. In silico analysis of nucleotide compositional skew has predicted the existence, in the germline, of replication N-domains bordered by putative replication origins and where the skew decreases rather linearly as the signature of a progressive inversion of the average fork polarity. Here, from the demonstration that the average fork polarity can be directly extracted from the derivative of replication timing profiles, we develop a wavelet-based pattern recognition methodology to delineate replication U-domains where the replication timing profile is shaped as a U and its derivative as a N. Replication U-domains are robustly found in seven cell lines as covering a significant portion (40-50%) of the human genome where the replication timing data actually displays some plasticity between cell lines. The early replication initiation zones at U-domains borders are found to be hypersensitive to DNase I cleavage, to be associated with transcriptional activity and to present a significant enrichment in insular-binding proteins CTCF, the hallmark of an open chromatin structure. A comparative analysis of genome-wide chromatin interaction (HiC) data shows that replication-U domains correspond to self-interacting structural high order chromatin units of megabase characteristic size. Taken together, these findings provide evidence that the epigenetic compartmentalization of the human genome into autonomous replication U-domains comes along with an extensive remodelling of the threedimensional chromosome architecture during development or in specific diseases. The observed cell specific conservation of the replication timing between the human and mouse genomes strongly suggests that this chromosome organization into self-interacting structural and functional units is a general feature of mammalian organisms.

Cultural traits as units of analysis.

PubMed

O'Brien, Michael J; Lyman, R Lee; Mesoudi, Alex; VanPool, Todd L

2010-12-12

Cultural traits have long been used in anthropology as units of transmission that ostensibly reflect behavioural characteristics of the individuals or groups exhibiting the traits. After they are transmitted, cultural traits serve as units of replication in that they can be modified as part of an individual's cultural repertoire through processes such as recombination, loss or partial alteration within an individual's mind. Cultural traits are analogous to genes in that organisms replicate them, but they are also replicators in their own right. No one has ever seen a unit of transmission, either behavioural or genetic, although we can observe the effects of transmission. Fortunately, such units are manifest in artefacts, features and other components of the archaeological record, and they serve as proxies for studying the transmission (and modification) of cultural traits, provided there is analytical clarity over how to define and measure the units that underlie this inheritance process.

Cultural traits as units of analysis

PubMed Central

O'Brien, Michael J.; Lyman, R. Lee; Mesoudi, Alex; VanPool, Todd L.

2010-01-01

Cultural traits have long been used in anthropology as units of transmission that ostensibly reflect behavioural characteristics of the individuals or groups exhibiting the traits. After they are transmitted, cultural traits serve as units of replication in that they can be modified as part of an individual's cultural repertoire through processes such as recombination, loss or partial alteration within an individual's mind. Cultural traits are analogous to genes in that organisms replicate them, but they are also replicators in their own right. No one has ever seen a unit of transmission, either behavioural or genetic, although we can observe the effects of transmission. Fortunately, such units are manifest in artefacts, features and other components of the archaeological record, and they serve as proxies for studying the transmission (and modification) of cultural traits, provided there is analytical clarity over how to define and measure the units that underlie this inheritance process. PMID:21041205

NACSA Charter School Replication Guide: The Spectrum of Replication Options. Authorizing Matters. Replication Brief 1

ERIC Educational Resources Information Center

O'Neill, Paul

2010-01-01

One of the most important and high-profile issues in public education reform today is the replication of successful public charter school programs. With more than 5,000 failing public schools in the United States, there is a tremendous need for strong alternatives for parents and students. Replicating successful charter school models is an…

SPRUCE S1 Bog Vegetation Survey and Peat Depth Data: 2009

DOE Data Explorer

Hanson, P. J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A

2009-12-31

This data set reports the results of a field survey of the S1 Bog to characterize the vegetation and to determine peat depth. The survey was conducted on September 21 and 22, 2009. The initial survey of vegetation and peat depth characteristics of the target bog was conducted to evaluate the logical locations for installing replicated experimental blocks for SPRUCE. The goal was to identify multiple locations of uniform aboveground vegetation and belowground peat depth for positioning experimental units within the bog.

Phosphorylated STAT5 directly facilitates parvovirus B19 DNA replication in human erythroid progenitors through interaction with the MCM complex.

PubMed

Ganaie, Safder S; Zou, Wei; Xu, Peng; Deng, Xuefeng; Kleiboeker, Steve; Qiu, Jianming

2017-05-01

Productive infection of human parvovirus B19 (B19V) exhibits high tropism for burst forming unit erythroid (BFU-E) and colony forming unit erythroid (CFU-E) progenitor cells in human bone marrow and fetal liver. This exclusive restriction of the virus replication to human erythroid progenitor cells is partly due to the intracellular factors that are essential for viral DNA replication, including erythropoietin signaling. Efficient B19V replication also requires hypoxic conditions, which upregulate the signal transducer and activator of transcription 5 (STAT5) pathway, and phosphorylated STAT5 is essential for virus replication. In this study, our results revealed direct involvement of STAT5 in B19V DNA replication. Consensus STAT5-binding elements were identified adjacent to the NS1-binding element within the minimal origins of viral DNA replication in the B19V genome. Phosphorylated STAT5 specifically interacted with viral DNA replication origins both in vivo and in vitro, and was actively recruited within the viral DNA replication centers. Notably, STAT5 interacted with minichromosome maintenance (MCM) complex, suggesting that STAT5 directly facilitates viral DNA replication by recruiting the helicase complex of the cellular DNA replication machinery to viral DNA replication centers. The FDA-approved drug pimozide dephosphorylates STAT5, and it inhibited B19V replication in ex vivo expanded human erythroid progenitors. Our results demonstrated that pimozide could be a promising antiviral drug for treatment of B19V-related diseases.

Topologically associating domains are stable units of replication-timing regulation.

PubMed

Pope, Benjamin D; Ryba, Tyrone; Dileep, Vishnu; Yue, Feng; Wu, Weisheng; Denas, Olgert; Vera, Daniel L; Wang, Yanli; Hansen, R Scott; Canfield, Theresa K; Thurman, Robert E; Cheng, Yong; Gülsoy, Günhan; Dennis, Jonathan H; Snyder, Michael P; Stamatoyannopoulos, John A; Taylor, James; Hardison, Ross C; Kahveci, Tamer; Ren, Bing; Gilbert, David M

2014-11-20

Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.

Phosphorylated STAT5 directly facilitates parvovirus B19 DNA replication in human erythroid progenitors through interaction with the MCM complex

PubMed Central

Ganaie, Safder S.; Zou, Wei; Xu, Peng; Deng, Xuefeng; Kleiboeker, Steve

2017-01-01

Productive infection of human parvovirus B19 (B19V) exhibits high tropism for burst forming unit erythroid (BFU-E) and colony forming unit erythroid (CFU-E) progenitor cells in human bone marrow and fetal liver. This exclusive restriction of the virus replication to human erythroid progenitor cells is partly due to the intracellular factors that are essential for viral DNA replication, including erythropoietin signaling. Efficient B19V replication also requires hypoxic conditions, which upregulate the signal transducer and activator of transcription 5 (STAT5) pathway, and phosphorylated STAT5 is essential for virus replication. In this study, our results revealed direct involvement of STAT5 in B19V DNA replication. Consensus STAT5-binding elements were identified adjacent to the NS1-binding element within the minimal origins of viral DNA replication in the B19V genome. Phosphorylated STAT5 specifically interacted with viral DNA replication origins both in vivo and in vitro, and was actively recruited within the viral DNA replication centers. Notably, STAT5 interacted with minichromosome maintenance (MCM) complex, suggesting that STAT5 directly facilitates viral DNA replication by recruiting the helicase complex of the cellular DNA replication machinery to viral DNA replication centers. The FDA-approved drug pimozide dephosphorylates STAT5, and it inhibited B19V replication in ex vivo expanded human erythroid progenitors. Our results demonstrated that pimozide could be a promising antiviral drug for treatment of B19V-related diseases. PMID:28459842

Replication Research and Special Education

ERIC Educational Resources Information Center

Travers, Jason C.; Cook, Bryan G.; Therrien, William J.; Coyne, Michael D.

2016-01-01

Replicating previously reported empirical research is a necessary aspect of an evidence-based field of special education, but little formal investigation into the prevalence of replication research in the special education research literature has been conducted. Various factors may explain the lack of attention to replication of special education…

Topological entropy of catalytic sets: Hypercycles revisited

NASA Astrophysics Data System (ADS)

Sardanyés, Josep; Duarte, Jorge; Januário, Cristina; Martins, Nuno

2012-02-01

The dynamics of catalytic networks have been widely studied over the last decades because of their implications in several fields like prebiotic evolution, virology, neural networks, immunology or ecology. One of the most studied mathematical bodies for catalytic networks was initially formulated in the context of prebiotic evolution, by means of the hypercycle theory. The hypercycle is a set of self-replicating species able to catalyze other replicator species within a cyclic architecture. Hypercyclic organization might arise from a quasispecies as a way to increase the informational containt surpassing the so-called error threshold. The catalytic coupling between replicators makes all the species to behave like a single and coherent evolutionary multimolecular unit. The inherent nonlinearities of catalytic interactions are responsible for the emergence of several types of dynamics, among them, chaos. In this article we begin with a brief review of the hypercycle theory focusing on its evolutionary implications as well as on different dynamics associated to different types of small catalytic networks. Then we study the properties of chaotic hypercycles with error-prone replication with symbolic dynamics theory, characterizing, by means of the theory of topological Markov chains, the topological entropy and the periods of the orbits of unimodal-like iterated maps obtained from the strange attractor. We will focus our study on some key parameters responsible for the structure of the catalytic network: mutation rates, autocatalytic and cross-catalytic interactions.

Melatonin and puberty in female lambs exposed to EMF: A replicate study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, J.M. Jr.; Stormshak, F.; Thompson, J.M.

1995-06-01

In an earlier study, the authors found no effects of 60 Hz electric and magnetic fields (EMF) from a 500 kV transmission line on serum melatonin patterns or on puberty in ten female Suffolk lambs (Ovis aries). The authors conducted a larger replicate study of 15 lambs exposed to a mean electric field of 6.3 kV/m and a mean magnetic field of 3.77 {mu}T and 15 controls exposed to EMF two orders of magnitude weaker than in the line area. The replicate produced essentially the same results as their previous study.

VIRUS instrument enclosures

NASA Astrophysics Data System (ADS)

Prochaska, T.; Allen, R.; Mondrik, N.; Rheault, J. P.; Sauseda, M.; Boster, E.; James, M.; Rodriguez-Patino, M.; Torres, G.; Ham, J.; Cook, E.; Baker, D.; DePoy, Darren L.; Marshall, Jennifer L.; Hill, G. J.; Perry, D.; Savage, R. D.; Good, J. M.; Vattiat, Brian L.

2014-08-01

The Visible Integral-Field Replicable Unit Spectrograph (VIRUS) instrument will be installed at the Hobby-Eberly Telescope† in the near future. The instrument will be housed in two enclosures that are mounted adjacent to the telescope, via the VIRUS Support Structure (VSS). We have designed the enclosures to support and protect the instrument, to enable servicing of the instrument, and to cool the instrument appropriately while not adversely affecting the dome environment. The system uses simple HVAC air handling techniques in conjunction with thermoelectric and standard glycol heat exchangers to provide efficient heat removal. The enclosures also provide power and data transfer to and from each VIRUS unit, liquid nitrogen cooling to the detectors, and environmental monitoring of the instrument and dome environments. In this paper, we describe the design and fabrication of the VIRUS enclosures and their subsystems.

Replicating annual North Atlantic hurricane activity 1878-2012 from environmental variables

NASA Astrophysics Data System (ADS)

Saunders, Mark A.; Klotzbach, Philip J.; Lea, Adam S. R.

2017-06-01

Statistical models can replicate annual North Atlantic hurricane activity from large-scale environmental field data for August and September, the months of peak hurricane activity. We assess how well the six environmental fields used most often in contemporary statistical modeling of seasonal hurricane activity replicate North Atlantic hurricane numbers and Accumulated Cyclone Energy (ACE) over the 135 year period from 1878 to 2012. We find that these fields replicate historical hurricane activity surprisingly well, showing that contemporary statistical models and their seasonal physical links have long-term robustness. We find that August-September zonal trade wind speed over the Caribbean Sea and the tropical North Atlantic is the environmental field which individually replicates long-term hurricane activity the best and that trade wind speed combined with the difference in sea surface temperature between the tropical Atlantic and the tropical mean is the best multi-predictor model. Comparing the performance of the best single-predictor and best multi-predictor models shows that they exhibit little difference in hindcast skill for predicting long-term ACE but that the best multipredictor model offers improved skill for predicting long-term hurricane numbers. We examine whether replicated real-time prediction skill 1983-2012 increases as the model training period lengthens and find evidence that this happens slowly. We identify a dropout in hurricane replication centered on the 1940s and show that this is likely due to a decrease in data quality which affects all data sets but Atlantic sea surface temperatures in particular. Finally, we offer insights on the implications of our findings for seasonal hurricane prediction.

Role of the Polymerase ϵ sub-unit DPB2 in DNA replication, cell cycle regulation and DNA damage response in Arabidopsis.

PubMed

Pedroza-Garcia, José Antonio; Domenichini, Séverine; Mazubert, Christelle; Bourge, Mickael; White, Charles; Hudik, Elodie; Bounon, Rémi; Tariq, Zakia; Delannoy, Etienne; Del Olmo, Ivan; Piñeiro, Manuel; Jarillo, Jose Antonio; Bergounioux, Catherine; Benhamed, Moussa; Raynaud, Cécile

2016-09-06

Faithful DNA replication maintains genome stability in dividing cells and from one generation to the next. This is particularly important in plants because the whole plant body and reproductive cells originate from meristematic cells that retain their proliferative capacity throughout the life cycle of the organism. DNA replication involves large sets of proteins whose activity is strictly regulated, and is tightly linked to the DNA damage response to detect and respond to replication errors or defects. Central to this interconnection is the replicative polymerase DNA Polymerase ϵ (Pol ϵ) which participates in DNA replication per se, as well as replication stress response in animals and in yeast. Surprisingly, its function has to date been little explored in plants, and notably its relationship with DNA Damage Response (DDR) has not been investigated. Here, we have studied the role of the largest regulatory sub-unit of Arabidopsis DNA Pol ϵ: DPB2, using an over-expression strategy. We demonstrate that excess accumulation of the protein impairs DNA replication and causes endogenous DNA stress. Furthermore, we show that Pol ϵ dysfunction has contrasting outcomes in vegetative and reproductive cells and leads to the activation of distinct DDR pathways in the two cell types. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Topologically-associating domains are stable units of replication-timing regulation

PubMed Central

Pope, Benjamin D.; Ryba, Tyrone; Dileep, Vishnu; Yue, Feng; Wu, Weisheng; Denas, Olgert; Vera, Daniel L.; Wang, Yanli; Hansen, R. Scott; Canfield, Theresa K.; Thurman, Robert E.; Cheng, Yong; Gülsoy, Günhan; Dennis, Jonathan H.; Snyder, Michael P.; Stamatoyannopoulos, John A.; Taylor, James; Hardison, Ross C.; Kahveci, Tamer; Ren, Bing; Gilbert, David M.

2014-01-01

Summary Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program1. During mammalian development, at least half the genome changes replication timing, primarily in units of 400–800 kb (“replication domains”; RDs), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements2–7. Early and late replication correlate strongly with open and closed chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, lamina-associated domains (LADs)4,5,8,9. Recent Hi-C mapping has unveiled a substructure of topologically-associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to RDs8,10. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale11,12. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure8,9,13. Here, we localize boundaries of RDs to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, RD boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure RD boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell type specific sub-nuclear compartmentalization with developmentally stable chromosome domains and offer a unified model for large-scale chromosome structure and function. PMID:25409831

A Replication of the Internal Validity Structure of Three Major Teaching Rating Scales

ERIC Educational Resources Information Center

Peters, Scott J.; Pereira, Nielsen

2017-01-01

Even as the importance of replication research has become more widely understood, the field of gifted education is almost completely devoid of replication studies. An area in which replication is a particular problem is in student identification research, since instrument validity is a necessary prerequisite for any sound psychometric decision. To…

Genetic analysis without replications: Model evaluation and application in spring wheat

USDA-ARS?s Scientific Manuscript database

Genetic data collected from plant breeding and genetic studies may not be replicated in field designs even though field variation is present. In this study, we addressed this problem using spring wheat (Triticum eastivum L.) trial data collected from two locations. There were no intra-location repl...

Replicating Social Programmes: Approaches, Strategies and Conceptual Issues. Management of Social Transformations (MOST) Discussion Paper Series, No. 18.

ERIC Educational Resources Information Center

van Oudenhoven, Nico; Wazir, Rekha

This paper reviews the key issues and methodologies involved in the replication of social programs, as they pertain to non-profit sector development in the United States and in international development. The related process of knowledge transfer and dissemination, as well as the more specific strategies involved in replication and going-to-scale…

Replication of clinical innovations in multiple medical practices.

PubMed

Henley, N S; Pearce, J; Phillips, L A; Weir, S

1998-11-01

Many clinical innovations had been successfully developed and piloted in individual medical practice units of Kaiser Permanente in North Carolina during 1995 and 1996. Difficulty in replicating these clinical innovations consistently throughout all 21 medical practice units led to development of the interdisciplinary Clinical Innovation Implementation Team, which was formed by using existing resources from various departments across the region. REPLICATION MODEL: Based on a model of transfer of best practices, the implementation team developed a process and tools (master schedule and activity matrix) to quickly replicate successful pilot projects throughout all medical practice units. The process involved the following steps: identifying a practice and delineating its characteristics and measures (source identification); identifying a team to receive the (new) practice; piloting the practice; and standardizing, including the incorporation of learnings. The model includes the following components for each innovation: sending and receiving teams, an innovation coordinator role, an innovation expert role, a location expert role, a master schedule, and a project activity matrix. Communication depended on a partnership among the location experts (local knowledge and credibility), the innovation coordinator (process expertise), and the innovation experts (content expertise). Results after 12 months of working with the 21 medical practice units include integration of diabetes care team services into the practices, training of more than 120 providers in the use of personal computers and an icon-based clinical information system, and integration of a planwide self-care program into the medical practices--all with measurable improved outcomes. The model for sequential replication and the implementation team structure and function should be successful in other organizational settings.

It's Time to Broaden the Replicability Conversation: Thoughts for and From Clinical Psychological Science.

PubMed

Tackett, Jennifer L; Lilienfeld, Scott O; Patrick, Christopher J; Johnson, Sheri L; Krueger, Robert F; Miller, Joshua D; Oltmanns, Thomas F; Shrout, Patrick E

2017-09-01

Psychology is in the early stages of examining a crisis of replicability stemming from several high-profile failures to replicate studies in experimental psychology. This important conversation has largely been focused on social psychology, with some active participation from cognitive psychology. Nevertheless, several other major domains of psychological science-including clinical science-have remained insulated from this discussion. The goals of this article are to (a) examine why clinical psychology and allied fields, such as counseling and school psychology, have not been central participants in the replicability conversation; (b) review concerns and recommendations that are less (or more) applicable to or appropriate for research in clinical psychology and allied fields; and (c) generate take-home messages for scholars and consumers of the literature in clinical psychology and allied fields, as well as reviewers, editors, and colleagues from other areas of psychological science.

Dedicated education unit: implementing an innovation in replication sites.

PubMed

Moscato, Susan R; Nishioka, Vicki M; Coe, Michael T

2013-05-01

An important measure of an innovation is the ease of replication and achievement of the same positive outcomes. The dedicated education unit (DEU) clinical education model uses a collaborative academic-service partnership to develop an optimal learning environment for students. The University of Portland adapted this model from Flinders University, Australia, to increase the teaching capacity and quality of nursing education. This article identifies DEU implementation essentials and reports on the outcomes of two replication sites that received consultation support from the University of Portland. Program operation information, including education requirements for clinician instructors, types of patient care units, and clinical faculty-to-student ratios is presented. Case studies of the three programs suggest the DEU model is adaptable to a range of different clinical settings and continues to show promise as one strategy for addressing the nurse faculty shortage and strengthening academic-clinical collaborations while maintaining quality clinical education for students. Copyright 2013, SLACK Incorporated.

Challenges in reproducibility of genetic association studies: lessons learned from the obesity field.

PubMed

Li, A; Meyre, D

2013-04-01

A robust replication of initial genetic association findings has proved to be difficult in human complex diseases and more specifically in the obesity field. An obvious cause of non-replication in genetic association studies is the initial report of a false positive result, which can be explained by a non-heritable phenotype, insufficient sample size, improper correction for multiple testing, population stratification, technical biases, insufficient quality control or inappropriate statistical analyses. Replication may, however, be challenging even when the original study describes a true positive association. The reasons include underpowered replication samples, gene × gene, gene × environment interactions, genetic and phenotypic heterogeneity and subjective interpretation of data. In this review, we address classic pitfalls in genetic association studies and provide guidelines for proper discovery and replication genetic association studies with a specific focus on obesity.

Self-replication with magnetic dipolar colloids

NASA Astrophysics Data System (ADS)

Dempster, Joshua M.; Zhang, Rui; Olvera de la Cruz, Monica

2015-10-01

Colloidal self-replication represents an exciting research frontier in soft matter physics. Currently, all reported self-replication schemes involve coating colloidal particles with stimuli-responsive molecules to allow switchable interactions. In this paper, we introduce a scheme using ferromagnetic dipolar colloids and preprogrammed external magnetic fields to create an autonomous self-replication system. Interparticle dipole-dipole forces and periodically varying weak-strong magnetic fields cooperate to drive colloid monomers from the solute onto templates, bind them into replicas, and dissolve template complexes. We present three general design principles for autonomous linear replicators, derived from a focused study of a minimalist sphere-dimer magnetic system in which single binding sites allow formation of dimeric templates. We show via statistical models and computer simulations that our system exhibits nonlinear growth of templates and produces nearly exponential growth (low error rate) upon adding an optimized competing electrostatic potential. We devise experimental strategies for constructing the required magnetic colloids based on documented laboratory techniques. We also present qualitative ideas about building more complex self-replicating structures utilizing magnetic colloids.

The Obligate Human Pathogen, Neisseria gonorrhoeae, Is Polyploid

PubMed Central

Tobiason, Deborah M; Seifert, H. Steven

2006-01-01

We show using several methodologies that the Gram-negative, diplococcal-bacterium Neisseria gonorrhoeae has more than one complete genome copy per cell. Gene dosage measurements demonstrated that only a single replication initiation event per chromosome occurs per round of cell division, and that there is a single origin of replication. The region containing the origin does not encode any genes previously associated with bacterial origins of replication. Quantitative PCR results showed that there are on average three genome copies per coccal cell unit. These findings allow a model for gonococcal DNA replication and cell division to be proposed, in which a minimum of two chromosomal copies exist per coccal unit within a monococcal or diplococcal cell, and these chromosomes replicate in unison to produce four chromosomal copies during cell division. Immune evasion via antigenic variation is an important mechanism that allows these organisms to continually infect a high risk population of people. We propose that polyploidy may be necessary for the high frequency gene conversion system that mediates pilin antigenic variation and the propagation of N. gonorrhoeae within its human hosts. PMID:16719561

Mass production of volume phase holographic gratings for the VIRUS spectrograph array

NASA Astrophysics Data System (ADS)

Chonis, Taylor S.; Frantz, Amy; Hill, Gary J.; Clemens, J. Christopher; Lee, Hanshin; Tuttle, Sarah E.; Adams, Joshua J.; Marshall, J. L.; DePoy, D. L.; Prochaska, Travis

2014-07-01

The Visible Integral-field Replicable Unit Spectrograph (VIRUS) is a baseline array of 150 copies of a simple, fiber-fed integral field spectrograph that will be deployed on the Hobby-Eberly Telescope (HET). VIRUS is the first optical astronomical instrument to be replicated on an industrial scale, and represents a relatively inexpensive solution for carrying out large-area spectroscopic surveys, such as the HET Dark Energy Experiment (HETDEX). Each spectrograph contains a volume phase holographic (VPH) grating with a 138 mm diameter clear aperture as its dispersing element. The instrument utilizes the grating in first-order for 350 < λ (nm) < 550. Including witness samples, a suite of 170 VPH gratings has been mass produced for VIRUS. Here, we present the design of the VIRUS VPH gratings and a discussion of their mass production. We additionally present the design and functionality of a custom apparatus that has been used to rapidly test the first-order diffraction efficiency of the gratings for various discrete wavelengths within the VIRUS spectral range. This device has been used to perform both in-situ tests to monitor the effects of adjustments to the production prescription as well as to carry out the final acceptance tests of the gratings' diffraction efficiency. Finally, we present the as-built performance results for the entire suite of VPH gratings.

Using stochastic cell division and death to probe minimal units of cellular replication

NASA Astrophysics Data System (ADS)

Chib, Savita; Das, Suman; Venkatesan, Soumya; Sai Narain Seshasayee, Aswin; Thattai, Mukund

2018-03-01

The invariant cell initiation mass measured in bacterial growth experiments has been interpreted as a minimal unit of cellular replication. Here we argue that the existence of such minimal units induces a coupling between the rates of stochastic cell division and death. To probe this coupling we tracked live and dead cells in Escherichia coli populations treated with a ribosome-targeting antibiotic. We find that the growth exponent from macroscopic cell growth or decay measurements can be represented as the difference of microscopic first-order cell division and death rates. The boundary between cell growth and decay, at which the number of live cells remains constant over time, occurs at the minimal inhibitory concentration (MIC) of the antibiotic. This state appears macroscopically static but is microscopically dynamic: division and death rates exactly cancel at MIC but each is remarkably high, reaching 60% of the antibiotic-free division rate. A stochastic model of cells as collections of minimal replicating units we term ‘widgets’ reproduces both steady-state and transient features of our experiments. Sub-cellular fluctuations of widget numbers stochastically drive each new daughter cell to one of two alternate fates, division or death. First-order division or death rates emerge as eigenvalues of a stationary Markov process, and can be expressed in terms of the widget’s molecular properties. High division and death rates at MIC arise due to low mean and high relative fluctuations of widget number. Isolating cells at the threshold of irreversible death might allow molecular characterization of this minimal replication unit.

How (and Whether) to Teach Undergraduates about the Replication Crisis in Psychological Science

ERIC Educational Resources Information Center

Chopik, William J.; Bremner, Ryan H.; Defever, Andrew M.; Keller, Victor N.

2018-01-01

Over the past 10 years, crises surrounding replication, fraud, and best practices in research methods have dominated discussions in the field of psychology. However, no research exists examining how to communicate these issues to undergraduates and what effect this has on their attitudes toward the field. We developed and validated a 1-hr lecture…

The Bimodal Lifestyle of Intracellular Salmonella in Epithelial Cells: Replication in the Cytosol Obscures Defects in Vacuolar Replication

PubMed Central

Steele-Mortimer, Olivia

2012-01-01

Salmonella enterica serovar Typhimurium invades and proliferates within epithelial cells. Intracellular bacteria replicate within a membrane bound vacuole known as the Salmonella containing vacuole. However, this bacterium can also replicate efficiently in the cytosol of epithelial cells and net intracellular growth is a product of both vacuolar and cytosolic replication. Here we have used semi-quantitative single-cell analyses to investigate the contribution of each of these replicative niches to intracellular proliferation in cultured epithelial cells. We show that cytosolic replication can account for the majority of net replication even though it occurs in less than 20% of infected cells. Consequently, assays for net growth in a population of infected cells, for example by recovery of colony forming units, are not good indicators of vacuolar proliferation. We also show that the Salmonella Type III Secretion System 2, which is required for SCV biogenesis, is not required for cytosolic replication. Altogether this study illustrates the value of single cell analyses when studying intracellular pathogens. PMID:22719929

Single molecule analysis of Trypanosoma brucei DNA replication dynamics

PubMed Central

Calderano, Simone Guedes; Drosopoulos, William C.; Quaresma, Marina Mônaco; Marques, Catarina A.; Kosiyatrakul, Settapong; McCulloch, Richard; Schildkraut, Carl L.; Elias, Maria Carolina

2015-01-01

Eukaryotic genome duplication relies on origins of replication, distributed over multiple chromosomes, to initiate DNA replication. A recent genome-wide analysis of Trypanosoma brucei, the etiological agent of sleeping sickness, localized its replication origins to the boundaries of multigenic transcription units. To better understand genomic replication in this organism, we examined replication by single molecule analysis of replicated DNA. We determined the average speed of replication forks of procyclic and bloodstream form cells and we found that T. brucei DNA replication rate is similar to rates seen in other eukaryotes. We also analyzed the replication dynamics of a central region of chromosome 1 in procyclic forms. We present evidence for replication terminating within the central part of the chromosome and thus emanating from both sides, suggesting a previously unmapped origin toward the 5′ extremity of chromosome 1. Also, termination is not at a fixed location in chromosome 1, but is rather variable. Importantly, we found a replication origin located near an ORC1/CDC6 binding site that is detected after replicative stress induced by hydroxyurea treatment, suggesting it may be a dormant origin activated in response to replicative stress. Collectively, our findings support the existence of more replication origins in T. brucei than previously appreciated. PMID:25690894

Single molecule analysis of Trypanosoma brucei DNA replication dynamics.

PubMed

Calderano, Simone Guedes; Drosopoulos, William C; Quaresma, Marina Mônaco; Marques, Catarina A; Kosiyatrakul, Settapong; McCulloch, Richard; Schildkraut, Carl L; Elias, Maria Carolina

2015-03-11

Eukaryotic genome duplication relies on origins of replication, distributed over multiple chromosomes, to initiate DNA replication. A recent genome-wide analysis of Trypanosoma brucei, the etiological agent of sleeping sickness, localized its replication origins to the boundaries of multigenic transcription units. To better understand genomic replication in this organism, we examined replication by single molecule analysis of replicated DNA. We determined the average speed of replication forks of procyclic and bloodstream form cells and we found that T. brucei DNA replication rate is similar to rates seen in other eukaryotes. We also analyzed the replication dynamics of a central region of chromosome 1 in procyclic forms. We present evidence for replication terminating within the central part of the chromosome and thus emanating from both sides, suggesting a previously unmapped origin toward the 5' extremity of chromosome 1. Also, termination is not at a fixed location in chromosome 1, but is rather variable. Importantly, we found a replication origin located near an ORC1/CDC6 binding site that is detected after replicative stress induced by hydroxyurea treatment, suggesting it may be a dormant origin activated in response to replicative stress. Collectively, our findings support the existence of more replication origins in T. brucei than previously appreciated. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Selectionist and Evolutionary Approaches to Brain Function: A Critical Appraisal

PubMed Central

Fernando, Chrisantha; Szathmáry, Eörs; Husbands, Phil

2012-01-01

We consider approaches to brain dynamics and function that have been claimed to be Darwinian. These include Edelman’s theory of neuronal group selection, Changeux’s theory of synaptic selection and selective stabilization of pre-representations, Seung’s Darwinian synapse, Loewenstein’s synaptic melioration, Adam’s selfish synapse, and Calvin’s replicating activity patterns. Except for the last two, the proposed mechanisms are selectionist but not truly Darwinian, because no replicators with information transfer to copies and hereditary variation can be identified in them. All of them fit, however, a generalized selectionist framework conforming to the picture of Price’s covariance formulation, which deliberately was not specific even to selection in biology, and therefore does not imply an algorithmic picture of biological evolution. Bayesian models and reinforcement learning are formally in agreement with selection dynamics. A classification of search algorithms is shown to include Darwinian replicators (evolutionary units with multiplication, heredity, and variability) as the most powerful mechanism for search in a sparsely occupied search space. Examples are given of cases where parallel competitive search with information transfer among the units is more efficient than search without information transfer between units. Finally, we review our recent attempts to construct and analyze simple models of true Darwinian evolutionary units in the brain in terms of connectivity and activity copying of neuronal groups. Although none of the proposed neuronal replicators include miraculous mechanisms, their identification remains a challenge but also a great promise. PMID:22557963

Termination of DNA replication forks: "Breaking up is hard to do".

PubMed

Bailey, Rachael; Priego Moreno, Sara; Gambus, Agnieszka

2015-01-01

To ensure duplication of the entire genome, eukaryotic DNA replication initiates from thousands of replication origins. The replication forks move through the chromatin until they encounter forks from neighboring origins. During replication fork termination forks converge, the replisomes disassemble and topoisomerase II resolves the daughter DNA molecules. If not resolved efficiently, terminating forks result in genomic instability through the formation of pathogenic structures. Our recent findings shed light onto the mechanism of replisome disassembly upon replication fork termination. We have shown that termination-specific polyubiquitylation of the replicative helicase component - Mcm7, leads to dissolution of the active helicase in a process dependent on the p97/VCP/Cdc48 segregase. The inhibition of terminating helicase disassembly resulted in a replication termination defect. In this extended view we present hypothetical models of replication fork termination and discuss remaining and emerging questions in the DNA replication termination field.

The binding efficiency of RPA to telomeric G-strands folded into contiguous G-quadruplexes is independent of the number of G4 units.

PubMed

Lancrey, Astrid; Safa, Layal; Chatain, Jean; Delagoutte, Emmanuelle; Riou, Jean-François; Alberti, Patrizia; Saintomé, Carole

2018-03-01

Replication protein A (RPA) is a single-stranded DNA binding protein involved in replication and in telomere maintenance. During telomere replication, G-quadruplexes (G4) can accumulate on the lagging strand template and need to be resolved. It has been shown that human RPA is able to unfold a single G4. Nevertheless, the G-strand of human telomeres is prone to fold into higher-order structures formed by contiguous G-quadruplexes. To understand how RPA deals with these structures, we studied its interaction with telomeric G-strands folding into an increasing number of contiguous G4s. The aim of this study was to determine whether the efficiency of binding/unfolding of hRPA to telomeric G-strands depends on the number of G4 units. Our data show that the number n of contiguous G4 units (n ≥ 2) does not affect the efficiency of hRPA to coat transiently exposed single-stranded telomeric G-strands. This feature may be essential in preventing instability due to G4 structures during telomere replication. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Validation of a 2 percent lactic acid antimicrobial rinse for mobile poultry slaughter operations.

PubMed

Killinger, Karen M; Kannan, Aditi; Bary, Andy I; Cogger, Craig G

2010-11-01

Poultry processing antimicrobial interventions are critical for pathogen control, and organic, mobile operations in Washington seek alternatives to chlorine. Laboratory and field studies (three replications each) evaluated lactic acid efficacy as a chlorine alternative. For the laboratory study, retail-purchased, conventionally processed chicken wings inoculated with Salmonella were randomly assigned to the following treatments: Salmonella inoculation followed by no treatment (10 wings) or by 3-min rinses of water, 50 to 100 ppm of chlorine, or 2% lactic acid (20 wings for each rinse treatment). Wings were sampled for Salmonella enumeration on xylose lysine desoxycholate agar. During pastured poultry processing at mobile slaughter units for each field study replication, 20 chicken carcasses were randomly assigned to each treatment: untreated control or 3-min immersion in lactic acid or chlorine. Whole-carcass rinses were examined for aerobic plate count (APC) on tryptic soy agar and coliforms on violet red bile agar. Untreated controls were also examined for Salmonella. In the laboratory study, lactic acid produced a significant (P < 0.01) Salmonella reduction compared with the inoculated no-rinse, water, and chlorine treatments, which were statistically similar to each other. In the field study, no Salmonella was detected on untreated controls. Lactic acid produced significant >2-log (P < 0.01) reductions in APC and coliforms, whereas chlorine resulted in slight, but significant 0.4-log reductions (P < 0.01) and 0.21-log reductions (P < 0.05) in APC and coliforms compared with untreated controls. Considering laboratory and field studies, lactic acid produced greater reductions in Salmonella, APC, and coliforms, validating its effectiveness as a chlorine alternative in mobile poultry slaughter operations.

Classroom-Based L2 Vocabulary Learning and Comprehension: Replications of Lesaux, Kieffer, Faller & Kelley (2010)

ERIC Educational Resources Information Center

Durgunoglu, Aydin Yücesan; Bigelow, Martha

2017-01-01

The field of language teaching and learning is in dire need of replications of vocabulary and comprehension research with diverse populations of learners. We propose for replication one large-scale vocabulary intervention carried out successfully in a middle-school with monolingual and multilingual students. This study was carried out several…

Designing perturbative metamaterials from discrete models.

PubMed

Matlack, Kathryn H; Serra-Garcia, Marc; Palermo, Antonio; Huber, Sebastian D; Daraio, Chiara

2018-04-01

Identifying material geometries that lead to metamaterials with desired functionalities presents a challenge for the field. Discrete, or reduced-order, models provide a concise description of complex phenomena, such as negative refraction, or topological surface states; therefore, the combination of geometric building blocks to replicate discrete models presenting the desired features represents a promising approach. However, there is no reliable way to solve such an inverse problem. Here, we introduce 'perturbative metamaterials', a class of metamaterials consisting of weakly interacting unit cells. The weak interaction allows us to associate each element of the discrete model with individual geometric features of the metamaterial, thereby enabling a systematic design process. We demonstrate our approach by designing two-dimensional elastic metamaterials that realize Veselago lenses, zero-dispersion bands and topological surface phonons. While our selected examples are within the mechanical domain, the same design principle can be applied to acoustic, thermal and photonic metamaterials composed of weakly interacting unit cells.

Current status of the HETDEX fiber optic support system

NASA Astrophysics Data System (ADS)

Good, John M.; Hill, Gary J.; Mollison, Nicholas T.; Vattiat, Brian L.; Murphy, Jeremy D.; Klez, Andreas; Roth, Martin M.; MacQueen, Phillip J.; Rafal, Marc D.; Savage, Richard D.; Smith, Michael P.; Bayless, Amanda J.

2008-07-01

The Hobby-Eberly Telescope Dark Energy eXperiment [HETDEX] will employ over 43,000 optical fibers to feed light to 192 Visible Integral-Field Replicable Unit Spectrographs [VIRUS]. Each VIRUS instrument is fed by 224 fibers. To reduce cost, the spectrographs are combined into pairs; thus, two bundles of 224 fibers are combined into a single Integral Field Unit [IFU] of 448 fibers. On the input end the fibers are arranged in a square 'dense-pack' array at the HET focal surface. At the output end the IFU terminates in two separate linear arrays which provide entry slits for each spectrometer unit. The IFU lengths must be kept to an absolute minimum to mitigate losses; however, consideration of overall project cost and duration of the science mission have resulted in the generation of two competing concepts. Multiple axes of motion are imposed on the IFUs as they span the shortest distance from the focal surface to each VIRUS unit. Arranging and supporting 96 IFUs, that have a total mass over 450 kg, in a manner that is compatible with these complex translations, together with the management of accompanying forces on the tracking mechanism of the HET, presents a significant technical challenge, which is further compounded by wind buffeting. The longer IFU concept is favored due to overall project cost, but requires tests to assure that the fibers can withstand forces associated with a height differential of 16.25 meters without FRD losses or breakage.

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

PubMed Central

Penton, C. Ryan; Gupta, Vadakattu V. S. R.; Yu, Julian; Tiedje, James M.

2016-01-01

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation. PMID:27313569

The Importance of Replication in Measurement Research: Using Curriculum-Based Measures with Postsecondary Students with Developmental Disabilities

ERIC Educational Resources Information Center

Hosp, John L.; Ford, Jeremy W.; Huddle, Sally M.; Hensley, Kiersten K.

2018-01-01

Replication is a foundation of the development of a knowledge base in an evidence-based field such as education. This study includes two direct replications of Hosp, Hensley, Huddle, and Ford which found evidence of criterion-related validity of curriculum-based measurement (CBM) for reading and mathematics with postsecondary students with…

Replication, falsification, and the crisis of confidence in social psychology

PubMed Central

Earp, Brian D.; Trafimow, David

2015-01-01

The (latest) crisis in confidence in social psychology has generated much heated discussion about the importance of replication, including how it should be carried out as well as interpreted by scholars in the field. For example, what does it mean if a replication attempt “fails”—does it mean that the original results, or the theory that predicted them, have been falsified? And how should “failed” replications affect our belief in the validity of the original research? In this paper, we consider the replication debate from a historical and philosophical perspective, and provide a conceptual analysis of both replication and falsification as they pertain to this important discussion. Along the way, we highlight the importance of auxiliary assumptions (for both testing theories and attempting replications), and introduce a Bayesian framework for assessing “failed” replications in terms of how they should affect our confidence in original findings. PMID:26042061

Rapid Communication: Effect of machine, anatomical location, and replication on instrumental color of boneless pork loins.

PubMed

Barkley, K E; Fields, B; Dilger, A C; Boler, D D

2018-06-07

The objective was to determine the effect of machine, anatomical location and replication (multiple readings) on instrumental color and to characterize the amount of variation each factor contributed to overall color. Instrumental color was measured 3 times on the anterior and 3 times on the posterior end of 250 pork loins with 2 different Minolta CR-400 Chroma meter devices. Each Minolta was programed to use a D65 illuminant, 2º observer with an 8 mm aperture, and calibrated with white tiles specific to each machine. Therefore, a total of 12 instrumental color measurements were collected on each loin. The VARCOMP procedure in SAS was used to estimate the proportion of variation contributed by each factor to CIE L*, a*, b*, chroma and hue. Based on previous research, the average untrained consumer is able to distinguish between 3-L* units, 0.4-a* units, and 0.9-hue angle units. Loins evaluated with machine 1 were 0.71 L* units darker (P < 0.01), 1.09 b* units more yellow (P < 0.01), 0.47 chroma units more saturated (P < 0.01), and had a hue angle 5.12 units greater (P < 0.01) than when evaluated with machine 2 but did not differ (P = 0.24) in redness. The anterior portion of the loin was lighter, less red, more yellow, more saturated and had a greater hue angle than the posterior end (P < 0.01). All color trait values decreased (P < 0.01) as replication number increased. Inherent color differences among loins contributed the greatest proportion of variability for lightness (58%), redness (57%), yellowness (70%), saturation (70%) and hue angle (49%). Machine contributed 1% variability to lightness 3% to saturation, 23% to yellowness and 31% to hue angle (31%) but did not contribute to variability for redness. Anatomical location contributed 41% to lightness, 43% to redness, 7% to yellowness, 27% to saturation and 31% to hue angle. Replication did not contribute to total variation for any color traits, even though it did differ among measurements. Overall, there were differences in instrumental color values between the two machines tested but those differences were likely less than the threshold for detection by a consumer. Even so, inherent color differences between loins were a greater contributor to total variability than the differences between the 2 machines. Therefore, it is more important to define the location of measurements than replication or machine when using a Minolta CR-400 when performing color evaluations, assuming the settings are the same.

Entanglement replication in driven dissipative many-body systems.

PubMed

Zippilli, S; Paternostro, M; Adesso, G; Illuminati, F

2013-01-25

We study the dissipative dynamics of two independent arrays of many-body systems, locally driven by a common entangled field. We show that in the steady state the entanglement of the driving field is reproduced in an arbitrarily large series of inter-array entangled pairs over all distances. Local nonclassical driving thus realizes a scale-free entanglement replication and long-distance entanglement distribution mechanism that has immediate bearing on the implementation of quantum communication networks.

Replication intermediates of the linear mitochondrial DNA of Candida parapsilosis suggest a common recombination based mechanism for yeast mitochondria.

PubMed

Gerhold, Joachim M; Sedman, Tiina; Visacka, Katarina; Slezakova, Judita; Tomaska, Lubomir; Nosek, Jozef; Sedman, Juhan

2014-08-15

Variation in the topology of mitochondrial DNA (mtDNA) in eukaryotes evokes the question if differently structured DNAs are replicated by a common mechanism. RNA-primed DNA synthesis has been established as a mechanism for replicating the circular animal/mammalian mtDNA. In yeasts, circular mtDNA molecules were assumed to be templates for rolling circle DNA-replication. We recently showed that in Candida albicans, which has circular mapping mtDNA, recombination driven replication is a major mechanism for replicating a complex branched mtDNA network. Careful analyses of C. albicans-mtDNA did not reveal detectable amounts of circular DNA molecules. In the present study we addressed the question of how the unit sized linear mtDNA of Candida parapsilosis terminating at both ends with arrays of tandem repeats (mitochondrial telomeres) is replicated. Originally, we expected to find replication intermediates diagnostic of canonical bi-directional replication initiation at the centrally located bi-directional promoter region. However, we found that the linear mtDNA of Candida parapsilosis also employs recombination for replication initiation. The most striking findings were that the mitochondrial telomeres appear to be hot spots for recombination driven replication, and that stable RNA:DNA hybrids, with a potential role in mtDNA replication, are also present in the mtDNA preparations. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Replication Intermediates of the Linear Mitochondrial DNA of Candida parapsilosis Suggest a Common Recombination Based Mechanism for Yeast Mitochondria*

PubMed Central

Gerhold, Joachim M.; Sedman, Tiina; Visacka, Katarina; Slezakova, Judita; Tomaska, Lubomir; Nosek, Jozef; Sedman, Juhan

2014-01-01

Variation in the topology of mitochondrial DNA (mtDNA) in eukaryotes evokes the question if differently structured DNAs are replicated by a common mechanism. RNA-primed DNA synthesis has been established as a mechanism for replicating the circular animal/mammalian mtDNA. In yeasts, circular mtDNA molecules were assumed to be templates for rolling circle DNA-replication. We recently showed that in Candida albicans, which has circular mapping mtDNA, recombination driven replication is a major mechanism for replicating a complex branched mtDNA network. Careful analyses of C. albicans-mtDNA did not reveal detectable amounts of circular DNA molecules. In the present study we addressed the question of how the unit sized linear mtDNA of Candida parapsilosis terminating at both ends with arrays of tandem repeats (mitochondrial telomeres) is replicated. Originally, we expected to find replication intermediates diagnostic of canonical bi-directional replication initiation at the centrally located bi-directional promoter region. However, we found that the linear mtDNA of Candida parapsilosis also employs recombination for replication initiation. The most striking findings were that the mitochondrial telomeres appear to be hot spots for recombination driven replication, and that stable RNA:DNA hybrids, with a potential role in mtDNA replication, are also present in the mtDNA preparations. PMID:24951592

Maternal Affective Expression and Infant's Mood in a Laboratory Situation: A Japanese Case.

ERIC Educational Resources Information Center

Chen, Shing-jen

The results of a Japanese replication of the vocalic social referencing experiment are discussed in comparison with original findings from the United States. The attempt to replicate failed. It is argued that the lack of success was due to (1) Japanese mothers' attitude toward laboratory situations, an attitude resulting from relative…

Cohesin organizes chromatin loops at DNA replication factories

PubMed Central

Guillou, Emmanuelle; Ibarra, Arkaitz; Coulon, Vincent; Casado-Vela, Juan; Rico, Daniel; Casal, Ignacio; Schwob, Etienne; Losada, Ana; Méndez, Juan

2010-01-01

Genomic DNA is packed in chromatin fibers organized in higher-order structures within the interphase nucleus. One level of organization involves the formation of chromatin loops that may provide a favorable environment to processes such as DNA replication, transcription, and repair. However, little is known about the mechanistic basis of this structuration. Here we demonstrate that cohesin participates in the spatial organization of DNA replication factories in human cells. Cohesin is enriched at replication origins and interacts with prereplication complex proteins. Down-regulation of cohesin slows down S-phase progression by limiting the number of active origins and increasing the length of chromatin loops that correspond with replicon units. These results give a new dimension to the role of cohesin in the architectural organization of interphase chromatin, by showing its participation in DNA replication. PMID:21159821

Meta-analysis of correlations revisited: attempted replication and extension of Field's (2001) simulation studies.

PubMed

Hafdahl, Adam R; Williams, Michelle A

2009-03-01

In 2 Monte Carlo studies of fixed- and random-effects meta-analysis for correlations, A. P. Field (2001) ostensibly evaluated Hedges-Olkin-Vevea Fisher-z and Schmidt-Hunter Pearson-r estimators and tests in 120 conditions. Some authors have cited those results as evidence not to meta-analyze Fisher-z correlations, especially with heterogeneous correlation parameters. The present attempt to replicate Field's simulations included comparisons with analytic values as well as results for efficiency and confidence-interval coverage. Field's results under homogeneity were mostly replicable, but those under heterogeneity were not: The latter exhibited up to over .17 more bias than ours and, for tests of the mean correlation and homogeneity, respectively, nonnull rejection rates up to .60 lower and .65 higher. Changes to Field's observations and conclusions are recommended, and practical guidance is offered regarding simulation evidence and choices among methods. Most cautions about poor performance of Fisher-z methods are largely unfounded, especially with a more appropriate z-to-r transformation. The Appendix gives a computer program for obtaining Pearson-r moments from a normal Fisher-z distribution, which is used to demonstrate distortion due to direct z-to-r transformation of a mean Fisher-z correlation.

Experimental Design and Data Analysis Issues Contribute to Inconsistent Results of C-Bouton Changes in Amyotrophic Lateral Sclerosis.

PubMed

Dukkipati, S Shekar; Chihi, Aouatef; Wang, Yiwen; Elbasiouny, Sherif M

2017-01-01

The possible presence of pathological changes in cholinergic synaptic inputs [cholinergic boutons (C-boutons)] is a contentious topic within the ALS field. Conflicting data reported on this issue makes it difficult to assess the roles of these synaptic inputs in ALS. Our objective was to determine whether the reported changes are truly statistically and biologically significant and why replication is problematic. This is an urgent question, as C-boutons are an important regulator of spinal motoneuron excitability, and pathological changes in motoneuron excitability are present throughout disease progression. Using male mice of the SOD1-G93A high-expresser transgenic ( G93A ) mouse model of ALS, we examined C-boutons on spinal motoneurons. We performed histological analysis at high statistical power, which showed no difference in C-bouton size in G93A versus wild-type motoneurons throughout disease progression. In an attempt to examine the underlying reasons for our failure to replicate reported changes, we performed further histological analyses using several variations on experimental design and data analysis that were reported in the ALS literature. This analysis showed that factors related to experimental design, such as grouping unit, sampling strategy, and blinding status, potentially contribute to the discrepancy in published data on C-bouton size changes. Next, we systematically analyzed the impact of study design variability and potential bias on reported results from experimental and preclinical studies of ALS. Strikingly, we found that practices such as blinding and power analysis are not systematically reported in the ALS field. Protocols to standardize experimental design and minimize bias are thus critical to advancing the ALS field.

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

DOE PAGES

Penton, C. Ryan; Gupta, Vadakattu V. S. R.; Yu, Julian; ...

2016-06-02

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungalmore » community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.« less

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Penton, C. Ryan; Gupta, Vadakattu V. S. R.; Yu, Julian

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungalmore » community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.« less

USP7/HAUSP: A SUMO deubiquitinase at the heart of DNA replication.

PubMed

Smits, Veronique A J; Freire, Raimundo

2016-09-01

DNA replication is both highly conserved and controlled. Problematic DNA replication can lead to genomic instability and therefore carcinogenesis. Numerous mechanisms work together to achieve this tight control and increasing evidence suggests that post-translational modifications (phosphorylation, ubiquitination, SUMOylation) of DNA replication proteins play a pivotal role in this process. Here we discuss such modifications in the light of a recent article that describes a novel role for the deubiquitinase (DUB) USP7/HAUSP in the control of DNA replication. USP7 achieves this function by an unusual and novel mechanism, namely deubiquitination of SUMOylated proteins at the replication fork, making USP7 also a SUMO DUB (SDUB). This work extends previous observations of increased levels of SUMO and low levels of ubiquitin at the on-going replication fork. Here, we discuss this novel study, its contribution to the DNA replication and genomic stability field and what questions arise from this work. © 2016 WILEY Periodicals, Inc.

Registered Replication Report: Strack, Martin, & Stepper (1988).

PubMed

Acosta, Alberto; Adams, Reginald B; Albohn, Daniel N; Allard, Eric S; Beek, Titia; Benning, Stephen D; Blouin- Hudon, Eve-Marie; Bulnes, Luis Carlo; Caldwell, Tracy L; Calin-Jageman, Robert J; Capaldi, Colin A; Carfagno, Nicholas S; Chasten, Kelsie T; Cleeremans, Axel; Connell, Louise; DeCicco, Jennifer M.; Dijkhoff, Laura; Dijkstra, Katinka; Fischer, Agneta H; Foroni, Francesco; Gronau, Quentin F; Hess, Ursula; Holmes, Kevin J; Jones, Jacob L H; Klein, Olivier; Koch, Christopher; Korb, Sebastian; Lewinski, Peter; Liao, Julia D; Lund, Sophie; Lupiáñez, Juan; Lynott, Dermot; Nance, Christin N; Oosterwijk, Suzanne; Özdog˘ru, Asil Ali; Pacheco-Unguetti, Antonia Pilar; Pearson, Bethany; Powis, Christina; Riding, Sarah; Roberts, Tomi-Ann; Rumiati, Raffaella I; Senden, Morgane; Shea-Shumsky, Noah B; Sobocko, Karin; Soto, Jose A; Steiner, Troy G; Talarico, Jennifer M; vanAllen, Zack M; Wagenmakers, E-J; Vandekerckhove, Marie; Wainwright, Bethany; Wayand, Joseph F; Zeelenberg, Rene; Zetzer, Emily E; Zwaan, Rolf A

2016-11-01

According to the facial feedback hypothesis, people's affective responses can be influenced by their own facial expression (e.g., smiling, pouting), even when their expression did not result from their emotional experiences. For example, Strack, Martin, and Stepper (1988) instructed participants to rate the funniness of cartoons using a pen that they held in their mouth. In line with the facial feedback hypothesis, when participants held the pen with their teeth (inducing a "smile"), they rated the cartoons as funnier than when they held the pen with their lips (inducing a "pout"). This seminal study of the facial feedback hypothesis has not been replicated directly. This Registered Replication Report describes the results of 17 independent direct replications of Study 1 from Strack et al. (1988), all of which followed the same vetted protocol. A meta-analysis of these studies examined the difference in funniness ratings between the "smile" and "pout" conditions. The original Strack et al. (1988) study reported a rating difference of 0.82 units on a 10-point Likert scale. Our meta-analysis revealed a rating difference of 0.03 units with a 95% confidence interval ranging from -0.11 to 0.16. © The Author(s) 2016.

Comparison of field-collected ascovirus isolates by DNA hybridization, host range, and histopathology.

PubMed

Hamm, J J; Styer, E L; Federici, B A

1998-09-01

Six field-collected ascovirus isolates obtained from five noctuid species in the continental United States were compared with respect to the general relatedness of their DNA, host range, and histopathology. Two isolates were from Spodoptera frugiperda, and the other four were from Autographa precationis, Heliothis virescens, Helicoverpa zea, and Trichoplusia ni. DNA-DNA hybridization studies showed that the six isolates belonged to three distinct viral species, with the isolates from S. frugiperda composing one species, those from A. precationis and H. virescens a second species, and those from H. zea and T. ni a third species. The host range and histopathology of each isolate was studied in eight noctuid species, S. frugiperda, Spodoptera ornithogalli, Spodoptera exigua, Spodoptera eridania, H. virescens, H. zea, A. precationis, and Feltia subterranea. Though some variation existed between the different isolates of each viral species, distinct patterns were apparent for each. The viral species from S. frugiperda had a host range that was limited primarily to Spodoptera species and both isolates of this virus only replicated and caused significant pathology in the fat body, whereas the viral species from A. precationis and H. virescens had a much broader host range that included most of the species tested, but also had a tissue tropism primarily restricted to the fat body. The viral species from T. ni and H. zea readily infected all the hosts tested, where the principal site of replication and significant pathology was the epidermis. In many test hosts, however, this viral species also replicated and caused significant pathology in the tracheal epithelium and to a lesser extent in the fat body. Aside from contributing to knowledge of ascovirus biology, these studies indicate that DNA hybridization profiles combined with studies of host range and tissue tropism can be used as characters for defining ascovirus species. Copyright 1998 Academic Press.

Accelerated Self-Replication under Non-Equilibrium, Periodic Energy Delivery

NASA Astrophysics Data System (ADS)

Zhang, Rui; Olvera de La Cruz, Monica

2014-03-01

Self-replication is a remarkable phenomenon in nature that has fascinated scientists for decades. In a self-replicating system, the original units are attracted to a template, which induce their binding. In equilibrium, the energy required to disassemble the newly assembled copy from the mother template is supplied by thermal energy. The possibility of optimizing self-replication is explored by controlling the frequency at which energy is supplied to the system. A model system inspired by a class of light switchable colloids is considered where light is used to control the interactions. Conditions under which self-replication can be significantly more effective under non-equilibrium, cyclic energy delivery than under equilibrium constant energy conditions are identified. Optimal self-replication does not require constant energy expenditure. Instead, the proper timing at which energy is delivered to the system is an essential controllable parameter to induce high replication rates. This work was supported by the Non-Equilibrium Energy Research Center (NERC), which is an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0000989.

Field testing of the experimental wood preservative N'N-naphtaloylhydroxylamine : five and eight years results

Treesearch

Frederick Green; Rachel A. Arango; Stan T. Lebow

2010-01-01

Field trials were designed to evaluate the ability of the experimental wood preservative N’N-naphthaloylhydroxylamine (NHA) to inhibit fungal decay and termite damage at the USDA Harrison Experimental Forest (HEF) in Saucier, MS. Twenty replicate 19 x 19 x 457 mm (0.75 x 0.75 x 18 in.) southern yellow pine stakes and 10 replicate 19 x 19 x 76 mm (0.75 x 0.75 x 3 in.)...

DNA Polymerase Eta and Chemotherapeutic Agents

PubMed Central

2011-01-01

Abstract The discovery of human DNA polymerase eta (pol η) has a major impact on the fields of DNA replication/repair fields. Since the discovery of human pol η, a number of new DNA polymerases with the ability to bypass various DNA lesions have been discovered. Among these polymerases, pol η is the most extensively studied lesion bypass polymerase with a defined major biological function, that is, to replicate across the cyclobutane pyrimidine dimers introduced by UV irradiation. Cyclobutane pyrimidine dimer is a major DNA lesion that causes distortion of DNA structure and block the replicative DNA polymerases during DNA replication process. Genetic defects in the pol η gene, Rad30, results in a disease called xeroderma pigmentosum variant. This review focuses on the overall properties of pol η and the mechanism that involved in regulating its activity in cells. In addition, the role of pol η in the action of DNA-targeting anticancer compounds is also discussed. Antioxid. Redox Signal. 14, 2521–2529. PMID:21050139

Statistical correction of the Winner’s Curse explains replication variability in quantitative trait genome-wide association studies

PubMed Central

Pe’er, Itsik

2017-01-01

Genome-wide association studies (GWAS) have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10−14), even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner’s Curse (p < 10−16). We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94). In contrast, ancestry differences between replication and discovery (13 studies, 385 loci) cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium. PMID:28715421

From the chromatin interaction network to the organization of the human genome into replication N/U-domains

NASA Astrophysics Data System (ADS)

Boulos, Rasha E.; Julienne, Hanna; Baker, Antoine; Chen, Chun-Long; Petryk, Nataliya; Kahli, Malik; dʼAubenton-Carafa, Yves; Goldar, Arach; Jensen, Pablo; Hyrien, Olivier; Thermes, Claude; Arneodo, Alain; Audit, Benjamin

2014-11-01

The three-dimensional (3D) architecture of the mammalian nucleus is now being unraveled thanks to the recent development of chromatin conformation capture (3C) technologies. Here we report the results of a combined multiscale analysis of genome-wide mean replication timing and chromatin conformation data that reveal some intimate relationships between chromatin folding and human DNA replication. We previously described megabase replication N/U-domains as mammalian multiorigin replication units, and showed that their borders are ‘master’ replication initiation zones that likely initiate cascades of origin firing responsible for the stereotypic replication of these domains. Here, we demonstrate that replication N/U-domains correspond to the structural domains of self-interacting chromatin, and that their borders act as insulating regions both in high-throughput 3C (Hi-C) data and high-resolution 3C (4C) experiments. Further analyses of Hi-C data using a graph-theoretical approach reveal that N/U-domain borders are long-distance, interconnected hubs of the chromatin interaction network. Overall, these results and the observation that a well-defined ordering of chromatin states exists from N/U-domain borders to centers suggest that ‘master’ replication initiation zones are at the heart of a high-order, epigenetically controlled 3D organization of the human genome.

Regulating DNA Replication in Plants

PubMed Central

Sanchez, Maria de la Paz; Costas, Celina; Sequeira-Mendes, Joana; Gutierrez, Crisanto

2012-01-01

Chromosomal DNA replication in plants has requirements and constraints similar to those in other eukaryotes. However, some aspects are plant-specific. Studies of DNA replication control in plants, which have unique developmental strategies, can offer unparalleled opportunities of comparing regulatory processes with yeast and, particularly, metazoa to identify common trends and basic rules. In addition to the comparative molecular and biochemical studies, genomic studies in plants that started with Arabidopsis thaliana in the year 2000 have now expanded to several dozens of species. This, together with the applicability of genomic approaches and the availability of a large collection of mutants, underscores the enormous potential to study DNA replication control in a whole developing organism. Recent advances in this field with particular focus on the DNA replication proteins, the nature of replication origins and their epigenetic landscape, and the control of endoreplication will be reviewed. PMID:23209151

Diversifying the STEM Pipeline: The Model Replication Institutions Program

ERIC Educational Resources Information Center

Cullinane, Jenna

2009-01-01

In 2006, the National Science Foundation (NSF) began funding the Model Replication Institutions (MRI) program, which sought to improve the quality, availability, and diversity of science, technology, engineering, and mathematics (STEM) education. Faced with pressing national priorities in the STEM fields and chronic gaps in postsecondary…

Television Ads in Singapore: A Content Analysis.

ERIC Educational Resources Information Center

Rehman, Sharaf N.; Aw, Annette; Kennan, William

1999-01-01

Appraises the information content of Singapore television advertising, and makes a comparison with relevant United States findings. Research reported in this paper is a replication of two empirical studies of the informational content of television advertising in the United States from 1977. (Author/LRW)

Modeling Agricultural Watersheds with the Soil and Water Assessment Tool (SWAT): Calibration and Validation with a Novel Procedure for Spatially Explicit HRUs.

PubMed

Teshager, Awoke Dagnew; Gassman, Philip W; Secchi, Silvia; Schoof, Justin T; Misgna, Girmaye

2016-04-01

Applications of the Soil and Water Assessment Tool (SWAT) model typically involve delineation of a watershed into subwatersheds/subbasins that are then further subdivided into hydrologic response units (HRUs) which are homogeneous areas of aggregated soil, landuse, and slope and are the smallest modeling units used within the model. In a given standard SWAT application, multiple potential HRUs (farm fields) in a subbasin are usually aggregated into a single HRU feature. In other words, the standard version of the model combines multiple potential HRUs (farm fields) with the same landuse/landcover, soil, and slope, but located at different places of a subbasin (spatially non-unique), and considers them as one HRU. In this study, ArcGIS pre-processing procedures were developed to spatially define a one-to-one match between farm fields and HRUs (spatially unique HRUs) within a subbasin prior to SWAT simulations to facilitate input processing, input/output mapping, and further analysis at the individual farm field level. Model input data such as landuse/landcover (LULC), soil, crop rotation, and other management data were processed through these HRUs. The SWAT model was then calibrated/validated for Raccoon River watershed in Iowa for 2002-2010 and Big Creek River watershed in Illinois for 2000-2003. SWAT was able to replicate annual, monthly, and daily streamflow, as well as sediment, nitrate and mineral phosphorous within recommended accuracy in most cases. The one-to-one match between farm fields and HRUs created and used in this study is a first step in performing LULC change, climate change impact, and other analyses in a more spatially explicit manner.

Modeling Agricultural Watersheds with the Soil and Water Assessment Tool (SWAT): Calibration and Validation with a Novel Procedure for Spatially Explicit HRUs

NASA Astrophysics Data System (ADS)

Teshager, Awoke Dagnew; Gassman, Philip W.; Secchi, Silvia; Schoof, Justin T.; Misgna, Girmaye

2016-04-01

Applications of the Soil and Water Assessment Tool (SWAT) model typically involve delineation of a watershed into subwatersheds/subbasins that are then further subdivided into hydrologic response units (HRUs) which are homogeneous areas of aggregated soil, landuse, and slope and are the smallest modeling units used within the model. In a given standard SWAT application, multiple potential HRUs (farm fields) in a subbasin are usually aggregated into a single HRU feature. In other words, the standard version of the model combines multiple potential HRUs (farm fields) with the same landuse/landcover, soil, and slope, but located at different places of a subbasin (spatially non-unique), and considers them as one HRU. In this study, ArcGIS pre-processing procedures were developed to spatially define a one-to-one match between farm fields and HRUs (spatially unique HRUs) within a subbasin prior to SWAT simulations to facilitate input processing, input/output mapping, and further analysis at the individual farm field level. Model input data such as landuse/landcover (LULC), soil, crop rotation, and other management data were processed through these HRUs. The SWAT model was then calibrated/validated for Raccoon River watershed in Iowa for 2002-2010 and Big Creek River watershed in Illinois for 2000-2003. SWAT was able to replicate annual, monthly, and daily streamflow, as well as sediment, nitrate and mineral phosphorous within recommended accuracy in most cases. The one-to-one match between farm fields and HRUs created and used in this study is a first step in performing LULC change, climate change impact, and other analyses in a more spatially explicit manner.

Replicated Wolter-I X-ray Optics for Lightweight, High Angular Resolution, Large Collecting Area X-Ray Telescopes

NASA Technical Reports Server (NTRS)

Joy, M.; Bilbro, J.; Elsner, R.; Jones, W.; Kolodziejczak, J.; Petruzzo, J.; ODell, S.; Weisskopf, M.

1997-01-01

The next generation of orbiting x-ray observatories will require high angular resolution telescopes that have an order of magnitude greater collecting area in the 0.1-10 keV spectral region than those currently under construction, but with a much lower weight and cost per unit area. Replicated Wolter-I x-ray optics have the potential to meet this requirement. The currently demonstrated capabilities of replicated Wolter-I optics will be described, and a development plan for creating lightweight, high angular resolution, large effective area x-ray telescopes will be presented.

Quantitative Simulations of MST Visual Receptive Field Properties Using a Template Model of Heading Estimation

NASA Technical Reports Server (NTRS)

Stone, Leland S.; Perrone, J. A.

1997-01-01

We previously developed a template model of primate visual self-motion processing that proposes a specific set of projections from MT-like local motion sensors onto output units to estimate heading and relative depth from optic flow. At the time, we showed that that the model output units have emergent properties similar to those of MSTd neurons, although there was little physiological evidence to test the model more directly. We have now systematically examined the properties of the model using stimulus paradigms used by others in recent single-unit studies of MST: 1) 2-D bell-shaped heading tuning. Most MSTd neurons and model output units show bell-shaped heading tuning. Furthermore, we found that most model output units and the finely-sampled example neuron in the Duffy-Wurtz study are well fit by a 2D gaussian (sigma approx. 35deg, r approx. 0.9). The bandwidth of model and real units can explain why Lappe et al. found apparent sigmoidal tuning using a restricted range of stimuli (+/-40deg). 2) Spiral Tuning and Invariance. Graziano et al. found that many MST neurons appear tuned to a specific combination of rotation and expansion (spiral flow) and that this tuning changes little for approx. 10deg shifts in stimulus placement. Simulations of model output units under the same conditions quantitatively replicate this result. We conclude that a template architecture may underlie MT inputs to MST.

Competitive replication kinetics and pathogenicity in pigs co-infected with historical and newly invading classical swine fever viruses.

PubMed

Huang, Yu-Liang; Deng, Ming-Chung; Tsai, Kuo-Jung; Liu, Hsin-Meng; Huang, Chin-Cheng; Wang, Fun-In; Chang, Chia-Yi

2017-01-15

Classical swine fever (CSF), an economically important and highly contagious disease of pigs, is caused by classical swine fever virus (CSFV). In Taiwan, CSFVs from field outbreaks belong to two distinct genotypes. The historical genotype 3.4 dominated from the 1920s to 1996, and since 1996, the newly invading genotype 2.1 has dominated. To explain the phenomenon of this virus shift in the field, representative viruses belonging to genotypes 2.1 and 3.4 were either inoculated alone (single infection) or co-inoculated (co-infection), both in vivo and in vitro, to compare the virus replication and pathogenesis. In pigs co-infected with the genotype 2.1 TD/96/TWN strain and the genotype 3.4 94.4/IL/94/TWN strain, the newly invading genotype 2.1 was detected earlier in the blood, oral fluid, and feces, and the viral loads were consistently and significantly higher than that of the historical genotype 3.4. In cell cultures, the ratio of secreted virus to cell-associated virus of the genotype 2.1 strain was higher than that of the genotype 3.4 strain. This study is the first to demonstrate a possible explanation of virus shift in the field, wherein the newly invading genotype 2.1 replicates more efficiently than did genotype 3.4 and outcompetes the replication and pathogenicity of genotype 3.4 in pigs in the field. Copyright © 2016 Elsevier B.V. All rights reserved.

A New Replicator: A theoretical framework for analysing replication

PubMed Central

2010-01-01

Background Replicators are the crucial entities in evolution. The notion of a replicator, however, is far less exact than the weight of its importance. Without identifying and classifying multiplying entities exactly, their dynamics cannot be determined appropriately. Therefore, it is importance to decide the nature and characteristics of any multiplying entity, in a detailed and formal way. Results Replication is basically an autocatalytic process which enables us to rest on the notions of formal chemistry. This statement has major implications. Simple autocatalytic cycle intermediates are considered as non-informational replicators. A consequence of which is that any autocatalytically multiplying entity is a replicator, be it simple or overly complex (even nests). A stricter definition refers to entities which can inherit acquired changes (informational replicators). Simple autocatalytic molecules (and nests) are excluded from this group. However, in turn, any entity possessing copiable information is to be named a replicator, even multicellular organisms. In order to deal with the situation, an abstract, formal framework is presented, which allows the proper identification of various types of replicators. This sheds light on the old problem of the units and levels of selection and evolution. A hierarchical classification for the partition of the replicator-continuum is provided where specific replicators are nested within more general ones. The classification should be able to be successfully applied to known replicators and also to future candidates. Conclusion This paper redefines the concept of the replicator from a bottom-up theoretical approach. The formal definition and the abstract models presented can distinguish between among all possible replicator types, based on their quantity of variable and heritable information. This allows for the exact identification of various replicator types and their underlying dynamics. The most important claim is that replication, in general, is basically autocatalysis, with a specific defined environment and selective force. A replicator is not valid unless its working environment, and the selective force to which it is subject, is specified. PMID:20219099

In Search of Circasemidian Rhythms

DTIC Science & Technology

2006-11-01

NUMBER James C. Miller, Ph.D 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7757P905 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION...circasemidian rhythmicity in task performance was attributed to the nature of task, itself. Future investigations should attempt to replicate our...circasemidian rhythmicity in task performance was attributed to the nature of task, itself. Future investigations should attempt to replicate our findings

Role of DNA polymerase I-associated 5'-exonuclease in replication of coliphage M13 replicative-form DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dasgupta, S.; Mitra, S.

The conversion of both parental- and progeny-nascent open circular M13 RF DNA into covalently closed RF I is drastically reduced in an E. coli mutant deficient in the 5' ..-->.. 3' exonuclease associated with DNA polymerase I. The nascent progeny RF DNA also contains a significant proportion of fragments of smaller than unit length.

An instrument design and sample strategy for measuring soil respiration in the coastal temperate rain forest

NASA Astrophysics Data System (ADS)

Nay, S. M.; D'Amore, D. V.

2009-12-01

The coastal temperate rainforest (CTR) along the northwest coast of North America is a large and complex mosaic of forests and wetlands located on an undulating terrain ranging from sea level to thousands of meters in elevation. This biome stores a dynamic portion of the total carbon stock of North America. The fate of the terrestrial carbon stock is of concern due to the potential for mobilization and export of this store to both the atmosphere as carbon respiration flux and ocean as dissolved organic and inorganic carbon flux. Soil respiration is the largest export vector in the system and must be accurately measured to gain any comprehensive understanding of how carbon moves though this system. Suitable monitoring tools capable of measuring carbon fluxes at small spatial scales are essential for our understanding of carbon dynamics at larger spatial scales within this complex assemblage of ecosystems. We have adapted instrumentation and developed a sampling strategy for optimizing replication of soil respiration measurements to quantify differences among spatially complex landscape units of the CTR. We start with the design of the instrument to ease the technological, ergonomic and financial barriers that technicians encounter in monitoring the efflux of CO2 from the soil. Our sampling strategy optimizes the physical efforts of the field work and manages for the high variation of flux measurements encountered in this difficult environment of rough terrain, dense vegetation and wet climate. Our soil respirometer incorporates an infra-red gas analyzer (LiCor Inc. LI-820) and an 8300 cm3 soil respiration chamber; the device is durable, lightweight, easy to operate and can be built for under $5000 per unit. The modest unit price allows for a multiple unit fleet to be deployed and operated in an intensive field monitoring campaign. We use a large 346 cm2 collar to accommodate as much micro spatial variation as feasible and to facilitate repeated measures for tracking temporal trends. Our collar design minimizes root interference yet provides a highly stable platform for coupling with the respirometer. Meso-scale variability characterized by large down woody debris, wind throw pits and mounds and surface roots is negotiated with by a hexagonal array of seven collars at two meter spacing (sample pod). Landscape scale variability is managed through stratification and replication amongst ecosystem types arrayed across a hydrologic gradient from bogs to forested wetlands to upland forests. Our strategy has allowed us to gather data sets consisting of approximately 1800 total observations with approximately 600 measurements per replication per year. Mean coefficients of variation (CV) at the collar (micro-scale) were approximately 0.67. The pod level mean CV was reduced to approximately 0.29 at the pod (meso-scale). The CV at the vegetation strata were 0.43, 0.18 and 0.21 for bog, forested wetland and upland forest respectively. With temperature and hydrological data we are able to measure and model carbon dynamics in this large and complex environment. The analysis of variability at the three spatial scales has confirmed that our approach is capturing and constraining the variability.

High-precision 40Ar/39Ar sanidine geochronology of ignimbrites in the Mogollon-Datil volcanic field, southwestern New Mexico

USGS Publications Warehouse

McIntosh, W.C.; Sutter, J.F.; Chapin, C.E.; Kedzie, L.L.

1990-01-01

40Ar/39Ar age spectra have been obtained from 85 sanidine separates from 36 ignimbrites and one rhyolitic lava in the latest Eocene-Oligocene Mogollon-Datil volcanic field of southwestern New Mexico. Of the 97 measured age spectra, 94 yield weighted-mean plateau ages each giving single-spectrum 1?? precision of??0.25%-0.4% (??0.07-0.14 Ma). Replicate plateau age determinations for eight different samples show within-sample 1?? precisions averaging ??0.25%. Plateau ages from multiple (n=3-8) samples of individual ignimbrites show 1?? within-unit precision of ??0.1%-0.4% (??0.04-0.13 Ma). This within-unit precision represents a several-fold improvement over published K-Ar data for the same ignimbrites, and is similar to the range of precisions reported from single-crystal laser fusion studies. A further indication of the high precision of unit-mean 40Ar/30Ar ages is their close agreement with independently established stratigraphic order. Two samples failed to meet plateau criteria, apparently due to geologic contamination by older feldspars. Effects of minor contamination are shown by six other samples, which yielded slightly anomalous plateau ages. 40Ar/39Ar plateau ages permit resolution of units differing in age by 0.5% (0.15 Ma) or less. This high resolution, combined with paleomagnetic studies, has helped to correlate ignimbrites among isolated ranges and has allowed development of an integrated timestratigraphic framework for the volcanic field. Mogollon-Datil ignimbrites range in age from 36.2 to 24.3 Ma. Ignimbrite activity was strongly episodic, being confined to four brief (<2.6 m.y.) eruptive episodes separated by 1-3 m.y. gaps. Ignimbrite activity generally tended to migrate from the southeast toward the north and west. ?? 1990 Springer-Verlag.

Diversifying the STEM Pipeline: Recommendations from the Model Replication Institutions Program

ERIC Educational Resources Information Center

Institute for Higher Education Policy, 2010

2010-01-01

Launched in 2006 to address issues of national competitiveness and equity in science, technology, engineering, and mathematics (STEM) fields, the National Science Foundation-funded Model Replication Institutions (MRI) program sought to improve the quality, availability, and diversity of STEM education. The project offered technical assistance to…

Replication, randomization, and treatment design concepts for on-farm research

USDA-ARS?s Scientific Manuscript database

For most agronomists, randomization and replication are fundamental concepts that have a nearly sacred or spiritual status. They are an integral part of nearly all of our field-based activities. Some on-farm research falls into this category, simply because it is driven and designed by researchers w...

Replication and Reporting: A Commentary.

ERIC Educational Resources Information Center

Polio, Charlene; Gass, Susan

1997-01-01

Addresses the need for replication studies in the field of second-language acquisition and discusses the problems surrounding standards of reporting research. Notes a lack of uniform standards in reporting second-language learners' proficiency levels and proposes ways to achieve more thorough reporting of research that will allow others to engage…

Prospective elementary teachers' conceptions of multidigit number: exemplifying a replication framework for mathematics education

NASA Astrophysics Data System (ADS)

Jacobson, Erik; Simpson, Amber

2018-04-01

Replication studies play a critical role in scientific accumulation of knowledge, yet replication studies in mathematics education are rare. In this study, the authors replicated Thanheiser's (Educational Studies in Mathematics 75:241-251, 2010) study of prospective elementary teachers' conceptions of multidigit number and examined the main claim that most elementary pre-service teachers think about digits incorrectly at least some of the time. Results indicated no statistically significant difference in the distribution of conceptions between the original and replication samples and, moreover, no statistically significant differences in the distribution of sub-conceptions among prospective teachers with the most common conception. These results suggest confidence is warranted both in the generality of the main claim and in the utility of the conceptions framework for describing prospective elementary teachers' conceptions of multidigit number. The report further contributes a framework for replication of mathematics education research adapted from the field of psychology.

Replication, lies and lesser-known truths regarding experimental design in environmental microbiology.

PubMed

Lennon, Jay T

2011-06-01

A recent analysis revealed that most environmental microbiologists neglect replication in their science (Prosser, 2010). Of all peer-reviewed papers published during 2009 in the field's leading journals, slightly more than 70% lacked replication when it came to analyzing microbial community data. The paucity of replication is viewed as an 'endemic' and 'embarrassing' problem that amounts to 'bad science', or worse yet, as the title suggests, lying (Prosser, 2010). Although replication is an important component of experimental design, it is possible to do good science without replication. There are various quantitative techniques - some old, some new - that, when used properly, will allow environmental microbiologists to make strong statistical conclusions from experimental and comparative data. Here, I provide examples where unreplicated data can be used to test hypotheses and yield novel information in a statistically robust manner. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Separation of replication and transcription domains in nucleoli.

PubMed

Smirnov, E; Borkovec, J; Kováčik, L; Svidenská, S; Schröfel, A; Skalníková, M; Švindrych, Z; Křížek, P; Ovesný, M; Hagen, G M; Juda, P; Michalová, K; Cardoso, M C; Cmarko, D; Raška, I

2014-12-01

In mammalian cells, active ribosomal genes produce the 18S, 5.8S and 28S RNAs of ribosomal particles. Transcription levels of these genes are very high throughout interphase, and the cell needs a special strategy to avoid collision of the DNA polymerase and RNA polymerase machineries. To investigate this problem, we measured the correlation of various replication and transcription signals in the nucleoli of HeLa, HT-1080 and NIH 3T3 cells using a specially devised software for analysis of confocal images. Additionally, to follow the relationship between nucleolar replication and transcription in living cells, we produced a stable cell line expressing GFP-RPA43 (subunit of RNA polymerase I, pol I) and RFP-PCNA (the sliding clamp protein) based on human fibrosarcoma HT-1080 cells. We found that replication and transcription signals are more efficiently separated in nucleoli than in the nucleoplasm. In the course of S phase, separation of PCNA and pol I signals gradually increased. During the same period, separation of pol I and incorporated Cy5-dUTP signals decreased. Analysis of single molecule localization microscopy (SMLM) images indicated that transcriptionally active FC/DFC units (i.e. fibrillar centers with adjacent dense fibrillar components) did not incorporate DNA nucleotides. Taken together, our data show that replication of the ribosomal genes is spatially separated from their transcription, and FC/DFC units may provide a structural basis for that separation. Copyright © 2014 Elsevier Inc. All rights reserved.

Short-term response of reptiles and amphibians to prescribed fire and mechanical fuel reduction in a southern Appalachian upland hardwood forest

Treesearch

Cathryn H. Greenberg; Thomas A. Waldrop

2008-01-01

We compared the effects of three fuel reduction techniques and a control on the relative abundance and richness of reptiles and amphibians using drift fence arrays with pitfall and funnel traps. Three replicate blocks were established at the Green River Game Land, Polk County, North Carolina. Each replicate block contained four experimental units that were each...

Crystallization and preliminary X-ray characterization of the eukaryotic replication terminator Reb1-Ter DNA complex.

PubMed

Jaiswal, Rahul; Singh, Samarendra K; Bastia, Deepak; Escalante, Carlos R

2015-04-01

The Reb1 protein from Schizosaccharomyces pombe is a member of a family of proteins that control programmed replication termination and/or transcription termination in eukaryotic cells. These events occur at naturally occurring replication fork barriers (RFBs), where Reb1 binds to termination (Ter) DNA sites and coordinates the polar arrest of replication forks and transcription approaching in opposite directions. The Reb1 DNA-binding and replication-termination domain was expressed in Escherichia coli, purified and crystallized in complex with a 26-mer DNA Ter site. Batch crystallization under oil was required to produce crystals of good quality for data collection. Crystals grew in space group P2₁, with unit-cell parameters a = 68.9, b = 162.9, c = 71.1 Å, β = 94.7°. The crystals diffracted to a resolution of 3.0 Å. The crystals were mosaic and required two or three cycles of annealing. This study is the first to yield structural information about this important family of proteins and will provide insights into the mechanism of replication and transcription termination.

Expanding Health Care Access Through Education: Dissemination and Implementation of the ECHO Model.

PubMed

Katzman, Joanna G; Galloway, Kevin; Olivas, Cynthia; McCoy-Stafford, Kimberly; Duhigg, Daniel; Comerci, George; Kalishman, Summers; Buckenmaier, Chester C; McGhee, Laura; Joltes, Kristin; Bradford, Andrea; Shelley, Brian; Hernandez, Jessica; Arora, Sanjeev

2016-03-01

Project ECHO (Extension for Community Healthcare Outcomes) is an evidence-based model that provides high-quality medical education for common and complex diseases through telementoring and comanagement of patients with primary care clinicians. In a one to many knowledge network, the ECHO model helps to bridge the gap between primary care clinicians and specialists by enhancing the knowledge, skills, confidence, and practice of primary care clinicians in their local communities. As a result, patients in rural and urban underserved areas are able to receive best practice care without long waits or having to travel long distances. The ECHO model has been replicated in 43 university hubs in the United States and five other countries. A new replication tool was developed by the Project ECHO Pain team and U.S. Army Medical Command to ensure a high-fidelity replication of the model. The adoption of the tool led to successful replication of ECHO in the Army Pain initiative. This replication tool has the potential to improve the fidelity of ECHO replication efforts around the world. Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.

Physics models of centriole replication.

PubMed

Cheng, Kang; Zou, Changhua

2006-01-01

Our previous pre-clinic experimental results have showed that the epithelialization can be enhanced by the externally applied rectangular pulsed electrical current stimulation (RPECS). The results are clinically significant for patients, especially for those difficult patients whose skin wounds need long periods to heal. However, the results also raise questions: How does the RPECS accelerate the epithelium cell proliferation? To answer these questions, we have previously developed several models for animal cells, in a view of physics, to explain mechanisms of mitosis and cytokinesis at a cellular level, and separation of nucleotide sequences and the unwinding of a double helix during DNA replication at a bio-molecular level. In this paper, we further model the mechanism of centriole replication during a natural and normal mitosis and cytokinesis to explore the mechanism of epithelialization enhanced with the externally applied RPECS at a bio-molecular level. Our models suggest: (1) Centriole replication is an information flowing. The direction of the information flowing is from centrioles to centrioles based on a cylindrical template of 9 x 3 protein microtubules (MTs) pattern. (2) A spontaneous and strong electromagnetic field (EMF) force is a pushing force that separates a mother and a daughter centrioles in centrosomes or in cells, while a pulling force of interacting fibers and pericentriolar materials delivers new babies. The newly born babies inherit the pattern information from their mother(s) and grow using microtubule fragments that come through the centrosome pores. A daughter centriole is always born and grows along stronger EMF. The EMF mostly determines centrioles positions and plays key role in centriole replication. We also hypothesize that the normal centriole replication could not been disturbed in centrosome in the epithelium cells by our RPECS, because the centrioles have two non-conducting envelope (cell and centrosome membranes), that protect the normal duplication. The induced electric field by externally applied RPECS could be mild compared with the spontaneous and natural electric field of the centrioles. Therefore, the centriole replication during the epithelium cellular proliferation may be directly, as well as indirectly (e.g., somatic reflex) accelerated by the RPECS.

Children's Understanding and Knowledge of Conception and Birth: Comparing Children from England, the Netherlands, Sweden, and the United States

ERIC Educational Resources Information Center

Caron, Sandra L.; Ahlgrim, Carie Jo

2012-01-01

The present study replicated research conducted decades earlier (Goldman & Goldman, 1982a; Koch, 197480) on what children in the United States know about conception and birth compared to those in other countries. Specifically, response drawings by 48 six-year-old boys and girls from England, the Netherlands, Sweden, and the United States were…

Measurement of replication structures at the nanometer scale using super-resolution light microscopy

PubMed Central

Baddeley, D.; Chagin, V. O.; Schermelleh, L.; Martin, S.; Pombo, A.; Carlton, P. M.; Gahl, A.; Domaing, P.; Birk, U.; Leonhardt, H.; Cremer, C.; Cardoso, M. C.

2010-01-01

DNA replication, similar to other cellular processes, occurs within dynamic macromolecular structures. Any comprehensive understanding ultimately requires quantitative data to establish and test models of genome duplication. We used two different super-resolution light microscopy techniques to directly measure and compare the size and numbers of replication foci in mammalian cells. This analysis showed that replication foci vary in size from 210 nm down to 40 nm. Remarkably, spatially modulated illumination (SMI) and 3D-structured illumination microscopy (3D-SIM) both showed an average size of 125 nm that was conserved throughout S-phase and independent of the labeling method, suggesting a basic unit of genome duplication. Interestingly, the improved optical 3D resolution identified 3- to 5-fold more distinct replication foci than previously reported. These results show that optical nanoscopy techniques enable accurate measurements of cellular structures at a level previously achieved only by electron microscopy and highlight the possibility of high-throughput, multispectral 3D analyses. PMID:19864256

Plasmid P1 replication: negative control by repeated DNA sequences.

PubMed Central

Chattoraj, D; Cordes, K; Abeles, A

1984-01-01

The incompatibility locus, incA, of the unit-copy plasmid P1 is contained within a fragment that is essentially a set of nine 19-base-pair repeats. One or more copies of the fragment destabilizes the plasmid when present in trans. Here we show that extra copies of incA interfere with plasmid DNA replication and that a deletion of most of incA increases plasmid copy number. Thus, incA is not essential for replication but is required for its control. When cloned in a high-copy-number vector, pieces of the incA fragment that each contain only three repeats destabilize P1 plasmids efficiently. This result makes it unlikely that incA specifies a regulatory product. Our in vivo results suggest that the repeating DNA sequence itself negatively controls replication by titrating a P1-determined protein, RepA, that is essential for replication. Consistent with this hypothesis is the observation that the RepA protein binds to the incA fragment in vitro. Images PMID:6387706

Random catalytic reaction networks

NASA Astrophysics Data System (ADS)

Stadler, Peter F.; Fontana, Walter; Miller, John H.

1993-03-01

We study networks that are a generalization of replicator (or Lotka-Volterra) equations. They model the dynamics of a population of object types whose binary interactions determine the specific type of interaction product. Such a system always reduces its dimension to a subset that contains production pathways for all of its members. The network equation can be rewritten at a level of collectives in terms of two basic interaction patterns: replicator sets and cyclic transformation pathways among sets. Although the system contains well-known cases that exhibit very complicated dynamics, the generic behavior of randomly generated systems is found (numerically) to be extremely robust: convergence to a globally stable rest point. It is easy to tailor networks that display replicator interactions where the replicators are entire self-sustaining subsystems, rather than structureless units. A numerical scan of random systems highlights the special properties of elementary replicators: they reduce the effective interconnectedness of the system, resulting in enhanced competition, and strong correlations between the concentrations.

Replication of transformation-defective mutants of the Prague strain of Rous sarcoma virus and isolation of a td mutant from duck-adapted PR-RSV-C.

PubMed

Geryk, J; Mazo, A; Svoboda, J; Hlozánek, I

1980-01-01

The replication of transformation-defective mutants of the Prague strain of Rous sarcoma virus subgroup C was studied using roller cultures. Under such conditions, 10(5)--10(6) infectous units of virus per 0.2 ml were produced, as revealed in both the reverse transcriptase and 16Q complementation tests. A new td daPR-RSV-C mutant was isolated from duck-adapted PR-RSV-C. This mutant replicated in roller cultures with equal efficiency as the original td PR-RSV-C. It was verified that td daPR-RSV-C does not transform chicken fibroblasts, is not oncogenic for 3-week-old chickens and has subgroup C host-range specificity. Both td mutants replicate in duck cells and reach the same titres.

Novel wide-field x-ray optics for space

NASA Astrophysics Data System (ADS)

Hudec, René; Pína, Ladislav; Inneman, Adolf

2017-11-01

We report on the program of design and development of innovative very wide field X-ray optics for space applications. We describe the idea of wide field X-ray optics of the lobster-eye type of both Angel and Schmidt arrangements. This optics was suggested in 70ies but not yet used in space experiment due to severe manufacturing problems. The lobster-eye X-ray optics may achieve up to 180 degrees (diameter) field of view at angular resolution of order of 1 arcmin. We report on various prototypes of lobster-eye X-ray lenses based on alternative technologies (replicated double sided X-ray reflecting flats, float glass, replicated square channels etc.) as well as on their optical and X-ray tests. We also discuss the importance and performance of lobster-eye X-ray telescopes in future X-ray astronomy projects.

Facts Are More Important than Novelty: Replication in the Education Sciences

ERIC Educational Resources Information Center

Makel, Matthew C.; Plucker, Jonathan A.

2014-01-01

Despite increased attention to methodological rigor in education research, the field has focused heavily on experimental design and not on the merit of replicating important results. The present study analyzed the complete publication history of the current top 100 education journals ranked by 5-year impact factor and found that only 0.13% of…

Immunochip Analyses of Epistasis in Rheumatoid Arthritis Confirm Multiple Interactions within MHC and Suggest Novel Non-MHC Epistatic Signals.

PubMed

Wei, Wen-Hua; Loh, Chia-Yin; Worthington, Jane; Eyre, Stephen

2016-05-01

Studying statistical gene-gene interactions (epistasis) has been limited by the difficulties in performance, both statistically and computationally, in large enough sample numbers to gain sufficient power. Three large Immunochip datasets from cohort samples recruited in the United Kingdom, United States, and Sweden with European ancestry were used to examine epistasis in rheumatoid arthritis (RA). A full pairwise search was conducted in the UK cohort using a high-throughput tool and the resultant significant epistatic signals were tested for replication in the United States and Swedish cohorts. A forward selection approach was applied to remove redundant signals, while conditioning on the preidentified additive effects. We detected abundant genome-wide significant (p < 1.0e-13) epistatic signals, all within the MHC region. These signals were reduced substantially, but a proportion remained significant (p < 1.0e-03) in conditional tests. We identified 11 independent epistatic interactions across the entire MHC, each explaining on average 0.12% of the phenotypic variance, nearly all replicated in both replication cohorts. We also identified non-MHC epistatic interactions between RA susceptible loci LOC100506023 and IRF5 with Immunochip-wide significance (p < 1.1e-08) and between 2 neighboring single-nucleotide polymorphism near PTPN22 that were in low linkage disequilibrium with independent interaction (p < 1.0e-05). Both non-MHC epistatic interactions were statistically replicated with a similar interaction pattern in the US cohort only. There are multiple but relatively weak interactions independent of the additive effects in RA and a larger sample number is required to confidently assign additional non-MHC epistasis.

Sensed presence and mystical experiences are predicted by suggestibility, not by the application of transcranial weak complex magnetic fields.

PubMed

Granqvist, Pehr; Fredrikson, Mats; Unge, Patrik; Hagenfeldt, Andrea; Valind, Sven; Larhammar, Dan; Larsson, Marcus

2005-04-29

Transcranial magnetic stimulation (TMS) with weak (micro Tesla) complex waveform fields have been claimed to evoke the sensed presence of a sentient being in up to 80% in the general population. These findings have had a questionable neurophysiological foundation as the fields are approximately six orders of magnitude weaker than ordinary TMS fields. Also, no independent replication has been reported. To replicate and extend previous findings, we performed a double-blind experiment (N=89), with a sham-field control group. Personality characteristics indicating suggestibility (absorption, signs of abnormal temporal lobe activity, and a "new age"-lifestyle orientation) were used as predictors. Sensed presence, mystical, and other somatosensory experiences previously reported from the magnetic field stimulation were outcome measures. We found no evidence for any effects of the magnetic fields, neither in the entire group, nor in individuals high in suggestibility. Because the personality characteristics significantly predicted outcomes, suggestibility may account for previously reported effects. Our results strongly question the earlier claims of experiential effects of weak magnetic fields.

The origin of replicators and reproducers

PubMed Central

Szathmáry, Eörs

2006-01-01

Replicators are fundamental to the origin of life and evolvability. Their survival depends on the accuracy of replication and the efficiency of growth relative to spontaneous decay. Infrabiological systems are built of two coupled autocatalytic systems, in contrast to minimal living systems that must comprise at least a metabolic subsystem, a hereditary subsystem and a boundary, serving respective functions. Some scenarios prefer to unite all these functions into one primordial system, as illustrated in the lipid world scenario, which is considered as a didactic example in detail. Experimentally produced chemical replicators grow parabolically owing to product inhibition. A selection consequence is survival of everybody. The chromatographized replicator model predicts that such replicators spreading on surfaces can be selected for higher replication rate because double strands are washed away slower than single strands from the surface. Analysis of real ribozymes suggests that the error threshold of replication is less severe by about one order of magnitude than thought previously. Surface-bound dynamics is predicted to play a crucial role also for exponential replicators: unlinked genes belonging to the same genome do not displace each other by competition, and efficient and accurate replicases can spread. The most efficient form of such useful population structure is encapsulation by reproducing vesicles. The stochastic corrector model shows how such a bag of genes can survive, and what the role of chromosome formation and intragenic recombination could be. Prebiotic and early evolution cannot be understood without the models of dynamics. PMID:17008217

Animal Mitochondrial DNA Replication

PubMed Central

Ciesielski, Grzegorz L.; Oliveira, Marcos T.; Kaguni, Laurie S.

2016-01-01

Recent advances in the field of mitochondrial DNA (mtDNA) replication highlight the diversity of both the mechanisms utilized and the structural and functional organization of the proteins at mtDNA replication fork, despite the simplicity of the animal mtDNA genome. DNA polymerase γ, mtDNA helicase and mitochondrial single-stranded DNA-binding protein- the key replisome proteins, have evolved distinct structural features and biochemical properties. These appear to be correlated with mtDNA genomic features in different metazoan taxa and with their modes of DNA replication, although a substantial integrative research is warranted to establish firmly these links. To date, several modes of mtDNA replication have been described for animals: rolling circle, theta, strand-displacement, and RITOLS/bootlace. Resolution of a continuing controversy relevant to mtDNA replication in mammals/vertebrates will have a direct impact on the mechanistic interpretation of mtDNA-related human diseases. Here we review these subjects, integrating earlier and recent data to provide a perspective on the major challenges for future research. PMID:27241933

On the cross-cultural replicability of the resilient, undercontrolled, and overcontrolled personality types.

PubMed

Alessandri, Guido; Vecchione, Michele; Donnellan, Brent M; Eisenberg, Nancy; Caprara, Gian Vittorio; Cieciuch, Jan

2014-08-01

Personality types reflect typical configurations of personality attributes within individuals. Over the last 20 years, researchers have identified a set of three replicable personality types: resilient (R), undercontrolled (U), and overcontrolled (O) types. In this study, we examined the cross-cultural replicability of the RUO types in Italy, Poland, Spain, and the United States. Personality types were identified using cluster analyses of Big Five profiles in large samples of college students from Italy (n = 322), the United States (n = 499), Spain (n = 420), and Poland (n = 235). Prior to clustering the profiles, the measurement invariance of the Big Five measure across samples was tested. We found evidence for the RUO types in all four samples. The three-cluster solution showed a better fit over alternative solutions and had a relatively high degree of cross-cultural generalizability. The RUO types are evident in samples from four countries with distinct linguistic and cultural traditions. Results were discussed in light of the importance of considering how traits are organized within individuals for advancing contemporary personality psychology. © 2013 Wiley Periodicals, Inc.

Comparison of the forage and grain composition from insect-protected and glyphosate-tolerant MON 88017 corn to conventional corn (Zea mays L.).

PubMed

McCann, Melinda C; Trujillo, William A; Riordan, Susan G; Sorbet, Roy; Bogdanova, Natalia N; Sidhu, Ravinder S

2007-05-16

The next generation of biotechnology-derived products with the combined benefit of herbicide tolerance and insect protection (MON 88017) was developed to withstand feeding damage caused by the coleopteran pest corn rootworm and over-the-top applications of glyphosate, the active ingredient in Roundup herbicides. As a part of a larger safety and characterization assessment, MON 88017 was grown under field conditions at geographically diverse locations within the United States and Argentina during the 2002 and 2003-2004 field seasons, respectively, along with a near-isogenic control and other conventional corn hybrids for compositional assessment. Field trials were conducted using a randomized complete block design with three replication blocks at each site. Corn forage samples were harvested at the late dough/early dent stage, ground, and analyzed for the concentration of proximate constituents, fibers, and minerals. Samples of mature grain were harvested, ground, and analyzed for the concentration of proximate constituents, fiber, minerals, amino acids, fatty acids, vitamins, antinutrients, and secondary metabolites. The results showed that the forage and grain from MON 88017 are compositionally equivalent to forage and grain from control and conventional corn hybrids.

Reverse genetics in high throughput: rapid generation of complete negative strand RNA virus cDNA clones and recombinant viruses thereof.

PubMed

Nolden, T; Pfaff, F; Nemitz, S; Freuling, C M; Höper, D; Müller, T; Finke, Stefan

2016-04-05

Reverse genetics approaches are indispensable tools for proof of concepts in virus replication and pathogenesis. For negative strand RNA viruses (NSVs) the limited number of infectious cDNA clones represents a bottleneck as clones are often generated from cell culture adapted or attenuated viruses, with limited potential for pathogenesis research. We developed a system in which cDNA copies of complete NSV genomes were directly cloned into reverse genetics vectors by linear-to-linear RedE/T recombination. Rapid cloning of multiple rabies virus (RABV) full length genomes and identification of clones identical to field virus consensus sequence confirmed the approache's reliability. Recombinant viruses were recovered from field virus cDNA clones. Similar growth kinetics of parental and recombinant viruses, preservation of field virus characters in cell type specific replication and virulence in the mouse model were confirmed. Reduced titers after reporter gene insertion indicated that the low level of field virus replication is affected by gene insertions. The flexibility of the strategy was demonstrated by cloning multiple copies of an orthobunyavirus L genome segment. This important step in reverse genetics technology development opens novel avenues for the analysis of virus variability combined with phenotypical characterization of recombinant viruses at a clonal level.

Fabrication of flexible grating sensing waveguide based on nano-imprint lithography and micro-replication process

NASA Astrophysics Data System (ADS)

Liu, Yueming; Tian, Weijian; Zhang, Shaojun

2009-05-01

Soft and flexible grating sensing waveguides is urgently demanded in application of micro-bending sensing and surface distortion sensing in medical catheter and smart skin sensing unit etc. Based on Nano-imprint Lithography and micro-replication process, polymer grating waveguides with core size 4μm×20μm and pitch 0.75μm are fabricated successfully in this paper. This novel grating waveguides is soft and flexible enough for related application and with the bio-medical safe feature when used in human body catheter. Fabricated processes are presented including the fabrication of micro mould and UV-replication process, and relative skills are discussed also in this paper.

Social Fears and Social Phobia in the United States: Results from the National Comorbidity Survey Replication

PubMed Central

Ruscio, Ayelet Meron; Brown, Timothy A.; Chiu, Wai Tat; Sareen, Jitender; Stein, Murray B.; Kessler, Ronald C.

2008-01-01

Background Despite heightened awareness of the clinical significance of social phobia, information is still lacking about putative subtypes, functional impairment, and treatment-seeking. New epidemiologic data on these topics are presented from the National Comorbidity Survey Replication (NCS-R). Methods The NCS-R is a nationally representative household survey fielded in 2001–2003. The WHO Composite International Diagnostic Interview (CIDI 3.0) was used to assess 14 performance and interactional fears and DSM-IV social phobia. Results The estimated lifetime and 12-month prevalence of social phobia are 12.1% and 7.1%. Performance and interactional fears load onto a single latent factor, and there is little evidence for distinct subtypes based either on the content or number of fears. Social phobia is associated with significant psychiatric comorbidity, role impairment, and treatment-seeking, all of which have a dose-response relationship with number of social fears. However, social phobia is the focus of clinical attention in only about half of cases where treatment is obtained. Among non-comorbid cases, those with the most fears were least likely to receive social phobia treatment. Conclusions Social phobia is a common, under-treated disorder that leads to significant functional impairment. Increasing numbers of social fears are associated with increasingly severe manifestations of the disorder. PMID:17976249

Grazing Incidence Nickel Replicated Optics for Hard X-ray Telescopes

NASA Technical Reports Server (NTRS)

Peturzzo, J. J., III; Elsner, R. F.; Joy, M. K.; ODell, S. L.; Weisskopf, M. C.

1997-01-01

The requirements for future hard x-ray (up to 50 keV) telescopes are lightweight, high angular resolution optics with large collecting areas. Grazing incidence replicated optics are an excellent candidate for this, type of mission, providing better angular resolution, comparable area/unit mass, and simpler fabrication than multilayer-coated foils. Most importantly, the technology to fabricate the required optics currently exists. A comparison of several hard x-ray telescope designs will be presented.

New filtration system for efficient recovery of waterborne Cryptosporidium oocysts and Giardia cysts.

PubMed

Al-Sabi, M N S; Gad, J A; Riber, U; Kurtzhals, J A L; Enemark, H L

2015-09-01

To develop a filtration unit for efficient recovery of waterborne Cryptosporidium oocysts and Giardia cysts ((oo-)cysts) in drinking water. This unit utilizes a metallic filter and an ultrasound transducer for eluting (oo-)cysts, with a fixed retentate backwash volume; approx. 400 μl. Changes in the viability was evaluated by seeding wild type (oo-)cysts (1 × 10(4)) followed by sonication for 5, 10, 20 or 40 s (five replicates for each period). Flow cytometry analysis showed negligible increase in the mortality of (oo-)cysts exposed to 5-10 s of sonication. Recovery rate was assessed by seeding ColorSeed(™) (10 replicates) into the filter unit followed by air backwash to a glass slide and counting of (oo-)cysts by epifluorescent microscopy. High recovery rates (mean ± SD) were found: 84·9% ± 4·8 for Giardia cysts and 70% ± 6·5 for Cryptosporidium oocysts. DNA of seeded wild type (oo-)cysts (1 × 10(2); 10 replicates) was successfully amplified using real-time PCR. The use of a metallic filter, sonication and 'air backwash' were key factors for creating a highly efficient system for recovery of apparently undamaged protozoa. This reagent-less system can be used for monitoring of parasite contamination in drinking water. © 2015 The Society for Applied Microbiology.

Review of Claims of Interaction Between Gravitation and High-Temperature Superconductors

NASA Astrophysics Data System (ADS)

Woods, R. Clive

2004-02-01

Recent reports have claimed that high-temperature superconductors can interact with gravitation under certain non-relativistic conditions. Only two such reports have been peer-reviewed: the first, describing changes in the weight of test masses, was by Podkletnov and Nieminen (1992) the other, reporting large-amplitude gravitational wave generation in a laboratory, was by Podkletnov and Modanese (2003). Common to these reports is the claim that the observed gravitational field may be modified using YBa2Cu3O7-δ (YBCO) below its superconducting critical temperature, Tc ~ 93K, and in a magnetic field B ~ 1T. Temperatures below 70K gave the largest effects. The first experiment used magnetically levitated YBCO rotated at ~5000 rpm; the second experiment did not spin or levitate the YBCO, but used a 2MV electrical discharge in a vacuum chamber. Several attempts have been made world-wide to replicate the first of these experiments, although no peer-reviewed reports have yet confirmed the observations. No known replications of the second experiment have been completed so far. A number of papers have presented theoretical models for the effects. This paper reviews the current experimental and theoretical scientific evidence regarding these experiments, together with further tests implied by the published explanations. The discussion includes a classical suggestion (due to Landau and Lifshitz) that gravitational waves can modify gravitational fields, Aquino's theory based upon electromagnetic fields, and Desbrandes's calculation to explain the Podkletnov and Nieminen results on the basis of gravity waves emitted from the Cooper pairs inside a superconductor. The conclusions are that these experiments are extremely difficult to replicate and that no complete replication confirming the effects has yet taken place. By contrast, no-one has conclusively disproved the existence of the effects.

De novo identification of replication-timing domains in the human genome by deep learning.

PubMed

Liu, Feng; Ren, Chao; Li, Hao; Zhou, Pingkun; Bo, Xiaochen; Shu, Wenjie

2016-03-01

The de novo identification of the initiation and termination zones-regions that replicate earlier or later than their upstream and downstream neighbours, respectively-remains a key challenge in DNA replication. Building on advances in deep learning, we developed a novel hybrid architecture combining a pre-trained, deep neural network and a hidden Markov model (DNN-HMM) for the de novo identification of replication domains using replication timing profiles. Our results demonstrate that DNN-HMM can significantly outperform strong, discriminatively trained Gaussian mixture model-HMM (GMM-HMM) systems and other six reported methods that can be applied to this challenge. We applied our trained DNN-HMM to identify distinct replication domain types, namely the early replication domain (ERD), the down transition zone (DTZ), the late replication domain (LRD) and the up transition zone (UTZ), using newly replicated DNA sequencing (Repli-Seq) data across 15 human cells. A subsequent integrative analysis revealed that these replication domains harbour unique genomic and epigenetic patterns, transcriptional activity and higher-order chromosomal structure. Our findings support the 'replication-domain' model, which states (1) that ERDs and LRDs, connected by UTZs and DTZs, are spatially compartmentalized structural and functional units of higher-order chromosomal structure, (2) that the adjacent DTZ-UTZ pairs form chromatin loops and (3) that intra-interactions within ERDs and LRDs tend to be short-range and long-range, respectively. Our model reveals an important chromatin organizational principle of the human genome and represents a critical step towards understanding the mechanisms regulating replication timing. Our DNN-HMM method and three additional algorithms can be freely accessed at https://github.com/wenjiegroup/DNN-HMM The replication domain regions identified in this study are available in GEO under the accession ID GSE53984. shuwj@bmi.ac.cn or boxc@bmi.ac.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Development and application of a Controlled Release Facility (CRF) to validate flux quantifying methodologies.

NASA Astrophysics Data System (ADS)

Helmore, Jonathan

2017-04-01

The National Physical Laboratory, the UK's National Measurement Institute, has developed a novel facility capable of replicating the gaseous emission flux characteristics of a variety of real-word scenarios as may be found in small to medium scale industry and agriculture. The Controlled Release Facility (CRF) can be used to challenge conventional remote sensing techniques, as well as validate new Unmanned Aerial Vehicle (UAV) and distributed sensor network based methods, for source identification and flux calculation. The CRF method will be described and the results from three case studies will be discussed: The replication of an operational on-shore shale gas well using emissions of natural gas to atmosphere and measurements using Differential Absorption LIDAR (DIAL); the replication of fugitive volatile organic compounds emissions from a petrochemical unit and measurements using DIAL; and the replication of methane and carbon dioxide emissions from landfill and measurements using both fixed wing and multi-rotor UAVs.

Mu-driven transposition of recombinant mini-Mu unit DNA in the Corynebacterium glutamicum chromosome.

PubMed

Gorshkova, Natalya V; Lobanova, Juliya S; Tokmakova, Irina L; Smirnov, Sergey V; Akhverdyan, Valerii Z; Krylov, Alexander A; Mashko, Sergey V

2018-03-01

A dual-component Mu-transposition system was modified for the integration/amplification of genes in Corynebacterium. The system consists of two types of plasmids: (i) a non-replicative integrative plasmid that contains the transposing mini-Mu(LR) unit bracketed by the L/R Mu ends or the mini-Mu(LER) unit, which additionally contains the enhancer element, E, and (ii) an integration helper plasmid that expresses the transposition factor genes for MuA and MuB. Efficient transposition in the C. glutamicum chromosome (≈ 2 × 10 -4 per cell) occurred mainly through the replicative pathway via cointegrate formation followed by possible resolution. Optimizing the E location in the mini-Mu unit significantly increased the efficiency of Mu-driven intramolecular transposition-amplification in C. glutamicum as well as in gram-negative bacteria. The new C. glutamicum genome modification strategy that was developed allows the consequent independent integration/amplification/fixation of target genes at high copy numbers. After integration/amplification of the first mini-Mu(LER) unit in the C. glutamicum chromosome, the E-element, which is bracketed by lox-like sites, is excised by Cre-mediated fashion, thereby fixing the truncated mini-Mu(LR) unit in its position for the subsequent integration/amplification of new mini-Mu(LER) units. This strategy was demonstrated using the genes for the citrine and green fluorescent proteins, yECitrine and yEGFP, respectively.

Single-Case Design Research: Building the Evidence-Base in the Field of Education of Deaf and Hard of Hearing Students.

PubMed

Cannon, Joanna E; Guardino, Caroline; Antia, Shirin D; Luckner, John L

2016-01-01

The field of education of deaf and hard of hearing (DHH) students has a paucity of evidence-based practices (EBPs) to guide instruction. The authors discussed how the research methodology of single-case design (SCD) can be used to build EBPs through direct and systematic replication of studies. An overview of SCD research methods is presented, including an explanation of how internal and external validity issues are addressed, and why SCD is appropriate for intervention research with DHH children. The authors then examine the SCD research in the field according to quality indicators (QIs; at the individual level and as a body of evidence) to determine the existing evidence base. Finally, future replication areas are recommended to fill the gaps in SCD research with students who are DHH in order to add to the evidence base in the field.

Missed Nursing Care and Unit-Level Nurse Workload in the Acute and Post-Acute Settings.

PubMed

Orique, Sabrina B; Patty, Christopher M; Woods, Ellen

2016-01-01

This study replicates previous research on the nature and causes of missed nursing care and adds an explanatory variable: unit-level nurse workload (patient turnover percentage). The study was conducted in California, which legally mandates nurse staffing ratios. Findings demonstrated no significant relationship between patient turnover and missed nursing care.

Songbird Community Variation Among Five Levels of Overstory Retention in Northern Alabama

Treesearch

Adrian A. Lesak; Yong Wang; Callie Jo Schweitzer

2004-01-01

We compared songbird communities among varying degrees of overstory tree retention in the oak-hickory forest of the southern Mid-Cumberland Plateau region. Three 20-ha complete block replicates of 5 experimental treatments (15 treatment units, 4 ha per unit) were used. The five treatments were operational shelterwood stands with target overstory retention levels of...

DNA replication stress restricts ribosomal DNA copy number.

PubMed

Salim, Devika; Bradford, William D; Freeland, Amy; Cady, Gillian; Wang, Jianmin; Pruitt, Steven C; Gerton, Jennifer L

2017-09-01

Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

Field of Vision Influences Sensory-Motor Control of Skilled and Less-Skilled Dart Players

PubMed Central

Rienhoff, Rebecca; Baker, Joseph; Fischer, Lennart; Strauss, Bernd; Schorer, Jörg

2012-01-01

One characteristic of perceptual expertise in sport and other domains is known as ’the quiet eye', which assumes that fixated information is processed during gaze stability and insufficient spatial information leads to a decrease in performance. The aims of this study were a) replicating inter- and intra-group variability and b) investigating the extent to which quiet eye supports information pick-up of varying fields of vision (i.e., central versus peripheral) using a specific eye-tracking paradigm to compare different skill levels in a dart throwing task. Differences between skill levels were replicated at baseline, but no significant differences in throwing performance were revealed among the visual occlusion conditions. Findings are generally in line with the association between quiet eye duration and aiming performance, but raise questions regarding the relevance of central vision information pick-up for the quiet eye. Key pointsInvestigation of throwing performance and quiet eye duration in dart throwing under several vision conditionsFirst investigation using a dynamic occlusion paradigm, manipulating field of vision in situReplication of previous findings concerning throwing performance and quiet eye durationNew insights about the role of central (and peripheral) vision concerning the quiet eye phenomena PMID:24149366

Water quality of flow through cured-in-place pipe (CIPP).

DOT National Transportation Integrated Search

2017-02-01

Though this study did not include replication, the preponderance of the data from field and simulated-field experiments indicates that Curedin- : Place Pipe (CIPP), with some care in enforcing the Caltrans specification and delaying the reintroductio...

Sample preparation composite and replicate strategy case studies for assay of solid oral drug products.

PubMed

Nickerson, Beverly; Harrington, Brent; Li, Fasheng; Guo, Michele Xuemei

2017-11-30

Drug product assay is one of several tests required for new drug products to ensure the quality of the product at release and throughout the life cycle of the product. Drug product assay testing is typically performed by preparing a composite sample of multiple dosage units to obtain an assay value representative of the batch. In some cases replicate composite samples may be prepared and the reportable assay value is the average value of all the replicates. In previously published work by Harrington et al. (2014) [5], a sample preparation composite and replicate strategy for assay was developed to provide a systematic approach which accounts for variability due to the analytical method and dosage form with a standard error of the potency assay criteria based on compendia and regulatory requirements. In this work, this sample preparation composite and replicate strategy for assay is applied to several case studies to demonstrate the utility of this approach and its application at various stages of pharmaceutical drug product development. Copyright © 2017 Elsevier B.V. All rights reserved.

Advancements in Hydrology and Erosion Process Understanding and Post-Fire Hydrologic and Erosion Model Development for Semi-Arid Landscapes

NASA Astrophysics Data System (ADS)

Williams, C. Jason; Pierson, Frederick B.; Al-Hamdan, Osama Z.; Robichaud, Peter R.; Nearing, Mark A.; Hernandez, Mariano; Weltz, Mark A.; Spaeth, Kenneth E.; Goodrich, David C.

2017-04-01

Fire activity continues to increase in semi-arid regions around the globe. Private and governmental land management entities are challenged with predicting and mitigating post-fire hydrologic and erosion responses on these landscapes. For more than a decade, a team of scientists with the US Department of Agriculture has collaborated on extensive post-fire hydrologic field research and the application of field research to development of post-fire hydrology and erosion predictive technologies. Experiments funded through this research investigated the impacts of fire on vegetation and soils and the effects of these fire-induced changes on infiltration, runoff generation, erodibility, and soil erosion processes. The distribution of study sites spans diverse topography across grassland, shrubland, and woodland landscapes throughout the western United States. Knowledge gleaned from the extensive field experiments was applied to develop and enhance physically-based models for hillslope- to watershed-scale runoff and erosion prediction. Our field research and subsequent data syntheses have identified key knowledge gaps and challenges regarding post-fire hydrology and erosion modeling. Our presentation details some consistent trends across a diverse domain and varying landscape conditions based on our extensive field campaigns. We demonstrate how field data have advanced our understanding of post-fire hydrology and erosion for semi-arid landscapes and highlight remaining key knowledge gaps. Lastly, we briefly show how our well-replicated experimental methodologies have contributed to advancements in hydrologic and erosion model development for the post-fire environment.

Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing.

PubMed

Senkevich, Tatiana G; Bruno, Daniel; Martens, Craig; Porcella, Stephen F; Wolf, Yuri I; Moss, Bernard

2015-09-01

Poxviruses reproduce in the host cytoplasm and encode most or all of the enzymes and factors needed for expression and synthesis of their double-stranded DNA genomes. Nevertheless, the mode of poxvirus DNA replication and the nature and location of the replication origins remain unknown. A current but unsubstantiated model posits only leading strand synthesis starting at a nick near one covalently closed end of the genome and continuing around the other end to generate a concatemer that is subsequently resolved into unit genomes. The existence of specific origins has been questioned because any plasmid can replicate in cells infected by vaccinia virus (VACV), the prototype poxvirus. We applied directional deep sequencing of short single-stranded DNA fragments enriched for RNA-primed nascent strands isolated from the cytoplasm of VACV-infected cells to pinpoint replication origins. The origins were identified as the switching points of the fragment directions, which correspond to the transition from continuous to discontinuous DNA synthesis. Origins containing a prominent initiation point mapped to a sequence within the hairpin loop at one end of the VACV genome and to the same sequence within the concatemeric junction of replication intermediates. These findings support a model for poxvirus genome replication that involves leading and lagging strand synthesis and is consistent with the requirements for primase and ligase activities as well as earlier electron microscopic and biochemical studies implicating a replication origin at the end of the VACV genome.

Safety profile of a replication-deficient human adenovirus-vectored foot-and-mouth disease virus serotype A24 subunit vaccine in cattle.

PubMed

Barrera, J; Brake, D A; Kamicker, B J; Purcell, C; Kaptur, R; Schieber, T; Lechtenberg, K; Miller, T D; Ettyreddy, D; Brough, D E; Butman, B T; Colby, M; Neilan, J G

2018-04-01

The safety of a replication-deficient, human adenovirus-vectored foot-and-mouth disease virus (FMDV) serotype A24 Cruzeiro capsid-based subunit vaccine (AdtA24) was evaluated in five independent safety studies. The target animal safety studies were designed in compliance with United States (U.S.) regulatory requirements (Title 9, U.S. Code of Federal Regulation [9CFR]) and international standard guidelines (VICH Topic GL-44) for veterinary live vaccines. The first three studies were conducted in a total of 22 vaccinees and demonstrated that the AdtA24 master seed virus (MSV) was safe, did not revert to virulence and was not shed or spread from vaccinees to susceptible cattle or pigs. The fourth safety study conducted in 10 lactating cows using an AdtA24 vaccine serial showed that the vaccine was completely absent from milk. The fifth safety study was conducted under typical U.S. production field conditions in 500 healthy beef and dairy cattle using two AdtA24 vaccine serials. These results demonstrated that the vaccine was safe when used per the product label recommendations. Additional data collected during these five studies confirmed that AdtA24 vaccinees developed FMDV A24 and the HAd5 vaccine vector serum neutralization antibodies that test negative in a FMDV non-structural protein antibody test, confirming AdtA24 vaccine's capability to differentiate infected from vaccinated animals (DIVA). In conclusion, results from this comprehensive set of cattle studies demonstrated the safety of the replication-deficient AdtA24 vaccine and fulfilled safety-related requirements for U.S. regulatory requirements. © 2017 The Authors. Transboundary and Emerging Diseases Published by Blackwell Verlag GmbH.

Quality-control results for ground-water and surface-water data, Sacramento River Basin, California, National Water-Quality Assessment, 1996-1998

USGS Publications Warehouse

Munday, Cathy; Domagalski, Joseph L.

2003-01-01

Evaluating the extent that bias and variability affect the interpretation of ground- and surface-water data is necessary to meet the objectives of the National Water-Quality Assessment (NAWQA) Program. Quality-control samples used to evaluate the bias and variability include annual equipment blanks, field blanks, field matrix spikes, surrogates, and replicates. This report contains quality-control results for the constituents critical to the ground- and surface-water components of the Sacramento River Basin study unit of the NAWQA Program. A critical constituent is one that was detected frequently (more than 50 percent of the time in blank samples), was detected at amounts exceeding water-quality standards or goals, or was important for the interpretation of water-quality data. Quality-control samples were collected along with ground- and surface-water samples during the high intensity phase (cycle 1) of the Sacramento River Basin NAWQA beginning early in 1996 and ending in 1998. Ground-water field blanks indicated contamination of varying levels of significance when compared with concentrations detected in environmental ground-water samples for ammonia, dissolved organic carbon, aluminum, and copper. Concentrations of aluminum in surface-water field blanks were significant when compared with environmental samples. Field blank samples collected for pesticide and volatile organic compound analyses revealed no contamination in either ground- or surface-water samples that would effect the interpretation of environmental data, with the possible exception of the volatile organic compound trichloromethane (chloroform) in ground water. Replicate samples for ground water and surface water indicate that variability resulting from sample collection, processing, and analysis was generally low. Some of the larger maximum relative percentage differences calculated for replicate samples occurred between samples having lowest absolute concentration differences and(or) values near the reporting limit. Surrogate recoveries for pesticides analyzed by gas chromatography/mass spectrometry (GC/MS), pesticides analyzed by high performance liquid chromatography (HPLC), and volatile organic compounds in ground- and surface-water samples were within the acceptable limits of 70 to 130 percent and median recovery values between 82 and 113 percent. The recovery percentages for surrogate compounds analyzed by HPLC had the highest standard deviation, 20 percent for ground-water samples and 16 percent for surface-water samples, and the lowest median values, 82 percent for ground-water samples and 91 percent for surface-water samples. Results were consistent with the recovery results described for the analytical methods. Field matrix spike recoveries for pesticide compounds analyzed using GC/MS in ground- and surface-water samples were comparable with published recovery data. Recoveries of carbofuran, a critical constituent in ground- and surface-water studies, and desethyl atrazine, a critical constituent in the ground-water study, could not be calculated because of problems with the analytical method. Recoveries of pesticides analyzed using HPLC in ground- and surface-water samples were generally low and comparable with published recovery data. Other methodological problems for HPLC analytes included nondetection of the spike compounds and estimated values of spike concentrations. Recovery of field matrix spikes for volatile organic compounds generally were within the acceptable range, 70 and 130 percent for both ground- and surface-water samples, and median recoveries from 62 to 127 percent. High or low recoveries could be related to errors in the field, such as double spiking or using spike solution past its expiration date, rather than problems during analysis. The methodological changes in the field spike protocol during the course of the Sacramento River Basin study, which included decreasing the amount of spike solu

Mechanisms to Control Rereplication and Implications for Cancer

PubMed Central

Hook, Sara S.; Lin, Jie Jessie; Dutta, Anindya

2007-01-01

Recent advances in the replication field have highlighted how the replication initiator proteins are negatively regulated by inhibitor proteins and ubiquitin-mediated degradation in mammalian cells to prevent rereplication. When these regulatory pathways go awry, uncontrolled rereplication ensues and a G2/M checkpoint is evoked to prevent cellular death. Many components of the checkpoints activated by rereplicaton are important for cancer prevention by facilitating DNA damage repair processes. The pathways that prevent rereplication themselves have also recently been implicated in preventing tumorigenesis. Studies from patient tumors, genetically altered mice, and mammalian cell culture suggest that deregulation of replication licensing proteins results in an increase in aneuploidy, chromosomal fusions, and DNA breaks. These studies provide a framework to address how regulators of replication function to maintain genomic stability. PMID:18053699

A reminder on millisecond timing accuracy and potential replication failure in computer-based psychology experiments: An open letter.

PubMed

Plant, Richard R

2016-03-01

There is an ongoing 'replication crisis' across the field of psychology in which researchers, funders, and members of the public are questioning the results of some scientific studies and the validity of the data they are based upon. However, few have considered that a growing proportion of research in modern psychology is conducted using a computer. Could it simply be that the hardware and software, or experiment generator, being used to run the experiment itself be a cause of millisecond timing error and subsequent replication failure? This article serves as a reminder that millisecond timing accuracy in psychology studies remains an important issue and that care needs to be taken to ensure that studies can be replicated on current computer hardware and software.

Genetic Diversity of Infectious Laryngotracheitis Virus during In Vivo Coinfection Parallels Viral Replication and Arises from Recombination Hot Spots within the Genome

PubMed Central

Hartley, Carol A.; Vaz, Paola K.; Diaz-Méndez, Andrés; García, Maricarmen; Spatz, Stephen; Devlin, Joanne M.

2017-01-01

ABSTRACT Recombination is a feature of many alphaherpesviruses that infect people and animals. Infectious laryngotracheitis virus (ILTV; Gallid alphaherpesvirus 1) causes respiratory disease in chickens, resulting in significant production losses in poultry industries worldwide. Natural (field) ILTV recombination is widespread, particularly recombination between attenuated ILTV vaccine strains to create virulent viruses. These virulent recombinants have had a major impact on animal health. Recently, the development of a single nucleotide polymorphism (SNP) genotyping assay for ILTV has helped to understand ILTV recombination in laboratory settings. In this study, we applied this SNP genotyping assay to further examine ILTV recombination in the natural host. Following coinoculation of specific-pathogen-free chickens, we examined the resultant progeny for evidence of viral recombination and characterized the diversity of the recombinants over time. The results showed that ILTV replication and recombination are closely related and that the recombinant viral progeny are most diverse 4 days after coinoculation, which is the peak of viral replication. Further, the locations of recombination breakpoints in a selection of the recombinant progeny, and in field isolates of ILTV from different geographical regions, were examined following full-genome sequencing and used to identify recombination hot spots in the ILTV genome. IMPORTANCE Alphaherpesviruses are common causes of disease in people and animals. Recombination enables genome diversification in many different species of alphaherpesviruses, which can lead to the evolution of higher levels of viral virulence. Using the alphaherpesvirus infectious laryngotracheitis virus (ILTV), we performed coinfections in the natural host (chickens) to demonstrate high levels of virus recombination. Higher levels of diversity in the recombinant progeny coincided with the highest levels of virus replication. In the recombinant progeny, and in field isolates, recombination occurred at greater frequency in recombination hot spot regions of the virus genome. Our results suggest that control measures that aim to limit viral replication could offer the potential to limit virus recombination and thus the evolution of virulence. The development and use of vaccines that are focused on limiting virus replication, rather than vaccines that are focused more on limiting clinical disease, may be indicated in order to better control disease. PMID:28939604

Open-field behavior of house mice selectively bred for high voluntary wheel-running.

PubMed

Bronikowski, A M; Carter, P A; Swallow, J G; Girard, I A; Rhodes, J S; Garland, T

2001-05-01

Open-field behavioral assays are commonly used to test both locomotor activity and emotionality in rodents. We performed open-field tests on house mice (Mus domesticus) from four replicate lines genetically selected for high voluntary wheel-running for 22 generations and from four replicate random-bred control lines. Individual mice were recorded by video camera for 3 min in a 1-m2 open-field arena on 2 consecutive days. Mice from selected lines showed no statistical differences from control mice with respect to distance traveled, defecation, time spent in the interior, or average distance from the center of the arena during the trial. Thus, we found little evidence that open-field behavior, as traditionally defined, is genetically correlated with wheel-running behavior. This result is a useful converse test of classical studies that report no increased wheel-running in mice selected for increased open-field activity. However, mice from selected lines turned less in their travel paths than did control-line mice, and females from selected lines had slower travel times (longer latencies) to reach the wall. We discuss these results in the context of the historical open-field test and newly defined measures of open-field activity.

Ethical and Legal Implications of the Methodological Crisis in Neuroimaging.

PubMed

Kellmeyer, Philipp

2017-10-01

Currently, many scientific fields such as psychology or biomedicine face a methodological crisis concerning the reproducibility, replicability, and validity of their research. In neuroimaging, similar methodological concerns have taken hold of the field, and researchers are working frantically toward finding solutions for the methodological problems specific to neuroimaging. This article examines some ethical and legal implications of this methodological crisis in neuroimaging. With respect to ethical challenges, the article discusses the impact of flawed methods in neuroimaging research in cognitive and clinical neuroscience, particularly with respect to faulty brain-based models of human cognition, behavior, and personality. Specifically examined is whether such faulty models, when they are applied to neurological or psychiatric diseases, could put patients at risk, and whether this places special obligations on researchers using neuroimaging. In the legal domain, the actual use of neuroimaging as evidence in United States courtrooms is surveyed, followed by an examination of ways that the methodological problems may create challenges for the criminal justice system. Finally, the article reviews and promotes some promising ideas and initiatives from within the neuroimaging community for addressing the methodological problems.

Commercial Building Partnerships Replication and Diffusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antonopoulos, Chrissi A.; Dillon, Heather E.; Baechler, Michael C.

2013-09-16

This study presents findings from survey and interview data investigating replication efforts of Commercial Building Partnership (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered directly with 12 organizations on new and retrofit construction projects, which represented approximately 28 percent of the entire U.S. Department of Energy (DOE) CBP program. Through a feedback survey mechanism, along with personal interviews, PNNL gathered quantitative and qualitative data relating to replication efforts by each organization. These data were analyzed to provide insight into two primary research areas: 1) CBP partners’ replication efforts of technologies and approaches used inmore » the CBP project to the rest of the organization’s building portfolio (including replication verification), and, 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the CBP program. The first area of this research focused specifically on replication efforts underway or planned by each CBP program participant. Factors that impact replication include motivation, organizational structure and objectives firms have for implementation of energy efficient technologies. Comparing these factors between different CBP partners revealed patterns in motivation for constructing energy efficient buildings, along with better insight into market trends for green building practices. The second area of this research develops a diffusion of innovations model to analyze potential broad market impacts of the CBP program on the commercial building industry in the United States.« less

Microgravity

NASA Image and Video Library

1998-07-01

The fundamental structural unit of chromatin and is the basis for organization within the genome by compaction of DNA within the nucleus of the cell and by making selected regions of chromosomes available for transcription and replication.

Nucleosome

NASA Technical Reports Server (NTRS)

1998-01-01

The fundamental structural unit of chromatin and is the basis for organization within the genome by compaction of DNA within the nucleus of the cell and by making selected regions of chromosomes available for transcription and replication.

Water quality of flow through cured-in-place pipe (CIPP) : final report.

DOT National Transportation Integrated Search

2017-02-01

Though this study did not include replication, the preponderance of the data from field and simulated-field experiments indicates that Curedin-Place : Pipe (CIPP), with some care in enforcing the Caltrans specification and delaying the reintroduction...

Paying for performance: Performance incentives increase desire for the reward object.

PubMed

Hur, Julia D; Nordgren, Loran F

2016-09-01

The current research examines how exposure to performance incentives affects one's desire for the reward object. We hypothesized that the flexible nature of performance incentives creates an attentional fixation on the reward object (e.g., money), which leads people to become more desirous of the rewards. Results from 5 laboratory experiments and 1 large-scale field study provide support for this prediction. When performance was incentivized with monetary rewards, participants reported being more desirous of money (Study 1), put in more effort to earn additional money in an ensuing task (Study 2), and were less willing to donate money to charity (Study 4). We replicated the result with nonmonetary rewards (Study 5). We also found that performance incentives increased attention to the reward object during the task, which in part explains the observed effects (Study 6). A large-scale field study replicated these findings in a real-world setting (Study 7). One laboratory experiment failed to replicate (Study 3). (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Regions flanking ori sequences affect the replication efficiency of the mitochondrial genome of ori+ petite mutants from yeast.

PubMed

Rayko, E; Goursot, R; Cherif-Zahar, B; Melis, R; Bernardi, G

1988-03-31

The mitochondrial genomes of progenies from 26 crosses between 17 cytoplasmic, spontaneous, suppressive, ori+ petite mutants of Saccharomyces cerevisiae have been studied by electrophoresis of restriction fragments. Only parental genomes (or occasionally, genomes derived from them by secondary excisions) were found in the progenies of the almost 500 diploids investigated; no evidence for illegitimate, site-specific mitochondrial recombination was detected. One of the parental genomes was always found to be predominate over the other one, although to different extents in different crosses. This predominance appears to be due to a higher replication efficiency, which is correlated with a greater density of ori sequences on the mitochondrial genome (and with a shorter repeat unit size of the latter). Exceptions to the 'repeat-unit-size rule' were found, however, even when the parental mitochondrial genomes carried the same ori sequence. This indicates that noncoding, intergenic sequences outside ori sequences also play a role in modulating replication efficiency. Since in different petites such sequences differ in primary structure, size, and position relative to ori sequences, this modulation is likely to take place through an indirect effect on DNA and nucleoid structure.

Ribosomal DNA Organization Before and After Magnification in Drosophila melanogaster

PubMed Central

Bianciardi, Alessio; Boschi, Manuela; Swanson, Ellen E.; Belloni, Massimo; Robbins, Leonard G.

2012-01-01

In all eukaryotes, the ribosomal RNA genes are stably inherited redundant elements. In Drosophila melanogaster, the presence of a Ybb− chromosome in males, or the maternal presence of the Ribosomal exchange (Rex) element, induces magnification: a heritable increase of rDNA copy number. To date, several alternative classes of mechanisms have been proposed for magnification: in situ replication or extra-chromosomal replication, either of which might act on short or extended strings of rDNA units, or unequal sister chromatid exchange. To eliminate some of these hypotheses, none of which has been clearly proven, we examined molecular-variant composition and compared genetic maps of the rDNA in the bb2 mutant and in some magnified bb+ alleles. The genetic markers used are molecular-length variants of IGS sequences and of R1 and R2 mobile elements present in many 28S sequences. Direct comparison of PCR products does not reveal any particularly intensified electrophoretic bands in magnified alleles compared to the nonmagnified bb2 allele. Hence, the increase of rDNA copy number is diluted among multiple variants. We can therefore reject mechanisms of magnification based on multiple rounds of replication of short strings. Moreover, we find no changes of marker order when pre- and postmagnification maps are compared. Thus, we can further restrict the possible mechanisms to two: replication in situ of an extended string of rDNA units or unequal exchange between sister chromatids. PMID:22505623

The cooperative forestry research unit Commercial Thinning Research Network--9-year results

Treesearch

Robert S. Seymour; Spencer R. Meyer; Robert G. Wagner

2014-01-01

The Commercial Thinning Research Network (CTRN) was established throughout the spruce-fir forest of Maine beginning in 2000 with substantial funding from the University of Maine's Cooperative Forestry Research Unit. One of six replicates of the precommercially thinned stand condition in the CTRN is located in compartment 23A in the U.S. Department of Agriculture,...

Crystallization and preliminary X-ray diffraction analysis of the Bacillus subtilis replication termination protein in complex with the 37-base-pair TerI-binding site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vivian, J. P.; Porter, C.; Wilce, J. A.

2006-11-01

A preparation of replication terminator protein (RTP) of B. subtilis and a 37-base-pair TerI sequence (comprising two binding sites for RTP) has been purified and crystallized. The replication terminator protein (RTP) of Bacillus subtilis binds to specific DNA sequences that halt the progression of the replisome in a polar manner. These terminator complexes flank a defined region of the chromosome into which they allow replication forks to enter but not exit. Forcing the fusion of replication forks in a specific zone is thought to allow the coordination of post-replicative processes. The functional terminator complex comprises two homodimers each of 29more » kDa bound to overlapping binding sites. A preparation of RTP and a 37-base-pair TerI sequence (comprising two binding sites for RTP) has been purified and crystallized. A data set to 3.9 Å resolution with 97.0% completeness and an R{sub sym} of 12% was collected from a single flash-cooled crystal using synchrotron radiation. The diffraction data are consistent with space group P622, with unit-cell parameters a = b = 118.8, c = 142.6 Å.« less

The phantom leaf effect: a replication, part 1.

PubMed

Hubacher, John

2015-02-01

To replicate the phantom leaf effect and demonstrate a possible means to directly observe properties of the biological field. Thirty percent to 60% of plant leaves were amputated, and the remaining leaf sections were photographed with corona discharge imaging. All leaves were cut before placement on film. A total of 137 leaves were used. Plant leaves of 14 different species. Ninety-six phantom leaf specimens were successfully obtained; 41 specimens did not yield the phantom leaf effect. A normally undetected phantom "structure," possibly evidence of the biological field, can persist in the area of an amputated leaf section, and corona discharge can occur from this invisible structure. This protocol may suggest a testable method to study properties of conductivity and other parameters through direct observation of the complete biological field in plant leaves, with broad implications for biology and physics.

The importance of replication in wildlife research

USGS Publications Warehouse

Johnson, D.H.

2002-01-01

Wildlife ecology and management studies have been widely criticized for deficiencies in design or analysis. Manipulative experiments--with controls, randomization, and replication in space and time--provide powerful ways of learning about natural systems and establishing causal relationships, but such studies are rare in our field. Observational studies and sample surveys are more common; they also require appropriate design and analysis. More important than the design and analysis of individual studies is metareplication: replication of entire studies. Similar conclusions obtained from studies of the same phenomenon conducted under widely differing conditions will give us greater confidence in the generality of those findings than would any single study, however well designed and executed.

[Natural history, diagnosis and treatment of chronic hepatitis B and C in hemodialysis patients].

PubMed

Nicolardi, Erica; Grieco, Antonio; Rapaccini, Gian Ludovico; Pompili, Maurizio

2010-01-01

Chronic hepatitis B and C are important causes of liver disease in hemodialysis units. The most important route of transmission is the inapparent parenteral route; known risk factors are the high prevalence of HBV and HCV infections in hemodialysis units, previous blood transfusions, long-term dialysis treatment, frequent changes of hemodialysis unit, and previous renal transplants. The source, time and duration of infection are often difficult to ascertain. The studies investigating the natural history of viral hepatitis in hemodialysis patients are few and limited by a short follow-up, but they show an independent and negative impact on survival due to an increased risk of liver cirrhosis and hepatocellular carcinoma. The treatment options include conventional or pegylated interferon (alone or in association with ribavirin) and the nucleoside/nucleotide analogs. The aim of treatment is viral eradication or persistent suppression of viral replication. The altered pharmacokinetics, the increased risk of drug-related toxicity, and the need for renal transplant complicate the management of antiviral therapy. In patients with chronic HBV infection and active replication the most common approach is persistent suppression of viral replication using nucleoside/nucleotide analogs. As regards hepatitis C, several clinical trials evaluating conventional interferon monotherapy have shown higher sustained virological response and dropout rates in dialysis patients than in patients with normal kidney function. Data about pegylated interferon as monotherapy or in association with ribavirin are promising but limited. Hemodialyzed patients obtaining a sustained virological response often maintain the response after kidney transplantation.

Interpreting the Dependence of Mutation Rates on Age and Time

PubMed Central

Gao, Ziyue; Wyman, Minyoung J.; Sella, Guy; Przeworski, Molly

2016-01-01

Mutations can originate from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that arise between replication cycles and are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell divisions, providing a framework for understanding how mutation rates depend on sex, age, and cell division rate. We show that the accrual of mutations should track cell divisions not only when mutations are replicative in origin but also when they are non-replicative and repaired efficiently. One implication is that observations from diverse fields that to date have been interpreted as pointing to a replicative origin of most mutations could instead reflect the accumulation of mutations arising from endogenous reactions or exogenous mutagens. We further find that only mutations that arise from inefficiently repaired lesions will accrue according to absolute time; thus, unless life history traits co-vary, the phylogenetic “molecular clock” should not be expected to run steadily across species. PMID:26761240

Noise-induced bistability in the quasi-neutral coexistence of viral RNAs under different replication modes.

PubMed

Sardanyés, Josep; Arderiu, Andreu; Elena, Santiago F; Alarcón, Tomás

2018-05-01

Evolutionary and dynamical investigations into real viral populations indicate that RNA replication can range between the two extremes represented by so-called 'stamping machine replication' (SMR) and 'geometric replication' (GR). The impact of asymmetries in replication for single-stranded (+) sense RNA viruses has been mainly studied with deterministic models. However, viral replication should be better described by including stochasticity, as the cell infection process is typically initiated with a very small number of RNA macromolecules, and thus largely influenced by intrinsic noise. Under appropriate conditions, deterministic theoretical descriptions of viral RNA replication predict a quasi-neutral coexistence scenario, with a line of fixed points involving different strands' equilibrium ratios depending on the initial conditions. Recent research into the quasi-neutral coexistence in two competing populations reveals that stochastic fluctuations fundamentally alter the mean-field scenario, and one of the two species outcompetes the other. In this article, we study this phenomenon for viral RNA replication modes by means of stochastic simulations and a diffusion approximation. Our results reveal that noise has a strong impact on the amplification of viral RNAs, also causing the emergence of noise-induced bistability. We provide analytical criteria for the dominance of (+) sense strands depending on the initial populations on the line of equilibria, which are in agreement with direct stochastic simulation results. The biological implications of this noise-driven mechanism are discussed within the framework of the evolutionary dynamics of RNA viruses with different modes of replication. © 2018 The Author(s).

The effectiveness of a single treatment with doramectin or ivermectin in the control of gastrointestinal nematodes in grazing yearling stocker cattle.

PubMed

Ballweber, L R; Smith, L L; Stuedemann, J A; Yazwinski, T A; Skogerboe, T L

1997-09-01

Four studies were conducted to a similar experimental design in the U.S. to evaluate the effectiveness of doramectin injectable administered to yearling stocker cattle in the control of gastrointestinal nematodiasis over the subsequent grazing period. Studies were conducted in Wisconsin (WI) and Arkansas (AR) during the summer season. The other two studies were conducted in Georgia (GA) and Mississippi (MS) during the winter/spring season. Doramectin was compared with both ivermectin injectable and ivermectin pour-on in the WI study, with ivermectin injectable alone in the GA study and with ivermectin pour-on alone in the other two studies. At each study site, an area of permanent pasture previously grazed by parasitized animals was subdivided by fencing into equal pasture units each with its own water supply. A treatment designation (non-medicated control, doramectin injectable, ivermectin injectable or ivermectin pour-on) was randomly assigned to each pasture unit. Weaned beef calves with confirmed gastrointestinal nematode infections were randomly allotted to a pasture unit and corresponding treatment group. Each treatment group consisted of three replicates of seven animals per pasture unit (total 21 animals) in the WI study, three replicates of four or six animals per pasture unit (total 16 animals) in the AR study, five replicates of six animals per pasture unit (total 30 animals) in the GA study and three replicates of 12 animals per pasture unit (total 36 animals) in the MS study. Treatments were 1% doramectin injectable solution, 1% ivermectin injectable solution, 0.5% ivermectin pour-on solution or non-medicated controls. The injectables were administered at a dose of 1 ml/50 kg body weight (200 micrograms doramectin or ivermectin/kg) by subcutaneous injection in the neck. Ivermectin pour-on solution was administered topically at a dose of 1 ml/10 kg body weight (500 micrograms ivermectin/kg). After receiving their prescribed treatment, animals were placed on their designated pasture unit where they remained for the entire grazing period (84-140 days). Fecal nematode egg counts and body weights were monitored at predetermined intervals throughout each study. Doramectin treatment reduced pretreatment egg counts by between 95 and 100% by 21 days post-treatment. Subsequent rises in egg output from exposure to infective pastures were delayed by two to four weeks resulting in substantial reductions in total egg deposition over the grazing period and, therefore, potential pasture recontamination. Doramectin treatment resulted in substantial average daily weight gain advantages (0.152-0.272 kg) over the grazing season compared to non-medicated controls. Advantages were statistically significant (P < 0.05) in three of the four studies. There were no significant differences (P > 0.05) in average daily gain between the doramectin and ivermectin injectable or ivermectin pour-on treated groups.

Correlative live and super-resolution imaging reveals the dynamic structure of replication domains.

PubMed

Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, Jan

2018-06-04

Chromosome organization in higher eukaryotes controls gene expression, DNA replication, and DNA repair. Genome mapping has revealed the functional units of chromatin at the submegabase scale as self-interacting regions called topologically associating domains (TADs) and showed they correspond to replication domains (RDs). A quantitative structural and dynamic description of RD behavior in the nucleus is, however, missing because visualization of dynamic subdiffraction-sized RDs remains challenging. Using fluorescence labeling of RDs combined with correlative live and super-resolution microscopy in situ, we determined biophysical parameters to characterize the internal organization, spacing, and mechanical coupling of RDs. We found that RDs are typically 150 nm in size and contain four co-replicating regions spaced 60 nm apart. Spatially neighboring RDs are spaced 300 nm apart and connected by highly flexible linker regions that couple their motion only <550 nm. Our pipeline allows a robust quantitative characterization of chromosome structure in situ and provides important biophysical parameters to understand general principles of chromatin organization. © 2018 Xiang et al.

Replication and robustness in developmental research.

PubMed

Duncan, Greg J; Engel, Mimi; Claessens, Amy; Dowsett, Chantelle J

2014-11-01

Replications and robustness checks are key elements of the scientific method and a staple in many disciplines. However, leading journals in developmental psychology rarely include explicit replications of prior research conducted by different investigators, and few require authors to establish in their articles or online appendices that their key results are robust across estimation methods, data sets, and demographic subgroups. This article makes the case for prioritizing both explicit replications and, especially, within-study robustness checks in developmental psychology. It provides evidence on variation in effect sizes in developmental studies and documents strikingly different replication and robustness-checking practices in a sample of journals in developmental psychology and a sister behavioral science-applied economics. Our goal is not to show that any one behavioral science has a monopoly on best practices, but rather to show how journals from a related discipline address vital concerns of replication and generalizability shared by all social and behavioral sciences. We provide recommendations for promoting graduate training in replication and robustness-checking methods and for editorial policies that encourage these practices. Although some of our recommendations may shift the form and substance of developmental research articles, we argue that they would generate considerable scientific benefits for the field. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

DNA replication through a chromatin environment.

PubMed

Bellush, James M; Whitehouse, Iestyn

2017-10-05

Compaction of the genome into the nuclear space is achieved by wrapping DNA around octameric assemblies of histone proteins to form nucleosomes, the fundamental repeating unit of chromatin. Aside from providing a means by which to fit larger genomes into the cell, chromatinization of DNA is a crucial means by which the cell regulates access to the genome. While the complex role that chromatin plays in gene transcription has been appreciated for a long time, it is now also apparent that crucial aspects of DNA replication are linked to the biology of chromatin. This review will focus on recent advances in our understanding of how the chromatin environment influences key aspects of DNA replication.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'. © 2017 The Author(s).

Propagation of Some Local Fig (Ficus carica L.) Cultivars by Hardwood Cuttings under the Field Conditions in Tunisia

PubMed Central

Aljane, Fateh; Nahdi, Sabrine

2014-01-01

This research was carried out in Southeast of Tunisia in 2009 and 2010, in order to study the propagation of six (Ficus carica L.) cultivars by using hardwood cuttings under the field conditions. The effect of the cultivars and the type of buds, shoots age, shoots length, and shoots diameter were recorded. Ten cuttings per cultivar and/or cutting types with three replications were planted in rooting unit. Percentage of root emergence and six morphological parameters of young fig plants were measured. Results showed that the responses of cuttings as fig nursery plants presented a high variability among the five cultivars. The most widely varied characters were % root emergence (RE) and cumulative growth of young plant (CG). The first one ranged from 10% to 90%, the second varied within 32 and 112 cm. Concerning the ‘‘BITHER” cultivar, 6 cutting types with different age, length, and diameter were evaluated. Results showed a great variation in % of root emergence (0–90%), length of nursery plant (3–77 cm), and number of roots/nursery plant (0–29 roots). The present research showed that the hardwood cutting of local fig cultivars can be propagated under field conditions in Southeast of Tunisia. PMID:27437458

West Pearl Queen CO2 sequestration pilot test and modeling project 2006-2008.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Engler, Bruce Phillip; Cooper, Scott Patrick; Symons, Neill Phillip

2008-08-01

The West Pearl Queen is a depleted oil reservoir that has produced approximately 250,000 bbl of oil since 1984. Production had slowed prior to CO{sub 2} injection, but no previous secondary or tertiary recovery methods had been applied. The initial project involved reservoir characterization and field response to injection of CO{sub 2}; the field experiment consisted of injection, soak, and venting. For fifty days (December 20, 2002, to February 11, 2003) 2090 tons of CO{sub 2} were injected into the Shattuck Sandstone Member of the Queen Formation at the West Pearl Queen site. This technical report highlights the test resultsmore » of the numerous research participants and technical areas from 2006-2008. This work included determination of lateral extents of the permeability units using outcrop observations, core results, and well logs. Pre- and post-injection 3D seismic data were acquired. To aid in interpreting seismic data, we performed numerical simulations of the effects of CO{sub 2} replacement of brine where the reservoir model was based upon correlation lengths established by the permeability studies. These numerical simulations are not intended to replicate field data, but to provide insight of the effects of CO{sub 2}.« less

The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum

PubMed Central

Koonin, Eugene V; Wolf, Yuri I

2009-01-01

Background The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject. Concept Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns and processes of evolution. We posit that replication of the genetic material is the singular fundamental biological process and that replication with an error rate below a certain threshold both enables and necessitates evolution by drift and selection. Starting from this proposition, we outline a general concept of evolution that consists of three major precepts. 1. The primary agency of evolution consists of Fundamental Units of Evolution (FUEs), that is, units of genetic material that possess a substantial degree of evolutionary independence. The FUEs include both bona fide selfish elements such as viruses, viroids, transposons, and plasmids, which encode some of the information required for their own replication, and regular genes that possess quasi-independence owing to their distinct selective value that provides for their transfer between ensembles of FUEs (genomes) and preferential replication along with the rest of the recipient genome. 2. The history of replication of a genetic element without recombination is isomorphously represented by a directed tree graph (an arborescence, in the graph theory language). Recombination within a FUE is common between very closely related sequences where homologous recombination is feasible but becomes negligible for longer evolutionary distances. In contrast, shuffling of FUEs occurs at all evolutionary distances. Thus, a tree is a natural representation of the evolution of an individual FUE on the macro scale, but not of an ensemble of FUEs such as a genome. 3. The history of life is properly represented by the "forest" of evolutionary trees for individual FUEs (Forest of Life, or FOL). Search for trends and patterns in the FOL is a productive direction of study that leads to the delineation of ensembles of FUEs that evolve coherently for a certain time span owing to a shared history of vertical inheritance or horizontal gene transfer; these ensembles are commonly known as genomes, taxa, or clades, depending on the level of analysis. A small set of genes (the universal genetic core of life) might show a (mostly) coherent evolutionary trend that transcends the entire history of cellular life forms. However, it might not be useful to denote this trend "the tree of life", or organismal, or species tree because neither organisms nor species are fundamental units of life. Conclusion A logical analysis of the units and processes of biological evolution suggests that the natural fundamental unit of evolution is a FUE, that is, a genetic element with an independent evolutionary history. Evolution of a FUE on the macro scale is naturally represented by a tree. Only the full compendium of trees for individual FUEs (the FOL) is an adequate depiction of the evolution of life. Coherent evolution of FUEs over extended evolutionary intervals is a crucial aspect of the history of life but a "species" or "organismal" tree is not a fundamental concept. Reviewers This articles was reviewed by Valerian Dolja, W. Ford Doolittle, Nicholas Galtier, and William Martin PMID:19788730

The effect of inhibition on the existence of traveling wave solutions for a neural field model of human seizure termination.

PubMed

González-Ramírez, L R; Kramer, M A

2018-06-01

In this paper we study the influence of inhibition on an activity-based neural field model consisting of an excitatory population with a linear adaptation term that directly regulates the activity of the excitatory population. Such a model has been used to replicate traveling wave data as observed in high density local field potential recordings (González-Ramírez et al. PLoS Computational Biology, 11(2), e1004065, 2015). In this work, we show that by adding an inhibitory population to this model we can still replicate wave properties as observed in human clinical data preceding seizure termination, but the parameter range over which such waves exist becomes more restricted. This restriction depends on the strength of the inhibition and the timescale at which the inhibition acts. In particular, if inhibition acts on a slower timescale relative to excitation then it is possible to still replicate traveling wave patterns as observed in the clinical data even with a relatively strong effect of inhibition. However, if inhibition acts on the same timescale as the excitation, or faster, then traveling wave patterns with the desired characteristics cease to exist when the inhibition becomes sufficiently strong.

Doctoral training in statistics, measurement, and methodology in psychology: replication and extension of Aiken, West, Sechrest, and Reno's (1990) survey of PhD programs in North America.

PubMed

Aiken, Leona S; West, Stephen G; Millsap, Roger E

2008-01-01

In a survey of all PhD programs in psychology in the United States and Canada, the authors documented the quantitative methodology curriculum (statistics, measurement, and research design) to examine the extent to which innovations in quantitative methodology have diffused into the training of PhDs in psychology. In all, 201 psychology PhD programs (86%) participated. This survey replicated and extended a previous survey (L. S. Aiken, S. G. West, L. B. Sechrest, & R. R. Reno, 1990), permitting examination of curriculum development. Most training supported laboratory and not field research. The median of 1.6 years of training in statistics and measurement was mainly devoted to the modally 1-year introductory statistics course, leaving little room for advanced study. Curricular enhancements were noted in statistics and to a minor degree in measurement. Additional coverage of both fundamental and innovative quantitative methodology is needed. The research design curriculum has largely stagnated, a cause for great concern. Elite programs showed no overall advantage in quantitative training. Forces that support curricular innovation are characterized. Human capital challenges to quantitative training, including recruiting and supporting young quantitative faculty, are discussed. Steps must be taken to bring innovations in quantitative methodology into the curriculum of PhD programs in psychology. PsycINFO Database Record (c) 2008 APA, all rights reserved.

Use of the Primitive Unit Cell in Understanding Subtle Features of the Cubic Closest-Packed Structure

ERIC Educational Resources Information Center

Hawkins, John A.; Rittenhouse, Jeffrey L.; Soper, Linda M.; Rittenhouse, Robert C.

2008-01-01

One of the most important crystal structures adopted by metals is characterized by the "abcabc"...stacking of close-packed layers. This structure is commonly referred to in textbooks as the cubic close-packed (ccp) or face-centered cubic (fcc) structure, since the entire lattice can be generated by replication of a face-centered cubic unit cell…

PTGER4 gene variant rs76523431 is a candidate risk factor for radiological joint damage in rheumatoid arthritis patients: a genetic study of six cohorts.

PubMed

Rodriguez-Rodriguez, Luis; Ivorra-Cortes, Jose; Carmona, F David; Martín, Javier; Balsa, Alejandro; van Steenbergen, Hanna W; van der Helm-van Mil, Annette H M; González-Álvaro, Isidoro; Fernandez-Gutiérrez, Benjamín

2015-11-05

Prostaglandin E receptor 4 (PTGER4) is implicated in immune regulation and bone metabolism. The aim of this study was to analyze its role in radiological joint damage in rheumatoid arthritis (RA). Six independent cohorts of patients with RA of European or North American descent were included, comprising 1789 patients with 5083 sets of X-rays. The Hospital Clínico San Carlos Rheumatoid Arthritis, Princesa Early Arthritis Register Longitudinal study, and Hospital Universitario de La Paz early arthritis (Spain) cohorts were used as discovery cohorts, and the Leiden Early Arthritis Clinic (The Netherlands), Wichita (United States), and National Databank for Rheumatic Diseases (United States and Canada) cohorts as replication cohorts. First, the PTGER4 rs6896969 single-nucleotide polymorphism (SNP) was genotyped using TaqMan assays and available Illumina Immunochip data and studied in the discovery and replication cohorts. Second, the PTGER4 gene and adjacent regions were analyzed using Immunochip genotyping data in the discovery cohorts. On the basis of pooled p values, linkage disequilibrium structure of the region, and location in regions with transcriptional properties, SNPs were selected for replication. The results from discovery, replication, and overall cohorts were pooled using inverse-variance-weighted meta-analysis. Influence of the polymorphisms on the overall radiological damage (constant effect) and on damage progression over time (time-varying effect) was analyzed. The rs6896969 polymorphism showed a significant association with radiological damage in the constant effect pooled analysis of the discovery cohorts, although no significant association was observed in the replication cohorts or the overall pooled analysis. Regarding the analysis of the PTGER4 region, 976 variants were analyzed in the discovery cohorts. From the constant and time-varying effect analyses, 12 and 20 SNPs, respectively, were selected for replication. Only the rs76523431 variant showed a significant association with radiographic progression in the time-varying effect pooled analysis of the discovery, replication, and overall cohorts. The overall pooled effect size was 1.10 (95 % confidence interval 1.05-1.14, p = 2.10 × 10(-5)), meaning that radiographic yearly progression was 10 % greater for each copy of the minor allele. The PTGER4 gene is a candidate risk factor for radiological progression in RA.

The evolutionary ecology of molecular replicators

PubMed Central

2016-01-01

By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology. PMID:27853598

The evolutionary ecology of molecular replicators.

PubMed

Nee, Sean

2016-08-01

By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology.

Hobby-Eberly Telescope Dark Energy Experiment Fiber Optic Testing System

NASA Astrophysics Data System (ADS)

Fuller, Lindsay

2011-01-01

The Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) is a spectroscopic survey that will collect data from nearly one million Lyman-α emitting galaxies at a redshift of 1.8 < z < 3.8 in order to characterize dark energy. To accomplish this, over 33,000 optical fibers will feed light from these galaxies into 150 Visible Integral-Field Replicable Unit Spectrographs (VIRUS), an order of magnitude greater than has been done before. A fiber optic test bench has been constructed at the University of Texas at Austin in order to test the transmission and focal ratio degradation (FRD) of individual fibers at several wavelengths ranging from 350-600nm. Furthermore, the fiber optic bundles are undergoing extensive lifetime tests at the Center for Electromechanics on the university’s research campus which will simulate 10 years of motion on the Hobby-Eberly Telescope.

Steering and filtering white light with resonant waveguide gratings

NASA Astrophysics Data System (ADS)

Quaranta, Giorgio; Basset, Guillaume; Martin, Olivier J. F.; Gallinet, Benjamin

2017-08-01

A novel thin-film single-layer structure based on resonant waveguide gratings (RWGs) allows to engineer selective color filtering and steering of white light. The unit cell of the structure consists of two adjacent finite-length and cross-talking RWGs, where the former acts as in-coupler and the latter acts as out-coupler. The structure is made by only one nano-imprint lithography replication and one thin film layer deposition, making it fully compatible with up-scalable fabrication processes. We characterize a fabricated optical security element designed to work with the flash and the camera of a smartphone in off-axis light steering configuration, where the pattern is revealed only by placing the smartphone in the proper position. Widespread applications are foreseen in a variety of fields, such as multifocal or monochromatic lenses, solar cells, biosensors, security devices and seethrough optical combiners for near-eye displays.

Self-shaping composites with programmable bioinspired microstructures.

PubMed

Erb, Randall M; Sander, Jonathan S; Grisch, Roman; Studart, André R

2013-01-01

Shape change is a prevalent function apparent in a diverse set of natural structures, including seed dispersal units, climbing plants and carnivorous plants. Many of these natural materials change shape by using cellulose microfibrils at specific orientations to anisotropically restrict the swelling/shrinkage of their organic matrices upon external stimuli. This is in contrast to the material-specific mechanisms found in synthetic shape-memory systems. Here we propose a robust and universal method to replicate this unusual shape-changing mechanism of natural systems in artificial bioinspired composites. The technique is based upon the remote control of the orientation of reinforcing inorganic particles within the composite using a weak external magnetic field. Combining this reinforcement orientational control with swellable/shrinkable polymer matrices enables the creation of composites whose shape change can be programmed into the material's microstructure rather than externally imposed. Such bioinspired approach can generate composites with unusual reversibility, twisting effects and site-specific programmable shape changes.

Self-shaping composites with programmable bioinspired microstructures

NASA Astrophysics Data System (ADS)

Erb, Randall M.; Sander, Jonathan S.; Grisch, Roman; Studart, André R.

2013-04-01

Shape change is a prevalent function apparent in a diverse set of natural structures, including seed dispersal units, climbing plants and carnivorous plants. Many of these natural materials change shape by using cellulose microfibrils at specific orientations to anisotropically restrict the swelling/shrinkage of their organic matrices upon external stimuli. This is in contrast to the material-specific mechanisms found in synthetic shape-memory systems. Here we propose a robust and universal method to replicate this unusual shape-changing mechanism of natural systems in artificial bioinspired composites. The technique is based upon the remote control of the orientation of reinforcing inorganic particles within the composite using a weak external magnetic field. Combining this reinforcement orientational control with swellable/shrinkable polymer matrices enables the creation of composites whose shape change can be programmed into the material’s microstructure rather than externally imposed. Such bioinspired approach can generate composites with unusual reversibility, twisting effects and site-specific programmable shape changes.

DNA replication stress restricts ribosomal DNA copy number

PubMed Central

Salim, Devika; Bradford, William D.; Freeland, Amy; Cady, Gillian; Wang, Jianmin

2017-01-01

Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100–200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how “normal” copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a “normal” rDNA copy number. PMID:28915237

Flow field measurements in the cell culture unit

NASA Technical Reports Server (NTRS)

Walker, Stephen; Wilder, Mike; Dimanlig, Arsenio; Jagger, Justin; Searby, Nancy

2002-01-01

The cell culture unit (CCU) is being designed to support cell growth for long-duration life science experiments on the International Space Station (ISS). The CCU is a perfused loop system that provides a fluid environment for controlled cell growth experiments within cell specimen chambers (CSCs), and is intended to accommodate diverse cell specimen types. Many of the functional requirements depend on the fluid flow field within the CSC (e.g., feeding and gas management). A design goal of the CCU is to match, within experimental limits, all environmental conditions, other than the effects of gravity on the cells, whether the hardware is in microgravity ( micro g), normal Earth gravity, or up to 2g on the ISS centrifuge. In order to achieve this goal, two steps are being taken. The first step is to characterize the environmental conditions of current 1g cell biology experiments being performed in laboratories using ground-based hardware. The second step is to ensure that the design of the CCU allows the fluid flow conditions found in 1g to be replicated from microgravity up to 2g. The techniques that are being used to take these steps include flow visualization, particle image velocimetry (PIV), and computational fluid dynamics (CFD). Flow visualization using the injection of dye has been used to gain a global perspective of the characteristics of the CSC flow field. To characterize laboratory cell culture conditions, PIV is being used to determine the flow field parameters of cell suspension cultures grown in Erlenmeyer flasks on orbital shakers. These measured parameters will be compared to PIV measurements in the CSCs to ensure that the flow field that cells encounter in CSCs is within the bounds determined for typical laboratory experiments. Using CFD, a detailed simulation is being developed to predict the flow field within the CSC for a wide variety of flow conditions, including microgravity environments. Results from all these measurements and analyses of the CSC flow environment are presented and discussed. The final configuration of the CSC employs magnetic stir bars with angled paddles to achieve the necessary flow requirements within the CSC.

A Simplified Integrated Fish Culture Hydroponics System.

ERIC Educational Resources Information Center

Emberger, Gary

1991-01-01

Investigations that facilitate experimental design, the concept of replication, data analysis, and other aspects of scientific study are described. A list of materials, the recommended plants, and the directions for building the hydroponics unit are included. (KR)

Low-cost replicable plastic HUD combiner element

NASA Astrophysics Data System (ADS)

Kress, Bernard; Raulot, Victorien; St. Hilaire, Pierre; Meyrueis, Patrick

2009-05-01

We present a novel technique to fabricate low cost mass replicable plastic HUDs for the transportation industry. HUD are implemented in numerous sectors today (in avionics, automobile, military, machinery,...). Typical implementations include an optical combiner which produces the desired virtual image while leaving the field mostly unaffected by the optics. Such combiners optics are usually implemented as cumbersome catadioptric devices in automobile, dichroic coated curved plates, or expensive volume holograms in commercial and military aviation. We propose a novel way to design, model and fabricate combiner masters which can be replicated in mass by UV casting in plastic. We review the various design techniques required for such elements and the novel mastering technology.

Ease of articulation: A replication.

PubMed

Shuster, Linda I; Cottrill, Claire

2015-01-01

Researchers, as well as the lay public and the popular press, have become increasingly concerned about the lack of reproducibility of research findings. Despite this concern, research has shown that replications of previously published work comprise a very small proportion of published studies. Moreover, there are fewer published direct replications of research studies by independent investigators, and this type of replication is much less likely to confirm the results of the original research than are replications by the original investigator or conceptual replications. A search of the communication disorders research literature reveals that direct replications by independent investigators are virtually non-existent. The purpose of this project was to describe the major issues related to research reproducibility and report the results of a direct replication of a study by Locke (1972) regarding ease of articulation. Two methods for rating ease of articulation were employed. We were able to reproduce the results of the original study for the first method, obtaining a moderate positive correlation between our rankings of phoneme difficulty and Locke's rankings. We obtained a very high positive correlation between our phoneme rankings and rankings obtained in the original study for the second method. Moreover, we found a higher correlation between difficulty rankings and order of speech sound acquisition for American English than was found in the original study. Direct replication is not necessary for all studies in communication disorders, but should be considered for high impact studies, treatment studies, and those that provide data to support models and theories. The reader will be able to: (1) describe the major concerns related to the replicability of research findings; (2) describe the status of research replications in communication disorders; (3) describe how ease of articulation may relate to the order of speech sound acquisition in children; (4) list some types/areas of research that might be candidates for replication in the field of communication disorders. Copyright © 2015 Elsevier Inc. All rights reserved.

Conditionally replicative adenovirus for gastrointestinal cancers.

PubMed

Yamamoto, Masato

2004-08-01

The clinical outcome of advanced gastrointestinal (GI) cancers (especially pancreatic and oesophageal cancers) is dismal, despite the advance of conventional therapeutic strategies. Cancer gene therapy is a category of new therapeutics, among which conditionally replicative adenovirus (CRAd) is one promising strategy to overcome existing obstacles of cancer gene therapy. Various CRAds have been developed for GI cancer treatment by taking advantage of the replication biology of adenovirus. Some CRAds have already been tested in clinical trials, but have fallen short of initial expectations. Concerns for clinical applicability include therapeutic potency, replication selectivity and interval end points in clinical trials. In addition, improvement of experimental animal models is needed for a deeper understanding of CRAd biology. Despite these obstacles, CRAds continue to be an exciting area of investigation with great potential for clinical utility. Further virological and oncological research will eventually lead to full realisation of the therapeutic potential of CRAds in the field of GI cancers.

Genetic Diversity of Infectious Laryngotracheitis Virus during In Vivo Coinfection Parallels Viral Replication and Arises from Recombination Hot Spots within the Genome.

PubMed

Loncoman, Carlos A; Hartley, Carol A; Coppo, Mauricio J C; Vaz, Paola K; Diaz-Méndez, Andrés; Browning, Glenn F; García, Maricarmen; Spatz, Stephen; Devlin, Joanne M

2017-12-01

Recombination is a feature of many alphaherpesviruses that infect people and animals. Infectious laryngotracheitis virus (ILTV; Gallid alphaherpesvirus 1 ) causes respiratory disease in chickens, resulting in significant production losses in poultry industries worldwide. Natural (field) ILTV recombination is widespread, particularly recombination between attenuated ILTV vaccine strains to create virulent viruses. These virulent recombinants have had a major impact on animal health. Recently, the development of a single nucleotide polymorphism (SNP) genotyping assay for ILTV has helped to understand ILTV recombination in laboratory settings. In this study, we applied this SNP genotyping assay to further examine ILTV recombination in the natural host. Following coinoculation of specific-pathogen-free chickens, we examined the resultant progeny for evidence of viral recombination and characterized the diversity of the recombinants over time. The results showed that ILTV replication and recombination are closely related and that the recombinant viral progeny are most diverse 4 days after coinoculation, which is the peak of viral replication. Further, the locations of recombination breakpoints in a selection of the recombinant progeny, and in field isolates of ILTV from different geographical regions, were examined following full-genome sequencing and used to identify recombination hot spots in the ILTV genome. IMPORTANCE Alphaherpesviruses are common causes of disease in people and animals. Recombination enables genome diversification in many different species of alphaherpesviruses, which can lead to the evolution of higher levels of viral virulence. Using the alphaherpesvirus infectious laryngotracheitis virus (ILTV), we performed coinfections in the natural host (chickens) to demonstrate high levels of virus recombination. Higher levels of diversity in the recombinant progeny coincided with the highest levels of virus replication. In the recombinant progeny, and in field isolates, recombination occurred at greater frequency in recombination hot spot regions of the virus genome. Our results suggest that control measures that aim to limit viral replication could offer the potential to limit virus recombination and thus the evolution of virulence. The development and use of vaccines that are focused on limiting virus replication, rather than vaccines that are focused more on limiting clinical disease, may be indicated in order to better control disease. Copyright © 2017 American Society for Microbiology.

Application of GPS and Near-Surface Geophysical Methods to Evaluate Agricultural Test Plot Differences

USDA-ARS?s Scientific Manuscript database

A field research facility with two pairs of replicated agricultural test plots (four total) was established at a location in northwest Ohio during 2005 for the purpose of studying water table management strategies. Initial efforts at this field research facility were devoted to evaluating difference...

Field Performance of Cowpea Genotypes Grown under Virus Pressure in Puerto Rico

USDA-ARS?s Scientific Manuscript database

Cowpea [Vigna unguiculata (L.) Walp.] is an important grain legume in many regions of the tropics. However, viral diseases, particularly Cucumber mosaic virus (CMV) and Blackeye cowpea mosaic virus (BlCMV), can be a limiting factor in cowpea production. We evaluated in replicated field plots and un...

Birth Order and Field Dependence-Independence: A Failure to Replicate

ERIC Educational Resources Information Center

Finley, Gordon E.; Solla, Joseph

1975-01-01

The Children's Embedded Figures Test was individually administered to 116 Caucasian, middle class, second grade children. Results suggest that a child's early experience in a particular birth order position may not be related to the development of field dependence-independence in any unambiguous and simple fashion. (Author/ED)

Measuring and Enhancing Creativity

ERIC Educational Resources Information Center

Mahboub, Kamyar C.; Portillo, Margaret B.; Liu, Yinhui; Chandraratna, Susantha

2004-01-01

The purpose of this study was to assess ways by which creativity may be enhanced in a design-oriented course. In order to demonstrate the validity of the approach, a statistically based study was employed. Additionally, the experiment was replicated in two design-oriented fields at the University of Kentucky. These fields were civil engineering…

Minimizing field time to get reasonable greenhouse gas flux estimates from many chambers

USDA-ARS?s Scientific Manuscript database

Greenhouse gas measurements from soil are typically derived from static chambers placed in several replicate field plots and in multiple locations within a plot. Inherent variability in emissions is due to a number of known and unknown factors. Getting robust emission estimates from numerous chamber...

[Formula: see text]The statistical crisis in science: how is it relevant to clinical neuropsychology?

PubMed

Gelman, Andrew; Geurts, Hilde M

There is currently increased attention to the statistical (and replication) crisis in science. Biomedicine and social psychology have been at the heart of this crisis, but similar problems are evident in a wide range of fields. We discuss three examples of replication challenges from the field of social psychology and some proposed solutions, and then consider the applicability of these ideas to clinical neuropsychology. In addition to procedural developments such as preregistration and open data and criticism, we recommend that data be collected and analyzed with more recognition that each new study is a part of a learning process. The goal of improving neuropsychological assessment, care, and cure is too important to not take good scientific practice seriously.

Characterization of multilayer coated replicated Wolter optics for imaging x-ray emission from pulsed power

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ames, Andrew; Ampleford, David; Bourdon, Chris

Here, we have developed a process for indirectly coating small diameter electroformed nickel replicated optics with multilayers to increase their response at high energy (i.e. >10 keV). The ability to fabricate small diameter multilayer-coated full-shell Wolter X-ray optics with narrow bandpass opens the door to several applications within astronomy and also provides a path for cross-fertilization to other fields. We report on the characterization and evaluation of the first two prototype X-ray Wolter optics to be delivered to the Z Pulsed Power Facility at Sandia National Laboratories. The intent is to develop and field several optics as part of anmore » imaging system with targeted spectral ranges.« less

Characterization of multilayer coated replicated Wolter optics for imaging x-ray emission from pulsed power

DOE PAGES

Ames, Andrew; Ampleford, David; Bourdon, Chris; ...

2017-08-29

Here, we have developed a process for indirectly coating small diameter electroformed nickel replicated optics with multilayers to increase their response at high energy (i.e. >10 keV). The ability to fabricate small diameter multilayer-coated full-shell Wolter X-ray optics with narrow bandpass opens the door to several applications within astronomy and also provides a path for cross-fertilization to other fields. We report on the characterization and evaluation of the first two prototype X-ray Wolter optics to be delivered to the Z Pulsed Power Facility at Sandia National Laboratories. The intent is to develop and field several optics as part of anmore » imaging system with targeted spectral ranges.« less

Characterization of multilayer coated replicated Wolter optics for imaging x-ray emission from pulsed power

NASA Astrophysics Data System (ADS)

Ames, A.; Ampleford, D.; Bourdon, C.; Bruni, R.; Kilaru, K.; Kozioziemski, B.; Pivovaroff, M.; Ramsey, B.; Romaine, S.; Vogel, J.; Walton, C.; Wu, M.

2017-08-01

We have developed a process for indirectly coating arbitrarily small diameter electroformed nickel replicated optics with multilayers to increase their response at high energy (i.e. >10 keV). The ability to fabricate small diameter multilayer coated full shell Wolter X-ray optics with narrow bandpass opens the door to several applications within astronomy and also provides a path for cross-fertilization to other fields. We report on the characterization and evaluation of the first two prototype X-ray Wolter optics to be delivered to the Z Pulsed Power Facility at Sandia National Laboratories. The intent is to develop and field several optics as part of an imaging system with targeted spectral ranges.

Methamphetamine inhibits HIV-1 replication in CD4+ T cells by modulating anti-HIV-1 miRNA expression.

PubMed

Mantri, Chinmay K; Mantri, Jyoti V; Pandhare, Jui; Dash, Chandravanu

2014-01-01

Methamphetamine is the second most frequently used illicit drug in the United States. Methamphetamine abuse is associated with increased risk of HIV-1 acquisition, higher viral loads, and enhanced HIV-1 pathogenesis. Although a direct link between methamphetamine abuse and HIV-1 pathogenesis remains to be established in patients, methamphetamine has been shown to increase HIV-1 replication in macrophages, dendritic cells, and cells of HIV transgenic mice. Intriguingly, the effects of methamphetamine on HIV-1 replication in human CD4(+) T cells that serve as the primary targets of infection in vivo are not clearly understood. Therefore, we examined HIV-1 replication in primary CD4(+) T cells in the presence of methamphetamine in a dose-dependent manner. Our results demonstrate that methamphetamine had a minimal effect on HIV-1 replication at concentrations of 1 to 50 μmol/L. However, at concentrations >100 μmol/L, it inhibited HIV-1 replication in a dose-dependent manner. We also discovered that methamphetamine up-regulated the cellular anti-HIV-1 microRNAs (miR-125b, miR-150, and miR-28-5p) in CD4(+) T cells. Knockdown experiments illustrated that up-regulation of the anti-HIV miRNAs inhibited HIV-1 replication. These results are contrary to the paradigm that methamphetamine accentuates HIV-1 pathogenesis by increasing HIV-1 replication. Therefore, our findings underline the complex interaction between drug use and HIV-1 and necessitate comprehensive understanding of the effects of methamphetamine on HIV-1 pathogenesis. Copyright © 2014 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Use of retrospective data to assess ecotoxicological monitoring needs for terrestrial vertebrates residing in Atlantic coast estuaries

USGS Publications Warehouse

Cohen, J.B.; Rattner, B.A.; Golden, N.H.

2003-01-01

The 'Contaminant Exposure and Effects--Terrestrial Vertebrates' (CEE-TV) database contains 4,336 records of ecotoxicological information for free-ranging amphibians, reptiles, birds, and mammals residing in Atlantic and Florida Gulf coast estuaries and their drainages. To identify spatial data gaps, those CEE-TV records for which the specific study location were known (n=2,740) were combined with watershed and wildlife management unit boundaries using Geographic Information Systems software. The U.S. Environmental Protection Agency's Index of Watershed Indicators (IWI), which classifies watersheds based on water quality and their vulnerability to pollution, was used to prioritize these data gaps. Of 136 watersheds in the study area, 15 that are classified by the IWI as having water quality problems or high vulnerability to pollution lacked terrestrial vertebrate ecotoxicological monitoring or research in the past decade. Older studies within some of these watersheds documented high levels of contaminants in wildlife tissues. Of 90 National Wildlife Refuge units, 42 without current data fall within watersheds of concern. Of 40 National Park units larger than 1 km2, 17 without current data fall within watersheds of concern. Issues encountered in this analysis highlighted the need for spatially and temporally replicated field monitoring programs that utilize random sampling. Without data from such studies, it will be difficult to perform unbiased assessments of regional trends in contaminant exposure and effects in terrestrial vertebrates.

Use of retrospective data to assess ecotoxicological monitoring needs for terrestrial vertebrates residing in Atlantic coast estuaries.

PubMed

Cohen, Jonathan B; Rattner, Barnett A; Golden, Nancy H

2003-01-01

The "Contaminant Exposure and Effects-Terrestrial Vertebrates" (CEE-TV) database contains 4,336 records of ecotoxicological information for free-ranging amphibians, reptiles, birds, and mammals residing in Atlantic and Florida Gulf coast estuaries and their drainages. To identify spatial data gaps, those CEE-TV records for which the specific study location were known (n = 2,740) were combined with watershed and wildlife management unit boundaries using Geographic Information Systems software. The US Environmental Protection Agency's Index of Watershed Indicators (IWI), which classifies watersheds based on water quality and their vulnerability to pollution, was used to prioritize these data gaps. Of 136 watersheds in the study area, 15 that are classified by the IWI as having water quality problems or high vulnerability to pollution lacked terrestrial vertebrate ecotoxicological monitoring or research in the past decade. Older studies within some of these watersheds documented high levels of contaminants in wildlife tissues. Of 90 National Wildlife Refuge units, 42 without current data fall within watersheds of concern. Of 40 National Park units larger than 1 km2, 17 without current data fall within watersheds of concern. Issues encountered in this analysis highlighted the need for spatially and temporally replicated field monitoring programs that utilize random sampling. Without data from such studies, it will be difficult to perform unbiased assessments of regional trends in contaminant exposure and effects in terrestrial vertebrates.

Case study: design may influence use of seclusion and restraint.

PubMed

McCurdy, John M; Haliburton, James R; Yadav, Hardik C; Yoder, Allison M; Norton, Lindsey R; Froehlich, Josef A; Kaur, Harpreet; Kramer, Nicholas F; Silman, Ayesha; Quinn, Brian J; Pudlo, Sharon; Terrell, Christina Butler; El-Mallakh, Rif S

2015-01-01

The psychiatric emergency room is a dynamic and sometimes volatile environment. Its design may be an important variable in patient care, but most design decisions are based on models of thought and treatment with a minimal evidence base. The concept of open design, increasing access of patients to nursing staff, for inpatient psychiatric units has recently gained widespread acceptance, despite a dearth of empirical data. We examined rates of seclusion and restraint before and after a design change that reduced the openness of the unit in a dedicated emergency psychiatric service in a general university hospital. Quality assurance data regarding the census, occurrence of assaults, and the use of seclusion and restraint were queried. Two independent analyses utilizing a test of proportional data were performed to replicate the findings. After placement of a door to restrict patients' access to the waiting area of the unit, the rate of the use of seclusion and restraint went from 0.03 (44/777) to 0.0185 (27/1,514; z = 2.02, p < .04). Replication over a separate time period saw reduction from 0.029 (67/2,277) to 0.018 (44/2,431), z = 2.44, p < .02). A design change that reduced the openness of the unit resulted in the reduction of seclusion and restraint. © The Author(s) 2015.

Replicating receptive fields of simple and complex cells in primary visual cortex in a neuronal network model with temporal and population sparseness and reliability.

PubMed

Tanaka, Takuma; Aoyagi, Toshio; Kaneko, Takeshi

2012-10-01

We propose a new principle for replicating receptive field properties of neurons in the primary visual cortex. We derive a learning rule for a feedforward network, which maintains a low firing rate for the output neurons (resulting in temporal sparseness) and allows only a small subset of the neurons in the network to fire at any given time (resulting in population sparseness). Our learning rule also sets the firing rates of the output neurons at each time step to near-maximum or near-minimum levels, resulting in neuronal reliability. The learning rule is simple enough to be written in spatially and temporally local forms. After the learning stage is performed using input image patches of natural scenes, output neurons in the model network are found to exhibit simple-cell-like receptive field properties. When the output of these simple-cell-like neurons are input to another model layer using the same learning rule, the second-layer output neurons after learning become less sensitive to the phase of gratings than the simple-cell-like input neurons. In particular, some of the second-layer output neurons become completely phase invariant, owing to the convergence of the connections from first-layer neurons with similar orientation selectivity to second-layer neurons in the model network. We examine the parameter dependencies of the receptive field properties of the model neurons after learning and discuss their biological implications. We also show that the localized learning rule is consistent with experimental results concerning neuronal plasticity and can replicate the receptive fields of simple and complex cells.

Gefitinib and pyrrolidine dithiocarbamate decrease viral replication and cytokine production in dengue virus infected human monocyte cultures.

PubMed

Duran, Anyelo; Valero, Nereida; Mosquera, Jesús; Fuenmayor, Edgard; Alvarez-Mon, Melchor

2017-12-15

The epidermal growth factor receptor (EGFR) and nucleotide-binding and oligomerization-domain containing 2 (NOD2) are important in cancer and in microbial recognition, respectively. These molecules trigger intracellular signaling pathways inducing the expression of inflammatory genes by NF-kB translocation. Gefitinib (GBTC) and pyrrolidine dithiocarbamate (PDTC) are capable of inhibiting EGFR/NOD2 and NF-kB, respectively. In earlier stages of dengue virus (DENV) infection, monocytes are capable of sustaining viral replication and increasing cytokine production, suggesting that monocyte/macrophages play an important role in early DENV replication. GBTC and PDTC have not been used to modify the pathogenesis of DENV in infected cells. This study was aimed to determine the effect of GBTC and PDTC on viral replication and cytokine production in DENV serotype 2 (DENV2)-infected human monocyte cultures. GBTC and PDTC were used to inhibit EGFR/NOD2 and NF-kB, respectively. Cytokine production was measured by ELISA and viral replication by plaque forming unit assay. Increased DENV2 replication and anti-viral cytokine production (IFN-α/β, TNF-α, IL-12 and IL-18) in infected cultures were found. These parameters were decreased after EGFR/NOD2 or NF-kB inhibitions. The inhibitory effects of GBTC and PDTC on viral replication and cytokine production can be beneficial in the treatment of patients infected by dengue and suggest a possible role of EGFR/NOD2 receptors and NF-kB in dengue pathogenesis. Copyright © 2017 Elsevier Inc. All rights reserved.

The prebiotic synthesis of oligonucleotides

NASA Technical Reports Server (NTRS)

Oro, J.; Stephen-Sherwood, E.

1974-01-01

This paper is primarily a review of recent developments in the abiotic synthesis of nucleotides, short chain oligonucleotides, and their mode of replication in solution. It also presents preliminary results from this laboratory on the prebiotic synthesis of thymidine oligodeoxynucleotides. A discussion, based on the physicochemical properties of RNA and DNA oligomers, relevant to the molecular evolution of these compounds leads to the tentative hypothesis that oligodeoxyribonucleotides of about 12 units may have been of sufficient length to initiate a self replicating coding system. Two models are suggested to account for the synthesis of high molecular weight oligomers using short chain templates and primers.

Groundwater-Quality Data in the South Coast Range-Coastal Study Unit, 2008: Results from the California GAMA Program

USGS Publications Warehouse

Mathany, Timothy M.; Burton, Carmen A.; Land, Michael; Belitz, Kenneth

2010-01-01

Groundwater quality in the approximately 766-square-mile South Coast Range-Coastal (SCRC) study unit was investigated from May to December 2008, as part of the Priority Basins Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basins Project was developed in response to legislative mandates (Supplemental Report of the 1999 Budget Act 1999-00 Fiscal Year; and, the Groundwater Quality Monitoring Act of 2001 [Sections 10780-10782.3 of the California Water Code, Assembly Bill 599]) to assess and monitor the quality of groundwater in California, and is being conducted by the U.S. Geological Survey (USGS) in cooperation with the California State Water Resources Control Board (SWRCB). The SCRC study unit was the 25th study unit to be sampled as part of the GAMA Priority Basins Project. The SCRC study unit was designed to provide a spatially unbiased assessment of untreated groundwater quality in the primary aquifer systems and to facilitate statistically consistent comparisons of untreated groundwater quality throughout California. The primary aquifer systems (hereinafter referred to as primary aquifers) were defined as that part of the aquifer corresponding to the perforation interval of wells listed in the California Department of Public Health (CDPH) database for the SCRC study unit. The quality of groundwater in shallow or deep water-bearing zones may differ from the quality of groundwater in the primary aquifers; shallow groundwater may be more vulnerable to surficial contamination. In the SCRC study unit, groundwater samples were collected from 70 wells in two study areas (Basins and Uplands) in Santa Barbara and San Luis Obispo Counties. Fifty-five of the wells were selected using a spatially distributed, randomized grid-based method to provide statistical representation of the study unit (grid wells), and 15 wells were selected to aid in evaluation of specific water-quality issues (understanding wells). In addition to the 70 wells sampled, 3 surface-water samples were collected in streams near 2 of the sampled wells in order to better comprehend the interaction between groundwater and surface water in the area. The groundwater samples were analyzed for organic constituents (volatile organic compounds [VOC], pesticides and pesticide degradates, polar pesticides and metabolites, and pharmaceutical compounds), constituents of special interest (perchlorate, N-nitrosodimethylamine [NDMA], and 1,2,3-TCP), naturally occurring inorganic constituents (trace elements, nutrients, dissolved organic carbon [DOC], major and minor ions, silica, total dissolved solids [TDS], and alkalinity), and radioactive constituents (gross alpha and gross beta radioactivity). Naturally occurring isotopes (stable isotopes of hydrogen and oxygen in water, stable isotopes of nitrogen and oxygen in dissolved nitrate, stable isotopes of sulfur in dissolved sulfate, stable isotopes of carbon in dissolved inorganic carbon, activities of tritium, and carbon-14 abundance), and dissolved gases (including noble gases) also were measured to help identify the sources and ages of the sampled groundwater. In total, 298 constituents and field water-quality indicators were investigated. Three types of quality-control samples (blanks, replicates, and matrix-spikes) were collected at approximately 3 to 12 percent of the wells in the SCRC study unit, and the results for these samples were used to evaluate the quality of the data for the groundwater samples. Field blanks rarely contained detectable concentrations of any constituent, suggesting that contamination from sample collection procedures was not a significant source of bias in the data for the groundwater samples. Differences between replicate samples generally were less than 10 percent relative and/or standard deviation, indicating acceptable analytical reproducibility. Matrix-spike recoveries were within the acceptable range (70 to 130 percent) for approximately 84

Correlation between Marek's disease virus pathotype and replication.

PubMed

Dunn, John R; Auten, Kiva; Heidari, Mohammad; Buscaglia, Celina

2014-06-01

Marek's disease (MD) virus (MDV) is an alphaherpesvirus that causes MD, a lymphoproliferative disease in chickens. Pathotyping has become an increasingly important assay for monitoring shifts in virulence of field strains; however, it is time-consuming and expensive, and alternatives are needed to provide fast answers in the face of current outbreaks. The purpose of this study was to determine whether differences in virus replication between pathotypes that have been reported using a small number of virulent (v) and very virulent plus (vv+) MDV strains could be confirmed with a large collection of MD viruses. Based on pilot study data, bursa, brain, and lung samples were collected at 9 and 11 days postinoculation (dpi) from birds challenged with 1 of 15 MDV strains. The correlation between virus replication and virulence was confirmed between vMDV strains and higher virulent strains, but in most cases, there was no significant difference between very virulent (vv) and vv+MDV groups. At both 9 and 11 dpi, chickens infected with vv and vv+MDV had significantly lower body weights and relative thymus and bursa weights compared with chickens challenged with vMDV. However, similar to virus quantity, there was no significant difference between weights in birds challenged with vv or vv+MDV. The significant differences observed in maternal antibody negative (ab-) chickens were not significant in maternal antibody positive (ab+) chickens, demonstrating the requirement of ab- birds for this type of comparison. These data do not support the use of virus replication or organ weights as an alternative to pathotyping for discrimination between all three virulent MDV pathotypes but may be useful for determining a virus replication threshold to choose which field strains meet a minimum virulence to be pathotyped by traditional methods.

Assessment of volatile organic compounds in surface water at West Branch Canal Creek, Aberdeen Proving Ground, Maryland, 1999

USGS Publications Warehouse

Olsen, Lisa D.; Spencer, Tracey A.

2000-01-01

The U.S. Geological Survey (USGS) collected 13 surface-water samples and 3 replicates from 5 sites in the West Branch Canal Creek area at Aberdeen Proving Ground from February through August 1999, as a part of an investigation of ground-water contamination and natural attenuation processes. The samples were analyzed for volatile organic compounds, including trichloroethylene, 1,1,2,2-tetrachloroethane, carbon tetrachloride, and chloroform, which are the four major contaminants that were detected in ground water in the Canal Creek area in earlier USGS studies. Field blanks were collected during the sampling period to assess sample bias. Field replicates were used to assess sample variability, which was expressed as relative percent difference. The mean variability of the surface-water replicate analyses was larger (35.4 percent) than the mean variability of ground-water replicate analyses (14.6 percent) determined for West Branch Canal Creek from 1995 through 1996. The higher variability in surface-water analyses is probably due to heterogeneities in the composition of the surface water rather than differences in sampling or analytical procedures. The most frequently detected volatile organic compound was 1,1,2,2- tetrachloroethane, which was detected in every sample and in two of the replicates. The surface-water contamination is likely the result of cross-media transfer of contaminants from the ground water and sediments along the West Branch Canal Creek. The full extent of surface-water contamination in West Branch Canal Creek and the locations of probable contaminant sources cannot be determined from this limited set of data. Tidal mixing, creek flow patterns, and potential effects of a drought that occurred during the sampling period also complicate the evaluation of surface-water contamination.

In vitro models of viral-induced congenital deafness.

PubMed

Davis, G L

1981-10-01

Cytomegalovirus (CMV) infects 1 to 2 percent of liveborn infants in the United States and causes varying degrees of perceptive hearing loss. There are eight reported pathologic studies of temporal bones in CMV-infected neonates. Viral replication occurs in nonsensory endolabyrinthine epithelium, but viral antigen is also found in the organ of Corti and spiral ganglion neurons, and CMV has been cultured from perilymph. Further clinicopathologic correlation is frustrated, since the inner ear cannot be biopsied during life, and the number of temporal bones available for study is limited, owing to the decrease in the number of autopsies being performed. Inoculation of CMV into newborn mice, and extracorporeal preparations of mouse and guinea pig fetal inner ears, either in organ culture or as grafts on chick chorioallantoic membranes, yields viral perilabyrinthitis. The different ultrastructural appearances of CMV replicating in epithelial and mesenchymal cells show that animal CMV replicates in mesenchymal cells and human CMV replicates in epithelial cells of the inner ear. These different ultrastructural patterns indicate that the chromophobe (transitional) cells of the stria vascularis of the guinea pig are of mesenchymal origin.

Effect of temperature on replicative aging of the budding yeast Saccharomyces cerevisiae.

PubMed

Molon, Mateusz; Zadrag-Tecza, Renata

2016-04-01

The use of the budding yeast Saccharomyces cerevisiae in gerontological studies was based on the assumption that the reproduction limit of a single cell (replicative aging) is a consequence of accumulation of a hypothetical universal "senescence factor" within the mother cell. However, some evidence suggests that molecules or structures proposed as the "aging factor", such as rDNA circles, oxidatively damaged proteins (with carbonyl groups) or mitochondria, have little effect on replicative lifespan of yeast cells. Our results also suggest that protein aggregates associated with Hsp104, treated as a marker of yeast aging, do not seem to affect the numeric value of replicative lifespan of yeast. What these results indicate, however, is the need for finding a different way of expressing age and longevity of yeast cells instead of the commonly used number of daughters produced over units of time, as in the case of other organisms. In this paper, we show that the temperature has a stronger influence on the time of life (the total lifespan) than on the reproductive potential of yeast cells.

Regulation of Flavivirus RNA synthesis and replication

PubMed Central

Selisko, Barbara; Wang, Chunling; Harris, Eva; Canard, Bruno

2014-01-01

RNA synthesis and replication of the members of the Flavivirus genus (including dengue, West Nile and Japanese encephalitis viruses) is regulated by a wide variety of mechanisms and actors. These include the sequestration of the RNA-dependent RNA polymerase (RdRp) for functions other than RNA synthesis, regulatory interactions with other viral and host proteins within the replication complex (RC), and regulatory elements within the RNA genome itself. In this review, we discuss our current knowledge of the multiple levels at which Flavivirus RNA synthesis is controlled. We aim to bring together two active research fields: the structural and functional biology of individual proteins of the RC and the impressive wealth of knowledge acquired regarding the viral genomic RNA. PMID:25462437

[Mediate evaluation of replicating a Training Program in Nonverbal Communication in Gerontology].

PubMed

Schimidt, Teresa Cristina Gioia; Duarte, Yeda Aparecida de Oliveira; Silva, Maria Julia Paes da

2015-04-01

Replicating the training program in non-verbal communication based on the theoretical framework of interpersonal communication; non-verbal coding, valuing the aging aspects in the perspective of active aging, checking its current relevance through the content assimilation index after 90 days (mediate) of its application. A descriptive and exploratory field study was conducted in three hospitals under direct administration of the state of São Paulo that caters exclusively to Unified Health System (SUS) patients. The training lasted 12 hours divided in three meetings, applied to 102 health professionals. Revealed very satisfactory and satisfactory mediate content assimilation index in 82.9%. The program replication proved to be relevant and updated the setting of hospital services, while remaining efficient for healthcare professionals.

Faithful replication of grating patterns in polymer through electrohydrodynamic instabilities

NASA Astrophysics Data System (ADS)

Li, H.; Yu, W.; Wang, T.; Zhang, H.; Cao, Y.; Abraham, E.; Desmulliez, M. P. Y.

2014-07-01

Electrohydrodynamic instability patterning (EHDIP) as an alternative patterning method has attracted a great deal of attention over the past decade. This article demonstrates the faithful transfer of patterns with a high aspect ratio onto a polymer film via electrohydrodynamic instabilities for a given patterned grating mask. We perform a simple mathematical analysis to determine the influence of process parameters on the pressure difference ▵P. Through numerical simulation, it is demonstrated that thick films subject to large electric fields are essential to realize this faithful replication. In particular, the influence of the material properties of the polymer on pattern replication is discussed in detail. It is found that, to achieve the smaller periodic patterns with a higher resolution, film with a larger value of the dielectric constant and smaller value of the surface tension should be chosen. In addition, an ideal replication of the mask pattern with a short evolution time is possible by reducing the viscosity of the polymer liquid. Finally, the experiments of the pattern replication with and without defects are demonstrated to compare with the numerical simulation results. It is found that experiments are in good agreement with the simulation results and prove that the numerical simulation method provides an effective way to predict faithful replication.

Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae.

PubMed

Soriano, Ignacio; Morafraile, Esther C; Vázquez, Enrique; Antequera, Francisco; Segurado, Mónica

2014-09-13

Eukaryotic genomes are replicated during S phase according to a temporal program. Several determinants control the timing of origin firing, including the chromatin environment and epigenetic modifications. However, how chromatin structure influences the timing of the activation of specific origins is still poorly understood. By performing high-resolution analysis of genome-wide nucleosome positioning we have identified different chromatin architectures at early and late replication origins. These different patterns are already established in G1 and are tightly correlated with the organization of adjacent transcription units. Moreover, specific early and late nucleosomal patterns are fixed robustly, even in rpd3 mutants in which histone acetylation and origin timing have been significantly altered. Nevertheless, higher histone acetylation levels correlate with the local modulation of chromatin structure, leading to increased origin accessibility. In addition, we conducted parallel analyses of replication and nucleosome dynamics that revealed that chromatin structure at origins is modulated during origin activation. Our results show that early and late replication origins present distinctive nucleosomal configurations, which are preferentially associated to different genomic regions. Our data also reveal that origin structure is dynamic and can be locally modulated by histone deacetylation, as well as by origin activation. These data offer novel insight into the contribution of chromatin structure to origin selection and firing in budding yeast.

Theory building, replication, and behavioral priming: where do we need to go from here?

PubMed

Locke, Edwin A

2015-05-01

This article suggests that the field of behavioral priming, which is basically a technique, is in need of theory building. Guidelines from successful theory building by induction in the realm of conscious motivation (namely, goal setting and self-efficacy) are suggested. The process would include replication with variation, identifying the logical relation between a given prime and the action in question, discovering moderators and mediators, and clarifying the relationship between the conscious mind and the subconscious. © The Author(s) 2015.

Application of GPS and Near-Surface Geophysical Methods to Evaluate Differences Between Agricultural Test Plots

USDA-ARS?s Scientific Manuscript database

A field research facility with two pairs of replicated agricultural test plots (four total) was established at a location in northwest Ohio during 2005 for the purpose of studying water table management strategies. Initial efforts at this field research facility were devoted to evaluating difference...

Alternative fumigants and grafting for tomato and double-cropped muskmelon production in Florida

USDA-ARS?s Scientific Manuscript database

A field trial was conducted at the USDA, ARS Farm in Fort Pierce, FL in a field infested with root-knot nematodes (RKN) (Meloidogyne incognita), soil-borne pathogens, and weeds. A split plot experiment with four replications was used to evaluate rootstock/scion combinations in fumigated and herbicid...

Modeled alongshore circulation and morphologic evolution onshore of a large submarine canyon

NASA Astrophysics Data System (ADS)

Hansen, J. E.; Raubenheimer, B.; List, J. H.; Elgar, S.; Guza, R. T.; Lippmann, T. C.

2012-12-01

Alongshore circulation and morphologic evolution observed at an ocean beach during the Nearshore Canyon Experiment, onshore of a large submarine canyon in San Diego, CA (USA), are investigated using a two-dimensional depth-averaged numerical model (Delft3D). The model is forced with waves observed in ~500 m water depth and tidal constituents derived from satellite altimetry. Consistent with field observations, the model indicates that refraction of waves over the canyon results in wave focusing ~500 m upcoast of the canyon and shadowing onshore of the canyon. The spatial variability in the modeled wave field results in a corresponding non-uniform alongshore circulation field. In particular, when waves approach from the northwest the alongshore flow converges near the wave focal zone, while waves that approach from the southwest result in alongshore flow that diverges away from the wave focal zone. The direction and magnitude of alongshore flows are determined by a balance between the (often opposing) radiation stress and alongshore pressure gradients, consistent with observations and previous results. The largest observed morphologic evolution, vertical accretion of about 1.5 m in about 3 m water depth near the wave focal zone, occurred over a one-week period when waves from the northwest reached heights of 1.8 m. The model, with limited tuning, replicates the magnitude and spatial extent of the observed accretion and indicates that net accretion of the cross-shore profile was owing to alongshore transport from converging alongshore flows. The good agreement between the observed and modeled morphology change allows for an in-depth examination of the alongshore force balance that resulted in the sediment convergence. These results indicate that, at least in this case, a depth-averaged hydrodynamic model can replicate observed surfzone morphologic change resulting from forcing that is strongly non-uniform in the alongshore. Funding was provided by the Office of Naval Research, The National Science Foundation, a Woods Hole Oceanographic Institution and United States Geological Survey joint postdoctoral fellowship, and a National Security Science and Engineering Faculty Fellowship.

Falsifiability is not optional.

PubMed

LeBel, Etienne P; Berger, Derek; Campbell, Lorne; Loving, Timothy J

2017-08-01

Finkel, Eastwick, and Reis (2016; FER2016) argued the post-2011 methodological reform movement has focused narrowly on replicability, neglecting other essential goals of research. We agree multiple scientific goals are essential, but argue, however, a more fine-grained language, conceptualization, and approach to replication is needed to accomplish these goals. Replication is the general empirical mechanism for testing and falsifying theory. Sufficiently methodologically similar replications, also known as direct replications, test the basic existence of phenomena and ensure cumulative progress is possible a priori. In contrast, increasingly methodologically dissimilar replications, also known as conceptual replications, test the relevance of auxiliary hypotheses (e.g., manipulation and measurement issues, contextual factors) required to productively investigate validity and generalizability. Without prioritizing replicability, a field is not empirically falsifiable. We also disagree with FER2016's position that "bigger samples are generally better, but . . . that very large samples could have the downside of commandeering resources that would have been better invested in other studies" (abstract). We identify problematic assumptions involved in FER2016's modifications of our original research-economic model, and present an improved model that quantifies when (and whether) it is reasonable to worry that increasing statistical power will engender potential trade-offs. Sufficiently powering studies (i.e., >80%) maximizes both research efficiency and confidence in the literature (research quality). Given that we are in agreement with FER2016 on all key open science points, we are eager to start seeing the accelerated rate of cumulative knowledge development of social psychological phenomena such a sufficiently transparent, powered, and falsifiable approach will generate. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

PubMed

Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

2012-11-06

All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

A Rolling Circle Replication Mechanism Produces Multimeric Lariats of Mitochondrial DNA in Caenorhabditis elegans

PubMed Central

Lewis, Samantha C.; Joers, Priit; Willcox, Smaranda; Griffith, Jack D.; Jacobs, Howard T.; Hyman, Bradley C.

2015-01-01

Mitochondrial DNA (mtDNA) encodes respiratory complex subunits essential to almost all eukaryotes; hence respiratory competence requires faithful duplication of this molecule. However, the mechanism(s) of its synthesis remain hotly debated. Here we have developed Caenorhabditis elegans as a convenient animal model for the study of metazoan mtDNA synthesis. We demonstrate that C. elegans mtDNA replicates exclusively by a phage-like mechanism, in which multimeric molecules are synthesized from a circular template. In contrast to previous mammalian studies, we found that mtDNA synthesis in the C. elegans gonad produces branched-circular lariat structures with multimeric DNA tails; we were able to detect multimers up to four mtDNA genome unit lengths. Further, we did not detect elongation from a displacement-loop or analogue of 7S DNA, suggesting a clear difference from human mtDNA in regard to the site(s) of replication initiation. We also identified cruciform mtDNA species that are sensitive to cleavage by the resolvase RusA; we suggest these four-way junctions may have a role in concatemer-to-monomer resolution. Overall these results indicate that mtDNA synthesis in C. elegans does not conform to any previously documented metazoan mtDNA replication mechanism, but instead are strongly suggestive of rolling circle replication, as employed by bacteriophages. As several components of the metazoan mitochondrial DNA replisome are likely phage-derived, these findings raise the possibility that the rolling circle mtDNA replication mechanism may be ancestral among metazoans. PMID:25693201

Longleaf pine wood and straw yields from two old-field planted sites in Georgia

Treesearch

E. David Dickens; David J. Moorhead; Bryan C. McElvany; Ray Hicks

2012-01-01

Little is known or published concerning longleaf pine’s growth rate, or wood and pine straw yields on old-field sites. Two study areas were installed in unthinned longleaf plantations established on former old-fields in Screven and Tift Counties, Georgia to address pine growth and straw yields. Soil series were delineated and replicated plots with three levels of...

Predicting presidential performance in the United States: equation replication on recent survey results.

PubMed

Simonton, D K

2001-06-01

For more than 2 decades, researchers have tried to identify the variables that predict the overall performance of U.S. presidents. In 1986, there emerged a 6-variable prediction equation (D. K. Simonton, 1986c, 1987b) that has been replicated repeatedly. The predictors are years in office, war years, scandal, assassination, heroism in war, and intellectual brilliance. The author again replicated the equation on recent rankings of all presidents from George Washington through William Jefferson Clinton according to a survey of 719 experts (W. R. Ridings, Jr., & S. B. McIver, 1997). The original 6-variable equation successfully predicted both the overall rankings as well as the 5 core components of the rankings (leadership qualities, accomplishment, political skill, appointments, character and integrity). The predictive value of the equation was illustrated for the presidencies of Ronald W. Reagan, George H. W. Bush, and Clinton.

Analysis of HSV viral reactivation in explants of sensory neurons

PubMed Central

Turner, Anne-Marie W.; Kristie, Thomas M.

2014-01-01

As with all Herpesviruses, Herpes simplex virus (HSV) has both a lytic replication phase and a latency-reactivation cycle. During lytic replication, there is an ordered cascade of viral gene expression that leads to the synthesis of infectious viral progeny. In contrast, latency is characterized by the lack of significant lytic gene expression and the absence of infectious virus. Reactivation from latency is characterized by the re-entry of the virus into the lytic replication cycle and the production of recurrent disease. This unit describes the establishment of the mouse sensory neuron model of HSV-1 latency-reactivation as a useful in vivo system for the analysis of mechanisms involved in latency and reactivation. Assays including the determination of viral yields, immunohistochemical/immunofluorescent detection of viral antigens, and mRNA quantitation are used in experiments designed to investigate the network of cellular and viral proteins regulating HSV-1 lytic infection, latency, and reactivation. PMID:25367271

Communicative genes in the evolution of empathy and altruism.

PubMed

Buck, Ross

2011-11-01

This paper discusses spontaneous communication and its implications for understanding empathy and altruism. The question of the possibility of "true" altruism-giving up one's genetic potential in favor of the genetic potential of another-is a fundamental issue common to the biological, behavioral, and social sciences. Darwin regarded "social instincts and sympathies" to be critical to the social order, but the possibility of biologically-based prosocial motives and emotions was questioned when selection was interpreted as operating at the level of the gene. In the selfish gene hypothesis, Dawkins argued that the unit of evolutionary selection must be an active, germ-line replicator: a unit whose activities determine whether copies of it are made across evolutionary timescales. He argued that the only active replicator existing across evolutionary timescales is the gene, so that the "selfish gene" is a replicator motivated only to make copies of itself. The communicative gene hypothesis notes that genes function by communicating, and the phenotype communication involves not only the individual sending and receiving abilities of the individual genes involved, but also the relationship between them relative to other genes. Therefore the selection of communication as phenotype involves the selection of individual genes and also their relationship. Relationships become replicators, and are selected across evolutionary timescales including social relationships (e.g., sex, nurturance, dominance-submission). An interesting implication of this view: apparent altruism has been interpreted by selfish gene theorists as due to kin selection and reciprocity, in which the survival of kin and comrade indirectly favor the genetic potential of the altruist. From the viewpoint of the communicative gene hypothesis, rather than underlying altruism, kin selection and reciprocity are ways of restricting altruism to kin and comrade: they are mechanisms not of altruism but of xenophobia.

Study of the efficiency of some water treatment unit that present in houses in Erbil city-Iraq

NASA Astrophysics Data System (ADS)

Toma, Janan. Jabbar.; Hanna, Aveen. Matti.

2017-09-01

Many people in Erbil city started more than two decade to put special treatment units in their houses to purified water to become safer for drinking uses. The aim of this study was determine the efficiency of six kind water treatment units which include (two replicate of Crystal Water Purifier, So-Safe Water Filter, R O Water Purifier, Kontec Water Purified and Al-Kawther Purified Water). Water samples were collected in two sites one before and other after treatment unit. Each sample was collect with three replication during May to October-2016. Analyzed for Major cations concentration (calcium, magnesium, sodium and potassium), anions concentration (nitrate and chloride) and hydrogen ion concentration (pH), electrical conductivity (EC), total dissolved solids (TDS), alkalinity and total hardness by using standard methods. The water quality index values for all raw water sample befor and after treatment was good and excellent respectively for drinking purposes. Efficiency of So-Safe Water Filter was 66.32% it means was more efficiency than others special water treatment units while in RO Water Purifier was 27.14%, means less efficiency than other water purifier water under this study. Values for major cations, anions and others chemicals characteristics in the water samples after treatment became lower concentrations than befor treatment, likely an indication that these were removed by treatment. According to guideline of world health organization all of variables except total hardness befor treatment are safe and suitable for drinking purposes.

Two-Year Campus Newspapers Remain Healthy Businesses.

ERIC Educational Resources Information Center

Kopenhaver, Lillian Lodge

1994-01-01

Describes a 1994 survey examining the role, costs, revenue, and policies related to advertising in community college newspapers, which replicated a similar 1990 survey. Discusses school demographics, newspaper characteristics, page formats, advertising rates, inserts and standard advertising units, management, revenue, and advertising acceptance…

Temperature regulation of bud-burst phenology within and among years in a young Douglas-fir (Pseudotsuga menziesii) plantation in western Washington, USA.

PubMed

Bailey, John D; Harrington, Constance A

2006-04-01

Past research has established that terminal buds of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) seedlings from many seed sources have a chilling requirement of about 1200 h at 0-5 degrees C; once chilled, temperatures > 5 degrees C force bud burst via accumulation of heat units. We tested this sequential bud-burst model in the field to determine whether terminal buds of trees in cooler microsites, which receive less heat forcing, develop more slowly than those in warmer microsites. For three years we monitored terminal bud development in young saplings as well as soil and air temperatures on large, replicated plots in a harvest unit; plots differed in microclimate based on amount of harvest residue and shade from neighboring stands. In two of three years, trees on cooler microsites broke bud 2 to 4 days earlier than those on warmer microsites, despite receiving less heat forcing from March to May each year. A simple sequential model did not predict cooler sites having earlier bud burst nor did it correctly predict the order of bud burst across the three years. We modified the basic heat-forcing model to initialize, or reset to zero, the accumulation of heat units whenever significant freezing temperature events (> or = 3 degree-hours day(-1) < 0 degrees C) occurred; this modified model correctly predicted the sequence of bud burst across years. Soil temperature alone or in combination with air temperature did not improve our predictions of bud burst. Past models of bud burst have relied heavily on data from controlled experiments with simple temperature patterns; analysis of more variable temperature patterns from our 3-year field trial, however, indicated that simple models of bud burst are inaccurate. More complex models that incorporate chilling hours, heat forcing, photoperiod and the occurrence of freeze events in the spring may be needed to predict effects of future silvicultural treatments as well to interpret the implications of climate-change scenarios. Developing and testing new models will require data from both field and controlled-environment experiments.

Characterization of metal oxide field-effect transistors for first helical tomotherapy Hi-Art II unit in India.

PubMed

Kinhikar, Rajesh A; Pai, Rajeshree; Master, Zubin; Deshpande, Deepak D

2009-01-01

To characterize metal oxide semiconductor field-effect transistors (MOSFETs) for a 6-MV photon beam with a first helical tomotherapy Hi-Art II unit in India. Standard sensitivity MOSFETs were first calibrated and then characterized for reproducibility, field size dependence, angular dependence, fade effects, and temperature dependence. The detector sensitivity was estimated for static as well as rotational modes for three jaw settings (1.0 cm x 40 cm, 2.5 cm x 40 cm, and 5 cm x 40 cm) at 1.5-cm depth with a source-to-axis distance (SAD) of 85 cm in virtual water slabs. The A1SL ion chamber and thermoluminescence dosimeters (TLDs) were used to compare the results. No significant difference was found in the detector sensitivity for static and rotational procedures. The average detector sensitivity for static procedures was 1.10 mV/cGy (SD 0.02) while it was 1.12 mV/cGy (SD 0.02) for rotational procedures. The average detector sensitivity found was the same within the experimental uncertainty for static and rotational dose deliveries. The MOSFET reading was consistent and its reproducibility was excellent (+0.5%) while there was no significant dependence of field size. The angular dependence of less than 1.0% was observed. There was negligible fading effect of the MOSFET. The MOSFET response was found independent of temperature in the range 18 degrees-30 degrees. The ion chamber readings were assumed to be a reference for the estimation of the MOSFET calibration factor. The ion chamber and the TLD were in good agreement (+2%) with each other. This study deals only with the measurements and calibration performed on the surface of the phantom. MOSFET was calibrated and validated for phantom surface measurements for a 6-MV photon beam generated by a tomotherapy machine. The sensitivity of the detector was the same for both modes of treatment delivery with tomotherapy. The performance of the MOSFET was validated for and satisfactory for the helical tomotherapy Hi-Art II unit. However, MOSFET may be used for in vivo surface dosimetry only after it is calibrated under the conditions replicating as much as possible the manner in which the dosimeter will be used clinically.

Metatranscriptomics and Pyrosequencing Facilitate Discovery of Potential Viral Natural Enemies of the Invasive Caribbean Crazy Ant, Nylanderia pubens

PubMed Central

Valles, Steven M.; Oi, David H.; Yu, Fahong; Tan, Xin-Xing; Buss, Eileen A.

2012-01-01

Background Nylanderia pubens (Forel) is an invasive ant species that in recent years has developed into a serious nuisance problem in the Caribbean and United States. A rapidly expanding range, explosive localized population growth, and control difficulties have elevated this ant to pest status. Professional entomologists and the pest control industry in the United States are urgently trying to understand its biology and develop effective control methods. Currently, no known biological-based control agents are available for use in controlling N. pubens. Methodology and Principal Findings Metagenomics and pyrosequencing techniques were employed to examine the transcriptome of field-collected N. pubens colonies in an effort to identify virus infections with potential to serve as control agents against this pest ant. Pyrosequencing (454-platform) of a non-normalized N. pubens expression library generated 1,306,177 raw sequence reads comprising 450 Mbp. Assembly resulted in generation of 59,017 non-redundant sequences, including 27,348 contigs and 31,669 singlets. BLAST analysis of these non-redundant sequences identified 51 of potential viral origin. Additional analyses winnowed this list of potential viruses to three that appear to replicate in N. pubens. Conclusions Pyrosequencing the transcriptome of field-collected samples of N. pubens has identified at least three sequences that are likely of viral origin and, in which, N. pubens serves as host. In addition, the N. pubens transcriptome provides a genetic resource for the scientific community which is especially important at this early stage of developing a knowledgebase for this new pest. PMID:22384082

Design and evaluation of an aerial spray trial with true replicates to test the efficacy of Bacillus thuringiensis insecticide in a boreal forest.

PubMed

Cadogan, Beresford L; Scharbach, Roger D

2003-04-01

A field trial using true replicates was conducted successfully in a boreal forest in 1996 to evaluate the efficacy of two aerially applied Bacillus thuringiensis formulations, ABG 6429 and ABG 6430. A complete randomized design with four replicates per treatment was chosen. Twelve to 15 balsam fir (Abies balsamea [L.] Mill.) per plot were randomly selected as sample trees. Interplot buffer zones, > or = 200 m wide, adequately prevented cross contamination from sprays that were atomized with four rotary atomizers (volume median diameters ranging from 64.6 to 139.4 microm) and released approximately 30 m above the ground. The B. thuringiensis formulations were not significantly different (P > 0.05) from each other in reducing spruce budworm (Choristoneura fumiferana [Clem.]) populations and protecting balsam trees from defoliation but both formulations were significantly more efficacious than the controls. The results suggest that true replicates are a feasible alternative to pseudoreplication in experimental forest aerial applications.

Molecular turnover, the H3.3 dilemma and organismal aging (hypothesis)

PubMed Central

Saade, Evelyne; Pirozhkova, Iryna; Aimbetov, Rakhan; Lipinski, Marc; Ogryzko, Vasily

2015-01-01

The H3.3 histone variant has been a subject of increasing interest in the field of chromatin studies due to its two distinguishing features. First, its incorporation into chromatin is replication independent unlike the replication-coupled deposition of its canonical counterparts H3.1/2. Second, H3.3 has been consistently associated with an active state of chromatin. In accordance, this histone variant should be expected to be causally involved in the regulation of gene expression, or more generally, its incorporation should have downstream consequences for the structure and function of chromatin. This, however, leads to an apparent paradox: In cells that slowly replicate in the organism, H3.3 will accumulate with time, opening the way to aberrant effects on heterochromatin. Here, we review the indications that H3.3 is expected both to be incorporated in the heterochromatin of slowly replicating cells and to retain its functional downstream effects. Implications for organismal aging are discussed. PMID:25720734

Studies in Historical Replication in Psychology VII: The Relative Utility of ``Ancestor Analysis'' from Scientific and Educational Vantages

NASA Astrophysics Data System (ADS)

Ranney, Michael Andrew

2008-05-01

This article discusses, from various vantages, Ryan Tweney’s (this issue) pedagogical technique of employing historical replications of psychological experiments with graduate students in psychology. A prima facie perspective suggests great promise for this sort of academic “ancestor analysis,” particularly given the enthusiasm and skill represented in the activities that culminated in the replicators’ articles. It is suggested that such activities might be enhanced by requiring a contextualization that makes contact with more modern psychological research—particularly regarding expositions of the replications. From a scientific/cognitive methods perspective, the original experimenters’ inexplicit, ambiguous, descriptions provide both challenges and opportunities for students seeking to improve their understandings of their field. Three practical questions are posed herein regarding the general utility of this—or any—proposed instructional intervention. Ultimately, determining and integrating the diverse objectives that essential stakeholders have in graduate psychological training represent critical prerequisites in comprehensively assessing the relative advantages of such historical replications with respect to alternative experiences.

System-wide Analysis of SUMOylation Dynamics in Response to Replication Stress Reveals Novel Small Ubiquitin-like Modified Target Proteins and Acceptor Lysines Relevant for Genome Stability*

PubMed Central

Xiao, Zhenyu; Chang, Jer-Gung; Hendriks, Ivo A.; Sigurðsson, Jón Otti; Olsen, Jesper V.; Vertegaal, Alfred C.O.

2015-01-01

Genotoxic agents can cause replication fork stalling in dividing cells because of DNA lesions, eventually leading to replication fork collapse when the damage is not repaired. Small Ubiquitin-like Modifiers (SUMOs) are known to counteract replication stress, nevertheless, only a small number of relevant SUMO target proteins are known. To address this, we have purified and identified SUMO-2 target proteins regulated by replication stress in human cells. The developed methodology enabled single step purification of His10-SUMO-2 conjugates under denaturing conditions with high yield and high purity. Following statistical analysis on five biological replicates, a total of 566 SUMO-2 targets were identified. After 2 h of hydroxyurea treatment, 10 proteins were up-regulated for SUMOylation and two proteins were down-regulated for SUMOylation, whereas after 24 h, 35 proteins were up-regulated for SUMOylation, and 13 proteins were down-regulated for SUMOylation. A site-specific approach was used to map over 1000 SUMO-2 acceptor lysines in target proteins. The methodology is generic and is widely applicable in the ubiquitin field. A large subset of these identified proteins function in one network that consists of interacting replication factors, transcriptional regulators, DNA damage response factors including MDC1, ATR-interacting protein ATRIP, the Bloom syndrome protein and the BLM-binding partner RMI1, the crossover junction endonuclease EME1, BRCA1, and CHAF1A. Furthermore, centromeric proteins and signal transducers were dynamically regulated by SUMOylation upon replication stress. Our results uncover a comprehensive network of SUMO target proteins dealing with replication damage and provide a framework for detailed understanding of the role of SUMOylation to counteract replication stress. Ultimately, our study reveals how a post-translational modification is able to orchestrate a large variety of different proteins to integrate different nuclear processes with the aim of dealing with the induced DNA damage. PMID:25755297

The National Comorbidity Survey Adolescent Supplement (NCS-A): II. Overview and Design

PubMed Central

Kessler, Ronald C.; Avenevoli, Shelli; Costello, E. Jane; Green, Jennifer Greif; Gruber, Michael J.; Heeringa, Steven; Merikangas, Kathleen R.; Pennell, Beth-Ellen; Sampson, Nancy A.; Zaslavsky, Alan M.

2009-01-01

OBJECTIVE To present an overview of the design and field procedures of the National Comorbidity Survey Replication Adolescent Supplement (NCS-A) METHOD The NCS-A is a nationally representative face-to-face household survey of the prevalence and correlates of DSM-IV mental disorders among US adolescents (ages 13–17) that was carried out between February 2001 and January 2004 by the Survey Research Center of the Institute for Social Research at the University of Michigan. The sample was based on a dual-frame design that included 904 adolescent residents of the households that participated in the National Comorbidity Survey Replication (85.9% response rate) and 9244 adolescent students selected from a representative sample of 320 schools in the same nationally representative sample of counties as the NCS-R (74.7% response rate). RESULTS Comparisons of sample and population distributions on Census socio-demographic variables and, in the school sample, school characteristics documented only minor differences that were corrected with post-stratification weighting. Comparisons of DSM-IV disorder prevalence estimates among household vs. school sample respondents in counties that differed in the use of replacement schools for originally selected schools that refused to participate showed that the use of replacement schools did not introduce bias into prevalence estimates. CONCLUSIONS The NCS-A is a rich nationally representative dataset that will substantially increase understanding of the mental health and well-being of adolescents in the United States. PMID:19242381

Replication initiatives will not salvage the trustworthiness of psychology.

PubMed

Coyne, James C

2016-05-31

Replication initiatives in psychology continue to gather considerable attention from far outside the field, as well as controversy from within. Some accomplishments of these initiatives are noted, but this article focuses on why they do not provide a general solution for what ails psychology. There are inherent limitations to mass replications ever being conducted in many areas of psychology, both in terms of their practicality and their prospects for improving the science. Unnecessary compromises were built into the ground rules for design and publication of the Open Science Collaboration: Psychology that undermine its effectiveness. Some ground rules could actually be flipped into guidance for how not to conduct replications. Greater adherence to best publication practices, transparency in the design and publishing of research, strengthening of independent post-publication peer review and firmer enforcement of rules about data sharing and declarations of conflict of interest would make many replications unnecessary. Yet, it has been difficult to move beyond simple endorsement of these measures to consistent implementation. Given the strong institutional support for questionable publication practices, progress will depend on effective individual and collective use of social media to expose lapses and demand reform. Some recent incidents highlight the necessity of this.

Using prediction markets to estimate the reproducibility of scientific research.

PubMed

Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A; Johannesson, Magnus

2015-12-15

Concerns about a lack of reproducibility of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants' individual forecasts. This shows that prediction markets are a promising tool for assessing the reproducibility of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a "statistically significant" finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications.

Using prediction markets to estimate the reproducibility of scientific research

PubMed Central

Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A.; Johannesson, Magnus

2015-01-01

Concerns about a lack of reproducibility of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants’ individual forecasts. This shows that prediction markets are a promising tool for assessing the reproducibility of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a “statistically significant” finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications. PMID:26553988

We need more replication research - A case for test-retest reliability.

PubMed

Leppink, Jimmie; Pérez-Fuster, Patricia

2017-06-01

Following debates in psychology on the importance of replication research, we have also started to see pleas for a more prominent role for replication research in medical education. To enable replication research, it is of paramount importance to carefully study the reliability of the instruments we use. Cronbach's alpha has been the most widely used estimator of reliability in the field of medical education, notably as some kind of quality label of test or questionnaire scores based on multiple items or of the reliability of assessment across exam stations. However, as this narrative review outlines, Cronbach's alpha or alternative reliability statistics may complement but not replace psychometric methods such as factor analysis. Moreover, multiple-item measurements should be preferred above single-item measurements, and when using single-item measurements, coefficients as Cronbach's alpha should not be interpreted as indicators of the reliability of a single item when that item is administered after fundamentally different activities, such as learning tasks that differ in content. Finally, if we want to follow up on recent pleas for more replication research, we have to start studying the test-retest reliability of the instruments we use.

Meta-Analysis of Correlations Revisited: Attempted Replication and Extension of Field's (2001) Simulation Studies

ERIC Educational Resources Information Center

Hafdahl, Adam R.; Williams, Michelle A.

2009-01-01

In 2 Monte Carlo studies of fixed- and random-effects meta-analysis for correlations, A. P. Field (2001) ostensibly evaluated Hedges-Olkin-Vevea Fisher-[zeta] and Schmidt-Hunter Pearson-r estimators and tests in 120 conditions. Some authors have cited those results as evidence not to meta-analyze Fisher-[zeta] correlations, especially with…

A geropsychiatric unit without walls.

PubMed

Nadler-Moodie, Marlene; Gold, Jerry

2005-01-01

The continued population growth of people over the age of 65 correlates with the growth in the number of older people who experience a mental health crisis or frank mental illness. Currently there is a paucity of treatment programs that are specialized for the geropsychiatric patient. Given the limitations of finances and human resources as well as the constraints sometimes imposed by regulatory agencies, interdisciplinary health care workers are challenged to provide optimum care in traditional settings. This article describes how an inpatient psychiatric unit can be modified to replicate some of the best practices of a designated geropsychiatric unit with positive results.

Autonomous replication of nucleic acids by polymerization/nicking enzyme/DNAzyme cascades for the amplified detection of DNA and the aptamer-cocaine complex.

PubMed

Wang, Fuan; Freage, Lina; Orbach, Ron; Willner, Itamar

2013-09-03

The progressive development of amplified DNA sensors and aptasensors using replication/nicking enzymes/DNAzyme machineries is described. The sensing platforms are based on the tailoring of a DNA template on which the recognition of the target DNA or the formation of the aptamer-substrate complex trigger on the autonomous isothermal replication/nicking processes and the displacement of a Mg(2+)-dependent DNAzyme that catalyzes the generation of a fluorophore-labeled nucleic acid acting as readout signal for the analyses. Three different DNA sensing configurations are described, where in the ultimate configuration the target sequence is incorporated into a nucleic acid blocker structure associated with the sensing template. The target-triggered isothermal autonomous replication/nicking process on the modified template results in the formation of the Mg(2+)-dependent DNAzyme tethered to a free strand consisting of the target sequence. This activates additional template units for the nucleic acid self-replication process, resulting in the ultrasensitive detection of the target DNA (detection limit 1 aM). Similarly, amplified aptamer-based sensing platforms for cocaine are developed along these concepts. The modification of the cocaine-detection template by the addition of a nucleic acid sequence that enables the autonomous secondary coupled activation of a polymerization/nicking machinery and DNAzyme generation path leads to an improved analysis of cocaine (detection limit 10 nM).

Multiseason occupancy models for correlated replicate surveys

USGS Publications Warehouse

Hines, James; Nichols, James D.; Collazo, Jaime

2014-01-01

Occupancy surveys collecting data from adjacent (sometimes correlated) spatial replicates have become relatively popular for logistical reasons. Hines et al. (2010) presented one approach to modelling such data for single-season occupancy surveys. Here, we present a multiseason analogue of this model (with corresponding software) for inferences about occupancy dynamics. We include a new parameter to deal with the uncertainty associated with the first spatial replicate for both single-season and multiseason models. We use a case study, based on the brown-headed nuthatch, to assess the need for these models when analysing data from the North American Breeding Bird Survey (BBS), and we test various hypotheses about occupancy dynamics for this species in the south-eastern United States. The new model permits inference about local probabilities of extinction, colonization and occupancy for sampling conducted over multiple seasons. The model performs adequately, based on a small simulation study and on results of the case study analysis. The new model incorporating correlated replicates was strongly favoured by model selection for the BBS data for brown-headed nuthatch (Sitta pusilla). Latitude was found to be an important source of variation in local colonization and occupancy probabilities for brown-headed nuthatch, with both probabilities being higher near the centre of the species range, as opposed to more northern and southern areas. We recommend this new occupancy model for detection–nondetection studies that use potentially correlated replicates.

Visualization of the Charcoal Agar Resazurin Assay for Semi-quantitative, Medium-throughput Enumeration of Mycobacteria.

PubMed

Gold, Ben; Roberts, Julia; Ling, Yan; Lopez Quezada, Landys; Glasheen, Jou; Ballinger, Elaine; Somersan-Karakaya, Selin; Warrier, Thulasi; Nathan, Carl

2016-12-14

There is an urgent need to discover and progress anti-infectives that shorten the duration of tuberculosis (TB) treatment. Mycobacterium tuberculosis, the etiological agent of TB, is refractory to rapid and lasting chemotherapy due to the presence of bacilli exhibiting phenotypic drug resistance. The charcoal agar resazurin assay (CARA) was developed as a tool to characterize active molecules discovered by high-throughput screening campaigns against replicating and non-replicating M. tuberculosis. Inclusion of activated charcoal in bacteriologic agar medium helps mitigate the impact of compound carry-over, and eliminates the requirement to pre-dilute cells prior to spotting on CARA microplates. After a 7-10 day incubation period at 37 °C, the reduction of resazurin by mycobacterial microcolonies growing on the surface of CARA microplate wells permits semi-quantitative assessment of bacterial numbers via fluorometry. The CARA detects approximately a 2-3 log10 difference in bacterial numbers and predicts a minimal bactericidal concentration leading to ≥99% bacterial kill (MBC≥99). The CARA helps determine whether a molecule is active on bacilli that are replicating, non-replicating, or both. Pilot experiments using the CARA facilitate the identification of which concentration of test agent and time of compound exposure require further evaluation by colony forming unit (CFU) assays. In addition, the CARA can predict if replicating actives are bactericidal or bacteriostatic.

A cross-cultural clinical comparison between subjects with obsessive-compulsive disorder from the United States and Brazil.

PubMed

Medeiros, Gustavo C; Torres, Albina R; Boisseau, Christina L; Leppink, Eric W; Eisen, Jane L; Fontenelle, Leonardo F; do Rosário, Maria C; Mancebo, Maria C; Rasmussen, Steven A; Ferrão, Ygor A; Grant, Jon E

2017-08-01

Although OCD is a global problem, the literature comparing, in a direct and standardized way, the manifestations across countries is scarce. Therefore, questions remain as to whether some important clinical findings are replicable worldwide, especially in the developing world. The objective of this study was to perform a clinical comparison of OCD patients recruited in the United States (U.S.) and Brazil. Our sample consisted of 1187 adult, treatment-seeking OCD outpatients from the U.S. (n=236) and Brazil (n=951). With regards to the demographics, U.S. participants with OCD were older, more likely to identify as Caucasian, had achieved a higher educational level, and were less likely to be partnered when compared to Brazilians. Concerning the clinical variables, after controlling for demographics the two samples presented largely similar profiles. Brazilian participants with OCD, however, endorsed significantly greater rates of generalized anxiety disorder and post-traumatic stress disorder, whereas U.S. subjects were significantly more likely to endorse a lifetime history of addiction (alcohol-use and substance-use disorders). This is the largest direct cross-cultural comparison to date in the OCD field. Our results provide much needed insight regarding the development of culture-sensitive treatments. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Order, Disorder, Death: Lessons from a Superorganism

PubMed Central

Amdam, Gro V.; Seehuu, Siri-Christine

2008-01-01

Animal models contribute to the understanding of molecular mechanism of cancer, revealing complex roles of altered cellular-signaling networks and deficient surveillance systems. Analogous pathologies are documented in an unconventional model organism that receives attention in research on systems theory, evolution, and aging. The honeybee (Apis mellifera) colony is an advanced integrative unit, a “superorganism” in which order is controlled via complex signaling cascades and surveillance schemes. A facultatively sterile caste, the workers, regulates patterns of growth, differentiation, homeostasis, and death. Workers differentiate into temporal phenotypes in response to dynamic social cues; chemosensory signals that can translate into dramatic physiological responses, including programmed cell death. Temporal worker forms function together, and effectively identify and terminate abnormal colony members ranging from embryos to adults. As long as this regulatory system is operational at a colony level, the unit survives and propagates. However, if the worker phenotypes that collectively govern order become too few or change into malignant forms that bypass control mechanisms to replicate aberrantly; order is replaced by disorder that ultimately leads to the destruction of the society. In this chapter we describe fundamental properties of honeybee social organization, and explore conditions that lead to states of disorder. Our hope is that this chapter will be an inspirational source for ongoing and future work in the field of cancer research. PMID:16860655

Teaching the Scientific Method: It's All in the Perspective

ERIC Educational Resources Information Center

Ayers, James M.; Ayers, Kathleen M.

2007-01-01

A three unit module of inquiry, including morphological comparison, cladogram construction, and data mining has been developed to teach students the nature of experimental science. Students generate angiosperm morphological data, form cladistic hypotheses, then mine taxonomic, bioinformatic and historical data from many sources to replicate and…

A NEW COPPER (II)-IMIDAZOLE DERIVATIVE EFFECTIVELY INHIBITS REPLICATION OF DENV-2 IN VERO CELL

PubMed Central

Sucipto, Teguh Hari; Churrotin, Siti; Setyawati, Harsasi; Martak, Fahimah; Mulyatno, Kris Cahyo; Amarullah, Ilham Harlan; Kotaki, Tomohiro; Kameoka, Masanori; Yotopranoto, Subagyo; Soegijanto, and Soegeng

2018-01-01

Background: Dengue is a kind of infectious disease that was distributed in the tropical and sub-tropical areas. To date, there is no clinically approved dengue vaccine or antiviral for humans, even though there have been great efforts towards this end. Therefore, finding the effective compound against dengue virus (DENV) replication is very important. Among the complex compounds, copper(II)-imidazole derivatives are of interest because of their biological and medicinal benefits. Materials and Methods: In the present study, antiviral activity of [Cu(2,4,5-triphenylimidazole)2]n, was evaluated against different stages of dengue virus type 2 (DENV-2) replication in Vero cell using focus forming unit reduction assay and quantitative ELISA. Results: [Cu(2,4,5-triphenylimidazole)2]n inhibited DENV-2 replication in Vero cells with IC50 = 2.3 μg/ml and SI= 19.42 when cells were treated 2 days after virus infection, whereas its CC50 for cytotoxicity to Vero cells was 44.174 μg/ml. Conclusion: The compound has high anti-DENV2 activity, less toxicity, and a high possibility to be considered a drug candidate. PMID:29619441

The biological control of Pomacea canaliculata population by rice-duck mutualism in paddy fields

Treesearch

Kiang Liang; Jia-en Zhang; Li Fang; Benliang Zaho; Mingzhu Luo; Prem Parajuli; Ying Ouyang

2013-01-01

Duck has been used as a non-chemical control method against Pomacea canaliculata Lamarck, but little is known about its principles that underlie the control of snail populations. An indoor experiment was initially used to observe the predation potential of ducks, followed by replicated field trials. In the indoor studies, ducks effectively preyed on...

2017 Update of the field evaluation of new and underutilized fig cultivars for fresh and dried markets

USDA-ARS?s Scientific Manuscript database

There are new and underutilized fig cultivars in the national collection of figs at the National Clonal Germplasm Repository, Davis, CA. This study is a replicated field trial of 12 cultivars that may potentially impact the fresh market and/or dry market fig industry. On April 16, 2015, the fig tree...

Proteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells.

PubMed

Bursomanno, Sara; Beli, Petra; Khan, Asif M; Minocherhomji, Sheroy; Wagner, Sebastian A; Bekker-Jensen, Simon; Mailand, Niels; Choudhary, Chunaram; Hickson, Ian D; Liu, Ying

2015-01-01

SUMOylation is a form of post-translational modification involving covalent attachment of SUMO (Small Ubiquitin-like Modifier) polypeptides to specific lysine residues in the target protein. In human cells, there are four SUMO proteins, SUMO1-4, with SUMO2 and SUMO3 forming a closely related subfamily. SUMO2/3, in contrast to SUMO1, are predominantly involved in the cellular response to certain stresses, including heat shock. Substantial evidence from studies in yeast has shown that SUMOylation plays an important role in the regulation of DNA replication and repair. Here, we report a proteomic analysis of proteins modified by SUMO2 in response to DNA replication stress in S phase in human cells. We have identified a panel of 22 SUMO2 targets with increased SUMOylation during DNA replication stress, many of which play key functions within the DNA replication machinery and/or in the cellular response to DNA damage. Interestingly, POLD3 was found modified most significantly in response to a low dose aphidicolin treatment protocol that promotes common fragile site (CFS) breakage. POLD3 is the human ortholog of POL32 in budding yeast, and has been shown to act during break-induced recombinational repair. We have also shown that deficiency of POLD3 leads to an increase in RPA-bound ssDNA when cells are under replication stress, suggesting that POLD3 plays a role in the cellular response to DNA replication stress. Considering that DNA replication stress is a source of genome instability, and that excessive replication stress is a hallmark of pre-neoplastic and tumor cells, our characterization of SUMO2 targets during a perturbed S-phase should provide a valuable resource for future functional studies in the fields of DNA metabolism and cancer biology. Copyright © 2014 Elsevier B.V. All rights reserved.

Looking in a science classroom: exploring possibilities of creative cultural divergence in science teaching and learning

NASA Astrophysics Data System (ADS)

Baron, Alex; Chen, Hsiao-Lan Sharon

2012-03-01

Worldwide proliferation of pedagogical innovations creates expanding potential in the field of science education. While some teachers effectively improve students' scientific learning, others struggle to achieve desirable student outcomes. This study explores a Taiwanese science teacher's ability to effectively enhance her students' science learning. The authors visited a Taipei city primary school class taught by an experienced science teacher during a 4-week unit on astronomy, with a total of eight, 90-minute periods. Research methods employed in this study included video capture of each class as well as reflective interviews with the instructor, eliciting the teacher's reflection upon both her pedagogical choices and the perceived results of these choices. We report that the teacher successfully teaches science by creatively diverging from culturally generated educational expectations. Although the pedagogical techniques and ideas enumerated in the study are relevant specifically to Taiwan, creative cultural divergence might be replicated to improve science teaching worldwide.

Can emotion regulation change political attitudes in intractable conflicts? From the laboratory to the field.

PubMed

Halperin, Eran; Porat, Roni; Tamir, Maya; Gross, James J

2013-01-01

We hypothesized that an adaptive form of emotion regulation-cognitive reappraisal-would decrease negative emotion and increase support for conflict-resolution policies. In Study 1, Israeli participants were invited to a laboratory session in which they were randomly assigned to either a cognitive-reappraisal condition or a control condition; they were then presented with anger-inducing information related to the Israeli-Palestinian conflict. Participants in the reappraisal condition were more supportive of conciliatory policies and less supportive of aggressive policies compared with participants in the control condition. In Study 2, we replicated these findings in responses to a real political event (the recent Palestinian bid for United Nations recognition). When assessed 1 week after training, participants trained in cognitive reappraisal showed greater support for conciliatory policies and less support for aggressive policies toward Palestinians compared with participants in a control condition. These effects persisted when participants were reassessed 5 months after training, and at both time points, negative emotion mediated the effects of reappraisal.

Composition of forage and grain from second-generation insect-protected corn MON 89034 is equivalent to that of conventional corn (Zea mays L.).

PubMed

Drury, Suzanne M; Reynolds, Tracey L; Ridley, William P; Bogdanova, Natalia; Riordan, Susan; Nemeth, Margaret A; Sorbet, Roy; Trujillo, William A; Breeze, Matthew L

2008-06-25

Insect-protected corn hybrids containing Cry insecticidal proteins derived from Bacillus thuringiensis have protection from target pests and provide effective management of insect resistance. MON 89034 hybrids have been developed that produce both the Cry1A.105 and Cry2Ab2 proteins, which provide two independent modes of insecticidal action against the European corn borer ( Ostrinia nubilalis ) and other lepidopteran insect pests of corn. The composition of MON 89034 corn was compared to conventional corn by measuring proximates, fiber, and minerals in forage and by measuring proximates, fiber, amino acids, fatty acids, vitamins, minerals, antinutrients, and secondary metabolites in grain collected from 10 replicated field sites across the United States and Argentina during the 2004-2005 growing seasons. Analyses established that the forage and grain from MON 89034 are compositionally comparable to the control corn hybrid and conventional corn reference hybrids. These findings support the conclusion that MON 89034 is compositionally equivalent to conventional corn hybrids.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Layton, Alice; Smart, Abby E.; Chauhan, Archana

Pseudomonas fluorescens HK44 represented the first genetically engineered microorganism to be approved in the United States for field release for applications related to subsurface soil bioremediation. In October 1996, strain HK44 was introduced into a replicated semi-contained array of soil lysimeters where its luciferase (luxCDABE)-based bioluminescent response to soil-borne polycyclic aromatic hydrocarbon (PAH) contaminants was detected and monitored for the next two years. At the termination of this experiment, it was decided that the lysimeters remain available for future longer-term monitoring efforts, and were thus covered and left essentially undisturbed until the initiation of a large sampling event in 2010,more » fourteen years after the original release. Although after extensive sampling culturable HK44 cells were not found, additional molecular and metagenomic analyses indicated that genetic signatures of HK44 cells still persisted, with genes diagnostic for the bioluminescent transposon carried by strain HK44 (luxA and tetA) being found at low concentrations (< 5000 copies/g).« less

Extrapolating Accelerated UV Weathering Data: Perspective From PVQAT Task Group 5 (Presentation)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, D.; Annigoni, E.; Ballion, A.

2015-02-01

Taskgroup 5 (TG5) is concerned with a accelerated aging standard incorporating factors including ultraviolet radiation, temperature, and moisture. Separate experiments are being conducted in support of a test standard via the regional sub-groups in Asia, Europe, and the United States. The authors will describe the objectives and timeline for the TG5 interlaboratory study being directed out of the USA. Qualitative preliminary data from the experiment is presented. To date, the encapsulation transmittance experiment has: replicated behaviors of fielded materials (including specimen location- and formulation additive-specific discoloration); demonstrated coupling between UV aging and temperature; demonstrated that degradation in EVA results frommore » UV- aging; and obtained good qualitative comparison between Xe and UVA-340 sources for EVA. To date, the encapsulation adhesion experiment (using the compressive shear test to quantify strength of attachment) has demonstrated that attachment strength can decrease drastically (>50%) with age; however, early results suggest significant factor (UV, T, RH) dependence. Much remains to be learned about adhesion.« less

Applying Questioning or Reading Strategy to Review Technology Enhanced Coedited Notes of Elementary School Students

ERIC Educational Resources Information Center

Chiu, Chiung-Hui; Cheng, Hsiao-Wei; Wu, Chiu-Yi

2016-01-01

The authors examined whether applying questioning review better enhances elementary level students' learning from technology-enhanced coediting-based note taking than does traditional reading review. A nonequivalent comparison group quasi-experimental design was implemented and replicated on four independent units. Two sixth grade elementary…

Sex Stereotypes in the United States Revisited: 1972-1988.

ERIC Educational Resources Information Center

Bergen, David J.; Williams, John E.

1991-01-01

Reports the results of a 1988 replication of a sex stereotype study done in 1972. There were minor qualitative changes such as the perception of women as more and men as less reality-oriented, but there was no evidence that the two stereotypes had become significantly less differentiated. (CJS)

Losing My Religion? The Impact of Spiritual Cues on Noncognitive Skills

ERIC Educational Resources Information Center

Bowen, Daniel H.; Cheng, Albert

2016-01-01

Studies consistently show that Catholic schools produce positive impacts on educational outcomes. Many charter school networks in the United States now provide, what are essentially, secularized versions of the Catholic education model. However, charter schools cannot legally replicate the overt religious curriculum and mission of Catholic…

Taking Workforce Initiatives to Scale: Workforce Initiatives Discussion Paper #2

ERIC Educational Resources Information Center

Academy for Educational Development, 2011

2011-01-01

The System-wide Collaborative Action for Livelihoods and Environment, or SCALE process, has become one of the Academy for Educational Development's (AED's) and the United States Agency for International Development's (USAID's) most utilized and replicated models, with applications in education, health, natural resources management, tourism,…

Plethodontid salamander response to Silvilcultural Practices in Missouri Ozark forests

Treesearch

Laura A. Herbeck; David R. Larsen

1999-01-01

There is little information on the effects of tree harvest on salamander populations in the midwestern United States. We present data on plethodontid salamander densities in replicated stands of three forest age classes in the southeastern Ozarks of Missouri. Forest age classes consisted of regeneration-cut sites

Show me the Monet.

PubMed

Duffin, Christian

2009-10-01

Experts in the United States believe that observation of art can help healthcare professionals diagnose illnesses and injuries in patients. This article reports on an art observation programme involving the University of Chicago Medical Center and the Art Institute of Chicago, Illinois, and reflects on whether such programmes can be replicated in the U.K.

Sugarcane aphid resistant sorghums found within USDA-ARS Lubbock, TX genotypes

USDA-ARS?s Scientific Manuscript database

The sugarcane aphid, Melanaphis sacchari, was discovered infesting grain sorghum in the southern United States in 2013 and has been a perennial pest through 2016. We evaluated 25 sorghum genotypes in a search for host plant resistance to this pest. Plants were started from seed (N = 16 replication...

Microgravity

NASA Image and Video Library

1997-01-12

Nucleosome Core Particle grown on STS-81. The fundamental structural unit of chromatin and is the basis for organization within the genome by compaction of DNA within the nucleus of the cell and by making selected regions of chromosomes available for transcription and replication. Principal Investigator's are Dr. Dan Carter and Dr. Gerard Bunick of New Century Pharmaceuticals.

Training Level, Acculturation, Role Ambiguity, and Multicultural Discussions in Training and Supervising International Counseling Students in the United States

ERIC Educational Resources Information Center

Ng, Kok-Mun; Smith, Shannon D.

2012-01-01

This research partially replicated Nilsson and Anderson's "Professional Psychology: Research and Practice" (2004) study on training and supervising international students. It investigated the relationships among international counseling students' training level, acculturation, supervisory working alliance (SWA), counseling self-efficacy (COSE),…

Promoting Community Language Learning in the United Kingdom

ERIC Educational Resources Information Center

Handley, Sharon

2011-01-01

The COLT (Community and Lesser Taught Languages) project is a consortium of five UK universities, working with various other regional organisations to set up replicable projects and structures to promote languages in North West England. It received funding under the UK's national "Routes into Languages" initiative. One objective was to…

Successive Research: A Strategy for Building on Previous Research.

ERIC Educational Resources Information Center

Noble, Mary Anne

1979-01-01

Describes an approach to clinical research used by the author in teaching graduate nursing students, involving replication and expansion of a primary study of hospital intensive care units. This approach provided valuable experience as well as validated data about clinical practice. Discusses advantages and disadvantages in the approach. (MF)

A Phonological Exploration of Oral Reading Errors.

ERIC Educational Resources Information Center

Moscicki, Eve K.; Tallal, Paula

1981-01-01

Presents study exploring oral reading errors of normally developing readers to determine any developmental differences in learning phoneme-grapheme units; to discover if the grapheme representations of some phonemes are more difficult to read than others; and to replicate results reported by Fowler, et. al. Findings show most oral reading errors…

Parent Involvement in the USA and in Austria.

ERIC Educational Resources Information Center

Krumm, Volker; And Others

Teachers' educational methods to procure or enhance parent involvement in their children's learning processes in schools in German-speaking countries are examined in this comparative study. This Austrian replication of a study conducted in the United States (Epstein, 1986) administered questionnaires to 124 first-, third-, and fifth-grade teachers…

Hazards in Motion: Development of Mobile Geofences for Use in Logging Safety

PubMed Central

Zimbelman, Eloise G.; Keefe, Robert F.; Strand, Eva K.; Kolden, Crystal A.; Wempe, Ann M.

2017-01-01

Logging is one of the most hazardous occupations in the United States. Real-time positioning that uses global navigation satellite system (GNSS) technology paired with radio frequency transmission (GNSS-RF) has the potential to reduce fatal and non-fatal accidents on logging operations through the use of geofences that define safe work areas. Until recently, most geofences have been static boundaries. The aim of this study was to evaluate factors affecting mobile geofence accuracy in order to determine whether virtual safety zones around moving ground workers or equipment are a viable option for improving situational awareness on active timber sales. We evaluated the effects of walking pace, transmission interval, geofence radius, and intersection angle on geofence alert delay using a replicated field experiment. Simulation was then used to validate field results and calculate the proportion of GNSS error bearings resulting in early alerts. The interaction of geofence radius and intersection angle affected safety geofence alert delay in the field experiment. The most inaccurate alerts were negative, representing early warning. The magnitude of this effect was largest at the greatest intersection angles. Simulation analysis supported these field results and also showed that larger GNSS error corresponded to greater variability in alert delay. Increasing intersection angle resulted in a larger proportion of directional GNSS error that triggered incorrect, early warnings. Because the accuracy of geofence alerts varied greatly depending on GNSS error and angle of approach, geofencing for occupational safety is most appropriate for general situational awareness unless real-time correction methods to improve accuracy or higher quality GNSS-RF transponders are used. PMID:28394303

The need for transparency and reproducibility in documenting values for regulatory decision making and evaluating causality: The example of formaldehyde.

PubMed

Van Landingham, Cynthia; Mundt, Kenneth A; Allen, Bruce C; Gentry, P Robinan

2016-11-01

Reproducibility and transparency in scientific reporting is paramount to advancing science and providing the foundation required for sound regulation. Recent examples demonstrate that pivotal scientific findings cannot be replicated, due to poor documentation or methodological bias, sparking debate across scientific and regulatory communities. However, there is general agreement that improvements in communicating and documenting research and risk assessment methods are needed. In the case of formaldehyde, the peer-review conducted by a National Academy of Sciences (NAS) Committee questioned the approaches used by the Integrated Risk Information System (IRIS) in developing draft unit risk values. Using the original data from the key study (Beane Freeman et al., 2009) and documentation provided in the draft IRIS profile, we attempted to duplicate the reported inhalation unit risk values and address the NAS Committee's questions regarding application of the appropriate dose-response model. Overall, documentation of the methods lacked sufficient detail to allow for replication of the unit risk estimates, specifically for Hodgkin lymphoma and leukemias, the key systemic endpoints selected by IRIS. The lack of apparent exposure-response relationships for selected endpoints raises the question whether quantitative analyses are appropriate for these endpoints, and if so, how results are to be interpreted. Copyright © 2016. Published by Elsevier Inc.

Two Bayesian tests of the GLOMOsys Model.

PubMed

Field, Sarahanne M; Wagenmakers, Eric-Jan; Newell, Ben R; Zeelenberg, René; van Ravenzwaaij, Don

2016-12-01

Priming is arguably one of the key phenomena in contemporary social psychology. Recent retractions and failed replication attempts have led to a division in the field between proponents and skeptics and have reinforced the importance of confirming certain priming effects through replication. In this study, we describe the results of 2 preregistered replication attempts of 1 experiment by Förster and Denzler (2012). In both experiments, participants first processed letters either globally or locally, then were tested using a typicality rating task. Bayes factor hypothesis tests were conducted for both experiments: Experiment 1 (N = 100) yielded an indecisive Bayes factor of 1.38, indicating that the in-lab data are 1.38 times more likely to have occurred under the null hypothesis than under the alternative. Experiment 2 (N = 908) yielded a Bayes factor of 10.84, indicating strong support for the null hypothesis that global priming does not affect participants' mean typicality ratings. The failure to replicate this priming effect challenges existing support for the GLOMO sys model. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Nanotherapeutics Using an HIV-1 Poly A and Transactivator of the HIV-1 LTR-(TAR-) Specific siRNA

PubMed Central

Mahajan, Supriya D.; Aalinkeel, Ravikumar; Reynolds, Jessica L.; Nair, Bindukumar; Sykes, Donald E.; Law, Wing-Cheung; Ding, Hong; Bergey, Earl J.; Prasad, Paras N.; Schwartz, Stanley A.

2011-01-01

HIV-1 replication can be efficiently inhibited by intracellular expression of an siRNA targeting the viral RNA. We used a well-validated siRNA (si510) which targets the poly A/TAR (transactivator of the HIV-1 LTR) site and suppresses viral replication. Nanotechnology holds much potential for impact in the field of HIV-1 therapeutics, and nanoparticles such as quantum rods (QRs) can be easily functionalized to incorporate siRNA forming stable nanoplexes that can be used for gene silencing. We evaluated the efficacy of the QR-si510 HIV-1 siRNA nanoplex in suppressing viral replication in the HIV-1-infected monocytic cell line THP-1 by measuring p24 antigen levels and gene expression levels of HIV-1 LTR. Our results suggest that the QR-si510 HIV-1 siRNA nanoplex is not only effective in delivering siRNA, but also in suppressing HIV-1 viral replication for a longer time period. HIV-1 nanotherapeutics can thus enhance systemic bioavailability and offer multifunctionality. PMID:21660279

Molecular turnover, the H3.3 dilemma and organismal aging (hypothesis).

PubMed

Saade, Evelyne; Pirozhkova, Iryna; Aimbetov, Rakhan; Lipinski, Marc; Ogryzko, Vasily

2015-06-01

The H3.3 histone variant has been a subject of increasing interest in the field of chromatin studies due to its two distinguishing features. First, its incorporation into chromatin is replication independent unlike the replication-coupled deposition of its canonical counterparts H3.1/2. Second, H3.3 has been consistently associated with an active state of chromatin. In accordance, this histone variant should be expected to be causally involved in the regulation of gene expression, or more generally, its incorporation should have downstream consequences for the structure and function of chromatin. This, however, leads to an apparent paradox: In cells that slowly replicate in the organism, H3.3 will accumulate with time, opening the way to aberrant effects on heterochromatin. Here, we review the indications that H3.3 is expected both to be incorporated in the heterochromatin of slowly replicating cells and to retain its functional downstream effects. Implications for organismal aging are discussed. © 2015 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Evolutionary game theory: Temporal and spatial effects beyond replicator dynamics

NASA Astrophysics Data System (ADS)

Roca, Carlos P.; Cuesta, José A.; Sánchez, Angel

2009-12-01

Evolutionary game dynamics is one of the most fruitful frameworks for studying evolution in different disciplines, from Biology to Economics. Within this context, the approach of choice for many researchers is the so-called replicator equation, that describes mathematically the idea that those individuals performing better have more offspring and thus their frequency in the population grows. While very many interesting results have been obtained with this equation in the three decades elapsed since it was first proposed, it is important to realize the limits of its applicability. One particularly relevant issue in this respect is that of non-mean-field effects, that may arise from temporal fluctuations or from spatial correlations, both neglected in the replicator equation. This review discusses these temporal and spatial effects focusing on the non-trivial modifications they induce when compared to the outcome of replicator dynamics. Alongside this question, the hypothesis of linearity and its relation to the choice of the rule for strategy update is also analyzed. The discussion is presented in terms of the emergence of cooperation, as one of the current key problems in Biology and in other disciplines.

Does Promotion Orientation Help Explain Why Future-Orientated People Exercise and Eat Healthy?

PubMed

Milfont, Taciano L; Vilar, Roosevelt; Araujo, Rafaella C R; Stanley, Robert

2017-01-01

A study with United States undergraduate students showed individuals high in concern with future consequences engage in exercise and healthy eating because they adopt a promotion orientation, which represents the extent to which individuals are inclined to pursue positive gains. The present article reports a cross-cultural replication of the mediation findings with undergraduate samples from Brazil and New Zealand. Promotion orientation mediated the association between concern with future consequences and exercise attitudes in both countries, but the associations for healthy eating were not replicated-which could be explained by distinct obesity prevalence and eating habits in these socio-cultural contexts. We discuss theoretical and practical implications of the findings for promoting health behavior.

Maximal gene number maintainable by stochastic correction - The second error threshold.

PubMed

Hubai, András G; Kun, Ádám

2016-09-21

There is still no general solution to Eigen׳s Paradox, the chicken-or-egg problem of the origin of life: neither accurate copying, nor long genomes could have evolved without one another being established beforehand. But an array of small, individually replicating genes might offer a workaround, provided that multilevel selection assists the survival of the ensemble. There are two key difficulties that such a system has to overcome: the non-synchronous replication of genes, and their random assortment into daughter cells (the units of higher-level selection) upon fission. Here we find, using the Stochastic Corrector Model framework, that a large number (τ≥90) of genes can coexist. Furthermore, the system can tolerate about 10% replication rate asymmetry (competition) among the genes. On this basis, we put forward a plausible (and testable!) scenario for how novel genes could have been incorporated into early living systems: a route to complex metabolism. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tallgrass prairie restoration: seeding for success

USGS Publications Warehouse

Larson, Diane L.

2013-01-01

Tallgrass prairie is one of the most imperiled ecosystems on Earth. A 2004 estimate indicated that only 2.4 percent of the original northern tallgrass prairie remained in the United States. If tallgrass prairie and the species dependent on it are to survive, management must include restoration of cropland and degraded prairies, in addition to preservation of the few remaining fragments. Despite the importance of restoration and its long history (the first tallgrass prairie restoration was started in 1935 at Curtis Prairie in Wisconsin), few studies have been undertaken with the goal of refining restoration practice. This fact sheet contains the results of one such study, started in 2005, in which we compared three seeding methods (dormant-season broadcast, growing-season broadcast, and growing-season drill) fully crossed with low (10-), medium (20-), and high (34-species) seed mixes replicated 12 times on each of 9 former agricultural fields in Minnesota and Iowa. Plots were 12.2 x 12.2 meters (m) and occupied about 1.6 hectares (ha) (4 acres) of each field. A “successful” restoration is one in which cover and richness of planted species is maximized and cover of exotic and invasive species, especially the noxious weed Canada thistle (Cirsium arvense), is minimized. Details of the planting methods can be located in Larson and others (2011).

Modeling place field activity with hierarchical slow feature analysis

PubMed Central

Schönfeld, Fabian; Wiskott, Laurenz

2015-01-01

What are the computational laws of hippocampal activity? In this paper we argue for the slowness principle as a fundamental processing paradigm behind hippocampal place cell firing. We present six different studies from the experimental literature, performed with real-life rats, that we replicated in computer simulations. Each of the chosen studies allows rodents to develop stable place fields and then examines a distinct property of the established spatial encoding: adaptation to cue relocation and removal; directional dependent firing in the linear track and open field; and morphing and scaling the environment itself. Simulations are based on a hierarchical Slow Feature Analysis (SFA) network topped by a principal component analysis (ICA) output layer. The slowness principle is shown to account for the main findings of the presented experimental studies. The SFA network generates its responses using raw visual input only, which adds to its biological plausibility but requires experiments performed in light conditions. Future iterations of the model will thus have to incorporate additional information, such as path integration and grid cell activity, in order to be able to also replicate studies that take place during darkness. PMID:26052279

The Molecular Biology of Frog Virus 3 and other Iridoviruses Infecting Cold-Blooded Vertebrates

PubMed Central

Chinchar, V. Gregory; Yu, Kwang H.; Jancovich, James K.

2011-01-01

Frog virus 3 (FV3) is the best characterized member of the family Iridoviridae. FV3 study has provided insights into the replication of other family members, and has served as a model of viral transcription, genome replication, and virus-mediated host-shutoff. Although the broad outlines of FV3 replication have been elucidated, the precise roles of most viral proteins remain unknown. Current studies using knock down (KD) mediated by antisense morpholino oligonucleotides (asMO) and small, interfering RNAs (siRNA), knock out (KO) following replacement of the targeted gene with a selectable marker by homologous recombination, ectopic viral gene expression, and recombinant viral proteins have enabled researchers to systematically ascertain replicative- and virulence-related gene functions. In addition, the application of molecular tools to ecological studies is providing novel ways for field biologists to identify potential pathogens, quantify infections, and trace the evolution of ecologically important viral species. In this review, we summarize current studies using not only FV3, but also other iridoviruses infecting ectotherms. As described below, general principles ascertained using FV3 served as a model for the family, and studies utilizing other ranaviruses and megalocytiviruses have confirmed and extended our understanding of iridovirus replication. Collectively, these and future efforts will elucidate molecular events in viral replication, intrinsic and extrinsic factors that contribute to disease outbreaks, and the role of the host immune system in protection from disease. PMID:22069524

Contextual sensitivity in scientific reproducibility

PubMed Central

Van Bavel, Jay J.; Mende-Siedlecki, Peter; Brady, William J.; Reinero, Diego A.

2016-01-01

In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher’s degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed “hidden moderators”) between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility. PMID:27217556

Contextual sensitivity in scientific reproducibility.

PubMed

Van Bavel, Jay J; Mende-Siedlecki, Peter; Brady, William J; Reinero, Diego A

2016-06-07

In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher's degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed "hidden moderators") between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility.

Cross-validation of the Student Perceptions of Team-Based Learning Scale in the United States.

PubMed

Lein, Donald H; Lowman, John D; Eidson, Christopher A; Yuen, Hon K

2017-01-01

The purpose of this study was to cross-validate the factor structure of the previously developed Student Perceptions of Team-Based Learning (TBL) Scale among students in an entry-level doctor of physical therapy (DPT) program in the United States. Toward the end of the semester in 2 patient/client management courses taught using TBL, 115 DPT students completed the Student Perceptions of TBL Scale, with a response rate of 87%. Principal component analysis (PCA) and confirmatory factor analysis (CFA) were conducted to replicate and confirm the underlying factor structure of the scale. Based on the PCA for the validation sample, the original 2-factor structure (preference for TBL and preference for teamwork) of the Student Perceptions of TBL Scale was replicated. The overall goodness-of-fit indices from the CFA suggested that the original 2-factor structure for the 15 items of the scale demonstrated a good model fit (comparative fit index, 0.95; non-normed fit index/Tucker-Lewis index, 0.93; root mean square error of approximation, 0.06; and standardized root mean square residual, 0.07). The 2 factors demonstrated high internal consistency (alpha= 0.83 and 0.88, respectively). DPT students taught using TBL viewed the factor of preference for teamwork more favorably than preference for TBL. Our findings provide evidence supporting the replicability of the internal structure of the Student Perceptions of TBL Scale when assessing perceptions of TBL among DPT students in patient/client management courses.

Relationship and variation of qPCR and culturable enterococci estimates in ambient surface waters are predictable

USGS Publications Warehouse

Whitman, Richard L.; Ge, Zhongfu; Nevers, Meredith B.; Boehm, Alexandria B.; Chern, Eunice C.; Haugland, Richard A.; Lukasik, Ashley M.; Molina, Marirosa; Przybyla-Kelly, Kasia; Shively, Dawn A.; White, Emily M.; Zepp, Richard G.; Byappanahalli, Muruleedhara N.

2010-01-01

The quantitative polymerase chain reaction (qPCR) method provides rapid estimates of fecal indicator bacteria densities that have been indicated to be useful in the assessment of water quality. Primarily because this method provides faster results than standard culture-based methods, the U.S. Environmental Protection Agency is currently considering its use as a basis for revised ambient water quality criteria. In anticipation of this possibility, we sought to examine the relationship between qPCR-based and culture-based estimates of enterococci in surface waters. Using data from several research groups, we compared enterococci estimates by the two methods in water samples collected from 37 sites across the United States. A consistent linear pattern in the relationship between cell equivalents (CCE), based on the qPCR method, and colony-forming units (CFU), based on the traditional culturable method, was significant (P 10CFU > 2.0/100 mL) while uncertainty increases at lower CFU values. It was further noted that the relative error in replicated qPCR estimates was generally higher than that in replicated culture counts even at relatively high target levels, suggesting a greater need for replicated analyses in the qPCR method to reduce relative error. Further studies evaluating the relationship between culture and qPCR should take into account analytical uncertainty as well as potential differences in results of these methods that may arise from sample variability, different sources of pollution, and environmental factors.

In vivo analysis of replication and immunogenicity of proviral clones of human T-lymphotropic virus type 1 with selective envelope surface-unit mutations

PubMed Central

Silverman, Lee R.; Phipps, Andrew J.; Montgomery, Andy; Fernandez, Soledad; Tsukahara, Tomonori; Ratner, Lee; Lairmore, Michael D.

2005-01-01

Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of adult T-cell lymphoma/leukemia (ATL). The HTLV-1 envelope gene exhibits limited variability when examined from infected individuals, but has not been tested using infectious clones of the virus in animal models. In vitro assays indicate that HTLV-1 envelope (Env) Ser75Ile, Asn95Asp, and Asn195Asp surface unit (SU) mutants are able to replicate in and immortalize lymphocytes. Herein, we examined the effects of these Env mutants in rabbits inoculated with HTLV-1 immortalized ACH.75, ACH.95, or ACH.195 cell lines (expressing full-length molecular clones with the SU mutations) or the ACH.1 cell line (expressing wild-type SU). All rabbits became infected, and the fidelity of the mutations was maintained throughout the 8-week study. However, SU point mutations resulted in decreased antibody responses to viral group-associated antigen (Gag) and Env antigens. ACH.195 rabbits had a selective decreased antibody response to SU, and one ACH.195 rabbit had an antibody response to both HTLV-1 and HTLV-2 SUs. Some mutant inoculation groups had altered proviral loads. However, peripheral-blood mononuclear cell (PBMC) proviral loads did not correlate with antibody responses. Our data are the first to demonstrate that mutations in critical determinants of HTLV-1 Env SU altered antibody responses and proviral loads, but do not prevent viral replication in vivo. PMID:16046523

Mindlessly Polite: A Conceptual Replication of the Emotional Seesaw Effect on Compliance and Information Processing

PubMed Central

Kaczmarek, Magdalena C.; Steffens, Melanie C.

2017-01-01

Recent studies demonstrated that the sequential induction of contrasting negative and positive emotions can be used as a social influence technique. The original field experiments found that whenever a sudden change in the emotional dynamic occurs – from negative to positive or vice versa – an increase in compliant behavior and an impairment in cognitive functioning can be observed. The goal of the present experiments was a conceptual replication and extension of the results in a more controlled and counterbalanced fashion. To this aim a novel emotion induction technique was created using an outcome related expectancy violation to induce and change emotions. In a first experiment, the influence of contrasting emotions (vs. only one emotion) on compliance, message processing and information recall was assessed among 80 undergraduate students. We were able to show that a positive, then negative experience, and vice versa, led to losses in processing efficacy, not only leaving individuals momentarily vulnerable to social influence attempts, but also impairing information recall. We replicated this pattern of findings in a second experiment (N = 41). The implications of this innovative induction technique and its findings for theory and future research on the emerging field on contrasting emotions as social-influence techniques are discussed. PMID:28270788

Mindlessly Polite: A Conceptual Replication of the Emotional Seesaw Effect on Compliance and Information Processing.

PubMed

Kaczmarek, Magdalena C; Steffens, Melanie C

2017-01-01

Recent studies demonstrated that the sequential induction of contrasting negative and positive emotions can be used as a social influence technique. The original field experiments found that whenever a sudden change in the emotional dynamic occurs - from negative to positive or vice versa - an increase in compliant behavior and an impairment in cognitive functioning can be observed. The goal of the present experiments was a conceptual replication and extension of the results in a more controlled and counterbalanced fashion. To this aim a novel emotion induction technique was created using an outcome related expectancy violation to induce and change emotions. In a first experiment, the influence of contrasting emotions (vs. only one emotion) on compliance, message processing and information recall was assessed among 80 undergraduate students. We were able to show that a positive, then negative experience, and vice versa, led to losses in processing efficacy, not only leaving individuals momentarily vulnerable to social influence attempts, but also impairing information recall. We replicated this pattern of findings in a second experiment ( N = 41). The implications of this innovative induction technique and its findings for theory and future research on the emerging field on contrasting emotions as social-influence techniques are discussed.

Putting Working-Class Mothers in Their Place: Social Stratification, the Field of Education, and Pierre Bourdieu's Theory of Practice

ERIC Educational Resources Information Center

O'Donoghue, Mary

2013-01-01

This article explores how a small sample of working-class mothers encounters the field of education. In the management of family and their children's schooling, mothers bring to bear and replicate ways of knowing that are embodied, are historical and that offer many-sided insights into profoundly stratified societies. Here I draw on Bourdieu's…

Spot Application of Diammonium Phosphate and Poultry Litter at Establishment in an Old-Field Planted Loblolly Pine Plantation

Treesearch

Bryan C. McElvany; E. David Dickens; Tucker Price

2004-01-01

A study area was installed in the Coastal Plain (Quitman County) of Georgia to determine the benefits of surface microsite application of diammonium phosphate (DAP) and poultry litter to planted loblolly pine (Pinus taeda L.) seedlings on an old-field site. Soils were Bonneau and Orangeburg. Experimental design was complete block with 3 replications...

Redesigning existing transcranial magnetic stimulation coils to reduce energy: application to low field magnetic stimulation

NASA Astrophysics Data System (ADS)

Wang, Boshuo; Shen, Michael R.; Deng, Zhi-De; Smith, J. Evan; Tharayil, Joseph J.; Gurrey, Clement J.; Gomez, Luis J.; Peterchev, Angel V.

2018-06-01

Objective. To present a systematic framework and exemplar for the development of a compact and energy-efficient coil that replicates the electric field (E-field) distribution induced by an existing transcranial magnetic stimulation coil. Approach. The E-field generated by a conventional low field magnetic stimulation (LFMS) coil was measured for a spherical head model and simulated in both spherical and realistic head models. Then, using a spherical head model and spatial harmonic decomposition, a spherical-shaped cap coil was synthesized such that its windings conformed to a spherical surface and replicated the E-field on the cortical surface while requiring less energy. A prototype coil was built and electrically characterized. The effect of constraining the windings to the upper half of the head was also explored via an alternative coil design. Main results. The LFMS E-field distribution resembled that of a large double-cone coil, with a peak field strength around 350 mV m‑1 in the cortex. The E-field distributions of the cap coil designs were validated against the original coil, with mean errors of 1%–3%. The cap coil required as little as 2% of the original coil energy and was significantly smaller in size. Significance. The redesigned LFMS coil is substantially smaller and more energy-efficient than the original, improving cost, power consumption, and portability. These improvements could facilitate deployment of LFMS in the clinic and potentially at home. This coil redesign approach can also be applied to other magnetic stimulation paradigms. Finally, the anatomically-accurate E-field simulation of LFMS can be used to interpret clinical LFMS data.

Variability of pesticide detections and concentrations in field replicate water samples collected for the National Water-Quality Assessment Program, 1992-97

USGS Publications Warehouse

Martin, Jeffrey D.

2002-01-01

Correlation analysis indicates that for most pesticides and concentrations, pooled estimates of relative standard deviation rather than pooled estimates of standard deviation should be used to estimate variability because pooled estimates of relative standard deviation are less affected by heteroscedasticity. The 2 Variability of Pesticide Detections and Concentrations in Field Replicate Water Samples, 1992–97 median pooled relative standard deviation was calculated for all pesticides to summarize the typical variability for pesticide data collected for the NAWQA Program. The median pooled relative standard deviation was 15 percent at concentrations less than 0.01 micrograms per liter (µg/L), 13 percent at concentrations near 0.01 µg/L, 12 percent at concentrations near 0.1 µg/L, 7.9 percent at concentrations near 1 µg/L, and 2.7 percent at concentrations greater than 5 µg/L. Pooled estimates of standard deviation or relative standard deviation presented in this report are larger than estimates based on averages, medians, smooths, or regression of the individual measurements of standard deviation or relative standard deviation from field replicates. Pooled estimates, however, are the preferred method for characterizing variability because they provide unbiased estimates of the variability of the population. Assessments of variability based on standard deviation (rather than variance) underestimate the true variability of the population. Because pooled estimates of variability are larger than estimates based on other approaches, users of estimates of variability must be cognizant of the approach used to obtain the estimate and must use caution in the comparison of estimates based on different approaches.

Differential Activation of Cellular DNA Damage Responses by Replication-Defective and Replication-Competent Adenovirus Mutants

PubMed Central

Prakash, Anand; Jayaram, Sumithra

2012-01-01

Adenovirus (Ad) mutants that lack early region 4 (E4) activate the phosphorylation of cellular DNA damage response proteins. In wild-type Ad type 5 (Ad5) infections, E1b and E4 proteins target the cellular DNA repair protein Mre11 for redistribution and degradation, thereby interfering with its ability to activate phosphorylation cascades important during DNA repair. The characteristics of Ad infection that activate cellular DNA repair processes are not yet well understood. We investigated the activation of DNA damage responses by a replication-defective Ad vector (AdRSVβgal) that lacks E1 and fails to produce the immediate-early E1a protein. E1a is important for activating early gene expression from the other viral early transcription units, including E4. AdRSVβgal can deliver its genome to the cell, but it is subsequently deficient for viral early gene expression and DNA replication. We studied the ability of AdRSVβgal-infected cells to induce cellular DNA damage responses. AdRSVβgal infection does activate formation of foci containing the Mdc1 protein. However, AdRSVβgal fails to activate phosphorylation of the damage response proteins Nbs1 and Chk1. We found that viral DNA replication is important for Nbs1 phosphorylation, suggesting that this step in the viral life cycle may provide an important trigger for activating at least some DNA repair proteins. PMID:23015708

Patient visibility and ICU mortality: a conceptual replication.

PubMed

Lu, Yi; Ossmann, Michelle M; Leaf, David E; Factor, Philip H

2014-01-01

This study reanalyzes the data from a study by Leaf, Homel, and Factor (2010) titled "Relationship between ICU Design and Mortality" by adopting and developing objective visibility measures. Various studies attribute healthcare outcomes (patient falls, satisfaction) to a vague notion of patient room visibility. The study by Leaf and colleagues was the first to draw an independent association between patient mortality and patient room visibility, however "visibility" remains imprecise. The original patient dataset was obtained from Dr. Leaf. The 664 patient sample assigned across 12 rooms at the medical ICU at Columbia University Medical Center was reanalyzed in terms of targeted visibility; the unit of analysis was the room, n = 12. Several computer-based visibility measures of patient rooms were used: patient head visibility, patient room visibility, and field of view to nursing station. Patient head visibility was defined as the percentage of area within the central nursing station from which the patient head could be seen; patient room visibility was defined as the percentage of area within the central nursing station that could see the patient room (average value of all patient room grids); field of view was defined as the maximum viewing angle from the patient head to the central nursing station. Among the sickest patients (those with Acute Physiology and Chronic Health Evaluation II > 30), field of view accounted for 33.5% of the variance in ICU mortality, p = 0.049. Subtle differences in patient room visibility may have important effects on clinical outcomes. Case study, critical care/intensive care, methodology, outcomes.

Success and failure in replication of genotype-phenotype associations: How does replication help in understanding the genetic basis of phenotypic variation in outbred populations?

PubMed

Schielzeth, Holger; Rios Villamil, Alejandro; Burri, Reto

2018-03-25

Recent developments in sequencing technologies have facilitated genomewide mapping of phenotypic variation in natural populations. Such mapping efforts face a number of challenges potentially leading to low reproducibility. However, reproducible research forms the basis of scientific progress. We here discuss the options for replication and the reasons for potential nonreproducibility. We then review the evidence for reproducible quantitative trait loci (QTL) with a focus on natural animal populations. Existing case studies of replication fall into three categories: (i) traits that have been mapped to major effect loci (including chromosomal inversion and supergenes) by independent research teams; (ii) QTL fine-mapped in discovery populations; and (iii) attempts to replicate QTL across multiple populations. Major effect loci, in particular those associated with inversions, have been successfully replicated in several cases within and across populations. Beyond such major effect variants, replication has been more successful within than across populations, suggesting that QTL discovered in natural populations may often be population-specific. This suggests that biological causes (differences in linkage patterns, allele frequencies or context-dependencies of QTL) contribute to nonreproducibility. Evidence from other fields, notably animal breeding and QTL mapping in humans, suggests that a significant fraction of QTL is indeed reproducible in direction and magnitude at least within populations. However, there is also a large number of QTL that cannot be easily reproduced. We put forward that more studies should explicitly address the causes and context-dependencies of QTL signals, in particular to disentangle linkage differences, allele frequency differences and gene-by-environment interactions as biological causes of nonreproducibility of QTL, especially between populations. © 2018 John Wiley & Sons Ltd.

Improved replication of the baculovirus Anticarsia gemmatalis nucleopolyhedrovirus (AgMNPV) in vitro using proteins from Lonomia obliqua hemolymph.

PubMed

Sousa, Álvaro P B; Moraes, Roberto H P; Mendonça, Ronaldo Z

2015-03-01

The baculovirus Anticarsia gemmatalis nucleopolyhedrovirus (AgMNPV), a member of the family Baculoviridae, has been widely applied as a biopesticide for the control of the velvetbean caterpillar, a pest of soybean crop field. Baculoviruses are considered safe and efficient agents for this purpose, because they do not infect vertebrates, being safe for the health of humans and animals, as well as to the environment. The objective of this work was to identify proteins obtained from Lonomia obliqua hemolymph with potential application in the optimization of baculovirus AgMNPV replication in Sf9 insect cell culture. In this work the improvement of the cell culture and viral replication of the AgMNPV baculovirus was observed when Grace medium was supplemented with 10 % (v/v) Fetal Bovine Serum (FBS), 1 % (v/v) hemolymph extract, or 3 % (v/v) of hemolymph fractions or hemolymph sub-fractions obtained by purifying hemolymph through High Performance Liquid Chromatography. Hemolymph presented a positive effect on the synthesis of polyhedra and enhanced baculovirus replication in Spodoptera frugiperda (Sf9) cells (TCID50/mL), and led to Sf9 cell culture improvement. Grace medium supplemented with 10 % (v/v) FBS and 1 % (v/v) hemolymph provided an increase of baculovirus replication, when the cells were infected with multiplicity of infection of 1. In this case, the baculovirus replication was 6,443.91 times greater than that obtained with the control: Grace medium supplemented with 10 % (v/v) FBS. In addition, this work suggests that hemolymph from L. obliqua could have an interesting application in biotechnology, due to an increase in the viability of the cells and virus replication.

Comparison of Rift Valley fever virus replication in North American livestock and wildlife cell lines.

PubMed

Gaudreault, Natasha N; Indran, Sabarish V; Bryant, P K; Richt, Juergen A; Wilson, William C

2015-01-01

Rift Valley fever virus (RVFV) causes disease outbreaks across Africa and the Arabian Peninsula, resulting in high morbidity and mortality among young domestic livestock, frequent abortions in pregnant animals, and potentially severe or fatal disease in humans. The possibility of RVFV spreading to the United States or other countries worldwide is of significant concern to animal and public health, livestock production, and trade. The mechanism for persistence of RVFV during inter-epidemic periods may be through mosquito transovarial transmission and/or by means of a wildlife reservoir. Field investigations in endemic areas and previous in vivo studies have demonstrated that RVFV can infect a wide range of animals, including indigenous wild ruminants of Africa. Yet no predominant wildlife reservoir has been identified, and gaps in our knowledge of RVFV permissive hosts still remain. In North America, domestic goats, sheep, and cattle are susceptible hosts for RVFV and several competent vectors exist. Wild ruminants such as deer might serve as a virus reservoir and given their abundance, wide distribution, and overlap with livestock farms and human populated areas could represent an important risk factor. The objective of this study was to assess a variety of cell lines derived from North American livestock and wildlife for susceptibility and permissiveness to RVFV. Results of this study suggest that RVFV could potentially replicate in native deer species such as white-tailed deer, and possibly a wide range of non-ruminant animals. This work serves to guide and support future animal model studies and risk model assessment regarding this high-consequence zoonotic pathogen.

Factors Related to Students' Learning of Biomechanics Concepts

ERIC Educational Resources Information Center

Hsieh, ChengTu; Smith, Jeremy D.; Bohne, Michael; Knudson, Duane

2012-01-01

The purpose of this study was to replicate and expand a previous study to identify the factors that affect students' learning of biomechanical concepts. Students were recruited from three universities (N = 149) located in the central and western regions of the United States. Data from 142 students completing the Biomechanics Concept Inventory…

Revisiting the Factor Structure of the Strengths and Difficulties Questionnaire: United States, 2001.

ERIC Educational Resources Information Center

Dickey, Wayne C.; Blumberg, Stephen J.

2004-01-01

Objective: The Strengths and Difficulties Questionnaire is a 25-item instrument developed to assess emotional and behavioral problems. The current study attempted to replicate previous European structural analyses and to describe the latent dimensions that underlie responses to the parent-reported version of the Strengths and Difficulties…

Factors Influencing Principals' Retirement Decisions: A Southern US Perspective

ERIC Educational Resources Information Center

Reames, Ellen H.; Kochan, Frances K.; Zhu, Linxiang

2014-01-01

This study, conducted in one state in the United States, replicated similar research from over a decade ago to compare principal demographics and reasons for remaining or leaving the profession. Demographics have trended with the nation. Principals are older, more diverse and are largely eligible for retirement within the next five years. Similar…

Nucleosome Core Particle

NASA Technical Reports Server (NTRS)

1997-01-01

Nucleosome Core Particle grown on STS-81. The fundamental structural unit of chromatin and is the basis for organization within the genome by compaction of DNA within the nucleus of the cell and by making selected regions of chromosomes available for transcription and replication. Principal Investigator's are Dr. Dan Carter and Dr. Gerard Bunick of New Century Pharmaceuticals.

Rhyme and Analogy in Beginning Reading: Conceptual and Methodological Issues.

ERIC Educational Resources Information Center

Goswami, Usha; East, Martin

2000-01-01

Two experiments replicated an earlier study on the causal connection between rhyming skills and reading development found in English. Different results were found from the first study. Argues that methodological and instructional factors may be very important for the conceptual interpretation of studies attempting to pit small units (phonemes)…

Maryland Day Care Voucher System.

ERIC Educational Resources Information Center

Hildebrand, Joan M.

This manual was written to assist States and other governmental units wishing to replicate the Maryland Day Care Voucher Program, a system of providing child care subsidies to eligible families. Chapter I provides brief histories of day care in Maryland and that State's grant to demonstrate the viability of a day care voucher system. Chapter II…

International Tests and the U.S. Educational Reforms: Can Success Be Replicated?

ERIC Educational Resources Information Center

Turgut, Guliz

2013-01-01

The ranking of the United States in major international tests such as the Progress in International Reading Literacy Study (PIRLS), Trends in International Mathematics and Science Study (TIMSS), and Program for International Student Assessment (PISA) is used as the driving force and rationale for the current educational reforms in the United…

Rehabilitation Counselor Education Students' Career Goals: A Partial Replication Study

ERIC Educational Resources Information Center

Chapin, Martha H.; Goodwin, Lloyd R., Jr.

2006-01-01

Rehabilitation counselor education (RCE) students from one RCE program in the Southeastern region of the United States were surveyed in 1993 and 2003 to determine their career goals and if career goals changed a decade later. Other goals were to assess influencing factors for entering rehabilitation counseling or rehabilitation related professions…

Recycling In The U.S. Pallet Industry: 1993

Treesearch

Bruce G. Hansen; Robert Bush; John Punches; Philip A. Araman

1995-01-01

This report provides the details of a study which investigated pallet recycling activity in the United States pallet industry (Standard Industrial Classification 2448) during 1993. The study was conducted by the Center for Forest Products Marketing at Virginia Tech and replicates a similar study that investigated pallet recycling during 1992. The report provides the...

Intracistronic complementation in the simian virus 40 A gene.

PubMed Central

Tornow, J; Cole, C N

1983-01-01

A set of eight simian virus 40 mutants was constructed with lesions in the A gene, which encodes the large tumor (T) antigen. These mutants have small deletions (3-20 base pairs) at either 0.497, 0.288, or 0.243 map units. Mutants having both in-phase and frameshift mutations at each site were isolated. Neither plaque formation nor replication of the mutant DNAs could be detected after transfection of monkey kidney cells. Another nonviable mutant, dlA2459, had a 14-base-pair deletion at 0.193 map unit and was positive for viral DNA replication. Each of the eight mutants were tested for ability to form plaques after cotransfection with dlA2459 DNA. The four mutants that had in-phase deletions were able to complement dlA2459. The other four, which had frameshift deletions, did not. No plaques were formed after cotransfection of cells with any other pair of group A mutants. This suggests that the defect in dlA2459 defines a distinct functional domain of simian virus 40 T antigen. Images PMID:6312452

Design and development of a novel viscoelastic ankle-foot prosthesis based on the human ankle biomechanics.

PubMed

Safaeepour, Zahra; Esteki, Ali; Tabatabai Ghomshe, Farhad; Mousavai, Mohammad E

2014-10-01

In the present study, a new approach was applied to design and develop a viscoelastic ankle-foot prosthesis. The aim was to replicate the intact ankle moment-angle loop in the normal walking speed. The moment-angle loop of intact ankle was divided into four parts, and the appropriate models including two viscoelastic units of spring-damper mechanism were considered to replicate the passive ankle dynamics. The developed prototype was then tested on a healthy subject with the amputee gait simulator. The result showed that prosthetic ankle moment-angle loop was similar to that of intact ankle with the distinct four periods. The findings suggest that the prototype successfully provided the human ankle passive dynamics. Therefore, the viscoelastic units could imitate the four periods of a normal gait. The novel viscoelastic foot prosthesis could provide natural ankle dynamics in a gait cycle. Applying simple but biomechanical approach is suggested in conception of new designs for prosthetic ankle-foot mechanisms. © The International Society for Prosthetics and Orthotics 2014.

Seasonal Patterns of Melatonin, Cortisol, and Progesterone Secretion in Female Lambs Raised Beneath a 500-kV Transmission Line.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Jack M.

Although several kinds of biological effects of electric and magnetic fields have been reported from laboratory studies, few have been independently replicated. When this study was being planned, the suppression of nighttime melatonin in rodents was thought to represent one of the strongest known effects of these fields. The effect had been replicated by a single laboratory for 60-Hz electric fields, and by multiple laboratories for d-c magnetic fields. The primary objective of this study was to determine whether the effect of electric and magnetic fields on melatonin would also occur in sheep exposed to a high voltage transmission line.more » The specific hypothesis tested by this experiment was as follows: The electrical environment produced by a 60-Hz, 500-kV transmission line causes a depression in nocturnal melatonin in chronically exposed female lambs. This may mimic effects of pinealectomy or constant long-day photoperiods, thus delaying the onset of reproductive cycles. Results of the study do not provide evidence to support the hypothesis. Melatonin concentrations in the sheep exposed to the transmission line showed the normal pattern of low daytime and high nighttime serum levels. As compared to the control group, there were no statistically significant group differences in the mean amplitude, phase, or duration of the nighttime melatonin elevation.« less

Serine 192 in the tiny RS repeat of the adenoviral L4-33K splicing enhancer protein is essential for function and reorganization of the protein to the periphery of viral replication centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oestberg, Sara, E-mail: sara.ostberg@imbim.uu.se; Toermaenen Persson, Heidi, E-mail: heidi.tormanen.persson@imbim.uu.se; Akusjaervi, Goeran, E-mail: goran.akusjarvi@imbim.uu.se

2012-11-25

The adenovirus L4-33K protein is a key regulator involved in the temporal shift from early to late pattern of mRNA expression from the adenovirus major late transcription unit. L4-33K is a virus-encoded alternative splicing factor, which enhances processing of 3 Prime splice sites with a weak sequence context. Here we show that L4-33K expressed from a plasmid is localized at the nuclear margin of uninfected cells. During an infection L4-33K is relocalized to the periphery of E2A-72K containing viral replication centers. We also show that serine 192 in the tiny RS repeat of the conserved carboxy-terminus of L4-33K, which ismore » critical for the splicing enhancer function of L4-33K, is necessary for the nuclear localization and redistribution of the protein to viral replication sites. Collectively, our results show a good correlation between the activity of L4-33K as a splicing enhancer protein and its localization to the periphery of viral replication centers.« less

Replication, pathogenicity, shedding, and transmission of Zaire ebolavirus in pigs.

PubMed

Kobinger, Gary P; Leung, Anders; Neufeld, James; Richardson, Jason S; Falzarano, Darryl; Smith, Greg; Tierney, Kevin; Patel, Ami; Weingartl, Hana M

2011-07-15

(See the editorial commentary by Bausch, on pages 179-81.) Reston ebolavirus was recently detected in pigs in the Philippines. Specific antibodies were found in pig farmers, indicating exposure to the virus. This important observation raises the possibility that pigs may be susceptible to Ebola virus infection, including from other species, such as Zaire ebolavirus (ZEBOV), and can transmit to other susceptible hosts. This study investigated whether ZEBOV, a species commonly reemerging in central Africa, can replicate and induce disease in pigs and can be transmitted to naive animals. Domesticated Landrace pigs were challenged through mucosal exposure with a total of 1 ×10(6) plaque-forming units of ZEBOV and monitored for virus replication, shedding, and pathogenesis. Using similar conditions, virus transmission from infected to naive animals was evaluated in a second set of pigs. Following mucosal exposure, pigs replicated ZEBOV to high titers (reaching 10(7) median tissue culture infective doses/mL), mainly in the respiratory tract, and developed severe lung pathology. Shedding from the oronasal mucosa was detected for up to 14 days after infection, and transmission was confirmed in all naive pigs cohabiting with inoculated animals. These results shed light on the susceptibility of pigs to ZEBOV infection and identify an unexpected site of virus amplification and shedding linked to transmission of infectious virus.

Single-Case Design Research: Building the Evidence-Base in the Field of Education of Deaf and Hard of Hearing Students

ERIC Educational Resources Information Center

Cannon, Joanna E.; Guardino, Caroline; Antia, Shirin D.; Luckner, John L.

2015-01-01

The field of education of deaf and hard of hearing (DHH) students has a paucity of evidence-based practices (EBPs) to guide instruction. The authors discussed how the research methodology of single-case design (SCD) can be used to build EBPs through direct and systematic replication of studies. An overview of SCD research methods is presented,…

Preplanting Treatments and Natural Invasion of Tree Species Onto Former Agricultural Fields at the Tensas River National Wildlife Refuge, Louisiana

Treesearch

John W. McCoy; Bobby D. Keeland; Brian Roy Lockhart; Thomas Dean

2002-01-01

As part of a study of oak planting techniques for bottomland hardwood afforestation we examined the natural invasion of woody species onto former agricultural fields at Tensas River National Wildlife Refuge. Three replications of 14 treatments were established as 0.4 hectare (1 acre) plots in a complete randomized block design. Combinations of these treatments were...

Evaluation of the 3D BacT/ALERT automated culture system for the detection of microbial contamination of platelet concentrates.

PubMed

McDonald, C P; Rogers, A; Cox, M; Smith, R; Roy, A; Robbins, S; Hartley, S; Barbara, J A J; Rothenberg, S; Stutzman, L; Widders, G

2002-10-01

Bacterial transmission remains the major component of morbidity and mortality associated with transfusion-transmitted infections. Platelet concentrates are the most common cause of bacterial transmission. The BacT/ALERT 3D automated blood culture system has the potential to screen platelet concentrates for the presence of bacteria. Evaluation of this system was performed by spiking day 2 apheresis platelet units with individual bacterial isolates at final concentrations of 10 and 100 colony-forming units (cfu) mL-1. Fifteen organisms were used which had been cited in platelet transmission and monitoring studies. BacT/ALERT times to detection were compared with thioglycollate broth cultures, and the performance of five types of BacT/ALERT culture bottles was evaluated. Sampling was performed immediately after the inoculation of the units, and 10 replicates were performed per organism concentration for each of the five types of BacT/ALERT bottles. The mean times for the detection of these 15 organisms by BacT/ALERT, with the exception of Propionibacterium acnes, ranged from 9.1 to 48.1 h (all 10 replicates were positive). In comparison, the time range found using thioglycollate was 12.0-32.3 h (all 10 replicates were positive). P. acnes' BacT/ALERT mean detection times ranged from 89.0 to 177.6 h compared with 75.6-86.4 h for the thioglycollate broth. BacT/ALERT, with the exception of P. acnes, which has dubious clinical significance, gave equivalent or shorter detection times when compared with the thioglycollate broth system. The BacT/ALERT system detected a range of organisms at levels of 10 and 100 cfu mL-1. This study validates the BacT/ALERT microbial detection system for screening platelets. Currently, the system is the only practically viable option available for routinely screening platelet concentrates to prevent bacterial transmission.

A field experiment demonstrating plant life-history evolution and its eco-evolutionary feedback to seed predator populations.

PubMed

Agrawal, Anurag A; Johnson, Marc T J; Hastings, Amy P; Maron, John L

2013-05-01

The extent to which evolutionary change occurs in a predictable manner under field conditions and how evolutionary changes feed back to influence ecological dynamics are fundamental, yet unresolved, questions. To address these issues, we established eight replicate populations of native common evening primrose (Oenothera biennis). Each population was planted with 18 genotypes in identical frequency. By tracking genotype frequencies with microsatellite DNA markers over the subsequent three years (up to three generations, ≈5,000 genotyped plants), we show rapid and consistent evolution of two heritable plant life-history traits (shorter life span and later flowering time). This rapid evolution was only partially the result of differential seed production; genotypic variation in seed germination also contributed to the observed evolutionary response. Since evening primrose genotypes exhibited heritable variation for resistance to insect herbivores, which was related to flowering time, we predicted that evolutionary changes in genotype frequencies would feed back to influence populations of a seed predator moth that specializes on O. biennis. By the conclusion of the experiment, variation in the genotypic composition among our eight replicate field populations was highly predictive of moth abundance. These results demonstrate how rapid evolution in field populations of a native plant can influence ecological interactions.

Nanoimprint wafer and mask tool progress and status for high volume semiconductor manufacturing

NASA Astrophysics Data System (ADS)

Matsuoka, Yoichi; Seki, Junichi; Nakayama, Takahiro; Nakagawa, Kazuki; Azuma, Hisanobu; Yamamoto, Kiyohito; Sato, Chiaki; Sakai, Fumio; Takabayashi, Yukio; Aghili, Ali; Mizuno, Makoto; Choi, Jin; Jones, Chris E.

2016-10-01

Imprint lithography has been shown to be an effective technique for replication of nano-scale features. Jet and Flash* Imprint Lithography (J-FIL*) involves the field-by-field deposition and exposure of a low viscosity resist deposited by jetting technology onto the substrate. The patterned mask is lowered into the fluid which then quickly flows into the relief patterns in the mask by capillary action. Following this filling step, the resist is crosslinked under UV radiation, and then the mask is removed, leaving a patterned resist on the substrate. There are many criteria that determine whether a particular technology is ready for wafer manufacturing. Defectivity and mask life play a significant role relative to meeting the cost of ownership (CoO) requirements in the production of semiconductor devices. Hard particles on a wafer or mask create the possibility of inducing a permanent defect on the mask that can impact device yield and mask life. By using material methods to reduce particle shedding and by introducing an air curtain system, the lifetime of both the master mask and the replica mask can be extended. In this work, we report results that demonstrate a path towards achieving mask lifetimes of better than 1000 wafers. On the mask side, a new replication tool, the FPA-1100 NR2 is introduced. Mask replication is required for nanoimprint lithography (NIL), and criteria that are crucial to the success of a replication platform include both particle control, resolution and image placement accuracy. In this paper we discuss the progress made in both feature resolution and in meeting the image placement specification for replica masks.

eDNAoccupancy: An R package for multi-scale occupancy modeling of environmental DNA data

USGS Publications Warehouse

Dorazio, Robert; Erickson, Richard A.

2017-01-01

In this article we describe eDNAoccupancy, an R package for fitting Bayesian, multi-scale occupancy models. These models are appropriate for occupancy surveys that include three, nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit, and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). eDNAoccupancy allows users to specify and fit multi-scale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model-selection criteria. We illustrate these features by analyzing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species.

The (non-)replicability of regulatory resource depletion: A field report employing non-invasive brain stimulation

PubMed Central

Martijn, Carolien; Alberts, Hugo J. E. M.; Thomson, Alix C.; David, Bastian; Kessler, Daniel

2017-01-01

Cognitive effort and self-control are exhausting. Although evidence is ambiguous, behavioural studies have repeatedly suggested that control-demanding tasks seem to deplete a limited cache of self-regulatory resources leading to performance degradations and fatigue. While resource depletion has indirectly been associated with a decline in right prefrontal cortex capacity, its precise neural underpinnings have not yet been revealed. This study consisted of two independent experiments, which set out to investigate the causal role of the right dorsolateral prefrontal cortex (DLPFC) in a classic dual phase depletion paradigm employing non-invasive brain stimulation. In Experiment 1 we demonstrated a general depletion effect, which was significantly eliminated by anodal transcranial Direct Current Stimulation to the right DLPFC. In Experiment 2, however, we failed to replicate the basic psychological depletion effect within a second independent sample. The dissimilar results are discussed in the context of the current ‘replication crisis’ and suggestions for future studies are offered. While our current results do not allow us to firmly argue for or against the existence of resource depletion, we outline why it is crucial to further clarify which specific external and internal circumstances lead to limited replicability of the described effect. We showcase and discuss the current inter-lab replication problem based on two independent samples tested within one research group (intra-lab). PMID:28362843

Immunogenic HSV-mediated oncolysis shapes the antitumor immune response and contributes to therapeutic efficacy.

PubMed

Workenhe, Samuel T; Simmons, Graydon; Pol, Jonathan G; Lichty, Brian D; Halford, William P; Mossman, Karen L

2014-01-01

Within the oncolytic virus field, the extent of virus replication that is essential for immune stimulation to control tumor growth remains unresolved. Using infected cell protein 0 (ICP0)-defective oncolytic Herpes simplex virus type 1 (HSV-1) and HSV-2 viruses (dICP0 and dNLS) that show differences in their in vitro replication and cytotoxicity, we investigated the inherent features of oncolytic HSV viruses that are required for potent antitumor activity. In vitro, the HSV-2 vectors showed rapid cytotoxicity despite lower viral burst sizes compared to HSV-1 vectors. In vivo, although both of the dICP0 vectors initially replicated to a similar level, HSV-1 dICP0 was rapidly cleared from the tumors. In spite of this rapid clearance, HSV-1 dICP0 treatment conferred significant survival benefit. HSV-1 dICP0-treated tumors showed significantly higher levels of danger-associated molecular patterns that correlated with higher numbers of antigen-presenting cells within the tumor and increased antigen-specific CD8+ T-cell levels in the peripheral blood. This study suggests that, at least in the context of oncolytic HSV, the initial stages of immunogenic virus replication leading to activation of antitumor immunity are more important than persistence of a replicating virus within the tumor. This knowledge provides important insight for the design of therapeutically successful oncolytic viruses.

SUMO1 depletion prevents lipid droplet accumulation and HCV replication.

PubMed

Akil, Abdellah; Wedeh, Ghaith; Zahid Mustafa, Mohammad; Gassama-Diagne, Ama

2016-01-01

Infection by hepatitis C virus (HCV) is a major public-health problem. Chronic infection often leads to cirrhosis, steatosis, and hepatocellular carcinoma. The life cycle of HCV depends on the host cell machinery and involves intimate interaction between viral and host proteins. However, the role of host proteins in the life cycle of HCV remains poorly understood. Here, we identify the small ubiquitin-related modifier (SUMO1) as a key host factor required for HCV replication. We performed a series of cell biology and biochemistry experiments using the HCV JFH-1 (Japanese fulminate hepatitis 1) genotype 2a strain, which produces infectious particles and recapitulates all the steps of the HCV life cycle. We observed that SUMO1 is upregulated in Huh7.5 infected cells. Reciprocally, SUMO1 was found to regulate the expression of viral core protein. Moreover, knockdown of SUMO1 using specific siRNA influenced the accumulation of lipid droplets and reduced HCV replication as measured by qRT-PCR. Thus, we identify SUMO1 as a key host factor required for HCV replication. To our knowledge, this is the first report showing that SUMO1 regulates lipid droplets in the context of viral infection. Our report provides a meaningful insight into how HCV replicates and interacts with host proteins and is of significant importance for the field of HCV and RNA viruses.

Groundwater-quality data for the Sierra Nevada study unit, 2008: Results from the California GAMA program

USGS Publications Warehouse

Shelton, Jennifer L.; Fram, Miranda S.; Munday, Cathy M.; Belitz, Kenneth

2010-01-01

Groundwater quality in the approximately 25,500-square-mile Sierra Nevada study unit was investigated in June through October 2008, as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basin Project is being conducted by the U.S. Geological Survey (USGS) in cooperation with the California State Water Resources Control Board (SWRCB). The Sierra Nevada study was designed to provide statistically robust assessments of untreated groundwater quality within the primary aquifer systems in the study unit, and to facilitate statistically consistent comparisons of groundwater quality throughout California. The primary aquifer systems (hereinafter, primary aquifers) are defined by the depth of the screened or open intervals of the wells listed in the California Department of Public Health (CDPH) database of wells used for public and community drinking-water supplies. The quality of groundwater in shallower or deeper water-bearing zones may differ from that in the primary aquifers; shallow groundwater may be more vulnerable to contamination from the surface. In the Sierra Nevada study unit, groundwater samples were collected from 84 wells (and springs) in Lassen, Plumas, Butte, Sierra, Yuba, Nevada, Placer, El Dorado, Amador, Alpine, Calaveras, Tuolumne, Madera, Mariposa, Fresno, Inyo, Tulare, and Kern Counties. The wells were selected on two overlapping networks by using a spatially-distributed, randomized, grid-based approach. The primary grid-well network consisted of 30 wells, one well per grid cell in the study unit, and was designed to provide statistical representation of groundwater quality throughout the entire study unit. The lithologic grid-well network is a secondary grid that consisted of the wells in the primary grid-well network plus 53 additional wells and was designed to provide statistical representation of groundwater quality in each of the four major lithologic units in the Sierra Nevada study unit: granitic, metamorphic, sedimentary, and volcanic rocks. One natural spring that is not used for drinking water was sampled for comparison with a nearby primary grid well in the same cell. Groundwater samples were analyzed for organic constituents (volatile organic compounds [VOC], pesticides and pesticide degradates, and pharmaceutical compounds), constituents of special interest (N-nitrosodimethylamine [NDMA] and perchlorate), naturally occurring inorganic constituents (nutrients, major ions, total dissolved solids, and trace elements), and radioactive constituents (radium isotopes, radon-222, gross alpha and gross beta particle activities, and uranium isotopes). Naturally occurring isotopes and geochemical tracers (stable isotopes of hydrogen and oxygen in water, stable isotopes of carbon, carbon-14, strontium isotopes, and tritium), and dissolved noble gases also were measured to help identify the sources and ages of the sampled groundwater. Three types of quality-control samples (blanks, replicates, and samples for matrix spikes) each were collected at approximately 10 percent of the wells sampled for each analysis, and the results for these samples were used to evaluate the quality of the data for the groundwater samples. Field blanks rarely contained detectable concentrations of any constituent, suggesting that contamination from sample collection, handling, and analytical procedures was not a significant source of bias in the data for the groundwater samples. Differences between replicate samples were within acceptable ranges, with few exceptions. Matrix-spike recoveries were within acceptable ranges for most compounds. This study did not attempt to evaluate the quality of water delivered to consumers; after withdrawal from the ground, groundwater typically is treated, disinfected, or blended with other waters to maintain water quality. Regulatory benchmarks apply to finished drinking water that is served to the consumer, not to untre

Simulated workplace neutron fields

NASA Astrophysics Data System (ADS)

Lacoste, V.; Taylor, G.; Röttger, S.

2011-12-01

The use of simulated workplace neutron fields, which aim at replicating radiation fields at practical workplaces, is an alternative solution for the calibration of neutron dosemeters. They offer more appropriate calibration coefficients when the mean fluence-to-dose equivalent conversion coefficients of the simulated and practical fields are comparable. Intensive Monte Carlo modelling work has become quite indispensable for the design and/or the characterization of the produced mixed neutron/photon fields, and the use of Bonner sphere systems and proton recoil spectrometers is also mandatory for a reliable experimental determination of the neutron fluence energy distribution over the whole energy range. The establishment of a calibration capability with a simulated workplace neutron field is not an easy task; to date only few facilities are available as standard calibration fields.

[Design method of convex master gratings for replicating flat-field concave gratings].

PubMed

Zhou, Qian; Li, Li-Feng

2009-08-01

Flat-field concave diffraction grating is the key device of a portable grating spectrometer with the advantage of integrating dispersion, focusing and flat-field in a single device. It directly determines the quality of a spectrometer. The most important two performances determining the quality of the spectrometer are spectral image quality and diffraction efficiency. The diffraction efficiency of a grating depends mainly on its groove shape. But it has long been a problem to get a uniform predetermined groove shape across the whole concave grating area, because the incident angle of the ion beam is restricted by the curvature of the concave substrate, and this severely limits the diffraction efficiency and restricts the application of concave gratings. The authors present a two-step method for designing convex gratings, which are made holographically with two exposure point sources placed behind a plano-convex transparent glass substrate, to solve this problem. The convex gratings are intended to be used as the master gratings for making aberration-corrected flat-field concave gratings. To achieve high spectral image quality for the replicated concave gratings, the refraction effect at the planar back surface and the extra optical path lengths through the substrate thickness experienced by the two divergent recording beams are considered during optimization. This two-step method combines the optical-path-length function method and the ZEMAX software to complete the optimization with a high success rate and high efficiency. In the first step, the optical-path-length function method is used without considering the refraction effect to get an approximate optimization result. In the second step, the approximate result of the first step is used as the initial value for ZEMAX to complete the optimization including the refraction effect. An example of design problem was considered. The simulation results of ZEMAX proved that the spectral image quality of a replicated concave grating is comparable with that of a directly recorded concave grating.

Characterization of Novel Calorimeters in the Annular Core Research Reactor

NASA Astrophysics Data System (ADS)

Hehr, Brian D.; Parma, Edward J.; Peters, Curtis D.; Naranjo, Gerald E.; Luker, S. Michael

2016-02-01

A series of pulsed irradiation experiments have been performed in the central cavity of Sandia National Laboratories' Annular Core Research Reactor (ACRR) to characterize the responses of a set of elemental calorimeter materials including Si, Zr, Sn, Ta, W, and Bi. Of particular interest was the perturbing effect of the calorimeter itself on the ambient radiation field - a potential concern in dosimetry applications. By placing the calorimeter package into a neutron-thermalizing lead/polyethylene (LP) bucket and irradiating both with and without a cadmium wrapper, it was demonstrated that prompt capture gammas generated inside the calorimeters can be a significant contributor to the measured dose in the active disc region. An MCNP model of the experimental setup was shown to replicate measured dose responses to within 10%. The internal (n,γ) contribution was found to constitute as much as 50% of the response inside the LP bucket and up to 20% inside the nominal (unmodified) cavity environment, with Ta and W exhibiting the largest enhancement due to their sizable (n,γ) cross sections. Capture reactions in non-disc components of the calorimeter were estimated to be responsible for up to a few percent of the measured response. This work was supported by the United States Department of Energy under Contract DE-AC04-94AL85000. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy.

SOYBEAN.APHID.LH.2009

USDA-ARS?s Scientific Manuscript database

Expression of soybean aphid (SA) resistance was characterized among 496 soybean lines in a twice-replicated field-plot test at the Eastern South Dakota Soil and Water Research Farm near Brookings, SD, in 2009. Natural infestations of SA occurred but were supplemented by placing individual stems of ...

Design of experiments on 135 cloned poplar trees to map environmental influence in greenhouse.

PubMed

Pinto, Rui Climaco; Stenlund, Hans; Hertzberg, Magnus; Lundstedt, Torbjörn; Johansson, Erik; Trygg, Johan

2011-01-31

To find and ascertain phenotypic differences, minimal variation between biological replicates is always desired. Variation between the replicates can originate from genetic transformation but also from environmental effects in the greenhouse. Design of experiments (DoE) has been used in field trials for many years and proven its value but is underused within functional genomics including greenhouse experiments. We propose a strategy to estimate the effect of environmental factors with the ultimate goal of minimizing variation between biological replicates, based on DoE. DoE can be analyzed in many ways. We present a graphical solution together with solutions based on classical statistics as well as the newly developed OPLS methodology. In this study, we used DoE to evaluate the influence of plant specific factors (plant size, shoot type, plant quality, and amount of fertilizer) and rotation of plant positions on height and section area of 135 cloned wild type poplar trees grown in the greenhouse. Statistical analysis revealed that plant position was the main contributor to variability among biological replicates and applying a plant rotation scheme could reduce this variation. Copyright © 2010 Elsevier B.V. All rights reserved.

A Longitudinal Examination of the Relationship of Selected Institutional Variables to Community College Foundation Revenue

ERIC Educational Resources Information Center

Patterson, Van; Justice, Madeline; Scott, Joyce A.

2012-01-01

The primary purpose of this study was to examine the annual revenue received by United States public Community College Foundations from 2008-2009 in relation to selected variables associated in the literature with successful foundation performance. This study also collected longitudinal data by replicating and expanding upon a similar study…

A Longitudinal Examination of the Relationship of Selected Institutional Variables to Community College Foundation Revenue

ERIC Educational Resources Information Center

Patterson, Vandiver L.

2011-01-01

The primary purpose of this study was to examine the annual revenue received by United States public community college foundations from 2008-2009 in relation to selected variables associated in the literature with successful foundation performance. This study also attempted to collect longitudinal data by replicating and expanding upon a similar…

When Dollars Follow Students: The Political Viability, Equity and Workability of Weighted Funding Formulas

ERIC Educational Resources Information Center

Deroche, Timothy R.; Cooper, Bruce S.; Ouchi, William G.

2004-01-01

For more than a decade, education reformers have admired the achievements of the Edmonton Public Schools in Canada, and school districts across the United States have attempted to replicate Edmonton's success with school-site decision making. However, most districts have stopped short of implementing one policy that is central to Edmonton's…

Enculturation Effects in Music Cognition: The Role of Age and Music Complexity

ERIC Educational Resources Information Center

Morrison, Steven J.; Demorest, Steven M.; Stambaugh, Laura A.

2008-01-01

The authors replicate and extend findings from previous studies of music enculturation by comparing music memory performance of children to that of adults when listening to culturally familiar and unfamiliar music. Forty-three children and 50 adults, all born and raised in the United States, completed a music memory test comprising unfamiliar…

Ethical Issues and Codes of Ethics: Views of Adult Education Practitioners in Canada and the United States.

ERIC Educational Resources Information Center

Gordon, Wanda; Sork, Thomas J.

2001-01-01

Replicating an Indiana study, 261 responses from British Columbia adult educators revealed a high degree of support for codes of ethics and identified ethical dilemmas in practice. Half currently operated under a code. Responses to whether codes should have a regulatory function were mixed. (Contains 44 references.) (SK)

Reducing Hispanic Teenage Pregnancy and Family Poverty: A Replication Guide. Final Version.

ERIC Educational Resources Information Center

Perez, Sonia M.; Duany, Luis A.

This guide was designed to help Hispanic American community-based organizations develop and establish a teenage pregnancy prevention or teenage parenting program for Hispanic American adolescents. The guide does not assume prior knowledge of the scope of the teenage pregnancy problem in the United States, but it does underscore the critical role…

Trends in Residential Services for Mentally Retarded People: 1977-1982. Brief #23.

ERIC Educational Resources Information Center

Hill, B. K.; Lakin, K. C.

In 1977 a survey was conducted of all state-licensed, state-contracted, and state-operated residential facilities serving mentally retarded people in the United States. The survey was replicated in 1982 and this report summarizes and compares the results of the two surveys. Results indicate that the overall size of the residential service system…

Sight-Reading Requirements at Concert Band Festivals: A National Survey

ERIC Educational Resources Information Center

Paul, Timothy A.

2010-01-01

This study, a replication and extension of work by Norris (2004), examined sight-reading requirements at middle and high school large-group band festivals across the United States. As in the earlier investigation, answers to the following questions were solicited from all 50 states: (1) Are there ratings-based large-group band festivals? (2) Is…

Further Evidence That Creativity and Innovation Are Inhibited by Conservative Thinking: Analyses of the 2016 Presidential Election

ERIC Educational Resources Information Center

Runco, Mark A.; Acar, Selcuk; Cayirdag, Nur

2017-01-01

The investigation replicated and extended previous research showing a negative relationship between conservatism and creative accomplishment. Conservatism was estimated, as in previous research, from voting patterns. The voting data used here were from the 2016 US Presidential election. The number of patents granted per county in the United States…

Career Services at Colleges and Universities: A 30-Year Replication Study

ERIC Educational Resources Information Center

Vinson, Bonita M.; Reardon, Robert C.; Bertoch, Sara C.

2014-01-01

This study examines career planning programs and career services offices at colleges and universities in the United States as viewed by senior student affairs officers (SSAOs). Findings from a 1979 study of career services offices (CSOs) were compared to the current findings. Additionally, new areas of research were examined in order to provide…

Comparison of Rift Valley fever virus and MP-12 replication in domestic livestock and North American wildlife cell lines.

USDA-ARS?s Scientific Manuscript database

Rift Valley fever virus (RVFV) is a mosquito-transmitted pathogen that primarily affects livestock, but can also cause mild to fatal disease in humans. Currently, there is no approved vaccine for use in the United States if it were introduced. Domestic goats, sheep and cattle are susceptible hosts ...

U.S. Elementary and Secondary Schools: Equalizing Opportunity or Replicating the Status Quo?

ERIC Educational Resources Information Center

Rouse, Cecilia Elena; Barrow, Lisa

2006-01-01

Although education pays off handsomely in the United States, children from low-income families attain less education than children from more advantaged families. In this article, Cecilia Elena Rouse and Lisa Barrow investigate why family background is so strongly linked to education. The authors show that family socioeconomic status affects such…

Two Asian highly pathogenic strains of Type 2 PRRSV in United States swine

USDA-ARS?s Scientific Manuscript database

Highly pathogenic PRRSV (HP-PRRSV) has been circulating in Asia for 7 years. rJXwn06 and rSRV07 were rescued from infectious clones of two HP-PRRSV for investigation at the National Animal Disease Center. The clinical disease and viral replication kinetics of HP-PRRSV were compared to prototype stra...

Development and Validation of the Internalized Racial Oppression Scale for Black Individuals

ERIC Educational Resources Information Center

Bailey, Tamba-Kuii M.; Chung, Y. Barry; Williams, Wendi S.; Singh, Anneliese A.; Terrell, Heather K.

2011-01-01

This article describes the development and validation of the Internalized Racial Oppression Scale (IROS) for Black individuals in 2 studies using a total sample of 468 Black college students. The IROS is intended to measure the degree to which racial oppression is internalized and replicated by Black individuals in the United States. An…

BETTER STATISTICS FOR BETTER DECISIONS: REJECTING NULL HYPOTHESES STATISTICAL TESTS IN FAVOR OF REPLICATION STATISTICS

PubMed Central

SANABRIA, FEDERICO; KILLEEN, PETER R.

2008-01-01

Despite being under challenge for the past 50 years, null hypothesis significance testing (NHST) remains dominant in the scientific field for want of viable alternatives. NHST, along with its significance level p, is inadequate for most of the uses to which it is put, a flaw that is of particular interest to educational practitioners who too often must use it to sanctify their research. In this article, we review the failure of NHST and propose prep, the probability of replicating an effect, as a more useful statistic for evaluating research and aiding practical decision making. PMID:19122766

Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

PubMed

Ruhlman, Tracey A; Zhang, Jin; Blazier, John C; Sabir, Jamal S M; Jansen, Robert K

2017-04-01

There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats. © 2017 Botanical Society of America.

Family environment and the malleability of cognitive ability: A Swedish national home-reared and adopted-away cosibling control study

PubMed Central

Kendler, Kenneth S.; Turkheimer, Eric; Ohlsson, Henrik; Sundquist, Jan; Sundquist, Kristina

2015-01-01

Cognitive ability strongly aggregates in families, and prior twin and adoption studies have suggested that this is the result of both genetic and environmental factors. In this study, we used a powerful design—home-reared and adopted-away cosibling controls—to investigate the role of the rearing environment in cognitive ability. We identified, from a complete national Swedish sample of male–male siblings, 436 full-sibships in which at least one member was reared by one or more biological parents and the other by adoptive parents. IQ was measured at age 18–20 as part of the Swedish military service conscription examination. Parental educational level was rated on a 5-point scale. Controlling for clustering of offspring within biological families, the adopted siblings had an IQ 4.41 (SE = 0.75) points higher than their nonadopted siblings. Each additional unit of rearing parental education was associated with 1.71 (SE = 0.44) units of IQ. We replicated these results in 2,341 male–male half-sibships, in which, controlling for clustering within families, adoption was associated with a gain of IQ of 3.18 (SE = 0.34) points. Each additional unit of rearing parental education was associated with 1.94 (SE = 0.18) IQ units. Using full- and half-sibling sets matched for genetic background, we found replicated evidence that (i) rearing environment affects IQ measured in late adolescence, and (ii) a portion of the IQ of adopted siblings could be explained by the educational level of their adoptive parents. PMID:25831538

Effect of superdosing phytase on productive performance and egg quality in laying hens.

PubMed

Kim, Jong Hyuk; Pitargue, Franco Martinez; Jung, Hyunjung; Han, Gi Ppeum; Choi, Hyeon Seok; Kil, Dong Yong

2017-07-01

An experiment was conducted to determine the effect of superdosing phytase on productive performance and egg quality in laying hens. A total of 200 42-wk-old Hy-Line Brown laying hens were allotted into 1 of 5 dietary treatments with 5 replicates consisting of 8 hens per replicate. The positive control (PC) and negative control diets (NC) were prepared based on the recommended P levels in layer diets. Supplemental phytase was added to the negative control diet at 10,000 (SD10), 20,000 (SD20), or 30,000 (SD30) fytase units (FTU)/kg. Productive performance was summarized for 6 weeks from 42 weeks to 47 weeks of age. Egg quality was assessed from 4 eggs per replicate randomly collected at the conclusion of the experiment. The SD20 treatment had greater (p<0.05) hen-day egg production than PC, NC, and SD10 treatment groups. There was no difference in hen-day egg production between SD20 and SD30 treatment groups. However, SD30 treatment had greater (p<0.05) hen-day egg production than PC treatment, but showed no difference in hen-day egg production as compared to NC and SD10 treatment groups. However, egg weight, egg mass, feed intake, and feed conversion ratio were not affected by dietary treatments. Egg quality including eggshell strength, eggshell color, egg yolk color, and haugh unit was not influenced by dietary treatments. Superdosing level of 20,000 FTU/kg phytase in diets has a positive effect on egg production rate, but no beneficial effect on egg quality in laying hens.

Characterization of the Campylobacter jejuni cryptic plasmid pTIW94 recovered from wild birds in the southeastern United States.

PubMed

Hiett, Kelli L; Rothrock, Michael J; Seal, Bruce S

2013-09-01

The complete nucleotide sequence was determined for a cryptic plasmid, pTIW94, recovered from several Campylobacter jejuni isolates from wild birds in the southeastern United States. pTIW94 is a circular molecule of 3860 nucleotides, with a G+C content (31.0%) similar to that of many Campylobacter spp. genomes. A typical origin of replication, with iteron sequences, was identified upstream of DNA sequences that demonstrated similarity to replication initiation proteins. A total of five open reading frames (ORFs) were identified; two of the five ORFs demonstrated significant similarity to plasmid pCC2228-2 found within Campylobacter coli. These two ORFs were similar to essential replication proteins RepA (100%; 26/26 aa identity) and RepB (95%; 327/346 aa identity). A third identified ORF demonstrated significant similarity (99%; 421/424 aa identity) to the MOB protein from C. coli 67-8, originally recovered from swine. The other two identified ORFs were either similar to hypothetical proteins from other Campylobacter spp., or exhibited no significant similarity to any DNA or protein sequence in the GenBank database. Promoter regions (-35 and -10 signal sites), ribosomal binding sites upstream of ORFs, and stem-loop structures were also identified within the plasmid. These results demonstrate that pTIW94 represents a previously un-reported small cryptic plasmid with unique sequences as well as highly similar sequences to other small plasmids found within Campylobacter spp., and that this cryptic plasmid is present among Campylobacter spp. recovered from different genera of wild birds. Copyright © 2013. Published by Elsevier Inc.

Cure-WISE: HETDEX Data Reduction with Astro-WISE

NASA Astrophysics Data System (ADS)

Snigula, J. M.; Drory, N.; Fabricius, M.; Landriau, M.; Montesano, F.; Hill, G. J.; Gebhardt, K.; Cornell, M. E.

2014-05-01

The Hobby-Eberly Telescope Dark Energy Experiment (HETDEX, Hill et al. 2012b) is a blind spectroscopic survey to map the evolution of dark energy using Lyman-alpha emitting galaxies at redshifts 1.9< ɀ <3.5 as tracers. The survey will use an array of 75 integral field spectrographs called the Visible Integral field Replicable Unit (IFU) Spectrograph (VIRUS, Hill et al. 2012c). The 10m HET (Ramsey et al. 1998) currently receives a wide-field upgrade (Hill et al. 2012a) to accomodate the spectrographs and to provide the needed field of view. Over the projected five year run of the survey we expect to obtain approximately 170 GB of data each night. For the data reduction we developed the Cure pipeline, to automatically find and calibrate the observed spectra, subtract the sky background, and detect and classify different types of sources. Cure employs rigorous statistical methods and complete pixel-level error propagation throughout the reduction process to ensure Poisson-limited performance and meaningful significance values. To automate the reduction of the whole dataset we implemented the Cure pipeline in the Astro-WISE framework. This integration provides for HETDEX a database backend with complete dependency tracking of the various reduction steps, automated checks, and a searchable interface to the detected sources and user management. It can be used to create various web interfaces for data access and quality control. Astro-WISE allows us to reduce the data from all the IFUs in parallel on a compute cluster. This cluster allows us to reduce the observed data in quasi real time and still have excess capacity for rerunning parts of the reduction. Finally, the Astro-WISE interface will be used to provide access to reduced data products to the general community.

Design and Field Procedures in the US National Comorbidity Survey Replication Adolescent Supplement (NCS-A)

PubMed Central

Kessler, Ronald C.; Avenevoli, Shelli; Costello, E. Jane; Green, Jennifer Greif; Gruber, Michael J.; Heeringa, Steven; Merikangas, Kathleen R.; Pennell, Beth-Ellen; Sampson, Nancy A.; Zaslavsky, Alan M.

2009-01-01

An overview is presented of the design and field procedures of the US National Comorbidity Survey Replication Adolescent Supplement (NCS-A), a US face-to-face household survey of the prevalence and correlates of DSM-IV mental disorders. The survey was based on a dual-frame design that included 904 adolescent residents of the households that participated in the US National Comorbidity Survey Replication (85.9% response rate) and 9,244 adolescent students selected from a nationally representative sample of 320 schools (74.7% response rate). After expositing the logic of dual-frame designs, comparisons are presented of sample and population distributions on Census socio-demographic variables and, in the school sample, school characteristics. These document only minor differences between the samples and the population. The results of statistical analysis of the bias-efficiency trade-off in weight trimming are then presented. These show that modest trimming meaningfully reduces mean squared error. Analysis of comparative sample efficiency shows that the household sample is more efficient than the school sample, leading to the household sample getting a higher weight relative to its size in the consolidated sample relative to the school sample. Taken together, these results show that the NCS-A is an efficient sample of the target population with good representativeness on a range of socio-demographic and geographic variables. PMID:19507169

Antiviral properties of deazaadenine nucleoside derivatives.

PubMed

Vittori, S; Dal Ben, D; Lambertucci, C; Marucci, G; Volpini, R; Cristalli, G

2006-01-01

Viral infections have menaced human beings since time immemorial, and even today new viral strains that cause lethal diseases are being discovered with alarming frequency. One major example is HIV, the etiological agent of AIDS, which spread up in the last two decades. Very recently, other virus based diseases such as avian flu have spread fear around the world, and hemorrhagic fevers from central Africa serious threaten human health because of their very deadly effects. New antiviral agents are still greatly needed to counter these menaces. Many scientists are involved in this field of research, and many of the recently discovered effective antiviral compounds are nucleoside analogues. Among those derivatives, deazapurine nucleoside analogues have demonstrated potent inhibitory effect of viral replication. This review reports on recently generated data from preparing and testing deazapurine nucleoside derivatives as inhibitors in virus replication systems. Although most of the reported data have been produced in antiHIV, antiHCMV, and antiHSV biological testing, very recently other new important fields of application have been discovered, all in topical subjects of strong interest. In fact, deazapurine nucleosides have been found to be active as chemotherapeutics for some veterinary systemic viral infections, for which no antiviral drugs are licensed yet. Furthermore, they demonstrated efficacy in the inhibition of Hepatitis C virus replication. Finally, these compounds showed high potency as virucides against Ebola Virus, curing Ebola infected mice with a single dose administration.

MicroRNA reduction of neuronal West Nile virus replication attenuates and affords a protective immune response in mice

PubMed Central

Brostoff, Terza; Pesavento, Patricia A.; Barker, Christopher M.; Kenney, Joan L.; Dietrich, Elizabeth A.; Duggal, Nisha K.; Bosco-Lauth, Angela M.; Brault, Aaron C.

2017-01-01

West Nile virus (WNV) is an important agent of human encephalitis that has quickly become endemic across much of the United States since its identification in North America in 1999. While the majority (~75%) of infections are subclinical, neurologic disease can occur in a subset of cases, with outcomes including permanent neurologic damage and death. Currently, there are no WNV vaccines approved for use in humans. This study introduces a novel vaccine platform for WNV to reduce viral replication in the central nervous system while maintaining peripheral replication to elicit strong neutralizing antibody titers. Vaccine candidates were engineered to incorporate microRNA (miRNA) target sequences for a cognate miRNA expressed only in neurons, allowing the host miRNAs to target viral transcription through endogenous RNA silencing. To maintain stability, these targets were incorporated in multiple locations within the 3′-untranslated region, flanking sequences essential for viral replication without affecting the viral open reading frame. All candidates replicated comparably to wild type WNV in vitro within cells that did not express the cognate miRNA. Insertional control viruses were also capable of neuroinvasion and neurovirulence in vivo in CD-1 mice. Vaccine viruses were safe at all doses tested and did not demonstrate mutations associated with a reversion to virulence when serially passaged in mice. All vaccine constructs were protective from lethal challenge in mice, producing 93–100% protection at the highest dose tested. Overall, this is a safe and effective attenuation strategy with broad potential application for vaccine development. PMID:27637937

MicroRNA reduction of neuronal West Nile virus replication attenuates and affords a protective immune response in mice.

PubMed

Brostoff, Terza; Pesavento, Patricia A; Barker, Christopher M; Kenney, Joan L; Dietrich, Elizabeth A; Duggal, Nisha K; Bosco-Lauth, Angela M; Brault, Aaron C

2016-10-17

West Nile virus (WNV) is an important agent of human encephalitis that has quickly become endemic across much of the United States since its identification in North America in 1999. While the majority (∼75%) of infections are subclinical, neurologic disease can occur in a subset of cases, with outcomes including permanent neurologic damage and death. Currently, there are no WNV vaccines approved for use in humans. This study introduces a novel vaccine platform for WNV to reduce viral replication in the central nervous system while maintaining peripheral replication to elicit strong neutralizing antibody titers. Vaccine candidates were engineered to incorporate microRNA (miRNA) target sequences for a cognate miRNA expressed only in neurons, allowing the host miRNAs to target viral transcription through endogenous RNA silencing. To maintain stability, these targets were incorporated in multiple locations within the 3'-untranslated region, flanking sequences essential for viral replication without affecting the viral open reading frame. All candidates replicated comparably to wild type WNV in vitro within cells that did not express the cognate miRNA. Insertional control viruses were also capable of neuroinvasion and neurovirulence in vivo in CD-1 mice. Vaccine viruses were safe at all doses tested and did not demonstrate mutations associated with a reversion to virulence when serially passaged in mice. All vaccine constructs were protective from lethal challenge in mice, producing 93-100% protection at the highest dose tested. Overall, this is a safe and effective attenuation strategy with broad potential application for vaccine development. Published by Elsevier Ltd.

Further assessment of houseflies (Musca domestica) as vectors for the mechanical transport and transmission of porcine reproductive and respiratory syndrome virus under field conditions.

PubMed

Pitkin, Andrea; Deen, John; Otake, Satoshi; Moon, Roger; Dee, Scott

2009-04-01

The purpose of this study was to evaluate the potential for houseflies (Musca domestica) to mechanically transport and transmit porcine reproductive and respiratory syndrome virus (PRRSV) between pig populations under controlled field conditions. The study employed swine housed in commercial livestock facilities and a release-recapture protocol involving marked (ochre-eyed) houseflies. To assess whether transport of PRRSV by insects occurred, ochre-eyed houseflies were released and collected from a facility housing an experimentally PRRSV-inoculated population of pigs (facility A) and collected from a neighboring facility located 120 m to the northwest that housed a naïve pig population (facility B). All samples were tested for PRRSV RNA by polymerase chain reaction (PCR). To assess transmission between the 2 populations, blood samples were collected from naïve pigs in facility B at designated intervals and tested by PCR. A total of 7 replicates were conducted. During 2 of 7 replicates (1 and 5), PCR-positive ochre-eyed houseflies were recovered in facility B and pigs in this facility became infected with PRRSV. Chi-squared analysis indicated that the presence of PRRSV in an insect sample was significantly (P = 0.0004) associated with infection of facility B pigs. Porcine reproductive and respiratory syndrome virus was not recovered from other reported routes of transmission during the study period, including air, fomites, and personnel. In conclusion, while an insufficient number of replicates were conducted to predict the frequency of the event, houseflies may pose some level of risk for the transport and transmission of PRRSV between pig populations under field conditions.

Further assessment of houseflies (Musca domestica) as vectors for the mechanical transport and transmission of porcine reproductive and respiratory syndrome virus under field conditions

PubMed Central

Pitkin, Andrea; Deen, John; Otake, Satoshi; Moon, Roger; Dee, Scott

2009-01-01

The purpose of this study was to evaluate the potential for houseflies (Musca domestica) to mechanically transport and transmit porcine reproductive and respiratory syndrome virus (PRRSV) between pig populations under controlled field conditions. The study employed swine housed in commercial livestock facilities and a release-recapture protocol involving marked (ochre-eyed) houseflies. To assess whether transport of PRRSV by insects occurred, ochre-eyed houseflies were released and collected from a facility housing an experimentally PRRSV-inoculated population of pigs (facility A) and collected from a neighboring facility located 120 m to the northwest that housed a naïve pig population (facility B). All samples were tested for PRRSV RNA by polymerase chain reaction (PCR). To assess transmission between the 2 populations, blood samples were collected from naïve pigs in facility B at designated intervals and tested by PCR. A total of 7 replicates were conducted. During 2 of 7 replicates (1 and 5), PCR-positive ochre-eyed houseflies were recovered in facility B and pigs in this facility became infected with PRRSV. Chi-squared analysis indicated that the presence of PRRSV in an insect sample was significantly (P = 0.0004) associated with infection of facility B pigs. Porcine reproductive and respiratory syndrome virus was not recovered from other reported routes of transmission during the study period, including air, fomites, and personnel. In conclusion, while an insufficient number of replicates were conducted to predict the frequency of the event, houseflies may pose some level of risk for the transport and transmission of PRRSV between pig populations under field conditions. PMID:19436589

A field test of the effect of spiked ivermectin concentrations on the biodiversity of coprophagous dung insects in Switzerland.

PubMed

Jochmann, Ralf; Lipkow, Erhard; Blanckenhorn, Wolf U

2016-08-01

Veterinary medical product residues can cause severe damage in the dung ecosystem. Depending on the manner of application and the time after treatment, the excreted concentration of a given pharmaceutical varies. The popular anthelmintic drug ivermectin can be applied to livestock in several different ways and is fecally excreted over a period of days to months after application. In a field experiment replicated in summer and autumn, the authors mixed 6 ivermectin concentrations plus a null control into fresh cow dung to assess the reaction of the dung insect community. Taxon richness of the insect dung fauna emerging from the dung, but not Hill diversity ((1) D) or the total number of individuals (abundance), decreased as ivermectin concentration increased. Corresponding declines in the number of emerging insects were found for most larger brachyceran flies and hymenopteran parasitoids, but not for most smaller nematoceran flies or beetles (except Hydrophilidae). Parallel pitfall traps recovered all major dung organism groups that emerged from the experimental dung, although at times in vastly different numbers. Ivermectin generally did not change the attractiveness of dung: differences in emergence therefore reflect differences in survival of coprophagous offspring of colonizing insects. Because sample size was limited to 6 replicates, the authors generally recommend more than 10 (seasonal) replicates and also testing higher concentrations than used in the present study as positive controls in future studies. Results accord with parallel experiments in which the substance was applied and passed through the cow's digestive system. In principle, therefore, the authors' experimental design is suitable for such higher-tier field tests of the response of the entire dung community to pharmaceutical residues, at least for ivermectin. Environ Toxicol Chem 2016;35:1947-1952. © 2015 SETAC. © 2015 SETAC.

A Culturally Responsive Approach to Improving Replication of a Youth Sexual Health Program.

PubMed

Mwaria, Mercy; Chen, ChiaChing; Coppola, Nanci; Maurice, Ingrid; Phifer, Mary

2016-11-01

Youth-serving agencies continually turn to evidence-based interventions that have been empirically assessed for effectiveness in influencing young people's lives, particularly those living in communities with considerable health inequities. Replicating promising evidence-based interventions requires thoughtful adaptation and modification to better fit participants' sociocultural context and to enhance their learning experiences. Due to the restrictive nature of a replication model, adaptations to the intervention curriculum must be minimized during full implementation. Implementers must find innovative ways to ensure content is relevant and engaging to participants without altering core elements of the curriculum. This article describes practical best practice strategies used in implementing a sexual health education program among socioculturally diverse youth in a northeastern city in the United States. The implementing agency applied Richard, Brown and Forde's framework for culturally responsive pedagogy as a heuristic approach to describe the application of implementation practices across three dimensions: institutional, personal, and instructional. The results not only highlight successful culturally responsive practices that enhanced the implementation process but also acknowledge areas in which such practices proved daunting to implement. © 2016 Society for Public Health Education.

5′CAG and 5′CTG Repeats Create Differential Impediment to the Progression of a Minimal Reconstituted T4 Replisome Depending on the Concentration of dNTPs

PubMed Central

Delagoutte, Emmanuelle; Baldacci, Giuseppe

2011-01-01

Instability of repetitive sequences originates from strand misalignment during repair or replicative DNA synthesis. To investigate the activity of reconstituted T4 replisomes across trinucleotide repeats (TNRs) during leading strand DNA synthesis, we developed a method to build replication miniforks containing a TNR unit of defined sequence and length. Each minifork consists of three strands, primer, leading strand template, and lagging strand template with a 5′ single-stranded (ss) tail. Each strand is prepared independently, and the minifork is assembled by hybridization of the three strands. Using these miniforks and a minimal reconstituted T4 replisome, we show that during leading strand DNA synthesis, the dNTP concentration dictates which strand of the structure-forming 5′CAG/5′CTG repeat creates the strongest impediment to the minimal replication complex. We discuss this result in the light of the known fluctuation of dNTP concentration during the cell cycle and cell growth and the known concentration balance among individual dNTPs. PMID:22096622

Copy number determination of genetically-modified hematopoietic stem cells.

PubMed

Schuesler, Todd; Reeves, Lilith; Kalle, Christof von; Grassman, Elke

2009-01-01

Human gene transfer with gammaretroviral, murine leukemia virus (MLV) based vectors has been shown to effectively insert and express transgene sequences at a level of therapeutic benefit. However, there are numerous reports of disruption of the normal cellular processes caused by the viral insertion, even of replication deficient gammaretroviral vectors. Current gammaretroviral and lentiviral vectors do not control the site of insertion into the genome, hence, the possibility of disruption of the target cell genome. Risk related to viral insertions is linked to the number of insertions of the transgene into the cellular DNA, as has been demonstrated for replication competent and replication deficient retroviruses in experiments. At high number of insertions per cell, cell transformation due to vector induced activation of proto-oncogenes is more likely to occur, in particular since more than one transforming event is needed for oncogenesis. Thus, determination of the vector copy number in bulk transduced populations, individual colony forming units, and tissue from the recipient of the transduced cells is an increasingly important safety assay and has become a standard, though not straightforward assay, since the inception of quantitative PCR.

Insect pests and yield potential of vegetable soybean (Endamame) produced in Georgia

USDA-ARS?s Scientific Manuscript database

A series of replicated field experiments was conducted with vegetable soybean (edamame), Glycine max (L.) Merrill, to assess the impacts of cultivars, planting dates, and insecticidal controls on insect pest abundance, crop damage and yield potential. The velvetbean caterpillar, Anticarsia gemmatali...

A Research Agenda for Geospatial Technologies and Learning

ERIC Educational Resources Information Center

Baker, Tom R.; Battersby, Sarah; Bednarz, Sarah W.; Bodzin, Alec M.; Kolvoord, Bob; Moore, Steven; Sinton, Diana; Uttal, David

2015-01-01

Knowledge around geospatial technologies and learning remains sparse, inconsistent, and overly anecdotal. Studies are needed that are better structured; more systematic and replicable; attentive to progress and findings in the cognate fields of science, technology, engineering, and math education; and coordinated for multidisciplinary approaches.…

Groundwater-Quality Data in the South Coast Interior Basins Study Unit, 2008: Results from the California GAMA Program

USGS Publications Warehouse

Mathany, Timothy M.; Kulongoski, Justin T.; Ray, Mary C.; Belitz, Kenneth

2009-01-01

Groundwater quality in the approximately 653-square-mile South Coast Interior Basins (SCI) study unit was investigated from August to December 2008, as part of the Priority Basins Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basins Project was developed in response to Legislative mandates (Supplemental Report of the 1999 Budget Act 1999-00 Fiscal Year; and, the Groundwater-Quality Monitoring Act of 2001 [Sections 10780-10782.3 of the California Water Code, Assembly Bill 599]) to assess and monitor the quality of groundwater used as public supply for municipalities in California, and is being conducted by the U.S. Geological Survey (USGS) in cooperation with the California State Water Resources Control Board (SWRCB). SCI was the 27th study unit to be sampled as part of the GAMA Priority Basins Project. This study was designed to provide a spatially unbiased assessment of the quality of untreated groundwater used for public water supplies within SCI, and to facilitate statistically consistent comparisons of groundwater quality throughout California. Samples were collected from 54 wells within the three study areas [Livermore, Gilroy, and Cuyama] of SCI in Alameda, Santa Clara, San Benito, Santa Barbara, Ventura, and Kern Counties. Thirty-five of the wells were selected using a spatially distributed, randomized grid-based method to provide statistical representation of the study unit (grid wells), and 19 were selected to aid in evaluation of specific water-quality issues (understanding wells). The groundwater samples were analyzed for organic constituents [volatile organic compounds (VOCs), pesticides and pesticide degradates, polar pesticides and metabolites, and pharmaceutical compounds], constituents of special interest [perchlorate and N-nitrosodimethylamine (NDMA)], naturally occurring inorganic constituents [trace elements, nutrients, major and minor ions, silica, total dissolved solids (TDS), and alkalinity], and radioactive constituents [gross alpha and gross beta radioactivity and radon-222]. Naturally occurring isotopes [stable isotopes of hydrogen, oxygen, and carbon, and activities of tritium and carbon-14] and dissolved noble gases also were measured to help identify the sources and ages of the sampled groundwater. In total, 288 constituents and water-quality indicators (field parameters) were investigated. Three types of quality-control samples (blanks, replicates, and matrix spikes) each were collected at approximately 4-11 percent of the wells, and the results for these samples were used to evaluate the quality of the data for the groundwater samples. Field blanks rarely contained detectable concentrations of any constituent, suggesting that contamination was not a significant source of bias in the data obtained from the groundwater samples. Differences between replicate samples generally were less than 10 percent relative standard deviation, indicating acceptable analytical reproducibility. Matrix spike recoveries were within the acceptable range (70 to 130 percent) for most compounds. This study did not attempt to evaluate the quality of water delivered to consumers; after withdrawal from the ground, untreated groundwater typically is treated, disinfected, and/or blended with other waters to maintain water quality. Regulatory thresholds apply to water that is served to the consumer, not to untreated groundwater. However, to provide some context for the results, concentrations of constituents measured in the untreated groundwater were compared with regulatory and nonregulatory health-based thresholds established by the U.S. Environmental Protection Agency (USEPA) and California Department of Public Health (CDPH), and to nonregulatory thresholds established for aesthetic and technical concerns by CDPH. Comparisons between data collected for this study and thresholds for drinking water are for illustrative purposes only, and are not indicative of complia

When the research is not reproducible: The importance of author-initiated and institution-driven responses and investigations.

PubMed

Tang, Bor Luen

2018-05-20

Important and potentially useful findings in the sciences are under more intense public scrutiny now more than ever. Other researchers in the field dive into replicating and expanding the findings while the media swamps the community and the public with peripheral reporting and analyses. How should authors and the hosting/funding institutions respond when other workers in the field could not reproduce or replicate their published results? To illustrate the importance of author-initiated and institution-driven investigations in response to outcries of research irreproducibility, I draw on comparisons between three recent and well-publicized cases in the life sciences: betatrophin, STAP cells, and NgAgo. Swift, transparent responses and investigations facilitate activation of the self-correcting mechanism of science and are likely also critical in preserving the community's resources, public trust, and the reputation of the institutions and individuals concerned. Operational guidelines for "author and institutional responses" towards external reports of irreproducibility should therefore be in place for all research intensive institutions.

A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate.

PubMed

Bataillon, Thomas; Galtier, Nicolas; Bernard, Aurelien; Cryer, Nicolai; Faivre, Nicolas; Santoni, Sylvain; Severac, Dany; Mikkelsen, Teis N; Larsen, Klaus S; Beier, Claus; Sørensen, Jesper G; Holmstrup, Martin; Ehlers, Bodil K

2016-07-01

Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Evaluation of VIDAS Salmonella (SLM) easy Salmonella method for the detection of Salmonella in a variety of foods: collaborative study.

PubMed

Crowley, Erin; Bird, Patrick; Fisher, Kiel; Goetz, Katherine; Benzinger, M Joseph; Agin, James; Goins, David; Johnson, Ronald L

2011-01-01

The VIDAS Salmonella (SLM) Easy Salmonella method is a specific enzyme-linked fluorescent immunoassay performed in the automated VIDAS instrument. The VIDAS Easy Salmonella method is a simple 2-step enrichment procedure, using pre-enrichment followed by selective enrichment in a newly formulated broth, SX2 broth. This new method was compared in a multilaboratory collaborative study to the U.S. Food and Drug Administration's Bacteriological Analytical Manual, Chapter 5 method for five food matrixes (liquid egg, vanilla ice cream, spinach, raw shrimp, and peanut butter) and the U.S. Department of Agriculture's Microbiology Laboratory Guidebook 4.04 method for deli turkey. Each food type was artificially contaminated with Salmonella at three inoculation levels. A total of 15 laboratories representing government, academia, and industry, throughout the United States, participated. In this study, 1583 samples were analyzed, of which 792 were paired replicates and 791 were unpaired replicates. Of the 792 paired replicates, 285 were positive by both the VIDAS and reference methods. Of the 791 unpaired replicates, 341 were positive by the VIDAS method and 325 were positive by the cultural reference method. A Chi-square analysis of each of the six food types was performed at the three inoculation levels tested. For all foods evaluated, the VIDAS Easy SLM method demonstrated results comparable to those of the reference methods for the detection of Salmonella.

Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013

PubMed Central

2013-01-01

An HIV-1 diagnostic laboratory was established in the Academic Medical Center (AMC) of the University of Amsterdam after the discovery of human immunodeficiency virus (HIV) as the cause of the acquired immunodeficiency syndrome (AIDS). The first AIDS patients were diagnosed here in 1981 and since 1983 we have tested the samples of 50992 patients using a variety of assays that greatly improved over the years. We will describe some of the basic results from this diagnostic laboratory and then focus on the spin-off in terms of the development of novel virus assays to detect super-infections and ultra-sensitive assays to measure the intracellular HIV-1 RNA load. We also review several original research findings in the field of HIV-1 virology that stem from initial observations made in the diagnostic unit. This includes the study of genetic defects in the HIV-1 genome and time trends of the replication fitness over 30 years of viral evolution, but also the description of novel HIV-1 variants in difficult-to-diagnose clinical specimen. PMID:23985078

Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013.

PubMed

van der Kuyl, Antoinette C; Bakker, Margreet; Jurriaans, Suzanne; Back, Nicole K T; Pasternak, Alexander O; Cornelissen, Marion; Berkhout, Ben

2013-08-28

An HIV-1 diagnostic laboratory was established in the Academic Medical Center (AMC) of the University of Amsterdam after the discovery of human immunodeficiency virus (HIV) as the cause of the acquired immunodeficiency syndrome (AIDS). The first AIDS patients were diagnosed here in 1981 and since 1983 we have tested the samples of 50992 patients using a variety of assays that greatly improved over the years. We will describe some of the basic results from this diagnostic laboratory and then focus on the spin-off in terms of the development of novel virus assays to detect super-infections and ultra-sensitive assays to measure the intracellular HIV-1 RNA load. We also review several original research findings in the field of HIV-1 virology that stem from initial observations made in the diagnostic unit. This includes the study of genetic defects in the HIV-1 genome and time trends of the replication fitness over 30 years of viral evolution, but also the description of novel HIV-1 variants in difficult-to-diagnose clinical specimen.

Cannabis Epidemiology: A Selective Review.

PubMed

Anthony, James C; Lopez-Quintero, Catalina; Alshaarawy, Omayma

2017-01-04

Globally, the most widely used set of compounds among the internationally regulated drugs is cannabis. To review evidence from epidemiological research on cannabis, organized in relation to this field's five main rubrics: quantity, location, causes, mechanisms, and prevention/ control. The review covers a selection of evidence from standardized population surveys, official statistics, and governmental reports, as well as published articles and books identified via MEDLINE, Web of Science, and Google Scholar as of July 2016. In relation to quantity, an estimated 3% to 5% of the world population is thought to have tried a cannabis product, with at least one fairly recent use, mainly extra-medical and outside boundaries of prescribed use. Among cannabis users in the United States, roughly one in 7-8 has engaged in medical marijuana use. In relation to location, prevalence proportions reveal important variations across countries and between subgroups within countries. Regarding causes and mechanisms of starting to use cannabis, there is no compelling integrative and replicable conceptual model or theoretical formulation. Most studies of mechanisms have focused upon a 'gateway sequence' and person-to-person diffusion, with some recent work on disability-adjusted life years. A brief review of cannabis use consequences, as well as prevention and control strategies is also provided. At present, we know much about the frequency and occurrence of cannabis use, with too little replicable definitive evidence with respect to the other main rubrics. Given a changing regulatory environment for cannabis products, new institutions such as an independent International Cannabis Products Safety Commission may be required to produce evidence required to weigh benefits versus costs. It is not clear that governmentsponsored research will be sufficient to meet consumer demand for balanced points of view and truly definitive evidence. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Composition of arthropod species assemblages in Bt-expressing and near isogenic eggplants in experimental fields.

PubMed

Arpaia, Salvatore; Di Leo, Grazia M; Fiore, Maria C; Schmidt, Jörg E U; Scardi, Michele

2007-02-01

The environmental impact of genetically modified (GM) plants in experimental fields has been examined in several ways, in particular with respect to the dynamics of specific nontarget organisms. The approach of sampling for biodiversity in agroecosystems to compare complex patterns could also be useful in studying potential disruptions caused by GM crops. In this study, we set up replicated field plots of Bt-expressing eggplants and near isogenic untransformed eggplants as a control. We monitored the presence and abundance of herbivore and predator arthropods in weekly visual samplings of the plant canopy for three growing seasons (2001-2003). Insect species were pooled in organismal taxonomic units (OTUs); three multivariate methods were used to compare species assemblage as an estimate of insect biodiversity. This multistep statistical approach proved to be efficient in recognizing association patterns, as evidenced by the data for the target species Leptinotarsa decemlineata Say (Coleoptera: Chrysomelidae) clearly showing a significant association with the control plots. All the analyses indicate a comparable species assemblage between transgenic and near isogenic eggplant areas. Our results suggest that some taxa may warrant more specific study. For example, Alticinae beetles (Coleoptera: Chrysomelidae) were alternatively more abundant in either of the two treatments, and their overall abundance was significantly higher on transgenic eggplants. In light of these results and because of their taxonomic proximity to the target species, these herbivores may represent an important nontarget group to be further studied. Moreover, some sap feeders (e.g., Homoptera: Cicadellidae) were more abundant on Bt-expressing plants in some samples in all 3 yr.

Membrane Accelerated Stress Test Development for Polymer Electrolyte Fuel Cell Durability Validated Using Field and Drive Cycle Testing

DOE PAGES

Mukundan, Rangachary; Baker, Andrew M.; Kusoglu, Ahmet; ...

2018-03-01

A combined chemical/mechanical accelerated stress test (AST) was developed for proton exchange membrane (PEM) fuel cells based on relative humidity cycling (RHC) between dry and saturated gases at open circuit voltage (OCV). Membrane degradation and failure were investigated using scanning electron microscopy and small- and wide-angle X-ray scattering. Changes to membrane thickness, hydrophilic domain spacing, and crystallinity were observed to be most similar between field-operated cells and OCV RHC ASTs, where local thinning and divot-type defects are the primary failure modes. While RHC in air also reproduces these failure modes, it is not aggressive enough to differentiate between different membranemore » types in >1,333 hours (55 days) of testing. Conversely, steady-state OCV tests result in significant ionomer morphology changes and global thinning, which do not replicate field degradation and failure modes. It is inferred that during the OCV RHC AST, the decay of the membrane's mechanical properties is accelerated such that materials can be evaluated in hundreds, instead of thousands, of hours, while replicating the degradation and failure modes of field operation; associated AST protocols are recommended as OCV RHC at 90°C for 500 hours with wet/dry cycle durations of 30s/45s and 2m/2m for automotive and bus operation, respectively.« less

Membrane Accelerated Stress Test Development for Polymer Electrolyte Fuel Cell Durability Validated Using Field and Drive Cycle Testing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukundan, Rangachary; Baker, Andrew M.; Kusoglu, Ahmet

A combined chemical/mechanical accelerated stress test (AST) was developed for proton exchange membrane (PEM) fuel cells based on relative humidity cycling (RHC) between dry and saturated gases at open circuit voltage (OCV). Membrane degradation and failure were investigated using scanning electron microscopy and small- and wide-angle X-ray scattering. Changes to membrane thickness, hydrophilic domain spacing, and crystallinity were observed to be most similar between field-operated cells and OCV RHC ASTs, where local thinning and divot-type defects are the primary failure modes. While RHC in air also reproduces these failure modes, it is not aggressive enough to differentiate between different membranemore » types in >1,333 hours (55 days) of testing. Conversely, steady-state OCV tests result in significant ionomer morphology changes and global thinning, which do not replicate field degradation and failure modes. It is inferred that during the OCV RHC AST, the decay of the membrane's mechanical properties is accelerated such that materials can be evaluated in hundreds, instead of thousands, of hours, while replicating the degradation and failure modes of field operation; associated AST protocols are recommended as OCV RHC at 90°C for 500 hours with wet/dry cycle durations of 30s/45s and 2m/2m for automotive and bus operation, respectively.« less

Educational Leaders', Teachers' and Parents' Perceptions on Current Lesbian, Gay, Bisexual, Transgender, and Questioning Practices on the Elementary Level

ERIC Educational Resources Information Center

Ferrante, Pia Linda

2017-01-01

Schools in the United States often times replicate the heteronormative beliefs of the American culture which can make these institutions feel isolating and unsafe for the lesbian, gay, bisexual, transgender, and questioning (LGBTQ) community. Historically, schools were places that reinforced heterosexuality and gender conforming norms. Despite…

Has Adolescent Suicidality Decreased in the United States? Data from Two National Samples of Adolescents Interviewed in 1995 and 2005

ERIC Educational Resources Information Center

Wolitzky-Taylor, Kate B.; Ruggiero, Kenneth J.; McCart, Michael R.; Smith, Daniel W.; Hanson, Rochelle F.; Resnick, Heidi S.; de Arellano, Michael A.; Saunders, Benjamin E.; Kilpatrick, Dean G.

2010-01-01

We compared the prevalence and correlates of adolescent suicidal ideation and attempts in two nationally representative probability samples of adolescents interviewed in 1995 (National Survey of Adolescents; N = 4,023) and 2005 (National Survey of Adolescents-Replication; N = 3,614). Participants in both samples completed a telephone survey that…

Influence of a Hybrid Sport Education--Teaching Games for Understanding Unit on One Teacher and His Students

ERIC Educational Resources Information Center

Hastie, Peter A.; Curtner-Smith, Matthew D.

2006-01-01

Background: Sport Education (SE) and Teaching Games for Understanding (TGfU) are two curriculum models that were developed to help students participate in fair and equitable ways and challenge their thinking beyond the replication of techniques and skills. Given that the general aim of both models is to employ more democratic pedagogies and…

Promoting Teachers' Social and Emotional Competence: A Replication Study of the Cultivating Awareness and Resilience in Education (CARE) Program

ERIC Educational Resources Information Center

Jennings, Patricia A.; Brown, Joshua L.; Frank, Jennifer; Tanler, Regin; Doyle, Sebrina; Rasheed, Damira; DeWeese, Anna; Greenberg, Mark

2014-01-01

The present study, which takes place in a high-poverty section of a large urban area of the northeastern United States, is based upon the prosocial classroom theoretical model that emphasizes the significance of teachers' social and emotional competence (SEC) and well-being in the development and maintenance of supportive teacher-student…

Testing the Theory of Successful Intelligence in Teaching Grade 4 Language Arts, Mathematics, and Science

ERIC Educational Resources Information Center

Sternberg, Robert J.; Jarvin, Linda; Birney, Damian P.; Naples, Adam; Stemler, Steven E.; Newman, Tina; Otterbach, Renate; Parish, Carolyn; Randi, Judy; Grigorenko, Elena L.

2014-01-01

This study addressed whether prior successes with educational interventions grounded in the theory of successful intelligence could be replicated on a larger scale as the primary basis for instruction in language arts, mathematics, and science. A total of 7,702 4th-grade students in the United States, drawn from 223 elementary school classrooms in…

Nonfumigant Alternatives to Methyl Bromide for Production of Snapdragon (Antirrhinum majus)

USDA-ARS?s Scientific Manuscript database

Two field experiments were conducted in north Florida to examine effects of solarization and reduced-risk pesticides on weeds, nematodes, soil-borne diseases, and yield of snapdragon (Antirrhinum majus). Five treatments were replicated five times in a randomized complete block design: fumigation wit...

Shear repair methods for conventionally reinforced concrete girders and bent caps.

DOT National Transportation Integrated Search

2009-12-01

Thirteen large-scale girders and two bent caps that replicated as close as possible bridge components from the 1950s were cast and loaded to cause initial cracking similar to that observed in the field. The girders were repaired with epoxy crack inje...

Shear repair methods for conventionally reinforced concrete girders and bent caps : appendices.

DOT National Transportation Integrated Search

2009-12-01

Thirteen large-scale girders and two bent caps that replicated as close as possible bridge components from the 1950s were cast and loaded to cause initial cracking similar to that observed in the field. The girders were repaired with epoxy crack inje...

Lakes, landscapes, and R: A framework for open science on freshwater cyanobacteria

EPA Science Inventory

In the last several years scientific reproducibility has been a hot topic with several fields openly struggling with reproducing and replicating research results. One of the key tools to address reproducibility is the use of open source software. Increasingly in ecology, the R ...

Soil microbial communities under cacao agroforestry and cover crop systems in Peru

USDA-ARS?s Scientific Manuscript database

Cacao (Theobroma cacao) trees are grown in tropical regions worldwide for chocolate production. We studied the effects of agroforestry management systems and cover cropping on soil microbial communities under cacao in two different replicated field experiments in Peru. Two agroforestry systems, Imp...

Gender Disparity in Third World Technological, Social, and Economic Development.

ERIC Educational Resources Information Center

Akubue, Anthony I.

2001-01-01

Socialization of women in developing countries inhibits their education and employment in scientific and technical fields. This mindset perpetuates poverty and limits economic and social development. Solutions include elimination of gender bias, information dissemination, replication of successful development projects, use of role models, and…

Volatile communication between plants that affects herbivory: a meta-analysis.

PubMed

Karban, Richard; Yang, Louie H; Edwards, Kyle F

2014-01-01

Volatile communication between plants causing enhanced defence has been controversial. Early studies were not replicated, and influential reviews questioned the validity of the phenomenon. We collected 48 well-replicated studies and found overall support for the hypothesis that resistance increased for individuals with damaged neighbours. Laboratory or greenhouse studies and those conducted on agricultural crops showed stronger induced resistance than field studies on undomesticated species, presumably because other variation had been reduced. A cumulative analysis revealed that early, non-replicated studies were more variable and showed less evidence for communication. Effects of habitat and plant growth form were undetectable. In most cases, the mechanisms of resistance and alternative hypotheses were not considered. There was no indication that some response variables were more likely to produce large effects. These results indicate that plants of diverse taxonomic affinities and ecological conditions become more resistant to herbivores when exposed to volatiles from damaged neighbours. © 2013 John Wiley & Sons Ltd/CNRS.

Self-Replication of Localized Vegetation Patches in Scarce Environments

NASA Astrophysics Data System (ADS)

Bordeu, Ignacio; Clerc, Marcel G.; Couteron, Piere; Lefever, René; Tlidi, Mustapha

2016-09-01

Desertification due to climate change and increasing drought periods is a worldwide problem for both ecology and economy. Our ability to understand how vegetation manages to survive and propagate through arid and semiarid ecosystems may be useful in the development of future strategies to prevent desertification, preserve flora—and fauna within—or even make use of scarce resources soils. In this paper, we study a robust phenomena observed in semi-arid ecosystems, by which localized vegetation patches split in a process called self-replication. Localized patches of vegetation are visible in nature at various spatial scales. Even though they have been described in literature, their growth mechanisms remain largely unexplored. Here, we develop an innovative statistical analysis based on real field observations to show that patches may exhibit deformation and splitting. This growth mechanism is opposite to the desertification since it allows to repopulate territories devoid of vegetation. We investigate these aspects by characterizing quantitatively, with a simple mathematical model, a new class of instabilities that lead to the self-replication phenomenon observed.

Whole-Exome Sequencing in Familial Parkinson Disease

PubMed Central

Farlow, Janice L.; Robak, Laurie A.; Hetrick, Kurt; Bowling, Kevin; Boerwinkle, Eric; Coban-Akdemir, Zeynep H.; Gambin, Tomasz; Gibbs, Richard A.; Gu, Shen; Jain, Preti; Jankovic, Joseph; Jhangiani, Shalini; Kaw, Kaveeta; Lai, Dongbing; Lin, Hai; Ling, Hua; Liu, Yunlong; Lupski, James R.; Muzny, Donna; Porter, Paula; Pugh, Elizabeth; White, Janson; Doheny, Kimberly; Myers, Richard M.; Shulman, Joshua M.; Foroud, Tatiana

2016-01-01

IMPORTANCE Parkinson disease (PD) is a progressive neurodegenerative disease for which susceptibility is linked to genetic and environmental risk factors. OBJECTIVE To identify genetic variants contributing to disease risk in familial PD. DESIGN, SETTING, AND PARTICIPANTS A 2-stage study design that included a discovery cohort of families with PD and a replication cohort of familial probands was used. In the discovery cohort, rare exonic variants that segregated in multiple affected individuals in a family and were predicted to be conserved or damaging were retained. Genes with retained variants were prioritized if expressed in the brain and located within PD-relevant pathways. Genes in which prioritized variants were observed in at least 4 families were selected as candidate genes for replication in the replication cohort. The setting was among individuals with familial PD enrolled from academic movement disorder specialty clinics across the United States. All participants had a family history of PD. MAIN OUTCOMES AND MEASURES Identification of genes containing rare, likely deleterious, genetic variants in individuals with familial PD using a 2-stage exome sequencing study design. RESULTS The 93 individuals from 32 families in the discovery cohort (49.5% [46 of 93] female) had a mean (SD) age at onset of 61.8 (10.0) years. The 49 individuals with familial PD in the replication cohort (32.6% [16 of 49] female) had a mean (SD) age at onset of 50.1 (15.7) years. Discovery cohort recruitment dates were 1999 to 2009, and replication cohort recruitment dates were 2003 to 2014. Data analysis dates were 2011 to 2015. Three genes containing a total of 13 rare and potentially damaging variants were prioritized in the discovery cohort. Two of these genes (TNK2 and TNR) also had rare variants that were predicted to be damaging in the replication cohort. All 9 variants identified in the 2 replicated genes in 12 families across the discovery and replication cohorts were confirmed via Sanger sequencing. CONCLUSIONS AND RELEVANCE TNK2 and TNR harbored rare, likely deleterious, variants in individuals having familial PD, with similar findings in an independent cohort. To our knowledge, these genes have not been previously associated with PD, although they have been linked to critical neuronal functions. Further studies are required to confirm a potential role for these genes in the pathogenesis of PD. PMID:26595808

Diffusion of Energy Efficient Technology in Commercial Buildings: An Analysis of the Commercial Building Partnerships Program

NASA Astrophysics Data System (ADS)

Antonopoulos, Chrissi Argyro

This study presents findings from survey and interview data investigating replication of green building measures by Commercial Building Partnership (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered directly with 12 organizations on new and retrofit construction projects, which represented approximately 28 percent of the entire U.S. Department of Energy (DOE) CBP program. Through a feedback survey mechanism, along with personal interviews, quantitative and qualitative data were gathered relating to replication efforts by each organization. These data were analyzed to provide insight into two primary research areas: 1) CBP partners' replication efforts of green building approaches used in the CBP project to the rest of the organization's building portfolio, and, 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the CBP program. The first area of this research focused specifically on replication efforts underway or planned by each CBP program participant. The second area of this research develops a diffusion of innovations model to analyze potential broad market impacts of the CBP program on the commercial building industry in the United States. Findings from this study provided insight into motivations and objectives CBP partners had for program participation. Factors that impact replication include motivation, organizational structure and objectives firms have for implementation of energy efficient technologies. Comparing these factors between different CBP partners revealed patterns in motivation for constructing energy efficient buildings, along with better insight into market trends for green building practices. The optimized approach to the CBP program allows partners to develop green building parameters that fit the specific uses of their building, resulting in greater motivation for replication. In addition, the diffusion model developed for this analysis indicates that this method of market prediction may be used to adequately capture cumulative construction metrics for a whole-building analysis as opposed to individual energy efficiency measures used in green building.

Zika virus preferentially replicates in the female reproductive tract after vaginal inoculation of rhesus macaques.

PubMed

Carroll, Timothy; Lo, Ming; Lanteri, Marion; Dutra, Joseph; Zarbock, Katie; Silveira, Paola; Rourke, Tracy; Ma, Zhong-Min; Fritts, Linda; O'Connor, Shelby; Busch, Michael; Miller, Christopher J

2017-07-01

Zika virus (ZIKV) is a mosquito-transmitted virus that can cause severe defects in an infected fetus. ZIKV is also transmitted by sexual contact, although the relative importance of sexual transmission is unclear. To better understand the role of sexual transmission in ZIKV pathogenesis, a nonhuman primate (NHP) model of vaginal transmission was developed. ZIKV was readily transmitted to mature cycling female rhesus macaque (RM) by vaginal inoculation with 104-106 plaque-forming units (PFU). However, there was variability in susceptibility between the individual RM with 1->8 vaginal inoculations required to establish infection. After treatment with Depoprovera, a widely used contraceptive progestin, two RM that initially resisted 8 vaginal ZIKV inoculations became infected after one ZIKV inoculation. Thus, Depoprovera seemed to enhance susceptibility to vaginal ZIKV transmission. Unexpectedly, the kinetics of virus replication and dissemination after intravaginal ZIKV inoculation were markedly different from RM infected with ZIKV by subcutaneous (SQ) virus inoculation. Several groups have reported that after SQ ZIKV inoculation vRNA is rapidly detected in blood plasma with vRNA less common in urine and saliva and only rarely detected in female reproductive tract (FRT) secretions. In contrast, in vaginally inoculated RM, plasma vRNA is delayed for several days and ZIKV replication in, and vRNA shedding from, the FRT was found in all 6 animals. Further, after intravaginal transmission ZIKV RNA shedding from FRT secretions was detected before or simultaneously with plasma vRNA, and persisted for at least as long. Thus, ZIKV replication in the FRT was independent of, and often preceded virus replication in the tissues contributing to plasma vRNA. These results support the conclusion that ZIKV preferentially replicates in the FRT after vaginal transmission, but not after SQ transmission, and raise the possibility that there is enhanced fetal infection and pathology after vaginal ZIKV transmission compared to a mosquito transmitted ZIKV.

Reproducibility and quantitation of amplicon sequencing-based detection

PubMed Central

Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

2011-01-01

To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the β-diversity of microbial communities. PMID:21346791

A journey through the microscopic ages of DNA replication.

PubMed

Reinhart, Marius; Cardoso, M Cristina

2017-05-01

Scientific discoveries and technological advancements are inseparable but not always take place in a coherent chronological manner. In the next, we will provide a seemingly unconnected and serendipitous series of scientific facts that, in the whole, converged to unveil DNA and its duplication. We will not cover here the many and fundamental contributions from microbial genetics and in vitro biochemistry. Rather, in this journey, we will emphasize the interplay between microscopy development culminating on super resolution fluorescence microscopy (i.e., nanoscopy) and digital image analysis and its impact on our understanding of DNA duplication. We will interlace the journey with landmark concepts and experiments that have brought the cellular DNA replication field to its present state.

A multi-functional high voltage experiment apparatus for vacuum surface flashover switch research.

PubMed

Zeng, Bo; Su, Jian-cang; Cheng, Jie; Wu, Xiao-long; Li, Rui; Zhao, Liang; Fang, Jin-peng; Wang, Li-min

2015-04-01

A multifunctional high voltage apparatus for experimental researches on surface flashover switch and high voltage insulation in vacuum has been developed. The apparatus is composed of five parts: pulse generating unit, axial field unit, radial field unit, and two switch units. Microsecond damped ringing pulse with peak-to-peak voltage 800 kV or unipolar pulse with maximum voltage 830 kV is generated, forming transient axial or radial electrical field. Different pulse waveforms and field distributions make up six experimental configurations in all. Based on this apparatus, preliminary experiments on vacuum surface flashover switch with different flashover dielectric materials have been conducted in the axial field unit, and nanosecond pulse is generated in the radial field unit which makes a pulse transmission line in the experiment. Basic work parameters of this kind of switch such as lifetime, breakdown voltage are obtained.

Oncolytic adenovirus that overproduces ADP and replicates selectively in tumors due to hTERT promoter-regulated E4 gene expression.

PubMed

Kuppuswamy, M; Spencer, J F; Doronin, K; Tollefson, A E; Wold, W S M; Toth, K

2005-11-01

We have constructed a novel oncolytic adenovirus (Ad) vector, named VRX-011, in which the replication of the vector is targeted to cancer cells by the replacement of the wild-type Ad E4 promoter with the human telomerase reverse transcriptase (hTERT) promoter. Genes in the Ad E4 transcription unit are essential for Ad replication; therefore, VRX-011 will grow efficiently only in cells in which the hTERT promoter is active, that is, in a wide range of cancer and immortalized cells but not in most somatic cells. Consistent with these expectations, VRX-011 replicated efficiently in all cancer cell lines examined, while its growth was restricted in various primary and normal cells. VRX-011 overexpresses ADP (also known as E3-11.6K), an Ad protein required for efficient cell lysis and release of virions from cells at late stages of infection. This overexpression enhances cell-to-cell spread and could significantly increase antitumor efficacy. In a xenograft model in nude mice, both intratumoral and intravenous administration of VRX-011 effectively suppressed the growth of subcutaneous Hep3B human liver tumors. Also, intravenous delivery of VRX-011 greatly reduced the number and size of A549 human lung cancer cell nodules in a disseminated lung tumor model in nude mice. Importantly, tail vein administration of different doses of VRX-011 in C57BL/6 mice showed minimal liver toxicity. Considering its broad range of lytic replication in cancer cells, its attenuated phenotype in primary cells, its efficacy in suppressing xenografts, and its low toxicity in mouse liver, VRX-011 is a promising candidate for further evaluation as an anticancer therapeutic.

Controllable Nanoparticle Assembly and Actuation with Modified Dipole Potentials in Simulation

NASA Astrophysics Data System (ADS)

Dempster, Joshua

Science at the nanoscale poses several recurring difficulties. How can we control the assembly of objects too small for direct manipulation to be practical? How can we extend that control to in vivo systems so we can make use of nanotechnology in medicine? And how can we recreate the extraordinary capacities of Nature: healing, replication, growth, adaptation, self-regulation? One of the most powerful tools for addressing these challenges is the simple, familiar dipole moment. Since their debut as fuel control devices at NASA in the early sixties, possible applications for dipole suspensions have grown to areas far beyond what their creators envisioned. A multitude of ambitious new medical and mechanical applications make use of dipolar colloids. Dipoles are attractive from a practical standpoint because one can use fields to control not just their orientation and location, but also their mutual interactions. From a physical standpoint, dipoles are compelling as an exceptionally simple form of symmetry-breaking that leads to a variety of complex phenomena. This thesis studies the assembly and control of spherical colloids with a dipolar interaction modified by additional conditions using simulations. Three cases are examined in detail. The first is the case of an electrical dipole moment created by regions of opposite charge density on the surface of a colloid. Here the dipole potential is modified by strong screening. Such a system is interesting as a model for certain proteins in a high-salt solution and suggests possible uses for inverse Janus colloids. The resulting phases have little resemblance to the usual dipole phases and can be controlled with small quantities of homogeneously charged particles. In the second case, superparamagnetic dipoles are linked into chains. Such chains have been realized in a wide variety of experimental schemes. A general theory is developed for the equilibrium shapes of the chains in a precessing field when their endpoints are fixed. This theory reveals that the chains are good candidates for contracting muscles in microscopic devices with a conveniently harmonic form for their potentials. Ensembles of free chains can be put to more elaborate uses. To illustrate, a regime is designed that spins the chains into a self-healing cross-linked gel. Finally, we will turn to self-replication. Decorating a permanent dipole with a single permanent binding site is enough to enable self-replication using dimers as the template. A periodic magnetic drive provides the energy to drive replication. Several theoretical principles regarding the statistics of linear self-replicators are deduced and used to optimize the dipole replicating system.

Use of a BOD oxygen probe for estimating primary productivity

Treesearch

Raymond L. Czaplewski; Michael Parker

1973-01-01

The accuracy of a BOD oxygen probe for field measurements of primary production by the light and dark bottle oxygen technique is analyzed. A figure is presented with which to estimate the number of replicate bottles needed to obtain a given accuracy in estimating photosynthetic rates.

A Call for Examining Replication and Bias in Special Education Research

ERIC Educational Resources Information Center

Cook, Bryan G.

2014-01-01

Valid, scientific research is critical for ascertaining the effects of instructional techniques on learners with disabilities and for guiding effective special education practice and policy. Researchers in fields such as psychology and medicine have identified serious and widespread shortcomings in their research literatures related to replication…

INDEPENDENT AND CONTRASTING EFFECTS OF ELEVATED CO2 AND N-FERTILIZATION ROOT ARCHITECTURE

EPA Science Inventory

The effects of elevated CO2 and N fertilization on architecture of Pinus ponderosa fine roots and their associated mycorrhizal symbionts were measured over a 4-year period. The study was conducted in open-top field-exposure chambers located near Placerville, CA. A replicated (thr...

Understanding the Etiology of Complex Traits: Symbiotic Relationships between Psychology and Genetics

ERIC Educational Resources Information Center

Grigorenko, Elena L.

2007-01-01

The present article offers comments on the infusion of methodologies, approaches, reasoning strategies, and findings from the fields of genetics and genomics into studies of complex human behaviors (hereafter, complex phenotypes). Specifically, I discuss issues of generality and specificity, causality, and replicability as they pertain to…

Fumigant distribution in forest nursery soils

Treesearch

Dong Wang; Stephen W. Fraedrich; Jennifer Juzwik; Kurt Spokas; Yi Zhang; William C. Koskinen

2006-01-01

Adequate concentration, exposure time and distribution uniformity of activated fumigant gases are prerequisites for successful soil fumigation. Field experiments were conducted to evaluate gas phase distributions of methyl isothiocyanate (MITC) and chloropicrin (CP) in two forest-tree nurseries. Concentrations of MITC and CP in soil air were measured from replicated...

INVESTIGATION OF ORGANIC WEED CONTROL METHODS, PESTICIDE SPECIAL STUDY, COLORADO STATE UNIVERSITY

EPA Science Inventory

The project is proposed for the 2003 and 2004 growing seasons. Corn gluten meal (CGM), treated paper mulch and plastic mulch, along with conventional herbicide, will be applied to fields of drip irrigated broccoli in a randomized complete block design with 6 replicates. Due to ...

Success and challenges met during the calibration of APEX on large plots

USDA-ARS?s Scientific Manuscript database

As the APEX model is increasingly considered for the evaluation of agricultural systems, satisfactory performance of APEX on fields is critical. APEX was applied to 16 replicated large plots established in 1991 in Northeast Missouri. Until 2009, each phase of each rotation was represented every year...

Shear repair methods for conventionally reinforced concrete girders and bent caps : final report, December 2009.

DOT National Transportation Integrated Search

2009-12-01

Thirteen large-scale girders and two bent caps that replicated as close as possible bridge components from the 1950s were cast and loaded to cause initial cracking similar to that observed in the field. The girders were repaired with epoxy crack inje...

Functional and nutritional characteristics of wheat grown in organic and conventional cropping systems

USDA-ARS?s Scientific Manuscript database

The effects of organic vs. conventional farming practices on wheat functional and nutritional characteristics were compared. Soft white winter wheat and hard red spring wheat were obtained from long-term replicated field plots near Pullman, Washington and Bozeman, Montana. Test weight, kernel weight...

Twelve-month use of herbal medicines as a remedy for mental health problems in Japan: A cross-national analysis of World Mental Health Survey data.

PubMed

Iwanaga, Mai; Iwanaga, Hiroo; Kawakami, Norito

2017-09-01

The purpose of this study was to clarify the frequencies and sociodemographic and other characteristics around use of herbal medicine as a remedy for mental health problems in Japan. Data from the World Mental Health Japan (WMHJ) Survey and US National Comorbidity Survey Replications were analyzed. The WMHJ was conducted in 2002 to 2006, with 4129 respondents. National Comorbidity Survey Replications was conducted in 2002 to 2003, with 9282 respondents. The interview asked the respondents about their use of several types of herbs for mental health problems. Frequencies of use of herbal medicine were compared between Japan and the United States. Multiple logistic regression analyses were conducted to determine sociodemographic and mental health-related correlates of 12-month herbal medicine use. Relevant sampling weights were used to adjust for the sampling designs. The proportion for use of herbal medicines as a remedy for mental health problems in the past 12 months was lower (0.4%) in Japan than that in the United States (3.7%). Low education in both countries (P < .05) was significantly associated with nonuse of herbal medicine. Any anxiety disorder in Japan was significantly associated with herbal medicine use (P < .01), while any mental disorder categories were significantly associated in the United States (P < .01). The frequency for use of herbal medicine among patients with mental health problems in the past 12 months was much lower in Japan compared to the United States. Persons with high educational attainment and anxiety disorders used herbal medicine as a remedy for mental health problems more frequently in Japan. © 2017 John Wiley & Sons Australia, Ltd.

Permanent magnets composed of high temperature superconductors

NASA Technical Reports Server (NTRS)

Weinstein, Roy; Chen, In-Gann; Liu, Jay; Lau, Kwong

1991-01-01

A study of persistent, trapped magnetic field has been pursued with high-temperature superconducting (HTS) materials. The main effort is to study the feasibility of utilization of HTS to fabricate magnets for various devices. The trapped field, when not in saturation, is proportional to the applied field. Thus, it should be possible to replicate complicated field configurations with melt-textured YBa2Cu3O7 (MT-Y123) material, bypassing the need for HTS wires. Presently, materials have been developed from which magnets of 1.5 T, at 77 K, can be fabricated. Much higher field is available at lower operating temperature. Stability of a few percent per year is readily attainable. Results of studies on prototype motors and minimagnets are reported.

Groundwater-quality data in the Klamath Mountains study unit, 2010: results from the California GAMA Program

USGS Publications Warehouse

Mathany, Timothy M.; Belitz, Kenneth

2014-01-01

Groundwater quality in the 8,806-square-mile Klamath Mountains (KLAM) study unit was investigated by the U.S. Geological Survey (USGS) from October to December 2010, as part of the California State Water Resources Control Board (SWRCB) Groundwater Ambient Monitoring and Assessment (GAMA) Program’s Priority Basin Project (PBP). The GAMA-PBP was developed in response to the California Groundwater Quality Monitoring Act of 2001 and is being conducted in collaboration with the SWRCB and Lawrence Livermore National Laboratory (LLNL). The KLAM study unit was the thirty-third study unit to be sampled as part of the GAMA-PBP. The GAMA Klamath Mountains study was designed to provide a spatially unbiased assessment of untreated-groundwater quality in the primary aquifer system and to facilitate statistically consistent comparisons of untreated-groundwater quality throughout California. The primary aquifer system is defined by the perforation intervals of wells listed in the California Department of Public Health (CDPH) database for the KLAM study unit. Groundwater quality in the primary aquifer system may differ from the quality in the shallower or deeper water-bearing zones; shallower groundwater may be more vulnerable to surficial contamination. In the KLAM study unit, groundwater samples were collected from sites in Del Norte, Siskiyou, Humboldt, Trinity, Tehama, and Shasta Counties, California. Of the 39 sites sampled, 38 were selected by using a spatially distributed, randomized grid-based method to provide statistical representation of the primary aquifer system in the study unit (grid sites), and the remaining site was non-randomized (understanding site). The groundwater samples were analyzed for basic field parameters, organic constituents (volatile organic compounds [VOCs] and pesticides and pesticide degradates), inorganic constituents (trace elements, nutrients, major and minor ions, total dissolved solids [TDS]), radon-222, gross alpha and gross beta radioactivity, and microbial indicators (total coliform and Escherichia coli [E. coli]). Isotopic tracers (stable isotopes of hydrogen and oxygen in water, isotopic ratios of dissolved strontium in water, and stable isotopes of carbon in dissolved inorganic carbon), dissolved noble gases, and age-dating tracers (tritium and carbon-14) were measured to help identify sources and ages of sampled groundwater. Quality-control samples (field blanks, replicate sample pairs, and matrix spikes) were collected at 13 percent of the sites in the KLAM study unit, and the results were used to evaluate the quality of the data from the groundwater samples. Field blank samples rarely contained detectable concentrations of any constituent, indicating that contamination from sample collection or analysis was not a significant source of bias in the data for the groundwater samples. More than 99 percent of the replicate pair samples were within acceptable limits of variability. Matrix-spike sample recoveries were within the acceptable range (70 to 130 percent) for approximately 91 percent of the compounds. This study did not evaluate the quality of water delivered to consumers. After withdrawal, groundwater typically is treated, disinfected, and (or) blended with other waters to maintain water quality. Regulatory benchmarks apply to water that is delivered to the consumer, not to untreated groundwater. However, to provide some context for the results, concentrations of constituents measured in the untreated groundwater were compared with regulatory and non-regulatory health-based benchmarks established by the U.S. Environmental Protection Agency (USEPA) and CDPH, and to non-health-based benchmarks established for aesthetic concerns by the CDPH. Comparisons between data collected for this study and benchmarks for drinking water are for illustrative purposes only and are not indicative of compliance or non-compliance with those benchmarks. All concentrations of organic constituents from grid sites sampled in the KLAM study unit were less than health-based benchmarks. In total, VOCs were detected in 16 of the 38 grid sites sampled (approximately 42 percent), pesticides and pesticide degradates were detected in 8 grid sites (about 21 percent), and microbial indicators were detected in 14 grid sites (approximately 37 percent). Inorganic constituents (trace elements, major and minor ions, nutrients, and uranium and other radioactive constituents) and microbial indicators were sampled for at 38 grid sites, and all concentrations were less than health-based benchmarks, with the exception of one detection of boron greater than the CDPH notification level of 1,000 micrograms per liter (μg/L). Generally, concentrations of inorganic constituents with non-health-based benchmarks (iron, manganese, chloride, and TDS) were less than the CDPH secondary maximum contaminant level (SMCL-CA). Exceptions include three detections of iron greater than the SMCL-CA of 300 μg/L, four detections of manganese greater than the SMCL-CA of 50 μg/L, one detection of chloride greater than the recommended SMCL-CA of 250 μg/L, and one detection of TDS greater than the recommended SMCL-CA of 500 μg/L.

Registered report: the androgen receptor induces a distinct transcriptional program in castration-resistant prostate cancer in man

PubMed Central

Chronscinski, Denise; Cherukeri, Srujana; Tan, Fraser; Lomax, Joelle; Iorns, Elizabeth

2015-01-01

The Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative (PCFMFRI) seeks to address growing concerns about reproducibility in scientific research by conducting replications of recent papers in the field of prostate cancer. This Registered Report describes the proposed replication plan of key experiments from “The Androgen Receptor Induces a Distinct Transcriptional Program in Castration-Resistant Prostate Cancer in Man” by Sharma and colleagues (2013), published in Cancer Cell in 2013. Of thousands of targets for the androgen receptor (AR), the authors elucidated a subset of 16 core genes that were consistently downregulated with castration and re-emerged with castration resistance. These 16 AR binding sites were distinct from those observed in cells in culture. The authors suggested that cellular context can have dramatic effects on downstream transcriptional regulation of AR binding sites. The present study will attempt to replicate Fig. 7C by comparing gene expression of the 16 core genes identified by Sharma and colleagues in xenograft tumor tissue compared to androgen treated LNCaP cells in vitro. The Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative is a collaboration between the Prostate Cancer Foundation, the Movember Initiative, and Science Exchange, and the results of the replications will be published by PeerJ. PMID:26401447

A biologically inspired two-species exclusion model: effects of RNA polymerase motor traffic on simultaneous DNA replication

NASA Astrophysics Data System (ADS)

Ghosh, Soumendu; Mishra, Bhavya; Patra, Shubhadeep; Schadschneider, Andreas; Chowdhury, Debashish

2018-04-01

We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication forks on the same DNA segment. One of the species of particles (P) represents RNAP motors while the other (R) represents the replication forks. Motivated by the biological phenomena that this model is intended to capture, a maximum of two R particles only are allowed to enter the lattice from two opposite ends whereas the unrestricted number of P particles constitutes a totally asymmetric simple exclusion process (TASEP) in a segment in the middle of the lattice. The model captures three distinct pathways for resolving the co-directional as well as head-on collision between the P and R particles. Using Monte Carlo simulations and heuristic analytical arguments that combine exact results for the TASEP with mean-field approximations, we predict the possible outcomes of the conflict between the traffic of RNAP motors (P particles engaged in transcription) and the replication forks (R particles). In principle, the model can be adapted to experimental conditions to account for the data quantitatively.

HIV vaccine research and discovery in the nonhuman primates model: a unified theory in acquisition prevention and control of SIV infection.

PubMed

Lynch, Rebecca M; Yamamoto, Takuya; McDermott, Adrian B

2013-07-01

Here we highlight the latest advances in HIV vaccine concepts that will expand our knowledge on how to elicit effective acquisition-prevention and/or control of simian immunodeficiency virus (SIV) replication in the nonhuman primate (NHP) model. In the context of the promising analyses from the RV144 Thai Trial and the effective control of SIV replication exerted by rhCMV-(SIV) elicited EM CD8 T cells, the HIV field has recently shifted toward vaccine concepts that combine protection from acquisition with effective control of SIV replication. Current studies in the NHP model have demonstrated the efficacy of HIV-neutralizing antibodies via passive transfer, the potential importance of the CD4 Tfh subset, the ability to effectively model the RV144 vaccine trial and the capacity of an Ad26 prime and modified vaccinia Ankara virus boost to elicit Env-specific antibody and cellular responses that both limit acquisition and control heterologous SIVmac251 challenge. The latest work in the NHP model suggests that the next generation HIV-1 vaccines should aim to provoke a comprehensive adaptive immune response for both prevention of SIV acquisition as well as control of replication in breakthrough infection.

Using organotypic (raft) epithelial tissue cultures for the biosynthesis and isolation of infectious human papillomaviruses.

PubMed

Ozbun, Michelle A; Patterson, Nicole A

2014-08-01

Papillomaviruses have a strict tropism for epithelial cells, and they are fully reliant on cellular differentiation for completion of their life cycles, resulting in the production of progeny virions. Thus, a permissive environment for full viral replication in vitro-wherein virion morphogenesis occurs under cooperative viral and cellular cues-requires the cultivation of epithelium. Presented in the first section of this unit is a protocol to grow differentiating epithelial tissues that mimic many important morphological and biochemical aspects of normal skin. The technique involves growing epidermal cells atop a dermal equivalent consisting of live fibroblasts and a collagen lattice. Epithelial stratification and differentiation ensues when the keratinocyte-dermal equivalent is placed at the air-liquid interface. The apparent floating nature of the cell-matrix in this method led to the nickname "raft" cultures. The general technique can be applied to normal low passage keratinocytes, to cells stably transfected with papillomavirus genes or genomes, or keratinocytes established from neoplastic lesions. However, infectious papillomavirus particles have only been isolated from organotypic epithelial cultures initiated with cells that maintain oncogenic human papillomavirus genomes in an extrachomosomal replicative form. The second section of this unit is dedicated to a virion isolation method that minimizes aerosol and skin exposure to these human carcinogens. Although the focus of the protocols is on the growth of tissues that yields infectious papillomavirus progeny, this culture system facilitates the investigation of these fastidious viruses during their complex replicative cycles, and raft tissues can be manipulated and harvested at any point during the process. Importantly, a single-step virus growth cycle is achieved in this process, as it is unlikely that progeny virions are released to initiate subsequent rounds of infection. Copyright © 2014 John Wiley & Sons, Inc.

Electromagnetic Fields and Human Health: Fundamental and Applied Research. Proceeding of the International Conference (3rd) Held in Moscow and St. Petersburg, Russia, September 17-25 2002

DTIC Science & Technology

2002-10-28

repeatedly similar to those observed in a standard hatchery. In a series of seven replicates, eggs issued from artificially inseminated hens (200 x 106 spz...intercellular information channel leading to the negative con- sequences for the organism. Likely the magnet storms the artificial change of magnet field...biochemical reactions that can be affected by such pulses. We shall present data that shows an artificially contrived biochemical reaction, the

Effect of the Salary Model on Sustainability of a Professional Practice Environment.

PubMed

Hickey, Rosa G; Buchko, Barbara L; Coe, Paula F; Woods, Anne B

2017-10-01

This replication study examined differences in RN perception of the professional practice environment (PPE) between salary- and hourly-wage compensation models over time. A previous study demonstrated that nurses in a salary-wage model had a significantly higher perception of the PPE compared with their peers receiving hourly wages. A descriptive, comparative design was used to examine the Revised Professional Practice Environment (RPPE) scale of nurses in the same units surveyed in the previous study 2 years later. Mean scores on the RPPE continued to be significantly lower for hourly-wage RNs compared with the RNs in the salary-wage model. Nurses in an hourly-wage unit have significantly lower perceptions of the clinical practice environment than their peers in a salary-wage unit, indicating that professional practice perceptions in a salary-wage unit were sustained for a 2-year period and may provide a more effective PPE.

Multiple-scale hydraulic characterization of a surficial clayey aquitard overlying a regional aquifer in Louisiana

NASA Astrophysics Data System (ADS)

Chapman, Steven W.; Cherry, John A.; Parker, Beth L.

2018-03-01

The vertical hydraulic conductivity (Kv) of a 30-m thick surficial clayey aquitard overlying a regional aquifer at an industrial site in the Mississippi River Valley in Louisiana was investigated via intensive hydraulic characterization using high resolution vertical hydraulic head profiles with temporal monitoring and laboratory tests. A study area was instrumented with a semi-circular array of piezometers at many depths in the aquitard at equal distance from a large capacity pumping well including replicate piezometers. Profiles showed negligible head differential to 20 m bgs, below which there was an abrupt change in vertical gradients over the lower 8-10 m of the aquitard. Hydraulic characteristics are strongly associated with depositional environment; the upper zone of minimal head differentials with depth and minimal variation over time correlates with Paleo-Mississippi River backswamp deposits, while the lower zone with large head differentials and slow but moderate head changes correlates with lacustrine deposits. The lower zone restricts groundwater flow between the surface and underlying regional aquifer, which is hydraulically connected to the Mississippi River. Lab tests on lacustrine samples show low Kv (8 × 10-11-4 × 10-9 m/s) bracketing field estimates (6 × 10-10 m/s) from 1-D model fits to piezometric data in response to large aquifer head changes. The slow response indicates absence of through-going open fractures in the lacustrine unit, consistent with geotechnical properties (high plasticity, normal consolidation), suggesting high integrity that protects the underlying aquifer from surficial contamination. The lack of vertical gradients in the overlying backswamp unit indicates abundant secondary permeability features (e.g. fractures, rootholes) consistent with depositional and weathering conditions. 2-D stylized transient flow simulations including both units supports this interpretation. Other published reports on surficial aquitards in the Gulf Coast Region pertain to Pleistocene deposits that lack laterally extensive lacustrine units and where Kv is enhanced by secondary permeability features, resulting in clayey aquitards with poor integrity.

Ponderosa pine growth response to soil strength in the volcanic ash soils of central Oregon.

Treesearch

R.T. Parker; D.A. Maguire; D.D. Marshall; P. Cochran

2007-01-01

Mechanical harvesting and associated logging activities have the capacity to compact soil across large portions of harvest units. Two thinning treatments (felled only versus felled and skidded) in 70- to 80-year-old ponderosa pine stands were replicated at three sites with volcanic soils in central Oregon. Growth in diameter, height, and volume of residual trees were...

Transparency in Distributed File Systems

DTIC Science & Technology

1989-01-01

ORGANIZATION NAME AND ADDRESS 10. PROGRAM ELEMENT. PROJECT, TASK Computer Science Department AREA & WORK UNIT NUMBERS 734 Comouter Studies Bldc . University of...sistency control , file and director) placement, and file and directory migration in a way that pro- 3 vides full network transparency. This transparency...areas of naming, replication, con- sistency control , file and directory placement, and file and directory migration in a way that pro- 3 vides full

Improved Reflections: American Magazines, Higher Education, and the Construction of a Middle-Class Male Identity through European Comparisons, 1890-1915

ERIC Educational Resources Information Center

Clark, Daniel

2010-01-01

Historians of American education readily acknowledge that in the mid-19th century the German university and academic ideal rose in prominence among American academicians, who then worked diligently to replicate the German university model in the United States. During this same time, however, many more Americans were exposed to a different…

Production dynamics of intensively managed loblolly pine stands in the southern United States: a synthesis of seven long-term experiments

Treesearch

Eric J. Jokela; Philip M. Dougherty; Timothy A. Martin

2004-01-01

Results from seven long-term experiments in the southern US were summarized to understand production dynamics of intensively managed loblolly pine plantations. Replicated studies that spanned a wide range of soil and climatic conditions were established (North Carolina-NC; Georgia-GA (three sites); Florida-F%; Louisiana-LA; Oklahoma--OK). A11 experiments received some...

Reading, Equivalence, and Recombination of Units: A Replication with Students with Different Learning Histories.

ERIC Educational Resources Information Center

Melchiori, Ligia Ebner; de Souza, Deisy G.; de Rose, Julio C.

2000-01-01

First graders (n=5), preschoolers (n=5), special education first-graders (n=5), and adults (n=8) in Brazil received a reading program in which they learned to match printed to dictated words and to construct (copy) printed words. The students not only learned to match the training words but also learned to read them. (Contains references.)…

Fuel mass and stand structure after post-fire logging of a severely burned ponderosa pine forest in northeastern Oregon.

Treesearch

J.D. McIver; R. Ottmar

2006-01-01

Stand structure and downed woody fuel mass were measured in four replicate units for each of three treatments (unlogged control, commercial harvest, and fuel reduction harvest) following the 1996 Summit Wildfire in northeastern Oregon. Commercial and fuel-reduction harvest resulted in a significant decrease in tree density and tree basal areas. The total downed woody...

Can We Generalize from Student Experiments to the Real World in Political Science, Military Affairs, and International Relations?

ERIC Educational Resources Information Center

Mintz, Alex; Redd, Steven B.; Vedlitz, Arnold

2006-01-01

The authors conducted an experiment with a group of military officers and replicated it with a group of students at a public university in the United States. The experimental scenario dealt with a decision problem in the area of counterterrorism. The authors found that while more than one-third of students recommended doing nothing, the…

Systematic Review of Plant-Based Homeopathic Basic Research: An Update.

PubMed

Ücker, Annekathrin; Baumgartner, Stephan; Sokol, Anezka; Huber, Roman; Doesburg, Paul; Jäger, Tim

2018-05-01

 Plant-based test systems have been described as a useful tool for investigating possible effects of homeopathic preparations. The last reviews of this research field were published in 2009/2011. Due to recent developments in the field, an update is warranted. Publications on plant-based test systems were analysed with regard to publication quality, reproducibility and potential for further research.  A literature search was conducted in online databases and specific journals, including publications from 2008 to 2017 dealing with plant-based test systems in homeopathic basic research. To be included, they had to contain statistical analysis and fulfil quality criteria according to a pre-defined manuscript information score (MIS). Publications scoring at least 5 points (maximum 10 points) were assumed to be adequate. They were analysed for the use of adequate controls, outcome and reproducibility.  Seventy-four publications on plant-based test systems were found. Thirty-nine publications were either abstracts or proceedings of conferences and were excluded. From the remaining 35 publications, 26 reached a score of 5 or higher in the MIS. Adequate controls were used in 13 of these publications. All of them described specific effects of homeopathic preparations. The publication quality still varied: a substantial number of publications (23%) did not adequately document the methods used. Four reported on replication trials. One replication trial found effects of homeopathic preparations comparable to the original study. Three replication trials failed to confirm the original study but identified possible external influencing factors. Five publications described novel plant-based test systems. Eight trials used systematic negative control experiments to document test system stability.  Regarding research design, future trials should implement adequate controls to identify specific effects of homeopathic preparations and include systematic negative control experiments. Further external and internal replication trials, and control of influencing factors, are needed to verify results. Standardised test systems should be developed. The Faculty of Homeopathy.

The effect of sociodemographic (mis)match between interviewers and respondents on unit and item nonresponse in Belgium.

PubMed

Vercruyssen, Anina; Wuyts, Celine; Loosveldt, Geert

2017-09-01

Interviewer characteristics affect nonresponse and measurement errors in face-to-face surveys. Some studies have shown that mismatched sociodemographic characteristics - for example gender - affect people's behavior when interacting with an interviewer at the door and during the survey interview, resulting in more nonresponse. We investigate the effect of sociodemographic (mis)matching on nonresponse in two successive rounds of the European Social Survey in Belgium. As such, we replicate the analyses of the effect of (mis)matching gender and age on unit nonresponse on the one hand, and of gender, age and education level (mis)matching on item nonresponse on the other hand. Recurring effects of sociodemographic (mis)match are found for both unit and item nonresponse. Copyright © 2017 Elsevier Inc. All rights reserved.

[New hypothesis on the replication of centrioles and basal bodies].

PubMed

Mignot, J P

1996-12-01

Certain morphological data, obtained in studies of the ultrastructure of centrioles and basal bodies in cells of metazoa and protists, lead us to think that the cartwheel represents of the most appropriate organization for a self-reproducing and transmissible centriolar organizer. Centrioles and basal bodies might then not be simply the centres of replication of those organizers, but also reservoirs containing several superposed centriolar organizers, which are released depending on the requirements of the cell. As an isolated cartwheel is extremely unlikely to be detected, either in conventional electron microscopy or in immunocytochemistry, it is thus the reservoir which has so far been under consideration. Such a hypothesis would permit the explanation that biogenesis de novo and biogenesis in proximity to preexisting organelles may differ only in terms of the number of morphogenetic units involved.

Mitochondrial fission proteins Fis1 and Mdv1, but not Dnm1, play a role in maintenance of heteroplasmy in budding yeast.

PubMed

Bradshaw, Elliot; Yoshida, Minoru; Ling, Feng

2012-04-24

In budding yeast, the mitochondrial DNA (mtDNA) replication pathway involving the homologous DNA pairing protein Mhr1 promotes mitochondrial allele segregation. Mitochondrial fusion facilitates the recombination-mediated replication pathway; however, the role of fission remains largely unknown. By monitoring mitochondrial allele segregation during zygotic division, we found that the absence of fission proteins Fis1 or Mdv1, but not Dnm1, resulted in increased initial homoplasmy levels and decreased mtDNA copy number. However, decreases in mtDNA copy number alone were not sufficient for rapid establishment of homoplasmy, suggesting that inhibiting the activities of certain fission proteins promotes homoplasmy by reducing the number of mtDNA segregation units. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

A Comparison of Pathophysiology in Humans and Rodent Models of Subarachnoid Hemorrhage

PubMed Central

Leclerc, Jenna L.; Garcia, Joshua M.; Diller, Matthew A.; Carpenter, Anne-Marie; Kamat, Pradip K.; Hoh, Brian L.; Doré, Sylvain

2018-01-01

Non-traumatic subarachnoid hemorrhage (SAH) affects an estimated 30,000 people each year in the United States, with an overall mortality of ~30%. Most cases of SAH result from a ruptured intracranial aneurysm, require long hospital stays, and result in significant disability and high fatality. Early brain injury (EBI) and delayed cerebral vasospasm (CV) have been implicated as leading causes of morbidity and mortality in these patients, necessitating intense focus on developing preclinical animal models that replicate clinical SAH complete with delayed CV. Despite the variety of animal models currently available, translation of findings from rodent models to clinical trials has proven especially difficult. While the explanation for this lack of translation is unclear, possibilities include the lack of standardized practices and poor replication of human pathophysiology, such as delayed cerebral vasospasm and ischemia, in rodent models of SAH. In this review, we summarize the different approaches to simulating SAH in rodents, in particular elucidating the key pathophysiology of the various methods and models. Ultimately, we suggest the development of standardized model of rodent SAH that better replicates human pathophysiology for moving forward with translational research. PMID:29623028

Electrotransformation and clonal isolation of Rickettsia species

PubMed Central

Riley, Sean P; Macaluso, Kevin R; Martinez, Juan J

2015-01-01

Genetic manipulation of obligate intracellular bacteria of the genus Rickettsia is currently undergoing a rapid period of change. The development of viable genetic tools, including replicative plasmids, transposons, homologous recombination, fluorescent protein-encoding genes, and antibiotic selectable markers has provided the impetus for future research development. This unit is designed to coalesce the basic methods pertaining to creation of genetically modified Rickettsia. The unit describes a series of methods, from inserting exogenous DNA into Rickettsia to the final isolation of genetically modified bacterial clones. Researchers working towards genetic manipulation of Rickettsia or similar obligate intracellular bacteria will find these protocols to be a valuable reference. PMID:26528784

Big five personality factors and suicide rates in the United States: a state-level analysis.

PubMed

Voracek, Martin

2009-08-01

Partly replicating findings from several cross-national studies (of Lester and of Voracek) on possible aggregate-level associations between personality and suicide prevalence, state-level analysis within the United States yielded significantly negative associations between the Big Five factor of Neuroticism and suicide rates. This effect was observed for historical as well as contemporary suicide rates of the total or the elderly population and was preserved with controls for the four other Big Five factors and measures of state wealth. Also conforming to cross-national findings, the Big Five factors of Agreeableness and Extraversion were negatively, albeit not reliably, associated with suicide rates.

Magnetic resonance imaging compatible remote catheter navigation system with 3 degrees of freedom.

PubMed

Tavallaei, M A; Lavdas, M K; Gelman, D; Drangova, M

2016-08-01

To facilitate MRI-guided catheterization procedures, we present an MRI-compatible remote catheter navigation system that allows remote navigation of steerable catheters with 3 degrees of freedom. The system consists of a user interface (master), a robot (slave), and an ultrasonic motor control servomechanism. The interventionalist applies conventional motions (axial, radial and plunger manipulations) on an input catheter in the master unit; this user input is measured and used by the servomechanism to control a compact catheter manipulating robot, such that it replicates the interventionalist's input motion on the patient catheter. The performance of the system was evaluated in terms of MRI compatibility (SNR and artifact), feasibility of remote navigation under real-time MRI guidance, and motion replication accuracy. Real-time MRI experiments demonstrated that catheter was successfully navigated remotely to desired target references in all 3 degrees of freedom. The system had an absolute value error of [Formula: see text]1 mm in axial catheter motion replication over 30 mm of travel and [Formula: see text] for radial catheter motion replication over [Formula: see text]. The worst case SNR drop was observed to be [Formula: see text]3 %; the robot did not introduce any artifacts in the MR images. An MRI-compatible compact remote catheter navigation system has been developed that allows remote navigation of steerable catheters with 3 degrees of freedom. The proposed system allows for safe and accurate remote catheter navigation, within conventional closed-bore scanners, without degrading MR image quality.

Genetic and phenotypic correlations of quantitative traits in two long-term randomly mated soybean populations

USDA-ARS?s Scientific Manuscript database

The genetic effects of long term random mating and natural selection aided by genetic male sterility (gms) were evaluated in two soybean [Glycine max (L.) Merr.] populations designated: RSII and RSIII. These populations were evaluated in the field at three locations each with two replications. Genot...

The Relevance of Relationship Satisfaction and Continuation to the Gender Symmetry Debate

ERIC Educational Resources Information Center

Ackerman, Jeffrey M.

2012-01-01

In prior research, Ackerman and Field (2011) found that intimate partner violence (IPV) affects the relationship satisfaction of females more than the relationship satisfaction of males. The current research replicated those findings on a different sample of men and women. In addition to confirming past findings, it also found that gendered…

Diversity in Information Technology Education: Issues and Controversies

ERIC Educational Resources Information Center

Trajkovski, Goran, Ed.

2006-01-01

"Diversity in Information Technology Education: Issues and Controversies" sheds light on the status of diversity in the field of IT education. It identifies a wide range of problems that educators face on a daily basis, and gives practical, applicable solutions, mainly by showcasing successful and replicable examples. The chapters in "Diversity in…

Characterizing a point mutation within the UL5 gene that reduces in vivo replication and MD incidence

USDA-ARS?s Scientific Manuscript database

Marek’s disease virus (MDV) is an oncogenic alphaherpesvirus of chickens and the causative agent for Marek’s disease (MD). Vaccination is the primary method to control MD. Despite the success of vaccination, more virulent field strains are evolving, requiring the development of new vaccines. Attenua...

Evaluation of fungicide rotations for management of Phytophthora fruit rot of watermelon, 2015

USDA-ARS?s Scientific Manuscript database

The experiment was conducted at the U.S. Vegetable Laboratory farm in Charleston, SC. The soil was Yonges loamy fine sand. For the past 6 years, the field has been infested with Phytophthora capsici. The experimental design was a randomized complete block with four replications. Five-week-old seedli...

Modeling uncertainty of evapotranspiration measurements from multiple eddy covariance towers over a crop canopy

USDA-ARS?s Scientific Manuscript database

All measurements have random error associated with them. With fluxes in an eddy covariance system, measurement error can been modelled in several ways, often involving a statistical description of turbulence at its core. Using a field experiment with four towers, we generated four replicates of meas...

Influence of liquid surface area on hydrogen sulfide oxidation during micro-aeration in dairy manure digesters

USDA-ARS?s Scientific Manuscript database

The specific objectives of this study were to evaluate headspace aeration for reducing hydrogen sulfide levels in low cost plug flow digesters, and to characterize the relationship between the liquid surface area and hydrogen sulfide oxidation rates. Experiments with replicate field scale plug flow ...

An Analysis of State Guidelines for Intellectual Disability

ERIC Educational Resources Information Center

Polloway, Edward A.; Auguste, Maryleen; Smith, J. David; Peters, Delia

2017-01-01

This study provides an updated analysis of state guidelines with respect to terminology and definitions in the field of intellectual disability (ID). The study serves as a methodological replication of prior work that has been reported in the literature in earlier decades. The data were acquired by reviewing web-based state guidelines for ID…

Reference conditions for silvicultural field studies in Maine: limitations and opportunities

Treesearch

Laura S. Kenefic; Alan S. White; Shawn Fraver

2004-01-01

There are many types of controls or reference conditions for silvicultural experiments. The most basic are pretreatment records of composition and structure, but such data provide little information about response to treatment compared to natural developmental and disturbance patterns. Ideally, experiments should have untreated stand replicates in which development can...

Reference Stands for Silvicultural Research: A Maine Perspective

Treesearch

Laura S. Kenefic; Alan S. White; Andrew R. Cutko; Shawn Fraver

2005-01-01

Silvicultural experiments should have untreated stand replicates in which development can be tracked over time. Unfortunately, field studies are seldom ideal. This article is one of six in this issue addressing experimental controls. Our focus is the Penobscot Experimental Forest (PEF) in Maine, where a 55-year-old experiment in northern conifer silviculture has an...

Field testing existence values for riparian ecosystems

Treesearch

John W. Duffield; Chris J. Neher; David A. Patterson; Patricia A. Champ

2007-01-01

This paper presents preliminary findings on a cash and contingent valuation (cv) experiment. The study replicates major elements of an earlier (1990) experiment, which solicited hypothetical and actual donations to benefit instream flows for Montana fisheries. Extensions of the earlier work include: repeat contacts to increase response rate, follow-up of the contingent...

Association of Verde plant bug, Creontiades signatus (Hemiptera: Miridae), with cotton boll rot

USDA-ARS?s Scientific Manuscript database

Cotton along the Gulf Coast of south Texas has experienced loss from cotton boll rot especially during the last 10 to 15 years, and stink bugs and plant bugs (Hemiptera: Pentatomidae and Miridae) that feed on cotton bolls have been suspected in introducing the disease. A replicated grower field surv...

Evaluation of dry-fleshed sweetpotato genotypes for resistance to soil insect pests, 2012

USDA-ARS?s Scientific Manuscript database

An insect susceptible check cultivar (‘SC1149 19’), an insect resistant check cultivar (‘Ruddy’), 20 advanced dry-fleshed genotypes, and five dry-fleshed cultivars (‘Bonita’, ‘Liberty’, ‘NC Japanese’, ‘Picadito’, and ‘Sumor’) were evaluated for insect resistance in replicated field trials at Charles...

Bioassay of plant growth from soils varying in active C and N fractions

USDA-ARS?s Scientific Manuscript database

Biologically active soil C and N fractions are important attributes of healthy soil. As a bioassay, we hypothesized that active soil C and N fractions would relate with plant dry matter production from unamended soil. Four replicate soil samples from 22 tall fescue fields in North Carolina and Virgi...

Virtual Virtuosos: A Case Study in Learning Music in Virtual Learning Environments in Spain

ERIC Educational Resources Information Center

Alberich-Artal, Enric; Sangra, Albert

2012-01-01

In recent years, the development of Information and Communication Technologies (ICT) has contributed to the generation of a number of interesting initiatives in the field of music education and training in virtual learning environments. However, music education initiatives employing virtual learning environments have replicated and perpetuated the…

Seasonal trends in response to inoculation of coast live oak with Phytophthora ramorum

Treesearch

Richard S. Dodd; Daniel Hüberli; Tamar Y. Harnik; Brenda O' Dell; Matteo Garbelotto

2006-01-01

We developed a branch cutting inoculation method to provide a controlled system for studying variation in response to inoculation of coast live oak (Quercus agrifolia) with Phytophthora ramorum. This method has advantages over inoculations of trees in the field, in containing the inoculum and in allowing high levels of replication...

Multiple rolling/crimping effects on termination of two summer cover crops in a conservation system

USDA-ARS?s Scientific Manuscript database

A field experiment was initiated in the 2015 growing season at the USDA-NSDL to determine the effectiveness of a prototype two-stage roller/crimper in mechanical termination of two summer cover crops intended for organic systems. The experiment was a randomized complete block design with four replic...

Research Areas in Adult and Continuing Education

ERIC Educational Resources Information Center

Zawacki-Richter, Olaf; Röbken, Heinke; Ehrenspeck-Kolasa, Yvonne; von Ossietzky, Carl

2014-01-01

This study builds upon a Delphi study carried out by Zawacki-Richter (2009) which posited a validated classification of research areas in the special area of distance education. We now replicate the study for the broader field of adult and continuing education (ACE). The aims of this paper are: firstly, to develop a categorisation of research…

Development of criteria for the use of asphalt-rubber as a Stress-Absorbing Membrane Interlayer (SAMI)

NASA Astrophysics Data System (ADS)

Newcomb, D. E.; McKeen, R. G.

1983-12-01

This report documents over 2 years of research efforts to characterize asphalt-rubber mixtures to be used in Stress-Absorbing Membrane Interlayers (SAMI). The purpose of these SAMIs is to retard or prevent reflection cracking in asphalt-concrete overlays. Several laboratory experiments and one field trial were conducted to define significant test methods and parameters for incorporation into construction design and specification documents. Test methods used in this study included a modified softening point test, force-ductility, and Schweyer viscosity. Variables investigated included (1) Laboratory-mixing temperature; (2) Rubber type; (3) Laboratory storage time; (4) Laboratory storage condition; (5) Laboratory batch replication; (6) Laboratory mixing time; (7) Field mixing time; (8) Laboratory test temperature; (9) Force-Ductility elongation rates; and (10) Asphalt grade. It was found that mixing temperature, mixing time, rubber type, and asphalt grade all have significant effects upon the behavior of asphalt-rubber mixtures. Significant variability was also noticed in different laboratory batch replications. Varying laboratory test temperature and force-ductility elongation rate revealed further differences in asphalt-rubber mixtures.

The secret lives of experiments: methods reporting in the fMRI literature.

PubMed

Carp, Joshua

2012-10-15

Replication of research findings is critical to the progress of scientific understanding. Accordingly, most scientific journals require authors to report experimental procedures in sufficient detail for independent researchers to replicate their work. To what extent do research reports in the functional neuroimaging literature live up to this standard? The present study evaluated methods reporting and methodological choices across 241 recent fMRI articles. Many studies did not report critical methodological details with regard to experimental design, data acquisition, and analysis. Further, many studies were underpowered to detect any but the largest statistical effects. Finally, data collection and analysis methods were highly flexible across studies, with nearly as many unique analysis pipelines as there were studies in the sample. Because the rate of false positive results is thought to increase with the flexibility of experimental designs, the field of functional neuroimaging may be particularly vulnerable to false positives. In sum, the present study documented significant gaps in methods reporting among fMRI studies. Improved methodological descriptions in research reports would yield significant benefits for the field. Copyright © 2012 Elsevier Inc. All rights reserved.

Nanoimprint system development and status for high volume semiconductor manufacturing

NASA Astrophysics Data System (ADS)

Hiura, Hiromi; Takabayashi, Yukio; Takashima, Tsuneo; Emoto, Keiji; Choi, Jin; Schumaker, Phil

2016-10-01

Imprint lithography has been shown to be an effective technique for replication of nano-scale features. Jet and Flash Imprint Lithography* (J-FIL*) involves the field-by-field deposition and exposure of a low viscosity resist deposited by jetting technology onto the substrate. The patterned mask is lowered into the fluid which then quickly flows into the relief patterns in the mask by capillary action. Following this filling step, the resist is crosslinked under UV radiation, and then the mask is removed, leaving a patterned resist on the substrate. There are many criteria that determine whether a particular technology is ready for wafer manufacturing. For imprint lithography, recent attention has been given to the areas of overlay, throughput, defectivity, and mask replication. This paper reviews progress in these critical areas. Recent demonstrations have proven that mix and match overlay of less than 5nm can achieved. Further reductions require a higher order correction system. Modeling and experimental data are presented which provide a path towards reducing the overlay errors to less than 3nm. Throughput is mainly impacted by the fill time of the relief images on the mask. Improvement in resist materials provides a solution that allows 15 wafers per hour per station, or a tool throughput of 60 wafers per hour. Defectivity and mask life play a significant role relative to meeting the cost of ownership (CoO) requirements in the production of semiconductor devices. Hard particles on a wafer or mask create the possibility of inducing a permanent defect on the mask that can impact device yield and mask life. By using material methods to reduce particle shedding and by introducing an air curtain system, the lifetime of both the master mask and the replica mask can be extended. In this work, we report results that demonstrate a path towards achieving mask lifetimes of better than 1000 wafers. Finally, on the mask side, a new replication tool, the FPA-1100NR2 is introduced. Mask replication is required for nanoimprint lithography (NIL), and criteria that are crucial to the success of a replication platform include both particle control and IP accuracy. In particular, by improving the specifications on the mask chuck, residual errors of only 1nm can be realized.

Comparison of feed energy costs of maintenance, lean deposition, and fat deposition in three lines of mice selected for heat loss.

PubMed

Eggert, D L; Nielsen, M K

2006-02-01

Three replications of mouse selection populations for high heat loss (MH), low heat loss (ML), and a nonselected control (MC) were used to estimate the feed energy costs of maintenance and gain and to test whether selection had changed these costs. At 21 and 49 d of age, mice were weighed and subjected to dual x-ray densitometry measurement for prediction of body composition. At 21 d, mice were randomly assigned to an ad libitum, an 80% of ad libitum, or a 60% of ad libitum feeding group for 28-d collection of individual feed intake. Data were analyzed using 3 approaches. The first approach was an attempt to partition energy intake between costs for maintenance, fat deposition, and lean deposition for each replicate, sex, and line by multiple regression of feed intake on the sum of daily metabolic weight (kg(0.75)), fat gain, and lean gain. Approach II was a less restrictive attempt to partition energy intake between costs for maintenance and total gain for each replicate, sex, and line by multiple regression of feed intake on the sum of daily metabolic weight and total gain. Approach III used multiple regression on the entire data set with pooled regressions on fat and lean gains, and subclass regressions for maintenance. Contrasts were conducted to test the effect of selection (MH - ML) and asymmetry of selection [(MH + ML)/2 - MC] for the various energy costs. In approach I, there were no differences between lines for costs of maintenance, fat deposition, or protein deposition, but we question our ability to estimate these accurately. In approach II, selection changed both cost of maintenance (P = 0.03) and gain (P = 0.05); MH mice had greater per unit costs than ML mice for both. Asymmetry of the selection response was found in approach II for the cost of maintenance (P = 0.06). In approach III, the effect of selection (P < 0.01) contributed to differences in the maintenance cost, but asymmetry of selection (P > 0.17) was not evident. Sex effects were found for the cost of fat deposition (P = 0.02) in approach I and the cost of gain (P = 0.001) in approach II; females had a greater cost per unit than males. When costs per unit of fat and per unit of lean gain were assumed to be the same for both sexes (approach III), females had a somewhat greater estimate for maintenance cost (P = 0.10). We conclude that selection for heat loss has changed the costs for maintenance per unit size but probably not the costs for gain.

Visual evoked potentials and selective attention to points in space

NASA Technical Reports Server (NTRS)

Van Voorhis, S.; Hillyard, S. A.

1977-01-01

Visual evoked potentials (VEPs) were recorded to sequences of flashes delivered to the right and left visual fields while subjects responded promptly to designated stimuli in one field at a time (focused attention), in both fields at once (divided attention), or to neither field (passive). Three stimulus schedules were used: the first was a replication of a previous study (Eason, Harter, and White, 1969) where left- and right-field flashes were delivered quasi-independently, while in the other two the flashes were delivered to the two fields in random order (Bernoulli sequence). VEPs to attended-field stimuli were enhanced at both occipital (O2) and central (Cz) recording sites under all stimulus sequences, but different components were affected at the two scalp sites. It was suggested that the VEP at O2 may reflect modality-specific processing events, while the response at Cz, like its auditory homologue, may index more general aspects of selective attention.

The permuted generator hypothesis for the origin of a genetic code

NASA Technical Reports Server (NTRS)

Folsome, C.

1977-01-01

Protocells had no known means of ensuring that their randomly collected proteins would be duplicated. A possible, albeit inexact, mechanism for protein synthesis in a primitive t-RNA is presented, whereby an oligonucleotide (12 units) in a circular configuration is able to align a generator site with amino acid discriminator sites. In this way, unique anticodons could be specified for each site and replication could occur.

Response of white-footed mice (Peromyscus leucopus) to fire and fire surrogate fuel reduction treatments in a southern Appalachian hardwood forest

Treesearch

Cathryn H. Greenberg; David L. Otis; Thomas A. Waldrop

2006-01-01

An experiment conducted as part of the multidisciplinary National Fire and Fire Surrogate Study was designed to determine effects of three fuel reduction techniques on small mammals and habitat structure in the southern Appalachian mountains. Four experimental units, each >14-ha were contained within each of three replicate blocks at the Green River Game Land,...

An Empirical Model-based MOE for Friction Reduction by Slot-Ejected Polymer Solutions in an Aqueous Environment

DTIC Science & Technology

2007-12-21

of hydrodynamics and the physical characteristics of the polymers. The physics models include both analytical models and numerical simulations ...the experimental observations. The numerical simulations also succeed in replicating some experimental measurements. However, there is still no...become quite significant. 4.5 Documentation The complete model is coded in MatLab . In the model, all units are cgs, so distances are in

A comparison of tools for remotely estimating leaf area index in loblolly pine plantations

Treesearch

Janet C. Dewey; Scott D. Roberts; Isobel Hartley

2006-01-01

Light interception is critical to forest growth and is largely determined by foliage area per unit ground, the measure of which is leaf area index (LAI). Summer and winter LAI estimates were obtained in a 17-year-old loblolly pine (Pinus taeda L.) spacing trial in Mississippi, using three replications with initial spacings of 1.5, 2.4, and 3.0 m....

Effects of fire and fire surrogate treatments on bark beetle-caused tree mortality in the Southern Cascades, California

Treesearch

C.J. Fettig; R.R. Borys; C.P. and Dabney

2010-01-01

We examined bark beetle responses to fire and fire surrogate treatments 2 and 4 years after the application of prescribed fire in a mixed-conifer forest in northern California. Treatments included an untreated control (C), thinning from below (T), and applications of prescribed fire (B) and T + B replicated three times in 10-ha experimental units. A total of 1,822...

Self-Replication of Localized Vegetation Patches in Scarce Environments

PubMed Central

Bordeu, Ignacio; Clerc, Marcel G.; Couteron, Piere; Lefever, René; Tlidi, Mustapha

2016-01-01

Desertification due to climate change and increasing drought periods is a worldwide problem for both ecology and economy. Our ability to understand how vegetation manages to survive and propagate through arid and semiarid ecosystems may be useful in the development of future strategies to prevent desertification, preserve flora—and fauna within—or even make use of scarce resources soils. In this paper, we study a robust phenomena observed in semi-arid ecosystems, by which localized vegetation patches split in a process called self-replication. Localized patches of vegetation are visible in nature at various spatial scales. Even though they have been described in literature, their growth mechanisms remain largely unexplored. Here, we develop an innovative statistical analysis based on real field observations to show that patches may exhibit deformation and splitting. This growth mechanism is opposite to the desertification since it allows to repopulate territories devoid of vegetation. We investigate these aspects by characterizing quantitatively, with a simple mathematical model, a new class of instabilities that lead to the self-replication phenomenon observed. PMID:27650430

Reproducibility and replicability of rodent phenotyping in preclinical studies.

PubMed

Kafkafi, Neri; Agassi, Joseph; Chesler, Elissa J; Crabbe, John C; Crusio, Wim E; Eilam, David; Gerlai, Robert; Golani, Ilan; Gomez-Marin, Alex; Heller, Ruth; Iraqi, Fuad; Jaljuli, Iman; Karp, Natasha A; Morgan, Hugh; Nicholson, George; Pfaff, Donald W; Richter, S Helene; Stark, Philip B; Stiedl, Oliver; Stodden, Victoria; Tarantino, Lisa M; Tucci, Valter; Valdar, William; Williams, Robert W; Würbel, Hanno; Benjamini, Yoav

2018-04-01

The scientific community is increasingly concerned with the proportion of published "discoveries" that are not replicated in subsequent studies. The field of rodent behavioral phenotyping was one of the first to raise this concern, and to relate it to other methodological issues: the complex interaction between genotype and environment; the definitions of behavioral constructs; and the use of laboratory mice and rats as model species for investigating human health and disease mechanisms. In January 2015, researchers from various disciplines gathered at Tel Aviv University to discuss these issues. The general consensus was that the issue is prevalent and of concern, and should be addressed at the statistical, methodological and policy levels, but is not so severe as to call into question the validity and the usefulness of model organisms as a whole. Well-organized community efforts, coupled with improved data and metadata sharing, have a key role in identifying specific problems and promoting effective solutions. Replicability is closely related to validity, may affect generalizability and translation of findings, and has important ethical implications. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Cryo-EM visualization of the protein machine that replicates the chromosome

NASA Astrophysics Data System (ADS)

Li, Huilin

Structural knowledge is key to understanding biological functions. Cryo-EM is a physical method that uses transmission electron microscopy to visualize biological molecules that are frozen in vitreous ice. Due to recent advances in direct electron detector and image processing algorithm, cryo-EM has become a high-resolution technique. Cryo-EM field is undergoing a rapid expansion and vast majority research institutions and research universities around the world are setting up cryo-EM research. Indeed, the method is revolutionizing structural and molecular biology. We have been using cryo-EM to study the structure and mechanism of eukaryotic chromosome replication. Despite an abundance of cartoon drawings found in review articles and biology textbooks, the structure of the eukaryotic helicase that unwinds the double stranded DNA has been unknown. It has also been unknown how the helicase works with DNA polymerases to accomplish the feat of duplicating the genome. In my presentation, I will show how we have used cryo-EM to derive at structures of the eukaryotic chromosome replication machinery and describe mechanistic insights we have gleaned from the structures.

Adenovirus-mediated p53 gene delivery inhibits 9L glioma growth in rats.

PubMed

Badie, B; Drazan, K E; Kramar, M H; Shaked, A; Black, K L

1995-06-01

Adenoviral vectors have recently been shown to effectively deliver genes into a variety of tissues. Since these vectors have some advantages over the more extensively investigated retroviruses, we studied the effect of two replication-defective adenovectors bearing human wild type tumor suppressor gene p53 (Adp53) and Escherichia coli beta-galactosidase gene (AdLacZ) on 9L glioma cells. Successful in vitro gene transfer was shown by DNA polymerase chain reaction (PCR), and expression was confirmed by reverse transcriptase RNA PCR and Western blot analyses. Transduction of 9L cells with the Adp53 inhibited cell growth and induced phenotypic changes consistent with cell death at low titers, while AdLacZ caused cytopathic changes only at high titers. Stereotactic injection of AdLacZ (10(7) plaque forming units) into tumor bed stained 25 to 30% of tumor cells at the site of vector delivery. Injection of Adp53 (10(7) plaque forming units), but not AdLacZ (controls), into established 4-day old 9L glioma brain tumors decreased tumor volume by 40% after 14 days. As a step toward gene therapy of brain tumors using replication-defective adenoviruses, these data support the use of tumor suppressor gene transfer for in vivo treatment of whole animal brain tumor models.

Method for Estimating Three-Dimensional Knee Rotations Using Two Inertial Measurement Units: Validation with a Coordinate Measurement Machine

PubMed Central

Vitali, Rachel V.; Cain, Stephen M.; Zaferiou, Antonia M.; Ojeda, Lauro V.; Perkins, Noel C.

2017-01-01

Three-dimensional rotations across the human knee serve as important markers of knee health and performance in multiple contexts including human mobility, worker safety and health, athletic performance, and warfighter performance. While knee rotations can be estimated using optical motion capture, that method is largely limited to the laboratory and small capture volumes. These limitations may be overcome by deploying wearable inertial measurement units (IMUs). The objective of this study is to present a new IMU-based method for estimating 3D knee rotations and to benchmark the accuracy of the results using an instrumented mechanical linkage. The method employs data from shank- and thigh-mounted IMUs and a vector constraint for the medial-lateral axis of the knee during periods when the knee joint functions predominantly as a hinge. The method is carefully validated using data from high precision optical encoders in a mechanism that replicates 3D knee rotations spanning (1) pure flexion/extension, (2) pure internal/external rotation, (3) pure abduction/adduction, and (4) combinations of all three rotations. Regardless of the movement type, the IMU-derived estimates of 3D knee rotations replicate the truth data with high confidence (RMS error < 4° and correlation coefficient r≥0.94). PMID:28846613

Structural Protein VP2 of African Horse Sickness Virus Is Not Essential for Virus Replication In Vitro

PubMed Central

van de Water, Sandra G. P.; Potgieter, Christiaan A.; van Rijn, Piet A.

2016-01-01

ABSTRACT The Reoviridae family consists of nonenveloped multilayered viruses with a double-stranded RNA genome consisting of 9 to 12 genome segments. The Orbivirus genus of the Reoviridae family contains African horse sickness virus (AHSV), bluetongue virus, and epizootic hemorrhagic disease virus, which cause notifiable diseases and are spread by biting Culicoides species. Here, we used reverse genetics for AHSV to study the role of outer capsid protein VP2, encoded by genome segment 2 (Seg-2). Expansion of a previously found deletion in Seg-2 indicates that structural protein VP2 of AHSV is not essential for virus replication in vitro. In addition, in-frame replacement of RNA sequences in Seg-2 by that of green fluorescence protein (GFP) resulted in AHSV expressing GFP, which further confirmed that VP2 is not essential for virus replication. In contrast to virus replication without VP2 expression in mammalian cells, virus replication in insect cells was strongly reduced, and virus release from insect cells was completely abolished. Further, the other outer capsid protein, VP5, was not copurified with virions for virus mutants without VP2 expression. AHSV without VP5 expression, however, could not be recovered, indicating that outer capsid protein VP5 is essential for virus replication in vitro. Our results demonstrate for the first time that a structural viral protein is not essential for orbivirus replication in vitro, which opens new possibilities for research on other members of the Reoviridae family. IMPORTANCE Members of the Reoviridae family cause major health problems worldwide, ranging from lethal diarrhea caused by rotavirus in humans to economic losses in livestock production caused by different orbiviruses. The Orbivirus genus contains many virus species, of which bluetongue virus, epizootic hemorrhagic disease virus, and African horse sickness virus (AHSV) cause notifiable diseases according to the World Organization of Animal Health. Recently, it has been shown that nonstructural proteins NS3/NS3a and NS4 are not essential for virus replication in vitro, whereas it is generally assumed that structural proteins VP1 to -7 of these nonenveloped, architecturally complex virus particles are essential. Here we demonstrate for the first time that structural protein VP2 of AHSV is not essential for virus replication in vitro. Our findings are very important for virologists working in the field of nonenveloped viruses, in particular reoviruses. PMID:27903804

Collection methods and quality assessment for Esche-richia coli, water quality, and microbial source tracking data within Tumacácori National Historical Park and the upper Santa Cruz River, Arizona, 2015-16

USGS Publications Warehouse

Paretti, Nicholas; Coes, Alissa L.; Kephart, Christopher M.; Mayo, Justine

2018-03-05

Tumacácori National Historical Park protects the culturally important Mission, San José de Tumacácori, while also managing a portion of the ecologically diverse riparian corridor of the Santa Cruz River. This report describes the methods and quality assurance procedures used in the collection of water samples for the analysis of Escherichia coli (E. coli), microbial source tracking markers, suspended sediment, water-quality parameters, turbidity, and the data collection for discharge and stage; the process for data review and approval is also described. Finally, this report provides a quantitative assessment of the quality of the E. coli, microbial source tracking, and suspended sediment data.The data-quality assessment revealed that bias attributed to field and laboratory contamination was minimal, with E. coli detections in only 3 out of 33 field blank samples analyzed. Concentrations in the field blanks were several orders of magnitude lower than environmental concentrations. The microbial source tracking (MST) field blank was below the detection limit for all MST markers analyzed. Laboratory blanks for E. coli at the USGS Arizona Water Science Center and laboratory blanks for MST markers at the USGS Ohio Water Microbiology Laboratory were all below the detection limit. Irreplicate data for E. coli and suspended sediment indicated that bias was not introduced to the data by combining samples collected using discrete sampling methods with samples collected using automatic sampling methods.The split and sequential E. coli replicate data showed consistent analytical variability and a single equation was developed to explain the variability of E. coli concentrations. An additional analysis of analytical variability for E. coli indicated analytical variability around 18 percent relative standard deviation and no trend was observed in the concentration during the processing and analysis of multiple split-replicates. Two replicate samples were collected for MST and individual markers were compared for a base flow and flood sample. For the markers found in common between the two types of samples, the relative standard deviation for the base flow sample was more than 3 times greater than the markers in the flood sample. Sequential suspended sediment replicates had a relative standard deviation of about 1.3 percent, indicating that environmental and analytical variability was minimal.A holding time review and laboratory study analysis supported the extended holding times required for this investigation. Most concentrations for flood and base-flow samples were within the theoretical variability specified in the most probable number approach suggesting that extended hold times did not overly influence the final concentrations reported.

Hardware Verification of Laser Noise Cancellation and Gravitational Wave Extraction using Time-Delay Interferometry

NASA Astrophysics Data System (ADS)

Mitryk, Shawn; Mueller, Guido

The Laser Interferometer Space Antenna (LISA) is a space-based modified Michelson interfer-ometer designed to measure gravitational radiation in the frequency range from 30 uHz to 1 Hz. The interferometer measurement system (IMS) utilizes one-way laser phase measurements to cancel the laser phase noise, reconstruct the proof-mass motion, and extract the gravitational wave (GW) induced laser phase modulations in post-processing using a technique called time-delay interferometry (TDI). Unfortunately, there exist few hard-ware verification experiments of the IMS. The University of Florida LISA Interferometry Simulator (UFLIS) is designed to perform hardware-in-the-loop simulations of the LISA interferometry system, modeling the characteris-tics of the LISA mission as accurately as possible. This depends, first, on replicating the laser pre-stabilization by locking the laser phase to an ultra-stable Zerodur cavity length reference using the PDH locking method. Phase measurements of LISA-like photodetector beat-notes are taken using the UF-phasemeter (PM) which can measure the laser BN frequency to within an accuracy of 0.22 uHz. The inter-space craft (SC) laser links including the time-delay due to the 5 Gm light travel time along the LISA arms, the laser Doppler shifts due to differential SC motion, and the GW induced laser phase modulations are simulated electronically using the electronic phase delay (EPD) unit. The EPD unit replicates the laser field propagation between SC by measuring a photodetector beat-note frequency with the UF-phasemeter and storing the information in memory. After the requested delay time, the frequency information is added to a Doppler offset and a GW-like frequency modulation. The signal is then regenerated with the inter-SC laser phase affects applied. Utilizing these components, I will present the first complete TDI simulations performed using the UFLIS. The LISA model is presented along-side the simulation, comparing the generation and measurement of LISA-like signals. Phasemeter measurements are used in post-processing and combined in the linear combinations defined by TDI, thus, canceling the laser phase and phase-lock loop noise to extract the applied GW modulation buried under the noise. Nine order of magnitude common mode laser noise cancellation is achieved at a frequency of 1 mHz and the GW signal is clearly visible after the laser and PLL noise cancellation.

Recovery from Proactive Semantic Interference and MRI Volume: A Replication and Extension Study.

PubMed

Loewenstein, David A; Curiel, Rosie E; DeKosky, Steven; Rosselli, Monica; Bauer, Russell; Grieg-Custo, Maria; Penate, Ailyn; Li, Chunfei; Lizagarra, Gabriel; Golde, Todd; Adjouadi, Malek; Duara, Ranjan

2017-01-01

The rise in incidence of Alzheimer's disease (AD) has led to efforts to advance early detection of the disease during its preclinical stages. To achieve this, the field needs to develop more sensitive cognitive tests that relate to biological markers of disease pathology. Failure to recover from proactive interference (frPSI) is one such cognitive marker that is associated with volumetric reductions in the hippocampus, precuneus, and other AD-prone regions, and to amyloid load in the brain. The current study attempted to replicate and extend our previous findings that frPSI is a sensitive marker of early AD, and related to a unique pattern of volumetric loss in AD prone areas. Three different memory measures were examined relative to volumetric loss and cortical thickness among 45 participants with amnestic mild cognitive impairment. frPSI was uniquely associated with reduced volumes in the hippocampus (r = 0.50) precuneus (r = 0.41), and other AD prone regions, replicating previous findings. Strong associations between frPSI and lower entorhinal cortex volumes and cortical thickness (r≥0.60) and precuneus (r = 0.50) were also observed. Unique and strong associations between volumetric reductions and frPSI as observed by Loewenstein and colleagues were replicated. Together with cortical thickness findings, these results indicate that frPSI is worthy of further study as a sensitive and early cognitive marker of AD.

Replicability and other features of a high-quality science: Toward a balanced and empirical approach.

PubMed

Finkel, Eli J; Eastwick, Paul W; Reis, Harry T

2017-08-01

Finkel, Eastwick, and Reis (2015; FER2015) argued that psychological science is better served by responding to apprehensions about replicability rates with contextualized solutions than with one-size-fits-all solutions. Here, we extend FER2015's analysis to suggest that much of the discussion of best research practices since 2011 has focused on a single feature of high-quality science-replicability-with insufficient sensitivity to the implications of recommended practices for other features, like discovery, internal validity, external validity, construct validity, consequentiality, and cumulativeness. Thus, although recommendations for bolstering replicability have been innovative, compelling, and abundant, it is difficult to evaluate their impact on our science as a whole, especially because many research practices that are beneficial for some features of scientific quality are harmful for others. For example, FER2015 argued that bigger samples are generally better, but also noted that very large samples ("those larger than required for effect sizes to stabilize"; p. 291) could have the downside of commandeering resources that would have been better invested in other studies. In their critique of FER2015, LeBel, Campbell, and Loving (2016) concluded, based on simulated data, that ever-larger samples are better for the efficiency of scientific discovery (i.e., that there are no tradeoffs). As demonstrated here, however, this conclusion holds only when the replicator's resources are considered in isolation. If we widen the assumptions to include the original researcher's resources as well, which is necessary if the goal is to consider resource investment for the field as a whole, the conclusion changes radically-and strongly supports a tradeoff-based analysis. In general, as psychologists seek to strengthen our science, we must complement our much-needed work on increasing replicability with careful attention to the other features of a high-quality science. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Microscopy-based Assays for High-throughput Screening of Host Factors Involved in Brucella Infection of Hela Cells.

PubMed

Casanova, Alain; Low, Shyan H; Emmenlauer, Mario; Conde-Alvarez, Raquel; Salcedo, Suzana P; Gorvel, Jean-Pierre; Dehio, Christoph

2016-08-05

Brucella species are facultative intracellular pathogens that infect animals as their natural hosts. Transmission to humans is most commonly caused by direct contact with infected animals or by ingestion of contaminated food and can lead to severe chronic infections. Brucella can invade professional and non-professional phagocytic cells and replicates within endoplasmic reticulum (ER)-derived vacuoles. The host factors required for Brucella entry into host cells, avoidance of lysosomal degradation, and replication in the ER-like compartment remain largely unknown. Here we describe two assays to identify host factors involved in Brucella entry and replication in HeLa cells. The protocols describe the use of RNA interference, while alternative screening methods could be applied. The assays are based on the detection of fluorescently labeled bacteria in fluorescently labeled host cells using automated wide-field microscopy. The fluorescent images are analyzed using a standardized image analysis pipeline in CellProfiler which allows single cell-based infection scoring. In the endpoint assay, intracellular replication is measured two days after infection. This allows bacteria to traffic to their replicative niche where proliferation is initiated around 12 hr after bacterial entry. Brucella which have successfully established an intracellular niche will thus have strongly proliferated inside host cells. Since intracellular bacteria will greatly outnumber individual extracellular or intracellular non-replicative bacteria, a strain constitutively expressing GFP can be used. The strong GFP signal is then used to identify infected cells. In contrast, for the entry assay it is essential to differentiate between intracellular and extracellular bacteria. Here, a strain encoding for a tetracycline-inducible GFP is used. Induction of GFP with simultaneous inactivation of extracellular bacteria by gentamicin enables the differentiation between intracellular and extracellular bacteria based on the GFP signal, with only intracellular bacteria being able to express GFP. This allows the robust detection of single intracellular bacteria before intracellular proliferation is initiated.

Differences in replication kinetics and cell tropism between neurovirulent and non-neurovirulent EHV1 strains during the acute phase of infection in horses.

PubMed

Gryspeerdt, Annick C; Vandekerckhove, A P; Garré, B; Barbé, F; Van de Walle, G R; Nauwynck, H J

2010-05-19

Equine herpesvirus 1 (EHV1) replicates in the respiratory tract of horses, after which infected leukocytes transport virus throughout the body, resulting in abortion or nervous system disorders. Two EHV1 strains circulate in the field: neurovirulent and non-neurovirulent. To investigate differences in replication in the upper respiratory tract (URT), an experimental inoculation study in ponies was performed with both strains. Two groups of six ponies, were inoculated intranasally with 10(6.5) TCID(50) of either strain. Clinical signs, nasal shedding and viremia were evaluated. At early time points post-inoculation (pi), one pony of each group was euthanized. Tissues were collected for titration and immunostainings. Number and size of EHV1-induced plaques were calculated, and individual EHV1-infected cells were quantified and characterized. Inoculation with either strain resulted in nasal shedding and replication in several tissues of the URT. Both strains replicated in a plaquewise manner in epithelium of the nasal mucosa, but replication in epithelium of the nasopharynx was largely limited to non-neurovirulent EHV1. Plaques were never able to cross the basement membrane, but individual infected cells were noticed in the connective tissue of all examined tissues for both strains. The total number of these cells however, was 3-7 times lower with non-neurovirulent EHV1 compared to neurovirulent EHV1. CD172a(+) cells and CD5(+) lymphocytes were important target cells for both strains. Interestingly, in lymph nodes, B-lymphocytes were also important target cells for EHV1, irrespective of the strain. Viremia was detected very early pi and infected cells were mainly CD172a(+) for both strains. In summary, these results are valuable for understanding EHV1 pathogenesis at the port of entry, the URT. Copyright 2009 Elsevier B.V. All rights reserved.

Training General Aviation Pilots for Convective Weather Situations.

PubMed

Blickensderfer, Elizabeth L; Lanicci, John M; Vincent, Michael J; Thomas, Robert L; Smith, MaryJo; Cruit, Jessica K

2015-10-01

Over the past 10-15 yr, considerable research has occurred for the development, testing, and fielding of real-time Datalink weather products for general aviation (GA) pilots to use before and during flight. As is the case with the implementation of most new technologies, work is needed to ensure that the users (in this case, the pilots) understand both the capabilities and limitations of the new technologies as well as how to use the new systems to improve their task performance. The purpose of this study was to replicate and extend a previous study on training pilots how and when to use these new weather technologies. This field study used a quasi-experimental design (pre- vs. post-test with a control group). There were 91 GA pilots from the Midwest, Northeastern, and Southeastern United States who participated in a 2-h short course or a control activity. The lecture-based short course covered radar basics, Next Generation Weather Radar (NEXRAD), NEXRAD specifics/limitations, thunderstorm basics, radar products, and decision making. The pilots who participated in the course earned higher knowledge test scores, improved at applying the concepts in paper-based flight scenarios, had higher self-efficacy in post-training assessments as compared to pre-training assessments, and also performed better than did control subjects on post-test knowledge and skills assessments. GA pilots lack knowledge about real-time Datalink weather technology. This study indicates that a relatively short training program was effective for fostering Datalink weather-related knowledge and skills in GA pilots.

Reliable Method for Assessing Seed Germination, Dormancy, and Mortality under Field Conditions.

PubMed

Pace, Brian A; Alexander, Helen M; Emry, D Jason; Mercer, Kristin L

2016-11-06

We describe techniques for approximating seed bank dynamics over time using Helianthus annuus as an example study species. Strips of permeable polyester fabric and glue can be folded and glued to construct a strip of compartments that house seeds and identifying information, while allowing contact with soil leachate, water, microorganisms, and ambient temperature. Strips may be constructed with a wide range of compartment numbers and sizes and allow the researcher to house a variety of genotypes within a single species, different species, or seeds that have experienced different treatments. As opposed to individual seed packets, strips are more easily retrieved as a unit. While replicate packets can be included within a strip, different strips can act as blocks or can be retrieved at different times for observation of seed behavior over time. We used a high temperature glue gun to delineate compartments and sealed the strips once the seed and tags identifying block and removal times were inserted. The seed strips were then buried in the field at the desired depth, with the location marked for later removal. Burrowing animal predators were effectively excluded by use of a covering of metal mesh hardware cloth on the soil surface. After the selected time interval for burial, strips were dug up and seeds were assessed for germination, dormancy and mortality. While clearly dead seeds can often be distinguished from ungerminated living ones by eye, dormant seeds were conclusively identified using a standard Tetrazolium chloride colorimetric test for seed viability.

Plant-animal interactions in suburban environments: implications for floral evolution.

PubMed

Irwin, Rebecca E; Warren, Paige S; Carper, Adrian L; Adler, Lynn S

2014-03-01

Plant interactions with mutualists and antagonists vary remarkably across space, and have played key roles in the ecology and evolution of flowering plants. One dominant form of spatial variation is human modification of the landscape, including urbanization and suburbanization. Our goal was to assess how suburbanization affected plant-animal interactions in Gelsemium sempervirens in the southeastern United States, including interactions with mutualists (pollination) and antagonists (nectar robbing and florivory). Based on differences in plant-animal interactions measured in multiple replicate sites, we then developed predictions for how these differences would affect patterns of natural selection, and we explored the patterns using measurements of floral and defensive traits in the field and in a common garden. We found that Gelsemium growing in suburban sites experienced more robbing and florivory as well as more heterospecific but not conspecific pollen transfer. Floral traits, particularly corolla length and width, influenced the susceptibility of plants to particular interactors. Observational data of floral traits measured in the field and in a common garden provided some supporting but also some conflicting evidence for the hypothesis that floral traits evolved in response to differences in species interactions in suburban vs. wild sites. However, the degree to which plants can respond to any one interactor may be constrained by correlations among floral morphological traits. Taken together, consideration of the broader geographic context in which organisms interact, in both suburban and wild areas, is fundamental to our understanding of the forces that shape contemporary plant-animal interactions and selection pressures in native species.

Replicates, read numbers, and other important experimental design considerations for microbial RNA-seq identified using Bacillus thuringiensis datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Tse -Yuan; Mehlhorn, Tonia L; Pelletier, Dale A.

RNA-seq is being used increasingly for gene expression studies and it is revolutionizing the fields of genomics and transcriptomics. However, the field of RNA-seq analysis is still evolving. Therefore, we specifically designed this study to contain large numbers of reads and four biological replicates per condition so we could alter these parameters and assess their impact on differential expression results. Bacillus thuringiensis strains ATCC10792 and CT43 were grown in two Luria broth medium lots on four dates and transcriptomics data were generated using one lane of sequence output from an Illumina HiSeq2000 instrument for each of the 32 samples, whichmore » were then analyzed using DESeq2. Genome coverages across samples ranged from 87 to 465X with medium lots and culture dates identified as major variation sources. Significantly differentially expressed genes (5% FDR, two-fold change) were detected for cultures grown using different medium lots and between different dates. The highly differentially expressed iron acquisition and metabolism genes, were a likely consequence of differing amounts of iron in the two media lots. Indeed, in this study RNA-seq was a tool for predictive biology since we hypothesized and confirmed the two LB medium lots had different iron contents (~two-fold difference). Furthermore, this study shows that the noise in data can be controlled and minimized with appropriate experimental design and by having the appropriate number of replicates and reads for the system being studied. We outline parameters for an efficient and cost effective microbial transcriptomics study.« less

Apparatus and method for generating partially coherent illumination for photolithography

DOEpatents

Sweatt, W.C.

1999-07-06

The present invention relates an apparatus and method for creating a bright, uniform source of partially coherent radiation for illuminating a pattern, in order to replicate an image of said pattern with a high degree of acuity. The present invention introduces a novel scatter plate into the optical path of source light used for illuminating a replicated object. The scatter plate has been designed to interrupt a focused, incoming light beam by introducing between about 8 to 24 diffraction zones blazed onto the surface of the scatter plate which intercept the light and redirect it to a like number of different positions in the condenser entrance pupil each of which is determined by the relative orientation and the spatial frequency of the diffraction grating in each of the several zones. Light falling onto the scatter plate, therefore, generates a plurality of unphased sources of illumination as seen by the back half of the optical system. The system includes a high brightness source, such as a laser, creating light which is taken up by a beam forming optic which focuses the incoming light into a condenser which in turn, focuses light into a field lens creating Kohler illumination image of the source in a camera entrance pupil. The light passing through the field lens illuminates a mask which interrupts the source light as either a positive or negative image of the object to be replicated. Light passing by the mask is focused into the entrance pupil of the lithographic camera creating an image of the mask onto a receptive media. 7 figs.

Apparatus and method for generating partially coherent illumination for photolithography

DOEpatents

Sweatt, William C.

1999-01-01

The present invention relates an apparatus and method for creating a bright, uniform source of partially coherent radiation for illuminating a pattern, in order to replicate an image of said pattern with a high degree of acuity. The present invention introduces a novel scatter plate into the optical path of source light used for illuminating a replicated object. The scatter plate has been designed to interrupt a focused, incoming light beam by introducing between about 8 to 24 diffraction zones blazed onto the surface of the scatter plate which intercept the light and redirect it to a like number of different positions in the condenser entrance pupil each of which is determined by the relative orientation and the spatial frequency of the diffraction grating in each of the several zones. Light falling onto the scatter plate, therefore, generates a plurality of unphased sources of illumination as seen by the back half of the optical system. The system includes a high brightness source, such as a laser, creating light which is taken up by a beam forming optic which focuses the incoming light into a condenser which in turn, focuses light into a field lens creating Kohler illumination image of the source in a camera entrance pupil. The light passing through the field lens illuminates a mask which interrupts the source light as either a positive or negative image of the object to be replicated. Light passing by the mask is focused into the entrance pupil of the lithographic camera creating an image of the mask onto a receptive media.

Replicates, read numbers, and other important experimental design considerations for microbial RNA-seq identified using Bacillus thuringiensis datasets

DOE PAGES

Lu, Tse -Yuan; Mehlhorn, Tonia L; Pelletier, Dale A.; ...

2016-05-31

RNA-seq is being used increasingly for gene expression studies and it is revolutionizing the fields of genomics and transcriptomics. However, the field of RNA-seq analysis is still evolving. Therefore, we specifically designed this study to contain large numbers of reads and four biological replicates per condition so we could alter these parameters and assess their impact on differential expression results. Bacillus thuringiensis strains ATCC10792 and CT43 were grown in two Luria broth medium lots on four dates and transcriptomics data were generated using one lane of sequence output from an Illumina HiSeq2000 instrument for each of the 32 samples, whichmore » were then analyzed using DESeq2. Genome coverages across samples ranged from 87 to 465X with medium lots and culture dates identified as major variation sources. Significantly differentially expressed genes (5% FDR, two-fold change) were detected for cultures grown using different medium lots and between different dates. The highly differentially expressed iron acquisition and metabolism genes, were a likely consequence of differing amounts of iron in the two media lots. Indeed, in this study RNA-seq was a tool for predictive biology since we hypothesized and confirmed the two LB medium lots had different iron contents (~two-fold difference). Furthermore, this study shows that the noise in data can be controlled and minimized with appropriate experimental design and by having the appropriate number of replicates and reads for the system being studied. We outline parameters for an efficient and cost effective microbial transcriptomics study.« less

Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets.

PubMed

Manga, Punita; Klingeman, Dawn M; Lu, Tse-Yuan S; Mehlhorn, Tonia L; Pelletier, Dale A; Hauser, Loren J; Wilson, Charlotte M; Brown, Steven D

2016-01-01

RNA-seq is being used increasingly for gene expression studies and it is revolutionizing the fields of genomics and transcriptomics. However, the field of RNA-seq analysis is still evolving. Therefore, we specifically designed this study to contain large numbers of reads and four biological replicates per condition so we could alter these parameters and assess their impact on differential expression results. Bacillus thuringiensis strains ATCC10792 and CT43 were grown in two Luria broth medium lots on four dates and transcriptomics data were generated using one lane of sequence output from an Illumina HiSeq2000 instrument for each of the 32 samples, which were then analyzed using DESeq2. Genome coverages across samples ranged from 87 to 465X with medium lots and culture dates identified as major variation sources. Significantly differentially expressed genes (5% FDR, two-fold change) were detected for cultures grown using different medium lots and between different dates. The highly differentially expressed iron acquisition and metabolism genes, were a likely consequence of differing amounts of iron in the two media lots. Indeed, in this study RNA-seq was a tool for predictive biology since we hypothesized and confirmed the two LB medium lots had different iron contents (~two-fold difference). This study shows that the noise in data can be controlled and minimized with appropriate experimental design and by having the appropriate number of replicates and reads for the system being studied. We outline parameters for an efficient and cost effective microbial transcriptomics study.

Automated control and data acquisition for a tunable diode laser heterodyne spectrometer

NASA Technical Reports Server (NTRS)

Shull, T. S.; Rinsland, P. L.

1983-01-01

This paper describes the hardware and software design, development, and implementation of the control and data electronics of a laser heterodyne spectrometer instrument being built at NASA Langley Research Center for a technology demonstration. Functional partitioning, applied at all levels of hardware and software, has been found to provide expedient design, development, and testing of the instrument. The instrument is composed of distributed microprocessor-based units. A master/slave protocol is presented which can be simulated by a terminal for unit checkout. All but one of the units are implemented using a set of core boards, plus unique boards where necessary. This design has led to reduced hardware development, reduced parts inventory, and replication of software modules, while providing the flexibility needed for a development instrument. The development tools and documentation guidelines are discussed.

An Evaluation of Talent 4 . . . : A Programme to Identify Talent and Skills for Prisoners, Disadvantaged, Unemployed, and Vulnerable Groups.

PubMed

McGuire-Snieckus, Rebecca; Caulfield, Laura

2017-11-01

Previous research suggests that the relationship between employment and recidivism is complex, with more support needed to facilitate employability motivation for sustained change. An arts-based programme designed to facilitate vocational self-determinism among prisoners with evidence of impact across three prisons in the United Kingdom was replicated and delivered to 234 prisoners and long-term unemployed participants from six European countries, to explore whether the findings from the previous evaluation would be replicated on a much larger scale. The research presented in this article found that supporting prisoners and the long-term unemployed to articulate employability goals had a positive effect on personal growth as well as understanding of individual strengths and weaknesses with respect to work, employment, problem solving, and thinking styles. Future research might explore the longer term impact on employment and recidivism.

Stochastic DG Placement for Conservation Voltage Reduction Based on Multiple Replications Procedure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Zhaoyu; Chen, Bokan; Wang, Jianhui

2015-06-01

Conservation voltage reduction (CVR) and distributed-generation (DG) integration are popular strategies implemented by utilities to improve energy efficiency. This paper investigates the interactions between CVR and DG placement to minimize load consumption in distribution networks, while keeping the lowest voltage level within the predefined range. The optimal placement of DG units is formulated as a stochastic optimization problem considering the uncertainty of DG outputs and load consumptions. A sample average approximation algorithm-based technique is developed to solve the formulated problem effectively. A multiple replications procedure is developed to test the stability of the solution and calculate the confidence interval ofmore » the gap between the candidate solution and optimal solution. The proposed method has been applied to the IEEE 37-bus distribution test system with different scenarios. The numerical results indicate that the implementations of CVR and DG, if combined, can achieve significant energy savings.« less

Intuitive intellectual property law: A nationally-representative test of the plagiarism fallacy.

PubMed

Fast, Anne A; Olson, Kristina R; Mandel, Gregory N

2017-01-01

Studies with convenience samples have suggested that the lay public's conception of intellectual property laws, including how the laws should regulate and why they should exist, are largely incommensurate with the actual intended purpose of intellectual property laws and their history in the United States. In this paper, we test whether these findings generalize to a more diverse and representative sample. The major findings from past work were replicated in the current study. When presented with several potential reasons for IP protection, the lay public endorsed plagiarism and felt that acknowledging the original source of a creative work should make copying that work permissible-viewpoints strongly divergent from lawmakers' intent and the law itself. In addition, we replicate the finding that lay people know remarkably little about intellectual property laws more generally and report little experience as users or creators of creative works.

Base-unpaired regions in supercoiled replicative form DNA of coliphage M13

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dasgupta, S.; Allison, D.P.; Snyder, C.E.

Superhelical covalently closed circular replicative form DNA (RF I) of coliphage M13 appears as a relaxed molecule that has a base-unpaired region in the form of a bubble (100 to 200 base pairs long) seen in electron micrographs when spread in the presence of formaldehyde and formamide or after pretreatment with glyoxal. S1 endonuclease, specific for single-stranded DNA, converts superhelical M13 RF I DNA, but not nonsuperhelical M13 RF I to a significant extent, into unit-length linear molecules by sequential nicking of two strands. The locations of S1 nuclease-susceptible sites and glyoxal-fixed base-unpaired regions were both related to the fivemore » A-T-rich regions in M13 RF DNA. While S1 nuclease does not show preference for any of these sites, glyoxal-fixed bubbles occur predominantly at the major A-T-rich region in M13 RF DNA.« less

Social values as arguments: similar is convincing

PubMed Central

Maio, Gregory R.; Hahn, Ulrike; Frost, John-Mark; Kuppens, Toon; Rehman, Nadia; Kamble, Shanmukh

2014-01-01

Politicians, philosophers, and rhetors engage in co-value argumentation: appealing to one value in order to support another value (e.g., “equality leads to freedom”). Across four experiments in the United Kingdom and India, we found that the psychological relatedness of values affects the persuasiveness of the arguments that bind them. Experiment 1 found that participants were more persuaded by arguments citing values that fulfilled similar motives than by arguments citing opposing values. Experiments 2 and 3 replicated this result using a wider variety of values, while finding that the effect is stronger among people higher in need for cognition and that the effect is mediated by the greater plausibility of co-value arguments that link motivationally compatible values. Experiment 4 extended the effect to real-world arguments taken from political propaganda and replicated the mediating effect of argument plausibility. The findings highlight the importance of value relatedness in argument persuasiveness. PMID:25147529

Intuitive intellectual property law: A nationally-representative test of the plagiarism fallacy

PubMed Central

Olson, Kristina R.; Mandel, Gregory N.

2017-01-01

Studies with convenience samples have suggested that the lay public’s conception of intellectual property laws, including how the laws should regulate and why they should exist, are largely incommensurate with the actual intended purpose of intellectual property laws and their history in the United States. In this paper, we test whether these findings generalize to a more diverse and representative sample. The major findings from past work were replicated in the current study. When presented with several potential reasons for IP protection, the lay public endorsed plagiarism and felt that acknowledging the original source of a creative work should make copying that work permissible—viewpoints strongly divergent from lawmakers’ intent and the law itself. In addition, we replicate the finding that lay people know remarkably little about intellectual property laws more generally and report little experience as users or creators of creative works. PMID:28863170

Reproduction of the FC/DFC units in nucleoli.

PubMed

Smirnov, Evgeny; Hornáček, Matúš; Kováčik, Lubomír; Mazel, Tomáš; Schröfel, Adam; Svidenská, Silvie; Skalníková, Magdalena; Bartová, Eva; Cmarko, Dušan; Raška, Ivan

2016-04-25

The essential structural components of the nucleoli, Fibrillar Centers (FC) and Dense Fibrillar Components (DFC), together compose FC/DFC units, loci of rDNA transcription and early RNA processing. In the present study we followed cell cycle related changes of these units in 2 human sarcoma derived cell lines with stable expression of RFP-PCNA (the sliding clamp protein) and GFP-RPA43 (a subunit of RNA polymerase I, pol I) or GFP-fibrillarin. Correlative light and electron microscopy analysis showed that the pol I and fibrillarin positive nucleolar beads correspond to individual FC/DFC units. In vivo observations showed that at early S phase, when transcriptionally active ribosomal genes were replicated, the number of the units in each cell increased by 60-80%. During that period the units transiently lost pol I, but not fibrillarin. Then, until the end of interphase, number of the units did not change, and their duplication was completed only after the cell division, by mid G1 phase. This peculiar mode of reproduction suggests that a considerable subset of ribosomal genes remain transcriptionally silent from mid S phase to mitosis, but become again active in the postmitotic daughter cells.

In vitro assessment of sperm from bulls of high and low field fertility.

PubMed

Al Naib, A; Hanrahan, J P; Lonergan, P; Fair, S

2011-07-01

The aim of this study was to investigate the reasons for differences in field fertility of bulls following insemination with frozen-thawed semen. The study was carried out in two separate parts over two years and comparisons were made between 5 high and 4 low fertility Holstein Friesian bulls as determined by their either 90 day non-return rate (Year 1) or calving rate (Year 2). Two high fertility Limousin bulls were included in Year 1 for comparative purposes. The ability of sperm from each bull to penetrate artificial mucus was assessed (Year 1 = 7 replicates; Year 2 = 5 replicates). Glass capillary tubes (2 per bull per replicate) were filled with artificial mucus and incubated with sperm stained in 1% Hoechst 33342 for 30 min at 37 °C. The number of sperm were subsequently counted at 10 mm intervals along the tube between 40 and 80 mm markers. Sperm mitochondrial activity of each bull was assessed by the MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide) assay (4 replicates in each year). Sperm were incubated with MTT for 1 h at 37 °C following which the absorbance of formazan was read using a spectrophotometer. Sperm viability after thawing was assessed for each bull using a live/dead sperm viability kit (Year 1 = 3 replicates; Year 2 = 4 replicates). A minimum of 250 cells were assessed per bull in each replicate and classified as either live or dead. Finally, the ability of sperm to fertilize oocytes in vitro and their ability to develop to blastocyst stage embryos were assessed (5 replicates in each year involving 220 to 306 oocytes per bull). Data transformation to normalize residuals was required for mucus sperm penetration (square root) and IVF (cleavage and blastocyst rate) results (arcsin). The mean number of sperm counted at each 10 mm mark between 40 and 80 mm was higher in the high fertility (56.0; 95% CI 39.5 to 75.3) compared to the low fertility (42.9; 95% CI 29.3 to 59.1) Holstein Friesian bulls but the difference did not reach formal significance (P = 0.09). Fertility status had no effect on the ability of sperm to reduce MTT to formazan (mean absorbance 0.34 ± 0.051 and 0.30 ± 0.044) or on the percentage of live sperm per straw (mean 47.3 ± 5.47 and 32.4 ± 4.66) for high and low fertility Holstein Friesian bulls respectively. Oocyte cleavage rate following insemination with sperm from high fertility Holstein Friesian bulls was significantly higher than with sperm from low fertility Holstein Friesian bulls [76.7% (95% CI 60.9 to 89.4) and 55.3 (95% CI 40.4 to 69.7) respectively, P = 0.04]. There was no significant effect of bull fertility on blastocyst rate [34.7% (95% CI 21.1 to 49.6) and 24.2 % (95% CI 14.1 to 36.0) for the high and low fertility Holstein Friesian bulls, respectively; P = 0.2]. In conclusion, sperm from high fertility bulls tended to be more effective in penetrating artificial mucus and to have an increased ability to fertilize oocytes in vitro; however, once fertilization occurred subsequent embryo development was not significantly affected by fertility status. Copyright © 2011 Elsevier Inc. All rights reserved.

EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research.

PubMed

Van Deun, Jan; Mestdagh, Pieter; Agostinis, Patrizia; Akay, Özden; Anand, Sushma; Anckaert, Jasper; Martinez, Zoraida Andreu; Baetens, Tine; Beghein, Els; Bertier, Laurence; Berx, Geert; Boere, Janneke; Boukouris, Stephanie; Bremer, Michel; Buschmann, Dominik; Byrd, James B; Casert, Clara; Cheng, Lesley; Cmoch, Anna; Daveloose, Delphine; De Smedt, Eva; Demirsoy, Seyma; Depoorter, Victoria; Dhondt, Bert; Driedonks, Tom A P; Dudek, Aleksandra; Elsharawy, Abdou; Floris, Ilaria; Foers, Andrew D; Gärtner, Kathrin; Garg, Abhishek D; Geeurickx, Edward; Gettemans, Jan; Ghazavi, Farzaneh; Giebel, Bernd; Kormelink, Tom Groot; Hancock, Grace; Helsmoortel, Hetty; Hill, Andrew F; Hyenne, Vincent; Kalra, Hina; Kim, David; Kowal, Joanna; Kraemer, Sandra; Leidinger, Petra; Leonelli, Carina; Liang, Yaxuan; Lippens, Lien; Liu, Shu; Lo Cicero, Alessandra; Martin, Shaun; Mathivanan, Suresh; Mathiyalagan, Prabhu; Matusek, Támas; Milani, Gloria; Monguió-Tortajada, Marta; Mus, Liselot M; Muth, Dillon C; Németh, Andrea; Nolte-'t Hoen, Esther N M; O'Driscoll, Lorraine; Palmulli, Roberta; Pfaffl, Michael W; Primdal-Bengtson, Bjarke; Romano, Erminia; Rousseau, Quentin; Sahoo, Susmita; Sampaio, Natalia; Samuel, Monisha; Scicluna, Benjamin; Soen, Bieke; Steels, Anneleen; Swinnen, Johannes V; Takatalo, Maarit; Thaminy, Safia; Théry, Clotilde; Tulkens, Joeri; Van Audenhove, Isabel; van der Grein, Susanne; Van Goethem, Alan; van Herwijnen, Martijn J; Van Niel, Guillaume; Van Roy, Nadine; Van Vliet, Alexander R; Vandamme, Niels; Vanhauwaert, Suzanne; Vergauwen, Glenn; Verweij, Frederik; Wallaert, Annelynn; Wauben, Marca; Witwer, Kenneth W; Zonneveld, Marijke I; De Wever, Olivier; Vandesompele, Jo; Hendrix, An

2017-02-28

We argue that the field of extracellular vesicle (EV) biology needs more transparent reporting to facilitate interpretation and replication of experiments. To achieve this, we describe EV-TRACK, a crowdsourcing knowledgebase (http://evtrack.org) that centralizes EV biology and methodology with the goal of stimulating authors, reviewers, editors and funders to put experimental guidelines into practice.

Project SHAL: An Analysis of Implementation in the St. Louis Public Schools--Findings from the Replication Implementation Field Test, June 1984.

ERIC Educational Resources Information Center

Young, Rufus, Jr.

The Effective Schools Program in St. Louis, Missouri, public schools expanded the concept of effective schools developed in Project SHAL (1980-1984). The following five characteristics are considered effective school factors: (1) strong administrative leadership (2) high teacher expectations; (3) positive school climate; (4) total school…

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR REIMBURSEMENT FOR FIELD COLLECTION OF DIET SAMPLES (UA-F-23.1)

EPA Science Inventory

The purpose of this SOP is to provide a uniform procedure for the financial reimbursement of primary respondents for the collection of diet samples. Respondents were reimbursed for replicate food and beverage samples by type and amount collected over a 24-hour sampling period. ...

Evaluation of fungicide rotations and MELCAST for management of Phytophthora fruit rot of watermelon, 2014

USDA-ARS?s Scientific Manuscript database

The experiment was conducted at the U.S. Vegetable Laboratory farm in Charleston, SC. The soil was Yonges loamy fine sand, and for the past 5 years, the field has been infested with Phytophthora capsici. The experimental design was a randomized complete block with four replications. Four-week-old...

Reducing Achievement Gaps in Academic Writing for Latinos and English Learners in Grades 7-12

ERIC Educational Resources Information Center

Olson, Carol Booth; Matuchniak, Tina; Chung, Huy Q.; Stumpf, Rachel; Farkas, George

2017-01-01

This study reports 2 years of findings from a randomized controlled trial designed to replicate and demonstrate the efficacy of an existing, successful professional development program, the Pathway Project, that uses a cognitive strategies approach to text-based analytical writing. Building on an earlier randomized field trial in a large, urban,…

Going Underground: A Field Investigation and Lab Activity on Karst Topography and Water Systems

ERIC Educational Resources Information Center

O'Dell, Gary; Gonzalez-Espada, Wilson

2011-01-01

Students learn science best with activities that mirror the way scientists work. This article describes how geologists investigate groundwater flow systems in areas of karst topography--geologic formations shaped by dissolving bedrock--and provides a way for students to replicate this research. Students also use electric current to model water…

The Other Lottery: Are Philanthropists Backing the Best Charter Schools? Policy Analysis No. 677

ERIC Educational Resources Information Center

Coulson, Andrew J.

2011-01-01

The central problem confronting education systems around the world is not that people lack models of excellence; it is their inability to routinely replicate those models. In other fields, they take for granted an endless cycle of innovation and productivity growth that continually makes products and services better, more affordable, or both. That…

California's Title IV-E Partnership: A Statewide University-Agency Collaboration--Characteristics and Implications for Replication

ERIC Educational Resources Information Center

Mathias, Christine; Gilman, Elizabeth; Shin, Carolyn; Evans, William Todd

2015-01-01

University-agency partnerships funded by Title IV-E encourage students to enter the child welfare field by providing student stipends, thus supporting child welfare agency workforce development. This article examines the literature and historical roots of Title IV-E and other partnerships, identifies common structures and outcomes, and discusses…

Judgements about Knowledge: Searching for Factors that Influence Their Validity

ERIC Educational Resources Information Center

Mengelkamp, Christoph; Bannert, Maria

2009-01-01

Introduction: Research in the field of metacomprehension often uses the accuracy of judgements of own knowledge as a measure of monitoring which is a central component of metacognition. One aim of this study is to investigate if the accuracy above chance usually found in studies using traditional texts can be replicated with hypermedia. More…

Ceratapion basicorne (Illiger) (Coleoptera: Curculionidae): laboratory and open field trials to assess its specificity as biocontrol agent of Centaurea solstitialis (Asteraceae: Cardueae)

USDA-ARS?s Scientific Manuscript database

Prospective biological control agents generally must be demonstrated to not pose risks to non-target plants. Laboratory experiments evaluating host plant specificity are the most common method of evaluating such risk; however, they are constrained by limitations of space and number of replicates, gi...

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR REIMBURSEMENT FOR FIELD COLLECTION OF FOOD SAMPLES (UA-F-23.1)

EPA Science Inventory

The purpose of this SOP is to provide a uniform procedure for the financial reimbursement of primary respondents for the collection of diet samples. Respondents were reimbursed for replicate food and beverage samples by type and amount collected over a 24-hour sampling period. ...

The use of disease severity variables in predicting efficacy of FOV4 resistance selection

USDA-ARS?s Scientific Manuscript database

In 2015, 85 Upland (Gossypium hirsutum L.) accessions from the USDA-ARS Cotton Collection and 126 F6 Pima-S6 x Pima-S7 (G. barbadense L.) recombinant inbred lines were evaluated for disease performance under pressure of Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) in a replicated field trial ...

The unit field sanitation team: a square peg in a round hole.

PubMed

Bosetti, Timothy; Bridges, Davin

2009-01-01

Basic field sanitation and hygiene is a lost art in today's modern Army. Today, more than ever, there is a need for the unit field sanitation team (FST) to serve as advisors to unit commanders in the area of basic field sanitation and hygiene. Soldiers should know how to construct field latrines, construct waste disposal devices, conduct pest management and control activities, disinfect field water supplies, and practice personal hygiene under field conditions. The current unit FST concept is centered on company-sized formations operating in open terrain. This concept does not support current operations, transformed formations, rapidly changing doctrine, and the expeditionary nature of the Army. This article does not present a new concept, but rather a new look at an existing concept and practice based upon the lessons-learned and after-action reports from the Global War on Terrorism to support the Army in transformation during an era of persistent conflict.

Comparison of roll-to-roll replication approaches for microfluidic and optical functions in lab-on-a-chip diagnostic devices

NASA Astrophysics Data System (ADS)

Brecher, Christian; Baum, Christoph; Bastuck, Thomas

2015-03-01

Economically advantageous microfabrication technologies for lab-on-a-chip diagnostic devices substituting commonly used glass etching or injection molding processes are one of the key enablers for the emerging market of microfluidic devices. On-site detection in fields of life sciences, point of care diagnostics and environmental analysis requires compact, disposable and highly functionalized systems. Roll-to-roll production as a high volume process has become the emerging fabrication technology for integrated, complex high technology products within recent years (e.g. fuel cells). Differently functionalized polymer films enable researchers to create a new generation of lab-on-a-chip devices by combining electronic, microfluidic and optical functions in multilayer architecture. For replication of microfluidic and optical functions via roll-to-roll production process competitive approaches are available. One of them is to imprint fluidic channels and optical structures of micro- or nanometer scale from embossing rollers into ultraviolet (UV) curable lacquers on polymer substrates. Depending on dimension, shape and quantity of those structures there are alternative manufacturing technologies for the embossing roller. Ultra-precise diamond turning, electroforming or casting polymer materials are used either for direct structuring or manufacturing of roller sleeves. Mastering methods are selected for application considering replication quality required and structure complexity. Criteria for the replication quality are surface roughness and contour accuracy. Structure complexity is evaluated by shapes producible (e.g. linear, circular) and aspect ratio. Costs for the mastering process and structure lifetime are major cost factors. The alternative replication approaches are introduced and analyzed corresponding to the criteria presented. Advantages and drawbacks of each technology are discussed and exemplary applications are presented.

The Idea Is Good, but…: Failure to Replicate Associations of Oxytocinergic Polymorphisms with Face-Inversion in the N170

PubMed Central

Munk, Aisha J. L.; Hermann, Andrea; El Shazly, Jasmin; Grant, Phillip; Hennig, Jürgen

2016-01-01

Background In event-related potentials, the N170 manifests itself especially in reaction to faces. In the healthy population, face-inversion leads to stronger negative amplitudes and prolonged latencies of the N170, effects not being present in patients with autism-spectrum-disorder (ASD). ASD has frequently been associated with differences in oxytocinergic neurotransmission. This ERP-study aimed to investigate the face-inversion effect in association with oxytocinergic candidate genes. It was expected that risk-allele-carriers of the oxytocin-receptor-gene-polymorphism (rs53576) and of CD38 (rs379863) responded similar to upright and inverted faces as persons with ASD. Additionally, reactions to different facial emotional expressions were studied. As there have been difficulties with replications of those molecular genetic association studies, we aimed to replicate our findings in a second study. Method Seventy-two male subjects in the first-, and seventy-eight young male subjects in the replication-study conducted a face-inversion-paradigm, while recording EEG. DNA was extracted from buccal cells. Results Results revealed stronger N170-amplitudes and longer latencies in reaction to inverted faces in comparison to upright ones. Furthermore, effects of emotion on N170 were evident. Those effects were present in the first and in the second study. Whereas we found molecular-genetic associations of oxytocinergic polymorphisms with the N170 in the first study, we failed to do so in the replication sample. Conclusion Results indicate that a deeper theoretical understanding of this research-field is needed, in order to generate possible explanations for these findings. Results, furthermore, support the hypotheses that success of reproducibility is correlated with strength of lower original p-values and larger effect sizes in the original study. PMID:27015428

A model marine-science curriculum for fourth-grade pupils in Florida

NASA Astrophysics Data System (ADS)

Schulte, Philip James

This dissertation focused on the development of a model marine-science curriculum for fourth-grade pupils in the State of Florida. The curriculum was developed using grounded theory research method, including a component of data collected from an on-line survey administered to 106 professional educators and marine biologists. The results of the data collection and analysis showed a definitive necessity for teacher preparedness, multidisciplinary content, and inquiry-based science instruction. Further, three important factors emerged: (a) collaborative grouping increases achievement; (b) field excursions significantly impact student motivation; (c) standardized testing influences curriculum development. The curriculum is organized as an 11-day unit, with detailed lesson plans presented in standard curricular format and with all components correlated to the Florida State Educational Standards. The curriculum incorporates teacher preparation, multimedia presentations, computer-assisted instruction, scientific art appreciation, and replication as well as assessment factors. The curriculum addresses topics of ichthyology, marine animal identification, environmental conservation and protection, marine animal anatomy, water safety, environmental stewardship, and responsible angling techniques. The components of the curriculum were discussed with reference to the literature on which it was based and recommendations for future research were addressed.

An evaluation of the urban stormwater pollutant removal efficiency of catch basin inserts.

PubMed

Morgan, Robert A; Edwards, Findlay G; Brye, Kristofor R; Burian, Stephen J

2005-01-01

In a storm sewer system, the catch basin is the interface between surface runoff and the sewer. Responding to the need to improve the quality of stormwater from urban areas and transportation facilities, and spurred by Phase I and II Stormwater Rules from the U.S. Environmental Protection Agency, several companies market catch basin inserts as best management practices for urban water quality management. However, little data have been collected under controlled tests that indicate the pollutant removal efficiency of these inserts when the inflow is near what can be expected to occur in the field. A stormwater simulator was constructed to test inserts under controlled and replicable conditions. The inserts were tested for removal efficiency of total suspended solids (TSS) and total petroleum hydrocarbons (TPH) at an inflow rate of 757 to 814 L/min, with influent pollutant concentrations of 225 mg/L TSS and 30 mg/L TPH. These conditions are similar to stormwater runoff from small commercial sites in the southeastern United States. Results from the tests indicate that at the test flowrate and pollutant concentration, average TSS removal efficiencies ranged from 11 to 42% and, for TPH, the removal efficiency ranged from 10 to 19%.

Performance of Arrowroot (Marantha arundinacea) in various light intensities

NASA Astrophysics Data System (ADS)

Oktafani, M. B.; Supriyono; Budiastuti, MTh S.; Purnomo, D.

2018-03-01

Arrowroot (Marantha arundinacea) is one of the potential food crops to support food security programs. Light intensity is one of the important factors for plant growth. Arrowroot cultivation technology still need further development. Traditionally, arrowroot grows wild under canopy without intentisification of cultivating which have low productivity. The purpose of research was to investigate the suitable light intensity for arrowroot. The experiment was conducted at Jumantono as Experimental Field of Faculty of Agricultural, University of Sebelas Maret Surakarta located in Karanganyar, from March to September 2016. The experiment used a complete randomized block design (CRBD) of light intensity level there are 27400 lux (full sun light), 18900 lux (shaded 31%), 13500 lux (shaded 51%) and 7400 lux (shaded 72%). Each treatment was replicated six times so there were 24 experimental units. The results showed that arrowroot is a low light adaptive plant. Arrowroot under the light intensity 7400 lux (27% full light), the number of leaves and tillers is not significantly different than under full light, although the plant is higher. The highest tuber diameter and length were 1.91 and 25.06 cm, respectively, and tuber weight reached 607.5-651.67 g per plant.

Promoting physical activity: fertile ground for rehabilitation psychology.

PubMed

Uswatte, Gitendra

2013-02-01

Comments on the article by Schmacher et al. (see record 2013-06066-009). Readers of Rehabilitation Psychology might be surprised, or maybe even alarmed, to find an article on promoting physical activity in able-bodied people between the covers of their latest issue. This commentary contends that this area of research and practice might be one into which rehabilitation psychologists want to venture. Schumacher and coworkers describe a field test (N = 216) of a token system for reinforcing stair taking. The setting was an eight-story office building housing a single company in a midsized city in the southeastern United States. Schumacher et al. report an increase from 39 stair transactions per day by all study participants in the 6 months before implementation of the intervention to 301 transactions in the 6 months after the implementation of the intervention, which represents a 600% increase. The cost of the intervention was only $17 per person. Although replication of these results in a study with additional sources of control would increase confidence in the validity of the findings, the size of the gains in stair taking, the number of participants in the study, the length of the baseline and implementation periods, and the objective measurement of outcome warrant attention.

Millikan's Oil-Drop Experiment: A Centennial Setup Revisited in Virtual World

NASA Astrophysics Data System (ADS)

Gagnon, Michel

2012-02-01

Early in the last century, Robert Millikan developed a precise method of determining the electric charge carried by oil droplets.1-3 Using a microscope and a small incandescent lamp, he observed the fall of charged droplets under the influence of an electric field inside a small observation chamber. In so doing, Millikan demonstrated the existence of a fundamental unit of electric charge, and established its quantization. Now renowned as one of the most famous experiments of 20th-century physics, Millikan's oil-drop experiment has been reproduced with more or less success in most, if not all, high school and university physics classes. This has encouraged many improvements of the apparatus, now making this experiment much more accurate and easier to realize for advanced students. However, the required apparatus remains rather expensive, and for introductory college or high school students the experiment is still quite difficult to conduct. As an alternative to the traditional setup, a realistic computer-based simulator to replicate the Millikan oil-drop experiment has been developed. Using this software, students are able to undertake a complete experiment, obtain an accurate set of results, and thus gain a better understanding of the original experiment and its historical importance.

Linking Aerosol Optical Properties Between Laboratory, Field, and Model Studies

NASA Astrophysics Data System (ADS)

Murphy, S. M.; Pokhrel, R. P.; Foster, K. A.; Brown, H.; Liu, X.

2017-12-01

The optical properties of aerosol emissions from biomass burning have a significant impact on the Earth's radiative balance. Based on measurements made during the Fourth Fire Lab in Missoula Experiment, our group published a series of parameterizations that related optical properties (single scattering albedo and absorption due to brown carbon at multiple wavelengths) to the elemental to total carbon ratio of aerosols emitted from biomass burning. In this presentation, the ability of these parameterizations to simulate the optical properties of ambient aerosol is assessed using observations collected in 2017 from our mobile laboratory chasing wildfires in the Western United States. The ambient data includes measurements of multi-wavelength absorption, scattering, and extinction, size distribution, chemical composition, and volatility. In addition to testing the laboratory parameterizations, this combination of measurements allows us to assess the ability of core-shell Mie Theory to replicate observations and to assess the impact of brown carbon and mixing state on optical properties. Finally, both laboratory and ambient data are compared to the optical properties generated by a prominent climate model (Community Earth System Model (CESM) coupled with the Community Atmosphere Model (CAM 5)). The discrepancies between lab observations, ambient observations and model output will be discussed.

Designs of Empirical Evaluations of Nonexperimental Methods in Field Settings.

PubMed

Wong, Vivian C; Steiner, Peter M

2018-01-01

Over the last three decades, a research design has emerged to evaluate the performance of nonexperimental (NE) designs and design features in field settings. It is called the within-study comparison (WSC) approach or the design replication study. In the traditional WSC design, treatment effects from a randomized experiment are compared to those produced by an NE approach that shares the same target population. The nonexperiment may be a quasi-experimental design, such as a regression-discontinuity or an interrupted time-series design, or an observational study approach that includes matching methods, standard regression adjustments, and difference-in-differences methods. The goals of the WSC are to determine whether the nonexperiment can replicate results from a randomized experiment (which provides the causal benchmark estimate), and the contexts and conditions under which these methods work in practice. This article presents a coherent theory of the design and implementation of WSCs for evaluating NE methods. It introduces and identifies the multiple purposes of WSCs, required design components, common threats to validity, design variants, and causal estimands of interest in WSCs. It highlights two general approaches for empirical evaluations of methods in field settings, WSC designs with independent and dependent benchmark and NE arms. This article highlights advantages and disadvantages for each approach, and conditions and contexts under which each approach is optimal for addressing methodological questions.

Microengineering of Metals and Ceramics: Part II: Special Replication Techniques, Automation and Properties; Volume 4: Advanced Micro & Nanosystems

NASA Astrophysics Data System (ADS)

Baltes, Henry; Brand, Oliver; Fedder, Gary K.; Hierold, Christofer; Korvink, Jan G.; Tabata, Osamu; Löhe, Detlef; Haußelt, Jürgen

2005-10-01

Microstructures, electronics, nanotechnology - these vast fields of research are growing together as the size gap narrows and many different materials are combined. Current research, engineering sucesses and newly commercialized products hint at the immense innovative potentials and future applications that open up once mankind controls shape and function from the atomic level right up to the visible world without any gaps. Continuing from the previous volume, authors from three major competence centres for microengineering here cover all aspects of specialized replication techniques and how to employ state-of-the-art technologies for testing and characterizing micro-scale components, and illustrate quality control aspects and strategies for automation of production procedures in view of future industrial production and commercialisation.

Too good to be true: publication bias in two prominent studies from experimental psychology.

PubMed

Francis, Gregory

2012-04-01

Empirical replication has long been considered the final arbiter of phenomena in science, but replication is undermined when there is evidence for publication bias. Evidence for publication bias in a set of experiments can be found when the observed number of rejections of the null hypothesis exceeds the expected number of rejections. Application of this test reveals evidence of publication bias in two prominent investigations from experimental psychology that have purported to reveal evidence of extrasensory perception and to indicate severe limitations of the scientific method. The presence of publication bias suggests that those investigations cannot be taken as proper scientific studies of such phenomena, because critical data are not available to the field. Publication bias could partly be avoided if experimental psychologists started using Bayesian data analysis techniques.

The Male Produced Aggregation Pheromone of a Strawberry Sap Beetle, Lobiopa insularis (Coleoptera: Nitidulidae).

PubMed

Moliterno, Antonioni A C; Martins, Camila B C; Szczerbowski, Daiane; Zawadneak, Maria Aparecida C; Zarbin, Paulo H G

2017-06-01

The nitidulid beetle Lobiopa insularis is an important pest of strawberry crops in the United States and Brazil. Both larvae and adults feed on ripe strawberries, causing 20-70% loss in production during serious infestations. Aiming at the development of efficient, clean, and highly specific pest management systems, semiochemicals, especially pheromones, are particularly useful. Analyses of the extracts of both males and females obtained from aeration of live beetles showed the presence of three male specific compounds, 2-nonanone, 2-undecanone, and 2-undecanol (in an enantiomeric ratio of S:R = 3.5:1). This is the first record of ketones and an alcohol as pheromone components in Nitidulidae. These compounds were emitted by males in amounts of 0.3:6:1.5 ng per insect within 24 h (1:30:3), respectively, during the scotophase, indicating nocturnal sexual activity. Field tests with pitfall traps containing different mixtures of compounds and ripe strawberries as a co-attractant summed up to five treatments with 25 replications. As a result, 59% males and 41% females (1:0.7) were caught, indicating the L. insularis pheromone to cause aggregation of both sexes. Results of the field tests showed that the attractivity of the binary mixture of ketones (T3) differed from the control (T5), from traps with 2-undecanone alone (T4), and from the mixture of 2-undecanone and racemic 2-undecanol (T2). Moreover, the activity of the ternary mixture of compounds (T1) was not different from that of T3, indicating that the racemic alcohol did not positively influence trap catches. In future applications, a mixture of synthetic strawberry-derived compounds that are attractive to L. insularis may substitute rapidly decaying fruit in the field, maintaining catches for longer periods. Because of its efficiency and low cost, a mixture of 2-undecanone and 2-nonanone is recommended to catch adult L. insularis in the field.

Doctoral Training in Statistics, Measurement, and Methodology in Psychology: Replication and Extension of Aiken, West, Sechrest, and Reno's (1990) Survey of PhD Programs in North America

ERIC Educational Resources Information Center

Aiken, Leona S.; West, Stephen G.; Millsap, Roger E.

2008-01-01

In a survey of all PhD programs in psychology in the United States and Canada, the authors documented the quantitative methodology curriculum (statistics, measurement, and research design) to examine the extent to which innovations in quantitative methodology have diffused into the training of PhDs in psychology. In all, 201 psychology PhD…

Short-term effects of fire and other fuel reduction treatments on breeding birds in a Southern Appalachian upland hardwood forest

Treesearch

Cathryn H. Greenberg; Aimee Livings Tomcho; J. Drew Lanham; Thomas a. Waldrop; Jospeh Tomcho; Ross J. Phillips; Dean Simon

2007-01-01

We compared the effects of 3 fuel reduction techniques and a control on breeding birds during 2001–2005 using 50-m point counts. Four experimental units, each .14 ha, were contained within each of 3 replicate blocks at the Green River Game Land, Polk County, North Carolina, USA. Treatments were 1) prescribed burn, 2) mechanical understory reduction (chainsaw-felling...

A Measurement Invariance Examination of the Revised Child Anxiety and Depression Scale in a Southern Sample: Differential Item Functioning between African American and Caucasian Youth

ERIC Educational Resources Information Center

Trent, Lindsay Rae; Buchanan, Erin; Ebesutani, Chad; Ale, Chelsea M.; Heiden, Laurie; Hight, Terry L.; Damon, John D.; Young, John

2013-01-01

This study examined the psychometric properties of the Revised Child Anxiety and Depression Scale in a large sample of youth from the Southern United States. The authors aimed to determine (a) if the established six-factor Revised Child Anxiety and Depression Scale structure could be replicated in this Southern sample and (b) if scores were…

The United States Army Concept Capability Plan for Combating Weapons of Mass Destruction for the Futer Modular Force 2015-2024

DTIC Science & Technology

2009-03-25

development and pest control, also have deleterious dual use potential. By replicating themselves after introduction into a target population, a small...N national NATO North Atlantic Treaty Organization NEBC network-enabled battle command NMSCWMD National Military Strategy for Combating...within the continental U.S., Alaska, Hawaii, the District of Columbia, the Commonwealth of Puerto Rico, the U.S. Virgin Islands, Guam, American Samoa

Parameters of Mosquito-Enhanced West Nile Virus Infection.

PubMed

Moser, Lindsey A; Lim, Pei-Yin; Styer, Linda M; Kramer, Laura D; Bernard, Kristen A

2016-01-01

The arthropod-borne West Nile virus (WNV) emerged in New York State in 1999 and quickly spread throughout the United States. Transmission is maintained in an enzootic cycle in which infected mosquitoes transmit the virus to susceptible hosts during probing and feeding. Arthropod-derived components within the viral inoculum are increasingly acknowledged to play a role in infection of vertebrate hosts. We previously showed that Culex tarsalis mosquito saliva and salivary gland extract (SGE) enhance the in vivo replication of WNV. Here, we characterized the effective dose, timing, and proximity of saliva and SGE administration necessary for enhancement of WNV viremia using a mouse model. Mosquito saliva and SGE enhanced viremia in a dose-dependent manner, and a single mosquito bite or as little as 0.01 μg of SGE was effective at enhancing viremia, suggesting a potent active salivary factor. Viremia was enhanced when SGE was injected in the same location as virus inoculation from 24 h before virus inoculation through 12 h after virus inoculation. These results were confirmed with mosquito saliva deposited by uninfected mosquitoes. When salivary treatment and virus inoculation were spatially separated, viremia was not enhanced. In summary, the effects of mosquito saliva and SGE were potent, long lasting, and localized, and these studies have implications for virus transmission in nature, where vertebrate hosts are fed upon by both infected and uninfected mosquitoes over time. Furthermore, our model provides a robust system to identify the salivary factor(s) responsible for enhancement of WNV replication. Mosquito-borne viruses are a significant class of agents causing emerging infectious diseases. WNV has caused over 18,000 cases of neuroinvasive disease in the United States since its emergence. We have shown that Culex tarsalis mosquito saliva and SGE enhance the replication of WNV. We now demonstrate that saliva and SGE have potent, long-lasting, and localized effects. Our model provides a robust system to identify the salivary factor(s) and characterize the mechanism responsible for enhancement of WNV replication. These studies could lead to the identification of novel prophylactic or treatment options useful in limiting the spread of WNV, other mosquito-borne viruses, and the diseases that they cause. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The Human Cytomegalovirus UL51 Protein Is Essential for Viral Genome Cleavage-Packaging and Interacts with the Terminase Subunits pUL56 and pUL89

PubMed Central

Borst, Eva Maria; Kleine-Albers, Jennifer; Gabaev, Ildar; Babić, Marina; Wagner, Karen; Binz, Anne; Degenhardt, Inga; Kalesse, Markus; Jonjić, Stipan; Bauerfeind, Rudolf

2013-01-01

Cleavage of human cytomegalovirus (HCMV) genomes as well as their packaging into capsids is an enzymatic process mediated by viral proteins and therefore a promising target for antiviral therapy. The HCMV proteins pUL56 and pUL89 form the terminase and play a central role in cleavage-packaging, but several additional viral proteins, including pUL51, had been suggested to contribute to this process, although they remain largely uncharacterized. To study the function of pUL51 in infected cells, we constructed HCMV mutants encoding epitope-tagged versions of pUL51 and used a conditionally replicating virus (HCMV-UL51-ddFKBP), in which pUL51 levels could be regulated by a synthetic ligand. In cells infected with HCMV-UL51-ddFKBP, viral DNA replication was not affected when pUL51 was knocked down. However, no unit-length genomes and no DNA-filled C capsids were found, indicating that cleavage of concatemeric HCMV DNA and genome packaging into capsids did not occur in the absence of pUL51. pUL51 was expressed mainly with late kinetics and was targeted to nuclear replication compartments, where it colocalized with pUL56 and pUL89. Upon pUL51 knockdown, pUL56 and pUL89 were no longer detectable in replication compartments, suggesting that pUL51 is needed for their correct subnuclear localization. Moreover, pUL51 was found in a complex with the terminase subunits pUL56 and pUL89. Our data provide evidence that pUL51 is crucial for HCMV genome cleavage-packaging and may represent a third component of the viral terminase complex. Interference with the interactions between the terminase subunits by antiviral drugs could be a strategy to disrupt the HCMV replication cycle. PMID:23175377