Learning enhances the relative impact of top-down processing in the visual cortex

PubMed Central

Makino, Hiroshi; Komiyama, Takaki

2015-01-01

Theories have proposed that in sensory cortices learning can enhance top-down modulation by higher brain areas while reducing bottom-up sensory inputs. To address circuit mechanisms underlying this process, we examined the activity of layer 2/3 (L2/3) excitatory neurons in the mouse primary visual cortex (V1) as well as L4 neurons, the main bottom-up source, and long-range top-down projections from the retrosplenial cortex (RSC) during associative learning over days using chronic two-photon calcium imaging. During learning, L4 responses gradually weakened, while RSC inputs became stronger. Furthermore, L2/3 acquired a ramp-up response temporal profile with learning, coinciding with a similar change in RSC inputs. Learning also reduced the activity of somatostatin-expressing inhibitory neurons (SOM-INs) in V1 that could potentially gate top-down inputs. Finally, RSC inactivation or SOM-IN activation was sufficient to partially reverse the learning-induced changes in L2/3. Together, these results reveal a learning-dependent dynamic shift in the balance between bottom-up and top-down information streams and uncover a role of SOM-INs in controlling this process. PMID:26167904

The Nitrous Oxide (N2O) Budget: Constraints from Atmospheric Observations and Models

NASA Astrophysics Data System (ADS)

Tian, H.; Thompson, R.; Canadell, J.; Winiwarter, W.; Tian, H.; Thompson, R.; Prather, M. J.

2017-12-01

The increasing global abundance of N2O poses a threat to human health and society over this coming century through both climate change and ozone depletion. In the sense of greenhouse gases, N2O ranks third behind CO2 and CH4. In the sense of ozone depletion, N2O stands alone. In order to identify the cause of these increases and hopefully reverse them, we need to have a thorough understanding of the sources and sinks (a.k.a. the budget) of N2O and how they can be altered. A bottom-up approach to the budget evaluates individual biogeochemical sources of N2O from the land and ocean; whereas, a top-down approach uses atmospheric observations of the variability, combined with modeling of the atmospheric chemistry and transport, to infer the magnitude of sources and sinks throughout the Earth system. This paper reviews top-down approaches using atmospheric data; a similar top-down approach can be taken with oceanic measurements of N2O, but is not covered here. Stratospheric chemistry is the predominant loss of N2O, and here we review how a merging of new measurements with stratospheric chemistry models is able to provide a constrained budget for the global N2O sink. N2O surface sources are transported and mixed throughout the atmosphere, providing positive anomalies in the N2O abundance (mole fraction of N2O with respect to dry air); while N2O-depleted air from the stratosphere provides negative anomalies. With accurate atmospheric transport models, including for stratosphere-troposphere exchange, the observed tropospheric variability in N2O is effectively a fingerprint of the location and magnitude of sources. This inverse modeling of sources is part of the top-down constraints and is reviewed here.

Can bottom-up processes of attention be a source of 'interference' in situations where top-down control of attention is crucial?

PubMed

Nikolla, Dritan; Edgar, Graham; Catherwood, Dianne; Matthews, Tristan

2018-02-01

In this study, we investigate whether emotionally engaged bottom-up processes of attention can be a source of 'interference' in situations where top-down control of attention is necessary. Participants were asked to monitor and report on a video of a war scenario showing a developing battle in two conditions: emotionally positive and emotionally negative. Half of the participants (n = 15) were exposed to task-irrelevant pictures of positive emotional valence embedded within the scenario; the other half were exposed to task-irrelevant pictures of negative emotional valence. Sensitivity and Bias scores were calculated using signal detection theory. Overall, task accuracy scores were dependent upon the valence; negative pictures had an adverse effect on performance, whereas positive pictures improved performance. We concluded that negative emotional pictures interfered with top-down control of attention by attracting competing bottom-up processes of attention. We found the opposite effect for positive emotional stimuli. © 2017 The British Psychological Society.

A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis.

PubMed

Padula, Matthew P; Berry, Iain J; O Rourke, Matthew B; Raymond, Benjamin B A; Santos, Jerran; Djordjevic, Steven P

2017-04-07

Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O'Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single 'spots' in a polyacrylamide gel, allowing the quantitation of changes in a proteoform's abundance to ascertain changes in an organism's phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the 'Top-Down'. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O'Farrell's paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism's proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.

A fusion of top-down and bottom-up modeling techniques to constrain regional scale carbon budgets

NASA Astrophysics Data System (ADS)

Goeckede, M.; Turner, D. P.; Michalak, A. M.; Vickers, D.; Law, B. E.

2009-12-01

The effort to constrain regional scale carbon budgets benefits from assimilating as many high quality data sources as possible in order to reduce uncertainties. Two of the most common approaches used in this field, bottom-up and top-down techniques, both have their strengths and weaknesses, and partly build on very different sources of information to train, drive, and validate the models. Within the context of the ORCA2 project, we follow both bottom-up and top-down modeling strategies with the ultimate objective of reconciling their surface flux estimates. The ORCA2 top-down component builds on a coupled WRF-STILT transport module that resolves the footprint function of a CO2 concentration measurement in high temporal and spatial resolution. Datasets involved in the current setup comprise GDAS meteorology, remote sensing products, VULCAN fossil fuel inventories, boundary conditions from CarbonTracker, and high-accuracy time series of atmospheric CO2 concentrations. Surface fluxes of CO2 are normally provided through a simple diagnostic model which is optimized against atmospheric observations. For the present study, we replaced the simple model with fluxes generated by an advanced bottom-up process model, Biome-BGC, which uses state-of-the-art algorithms to resolve plant-physiological processes, and 'grow' a biosphere based on biogeochemical conditions and climate history. This approach provides a more realistic description of biomass and nutrient pools than is the case for the simple model. The process model ingests various remote sensing data sources as well as high-resolution reanalysis meteorology, and can be trained against biometric inventories and eddy-covariance data. Linking the bottom-up flux fields to the atmospheric CO2 concentrations through the transport module allows evaluating the spatial representativeness of the BGC flux fields, and in that way assimilates more of the available information than either of the individual modeling techniques alone. Bayesian inversion is then applied to assign scaling factors that align the surface fluxes with the CO2 time series. Our project demonstrates how bottom-up and top-down techniques can be reconciled to arrive at a more robust and balanced spatial carbon budget. We will show how to evaluate existing flux products through regionally representative atmospheric observations, i.e. how well the underlying model assumptions represent processes on the regional scale. Adapting process model parameterizations sets for e.g. sub-regions, disturbance regimes, or land cover classes, in order to optimize the agreement between surface fluxes and atmospheric observations can lead to improved understanding of the underlying flux mechanisms, and reduces uncertainties in the regional carbon budgets.

Reconciling Basin-Scale Top-Down and Bottom-Up Methane Emission Measurements for Onshore Oil and Gas Development: Cooperative Research and Development Final Report, CRADA Number CRD-14-572

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

Heath, Garvin A.

The overall objective of the Research Partnership to Secure Energy for America (RPSEA)-funded research project is to develop independent estimates of methane emissions using top-down and bottom-up measurement approaches and then to compare the estimates, including consideration of uncertainty. Such approaches will be applied at two scales: basin and facility. At facility scale, multiple methods will be used to measure methane emissions of the whole facility (controlled dual tracer and single tracer releases, aircraft-based mass balance and Gaussian back-trajectory), which are considered top-down approaches. The bottom-up approach will sum emissions from identified point sources measured using appropriate source-level measurement techniquesmore » (e.g., high-flow meters). At basin scale, the top-down estimate will come from boundary layer airborne measurements upwind and downwind of the basin, using a regional mass balance model plus approaches to separate atmospheric methane emissions attributed to the oil and gas sector. The bottom-up estimate will result from statistical modeling (also known as scaling up) of measurements made at selected facilities, with gaps filled through measurements and other estimates based on other studies. The relative comparison of the bottom-up and top-down estimates made at both scales will help improve understanding of the accuracy of the tested measurement and modeling approaches. The subject of this CRADA is NREL's contribution to the overall project. This project resulted from winning a competitive solicitation no. RPSEA RFP2012UN001, proposal no. 12122-95, which is the basis for the overall project. This Joint Work Statement (JWS) details the contributions of NREL and Colorado School of Mines (CSM) in performance of the CRADA effort.« less

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics*

PubMed Central

Cai, Wenxuan; Guner, Huseyin; Gregorich, Zachery R.; Chen, Albert J.; Ayaz-Guner, Serife; Peng, Ying; Valeja, Santosh G.; Liu, Xiaowen; Ge, Ying

2016-01-01

Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics. PMID:26598644

The global methane budget 2000-2012

NASA Astrophysics Data System (ADS)

Saunois, Marielle; Bousquet, Philippe; Poulter, Ben; Peregon, Anna; Ciais, Philippe; Canadell, Josep G.; Dlugokencky, Edward J.; Etiope, Giuseppe; Bastviken, David; Houweling, Sander; Janssens-Maenhout, Greet; Tubiello, Francesco N.; Castaldi, Simona; Jackson, Robert B.; Alexe, Mihai; Arora, Vivek K.; Beerling, David J.; Bergamaschi, Peter; Blake, Donald R.; Brailsford, Gordon; Brovkin, Victor; Bruhwiler, Lori; Crevoisier, Cyril; Crill, Patrick; Covey, Kristofer; Curry, Charles; Frankenberg, Christian; Gedney, Nicola; Höglund-Isaksson, Lena; Ishizawa, Misa; Ito, Akihiko; Joos, Fortunat; Kim, Heon-Sook; Kleinen, Thomas; Krummel, Paul; Lamarque, Jean-François; Langenfelds, Ray; Locatelli, Robin; Machida, Toshinobu; Maksyutov, Shamil; McDonald, Kyle C.; Marshall, Julia; Melton, Joe R.; Morino, Isamu; Naik, Vaishali; O'Doherty, Simon; Parmentier, Frans-Jan W.; Patra, Prabir K.; Peng, Changhui; Peng, Shushi; Peters, Glen P.; Pison, Isabelle; Prigent, Catherine; Prinn, Ronald; Ramonet, Michel; Riley, William J.; Saito, Makoto; Santini, Monia; Schroeder, Ronny; Simpson, Isobel J.; Spahni, Renato; Steele, Paul; Takizawa, Atsushi; Thornton, Brett F.; Tian, Hanqin; Tohjima, Yasunori; Viovy, Nicolas; Voulgarakis, Apostolos; van Weele, Michiel; van der Werf, Guido R.; Weiss, Ray; Wiedinmyer, Christine; Wilton, David J.; Wiltshire, Andy; Worthy, Doug; Wunch, Debra; Xu, Xiyan; Yoshida, Yukio; Zhang, Bowen; Zhang, Zhen; Zhu, Qiuan

2016-12-01

The global methane (CH4) budget is becoming an increasingly important component for managing realistic pathways to mitigate climate change. This relevance, due to a shorter atmospheric lifetime and a stronger warming potential than carbon dioxide, is challenged by the still unexplained changes of atmospheric CH4 over the past decade. Emissions and concentrations of CH4 are continuing to increase, making CH4 the second most important human-induced greenhouse gas after carbon dioxide. Two major difficulties in reducing uncertainties come from the large variety of diffusive CH4 sources that overlap geographically, and from the destruction of CH4 by the very short-lived hydroxyl radical (OH). To address these difficulties, we have established a consortium of multi-disciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate research on the methane cycle, and producing regular (˜ biennial) updates of the global methane budget. This consortium includes atmospheric physicists and chemists, biogeochemists of surface and marine emissions, and socio-economists who study anthropogenic emissions. Following Kirschke et al. (2013), we propose here the first version of a living review paper that integrates results of top-down studies (exploiting atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up models, inventories and data-driven approaches (including process-based models for estimating land surface emissions and atmospheric chemistry, and inventories for anthropogenic emissions, data-driven extrapolations). For the 2003-2012 decade, global methane emissions are estimated by top-down inversions at 558 Tg CH4 yr-1, range 540-568. About 60 % of global emissions are anthropogenic (range 50-65 %). Since 2010, the bottom-up global emission inventories have been closer to methane emissions in the most carbon-intensive Representative Concentrations Pathway (RCP8.5) and higher than all other RCP scenarios. Bottom-up approaches suggest larger global emissions (736 Tg CH4 yr-1, range 596-884) mostly because of larger natural emissions from individual sources such as inland waters, natural wetlands and geological sources. Considering the atmospheric constraints on the top-down budget, it is likely that some of the individual emissions reported by the bottom-up approaches are overestimated, leading to too large global emissions. Latitudinal data from top-down emissions indicate a predominance of tropical emissions (˜ 64 % of the global budget, < 30° N) as compared to mid (˜ 32 %, 30-60° N) and high northern latitudes (˜ 4 %, 60-90° N). Top-down inversions consistently infer lower emissions in China (˜ 58 Tg CH4 yr-1, range 51-72, -14 %) and higher emissions in Africa (86 Tg CH4 yr-1, range 73-108, +19 %) than bottom-up values used as prior estimates. Overall, uncertainties for anthropogenic emissions appear smaller than those from natural sources, and the uncertainties on source categories appear larger for top-down inversions than for bottom-up inventories and models. The most important source of uncertainty on the methane budget is attributable to emissions from wetland and other inland waters. We show that the wetland extent could contribute 30-40 % on the estimated range for wetland emissions. Other priorities for improving the methane budget include the following: (i) the development of process-based models for inland-water emissions, (ii) the intensification of methane observations at local scale (flux measurements) to constrain bottom-up land surface models, and at regional scale (surface networks and satellites) to constrain top-down inversions, (iii) improvements in the estimation of atmospheric loss by OH, and (iv) improvements of the transport models integrated in top-down inversions. The data presented here can be downloaded from the Carbon Dioxide Information Analysis Center (http://doi.org/10.3334/CDIAC/GLOBAL_METHANE_BUDGET_2016_V1.1) and the Global Carbon Project.

The Global Methane Budget 2000-2012

NASA Technical Reports Server (NTRS)

Saunois, Marielle; Bousquet, Philippe; Poulter, Benjamin; Peregon, Anna; Ciais, Philippe; Canadell, Josep G.; Dlugokencky, Edward J.; Etiope, Giuseppe; Bastviken, David; Houweling, Sander;

Geographical and experimental contexts modulate the effect of warming on top-down control: a meta-analysis.

PubMed

Marino, Nicholas Dos Anjos Cristiano; Romero, Gustavo Quevedo; Farjalla, Vinicius Fortes

2018-03-01

Ecologists have extensively investigated the effect of warming on consumer-resource interactions, with experiments revealing that warming can strengthen, weaken or have no net effect on top-down control of resources. These experiments have inspired a body of theoretical work to explain the variation in the effect of warming on top-down control. However, there has been no quantitative attempt to reconcile theory with outcomes from empirical studies. To address the gap between theory and experiment, we performed a meta-analysis to examine the combined effect of experimental warming and top-down control on resource biomass and determined potential sources of variation across experiments. We show that differences in experimental outcomes are related to systematic variation in the geographical distribution of studies. Specifically, warming strengthened top-down control when experiments were conducted in colder regions, but had the opposite effect in warmer regions. Furthermore, we found that differences in the thermoregulation strategy of the consumer and openness of experimental arenas to dispersal can contribute to some deviation from the overall geographical pattern. These results reconcile empirical findings and support the expectation of geographical variation in the response of consumer-resource interactions to warming. © 2018 John Wiley & Sons Ltd/CNRS.

Top-down and bottom-up interactions influence fledging success at North America’s largest colony of Caspian terns (Hydroprogne caspia)

USGS Publications Warehouse

Collar, Stefanie; Roby, Daniel D.; Lyons, Donald E.

2017-01-01

Our study investigated the influence of bottom-up and top-down drivers on the declining fledging success at a once thriving breeding colony of Caspian terns (Hydroprogne caspia). Situated at the mouth of the Columbia River, OR, East Sand Island (ESI) is home to the largest Caspian tern breeding colony in North America. Since 2001, the decline in fledging success of Caspian terns at ESI has been associated with a significant increase in average river discharge during May and June. During the years 2001–2011, the abundance of forage fish available to terns in the estuary was inversely related to river discharge. This relationship also apparently affected the reliance of nest predators on the tern colony as a food source, resulting in increased disturbance and decreased fledging success at the tern colony in years of higher river discharge. There was a significant longitudinal increase in disturbance rates by bald eagles (Haliaeetus leucocephalus) during June for terns nesting at the ESI colony, and eagle disturbance rates were positively associated with May river discharge. We also found a significant increase in kleptoparasitism rates of terns by hybrid glaucous-winged/western gulls (Larus glaucescens x Larus occidentalis) since 2001, and Caspian tern fledging success at ESI decreased with increasing average annual rates of gull kleptoparasitism. Our results support the hypothesis that the decline in Caspian tern fledging success at this large estuarine colony was primarily driven by the interaction of bottom-up and top-down factors, influencing tern fledging success through the food supply and triggering potential predators to identify the tern breeding colony as an alternative source of prey.

Physical stress modifies top-down and bottom-up forcing on plant growth and reproduction in a coastal ecosystem.

PubMed

Daleo, Pedro; Alberti, Juan; Bruschetti, Carlos Martin; Pascual, Jesos; Iribarne, Oscar; Silliman, Brian R

2015-08-01

Bottom-up and top-down effects act together to exert strong control over plant growth and reproduction, but how physical stress modifies those interactive forces remains unclear. Even though empirical evidence is scarce, theory predicts that the importance of both top-down- and bottom-up forces may decrease as physical stress increases. Here, we experimentally evaluate in the field the separate and interactive effect of salinity, nutrient availability, and crab herbivory on plant above- and belowground biomass, as well as on sexual and clonal reproduction in the salt marsh plant Spartina densiflora. Results show that the outcome of the interaction between nutrient availability and herbivory is highly context dependent, not only varying with the abiotic context (i.e., with or without increased salinity stress), but also with the dependent variable considered. Contrary to theoretical predictions, our results show that, consistently across different measured variables, salinity stress did not cancel bottom-up (i.e., nutrients) or top-down (i.e., consumers) control, but has additive effects. Our results support emerging theory by highlighting that, under many conditions, physical stress can act additively with, or even stimulate, consumer control, especially in cases where the physical stress is only experienced by basal levels of the trophic chain. Abiotic stress, as well as bottom-up and top-down factors, can affect salt marsh structure and function not only by affecting biomass production but also by having other indirect effects, such as changing patterns in plant biomass allocation and reproduction.

Reconciling Top-Down and Bottom-Up Estimates of Oil and Gas Methane Emissions in the Barnett Shale

NASA Astrophysics Data System (ADS)

Hamburg, S.

2015-12-01

Top-down approaches that use aircraft, tower, or satellite-based measurements of well-mixed air to quantify regional methane emissions have typically estimated higher emissions from the natural gas supply chain when compared to bottom-up inventories. A coordinated research campaign in October 2013 used simultaneous top-down and bottom-up approaches to quantify total and fossil methane emissions in the Barnett Shale region of Texas. Research teams have published individual results including aircraft mass-balance estimates of regional emissions and a bottom-up, 25-county region spatially-resolved inventory. This work synthesizes data from the campaign to directly compare top-down and bottom-up estimates. A new analytical approach uses statistical estimators to integrate facility emission rate distributions from unbiased and targeted high emission site datasets, which more rigorously incorporates the fat-tail of skewed distributions to estimate regional emissions of well pads, compressor stations, and processing plants. The updated spatially-resolved inventory was used to estimate total and fossil methane emissions from spatial domains that match seven individual aircraft mass balance flights. Source apportionment of top-down emissions between fossil and biogenic methane was corroborated with two independent analyses of methane and ethane ratios. Reconciling top-down and bottom-up estimates of fossil methane emissions leads to more accurate assessment of natural gas supply chain emission rates and the relative contribution of high emission sites. These results increase our confidence in our understanding of the climate impacts of natural gas relative to more carbon-intensive fossil fuels and the potential effectiveness of mitigation strategies.

Comprehensive Analysis of Low-Molecular-Weight Human Plasma Proteome Using Top-Down Mass Spectrometry.

PubMed

Cheon, Dong Huey; Nam, Eun Ji; Park, Kyu Hyung; Woo, Se Joon; Lee, Hye Jin; Kim, Hee Cheol; Yang, Eun Gyeong; Lee, Cheolju; Lee, Ji Eun

2016-01-04

While human plasma serves as a great source for disease diagnosis, low-molecular-weight (LMW) proteome (<30 kDa) has been shown to contain a rich source of diagnostic biomarkers. Here we employ top-down mass spectrometry to analyze the LMW proteoforms present in four types of human plasma samples pooled from three healthy controls (HCs) without immunoaffinity depletion and with depletion of the top two, six, and seven high-abundance proteins. The LMW proteoforms were first fractionated based on molecular weight using gel-eluted liquid fraction entrapment electrophoresis (GELFrEE). Then, the GELFrEE fractions containing up to 30 kDa were subjected to nanocapillary-LC-MS/MS, and the high-resolution MS and MS/MS data were processed using ProSightPC 3.0. As a result, a total of 442 LMW proteins and cleaved products, including those with post-translational modifications and single amino acid variations, were identified. From additional comparative analysis of plasma samples without immunoaffinity depletion between HCs and colorectal cancer (CRC) patients via top-down approach, tens of LMW proteoforms, including platelet factor 4, were found to show >1.5-fold changes between the plasma samples of HCs and CRC patients, and six of the LMW proteins were verified by Western blot analysis.

A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis

PubMed Central

Padula, Matthew P.; Berry, Iain J.; O′Rourke, Matthew B.; Raymond, Benjamin B.A.; Santos, Jerran; Djordjevic, Steven P.

2017-01-01

Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O′Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single ‘spots’ in a polyacrylamide gel, allowing the quantitation of changes in a proteoform′s abundance to ascertain changes in an organism′s phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the ‘Top-Down’. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O’Farrell’s paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism′s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer. PMID:28387712

A Routine 'Top-Down' Approach to Analysis of the Human Serum Proteome.

PubMed

D'Silva, Arlene M; Hyett, Jon A; Coorssen, Jens R

2017-06-06

Serum provides a rich source of potential biomarker proteoforms. One of the major obstacles in analysing serum proteomes is detecting lower abundance proteins owing to the presence of hyper-abundant species (e.g., serum albumin and immunoglobulins). Although depletion methods have been used to address this, these can lead to the concomitant removal of non-targeted protein species, and thus raise issues of specificity, reproducibility, and the capacity for meaningful quantitative analyses. Altering the native stoichiometry of the proteome components may thus yield a more complex series of issues than dealing directly with the inherent complexity of the sample. Hence, here we targeted method refinements so as to ensure optimum resolution of serum proteomes via a top down two-dimensional gel electrophoresis (2DE) approach that enables the routine assessment of proteoforms and is fully compatible with subsequent mass spectrometric analyses. Testing included various fractionation and non-fractionation approaches. The data show that resolving 500 µg protein on 17 cm 3-10 non-linear immobilised pH gradient strips in the first dimension followed by second dimension resolution on 7-20% gradient gels with a combination of lithium dodecyl sulfate (LDS) and sodium dodecyl sulfate (SDS) detergents markedly improves the resolution and detection of proteoforms in serum. In addition, well established third dimension electrophoretic separations in combination with deep imaging further contributed to the best available resolution, detection, and thus quantitative top-down analysis of serum proteomes.

Reconciling divergent estimates of oil and gas methane emissions

PubMed Central

Zavala-Araiza, Daniel; Lyon, David R.; Alvarez, Ramón A.; Davis, Kenneth J.; Harriss, Robert; Herndon, Scott C.; Karion, Anna; Kort, Eric Adam; Lamb, Brian K.; Lan, Xin; Marchese, Anthony J.; Pacala, Stephen W.; Robinson, Allen L.; Shepson, Paul B.; Sweeney, Colm; Talbot, Robert; Townsend-Small, Amy; Yacovitch, Tara I.; Zimmerle, Daniel J.; Hamburg, Steven P.

2015-01-01

Published estimates of methane emissions from atmospheric data (top-down approaches) exceed those from source-based inventories (bottom-up approaches), leading to conflicting claims about the climate implications of fuel switching from coal or petroleum to natural gas. Based on data from a coordinated campaign in the Barnett Shale oil and gas-producing region of Texas, we find that top-down and bottom-up estimates of both total and fossil methane emissions agree within statistical confidence intervals (relative differences are 10% for fossil methane and 0.1% for total methane). We reduced uncertainty in top-down estimates by using repeated mass balance measurements, as well as ethane as a fingerprint for source attribution. Similarly, our bottom-up estimate incorporates a more complete count of facilities than past inventories, which omitted a significant number of major sources, and more effectively accounts for the influence of large emission sources using a statistical estimator that integrates observations from multiple ground-based measurement datasets. Two percent of oil and gas facilities in the Barnett accounts for half of methane emissions at any given time, and high-emitting facilities appear to be spatiotemporally variable. Measured oil and gas methane emissions are 90% larger than estimates based on the US Environmental Protection Agency’s Greenhouse Gas Inventory and correspond to 1.5% of natural gas production. This rate of methane loss increases the 20-y climate impacts of natural gas consumed in the region by roughly 50%. PMID:26644584

Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin.

PubMed

Floris, Federico; Chiron, Lionel; Lynch, Alice M; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B

2018-06-04

Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about ~23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from ~23% to ~42%. Graphical Abstract Two-dimensional mass spectrometry, when applied to primary fragment ions from the source, allows deep-sequencing of the protein calmodulin.

Top-down Estimates of Greenhouse Gas Intensities and Emissions for Individual Oil Sands Facilities in Alberta Canada

NASA Astrophysics Data System (ADS)

Liggio, J.; Li, S. M.; Staebler, R. M.; Hayden, K. L.; Mittermeier, R. L.; McLaren, R.; Baray, S.; Darlington, A.; Worthy, D.; O'Brien, J.

2017-12-01

The oil sands (OS) region of Alberta contributes approximately 10% to Canada's overall anthropogenic greenhouse gas (GHG) emissions. Such emissions have traditionally been estimated through "bottom-up" methods which seek to account for all individual sources of GHGs within a given facility. However, it is recognized that bottom-up approaches for complex industrial facilities can be subject to uncertainties associated with incomplete or inaccurate emission factor and/or activity data. In order to quantify air pollutant emissions from oil sands activities an aircraft-based measurement campaign was performed in the summer of 2013. The aircraft measurements could also be used to quantify GHG emissions for comparison to the bottom up emissions estimates. Utilizing specific flight patterns, together with an emissions estimation algorithm and measurements of CO2 and methane, a "top-down" estimate of GHG intensities for several large surface mining operations was obtained. The results demonstrate that there is a wide variation in emissions intensities (≈80 - 220 kg CO2/barrel oil) across OS facilities, which in some cases agree with calculated intensities, and in other cases are larger than that estimated using industry reported GHG emission and oil production data. When translated to annual GHG emissions, the "top-down" approach results in a CO2 emission of approximately 41 Mega Tonnes (MT) CO2/year for the 4 OS facilities investigated, in contrast to the ≈26 MT CO2/year reported by industry. The results presented here highlight the importance of using "top-down" approaches as a complimentary method in evaluating GHG emissions from large industrial sources.

Systems Analysis of NASA Aviation Safety Program: Final Report

NASA Technical Reports Server (NTRS)

Jones, Sharon M.; Reveley, Mary S.; Withrow, Colleen A.; Evans, Joni K.; Barr, Lawrence; Leone, Karen

2013-01-01

A three-month study (February to April 2010) of the NASA Aviation Safety (AvSafe) program was conducted. This study comprised three components: (1) a statistical analysis of currently available civilian subsonic aircraft data from the National Transportation Safety Board (NTSB), the Federal Aviation Administration (FAA), and the Aviation Safety Information Analysis and Sharing (ASIAS) system to identify any significant or overlooked aviation safety issues; (2) a high-level qualitative identification of future safety risks, with an assessment of the potential impact of the NASA AvSafe research on the National Airspace System (NAS) based on these risks; and (3) a detailed, top-down analysis of the NASA AvSafe program using an established and peer-reviewed systems analysis methodology. The statistical analysis identified the top aviation "tall poles" based on NTSB accident and FAA incident data from 1997 to 2006. A separate examination of medical helicopter accidents in the United States was also conducted. Multiple external sources were used to develop a compilation of ten "tall poles" in future safety issues/risks. The top-down analysis of the AvSafe was conducted by using a modification of the Gibson methodology. Of the 17 challenging safety issues that were identified, 11 were directly addressed by the AvSafe program research portfolio.

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.

PubMed

Kou, Qiang; Wu, Si; Tolic, Nikola; Paša-Tolic, Ljiljana; Liu, Yunlong; Liu, Xiaowen

2017-05-01

Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a 'bird's eye view' of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry datasets showed that TopMG outperformed existing methods in identifying complex proteoforms. http://proteomics.informatics.iupui.edu/software/topmg/. xwliu@iupui.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Component processes in voluntary task switching.

PubMed

Demanet, Jelle; Liefooghe, Baptist

2014-05-01

The present study investigated the involvement of bottom-up and top-down control in task-switching situations in which tasks are selected on a voluntary basis. We tested for indices of both types of control in the reduction in switch cost that is observed when more time is available before executing a task. Participants had to indicate their task choice overtly prior to the actual task execution, and two time intervals were manipulated: the interval between the task-execution response of the previous trial and task-indication response of the current trial and the interval between task-indication response and task-execution response of a particular trial. In Experiment 1, the length of these intervals was manipulated orthogonally, and indices for top-down and bottom-up control were observed. Concerned with the validity of these results, Experiments 2-3 additionally discouraged participants from preparing the upcoming task before their task-indication response. Indices for bottom-up control remained, but not for top-down control. The characteristics of top-down and bottom-up control in voluntary task switching and task switching in general are discussed.

Top-down causation and emergence: some comments on mechanisms

PubMed Central

Ellis, George F. R.

2012-01-01

Both bottom-up and top-down causation occur in the hierarchy of structure and causation. A key feature is multiple realizability of higher level functions, and consequent existence of equivalence classes of lower level variables that correspond to the same higher level state. Five essentially different classes of top-down influence can be identified, and their existence demonstrated by many real-world examples. They are: algorithmic top-down causation; top-down causation via non-adaptive information control, top-down causation via adaptive selection, top-down causation via adaptive information control and intelligent top-down causation (the effect of the human mind on the physical world). Through the mind, abstract entities such as mathematical structures have causal power. The causal slack enabling top-down action to take place lies in the structuring of the system so as to attain higher level functions; in the way the nature of lower level elements is changed by context, and in micro-indeterminism combined with adaptive selection. Understanding top-down causation can have important effects on society. Two cases will be mentioned: medical/healthcare issues, and education—in particular, teaching reading and writing. In both cases, an ongoing battle between bottom-up and top-down approaches has important consequences for society. PMID:23386967

Great expectations: top-down attention modulates the costs of clutter and eccentricity.

PubMed

Steelman, Kelly S; McCarley, Jason S; Wickens, Christopher D

2013-12-01

An experiment and modeling effort examined interactions between bottom-up and top-down attentional control in visual alert detection. Participants performed a manual tracking task while monitoring peripheral display channels for alerts of varying salience, eccentricity, and spatial expectancy. Spatial expectancy modulated the influence of salience and eccentricity; alerts in low-probability locations engendered higher miss rates, longer detection times, and larger costs of visual clutter and eccentricity, indicating that top-down attentional control offset the costs of poor bottom-up stimulus quality. Data were compared to the predictions of a computational model of scanning and noticing that incorporates bottom-up and top-down sources of attentional control. The model accounted well for the overall pattern of miss rates and response times, predicting each of the observed main effects and interactions. Empirical results suggest that designers should expect the costs of poor bottom-up visibility to be greater for low expectancy signals, and that the placement of alerts within a display should be determined based on the combination of alert expectancy and response priority. Model fits suggest that the current model can serve as a useful tool for exploring a design space as a precursor to empirical data collection and for generating hypotheses for future experiments. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Top-down mass spectrometry imaging of intact proteins by laser ablation ESI FT-ICR MS.

PubMed

Kiss, András; Smith, Donald F; Reschke, Brent R; Powell, Matthew J; Heeren, Ron M A

2014-05-01

Laser ablation ESI (LAESI) is a recent development in MS imaging. It has been shown that lipids and small metabolites can be imaged in various samples such as plant material, tissue sections or bacterial colonies without any sample pretreatment. Further, LAESI has been shown to produce multiply charged protein ions from liquids or solid surfaces. This presents a means to address one of the biggest challenges in MS imaging; the identification of proteins directly from biological tissue surfaces. Such identification is hindered by the lack of multiply charged proteins in common MALDI ion sources and the difficulty of performing tandem MS on such large, singly charged ions. We present here top-down identification of intact proteins from tissue with a LAESI ion source combined with a hybrid ion-trap FT-ICR mass spectrometer. The performance of the system was first tested with a standard protein with electron capture dissociation and infrared multiphoton dissociation fragmentation to prove the viability of LAESI FT-ICR for top-down proteomics. Finally, the imaging of a tissue section was performed, where a number of intact proteins were measured and the hemoglobin α chain was identified directly from tissue using CID and infrared multiphoton dissociation fragmentation. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dividing to unveil protein microheterogeneities: A Traveling Wave Ion Mobility study

PubMed Central

Halgand, F.; Habchi, Johnny; Cravello, Laetitia; Martinho, Marlène; Guigliarelli, Bruno; Longhi, Sonia

2011-01-01

Over-expression of a protein in a foreign host is often the only route toward an exhaustive characterization especially when purification from the natural source(s) is hardly achievable. The key issue in these studies relies on quality control of the purified recombinant protein to precisely determining its identity as well as any undesirable micro-heterogeneities. While standard proteomics approaches preclude unbiased search for modifications, the optional technique of top down MSMS requires the use of highly accurate and highly resolved experiments to reveal subtle sequence modifications. In the present study, the top down MSMS approach combined with Traveling Wave Ion Mobility (TWIM) separation was evaluated for its ability to achieve high sequence coverage and to reveal subtle micro-heterogeneities that were hitherto only accessible with FTICR-MS instruments. The power of this approach is herein illustrated in an in-depth analysis of both wt and K496C variant of the recombinant X domain (XD, aa 459-507) of the measles virus phosphoprotein expressed in E. coli. Using top down MSMS combined to TWIM, we show that XD samples occasionally exhibit a micro-heterogeneity that could not be anticipated from the nucleotide sequence of the encoding constructs and that likely reflects a genetic drift, neutral or not, occurring during expression. In addition, an MTSL nitroxide probe that was grafted on the K496C XD variant was shown to undergo oxidation and/or protonation in the ESI source leading to artifactual mass increases. PMID:21800924

Variability and Quasi-Decadal Changes in the Methane Budget over the Period 2000-2012

NASA Technical Reports Server (NTRS)

Saunois, Marielle; Bousquet, Philippe; Poulter, Ben; Peregon, Anna; Ciais, Philippe; Canadell, Josep G.; Dlugokencky, Edward J.; Etiope, Giuseppe; Bastviken, David; Houweling, Sander;

Variability and quasi-decadal changes in the methane budget over the period 2000-2012

NASA Astrophysics Data System (ADS)

Saunois, Marielle; Bousquet, Philippe; Poulter, Ben; Peregon, Anna; Ciais, Philippe; Canadell, Josep G.; Dlugokencky, Edward J.; Etiope, Giuseppe; Bastviken, David; Houweling, Sander; Janssens-Maenhout, Greet; Tubiello, Francesco N.; Castaldi, Simona; Jackson, Robert B.; Alexe, Mihai; Arora, Vivek K.; Beerling, David J.; Bergamaschi, Peter; Blake, Donald R.; Brailsford, Gordon; Bruhwiler, Lori; Crevoisier, Cyril; Crill, Patrick; Covey, Kristofer; Frankenberg, Christian; Gedney, Nicola; Höglund-Isaksson, Lena; Ishizawa, Misa; Ito, Akihiko; Joos, Fortunat; Kim, Heon-Sook; Kleinen, Thomas; Krummel, Paul; Lamarque, Jean-François; Langenfelds, Ray; Locatelli, Robin; Machida, Toshinobu; Maksyutov, Shamil; Melton, Joe R.; Morino, Isamu; Naik, Vaishali; O'Doherty, Simon; Parmentier, Frans-Jan W.; Patra, Prabir K.; Peng, Changhui; Peng, Shushi; Peters, Glen P.; Pison, Isabelle; Prinn, Ronald; Ramonet, Michel; Riley, William J.; Saito, Makoto; Santini, Monia; Schroeder, Ronny; Simpson, Isobel J.; Spahni, Renato; Takizawa, Atsushi; Thornton, Brett F.; Tian, Hanqin; Tohjima, Yasunori; Viovy, Nicolas; Voulgarakis, Apostolos; Weiss, Ray; Wilton, David J.; Wiltshire, Andy; Worthy, Doug; Wunch, Debra; Xu, Xiyan; Yoshida, Yukio; Zhang, Bowen; Zhang, Zhen; Zhu, Qiuan

2017-09-01

Following the recent Global Carbon Project (GCP) synthesis of the decadal methane (CH4) budget over 2000-2012 (Saunois et al., 2016), we analyse here the same dataset with a focus on quasi-decadal and inter-annual variability in CH4 emissions. The GCP dataset integrates results from top-down studies (exploiting atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up models (including process-based models for estimating land surface emissions and atmospheric chemistry), inventories of anthropogenic emissions, and data-driven approaches. The annual global methane emissions from top-down studies, which by construction match the observed methane growth rate within their uncertainties, all show an increase in total methane emissions over the period 2000-2012, but this increase is not linear over the 13 years. Despite differences between individual studies, the mean emission anomaly of the top-down ensemble shows no significant trend in total methane emissions over the period 2000-2006, during the plateau of atmospheric methane mole fractions, and also over the period 2008-2012, during the renewed atmospheric methane increase. However, the top-down ensemble mean produces an emission shift between 2006 and 2008, leading to 22 [16-32] Tg CH4 yr-1 higher methane emissions over the period 2008-2012 compared to 2002-2006. This emission increase mostly originated from the tropics, with a smaller contribution from mid-latitudes and no significant change from boreal regions. The regional contributions remain uncertain in top-down studies. Tropical South America and South and East Asia seem to contribute the most to the emission increase in the tropics. However, these two regions have only limited atmospheric measurements and remain therefore poorly constrained. The sectorial partitioning of this emission increase between the periods 2002-2006 and 2008-2012 differs from one atmospheric inversion study to another. However, all top-down studies suggest smaller changes in fossil fuel emissions (from oil, gas, and coal industries) compared to the mean of the bottom-up inventories included in this study. This difference is partly driven by a smaller emission change in China from the top-down studies compared to the estimate in the Emission Database for Global Atmospheric Research (EDGARv4.2) inventory, which should be revised to smaller values in a near future. We apply isotopic signatures to the emission changes estimated for individual studies based on five emission sectors and find that for six individual top-down studies (out of eight) the average isotopic signature of the emission changes is not consistent with the observed change in atmospheric 13CH4. However, the partitioning in emission change derived from the ensemble mean is consistent with this isotopic constraint. At the global scale, the top-down ensemble mean suggests that the dominant contribution to the resumed atmospheric CH4 growth after 2006 comes from microbial sources (more from agriculture and waste sectors than from natural wetlands), with an uncertain but smaller contribution from fossil CH4 emissions. In addition, a decrease in biomass burning emissions (in agreement with the biomass burning emission databases) makes the balance of sources consistent with atmospheric 13CH4 observations. In most of the top-down studies included here, OH concentrations are considered constant over the years (seasonal variations but without any inter-annual variability). As a result, the methane loss (in particular through OH oxidation) varies mainly through the change in methane concentrations and not its oxidants. For these reasons, changes in the methane loss could not be properly investigated in this study, although it may play a significant role in the recent atmospheric methane changes as briefly discussed at the end of the paper.

Salivary Cystatins: Exploring New Post-Translational Modifications and Polymorphisms by Top-Down High-Resolution Mass Spectrometry.

PubMed

Manconi, Barbara; Liori, Barbara; Cabras, Tiziana; Vincenzoni, Federica; Iavarone, Federica; Castagnola, Massimo; Messana, Irene; Olianas, Alessandra

2017-11-03

Cystatins are a complex family of cysteine peptidase inhibitors. In the present study, various proteoforms of cystatin A, cystatin B, cystatin S, cystatin SN, and cystatin SA were detected in the acid-soluble fraction of human saliva and characterized by a top-down HPLC-ESI-MS approach. Proteoforms of cystatin D were also detected and characterized by an integrated top-down and bottom-up strategy. The proteoforms derive from coding sequence polymorphisms and post-translational modifications, in particular, phosphorylation, N-terminal processing, and oxidation. This study increases the current knowledge of salivary cystatin proteoforms and provides the basis to evaluate possible qualitative/quantitative variations of these proteoforms in different pathological states and reveal new potential salivary biomarkers of disease. Data are available via ProteomeXchange with identifier PXD007170.

Top-down analysis of protein samples by de novo sequencing techniques.

PubMed

Vyatkina, Kira; Wu, Si; Dekker, Lennard J M; VanDuijn, Martijn M; Liu, Xiaowen; Tolić, Nikola; Luider, Theo M; Paša-Tolić, Ljiljana; Pevzner, Pavel A

2016-09-15

Recent technological advances have made high-resolution mass spectrometers affordable to many laboratories, thus boosting rapid development of top-down mass spectrometry, and implying a need in efficient methods for analyzing this kind of data. We describe a method for analysis of protein samples from top-down tandem mass spectrometry data, which capitalizes on de novo sequencing of fragments of the proteins present in the sample. Our algorithm takes as input a set of de novo amino acid strings derived from the given mass spectra using the recently proposed Twister approach, and combines them into aggregated strings endowed with offsets. The former typically constitute accurate sequence fragments of sufficiently well-represented proteins from the sample being analyzed, while the latter indicate their location in the protein sequence, and also bear information on post-translational modifications and fragmentation patterns. Freely available on the web at http://bioinf.spbau.ru/en/twister vyatkina@spbau.ru or ppevzner@ucsd.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Integrating Top-down and Bottom-up Cybersecurity Guidance using XML

PubMed Central

Lubell, Joshua

2016-01-01

This paper describes a markup-based approach for synthesizing disparate information sources and discusses a software implementation of the approach. The implementation makes it easier for people to use two complementary, but differently structured, guidance specifications together: the (top-down) Cybersecurity Framework and the (bottom-up) National Institute of Standards and Technology Special Publication 800-53 security control catalog. An example scenario demonstrates how the software implementation can help a security professional select the appropriate safeguards for restricting unauthorized access to an Industrial Control System. The implementation and example show the benefits of this approach and suggest its potential application to disciplines other than cybersecurity. PMID:27795810

Top-Down Beta Enhances Bottom-Up Gamma

PubMed Central

Thompson, William H.

2017-01-01

Several recent studies have demonstrated that the bottom-up signaling of a visual stimulus is subserved by interareal gamma-band synchronization, whereas top-down influences are mediated by alpha-beta band synchronization. These processes may implement top-down control of stimulus processing if top-down and bottom-up mediating rhythms are coupled via cross-frequency interaction. To test this possibility, we investigated Granger-causal influences among awake macaque primary visual area V1, higher visual area V4, and parietal control area 7a during attentional task performance. Top-down 7a-to-V1 beta-band influences enhanced visually driven V1-to-V4 gamma-band influences. This enhancement was spatially specific and largest when beta-band activity preceded gamma-band activity by ∼0.1 s, suggesting a causal effect of top-down processes on bottom-up processes. We propose that this cross-frequency interaction mechanistically subserves the attentional control of stimulus selection. SIGNIFICANCE STATEMENT Contemporary research indicates that the alpha-beta frequency band underlies top-down control, whereas the gamma-band mediates bottom-up stimulus processing. This arrangement inspires an attractive hypothesis, which posits that top-down beta-band influences directly modulate bottom-up gamma band influences via cross-frequency interaction. We evaluate this hypothesis determining that beta-band top-down influences from parietal area 7a to visual area V1 are correlated with bottom-up gamma frequency influences from V1 to area V4, in a spatially specific manner, and that this correlation is maximal when top-down activity precedes bottom-up activity. These results show that for top-down processes such as spatial attention, elevated top-down beta-band influences directly enhance feedforward stimulus-induced gamma-band processing, leading to enhancement of the selected stimulus. PMID:28592697

Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria

NASA Astrophysics Data System (ADS)

Kocurek, Klaudia I.; Stones, Leanne; Bunch, Josephine; May, Robin C.; Cooper, Helen J.

2017-10-01

We have previously shown that liquid extraction surface analysis (LESA) mass spectrometry (MS) is a technique suitable for the top-down analysis of proteins directly from intact colonies of the Gram-negative bacterium Escherichia coli K-12. Here we extend the application of LESA MS to Gram-negative Pseudomonas aeruginosa PS1054 and Gram-positive Staphylococcus aureus MSSA476, as well as two strains of E. coli (K-12 and BL21 mCherry) and an unknown species of Staphylococcus. Moreover, we demonstrate the discrimination between three species of Gram-positive Streptococcus ( Streptococcus pneumoniae D39, and the viridans group Streptococcus oralis ATCC 35037 and Streptococcus gordonii ATCC35105), a recognized challenge for matrix-assisted laser desorption ionization time-of-flight MS. A range of the proteins detected were selected for top-down LESA MS/MS. Thirty-nine proteins were identified by top-down LESA MS/MS, including 16 proteins that have not previously been observed by any other technique. The potential of LESA MS for classification and characterization of novel species is illustrated by the de novo sequencing of a new protein from the unknown species of Staphylococcus. [Figure not available: see fulltext.

Oculomotor capture during real-world scene viewing depends on cognitive load.

PubMed

Matsukura, Michi; Brockmole, James R; Boot, Walter R; Henderson, John M

2011-03-25

It has been claimed that gaze control during scene viewing is largely governed by stimulus-driven, bottom-up selection mechanisms. Recent research, however, has strongly suggested that observers' top-down control plays a dominant role in attentional prioritization in scenes. A notable exception to this strong top-down control is oculomotor capture, where visual transients in a scene draw the eyes. One way to test whether oculomotor capture during scene viewing is independent of an observer's top-down goal setting is to reduce observers' cognitive resource availability. In the present study, we examined whether increasing observers' cognitive load influences the frequency and speed of oculomotor capture during scene viewing. In Experiment 1, we tested whether increasing observers' cognitive load modulates the degree of oculomotor capture by a new object suddenly appeared in a scene. Similarly, in Experiment 2, we tested whether increasing observers' cognitive load modulates the degree of oculomotor capture by an object's color change. In both experiments, the degree of oculomotor capture decreased as observers' cognitive resources were reduced. These results suggest that oculomotor capture during scene viewing is dependent on observers' top-down selection mechanisms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Revealing Ligand Binding Sites and Quantifying Subunit Variants of Noncovalent Protein Complexes in a Single Native Top-Down FTICR MS Experiment

NASA Astrophysics Data System (ADS)

Li, Huilin; Wongkongkathep, Piriya; Van Orden, Steve L.; Ogorzalek Loo, Rachel R.; Loo, Joseph A.

2014-12-01

"Native" mass spectrometry (MS) has been proven to be increasingly useful for structural biology studies of macromolecular assemblies. Using horse liver alcohol dehydrogenase (hADH) and yeast alcohol dehydrogenase (yADH) as examples, we demonstrate that rich information can be obtained in a single native top-down MS experiment using Fourier transform ion cyclotron mass spectrometry (FTICR MS). Beyond measuring the molecular weights of the protein complexes, isotopic mass resolution was achieved for yeast ADH tetramer (147 kDa) with an average resolving power of 412,700 at m/z 5466 in absorption mode, and the mass reflects that each subunit binds to two zinc atoms. The N-terminal 89 amino acid residues were sequenced in a top-down electron capture dissociation (ECD) experiment, along with the identifications of the zinc binding site at Cys46 and a point mutation (V58T). With the combination of various activation/dissociation techniques, including ECD, in-source dissociation (ISD), collisionally activated dissociation (CAD), and infrared multiphoton dissociation (IRMPD), 40% of the yADH sequence was derived directly from the native tetramer complex. For hADH, native top-down ECD-MS shows that both E and S subunits are present in the hADH sample, with a relative ratio of 4:1. Native top-down ISD of the hADH dimer shows that each subunit (E and S chains) binds not only to two zinc atoms, but also the NAD/NADH ligand, with a higher NAD/NADH binding preference for the S chain relative to the E chain. In total, 32% sequence coverage was achieved for both E and S chains.

Bottom-up and Top-down Input Augment the Variability of Cortical Neurons

PubMed Central

Nassi, Jonathan J.; Kreiman, Gabriel; Born, Richard T.

2016-01-01

SUMMARY Neurons in the cerebral cortex respond inconsistently to a repeated sensory stimulus, yet they underlie our stable sensory experiences. Although the nature of this variability is unknown, its ubiquity has encouraged the general view that each cell produces random spike patterns that noisily represent its response rate. In contrast, here we show that reversibly inactivating distant sources of either bottom-up or top-down input to cortical visual areas in the alert primate reduces both the spike train irregularity and the trial-to-trial variability of single neurons. A simple model in which a fraction of the pre-synaptic input is silenced can reproduce this reduction in variability, provided that there exist temporal correlations primarily within, but not between, excitatory and inhibitory input pools. A large component of the variability of cortical neurons may therefore arise from synchronous input produced by signals arriving from multiple sources. PMID:27427459

The time course of activity in dorsolateral prefrontal cortex and anterior cingulate cortex during top-down attentional control.

PubMed

Silton, Rebecca Levin; Heller, Wendy; Towers, David N; Engels, Anna S; Spielberg, Jeffrey M; Edgar, J Christopher; Sass, Sarah M; Stewart, Jennifer L; Sutton, Bradley P; Banich, Marie T; Miller, Gregory A

2010-04-15

A network of brain regions has been implicated in top-down attentional control, including left dorsolateral prefrontal cortex (LDLPFC) and dorsal anterior cingulate cortex (dACC). The present experiment evaluated predictions of the cascade-of-control model (Banich, 2009), which predicts that during attentionally-demanding tasks, LDLPFC imposes a top-down attentional set which precedes late-stage selection performed by dACC. Furthermore, the cascade-of-control model argues that dACC must increase its activity to compensate when top-down control by LDLPFC is poor. The present study tested these hypotheses using fMRI and dense-array ERP data collected from the same 80 participants in separate sessions. fMRI results guided ERP source modeling to characterize the time course of activity in LDLPFC and dACC. As predicted, dACC activity subsequent to LDLPFC activity distinguished congruent and incongruent conditions on the Stroop task. Furthermore, when LDLPFC activity was low, the level of dACC activity was related to performance outcome. These results demonstrate that dACC responds to attentional demand in a flexible manner that is dependent on the level of LDLPFC activity earlier in a trial. Overall, results were consistent with the temporal course of regional brain function proposed by the cascade-of-control model. Copyright 2009 Elsevier Inc. All rights reserved.

Top-down and bottom-up modeling in system pharmacology to understand clinical efficacy: An example with NRTIs of HIV-1.

PubMed

Duwal, Sulav; von Kleist, Max

2016-10-30

A major aim of Systems Pharmacology is to understand clinically relevant mechanisms of action (MOA) of drugs and to use this knowledge in order to optimize therapy. To enable this mission it is necessary to obtain knowledge on how in vitro testable insights translate into clinical efficacy. Mathematical modeling and data integration are essential components to achieve this goal. Two modeling philosophies are prevalent, each of which in isolation is not sufficient to achieve the above described: In a 'top-down' approach, a minimal pharmacokinetic-pharmacodynamic (PK-PD) model is derived from- and fitted to available clinical data. This model may lack interpretability in terms of mechanisms and may only be predictive for scenarios already covered by the data used to derive it. A 'bottom-up' approach builds on mechanistic insights derived from in vitro/ex vivo experiments, which can be conducted under controlled conditions, but may not be fully representative for the in vivo/clinical situation. In this work, we employ both approaches side-by-side to predict the clinical potency (IC 50 values) of the nucleoside reverse transcriptase inhibitors (NRTIs) lamivudine, emtricitabine and tenofovir. In the 'top-down' approach, this requires to establish the dynamic link between the intracellularly active NRTI-triphosphates (which exert the effect) and plasma prodrug PK and to subsequently link this composite PK model to viral kinetics. The 'bottom-up' approach assesses inhibition of reverse transcriptase-mediated viral DNA polymerization by the intracellular, active NRTI-triphosphates, which has to be brought into the context of target cell infection. By using entirely disparate sets of data to derive and parameterize the respective models, our approach serves as a means to assess the clinical relevance of the 'bottom-up' approach. We obtain very good qualitative and quantitative agreement between 'top-down' vs. 'bottom-up' predicted IC 50 values, arguing for the validity of the 'bottom-up' approach. We noted, however, that the 'top-down' approach is strongly dependent on the sparse and noisy intracellular pharmacokinetic data. All in all, our work provides confidence that we can translate in vitro parameters into measures of clinical efficacy using the 'bottom-up' approach. This may allow to infer the potency of various NRTIs in inhibiting e.g. mutant viruses, to distinguish sources of interaction of NRTI combinations and to assess the efficacy of different NRTIs for repurposing, e.g. for pre-exposure prophylaxis. Copyright © 2016 Elsevier B.V. All rights reserved.

How prior expectations shape multisensory perception.

PubMed

Gau, Remi; Noppeney, Uta

2016-01-01

The brain generates a representation of our environment by integrating signals from a common source, but segregating signals from different sources. This fMRI study investigated how the brain arbitrates between perceptual integration and segregation based on top-down congruency expectations and bottom-up stimulus-bound congruency cues. Participants were presented audiovisual movies of phonologically congruent, incongruent or McGurk syllables that can be integrated into an illusory percept (e.g. "ti" percept for visual «ki» with auditory /pi/). They reported the syllable they perceived. Critically, we manipulated participants' top-down congruency expectations by presenting McGurk stimuli embedded in blocks of congruent or incongruent syllables. Behaviorally, participants were more likely to fuse audiovisual signals into an illusory McGurk percept in congruent than incongruent contexts. At the neural level, the left inferior frontal sulcus (lIFS) showed increased activations for bottom-up incongruent relative to congruent inputs. Moreover, lIFS activations were increased for physically identical McGurk stimuli, when participants segregated the audiovisual signals and reported their auditory percept. Critically, this activation increase for perceptual segregation was amplified when participants expected audiovisually incongruent signals based on prior sensory experience. Collectively, our results demonstrate that the lIFS combines top-down prior (in)congruency expectations with bottom-up (in)congruency cues to arbitrate between multisensory integration and segregation. Copyright © 2015 Elsevier Inc. All rights reserved.

In Praise of Top-Down Leadership

ERIC Educational Resources Information Center

Dufour, Richard

2007-01-01

In the ongoing debate of the efficacy of top-down versus bottom-up strategies to improve school districts, top-down is clearly losing. Many district leaders are reluctant to champion improvement for fear of being labeled with the epithet "top-down leader," the unkindest cut of all. In this article, the author presents the change…

Conflict-Triggered Top-Down Control: Default Mode, Last Resort, or No Such Thing?

ERIC Educational Resources Information Center

Bugg, Julie M.

2014-01-01

The conflict monitoring account posits that globally high levels of conflict trigger engagement of top-down control; however, recent findings point to the mercurial nature of top-down control in high conflict contexts. The current study examined the potential moderating effect of associative learning on conflict-triggered top-down control…

Bottom-up vs. top-down effects on terrestrial insect herbivores: a meta-analysis.

PubMed

Vidal, Mayra C; Murphy, Shannon M

2018-01-01

Primary consumers are under strong selection from resource ('bottom-up') and consumer ('top-down') controls, but the relative importance of these selective forces is unknown. We performed a meta-analysis to compare the strength of top-down and bottom-up forces on consumer fitness, considering multiple predictors that can modulate these effects: diet breadth, feeding guild, habitat/environment, type of bottom-up effects, type of top-down effects and how consumer fitness effects are measured. We focused our analyses on the most diverse group of primary consumers, herbivorous insects, and found that in general top-down forces were stronger than bottom-up forces. Notably, chewing, sucking and gall-making herbivores were more affected by top-down than bottom-up forces, top-down forces were stronger than bottom-up in both natural and controlled (cultivated) environments, and parasitoids and predators had equally strong top-down effects on insect herbivores. Future studies should broaden the scope of focal consumers, particularly in understudied terrestrial systems, guilds, taxonomic groups and top-down controls (e.g. pathogens), and test for more complex indirect community interactions. Our results demonstrate the surprising strength of forces exerted by natural enemies on herbivorous insects, and thus the necessity of using a tri-trophic approach when studying insect-plant interactions. © 2017 John Wiley & Sons Ltd/CNRS.

Towards Understanding Methane Emissions from Abandoned Wells

EPA Science Inventory

Reconciliation of large-scale top-down methane measurements and bottom-up inventories requires complete accounting of source types. Methane emissions from abandoned oil and gas wells is an area of uncertainty. This presentation reviews progress to characterize the potential inv...

Conflict-triggered top-down control: default mode, last resort, or no such thing?

PubMed

Bugg, Julie M

2014-03-01

The conflict monitoring account posits that globally high levels of conflict trigger engagement of top-down control; however, recent findings point to the mercurial nature of top-down control in high conflict contexts. The current study examined the potential moderating effect of associative learning on conflict-triggered top-down control engagement by testing the Associations as Antagonists to Top-Down Control (AATC) hypothesis. In 4 experiments, list-wide proportion congruence was manipulated, and conflict-triggered top-down control engagement was examined by comparing interference for frequency-matched, 50% congruent items across mostly congruent (low conflict) and mostly incongruent (high conflict) lists. Despite the fact that global levels of conflict were varied identically across experiments, evidence of conflict-triggered top-down control engagement was selective to those experiments in which responses could not be predicted on the majority of trials via simple associative learning, consistent with the AATC hypothesis. In a 5th experiment, older adults showed no evidence of top-down control engagement under conditions in which young adults did, a finding that refined the interpretation of the patterns observed in the prior experiments. Collectively, these findings suggest that top-down control engagement in high conflict contexts is neither the default mode nor an unused (or nonexistent) strategy. Top-down control is best characterized as a last resort that is engaged when reliance on one's environment, and in particular associative responding, is unproductive for achieving task goals.

Conflict-Triggered Top-Down Control: Default Mode, Last Resort, or No Such Thing?

PubMed Central

Bugg, Julie M.

2014-01-01

The conflict monitoring account posits that globally high levels of conflict trigger engagement of top-down control; however, recent findings point to the mercurial nature of top-down control in high conflict contexts. The current study examined the potential moderating effect of associative learning on conflict-triggered top-down control engagement by testing the Associations as Antagonists to Top-Down Control (AATC) hypothesis. In 4 experiments, list-wide proportion congruence was manipulated, and conflict-triggered top-down control engagement was examined by comparing interference for 50% congruent items across mostly congruent (low conflict) and mostly incongruent (high conflict) lists. Despite the fact that global levels of conflict were varied identically across experiments, evidence of conflict-triggered top-down control engagement was selective to those experiments in which responses could not be predicted on the majority of trials via simple associative learning, consistent with the AATC hypothesis. In a fifth experiment, older adults showed no evidence of top-down control engagement under conditions in which young adults did, a finding that refined the interpretation of the patterns observed in the prior experiments. Collectively, these findings suggest that top-down control engagement in high conflict contexts is neither the default mode nor an unused (or non-existent) strategy. Top-down control is best characterized as a last resort that is engaged when reliance on one’s environment, and in particular associative responding, is unproductive for achieving task goals. PMID:24274385

The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics

NASA Astrophysics Data System (ADS)

Lyon, Yana A.; Riggs, Dylan; Fornelli, Luca; Compton, Philip D.; Julian, Ryan R.

2018-01-01

Analysis of whole proteins by mass spectrometry, or top-down proteomics, has several advantages over methods relying on proteolysis. For example, proteoforms can be unambiguously identified and examined. However, from a gas-phase ion-chemistry perspective, proteins are enormous molecules that present novel challenges relative to peptide analysis. Herein, the statistics of cleaving the peptide backbone multiple times are examined to evaluate the inherent propensity for generating internal versus terminal ions. The raw statistics reveal an inherent bias favoring production of terminal ions, which holds true regardless of protein size. Importantly, even if the full suite of internal ions is generated by statistical dissociation, terminal ions are predicted to account for at least 50% of the total ion current, regardless of protein size, if there are three backbone dissociations or fewer. Top-down analysis should therefore be a viable approach for examining proteins of significant size. Comparison of the purely statistical analysis with actual top-down data derived from ultraviolet photodissociation (UVPD) and higher-energy collisional dissociation (HCD) reveals that terminal ions account for much of the total ion current in both experiments. Terminal ion production is more favored in UVPD relative to HCD, which is likely due to differences in the mechanisms controlling fragmentation. Importantly, internal ions are not found to dominate from either the theoretical or experimental point of view. [Figure not available: see fulltext.

Simulation of Swap-Out Reliability For The Advance Photon Source Upgrade

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

Borland, M.

2017-06-01

The proposed upgrade of the Advanced Photon Source (APS) to a multibend-achromat lattice relies on the use of swap-out injection to accommodate the small dynamic acceptance, allow use of unusual insertion devices, and minimize collective effects at high single-bunch charge. This, combined with the short beam lifetime, will make injector reliability even more important than it is for top-up operation. We used historical data for the APS injector complex to obtain probability distributions for injector up-time and down-time durations. Using these distributions, we simulated several years of swap-out operation for the upgraded lattice for several operatingmodes. The results indicate thatmore » obtaining very high availability of beam in the storage ring will require improvements to injector reliability.« less

Depression and anxious apprehension distinguish frontocingulate cortical activity during top-down attentional control.

PubMed

Silton, Rebecca Levin; Heller, Wendy; Engels, Anna S; Towers, David N; Spielberg, Jeffrey M; Edgar, J Christopher; Sass, Sarah M; Stewart, Jennifer L; Sutton, Bradley P; Banich, Marie T; Miller, Gregory A

2011-05-01

A network consisting of left dorsolateral prefrontal cortex (LDLPFC) and dorsal anterior cingulate cortex (dACC) has been implicated in top-down attentional control. Few studies have systematically investigated how this network is altered in psychopathology, despite evidence that depression and anxiety are associated with attentional control impairments. Functional MRI and dense-array event-related brain potential (ERP) data were collected in separate sessions from 100 participants during a color-word Stroop task. Functional MRI results guided ERP source modeling to characterize the time course of activity in LDLPFC (300-440 ms) and dACC (520-680 ms). At low levels of depression, LDLPFC activity was indirectly related to Stroop interference and only via dACC activity. In contrast, at high levels of depression, dACC did not play an intervening role, and increased LDLPFC activity was directly related to decreased Stroop interference. Specific to high levels of anxious apprehension, higher dACC activity was related to more Stroop interference. Results indicate that depression and anxious apprehension modulate temporally and functionally distinct aspects of the frontocingulate network involved in top-down attention control.

Prefrontal cortex modulates posterior alpha oscillations during top-down guided visual perception

PubMed Central

Helfrich, Randolph F.; Huang, Melody; Wilson, Guy; Knight, Robert T.

2017-01-01

Conscious visual perception is proposed to arise from the selective synchronization of functionally specialized but widely distributed cortical areas. It has been suggested that different frequency bands index distinct canonical computations. Here, we probed visual perception on a fine-grained temporal scale to study the oscillatory dynamics supporting prefrontal-dependent sensory processing. We tested whether a predictive context that was embedded in a rapid visual stream modulated the perception of a subsequent near-threshold target. The rapid stream was presented either rhythmically at 10 Hz, to entrain parietooccipital alpha oscillations, or arrhythmically. We identified a 2- to 4-Hz delta signature that modulated posterior alpha activity and behavior during predictive trials. Importantly, delta-mediated top-down control diminished the behavioral effects of bottom-up alpha entrainment. Simultaneous source-reconstructed EEG and cross-frequency directionality analyses revealed that this delta activity originated from prefrontal areas and modulated posterior alpha power. Taken together, this study presents converging behavioral and electrophysiological evidence for frontal delta-mediated top-down control of posterior alpha activity, selectively facilitating visual perception. PMID:28808023

Top-down and bottom-up analysis of commercial enoxaparins.

PubMed

Liu, Xinyue; St Ange, Kalib; Lin, Lei; Zhang, Fuming; Chi, Lianli; Linhardt, Robert J

2017-01-13

A strategy for the comprehensive analysis of low molecular weight (LMW) heparins is described that relies on using an integrated top-down and bottom-up approach. Liquid chromatography-mass spectrometry, an essential component of this approach, is rapid, robust, and amenable to automated processing and interpretation. Nuclear magnetic resonance spectroscopy provides complementary top-down information on the chirality of the uronic acid residues comprising a low molecular weight heparin. Using our integrated approach four different low molecular weight heparins prepared from porcine heparin through chemical β-eliminative cleavage were comprehensively analyzed. Lovenox™ and Clexane™, the innovator versions of enoxaparin marketed in the US and Europe, respectively, and two generic enoxaparins, from Sandoz and Teva, were analyzed. The results which were supported by analysis of variation (ANOVA), while showing remarkable similarities between different versions of the product and good lot-to-lot consistency of each product, also detects subtle differences that may result from differences in their manufacturing processes or differences in the source (or parent) porcine heparin from which each product is prepared. Copyright © 2016 Elsevier B.V. All rights reserved.

Top-Down Control of MEG Alpha-Band Activity in Children Performing Categorical N-Back Task

ERIC Educational Resources Information Center

Ciesielski, Kristina T.; Ahlfors, Seppo P.; Bedrick, Edward J.; Kerwin, Audra A.; Hamalainen, Matti S.

2010-01-01

Top-down cognitive control has been associated in adults with the prefrontal-parietal network. In children the brain mechanisms of top-down control have rarely been studied. We examined developmental differences in top-down cognitive control by monitoring event-related desynchronization (ERD) and event-related synchronization (ERS) of alpha-band…

Animal water balance drives top-down effects in a riparian forest—implications for terrestrial trophic cascades

PubMed Central

Sabo, John L.

2016-01-01

Despite the clear importance of water balance to the evolution of terrestrial life, much remains unknown about the effects of animal water balance on food webs. Based on recent research suggesting animal water imbalance can increase trophic interaction strengths in cages, we hypothesized that water availability could drive top-down effects in open environments, influencing the occurrence of trophic cascades. We manipulated large spider abundance and water availability in 20 × 20 m open-air plots in a streamside forest in Arizona, USA, and measured changes in cricket and small spider abundance and leaf damage. As expected, large spiders reduced both cricket abundance and herbivory under ambient, dry conditions, but not where free water was added. When water was added (free or within moist leaves), cricket abundance was unaffected by large spiders, but spiders still altered herbivory, suggesting behavioural effects. Moreover, we found threshold-type increases in herbivory at moderately low soil moisture (between 5.5% and 7% by volume), suggesting the possibility that water balance may commonly influence top-down effects. Overall, our results point towards animal water balance as an important driver of direct and indirect species interactions and food web dynamics in terrestrial ecosystems. PMID:27534953

Top-down beta oscillatory signaling conveys behavioral context in early visual cortex.

PubMed

Richter, Craig G; Coppola, Richard; Bressler, Steven L

2018-05-03

Top-down modulation of sensory processing is a critical neural mechanism subserving numerous important cognitive roles, one of which may be to inform lower-order sensory systems of the current 'task at hand' by conveying behavioral context to these systems. Accumulating evidence indicates that top-down cortical influences are carried by directed interareal synchronization of oscillatory neuronal populations, with recent results pointing to beta-frequency oscillations as particularly important for top-down processing. However, it remains to be determined if top-down beta-frequency oscillations indeed convey behavioral context. We measured spectral Granger Causality (sGC) using local field potentials recorded from microelectrodes chronically implanted in visual areas V1/V2, V4, and TEO of two rhesus macaque monkeys, and applied multivariate pattern analysis to the spatial patterns of top-down sGC. We decoded behavioral context by discriminating patterns of top-down (V4/TEO-to-V1/V2) beta-peak sGC for two different task rules governing correct responses to identical visual stimuli. The results indicate that top-down directed influences are carried to visual cortex by beta oscillations, and differentiate task demands even before visual stimulus processing. They suggest that top-down beta-frequency oscillatory processes coordinate processing of sensory information by conveying global knowledge states to early levels of the sensory cortical hierarchy independently of bottom-up stimulus-driven processing.

Top-Down Proteomics and Direct Surface Sampling of Neonatal Dried Blood Spots: Diagnosis of Unknown Hemoglobin Variants

NASA Astrophysics Data System (ADS)

Edwards, Rebecca L.; Griffiths, Paul; Bunch, Josephine; Cooper, Helen J.

2012-11-01

We have previously shown that liquid microjunction surface sampling of dried blood spots coupled with high resolution top-down mass spectrometry may be used for screening of common hemoglobin variants HbS, HbC, and HbD. In order to test the robustness of the approach, we have applied the approach to unknown hemoglobin variants. Six neonatal dried blood spot samples that had been identified as variants, but which could not be diagnosed by current screening methods, were analyzed by direct surface sampling top-down mass spectrometry. Both collision-induced dissociation and electron transfer dissociation mass spectrometry were employed. Four of the samples were identified as β-chain variants: two were heterozygous Hb D-Iran, one was heterozygous Hb Headington, and one was heterozygous Hb J-Baltimore. The fifth sample was identified as the α-chain variant heterozygous Hb Phnom Penh. Analysis of the sixth sample suggested that it did not in fact contain a variant. Adoption of the approach in the clinic would require speed in both data collection and interpretation. To address that issue, we have compared manual data analysis with freely available data analysis software (ProsightPTM). The results demonstrate the power of top-down proteomics for hemoglobin variant analysis in newborn samples.

A new scoring function for top-down spectral deconvolution

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

Kou, Qiang; Wu, Si; Liu, Xiaowen

2014-12-18

Background: Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isotopomer envelopes from highly charged ions, which may overlap with one another. As a result, spectral deconvolution, which converts a complex top-down mass spectrum into a monoisotopic mass list, is a key step in top-down spectral interpretation. Results: In this paper, we propose a new scoring function, L-score, for evaluating isotopomer envelopes. By combining L-score with MS-Deconv, a new software tool, MS-Deconv+, was developed for top-down spectral deconvolution. Experimental results showedmore » that MS-Deconv+ outperformed existing software tools in top-down spectral deconvolution. Conclusions: L-score shows high discriminative ability in identification of isotopomer envelopes. Using L-score, MS-Deconv+ reports many correct monoisotopic masses missed by other software tools, which are valuable for proteoform identification and characterization.« less

Top-Down CMOS-NEMS Polysilicon Nanowire with Piezoresistive Transduction

PubMed Central

Marigó, Eloi; Sansa, Marc; Pérez-Murano, Francesc; Uranga, Arantxa; Barniol, Núria

2015-01-01

A top-down clamped-clamped beam integrated in a CMOS technology with a cross section of 500 nm × 280 nm has been electrostatic actuated and sensed using two different transduction methods: capacitive and piezoresistive. The resonator made from a single polysilicon layer has a fundamental in-plane resonance at 27 MHz. Piezoresistive transduction avoids the effect of the parasitic capacitance assessing the capability to use it and enhance the CMOS-NEMS resonators towards more efficient oscillator. The displacement derived from the capacitive transduction allows to compute the gauge factor for the polysilicon material available in the CMOS technology. PMID:26184222

Top-Down CMOS-NEMS Polysilicon Nanowire with Piezoresistive Transduction.

PubMed

Marigó, Eloi; Sansa, Marc; Pérez-Murano, Francesc; Uranga, Arantxa; Barniol, Núria

2015-07-14

A top-down clamped-clamped beam integrated in a CMOS technology with a cross section of 500 nm × 280 nm has been electrostatic actuated and sensed using two different transduction methods: capacitive and piezoresistive. The resonator made from a single polysilicon layer has a fundamental in-plane resonance at 27 MHz. Piezoresistive transduction avoids the effect of the parasitic capacitance assessing the capability to use it and enhance the CMOS-NEMS resonators towards more efficient oscillator. The displacement derived from the capacitive transduction allows to compute the gauge factor for the polysilicon material available in the CMOS technology.

Vulnerability Assessment of Water Supply Systems: Status, Gaps and Opportunities

NASA Astrophysics Data System (ADS)

Wheater, H. S.

2015-12-01

Conventional frameworks for assessing the impacts of climate change on water resource systems use cascades of climate and hydrological models to provide 'top-down' projections of future water availability, but these are subject to high uncertainty and are model and scenario-specific. Hence there has been recent interest in 'bottom-up' frameworks, which aim to evaluate system vulnerability to change in the context of possible future climate and/or hydrological conditions. Such vulnerability assessments are generic, and can be combined with updated information from top-down assessments as they become available. While some vulnerability methods use hydrological models to estimate water availability, fully bottom-up schemes have recently been proposed that directly map system vulnerability as a function of feasible changes in water supply characteristics. These use stochastic algorithms, based on reconstruction or reshuffling methods, by which multiple water supply realizations can be generated under feasible ranges of change in water supply conditions. The paper reports recent successes, and points to areas of future improvement. Advances in stochastic modeling and optimization can address some technical limitations in flow reconstruction, while various data mining and system identification techniques can provide possibilities to better condition realizations for consistency with top-down scenarios. Finally, we show that probabilistic and Bayesian frameworks together can provide a potential basis to combine information obtained from fully bottom-up analyses with projections available from climate and/or hydrological models in a fully integrated risk assessment framework for deep uncertainty.

Frontal top-down signals increase coupling of auditory low-frequency oscillations to continuous speech in human listeners.

PubMed

Park, Hyojin; Ince, Robin A A; Schyns, Philippe G; Thut, Gregor; Gross, Joachim

2015-06-15

Humans show a remarkable ability to understand continuous speech even under adverse listening conditions. This ability critically relies on dynamically updated predictions of incoming sensory information, but exactly how top-down predictions improve speech processing is still unclear. Brain oscillations are a likely mechanism for these top-down predictions [1, 2]. Quasi-rhythmic components in speech are known to entrain low-frequency oscillations in auditory areas [3, 4], and this entrainment increases with intelligibility [5]. We hypothesize that top-down signals from frontal brain areas causally modulate the phase of brain oscillations in auditory cortex. We use magnetoencephalography (MEG) to monitor brain oscillations in 22 participants during continuous speech perception. We characterize prominent spectral components of speech-brain coupling in auditory cortex and use causal connectivity analysis (transfer entropy) to identify the top-down signals driving this coupling more strongly during intelligible speech than during unintelligible speech. We report three main findings. First, frontal and motor cortices significantly modulate the phase of speech-coupled low-frequency oscillations in auditory cortex, and this effect depends on intelligibility of speech. Second, top-down signals are significantly stronger for left auditory cortex than for right auditory cortex. Third, speech-auditory cortex coupling is enhanced as a function of stronger top-down signals. Together, our results suggest that low-frequency brain oscillations play a role in implementing predictive top-down control during continuous speech perception and that top-down control is largely directed at left auditory cortex. This suggests a close relationship between (left-lateralized) speech production areas and the implementation of top-down control in continuous speech perception. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Frontal Top-Down Signals Increase Coupling of Auditory Low-Frequency Oscillations to Continuous Speech in Human Listeners

PubMed Central

Park, Hyojin; Ince, Robin A.A.; Schyns, Philippe G.; Thut, Gregor; Gross, Joachim

2015-01-01

Summary Humans show a remarkable ability to understand continuous speech even under adverse listening conditions. This ability critically relies on dynamically updated predictions of incoming sensory information, but exactly how top-down predictions improve speech processing is still unclear. Brain oscillations are a likely mechanism for these top-down predictions [1, 2]. Quasi-rhythmic components in speech are known to entrain low-frequency oscillations in auditory areas [3, 4], and this entrainment increases with intelligibility [5]. We hypothesize that top-down signals from frontal brain areas causally modulate the phase of brain oscillations in auditory cortex. We use magnetoencephalography (MEG) to monitor brain oscillations in 22 participants during continuous speech perception. We characterize prominent spectral components of speech-brain coupling in auditory cortex and use causal connectivity analysis (transfer entropy) to identify the top-down signals driving this coupling more strongly during intelligible speech than during unintelligible speech. We report three main findings. First, frontal and motor cortices significantly modulate the phase of speech-coupled low-frequency oscillations in auditory cortex, and this effect depends on intelligibility of speech. Second, top-down signals are significantly stronger for left auditory cortex than for right auditory cortex. Third, speech-auditory cortex coupling is enhanced as a function of stronger top-down signals. Together, our results suggest that low-frequency brain oscillations play a role in implementing predictive top-down control during continuous speech perception and that top-down control is largely directed at left auditory cortex. This suggests a close relationship between (left-lateralized) speech production areas and the implementation of top-down control in continuous speech perception. PMID:26028433

Depression-Biased Reverse Plasticity Rule Is Required for Stable Learning at Top-Down Connections

PubMed Central

Burbank, Kendra S.; Kreiman, Gabriel

2012-01-01

Top-down synapses are ubiquitous throughout neocortex and play a central role in cognition, yet little is known about their development and specificity. During sensory experience, lower neocortical areas are activated before higher ones, causing top-down synapses to experience a preponderance of post-synaptic activity preceding pre-synaptic activity. This timing pattern is the opposite of that experienced by bottom-up synapses, which suggests that different versions of spike-timing dependent synaptic plasticity (STDP) rules may be required at top-down synapses. We consider a two-layer neural network model and investigate which STDP rules can lead to a distribution of top-down synaptic weights that is stable, diverse and avoids strong loops. We introduce a temporally reversed rule (rSTDP) where top-down synapses are potentiated if post-synaptic activity precedes pre-synaptic activity. Combining analytical work and integrate-and-fire simulations, we show that only depression-biased rSTDP (and not classical STDP) produces stable and diverse top-down weights. The conclusions did not change upon addition of homeostatic mechanisms, multiplicative STDP rules or weak external input to the top neurons. Our prediction for rSTDP at top-down synapses, which are distally located, is supported by recent neurophysiological evidence showing the existence of temporally reversed STDP in synapses that are distal to the post-synaptic cell body. PMID:22396630

ATLAS Test Program Generator II (AGEN II). Volume I. Executive Software System.

DTIC Science & Technology

1980-08-01

features. l-1 C. To provide detailed descriptions of each of the system components and modules and their corresponding flowcharts. D. To describe methods of...contains the FORTRAN source code listings to enable programmer to do the expansions and modifications. The methods and details of adding another...characteristics of the network. The top-down implementa- tion method is therefore suggested. This method starts at the top by designing the IVT modules in

Individual differences in attentional modulation of cortical responses correlate with selective attention performance

PubMed Central

Choi, Inyong; Wang, Le; Bharadwaj, Hari; Shinn-Cunningham, Barbara

2014-01-01

Many studies have shown that attention modulates the cortical representation of an auditory scene, emphasizing an attended source while suppressing competing sources. Yet, individual differences in the strength of this attentional modulation and their relationship with selective attention ability are poorly understood. Here, we ask whether differences in how strongly attention modulates cortical responses reflect differences in normal-hearing listeners’ selective auditory attention ability. We asked listeners to attend to one of three competing melodies and identify its pitch contour while we measured cortical electroencephalographic responses. The three melodies were either from widely separated pitch ranges (“easy trials”), or from a narrow, overlapping pitch range (“hard trials”). The melodies started at slightly different times; listeners attended either the leading or lagging melody. Because of the timing of the onsets, the leading melody drew attention exogenously. In contrast, attending the lagging melody required listeners to direct top-down attention volitionally. We quantified how attention amplified auditory N1 response to the attended melody and found large individual differences in the N1 amplification, even though only correctly answered trials were used to quantify the ERP gain. Importantly, listeners with the strongest amplification of N1 response to the lagging melody in the easy trials were the best performers across other types of trials. Our results raise the possibility that individual differences in the strength of top-down gain control reflect inherent differences in the ability to control top-down attention. PMID:24821552

Top-down approach to biological therapy of Crohn's disease.

PubMed

Hirschmann, Simon; Neurath, Markus F

2017-03-01

Crohn's disease (CD) is a chronic, immune-mediated condition with a potentially disabling and destructive course. Despite growing data on when to use a therapeutic 'top-down' strategy, clinical management of this complex disorder is still challenging. Currently, the discussion of 'top-down' strategy in CD mostly includes biological therapy alone or in combination. Areas covered: This article is based on a review of existing literature regarding the use of biological therapy in a 'top-down' approach for the treatment of Crohn's disease. The authors reviewed all the major databases including MEDLINE as well as DDW and ECCO abstracts, respectively. Expert opinion: A 'top-down' therapeutic approach in Crohn's disease is strongly supported by existing data in patients with several risk factors for a severe course of disease. Moreover, there is an increasing amount of published data recommending a more individualised therapeutic strategy to identify candidates for 'top-down' treatment, based on enhanced diagnostics using biomarkers. Emerging therapeutic approaches besides existing therapy concepts using biologicals may possibly redefine the 'top-down' therapeutic strategy for Crohn's disease in the future.

High resolution top-down experimental strategies on the Orbitrap platform.

PubMed

Scheffler, Kai; Viner, Rosa; Damoc, Eugen

2018-03-20

Top-down mass spectrometry (MS) strategies allow in-depth characterization of proteins by fragmentation of the entire molecule(s) inside a mass spectrometer without requiring prior proteolytic digestion. Importantly, the fragmentation techniques on commercially available mass spectrometers have become more versatile over the past decade, with different characteristics in regards to the type and wealth of fragment ions that can be obtained while preserving labile protein post-translational modifications. Due to these and other improvements, top-down MS has become of broader interest and has started to be applied in more disciplines, such as the quality control of recombinant proteins, analysis and characterization of biopharmaceuticals, and clinical biochemistry to probe protein forms as potential disease biomarkers. This article provides a technical overview and guidance for data acquisition strategies on the Orbitrap platform for single proteins and low complexity protein mixtures. A protein standard mixture composed of six recombinant proteins is also introduced and analysis strategies are discussed in detail. The article provides a detailed overview and guidance on how to choose from the variety of available methods for protein characterization by top-down analysis on the Orbitrap platform. Technical details are provided explaining important observations and phenomena when working with intact proteins and data from a number of different samples should serve to provide a solid understanding on how experiments were and should be setup and to set the right expectations on the outcome of these types of experiments. Additionally, a new intact protein standard sample is introduced that will help as a QC sample to check the instrument's hardware and method setup conditions as a requirement for obtaining high quality data from biologically relevant samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Fiddler crabs facilitate Spartina alterniflora growth, mitigating periwinkle overgrazing of marsh habitat.

PubMed

Gittman, Rachel K; Keller, Danielle A

2013-12-01

Ecologists have long been interested in identifying and testing factors that drive top-down or bottom-up regulation of communities. Most studies have focused on factors that directly exert top-down (e.g., grazing) or bottom-up (e.g., nutrient availability) control on primary production. For example, recent studies in salt marshes have demonstrated that fronts of Littoraria irrorata periwinkles can overgraze Spartina alterniflora and convert marsh to mudflat. The importance of indirect, bottom-up effects, particularly facilitation, in enhancing primary production has also recently been explored. Previous field studies separately revealed that fiddler crabs, which burrow to depths of more than 30 cm, can oxygenate marsh sediments and redistribute nutrients, thereby relieving the stress of anoxia and enhancing S. alterniflora growth. However, to our knowledge, no studies to date have explored how nontrophic facilitators can mediate top-down effects (i.e., grazing) on primary-producer biomass. We conducted a field study testing whether fiddler crabs can facilitate S. alterniflora growth sufficiently to mitigate overgrazing by periwinkles and thus sustain S. alterniflora marsh. As inferred from contrasts to experimental plots lacking periwinkles and fiddler crabs, periwinkles alone exerted top-down control of total aboveground biomass and net growth of S. alterniflora. When fiddler crabs were included, they counteracted the effects of periwinkles on net S. alterniflora growth. Sediment oxygen levels were greater and S. alterniflora belowground biomass was lower where fiddler crabs were present, implying that fiddler crab burrowing enhanced S. alterniflora growth. Consequently, in the stressful interior S. alterniflora marsh, where subsurface soil anoxia is widespread, fiddler crab facilitation can mitigate top-down control by periwinkles and can limit and possibly prevent loss of biogenically structured marsh habitat and its ecosystem services.

Diurnal feeding behavior of the American Eel Anguilla rostrata

USGS Publications Warehouse

Engman, Augustin C.; Fischer, Jesse R.; Kwak, Thomas J.; Walter, Michael J.

2017-01-01

Despite potential to structure ecosystem food webs through top-down effects, the trophic interactions of the American Eel Anguilla rostrata remain largely understudied. All previous research on the trophic ecology of American Eel in inland aquatic ecosystems has been conducted in temperate continental regions of the species' range. These studies have led to a paradigm that American Eel is a nocturnally active benthic predator, which most commonly consumes benthic invertebrates. Tropical island streams and rivers have habitats and communities that are distinct from temperate counterparts, but comprise a large portion of the adult habitat in the American Eel's range. We documented a previously undescribed diurnal feeding behavior by American Eel in a Caribbean river and demonstrate that this behavior, and a shift toward more frequent daytime feeding, is linked to periodic mass migrations of postlarvae of amphidromous fish taxa, including the Sicydiine goby Sicydiumspp. Our findings indicate that periodic mass migrations of amphidromous postlarvae could function as a potentially important food source for American Eel in tropical regions of its distribution, despite the intermittence of availability. Furthermore, this suggests that the American Eel plays an important role in the structure of tropical lotic food webs through top-down effects that are potentially augmented by instream barriers.

Animal water balance drives top-down effects in a riparian forest-implications for terrestrial trophic cascades.

PubMed

McCluney, Kevin E; Sabo, John L

2016-08-17

Despite the clear importance of water balance to the evolution of terrestrial life, much remains unknown about the effects of animal water balance on food webs. Based on recent research suggesting animal water imbalance can increase trophic interaction strengths in cages, we hypothesized that water availability could drive top-down effects in open environments, influencing the occurrence of trophic cascades. We manipulated large spider abundance and water availability in 20 × 20 m open-air plots in a streamside forest in Arizona, USA, and measured changes in cricket and small spider abundance and leaf damage. As expected, large spiders reduced both cricket abundance and herbivory under ambient, dry conditions, but not where free water was added. When water was added (free or within moist leaves), cricket abundance was unaffected by large spiders, but spiders still altered herbivory, suggesting behavioural effects. Moreover, we found threshold-type increases in herbivory at moderately low soil moisture (between 5.5% and 7% by volume), suggesting the possibility that water balance may commonly influence top-down effects. Overall, our results point towards animal water balance as an important driver of direct and indirect species interactions and food web dynamics in terrestrial ecosystems. © 2016 The Author(s).

GlycCompSoft: Software for Automated Comparison of Low Molecular Weight Heparins Using Top-Down LC/MS Data

PubMed Central

Li, Lingyun; Zhang, Fuming; Hu, Min; Ren, Fuji; Chi, Lianli; Linhardt, Robert J.

2016-01-01

Low molecular weight heparins are complex polycomponent drugs that have recently become amenable to top-down analysis using liquid chromatography-mass spectrometry. Even using open source deconvolution software, DeconTools, and automatic structural assignment software, GlycReSoft, the comparison of two or more low molecular weight heparins is extremely time-consuming, taking about a week for an expert analyst and provides no guarantee of accuracy. Efficient data processing tools are required to improve analysis. This study uses the programming language of Microsoft Excel™ Visual Basic for Applications to extend its standard functionality for macro functions and specific mathematical modules for mass spectrometric data processing. The program developed enables the comparison of top-down analytical glycomics data on two or more low molecular weight heparins. The current study describes a new program, GlycCompSoft, which has a low error rate with good time efficiency in the automatic processing of large data sets. The experimental results based on three lots of Lovenox®, Clexane® and three generic enoxaparin samples show that the run time of GlycCompSoft decreases from 11 to 2 seconds when the data processed decreases from 18000 to 1500 rows. PMID:27942011

Increasing zooplankton size diversity enhances the strength of top-down control on phytoplankton through diet niche partitioning.

PubMed

Ye, Lin; Chang, Chun-Yi; García-Comas, Carmen; Gong, Gwo-Ching; Hsieh, Chih-Hao

2013-09-01

1. The biodiversity-ecosystem functioning debate is a central topic in ecology. Recently, there has been a growing interest in size diversity because body size is sensitive to environmental changes and is one of the fundamental characteristics of organisms linking many ecosystem properties. However, how size diversity affects ecosystem functioning is an important yet unclear issue. 2. To fill the gap, with large-scale field data from the East China Sea, we tested the novel hypothesis that increasing zooplankton size diversity enhances top-down control on phytoplankton (H1) and compared it with five conventional hypotheses explaining the top-down control: flatter zooplankton size spectrum enhances the strength of top-down control (H2); nutrient enrichment lessens the strength of top-down control (H3); increasing zooplankton taxonomic diversity enhances the strength of top-down control (H4); increasing fish predation decreases the strength of top-down control of zooplankton on phytoplankton through trophic cascade (H5); increasing temperature intensifies the strength of top-down control (H6). 3. The results of univariate analyses support the hypotheses based on zooplankton size diversity (H1), zooplankton size spectrum (H2), nutrient (H3) and zooplankton taxonomic diversity (H4), but not the hypotheses based on fish predation (H5) and temperature (H6). More in-depth analyses indicate that zooplankton size diversity is the most important factor in determining the strength of top-down control on phytoplankton in the East China Sea. 4. Our results suggest a new potential mechanism that increasing predator size diversity enhances the strength of top-down control on prey through diet niche partitioning. This mechanism can be explained by the optimal predator-prey body-mass ratio concept. Suppose each size group of zooplankton predators has its own optimal phytoplankton prey size, increasing size diversity of zooplankton would promote diet niche partitioning of predators and thus elevates the strength of top-down control. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Lipoaspirate fluid proteome: A preliminary investigation by LC-MS top-down/bottom-up integrated platform of a high potential biofluid in regenerative medicine.

PubMed

Inserra, Ilaria; Martelli, Claudia; Cipollina, Mara; Cicione, Claudia; Iavarone, Federica; Taranto, Giuseppe Di; Barba, Marta; Castagnola, Massimo; Desiderio, Claudia; Lattanzi, Wanda

2016-04-01

The lipoaspirate fluid (LAF) is emerging as a potentially valuable source in regenerative medicine. In particular, our group recently demonstrated that it is able to exert osteoinductive properties in vitro. This original observation stimulated the investigation of the proteomic component of LAF, by means of LC-ESI-LTQ-Orbitrap-MS top-down/bottom-up integrated approach, which represents the object of the present study. Top-down analyses required the optimization of sample pretreatment procedures to enable the correct investigation of the intact proteome. Bottom-up analyses have been directly applied to untreated samples after monodimensional SDS-PAGE separation. The analysis of the acid-soluble fraction of LAF by top-down approach allowed demonstrating the presence of albumin and hemoglobin fragments (i.e. VV- and LVV-hemorphin-7), thymosins β4 and β10 peptides, ubiquitin and acyl-CoA binding protein; adipogenesis regulatory factor, perilipin-1 fragments, and S100A6, along with their PTMs. Part of the bottom-up proteomic profile was reproducibly found in both tested samples. The bottom-up approach allowed demonstrating the presence of proteins, listed among the components of adipose tissue and/or comprised within the ASCs intracellular content and secreted proteome. Our data provide a first glance on the LAF molecular profile, which is consistent with its tissue environment. LAF appeared to contain bioactive proteins, peptides and paracrine factors, suggesting its potential translational exploitation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Top-down and bottom-up neurodynamic evidence in patients with tinnitus.

PubMed

Hong, Sung Kwang; Park, Sejik; Ahn, Min-Hee; Min, Byoung-Kyong

2016-12-01

Although a peripheral auditory (bottom-up) deficit is an essential prerequisite for the generation of tinnitus, central cognitive (top-down) impairment has also been shown to be an inherent neuropathological mechanism. Using an auditory oddball paradigm (for top-down analyses) and a passive listening paradigm (for bottom-up analyses) while recording electroencephalograms (EEGs), we investigated whether top-down or bottom-up components were more critical in the neuropathology of tinnitus, independent of peripheral hearing loss. We observed significantly reduced P300 amplitudes (reflecting fundamental cognitive processes such as attention) and evoked theta power (reflecting top-down regulation in memory systems) for target stimuli at the tinnitus frequency of patients with tinnitus but without hearing loss. The contingent negative variation (reflecting top-down expectation of a subsequent event prior to stimulation) and N100 (reflecting auditory bottom-up selective attention) were different between the healthy and patient groups. Interestingly, when tinnitus patients were divided into two subgroups based on their P300 amplitudes, their P170 and N200 components, and annoyance and distress indices to their tinnitus sound were different. EEG theta-band power and its Granger causal neurodynamic results consistently support a double dissociation of these two groups in both top-down and bottom-up tasks. Directed cortical connectivity corroborates that the tinnitus network involves the anterior cingulate and the parahippocampal areas, where higher-order top-down control is generated. Together, our observations provide neurophysiological and neurodynamic evidence revealing a differential engagement of top-down impairment along with deficits in bottom-up processing in patients with tinnitus but without hearing loss. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Voluntary task switching under load: contribution of top-down and bottom-up factors in goal-directed behavior.

PubMed

Demanet, Jelle; Verbruggen, Frederick; Liefooghe, Baptist; Vandierendonck, André

2010-06-01

The present study investigated the relative contribution of bottom-up and top-down control to task selection in the voluntary task-switching (VTS) procedure. In order to manipulate the efficiency of top-down control, a concurrent working memory load was imposed during VTS. In three experiments, bottom-up factors, such as stimulus repetitions, repetition of irrelevant information, and stimulus-task associations, were introduced in order to investigate their influence on task selection. We observed that the tendency to repeat tasks was stronger under load, suggesting that top-down control counteracts the automatic tendency to repeat tasks. The results also indicated that task selection can be guided by several elements in the environment, but that only the influence of stimulus repetitions depends on the efficiency of top-down control. The theoretical implications of these findings are discussed within the interplay between top-down and bottom-up control that underlies the voluntary selection of tasks.

Turning up the heat: temperature influences the relative importance of top-down and bottom-up effects.

PubMed

Hoekman, David

2010-10-01

Understanding how communities respond to changes in temperature is a major challenge for community ecology. Temperature influences the relative degree to which top-down and bottom-up forces structure ecological communities. In greenhouse experiments using the aquatic community found in pitcher plants (Sarracenia purpurea), I tested how temperature affected the relative importance of top-down (mosquito predation) and bottom-up (ant carcasses) forces on protozoa and bacteria populations. While bottom-up effects did not vary consistently with temperature, the top-down effects of predators on protozoa increased at higher temperatures. These results suggest that temperature could change the relative importance of top-down and bottom-up effects in ecological communities. Specifically, higher temperature may increase the strength of top-down effects by raising predator metabolic rate and concomitant processes (e.g., activity, foraging, digestion, growth) relative to cooler temperatures. These findings apply broadly to an understanding of trophic interactions in a variable environment and are especially relevant in the context of ongoing climate change.

Protein Identification Using Top-Down Spectra*

PubMed Central

Liu, Xiaowen; Sirotkin, Yakov; Shen, Yufeng; Anderson, Gordon; Tsai, Yihsuan S.; Ting, Ying S.; Goodlett, David R.; Smith, Richard D.; Bafna, Vineet; Pevzner, Pavel A.

2012-01-01

In the last two years, because of advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in their infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark various software tools on two top-down data sets from Saccharomyces cerevisiae and Salmonella typhimurium. We demonstrate that MS-Align+ significantly increases the number of identified spectra as compared with MASCOT and OMSSA on both data sets. Although MS-Align+ and ProSightPC have similar performance on the Salmonella typhimurium data set, MS-Align+ outperforms ProSightPC on the (more complex) Saccharomyces cerevisiae data set. PMID:22027200

Top-down causation and social structures

PubMed Central

Elder-Vass, Dave

2012-01-01

Top-down causation has been implicit in many sociological accounts of social structure and its influence on social events, but the social sciences have struggled to provide a coherent account of top-down causation itself. This paper summarizes a critical realist view of causation and emergence, shows how it supports a plausible account of top-down causation and then applies this account to the social world. The argument is illustrated by an examination of the concept of a norm circle, a kind of social entity that, it is argued, is causally responsible for the influence of normative social institutions. Nevertheless, social entities are structured rather differently from ordinary material ones, with the result that the compositional level structure of reality implicit in the concept of top-down causation has some limitations in the social world. The paper closes by considering what might be involved in examining how top-down causation can be shown to be at work in the social domain. PMID:23386963

Transgenic Bt Cotton Does Not Disrupt the Top-Down Forces Regulating the Cotton Aphid in Central China

PubMed Central

Yao, Yong-Sheng; Han, Peng; Niu, Chang-Ying; Dong, Yong-Cheng; Gao, Xi-Wu; Cui, Jin-Jie; Desneux, Nicolas

2016-01-01

Top-down force is referred to arthropod pest management delivered by the organisms from higher trophic levels. In the context of prevalent adoption of transgenic Bt crops that produce insecticidal Cry proteins derived from Bacillus thuringiensis (Bt), it still remains elusive whether the top-down forces are affected by the insect-resistant traits that introduced into the Bt crops. We explored how Bt cotton affect the strength of top-down forces via arthropod natural enemies in regulating a non-target pest species, the cotton aphid Aphis gossypii Glover, using a comparative approach (i.e. Bt cotton vs. conventional cotton) under field conditions. To determine top-down forces, we manipulated predation/parasitism exposure of the aphid to their natural enemies using exclusion cages. We found that the aphid population growth was strongly suppressed by the dominant natural enemies including Coccinellids, spiders and Aphidiines parasitoids. Coccinellids, spiders and the assemblage of other arthropod natural enemies (mainly lacewings and Hemipteran bugs) are similarly abundant in both plots, but with the parasitoid mummies less abundant in Bt cotton plots compared to the conventional cotton plots. However, the lower abundance of parasitoids in Bt cotton plots alone did not translate into differential top-down control on A. gossypii populations compared to conventional ones. Overall, the top-down forces were equally strong in both plots. We conclude that transgenic Bt cotton does not disrupt the top-down forces regulating the cotton aphid in central China. PMID:27870914

Top-down effects of a terrestrial frog on forest nutrient dynamics.

Treesearch

Karen H. Beard; Kristiina A. Vogt; Andrew Kulmatiski

2002-01-01

Many studies have found top-down effects of predators on prey, but few studies have linked top-down effects of vertebrate predators to nutrient cycling rates in terrestrial systems. In this study, large and significant effects of a terrestrial frog, Eleutherodactylus coqui (coqu

Top-down (Prior Knowledge) and Bottom-up (Perceptual Modality) Influences on Spontaneous Interpersonal Synchronization.

PubMed

Gipson, Christina L; Gorman, Jamie C; Hessler, Eric E

2016-04-01

Coordination with others is such a fundamental part of human activity that it can happen unintentionally. This unintentional coordination can manifest as synchronization and is observed in physical and human systems alike. We investigated the role of top-down influences (prior knowledge of the perceptual modality their partner is using) and bottom-up factors (perceptual modality combination) on spontaneous interpersonal synchronization. We examine this phenomena with respect to two different theoretical perspectives that differently emphasize top-down and bottom-up factors in interpersonal synchronization: joint-action/shared cognition theories and ecological-interactive theories. In an empirical study twelve dyads performed a finger oscillation task while attending to each other's movements through either visual, auditory, or visual and auditory perceptual modalities. Half of the participants were given prior knowledge of their partner's perceptual capabilities for coordinating across these different perceptual modality combinations. We found that the effect of top-down influence depends on the perceptual modality combination between two individuals. When people used the same perceptual modalities, top-down influence resulted in less synchronization and when people used different perceptual modalities, top-down influence resulted in more synchronization. Furthermore, persistence in the change in behavior as a result of having perceptual information about each other ('social memory') was stronger when this top-down influence was present.

Feature-Selective Attentional Modulations in Human Frontoparietal Cortex.

PubMed

Ester, Edward F; Sutterer, David W; Serences, John T; Awh, Edward

2016-08-03

Control over visual selection has long been framed in terms of a dichotomy between "source" and "site," where top-down feedback signals originating in frontoparietal cortical areas modulate or bias sensory processing in posterior visual areas. This distinction is motivated in part by observations that frontoparietal cortical areas encode task-level variables (e.g., what stimulus is currently relevant or what motor outputs are appropriate), while posterior sensory areas encode continuous or analog feature representations. Here, we present evidence that challenges this distinction. We used fMRI, a roving searchlight analysis, and an inverted encoding model to examine representations of an elementary feature property (orientation) across the entire human cortical sheet while participants attended either the orientation or luminance of a peripheral grating. Orientation-selective representations were present in a multitude of visual, parietal, and prefrontal cortical areas, including portions of the medial occipital cortex, the lateral parietal cortex, and the superior precentral sulcus (thought to contain the human homolog of the macaque frontal eye fields). Additionally, representations in many-but not all-of these regions were stronger when participants were instructed to attend orientation relative to luminance. Collectively, these findings challenge models that posit a strict segregation between sources and sites of attentional control on the basis of representational properties by demonstrating that simple feature values are encoded by cortical regions throughout the visual processing hierarchy, and that representations in many of these areas are modulated by attention. Influential models of visual attention posit a distinction between top-down control and bottom-up sensory processing networks. These models are motivated in part by demonstrations showing that frontoparietal cortical areas associated with top-down control represent abstract or categorical stimulus information, while visual areas encode parametric feature information. Here, we show that multivariate activity in human visual, parietal, and frontal cortical areas encode representations of a simple feature property (orientation). Moreover, representations in several (though not all) of these areas were modulated by feature-based attention in a similar fashion. These results provide an important challenge to models that posit dissociable top-down control and sensory processing networks on the basis of representational properties. Copyright © 2016 the authors 0270-6474/16/368188-12$15.00/0.

Top-down Proteomics in Health and Disease: Challenges and Opportunities

PubMed Central

Gregorich, Zachery R.; Ge, Ying

2014-01-01

Proteomics is essential for deciphering how molecules interact as a system and for understanding the functions of cellular systems in human disease; however, the unique characteristics of the human proteome, which include a high dynamic range of protein expression and extreme complexity due to a plethora of post-translational modifications (PTMs) and sequence variations, make such analyses challenging. An emerging “top-down” mass spectrometry (MS)-based proteomics approach, which provides a “bird’s eye” view of all proteoforms, has unique advantages for the assessment of PTMs and sequence variations. Recently, a number of studies have showcased the potential of top-down proteomics for unraveling of disease mechanisms and discovery of new biomarkers. Nevertheless, the top-down approach still faces significant challenges in terms of protein solubility, separation, and the detection of large intact proteins, as well as the under-developed data analysis tools. Consequently, new technological developments are urgently needed to advance the field of top-down proteomics. Herein, we intend to provide an overview of the recent applications of top-down proteomics in biomedical research. Moreover, we will outline the challenges and opportunities facing top-down proteomics strategies aimed at understanding and diagnosing human diseases. PMID:24723472

Functional overlap of top-down emotion regulation and generation: an fMRI study identifying common neural substrates between cognitive reappraisal and cognitively generated emotions.

PubMed

Otto, Benjamin; Misra, Supriya; Prasad, Aditya; McRae, Kateri

2014-09-01

One factor that influences the success of emotion regulation is the manner in which the regulated emotion was generated. Recent research has suggested that reappraisal, a top-down emotion regulation strategy, is more effective in decreasing self-reported negative affect when emotions were generated from the top-down, versus the bottom-up. On the basis of a process overlap framework, we hypothesized that the neural regions active during reappraisal would overlap more with emotions that were generated from the top-down, rather than from the bottom-up. In addition, we hypothesized that increased neural overlap between reappraisal and the history effects of top-down emotion generation would be associated with increased reappraisal success. The results of several analyses suggested that reappraisal and emotions that were generated from the top-down share a core network of prefrontal, temporal, and cingulate regions. This overlap is specific; no such overlap was observed between reappraisal and emotions that were generated in a bottom-up fashion. This network consists of regions previously implicated in linguistic processing, cognitive control, and self-relevant appraisals, which are processes thought to be crucial to both reappraisal and top-down emotion generation. Furthermore, individuals with high reappraisal success demonstrated greater neural overlap between reappraisal and the history of top-down emotion generation than did those with low reappraisal success. The overlap of these key regions, reflecting overlapping processes, provides an initial insight into the mechanism by which generation history may facilitate emotion regulation.

Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics.

PubMed

Valeja, Santosh G; Xiu, Lichen; Gregorich, Zachery R; Guner, Huseyin; Jin, Song; Ge, Ying

2015-01-01

To address the complexity of the proteome in mass spectrometry (MS)-based top-down proteomics, multidimensional liquid chromatography (MDLC) strategies that can effectively separate proteins with high resolution and automation are highly desirable. Although various MDLC methods that can effectively separate peptides from protein digests exist, very few MDLC strategies, primarily consisting of 2DLC, are available for intact protein separation, which is insufficient to address the complexity of the proteome. We recently demonstrated that hydrophobic interaction chromatography (HIC) utilizing a MS-compatible salt can provide high resolution separation of intact proteins for top-down proteomics. Herein, we have developed a novel 3DLC strategy by coupling HIC with ion exchange chromatography (IEC) and reverse phase chromatography (RPC) for intact protein separation. We demonstrated that a 3D (IEC-HIC-RPC) approach greatly outperformed the conventional 2D IEC-RPC approach. For the same IEC fraction (out of 35 fractions) from a crude HEK 293 cell lysate, a total of 640 proteins were identified in the 3D approach (corresponding to 201 nonredundant proteins) as compared to 47 in the 2D approach, whereas simply prolonging the gradients in RPC in the 2D approach only led to minimal improvement in protein separation and identifications. Therefore, this novel 3DLC method has great potential for effective separation of intact proteins to achieve deep proteome coverage in top-down proteomics.

Making a commercial carbon fiber cloth having comparable capacitances to carbon nanotubes and graphene in supercapacitors through a "top-down" approach.

PubMed

Zhang, Tianchang; Kim, Christine H J; Cheng, Yingwen; Ma, Yanwen; Zhang, Hongbo; Liu, Jie

2015-02-21

A "top-down" and scalable approach for processing carbon fiber cloth (CFC) into flexible and all-carbon electrodes with remarkable areal capacity and cyclic stability was developed. CFC is commercially available in large quantities but its use as an electrode material in supercapacitors is not satisfactory. The approach demonstrated in this work is based on the sequential treatment of CFC with KOH activation and high temperature annealing that can effectively improve its specific surface area to a remarkable 2780 m(2) g(-1) while at the same time achieving a good electrical conductivity of 320 S m(-1) without sacrificing its intrinsic mechanical strength and flexibility. The processed CFC can be directly used as an electrode for supercapacitors without any binders, conductive additives and current collectors while avoiding elaborate electrode processing steps to deliver a specific capacitance of ∼0.5 F cm(-2) and ∼197 F g(-1) with remarkable rate performance and excellent cyclic stability. The properties of these processed CFCs are comparable or better than graphene and carbon nanotube based electrodes. We further demonstrate symmetric solid-state supercapacitors based on these processed CFCs with very good flexibility. This "top-down" and scalable approach can be readily applied to other types of commercially available carbon materials and therefore can have a substantial significance for high performance supercapacitor devices.

A Top-Down Approach to Designing the Computerized Adaptive Multistage Test

ERIC Educational Resources Information Center

Luo, Xiao; Kim, Doyoung

2018-01-01

The top-down approach to designing a multistage test is relatively understudied in the literature and underused in research and practice. This study introduced a route-based top-down design approach that directly sets design parameters at the test level and utilizes the advanced automated test assembly algorithm seeking global optimality. The…

Transferring Codified Knowledge: Socio-Technical versus Top-Down Approaches

ERIC Educational Resources Information Center

Guzman, Gustavo; Trivelato, Luiz F.

2008-01-01

Purpose: This paper aims to analyse and evaluate the transfer process of codified knowledge (CK) performed under two different approaches: the "socio-technical" and the "top-down". It is argued that the socio-technical approach supports the transfer of CK better than the top-down approach. Design/methodology/approach: Case study methodology was…

Alternate Perspectives on Concept Internalization: Learning Top Down Vs. Learning Bottom Up.

ERIC Educational Resources Information Center

Pines, A. Leon

This paper outlines two alternate ways in which concepts are acquired, known as "top down" and "bottom up". "Bottom up" refers to learning the members of a category and then extracting their similarities or differences, the rule or criterial attributes used to make the categorization. In the "top down"…

Bottom-up and top-down influences at untrained conditions determine perceptual learning specificity and transfer

PubMed Central

Xiong, Ying-Zi; Zhang, Jun-Yun; Yu, Cong

2016-01-01

Perceptual learning is often orientation and location specific, which may indicate neuronal plasticity in early visual areas. However, learning specificity diminishes with additional exposure of the transfer orientation or location via irrelevant tasks, suggesting that the specificity is related to untrained conditions, likely because neurons representing untrained conditions are neither bottom-up stimulated nor top-down attended during training. To demonstrate these top-down and bottom-up contributions, we applied a “continuous flash suppression” technique to suppress the exposure stimulus into sub-consciousness, and with additional manipulations to achieve pure bottom-up stimulation or top-down attention with the transfer condition. We found that either bottom-up or top-down influences enabled significant transfer of orientation and Vernier discrimination learning. These results suggest that learning specificity may result from under-activations of untrained visual neurons due to insufficient bottom-up stimulation and/or top-down attention during training. High-level perceptual learning thus may not functionally connect to these neurons for learning transfer. DOI: http://dx.doi.org/10.7554/eLife.14614.001 PMID:27377357

Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins.

PubMed

Jebanathirajah, Judith A; Pittman, Jason L; Thomson, Bruce A; Budnik, Bogdan A; Kaur, Parminder; Rape, Michael; Kirschner, Marc; Costello, Catherine E; O'Connor, Peter B

2005-12-01

The use of a new electrospray qQq Fourier transform ion cyclotron mass spectrometer (qQq-FTICR MS) instrument for biologic applications is described. This qQq-FTICR mass spectrometer was designed for the study of post-translationally modified proteins and for top-down analysis of biologically relevant protein samples. The utility of the instrument for the analysis of phosphorylation, a common and important post-translational modification, was investigated. Phosphorylation was chosen as an example because it is ubiquitous and challenging to analyze. In addition, the use of the instrument for top-down sequencing of proteins was explored since this instrument offers particular advantages to this approach. Top-down sequencing was performed on different proteins, including commercially available proteins and biologically derived samples such as the human E2 ubiquitin conjugating enzyme, UbCH10. A good sequence tag was obtained for the human UbCH10, allowing the unambiguous identification of the protein. The instrument was built with a commercially produced front end: a focusing rf-only quadrupole (Q0), followed by a resolving quadrupole (Q1), and a LINAC quadrupole collision cell (Q2), in combination with an FTICR mass analyzer. It has utility in the analysis of samples found in substoichiometric concentrations, as ions can be isolated in the mass resolving Q1 and accumulated in Q2 before analysis in the ICR cell. The speed and efficacy of the Q2 cooling and fragmentation was demonstrated on an LCMS-compatible time scale, and detection limits for phosphopeptides in the 10 amol/muL range (pM) were demonstrated. The instrument was designed to make several fragmentation methods available, including nozzle-skimmer fragmentation, Q2 collisionally activated dissociation (Q2 CAD), multipole storage assisted dissociation (MSAD), electron capture dissociation (ECD), infrared multiphoton induced dissociation (IRMPD), and sustained off resonance irradiation (SORI) CAD, thus allowing a variety of MS(n) experiments. A particularly useful aspect of the system was the use of Q1 to isolate ions from complex mixtures with narrow windows of isolation less than 1 m/z. These features enable top-down protein analysis experiments as well structural characterization of minor components of complex mixtures.

Limited Role of Contextual Information in Adult Word Recognition. Technical Report No. 411.

ERIC Educational Resources Information Center

Durgunoglu, Aydin Y.

Recognizing a word in a meaningful text involves processes that combine information from many different sources, and both bottom-up processes (such as feature extraction and letter recognition) and top-down processes (contextual information) are thought to interact when skilled readers recognize words. Two similar experiments investigated word…

Quantification and source apportionment of the methane emission flux from the city of Indianapolis

USDA-ARS?s Scientific Manuscript database

We report the CH4 emission flux from the city of Indianapolis, IN, the site of the Indianapolis Flux Experiment (INFLUX) project for developing, assessing, and improving top-down and bottom-up approaches for quantifying urban greenhouse gas emissions. Using an aircraft-based mass balance approach, w...

The social-sensory interface: category interactions in person perception

PubMed Central

Freeman, Jonathan B.; Johnson, Kerri L.; Adams, Reginald B.; Ambady, Nalini

2012-01-01

Research is increasingly challenging the claim that distinct sources of social information—such as sex, race, and emotion—are processed in discrete fashion. Instead, there appear to be functionally relevant interactions that occur. In the present article, we describe research examining how cues conveyed by the human face, voice, and body interact to form the unified representations that guide our perceptions of and responses to other people. We explain how these information sources are often thrown into interaction through bottom-up forces (e.g., phenotypic cues) as well as top-down forces (e.g., stereotypes and prior knowledge). Such interactions point to a person perception process that is driven by an intimate interface between bottom-up perceptual and top-down social processes. Incorporating data from neuroimaging, event-related potentials (ERP), computational modeling, computer mouse-tracking, and other behavioral measures, we discuss the structure of this interface, and we consider its implications and adaptive purposes. We argue that an increased understanding of person perception will likely require a synthesis of insights and techniques, from social psychology to the cognitive, neural, and vision sciences. PMID:23087622

Brain Circuits of Methamphetamine Place Reinforcement Learning: The Role of the Hippocampus-VTA Loop.

PubMed

Keleta, Yonas B; Martinez, Joe L

2012-03-01

The reinforcing effects of addictive drugs including methamphetamine (METH) involve the midbrain ventral tegmental area (VTA). VTA is primary source of dopamine (DA) to the nucleus accumbens (NAc) and the ventral hippocampus (VHC). These three brain regions are functionally connected through the hippocampal-VTA loop that includes two main neural pathways: the bottom-up pathway and the top-down pathway. In this paper, we take the view that addiction is a learning process. Therefore, we tested the involvement of the hippocampus in reinforcement learning by studying conditioned place preference (CPP) learning by sequentially conditioning each of the three nuclei in either the bottom-up order of conditioning; VTA, then VHC, finally NAc, or the top-down order; VHC, then VTA, finally NAc. Following habituation, the rats underwent experimental modules consisting of two conditioning trials each followed by immediate testing (test 1 and test 2) and two additional tests 24 h (test 3) and/or 1 week following conditioning (test 4). The module was repeated three times for each nucleus. The results showed that METH, but not Ringer's, produced positive CPP following conditioning each brain area in the bottom-up order. In the top-down order, METH, but not Ringer's, produced either an aversive CPP or no learning effect following conditioning each nucleus of interest. In addition, METH place aversion was antagonized by coadministration of the N-methyl-d-aspartate (NMDA) receptor antagonist MK801, suggesting that the aversion learning was an NMDA receptor activation-dependent process. We conclude that the hippocampus is a critical structure in the reward circuit and hence suggest that the development of target-specific therapeutics for the control of addiction emphasizes on the hippocampus-VTA top-down connection.

Top-Down Prioritization of Salient Items May Produce the So-Called Stimulus-Driven Capture

PubMed Central

Benoni, Hanna

2018-01-01

The current study proposes that top-down attentional prioritization of salient items may produce the so-called stimulus-driven capture. To test this proposal, the “expectation-based paradigm” was designed on the basis of a visual search task. In Experiment 1, a task-irrelevant singleton frame was presented at the same location in 70% of the trials. The target was either presented at chance level within the singleton location, or away from it. In line with the singleton capture phenomenon, participants were faster in identifying the target when it appeared in the singleton location compared to non-singleton locations. However, leaving out the singleton frame in 30% of the trials led to a similar effect; participants were faster in identifying the target when it appeared in the expected singleton location compared to expected non-singletons locations (a “quasi-capture” effect). These results suggest that the participants allocated their attention to the expected singleton location, rather than that the singleton itself captured attention. In Experiment 2, the same task-irrelevant color singleton was presented in a random position in 70% of the trials. This color frame was shown as a non-singleton in all of the 30% singleton-absent multicolored trials. A similar facilitation effect was obtained when the target appeared in the expected singleton color frame compared to other frames, in singleton-absent trials as in singleton-present trials. These results further support the idea that instances of singleton capture can be explained by top-down attentional shifts toward singleton items. Theoretical implications of these results are discussed. Mostly, the study calls to consider the possibility that all sources of attentional control may be represented by a continuous variable of top-down control, including the category of “physical salience.” PMID:29599731

Top Cyber: Developing the Top One Percent to Defeat the Advanced Persistent Threat

DTIC Science & Technology

2014-02-13

Critical Infrastructure.” V3-CO-UK, 7 May 2013. http://www.v3.co.uk/v3-uk/news/2266397/us- government-chinese- hackers -have-the-skills-to-take-down...it is a source of great risk; and, for hackers , it is the super-highway to a target-rich environment. For the U.S. Government (USG), cyberspace is...worldwide. Ultimately, for all its benefits, the Internet presents an “Achilles’ Heel” in the defense of the nation’s Critical Infrastructure and Key

Estimating air emissions from ships: Meta-analysis of modelling approaches and available data sources

NASA Astrophysics Data System (ADS)

Miola, Apollonia; Ciuffo, Biagio

2011-04-01

Maritime transport plays a central role in the transport sector's sustainability debate. Its contribution to air pollution and greenhouse gases is significant. An effective policy strategy to regulate air emissions requires their robust estimation in terms of quantification and location. This paper provides a critical analysis of the ship emission modelling approaches and data sources available, identifying their limits and constraints. It classifies the main methodologies on the basis of the approach followed (bottom-up or top-down) for the evaluation and geographic characterisation of emissions. The analysis highlights the uncertainty of results from the different methods. This is mainly due to the level of uncertainty connected with the sources of information that are used as inputs to the different studies. This paper describes the sources of the information required for these analyses, paying particular attention to AIS data and to the possible problems associated with their use. One way of reducing the overall uncertainty in the results could be the simultaneous use of different sources of information. This paper presents an alternative methodology based on this approach. As a final remark, it can be expected that new approaches to the problem together with more reliable data sources over the coming years could give more impetus to the debate on the global impact of maritime traffic on the environment that, currently, has only reached agreement via the "consensus" estimates provided by IMO (2009).

Top-down knowledge modulates onset capture in a feedforward manner.

PubMed

Becker, Stefanie I; Lewis, Amanda J; Axtens, Jenna E

2017-04-01

How do we select behaviourally important information from cluttered visual environments? Previous research has shown that both top-down, goal-driven factors and bottom-up, stimulus-driven factors determine which stimuli are selected. However, it is still debated when top-down processes modulate visual selection. According to a feedforward account, top-down processes modulate visual processing even before the appearance of any stimuli, whereas others claim that top-down processes modulate visual selection only at a late stage, via feedback processing. In line with such a dual stage account, some studies found that eye movements to an irrelevant onset distractor are not modulated by its similarity to the target stimulus, especially when eye movements are launched early (within 150-ms post stimulus onset). However, in these studies the target transiently changed colour due to a colour after-effect that occurred during premasking, and the time course analyses were incomplete. The present study tested the feedforward account against the dual stage account in two eye tracking experiments, with and without colour after-effects (Exp. 1), as well when the target colour varied randomly and observers were informed of the target colour with a word cue (Exp. 2). The results showed that top-down processes modulated the earliest eye movements to the onset distractors (<150-ms latencies), without incurring any costs for selection of target matching distractors. These results unambiguously support a feedforward account of top-down modulation.

Top-Down Visual Saliency via Joint CRF and Dictionary Learning.

PubMed

Yang, Jimei; Yang, Ming-Hsuan

2017-03-01

Top-down visual saliency is an important module of visual attention. In this work, we propose a novel top-down saliency model that jointly learns a Conditional Random Field (CRF) and a visual dictionary. The proposed model incorporates a layered structure from top to bottom: CRF, sparse coding and image patches. With sparse coding as an intermediate layer, CRF is learned in a feature-adaptive manner; meanwhile with CRF as the output layer, the dictionary is learned under structured supervision. For efficient and effective joint learning, we develop a max-margin approach via a stochastic gradient descent algorithm. Experimental results on the Graz-02 and PASCAL VOC datasets show that our model performs favorably against state-of-the-art top-down saliency methods for target object localization. In addition, the dictionary update significantly improves the performance of our model. We demonstrate the merits of the proposed top-down saliency model by applying it to prioritizing object proposals for detection and predicting human fixations.

Global carbon monoxide cycle: Modeling and data analysis

NASA Astrophysics Data System (ADS)

Arellano, Avelino F., Jr.

The overarching goal of this dissertation is to develop robust, spatially and temporally resolved CO sources, using global chemical transport modeling, CO measurements from Climate Monitoring and Diagnostic Laboratory (CMDL) and Measurement of Pollution In The Troposphere (MOPITT), under the framework of Bayesian synthesis inversion. To rigorously quantify the CO sources, I conducted five sets of inverse analyses, with each set investigating specific methodological and scientific issues. The first two inverse analyses separately explored two different CO observations to estimate CO sources by region and sector. Under a range of scenarios relating to inverse methodology and data quality issues, top-down estimates using CMDL CO surface and MOPITT CO remote-sensed measurements show consistent results particularly on a significantly large fossil fuel/biofuel (FFBF) emission in East Asia than present bottom-up estimates. The robustness of this estimate is strongly supported by forward and inverse modeling studies in the region particularly from TRansport and Chemical Evolution over the Pacific (TRACE-P) campaign. The use of high-resolution measurement for the first time in CO inversion also draws attention to a methodology issue that the range of estimates from the scenarios is larger than posterior uncertainties, suggesting that estimate uncertainties may be underestimated. My analyses highlight the utility of top-down approach to provide additional constraints on present global estimates by also pointing to other discrepancies including apparent underestimation of FFBF from Africa/Latin America and biomass burning (BIOM) sources in Africa, southeast Asia and north-Latin America, indicating inconsistencies on our current understanding of fuel use and land-use patterns in these regions. Inverse analysis using MOPITT is extended to determine the extent of MOPITT information and estimate monthly regional CO sources. A major finding, which is consistent with other atmospheric observations but differ with satellite area-burned observations, is a significant overestimation in southern Africa for June/July relative to satellite-and-model-constrained BIOM emissions of CO. Sensitivity inverse analyses on observation error covariance and structure, and sequential inversion using NOAA CMDL to fully exploit available information, confirm the robustness of the estimates and further recognize the limitations of the approach, implying the need to further improve the methodology and to reconcile discrepancies.

Top-Down Influence in Young Children's Linguistic Ambiguity Resolution

ERIC Educational Resources Information Center

Rabagliati, Hugh; Pylkkanen, Liina; Marcus, Gary F.

2013-01-01

Language is rife with ambiguity. Do children and adults meet this challenge in similar ways? Recent work suggests that while adults resolve syntactic ambiguities by integrating a variety of cues, children are less sensitive to top-down evidence. We test whether this top-down insensitivity is specific to syntax or a general feature of children's…

Top-Down Management: An Effective Tool in Higher Education?

ERIC Educational Resources Information Center

Tsai, Yau; Beverton, Sue

2007-01-01

Purpose: The purpose of this paper is to explore the strengths and weaknesses of top-down management in a university that has embraced globalisation with a strong market-led ethos and to suggest the ways in which adjustments might be made to top-down management processes. Design/methodology/approach: The paper examines the strengths and weaknesses…

The Role of Person Versus Situation in Life Satisfaction: A Critical Examination

ERIC Educational Resources Information Center

Heller, Daniel; Watson, David; Hies, Remus

2004-01-01

Two main theoretical approaches have been put forward to explain individual differences in life satisfaction: top-down (i.e., personological) and bottom-up (i.e., situational). The authors examine the relative merit of these 2 approaches and the psychological processes underlying top-down models. Consistent with a top-down approach, meta-analytic…

Bottom-Up Guidance in Visual Search for Conjunctions

ERIC Educational Resources Information Center

Proulx, Michael J.

2007-01-01

Understanding the relative role of top-down and bottom-up guidance is crucial for models of visual search. Previous studies have addressed the role of top-down and bottom-up processes in search for a conjunction of features but with inconsistent results. Here, the author used an attentional capture method to address the role of top-down and…

Defining ecospace of Arctic marine food webs using a novel quantitative approach

NASA Astrophysics Data System (ADS)

Gale, M.; Loseto, L. L.

2011-12-01

The Arctic is currently facing unprecedented change with developmental, physical and climatological changes. Food webs within the marine Arctic environment are highly susceptible to anthropogenic stressors and have thus far been understudied. Stable isotopes, in conjunction with a novel set of metrics, may provide a framework that allows us to understand which areas of the Arctic are most vulnerable to change. The objective of this study was to use linear distance metrics applied to stable isotopes to a) define and quantify four Arctic marine food webs in ecospace; b) enable quantifiable comparisons among the four food webs and with other ecosystems; and, c) evaluate vulnerability of the four food webs to anthropogenic stressors such as climate change. The areas studied were Hudson Bay, Beaufort Sea, Lancaster Sound and North Water Polynya. Each region was selected based on the abundance of previous research and published and available stable isotope data in peer-review literature. We selected species to cover trophic levels ranging from particulate matter to polar bears with consideration of pelagic, benthic and ice-associated energy pathways. We interpret higher diversity in baseline carbon energy as signifying higher stability in food web structure. Based on this, the Beaufort Sea food web had the highest stability; the Beaufort Sea food web occupied the largest isotopic niche space and was supported by multiple carbon sources. Areas with top-down control system, such as Lancaster Sound and North Water Polynya, would be the first to experience an increase in trophic redundancy and possible hardships from external stressors, as they have fewer basal carbon sources and greater numbers of mid-high level consumers. We conclude that a diverse carbon energy based ecosystem such as the Beaufort Sea and Hudson Bay regions are more resilient to change than a top down control system.

Prey Vulnerability Limits Top-Down Control and Alters Reciprocal Feedbacks in a Subsidized Model Food Web

PubMed Central

Atlas, William I.; Palen, Wendy J.

2014-01-01

Resource subsidies increase the productivity of recipient food webs and can affect ecosystem dynamics. Subsidies of prey often support elevated predator biomass which may intensify top-down control and reduce the flow of reciprocal subsidies into adjacent ecosystems. However, top-down control in subsidized food webs may be limited if primary consumers posses morphological or behavioral traits that limit vulnerability to predation. In forested streams, terrestrial prey support high predator biomass creating the potential for strong top-down control, however armored primary consumers often dominate the invertebrate assemblage. Using empirically based simulation models, we tested the response of stream food webs to variations in subsidy magnitude, prey vulnerability, and the presence of two top predators. While terrestrial prey inputs increased predator biomass (+12%), the presence of armored primary consumers inhibited top-down control, and diverted most aquatic energy (∼75%) into the riparian forest through aquatic insect emergence. Food webs without armored invertebrates experienced strong trophic cascades, resulting in higher algal (∼50%) and detrital (∼1600%) biomass, and reduced insect emergence (−90%). These results suggest prey vulnerability can mediate food web responses to subsidies, and that top-down control can be arrested even when predator-invulnerable consumers are uncommon (20%) regardless of the level of subsidy. PMID:24465732

Top-down cortical input during NREM sleep consolidates perceptual memory.

PubMed

Miyamoto, D; Hirai, D; Fung, C C A; Inutsuka, A; Odagawa, M; Suzuki, T; Boehringer, R; Adaikkan, C; Matsubara, C; Matsuki, N; Fukai, T; McHugh, T J; Yamanaka, A; Murayama, M

2016-06-10

During tactile perception, long-range intracortical top-down axonal projections are essential for processing sensory information. Whether these projections regulate sleep-dependent long-term memory consolidation is unknown. We altered top-down inputs from higher-order cortex to sensory cortex during sleep and examined the consolidation of memories acquired earlier during awake texture perception. Mice learned novel textures and consolidated them during sleep. Within the first hour of non-rapid eye movement (NREM) sleep, optogenetic inhibition of top-down projecting axons from secondary motor cortex (M2) to primary somatosensory cortex (S1) impaired sleep-dependent reactivation of S1 neurons and memory consolidation. In NREM sleep and sleep-deprivation states, closed-loop asynchronous or synchronous M2-S1 coactivation, respectively, reduced or prolonged memory retention. Top-down cortical information flow in NREM sleep is thus required for perceptual memory consolidation. Copyright © 2016, American Association for the Advancement of Science.

Relative importance of top-down and bottom-up forces in food webs of Sarracenia pitcher communities at a northern and a southern site.

PubMed

Hoekman, David

2011-04-01

The relative importance of resources (bottom-up forces) and natural enemies (top-down forces) for regulating food web dynamics has been debated, and both forces have been found to be critical for determining food web structure. How the relative importance of top-down and bottom-up forces varies between sites with different abiotic conditions is not well understood. Using the pitcher plant inquiline community as a model system, I examine how the relative importance of top-down and bottom-up effects differs between two disparate sites. Resources (ant carcasses) and top predators (mosquito larvae) were manipulated in two identical 4 × 4 factorial press experiments, conducted at two geographically distant sites (Michigan and Florida) within the range of the purple pitcher plant, Sarracenia purpurea, and the aquatic community that resides in its leaves. Overall, top predators reduced the density of prey populations while additional resources bolstered them, and the relative importance of top-down and bottom-up forces varied between sites and for different trophic levels. Specifically, top-down effects on protozoa were stronger in Florida than in Michigan, while the opposite pattern was found for rotifers. These findings experimentally demonstrate that the strength of predator-prey interactions, even those involving the same species, vary across space. While only two sites are compared in this study, I hypothesize that site differences in temperature, which influences metabolic rate, may be responsible for variation in consumer-resource interactions. These findings warrant further investigation into the specific factors that modify the relative importance of top-down and bottom-up effects.

Direction with Discretion: Reading Recovery as an Example of Balancing Top-Down Policy and Bottom-Up Decision-Making.

ERIC Educational Resources Information Center

Scharer, Patricia L.; Zajano, Nancy C.

Educational policy analysts have recognized the need for an educational policy that combines the merits of "top-down" mandates with "bottom-up" teacher discretion. This paper describes the Reading Recovery program as an example of an educational program that balances top-down direction and bottom-up discretion by: (1) providing an overall…

Real-world visual search is dominated by top-down guidance.

PubMed

Chen, Xin; Zelinsky, Gregory J

2006-11-01

How do bottom-up and top-down guidance signals combine to guide search behavior? Observers searched for a target either with or without a preview (top-down manipulation) or a color singleton (bottom-up manipulation) among the display objects. With a preview, reaction times were faster and more initial eye movements were guided to the target; the singleton failed to attract initial saccades under these conditions. Only in the absence of a preview did subjects preferentially fixate the color singleton. We conclude that the search for realistic objects is guided primarily by top-down control. Implications for saliency map models of visual search are discussed.

Nine years of global hydrocarbon emissions based on source inversion of OMI formaldehyde observations

NASA Astrophysics Data System (ADS)

Bauwens, Maite; Stavrakou, Trissevgeni; Müller, Jean-François; De Smedt, Isabelle; Van Roozendael, Michel; van der Werf, Guido R.; Wiedinmyer, Christine; Kaiser, Johannes W.; Sindelarova, Katerina; Guenther, Alex

2016-08-01

As formaldehyde (HCHO) is a high-yield product in the oxidation of most volatile organic compounds (VOCs) emitted by fires, vegetation, and anthropogenic activities, satellite observations of HCHO are well-suited to inform us on the spatial and temporal variability of the underlying VOC sources. The long record of space-based HCHO column observations from the Ozone Monitoring Instrument (OMI) is used to infer emission flux estimates from pyrogenic and biogenic volatile organic compounds (VOCs) on the global scale over 2005-2013. This is realized through the method of source inverse modeling, which consists in the optimization of emissions in a chemistry-transport model (CTM) in order to minimize the discrepancy between the observed and modeled HCHO columns. The top-down fluxes are derived in the global CTM IMAGESv2 by an iterative minimization algorithm based on the full adjoint of IMAGESv2, starting from a priori emission estimates provided by the newly released GFED4s (Global Fire Emission Database, version 4s) inventory for fires, and by the MEGAN-MOHYCAN inventory for isoprene emissions. The top-down fluxes are compared to two independent inventories for fire (GFAS and FINNv1.5) and isoprene emissions (MEGAN-MACC and GUESS-ES). The inversion indicates a moderate decrease (ca. 20 %) in the average annual global fire and isoprene emissions, from 2028 Tg C in the a priori to 1653 Tg C for burned biomass, and from 343 to 272 Tg for isoprene fluxes. Those estimates are acknowledged to depend on the accuracy of formaldehyde data, as well as on the assumed fire emission factors and the oxidation mechanisms leading to HCHO production. Strongly decreased top-down fire fluxes (30-50 %) are inferred in the peak fire season in Africa and during years with strong a priori fluxes associated with forest fires in Amazonia (in 2005, 2007, and 2010), bushfires in Australia (in 2006 and 2011), and peat burning in Indonesia (in 2006 and 2009), whereas generally increased fluxes are suggested in Indochina and during the 2007 fires in southern Europe. Moreover, changes in fire seasonal patterns are suggested; e.g., the seasonal amplitude is reduced over southeast Asia. In Africa, the inversion indicates increased fluxes due to agricultural fires and decreased maxima when natural fires are dominant. The top-down fire emissions are much better correlated with MODIS fire counts than the a priori inventory in regions with small and agricultural fires, indicating that the OMI-based inversion is well-suited to assess the associated emissions. Regarding biogenic sources, significant reductions in isoprene fluxes are inferred in tropical ecosystems (30-40 %), suggesting overestimated basal emission rates in those areas in the bottom-up inventory, whereas strongly positive isoprene emission updates are derived over semiarid and desert areas, especially in southern Africa and Australia. This finding suggests that the parameterization of the soil moisture stress used in MEGAN greatly exaggerates the flux reduction due to drought in those regions. The isoprene emission trends over 2005-2013 are often enhanced after optimization, with positive top-down trends in Siberia (4.2 % year-1) and eastern Europe (3.9 % year-1), likely reflecting forest expansion and warming temperatures, and negative trends in Amazonia (-2.1 % year-1), south China (-1 % year-1), the United States (-3.7 % year-1), and western Europe (-3.3 % year-1), which are generally corroborated by independent studies, yet their interpretation warrants further investigation.

Ultrahigh pressure fast size exclusion chromatography for top-down proteomics.

PubMed

Chen, Xin; Ge, Ying

2013-09-01

Top-down MS-based proteomics has gained a solid growth over the past few years but still faces significant challenges in the LC separation of intact proteins. In top-down proteomics, it is essential to separate the high mass proteins from the low mass species due to the exponential decay in S/N as a function of increasing molecular mass. SEC is a favored LC method for size-based separation of proteins but suffers from notoriously low resolution and detrimental dilution. Herein, we reported the use of ultrahigh pressure (UHP) SEC for rapid and high-resolution separation of intact proteins for top-down proteomics. Fast separation of intact proteins (6-669 kDa) was achieved in < 7 min with high resolution and high efficiency. More importantly, we have shown that this UHP-SEC provides high-resolution separation of intact proteins using a MS-friendly volatile solvent system, allowing the direct top-down MS analysis of SEC-eluted proteins without an additional desalting step. Taken together, we have demonstrated that UHP-SEC is an attractive LC strategy for the size separation of proteins with great potential for top-down proteomics. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An integrative top-down and bottom-up qualitative model construction framework for exploration of biochemical systems.

PubMed

Wu, Zujian; Pang, Wei; Coghill, George M

Computational modelling of biochemical systems based on top-down and bottom-up approaches has been well studied over the last decade. In this research, after illustrating how to generate atomic components by a set of given reactants and two user pre-defined component patterns, we propose an integrative top-down and bottom-up modelling approach for stepwise qualitative exploration of interactions among reactants in biochemical systems. Evolution strategy is applied to the top-down modelling approach to compose models, and simulated annealing is employed in the bottom-up modelling approach to explore potential interactions based on models constructed from the top-down modelling process. Both the top-down and bottom-up approaches support stepwise modular addition or subtraction for the model evolution. Experimental results indicate that our modelling approach is feasible to learn the relationships among biochemical reactants qualitatively. In addition, hidden reactants of the target biochemical system can be obtained by generating complex reactants in corresponding composed models. Moreover, qualitatively learned models with inferred reactants and alternative topologies can be used for further web-lab experimental investigations by biologists of interest, which may result in a better understanding of the system.

Constraining regional scale carbon budgets at the US West Coast using a high-resolution atmospheric inverse modeling approach

NASA Astrophysics Data System (ADS)

Goeckede, M.; Michalak, A. M.; Vickers, D.; Turner, D.; Law, B.

2009-04-01

The study presented is embedded within the NACP (North American Carbon Program) West Coast project ORCA2, which aims at determining the regional carbon balance of the US states Oregon, California and Washington. Our work specifically focuses on the effect of disturbance history and climate variability, aiming at improving our understanding of e.g. drought stress and stand age on carbon sources and sinks in complex terrain with fine-scale variability in land cover types. The ORCA2 atmospheric inverse modeling approach has been set up to capture flux variability on the regional scale at high temporal and spatial resolution. Atmospheric transport is simulated coupling the mesoscale model WRF (Weather Research and Forecast) with the STILT (Stochastic Time Inverted Lagrangian Transport) footprint model. This setup allows identifying sources and sinks that influence atmospheric observations with highly resolved mass transport fields and realistic turbulent mixing. Terrestrial biosphere carbon fluxes are simulated at spatial resolutions of up to 1km and subdaily timesteps, considering effects of ecoregion, land cover type and disturbance regime on the carbon budgets. Our approach assimilates high-precision atmospheric CO2 concentration measurements and eddy-covariance data from several sites throughout the model domain, as well as high-resolution remote sensing products (e.g. LandSat, MODIS) and interpolated surface meteorology (DayMet, SOGS, PRISM). We present top-down modeling results that have been optimized using Bayesian inversion, reflecting the information on regional scale carbon processes provided by the network of high-precision CO2 observations. We address the level of detail (e.g. spatial and temporal resolution) that can be resolved by top-down modeling on the regional scale, given the uncertainties introduced by various sources for model-data mismatch. Our results demonstrate the importance of accurate modeling of carbon-water coupling, with the representation of water availability and drought stress playing a dominant role to capture spatially variable CO2 exchange rates in a region characterized by strong climatic gradients.

A New Top-Down Decadal Constraint on Black Carbon Emissions over Asia - Capturing The Influence of Widespread and Regularly Occurring Fires and Urbanization: Greater Atmospheric Loading and Variability, Larger Impacts on Radiative Forcing at the Surface and in the Atmosphere, and Possible Feedback Mechanisms

NASA Astrophysics Data System (ADS)

Cohen, J. B.

2014-12-01

A global top-down study of Black Carbon (BC) Emissions has found that sources are considerably higher than present day emissions datasets, with most of this underestimation stemming from the rapidly developing areas of East and Southeast Asia. An additional source in these regions is the frequent and sometimes annual influence of extreme biomass burning events, which emit additional BC and other aerosols into the atmosphere. An additional top-down study has shown that the emissions of BC from these biomass burning events in Southeast Asia contribute an additional 30% increase in the annual average BC emissions, and an additional 110% increase during the highest fire year. One important reason for this underestimation is that many of these source regions do not appear as fires, due to missing MODIS overpasses, intense cloud cover, and low fire temperatures at the wet surface. These new temporally and spatially varying emissions of BC are run in a state-of-the art combined model of aerosol physics, chemistry, and general circulation, including urban scale chemical processing and core/shell aerosol mixture impacts on radiation. The results reveal that this new dataset matches in space, time, and magnitude, an array of observations (remotely sensed, ground, and column) far better than other emission datasets: IPCC SRES, AEROCOM, BOND, and GFED. The modeled mean atmospheric extinction and loading are both much higher and more variable than previous modelling efforts, leading to a larger negative surface radiative forcing. At the same time, atmospheric absorption is enhanced and more variable, leading to intense atmospheric heating, with the average impact from 1.0-1.5 W/m2. This has impacts on the vertical stability in the source areas, and leads to changes in the dynamics such as a shifting of the ITCZ, reducing light precipitation and increasing strong convection. To support this, a bit of measurement-based evidence presented for each of these phenomena.

Crab regulation of cross-ecosystem resource transfer by marine foraging fire ants.

PubMed

Garcia, Erica A; Bertness, Mark D; Alberti, Juan; Silliman, Brian R

2011-08-01

Permeability of boundaries in biological systems is regulated by biotic and/or abiotic factors. Despite this knowledge, the role of biotic factors in regulating resource transfer across ecosystem boundaries has received little study. Additionally, little is known about how cross-ecosystem resource transfer affects source populations. We used experiments, observations and stable isotopes, to evaluate: (1) the proportion of intertidal-foraging black fire ant (Solenopsis richteri) diet derived from marine sources, (2) how black fire ant cross-ecosystem resource transfer is altered by the dominant bioengineer in the intertidal, a burrowing crab (Neohelice granulata), (3) the top-down impact of these terrestrial ants on a marine resource, and (4) the effect of marine resources on recipient black fire ants. We found that more than 85% of the black fire ant diet is derived from marine sources, the number of intertidal foraging ants doubles in the absence of crab burrows, and that ants cause a 50% reduction in intertidal polychaetes. Also, ant mound density is three times greater adjacent to marine systems. This study reveals that cross-ecosystem foraging terrestrial ants can clearly have strong impacts on marine resources. Furthermore, ecosystem engineers that modify and occupy habitat in these ecosystem boundaries can strongly regulate the degree of cross-ecosystem resource transfer and resultant top down impacts.

Low-Molecular-Weight Plasma Proteome Analysis Using Top-Down Mass Spectrometry.

PubMed

Cheon, Dong Huey; Yang, Eun Gyeong; Lee, Cheolju; Lee, Ji Eun

2017-01-01

While human plasma has a wealth of diagnostic information regarding the state of the human body in heath and disease, low molecular weight (LMW) proteome (<30 kDa) has been shown to contain a rich source of diagnostic biomarkers. Here we describe a protocol for top-down proteomic analysis to identify and characterize the LMW proteoforms present in four types of human plasma samples without immunoaffinity depletion and with depletion of the top two, six, and seven high-abundance proteins. Each type of plasma sample was first fractionated based on molecular weight using gel-eluted liquid fraction entrapment electrophoresis (GELFrEE). Then, the GELFrEE fractions containing up to 30 kDa were subjected to nanocapillary-LC-MS/MS, and the high-resolution MS and MS/MS data were processed using ProSightPC software. As a result, a total of 442 LMW proteins and cleaved products, including those with posttranslational modifications (PTMs) and single amino acid variations (SAAVs), were identified with a threshold E-value of 1 × 10 -4 from the four types of plasma samples.

Top-down proteomic identification of bacterial protein biomarkers and toxins using MALDI-TOF-TOF-MS/MS and post-source decay

USDA-ARS?s Scientific Manuscript database

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight mass spectrometry(MALDI-TOF-TOF-MS)has provided new capabilities for the rapid identification of digested and non-digested proteins. The tandem (MS/MS) capability of TOF-TOF instruments allows precursor ion selection/isolation...

The Evidence Informed School System in England: Where Should School Leaders Be Focusing Their Efforts?

ERIC Educational Resources Information Center

Greany, Toby; Brown, Chris

2017-01-01

This article examines the impetus for schools to engage both in and with evidence in England's self-improving school system. It begins with an examination of how the education policy environment has changed, shifting from predominantly top down approaches to school improvement to the current government's focus on schools themselves sourcing and…

The Evidence-Informed School System in England: Where Should School Leaders Be Focusing Their Efforts?

ERIC Educational Resources Information Center

Brown, Chris; Greany, Toby

2018-01-01

This article examines the impetus for schools to engage in and with evidence in England's self-improving school system. It begins with an examination of how the education policy environment has changed, shifting from predominantly top-down approaches to school improvement to the current government's focus on schools themselves sourcing and sharing…

Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem

PubMed Central

Rudman, Seth M.; Rodriguez-Cabal, Mariano A.; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W.; Crutsinger, Gregory M.

2015-01-01

Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. PMID:26203004

Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem.

PubMed

Rudman, Seth M; Rodriguez-Cabal, Mariano A; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W; Crutsinger, Gregory M

2015-08-07

Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. © 2015 The Author(s).

A Ubiquitin-Proteasome Pathway for the Repair of Topoisomerase I-DNA Covalent Complexes*S⃞

PubMed Central

Lin, Chao-Po; Ban, Yi; Lyu, Yi Lisa; Desai, Shyamal D.; Liu, Leroy F.

2008-01-01

Reversible topoisomerase I (Top1)-DNA cleavage complexes are the key DNA lesion induced by anticancer camptothecins (e.g. topotecan and irinotecan) as well as structurally perturbed DNAs (e.g. oxidatively damaged DNA, UV-irradiated DNA, alkylated DNA, uracil-substituted DNA, mismatched DNA, gapped and nicked DNA, and DNA with abasic sites). Top1 cleavage complexes arrest transcription and trigger transcription-dependent degradation of Top1, a phenomenon termed Top1 down-regulation. In the current study, we have investigated the role of Top1 down-regulation in the repair of Top1 cleavage complexes. Using quiescent (serum-starved) human WI-38 cells, camptothecin (CPT) was shown to induce Top1 down-regulation, which paralleled the induction of DNA single-strand breaks (SSBs) (assayed by comet assays) and ATM autophosphorylation (at Ser-1981). Interestingly, Top1 down-regulation, induction of DNA SSBs and ATM autophosphorylation were all abolished by the proteasome inhibitor MG132. Furthermore, studies using immunoprecipitation and dominant-negative ubiquitin mutants have suggested a specific requirement for the assembly of Lys-48-linked polyubiquitin chains for CPT-induced Top1 down-regulation. In contrast to the effect of proteasome inhibition, inactivation of PARP1 was shown to increase the amount of CPT-induced SSBs and the level of ATM autophosphorylation. Together, these results support a model in which Top1 cleavage complexes arrest transcription and activate a ubiquitin-proteasome pathway leading to the degradation of Top1 cleavage complexes. Degradation of Top1 cleavage complexes results in the exposure of Top1-concealed SSBs for repair through a PARP1-dependent process. PMID:18515798

Legacy of top-down herbivore pressure ricochets back up multiple trophic levels in forest canopies over 30 years

Treesearch

Tim Nuttle; Ellen H. Yerger; Scott H. Stoleson; Todd E. Ristau

2011-01-01

Removal of top-down control on herbivores can result in a trophic cascade where herbivore pressure on plants results in changes in plant communities. These altered plant communities are hypothesized to exert bottom-up control on subsequent herbivory via changes in plant quality or productivity. But it remains untested whether top-down perturbation causes long term...

Bottom-Up or Top-Down: English as a Foreign Language Vocabulary Instruction for Chinese University Students

ERIC Educational Resources Information Center

Moskovsky, Christo; Jiang, Guowu; Libert, Alan; Fagan, Seamus

2015-01-01

Whereas there has been some research on the role of bottom-up and top-down processing in the learning of a second or foreign language, very little attention has been given to bottom-up and top-down instructional approaches to language teaching. The research reported here used a quasi-experimental design to assess the relative effectiveness of two…

Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry.

PubMed

Anderson, Lissa C; DeHart, Caroline J; Kaiser, Nathan K; Fellers, Ryan T; Smith, Donald F; Greer, Joseph B; LeDuc, Richard D; Blakney, Greg T; Thomas, Paul M; Kelleher, Neil L; Hendrickson, Christopher L

2017-02-03

Successful high-throughput characterization of intact proteins from complex biological samples by mass spectrometry requires instrumentation capable of high mass resolving power, mass accuracy, sensitivity, and spectral acquisition rate. These limitations often necessitate the performance of hundreds of LC-MS/MS experiments to obtain reasonable coverage of the targeted proteome, which is still typically limited to molecular weights below 30 kDa. The National High Magnetic Field Laboratory (NHMFL) recently installed a 21 T FT-ICR mass spectrometer, which is part of the NHMFL FT-ICR User Facility and available to all qualified users. Here we demonstrate top-down LC-21 T FT-ICR MS/MS of intact proteins derived from human colorectal cancer cell lysate. We identified a combined total of 684 unique protein entries observed as 3238 unique proteoforms at a 1% false discovery rate, based on rapid, data-dependent acquisition of collision-induced and electron-transfer dissociation tandem mass spectra from just 40 LC-MS/MS experiments. Our identifications included 372 proteoforms with molecular weights over 30 kDa detected at isotopic resolution, which substantially extends the accessible mass range for high-throughput top-down LC-MS/MS.

Progress in Top-Down Proteomics and the Analysis of Proteoforms

PubMed Central

Toby, Timothy K.; Fornelli, Luca; Kelleher, Neil L.

2017-01-01

From a molecular perspective, enactors of function in biology are intact proteins that can be variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 years, mass spectrometry (MS) has become a powerful method for the analysis of proteomes. Prevailing bottom-up proteomics operates at the level of the peptide, leading to issues with protein inference, connectivity, and incomplete sequence/modification information. Top-down proteomics (TDP), alternatively, applies MS at the proteoform level to analyze intact proteins with diverse sources of intramolecular complexity preserved during analysis. Fortunately, advances in prefractionation workflows, MS instrumentation, and dissociation methods for whole-protein ions have helped TDP emerge as an accessible and potentially disruptive modality with increasingly translational value. In this review, we discuss technical and conceptual advances in TDP, along with the growing power of proteoform-resolved measurements in clinical and translational research. PMID:27306313

Human Decision Making Based on Variations in Internal Noise: An EEG Study

PubMed Central

Amitay, Sygal; Guiraud, Jeanne; Sohoglu, Ediz; Zobay, Oliver; Edmonds, Barrie A.; Zhang, Yu-Xuan; Moore, David R.

2013-01-01

Perceptual decision making is prone to errors, especially near threshold. Physiological, behavioural and modeling studies suggest this is due to the intrinsic or ‘internal’ noise in neural systems, which derives from a mixture of bottom-up and top-down sources. We show here that internal noise can form the basis of perceptual decision making when the external signal lacks the required information for the decision. We recorded electroencephalographic (EEG) activity in listeners attempting to discriminate between identical tones. Since the acoustic signal was constant, bottom-up and top-down influences were under experimental control. We found that early cortical responses to the identical stimuli varied in global field power and topography according to the perceptual decision made, and activity preceding stimulus presentation could predict both later activity and behavioural decision. Our results suggest that activity variations induced by internal noise of both sensory and cognitive origin are sufficient to drive discrimination judgments. PMID:23840904

Deterministic Placement of Quantum-Size Controlled Quantum Dots for Seamless Top-Down Integration

DOE PAGES

Fischer, Arthur J.; Anderson, P. Duke; Koleske, Daniel D.; ...

2017-08-18

We demonstrate a new route toward the integration and deterministic placement of quantum dots (QDs) within prepatterned nanostructures. Using standard electron-beam lithography (EBL) and inductively coupled plasma reactive-ion etching (ICP-RIE), we fabricate arrays of nanowires on a III-nitride platform. Next, we integrate QDs of controlled size within the prepatterned nanowires using a bandgap-selective, wet-etching technique: quantum-size-controlled photoelectrochemical (QSC-PEC) etching. Low-temperature microphotoluminescence (μ-PL) measurements of individual nanowires reveal sharp spectral signatures, indicative of QD formation. Further, internal quantum efficiency (IQE) measurements reveal a near order of magnitude improvement in emitter efficiency following QSC-PEC etching. Finally, second-order cross-correlation (g(2)(0)) measurements of individualmore » QDs directly confirm nonclassical, antibunching behavior. Lastly, our results illustrate an exciting approach toward the top-down integration of nonclassical light sources within nanophotonic platforms.« less

Deterministic Placement of Quantum-Size Controlled Quantum Dots for Seamless Top-Down Integration

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

Fischer, Arthur J.; Anderson, P. Duke; Koleske, Daniel D.

We demonstrate a new route toward the integration and deterministic placement of quantum dots (QDs) within prepatterned nanostructures. Using standard electron-beam lithography (EBL) and inductively coupled plasma reactive-ion etching (ICP-RIE), we fabricate arrays of nanowires on a III-nitride platform. Next, we integrate QDs of controlled size within the prepatterned nanowires using a bandgap-selective, wet-etching technique: quantum-size-controlled photoelectrochemical (QSC-PEC) etching. Low-temperature microphotoluminescence (μ-PL) measurements of individual nanowires reveal sharp spectral signatures, indicative of QD formation. Further, internal quantum efficiency (IQE) measurements reveal a near order of magnitude improvement in emitter efficiency following QSC-PEC etching. Finally, second-order cross-correlation (g(2)(0)) measurements of individualmore » QDs directly confirm nonclassical, antibunching behavior. Lastly, our results illustrate an exciting approach toward the top-down integration of nonclassical light sources within nanophotonic platforms.« less

Sponge communities on Caribbean coral reefs are structured by factors that are top-down, not bottom-up.

PubMed

Pawlik, Joseph R; Loh, Tse-Lynn; McMurray, Steven E; Finelli, Christopher M

2013-01-01

Caribbean coral reefs have been transformed in the past few decades with the demise of reef-building corals, and sponges are now the dominant habitat-forming organisms on most reefs. Competing hypotheses propose that sponge communities are controlled primarily by predatory fishes (top-down) or by the availability of picoplankton to suspension-feeding sponges (bottom-up). We tested these hypotheses on Conch Reef, off Key Largo, Florida, by placing sponges inside and outside predator-excluding cages at sites with less and more planktonic food availability (15 m vs. 30 m depth). There was no evidence of a bottom-up effect on the growth of any of 5 sponge species, and 2 of 5 species grew more when caged at the shallow site with lower food abundance. There was, however, a strong effect of predation by fishes on sponge species that lacked chemical defenses. Sponges with chemical defenses grew slower than undefended species, demonstrating a resource trade-off between growth and the production of secondary metabolites. Surveys of the benthic community on Conch Reef similarly did not support a bottom-up effect, with higher sponge cover at the shallower depth. We conclude that the structure of sponge communities on Caribbean coral reefs is primarily top-down, and predict that removal of sponge predators by overfishing will shift communities toward faster-growing, undefended species that better compete for space with threatened reef-building corals.

Sponge Communities on Caribbean Coral Reefs Are Structured by Factors That Are Top-Down, Not Bottom-Up

PubMed Central

Pawlik, Joseph R.; Loh, Tse-Lynn; McMurray, Steven E.; Finelli, Christopher M.

2013-01-01

Caribbean coral reefs have been transformed in the past few decades with the demise of reef-building corals, and sponges are now the dominant habitat-forming organisms on most reefs. Competing hypotheses propose that sponge communities are controlled primarily by predatory fishes (top-down) or by the availability of picoplankton to suspension-feeding sponges (bottom-up). We tested these hypotheses on Conch Reef, off Key Largo, Florida, by placing sponges inside and outside predator-excluding cages at sites with less and more planktonic food availability (15 m vs. 30 m depth). There was no evidence of a bottom-up effect on the growth of any of 5 sponge species, and 2 of 5 species grew more when caged at the shallow site with lower food abundance. There was, however, a strong effect of predation by fishes on sponge species that lacked chemical defenses. Sponges with chemical defenses grew slower than undefended species, demonstrating a resource trade-off between growth and the production of secondary metabolites. Surveys of the benthic community on Conch Reef similarly did not support a bottom-up effect, with higher sponge cover at the shallower depth. We conclude that the structure of sponge communities on Caribbean coral reefs is primarily top-down, and predict that removal of sponge predators by overfishing will shift communities toward faster-growing, undefended species that better compete for space with threatened reef-building corals. PMID:23667492

A case for ZnO nanowire field emitter arrays in advanced x-ray source applications

NASA Astrophysics Data System (ADS)

Robinson, Vance S.; Bergkvist, Magnus; Chen, Daokun; Chen, Jun; Huang, Mengbing

2016-09-01

Reviewing current efforts in X-ray source miniaturization reveals a broad spectrum of applications: Portable and/or remote nondestructive evaluation, high throughput protein crystallography, invasive radiotherapy, monitoring fluid flow and particulate generation in situ, and portable radiography devices for battle-front or large scale disaster triage scenarios. For the most part, all of these applications are being addressed with a top-down approach aimed at improving portability, weight and size. That is, the existing system or a critical sub-component is shrunk in some manner in order to miniaturize the overall package. In parallel to top-down x-ray source miniaturization, more recent efforts leverage field emission and semiconductor device fabrication techniques to achieve small scale x-ray sources via a bottom-up approach where phenomena effective at a micro/nanoscale are coordinated for macro-scale effect. The bottom-up approach holds potential to address all the applications previously mentioned but its entitlement extends into new applications with much more ground-breaking potential. One such bottom-up application is the distributed x-ray source platform. In the medical space, using an array of microscale x-ray sources instead of a single source promises significant reductions in patient dose as well as smaller feature detectability and fewer image artifacts. Cold cathode field emitters are ideal for this application because they can be gated electrostatically or via photonic excitation, they do not generate excessive heat like other common electron emitters, they have higher brightness and they are relatively compact. This document describes how ZnO nanowire field emitter arrays are well suited for distributed x-ray source applications because they hold promise in each of the following critical areas: emission stability, simple scalable fabrication, performance, radiation resistance and photonic coupling.

The role of attention in subliminal semantic processing: A mouse tracking study.

PubMed

Xiao, Kunchen; Yamauchi, Takashi

2017-01-01

Recent evidence suggests that top-down attention facilitates unconscious semantic processing. To clarify the role of attention in unconscious semantic processing, we traced trajectories of the computer mouse in a semantic priming task and scrutinized the extent to which top-down attention enhances unconscious semantic processing in four different stimulus-onset asynchrony (SOA: 50, 200, 500, or 1000ms) conditions. Participants judged whether a target digit (e.g., "6") was larger or smaller than five, preceded by a masked priming digit (e.g., "9"). The pre-prime duration changed randomly from trial to trial to disrupt participants' top-down attention in an uncued condition (in a cued condition, a green square cue was presented to facilitate participants' top-down attention). The results show that top-down attention modifies the time course of subliminal semantic processing, and the temporal attention window lasts more than 1000ms; attention facilitated by the cue may amplify semantic priming to some extent, yet the amplification effect of attention is relatively minor.

Effect of drug physico-chemical properties on the efficiency of top-down process and characterization of nanosuspension.

PubMed

Liu, Tao; Müller, Rainer H; Möschwitzer, Jan P

2015-01-01

The top-down approach is frequently used for drug nanocrystal production. A large number of review papers have referred to the top-down approach in terms of process parameters such as stabilizer selection. However, a very important factor, that is, the influence of drug properties, has been not addressed so far. This review will first discuss different nanocrystal technologies in brief. The focus will be on reviewing the different drug properties such as solid state and particle morphology on the efficiency of particle size reduction during top-down processes. Furthermore, the drug properties in the final nanosuspensions are critical for drug dissolution velocity. Therefore, another focus is the characterization of drugs in obtained nanosuspension. Drug physical properties play an important role in the production efficiency. The combinative technologies using modified drugs could significantly improve the performances of top-down processes. However, further understanding of the drug millability and homogenization will still be needed. In addition, a carefully established characterization system for nansuspension is essential.

How to (and how not to) think about top-down influences on visual perception.

PubMed

Teufel, Christoph; Nanay, Bence

2017-01-01

The question of whether cognition can influence perception has a long history in neuroscience and philosophy. Here, we outline a novel approach to this issue, arguing that it should be viewed within the framework of top-down information-processing. This approach leads to a reversal of the standard explanatory order of the cognitive penetration debate: we suggest studying top-down processing at various levels without preconceptions of perception or cognition. Once a clear picture has emerged about which processes have influences on those at lower levels, we can re-address the extent to which they should be considered perceptual or cognitive. Using top-down processing within the visual system as a model for higher-level influences, we argue that the current evidence indicates clear constraints on top-down influences at all stages of information processing; it does, however, not support the notion of a boundary between specific types of information-processing as proposed by the cognitive impenetrability hypothesis. Copyright © 2016 Elsevier Inc. All rights reserved.

Biodiversity mediates top-down control in eelgrass ecosystems: a global comparative-experimental approach.

PubMed

Duffy, J Emmett; Reynolds, Pamela L; Boström, Christoffer; Coyer, James A; Cusson, Mathieu; Donadi, Serena; Douglass, James G; Eklöf, Johan S; Engelen, Aschwin H; Eriksson, Britas Klemens; Fredriksen, Stein; Gamfeldt, Lars; Gustafsson, Camilla; Hoarau, Galice; Hori, Masakazu; Hovel, Kevin; Iken, Katrin; Lefcheck, Jonathan S; Moksnes, Per-Olav; Nakaoka, Masahiro; O'Connor, Mary I; Olsen, Jeanine L; Richardson, J Paul; Ruesink, Jennifer L; Sotka, Erik E; Thormar, Jonas; Whalen, Matthew A; Stachowicz, John J

2015-07-01

Nutrient pollution and reduced grazing each can stimulate algal blooms as shown by numerous experiments. But because experiments rarely incorporate natural variation in environmental factors and biodiversity, conditions determining the relative strength of bottom-up and top-down forcing remain unresolved. We factorially added nutrients and reduced grazing at 15 sites across the range of the marine foundation species eelgrass (Zostera marina) to quantify how top-down and bottom-up control interact with natural gradients in biodiversity and environmental forcing. Experiments confirmed modest top-down control of algae, whereas fertilisation had no general effect. Unexpectedly, grazer and algal biomass were better predicted by cross-site variation in grazer and eelgrass diversity than by global environmental gradients. Moreover, these large-scale patterns corresponded strikingly with prior small-scale experiments. Our results link global and local evidence that biodiversity and top-down control strongly influence functioning of threatened seagrass ecosystems, and suggest that biodiversity is comparably important to global change stressors. © 2015 John Wiley & Sons Ltd/CNRS.

The distributed neural system for top-down letter processing: an fMRI study

NASA Astrophysics Data System (ADS)

Liu, Jiangang; Feng, Lu; Li, Ling; Tian, Jie

2011-03-01

This fMRI study used Psychophysiological interaction (PPI) to investigate top-down letter processing with an illusory letter detection task. After an initial training that became increasingly difficult, participant was instructed to detect a letter from pure noise images where there was actually no letter. Such experimental paradigm allowed for isolating top-down components of letter processing and minimizing the influence of bottom-up perceptual input. A distributed cortical network of top-down letter processing was identified by analyzing the functional connectivity patterns of letter-preferential area (LA) within the left fusiform gyrus. Such network extends from the visual cortex to high level cognitive cortexes, including the left middle frontal gyrus, left medial frontal gyrus, left superior parietal gyrus, bilateral precuneus, and left inferior occipital gyrus. These findings suggest that top-down letter processing contains not only regions for processing of letter phonology and appearance, but also those involved in internal information generation and maintenance, and attention and memory processing.

Fine particulate matter emissions inventories: comparisons of emissions estimates with observations from recent field programs.

PubMed

Simon, Heather; Allen, David T; Wittig, Ann E

2008-02-01

Emissions inventories of fine particulate matter (PM2.5) were compared with estimates of emissions based on data emerging from U.S. Environment Protection Agency Particulate Matter Supersites and other field programs. Six source categories for PM2.5 emissions were reviewed: on-road mobile sources, nonroad mobile sources, cooking, biomass combustion, fugitive dust, and stationary sources. Ammonia emissions from all of the source categories were also examined. Regional emissions inventories of PM in the exhaust from on-road and nonroad sources were generally consistent with ambient observations, though uncertainties in some emission factors were twice as large as the emission factors. In contrast, emissions inventories of road dust were up to an order of magnitude larger than ambient observations, and estimated brake wear and tire dust emissions were half as large as ambient observations in urban areas. Although comprehensive nationwide emissions inventories of PM2.5 from cooking sources and biomass burning are not yet available, observational data in urban areas suggest that cooking sources account for approximately 5-20% of total primary emissions (excluding dust), and biomass burning sources are highly dependent on region. Finally, relatively few observational data were available to assess the accuracy of emission estimates for stationary sources. Overall, the uncertainties in primary emissions for PM2.s are substantial. Similar uncertainties exist for ammonia emissions. Because of these uncertainties, the design of PM2.5 control strategies should be based on inventories that have been refined by a combination of bottom-up and top-down methods.

Quantifying methane emissions from coal and natural gas sources along the northwestern Appalachian

NASA Astrophysics Data System (ADS)

Barkley, Z.; Lauvaux, T.; Davis, K. J.; Fried, A.

2017-12-01

According to the EPA's 2012 gridded inventory (Maasakkers et al., 2016), more than 10% of all CH4 emissions in the U.S. are located along the western edge of the Appalachian with the majority of these emissions coming from natural gas infrastructure and coal mines. However, top-down studies of unconventional wells in southwestern Pennsylvania have found emission rates to be much higher than EPA estimates (Caulton et al., 2014, Ren et al., 2017). Furthermore, although 9 of the 10 largest sources of CH4 in the EPA Greenhouse Gas Reporting Program are coal mines located in this region, no top down studies have been performed to assess the accuracy of these enormous point sources. This study uses aircraft data from the ACT-America flight campaign in conjunction with techniques previously used to solve for CH4 emissions from the northeastern Marcellus (Barkley et al., 2017) to quantify the total CH4 flux from the western Pennsylvania/West Virginia region and constrain emissions from natural gas and coal with an upper limit for each source. We use the WRF-Chem mesoscale model at 3 km resolution to simulate CH4 enhancements from a customized emissions inventory and compare the modelled enhancements to observations from 7 flights that were downwind of coal and gas sources. Coal and natural gas emissions are adjusted in the model to minimize a cost function that accounts for the difference between the modelled and observed CH4 values, and a range of likely combinations for natural gas and coal emission rates are obtained for each flight. We then overlap this range of likely emission rates across all flights to further limit the range of possible emission rates. Influence functions created using a lagrangian particle dispersion model for segments of each flight provide information on what area emissions are being optimized for. Preliminary results find that CH4 emissions from gas and coal along the northwestern Appalachian are lower than EPA estimates by 20-50%. In particular, upper limits on CH4 emissions from unconventional natural gas are less than 1% of total production, significantly lower than previous top-down estimates in the region. Future work will use ethane data to better distinguish between coal and natural gas emissions, and expand these analyses to other study regions explored in the ACT-America aircraft campaign.

Effect of infliximab top-down therapy on weight gain in pediatric Crohns disease.

PubMed

Kim, Mi Jin; Lee, Woo Yong; Choi, Kyong Eun; Choe, Yon Ho

2012-12-01

This retrospective-medical-record review was conducted to evaluate effect of infliximab therapy, particularly with a top-down strategy, on the nutritional parameters of children with Crohns disease (CD). 42 patients who were diagnosed with Crohns disease at the Pediatric Gastroenterology center of a tertiary care teaching hospital and achieved remission at two months and one year after beginning of treatment were divided into four subgroups according to the treatment regimen; azathioprine group (n = 11), steroid group (n = 11), infliximab top-down group (n = 11) and step-up group (n = 9). Weight, height, and serum albumin were measured at diagnosis, and then at two months and one year after the initiation of treatment. At 2 months, the Z score increment for weight was highest in the steroid group, followed by the top-down, step-up, and azathioprine groups. At one year, the Z score increment was highest in top-down group, followed by steroid, azathioprine, and step-up group. There were no significant differences between the four groups in Z score increment for height and serum albumin during the study period. The top-down infliximab treatment resulted in superior outcome for weight gain, compared to the step-up therapy and other treatment regimens.

Hierarchy, causation and explanation: ubiquity, locality and pluralism

PubMed Central

Love, Alan C.

2012-01-01

The ubiquity of top-down causal explanations within and across the sciences is prima facie evidence for the existence of top-down causation. Much debate has been focused on whether top-down causation is coherent or in conflict with reductionism. Less attention has been given to the question of whether these representations of hierarchical relations pick out a single, common hierarchy. A negative answer to this question undermines a commonplace view that the world is divided into stratified ‘levels’ of organization and suggests that attributions of causal responsibility in different hierarchical representations may not have a meaningful basis for comparison. Representations used in top-down and bottom-up explanations are primarily ‘local’ and tied to distinct domains of science, illustrated here by protein structure and folding. This locality suggests that no single metaphysical account of hierarchy for causal relations to obtain within emerges from the epistemology of scientific explanation. Instead, a pluralist perspective is recommended—many different kinds of top-down causation (explanation) can exist alongside many different kinds of bottom-up causation (explanation). Pluralism makes plausible why different senses of top-down causation can be coherent and not in conflict with reductionism, thereby illustrating a productive interface between philosophical analysis and scientific inquiry. PMID:23386966

Top-down Proteomics: Technology Advancements and Applications to Heart Diseases

PubMed Central

Cai, Wenxuan; Tucholski, Trisha M.; Gregorich, Zachery R.; Ge, Ying

2016-01-01

Introduction Diseases of the heart are a leading cause of morbidity and mortality for both men and women worldwide, and impose significant economic burdens on the healthcare systems. Despite substantial effort over the last several decades, the molecular mechanisms underlying diseases of the heart remain poorly understood. Areas covered Altered protein post-translational modifications (PTMs) and protein isoform switching are increasingly recognized as important disease mechanisms. Top-down high-resolution mass spectrometry (MS)-based proteomics has emerged as the most powerful method for the comprehensive analysis of PTMs and protein isoforms. Here, we will review recent technology developments in the field of top-down proteomics, as well as highlight recent studies utilizing top-down proteomics to decipher the cardiac proteome for the understanding of the molecular mechanisms underlying diseases of the heart. Expert commentary Top-down proteomics is a premier method for the global and comprehensive study of protein isoforms and their PTMs, enabling the identification of novel protein isoforms and PTMs, characterization of sequence variations, and quantification of disease-associated alterations. Despite significant challenges, continuous development of top-down proteomics technology will greatly aid the dissection of the molecular mechanisms underlying diseases of the hearts for the identification of novel biomarkers and therapeutic targets. PMID:27448560

De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.

PubMed

Liu, Xiaowen; Dekker, Lennard J M; Wu, Si; Vanduijn, Martijn M; Luider, Theo M; Tolić, Nikola; Kou, Qiang; Dvorkin, Mikhail; Alexandrova, Sonya; Vyatkina, Kira; Paša-Tolić, Ljiljana; Pevzner, Pavel A

2014-07-03

There are two approaches for de novo protein sequencing: Edman degradation and mass spectrometry (MS). Existing MS-based methods characterize a novel protein by assembling tandem mass spectra of overlapping peptides generated from multiple proteolytic digestions of the protein. Because each tandem mass spectrum covers only a short peptide of the target protein, the key to high coverage protein sequencing is to find spectral pairs from overlapping peptides in order to assemble tandem mass spectra to long ones. However, overlapping regions of peptides may be too short to be confidently identified. High-resolution mass spectrometers have become accessible to many laboratories. These mass spectrometers are capable of analyzing molecules of large mass values, boosting the development of top-down MS. Top-down tandem mass spectra cover whole proteins. However, top-down tandem mass spectra, even combined, rarely provide full ion fragmentation coverage of a protein. We propose an algorithm, TBNovo, for de novo protein sequencing by combining top-down and bottom-up MS. In TBNovo, a top-down tandem mass spectrum is utilized as a scaffold, and bottom-up tandem mass spectra are aligned to the scaffold to increase sequence coverage. Experiments on data sets of two proteins showed that TBNovo achieved high sequence coverage and high sequence accuracy.

Face processing pattern under top-down perception: a functional MRI study

NASA Astrophysics Data System (ADS)

Li, Jun; Liang, Jimin; Tian, Jie; Liu, Jiangang; Zhao, Jizheng; Zhang, Hui; Shi, Guangming

2009-02-01

Although top-down perceptual process plays an important role in face processing, its neural substrate is still puzzling because the top-down stream is extracted difficultly from the activation pattern associated with contamination caused by bottom-up face perception input. In the present study, a novel paradigm of instructing participants to detect faces from pure noise images is employed, which could efficiently eliminate the interference of bottom-up face perception in topdown face processing. Analyzing the map of functional connectivity with right FFA analyzed by conventional Pearson's correlation, a possible face processing pattern induced by top-down perception can be obtained. Apart from the brain areas of bilateral fusiform gyrus (FG), left inferior occipital gyrus (IOG) and left superior temporal sulcus (STS), which are consistent with a core system in the distributed cortical network for face perception, activation induced by top-down face processing is also found in these regions that include the anterior cingulate gyrus (ACC), right oribitofrontal cortex (OFC), left precuneus, right parahippocampal cortex, left dorsolateral prefrontal cortex (DLPFC), right frontal pole, bilateral premotor cortex, left inferior parietal cortex and bilateral thalamus. The results indicate that making-decision, attention, episodic memory retrieving and contextual associative processing network cooperate with general face processing regions to process face information under top-down perception.

Auditory top-down control and affective theory of mind in schizophrenia with and without hallucinations.

PubMed

Rominger, Christian; Bleier, Angelika; Fitz, Werner; Marksteiner, Josef; Fink, Andreas; Papousek, Ilona; Weiss, Elisabeth M

2016-07-01

Social cognitive impairments may represent a core feature of schizophrenia and above all are a strong predictor of positive psychotic symptoms. Previous studies could show that reduced inhibitory top-down control contributes to deficits in theory of mind abilities and is involved in the genesis of hallucinations. The current study aimed to investigate the relationship between auditory inhibition, affective theory of mind and the experience of hallucinations in patients with schizophrenia. In the present study, 20 in-patients with schizophrenia and 20 healthy controls completed a social cognition task (the Reading the Mind in the Eyes Test) and an inhibitory top-down Dichotic Listening Test. Schizophrenia patients with greater severity of hallucinations showed impaired affective theory of mind as well as impaired inhibitory top-down control. More dysfunctional top-down inhibition was associated with poorer affective theory of mind performance, and seemed to mediate the association between impairment to affective theory of mind and severity of hallucinations. The findings support the idea of impaired theory of mind as a trait marker of schizophrenia. In addition, dysfunctional top-down inhibition may give rise to hallucinations and may further impair affective theory of mind skills in schizophrenia. Copyright © 2016 Elsevier B.V. All rights reserved.

A category-specific top-down attentional set can affect the neural responses outside the current focus of attention.

PubMed

Jiang, Yunpeng; Wu, Xia; Gao, Xiaorong

2017-10-17

A top-down set can guide attention to enhance the processing of task-relevant objects. Many studies have found that the top-down set can be tuned to a category level. However, it is unclear whether the category-specific top-down set involving a central search task can exist outside the current area of attentional focus. To directly probe the neural responses inside and outside the current focus of attention, we recorded continuous EEG to measure the contralateral ERP components for central targets and the steady-state visual evoked potential (SSVEP) oscillations associated with a flickering checkerboard placed on the visual periphery. The relationship of color categories between targets and non-targets was manipulated to investigate the effect of category-specific top-down set. Results showed that when the color categories of targets and non-targets in the central search arrays were the same, larger SSVEP oscillations were evoked by target color peripheral checkerboards relative to the non-target color ones outside the current attentional focus. However, when the color categories of targets and non-targets were different, the peripheral checkerboards in two different colors of the same category evoked similar SSVEP oscillations, indicating the effects of category-specific top-down set. These results firstly demonstrate that the category-specific top-down set can affect the neural responses of peripheral distractors. The results could support the idea of a global selection account and challenge the attentional window account in selective attention. Copyright © 2017. Published by Elsevier B.V.

Ammonia emissions from an anaerobic digestion plant estimated using atmospheric measurements and dispersion modelling.

PubMed

Bell, Michael W; Tang, Y Sim; Dragosits, Ulrike; Flechard, Chris R; Ward, Paul; Braban, Christine F

2016-10-01

Anaerobic digestion (AD) is becoming increasingly implemented within organic waste treatment operations. The storage and processing of large volumes of organic wastes through AD has been identified as a significant source of ammonia (NH3) emissions, however the totality of ammonia emissions from an AD plant have not been previously quantified. The emissions from an AD plant processing food waste were estimated through integrating ambient NH3 concentration measurements, atmospheric dispersion modelling, and comparison with published emission factors (EFs). Two dispersion models (ADMS and a backwards Lagrangian stochastic (bLS) model) were applied to calculate emission estimates. The bLS model (WindTrax) was used to back-calculate a total (top-down) emission rate for the AD plant from a point of continuous NH3 measurement downwind from the plant. The back-calculated emission rates were then input to the ADMS forward dispersion model to make predictions of air NH3 concentrations around the site, and evaluated against weekly passive sampler NH3 measurements. As an alternative approach emission rates from individual sources within the plant were initially estimated by applying literature EFs to the available site parameters concerning the chemical composition of waste materials, room air concentrations, ventilation rates, etc. The individual emission rates were input to ADMS and later tuned by fitting the simulated ambient concentrations to the observed (passive sampler) concentration field, which gave an excellent match to measurements after an iterative process. The total emission from the AD plant thus estimated by a bottom-up approach was 16.8±1.8mgs(-1), which was significantly higher than the back-calculated top-down estimate (7.4±0.78mgs(-1)). The bottom-up approach offered a more realistic treatment of the source distribution within the plant area, while the complexity of the site was not ideally suited to the bLS method, thus the bottom-up method is believed to give a better estimate of emissions. The storage of solid digestate and the aerobic treatment of liquid effluents at the site were the greatest sources of NH3 emissions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Top-down NOX Emissions of European Cities Derived from Modelled and Spaceborne Tropospheric NO2 Columns

NASA Astrophysics Data System (ADS)

Verstraeten, W. W.; Boersma, K. F.; Douros, J.; Williams, J. E.; Eskes, H.; Delcloo, A. W.

2017-12-01

High nitrogen oxides (NOX = NO + NO2) concentrations near the surface impact humans and ecosystems badly and play a key role in tropospheric chemistry. NO2 is an important precursor of tropospheric ozone (O3) which in turn affects the production of the hydroxyl radical controlling the chemical lifetime of key atmospheric pollutants and reactive greenhouse gases. Combustion from industrial, traffic and household activities in large and densely populated urban areas result in high NOX emissions. Accurate mapping of these emissions is essential but hard to do since reported emissions factors may differ from real-time emissions in order of magnitude. Modelled NO2 levels and lifetimes also have large associated uncertainties and overestimation in the chemical lifetime which may mask missing NOX chemistry in current chemistry transport models (CTM's). The simultaneously estimation of both the NO2 lifetime and as well as the concentrations by applying the Exponentially Modified Gaussian (EMG) method on tropospheric NO2 columns lines densities should improve the surface NOX emission estimates. Here we evaluate if the EMG methodology applied on the tropospheric NO2 columns simulated by the LOTOS-EUROS (Long Term Ozone Simulation-European Ozone Simulation) CTM can reproduce the NOX emissions used as model input. First we process both the modelled tropospheric NO2 columns for the period April-September 2013 for 21 selected European urban areas under windy conditions (averaged vertical wind speeds between surface and 500 m from ECMWF > 2 m s-1) as well as the accompanying OMI (Ozone Monitoring Instrument) data providing us with real-time observation-based estimates of midday NO2 columns. Then we compare the top-down derived surface NOX emissions with the 2011 MACC-III emission inventory, used in the CTM as input to simulate the NO2 columns. For cities where NOX emissions can be assumed as originating from one large source good agreement is found between the top-down derived NOX emissions from CTM and OMI with the MACC-III inventory. For cities where multiple sources of NOX are observed (e.g. Brussels, London), an adapted methodology is required. For some cities such as St-Petersburg and Moscow the top-down NOX estimates from 2013 OMI data are biased low compared to the MACC-III inventory which uses a 2011 NOX emissions update.

Analysis of top-down and bottom-up North American CO2 and CH4 emissions estimates in the second State of the Carbon Cycle Report

NASA Astrophysics Data System (ADS)

Miller, J. B.; Jacobson, A. R.; Bruhwiler, L.; Michalak, A.; Hayes, D. J.; Vargas, R.

2017-12-01

In just ten years since publication of the original State of the Carbon Cycle Report in 2007, global CO2 concentrations have risen by more than 22 ppm to 405 ppm. This represents 18% of the increase over preindustrial levels of 280 ppm. This increase is being driven unequivocally by fossil fuel combustion with North American emissions comprising roughly 20% of the global total over the past decade. At the global scale, we know by comparing well-known fossil fuel inventories and rates of atmospheric CO2 increase that about half of all emissions are absorbed at Earth's surface. For North America, however, we can not apply a simple mass balance to determine sources and sinks. Instead, contributions from ecosystems must be estimated using top-down and bottom-up methods. SOCCR-2 estimates North American net CO2 uptake from ecosystems using bottom-up (inventory) methods as 577 +/- 433 TgC/yr and 634 +/- 288 TgC/yr from top-down atmospheric inversions. Although the global terrestrial carbon sink is not precisely known, these values represent possibly 30% of the global values. As with net sink estimates reported in SOCCR, these new top-down and bottom-up estimates are statistically consistent with one another. However, the uncertainties on each of these estimates are now substantially smaller, giving us more confidence about where the truth lies. Atmospheric inversions also yield estimates of interannual variations (IAV) in CO2 and CH4 fluxes. Our syntheses suggest that IAV of ecosystem CO2 fluxes is of order 100 TgC/yr, mainly originating in the conterminous US, with lower variability in boreal and arctic regions. Moreover, this variability is much larger than for inventory-based fluxes reported by the US to the UNFCCC. Unlike CO2, bottom-up CH4 emissions are larger than those derived from large-scale atmospheric data, with the continental discrepancy resulting primarily from differences in arctic and boreal regions. In addition to the current state of the science, we will also discuss the primary sources of uncertainty and how existing and emerging measurement and modeling technologies can address them.

Rivers: Nature's Wondrous Waterways.

ERIC Educational Resources Information Center

Harrison, David L.

Rivers play a vital role in the life of the planet. They provide water for wildlife, plant life, and people, and they help to fertilize fields where corn and other crops grow. But how were these rivers made? This children's book takes readers/students on a journey down a river from its source at the top of a mountain to its mouth where it meets…

Co-development, innovation and mutual learning--or how we need to turn the world upside down.

PubMed

Crisp, Nigel

2015-12-01

This paper describes the scope for mutual learning and the sharing of innovation between different parts of the world. It argues that the top-down concept of international development--with its connotations that low income countries need to develop in ways that emulate progress in richer more "developed" ones needs to be replaced with the idea of co-development and learning and sharing together. Similarly, it advocates for replacing the term of "reverse innovation" with the concept of global sourcing of innovation. Copyright © 2015. Published by Elsevier Inc.

Top-Down Proteomics and Farm Animal and Aquatic Sciences.

PubMed

Campos, Alexandre M O; de Almeida, André M

2016-12-21

Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry.

PubMed

Zhou, Mowei; Wu, Si; Stenoien, David L; Zhang, Zhaorui; Connolly, Lanelle; Freitag, Michael; Paša-Tolić, Ljiljana

2017-01-01

Top-down mass spectrometry is a valuable tool for understanding gene expression through characterization of combinatorial histone post-translational modifications (i.e., histone code). In this protocol, we describe a top-down workflow that employs liquid chromatography (LC) coupled to mass spectrometry (MS), for fast global profiling of changes in histone proteoforms, and apply LCMS top-down approach for comparative analysis of a wild-type and a mutant fungal species. The proteoforms exhibiting differential abundances can be subjected to further targeted studies by other MS or orthogonal (e.g., biochemical) assays. This method can be generally adapted for screening of changes in histone modifications between samples such as wild type vs. mutant or healthy vs. diseased.

Conformational Assessment of Adnectin and Adnectin-Drug Conjugate by Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Huang, Richard Y.-C.; O'Neil, Steven R.; Lipovšek, Daša; Chen, Guodong

2018-05-01

Higher-order structure (HOS) characterization of therapeutic protein-drug conjugates for comprehensive assessment of conjugation-induced protein conformational changes is an important consideration in the biopharmaceutical industry to ensure proper behavior of protein therapeutics. In this study, conformational dynamics of a small therapeutic protein, adnectin 1, together with its drug conjugate were characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) with different spatial resolutions. Top-down HDX allows detailed assessment of the residue-level deuterium content in the payload conjugation region. HDX-MS dataset revealed the ability of peptide-based payload/linker to retain deuterium in HDX experiments. Combined results from intact, top-down, and bottom-up HDX indicated no significant conformational changes of adnectin 1 upon payload conjugation. [Figure not available: see fulltext.

Top-down preparation modulates visual categorization but not subjective awareness of objects presented in natural backgrounds.

PubMed

Koivisto, Mika; Kahila, Ella

2017-04-01

Top-down processes are widely assumed to be essential in visual awareness, subjective experience of seeing. However, previous studies have not tried to separate directly the roles of different types of top-down influences in visual awareness. We studied the effects of top-down preparation and object substitution masking (OSM) on visual awareness during categorization of objects presented in natural scene backgrounds. The results showed that preparation facilitated categorization but did not influence visual awareness. OSM reduced visual awareness and impaired categorization. The dissociations between the effects of preparation and OSM on visual awareness and on categorization imply that they influence at different stages of cognitive processing. We propose that preparation influences at the top of the visual hierarchy, whereas OSM interferes with processes occurring at lower levels of the hierarchy. These lower level processes play an essential role in visual awareness. Copyright © 2017 Elsevier Ltd. All rights reserved.

Approach to characterization of the higher order structure of disulfide-containing proteins using hydrogen/deuterium exchange and top-down mass spectrometry.

PubMed

Wang, Guanbo; Kaltashov, Igor A

2014-08-05

Top-down hydrogen/deuterium exchange (HDX) with mass spectrometric (MS) detection has recently matured to become a potent biophysical tool capable of providing valuable information on higher order structure and conformational dynamics of proteins at an unprecedented level of structural detail. However, the scope of the proteins amenable to the analysis by top-down HDX MS still remains limited, with the protein size and the presence of disulfide bonds being the two most important limiting factors. While the limitations imposed by the physical size of the proteins gradually become more relaxed as the sensitivity, resolution and dynamic range of modern MS instrumentation continue to improve at an ever accelerating pace, the presence of the disulfide linkages remains a much less forgiving limitation even for the proteins of relatively modest size. To circumvent this problem, we introduce an online chemical reduction step following completion and quenching of the HDX reactions and prior to the top-down MS measurements of deuterium occupancy of individual backbone amides. Application of the new methodology to the top-down HDX MS characterization of a small (99 residue long) disulfide-containing protein β2-microglobulin allowed the backbone amide protection to be probed with nearly a single-residue resolution across the entire sequence. The high-resolution backbone protection pattern deduced from the top-down HDX MS measurements carried out under native conditions is in excellent agreement with the crystal structure of the protein and high-resolution NMR data, suggesting that introduction of the chemical reduction step to the top-down routine does not trigger hydrogen scrambling either during the electrospray ionization process or in the gas phase prior to the protein ion dissociation.

Comprehensive Analysis of Protein Modifications by Top-down Mass Spectrometry

PubMed Central

Zhang, Han; Ge, Ying

2012-01-01

Mass spectrometry (MS)-based proteomics is playing an increasingly important role in cardiovascular research. Proteomics includes not only identification and quantification of proteins, but also the characterization of protein modifications such as post-translational modifications and sequence variants. The conventional bottom-up approach, involving proteolytic digestion of proteins into small peptides prior to MS analysis, is routinely used for protein identification and quantification with high throughput and automation. Nevertheless, it has limitations in the analysis of protein modifications mainly due to the partial sequence coverage and loss of connections among modifications on disparate portions of a protein. An alternative approach, top-down MS, has emerged as a powerful tool for the analysis of protein modifications. The top-down approach analyzes whole proteins directly, providing a “bird’s eye” view of all existing modifications. Subsequently, each modified protein form can be isolated and fragmented in the mass spectrometer to locate the modification site. The incorporation of the non-ergodic dissociation methods such as electron capture dissociation (ECD) greatly enhances the top-down capabilities. ECD is especially useful for mapping labile post-translational modifications which are well-preserved during the ECD fragmentation process. Top-down MS with ECD has been successfully applied to cardiovascular research with the unique advantages in unraveling the molecular complexity, quantifying modified protein forms, complete mapping of modifications with full sequence coverage, discovering unexpected modifications, and identifying and quantifying positional isomers and determining the order of multiple modifications. Nevertheless, top-down MS still needs to overcome some technical challenges to realize its full potential. Herein, we reviewed the advantages and challenges of top-down methodology with a focus on its application in cardiovascular research. PMID:22187450

Event-Related Potentials of Bottom-Up and Top-Down Processing of Emotional Faces

PubMed Central

Moradi, Afsane; Mehrinejad, Seyed Abolghasem; Ghadiri, Mohammad; Rezaei, Farzin

2017-01-01

Introduction: Emotional stimulus is processed automatically in a bottom-up way or can be processed voluntarily in a top-down way. Imaging studies have indicated that bottom-up and top-down processing are mediated through different neural systems. However, temporal differentiation of top-down versus bottom-up processing of facial emotional expressions has remained to be clarified. The present study aimed to explore the time course of these processes as indexed by the emotion-specific P100 and late positive potential (LPP) event-related potential (ERP) components in a group of healthy women. Methods: Fourteen female students of Alzahra University, Tehran, Iran aged 18–30 years, voluntarily participated in the study. The subjects completed 2 overt and covert emotional tasks during ERP acquisition. Results: The results indicated that fearful expressions significantly produced greater P100 amplitude compared to other expressions. Moreover, the P100 findings showed an interaction between emotion and processing conditions. Further analysis indicated that within the overt condition, fearful expressions elicited more P100 amplitude compared to other emotional expressions. Also, overt conditions created significantly more LPP latencies and amplitudes compared to covert conditions. Conclusion: Based on the results, early perceptual processing of fearful face expressions is enhanced in top-down way compared to bottom-up way. It also suggests that P100 may reflect an attentional bias toward fearful emotions. However, no such differentiation was observed within later processing stages of face expressions, as indexed by the ERP LPP component, in a top-down versus bottom-up way. Overall, this study provides a basis for further exploring of bottom-up and top-down processes underlying emotion and may be typically helpful for investigating the temporal characteristics associated with impaired emotional processing in psychiatric disorders. PMID:28446947

Salient region detection by fusing bottom-up and top-down features extracted from a single image.

PubMed

Tian, Huawei; Fang, Yuming; Zhao, Yao; Lin, Weisi; Ni, Rongrong; Zhu, Zhenfeng

2014-10-01

Recently, some global contrast-based salient region detection models have been proposed based on only the low-level feature of color. It is necessary to consider both color and orientation features to overcome their limitations, and thus improve the performance of salient region detection for images with low-contrast in color and high-contrast in orientation. In addition, the existing fusion methods for different feature maps, like the simple averaging method and the selective method, are not effective sufficiently. To overcome these limitations of existing salient region detection models, we propose a novel salient region model based on the bottom-up and top-down mechanisms: the color contrast and orientation contrast are adopted to calculate the bottom-up feature maps, while the top-down cue of depth-from-focus from the same single image is used to guide the generation of final salient regions, since depth-from-focus reflects the photographer's preference and knowledge of the task. A more general and effective fusion method is designed to combine the bottom-up feature maps. According to the degree-of-scattering and eccentricities of feature maps, the proposed fusion method can assign adaptive weights to different feature maps to reflect the confidence level of each feature map. The depth-from-focus of the image as a significant top-down feature for visual attention in the image is used to guide the salient regions during the fusion process; with its aid, the proposed fusion method can filter out the background and highlight salient regions for the image. Experimental results show that the proposed model outperforms the state-of-the-art models on three public available data sets.

Characterization and Quantification of Intact 26S Proteasome Proteins by Real-Time Measurement of Intrinsic Fluorescence Prior to Top-down Mass Spectrometry

PubMed Central

Russell, Jason D.; Scalf, Mark; Book, Adam J.; Ladror, Daniel T.; Vierstra, Richard D.; Smith, Lloyd M.; Coon, Joshua J.

2013-01-01

Quantification of gas-phase intact protein ions by mass spectrometry (MS) is impeded by highly-variable ionization, ion transmission, and ion detection efficiencies. Therefore, quantification of proteins using MS-associated techniques is almost exclusively done after proteolysis where peptides serve as proxies for estimating protein abundance. Advances in instrumentation, protein separations, and informatics have made large-scale sequencing of intact proteins using top-down proteomics accessible to the proteomics community; yet quantification of proteins using a top-down workflow has largely been unaddressed. Here we describe a label-free approach to determine the abundance of intact proteins separated by nanoflow liquid chromatography prior to MS analysis by using solution-phase measurements of ultraviolet light-induced intrinsic fluorescence (UV-IF). UV-IF is measured directly at the electrospray interface just prior to the capillary exit where proteins containing at least one tryptophan residue are readily detected. UV-IF quantification was demonstrated using commercially available protein standards and provided more accurate and precise protein quantification than MS ion current. We evaluated the parallel use of UV-IF and top-down tandem MS for quantification and identification of protein subunits and associated proteins from an affinity-purified 26S proteasome sample from Arabidopsis thaliana. We identified 26 unique proteins and quantified 13 tryptophan-containing species. Our analyses discovered previously unidentified N-terminal processing of the β6 (PBF1) and β7 (PBG1) subunit - such processing of PBG1 may generate a heretofore unknown additional protease active site upon cleavage. In addition, our approach permitted the unambiguous identification and quantification both isoforms of the proteasome-associated protein DSS1. PMID:23536786

Characterization and quantification of intact 26S proteasome proteins by real-time measurement of intrinsic fluorescence prior to top-down mass spectrometry.

PubMed

Russell, Jason D; Scalf, Mark; Book, Adam J; Ladror, Daniel T; Vierstra, Richard D; Smith, Lloyd M; Coon, Joshua J

2013-01-01

Quantification of gas-phase intact protein ions by mass spectrometry (MS) is impeded by highly-variable ionization, ion transmission, and ion detection efficiencies. Therefore, quantification of proteins using MS-associated techniques is almost exclusively done after proteolysis where peptides serve as proxies for estimating protein abundance. Advances in instrumentation, protein separations, and informatics have made large-scale sequencing of intact proteins using top-down proteomics accessible to the proteomics community; yet quantification of proteins using a top-down workflow has largely been unaddressed. Here we describe a label-free approach to determine the abundance of intact proteins separated by nanoflow liquid chromatography prior to MS analysis by using solution-phase measurements of ultraviolet light-induced intrinsic fluorescence (UV-IF). UV-IF is measured directly at the electrospray interface just prior to the capillary exit where proteins containing at least one tryptophan residue are readily detected. UV-IF quantification was demonstrated using commercially available protein standards and provided more accurate and precise protein quantification than MS ion current. We evaluated the parallel use of UV-IF and top-down tandem MS for quantification and identification of protein subunits and associated proteins from an affinity-purified 26S proteasome sample from Arabidopsis thaliana. We identified 26 unique proteins and quantified 13 tryptophan-containing species. Our analyses discovered previously unidentified N-terminal processing of the β6 (PBF1) and β7 (PBG1) subunit - such processing of PBG1 may generate a heretofore unknown additional protease active site upon cleavage. In addition, our approach permitted the unambiguous identification and quantification both isoforms of the proteasome-associated protein DSS1.

Analysis of epididymal sperm maturation by MALDI profiling and top-down mass spectrometry.

PubMed

Labas, Valérie; Spina, Lucie; Belleannee, Clémence; Teixeira-Gomes, Ana-Paula; Gargaros, Audrey; Dacheux, Françoise; Dacheux, Jean-Louis

2015-01-15

The fertilization ability of male gametes is achieved after their transit through the epididymis where important post-gonadal differentiation occurs in different cellular compartments. Most of these maturational modifications occur at the protein level. The epididymal sperm maturation process was investigated using the ICM-MS (Intact Cell MALDI-TOF MS) approach on boar spermatozoa isolated from four different epididymal regions (immature to mature stage). Differential and quantitative MALDI-TOF profiling for whole cells or sub-cellular fractions was combined with targeted top-down MS in order to identify endogenous biomolecules. Using this approach, 172m/z peaks ranging between 2 and 20kDa were found to be modified during maturation of sperm. Using top-down MS, 62m/z were identified corresponding to peptidoforms/proteoforms with post-translational modifications (MS data are available via ProteomeXchange with identifier PXD001303). Many of the endogenous peptides were characterized as N-, C-terminal sequences or internal fragments of proteins presenting specific cleavages, suggesting the presence of sequential protease activities in the spermatozoa. This is the first time that such proteolytic activities could be evidenced for various sperm proteins through quantification of their proteolytic products. ICM-MS/top-down MS thus proved to be a valid approach for peptidome/degradome studies and provided new contributions to understanding of the maturation process of the male gamete involved in the development of male fertility. This peptidomic study (i) characterized the peptidome of epididymal spermatozoa from boar (Sus scrofa); (ii) established characteristic molecular phenotypes distinguishing degrees of maturation of spermatozoa during epididymal transit, and (iii) revealed that protease activities were at the origin of numerous peptides from known and unknown proteins involved in sperm maturation and/or fertility processes. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Jiang; Loo, Rachel R. Ogorzalek; Loo, Joseph A.

2017-09-01

Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH4OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin-TBA complex and 1 M NH4OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin-TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein-DNA complexes. [Figure not available: see fulltext.

Defining Gas-Phase Fragmentation Propensities of Intact Proteins During Native Top-Down Mass Spectrometry

NASA Astrophysics Data System (ADS)

Haverland, Nicole A.; Skinner, Owen S.; Fellers, Ryan T.; Tariq, Areeba A.; Early, Bryan P.; LeDuc, Richard D.; Fornelli, Luca; Compton, Philip D.; Kelleher, Neil L.

2017-06-01

Fragmentation of intact proteins in the gas phase is influenced by amino acid composition, the mass and charge of precursor ions, higher order structure, and the dissociation technique used. The likelihood of fragmentation occurring between a pair of residues is referred to as the fragmentation propensity and is calculated by dividing the total number of assigned fragmentation events by the total number of possible fragmentation events for each residue pair. Here, we describe general fragmentation propensities when performing top-down mass spectrometry (TDMS) using denaturing or native electrospray ionization. A total of 5311 matched fragmentation sites were collected for 131 proteoforms that were analyzed over 165 experiments using native top-down mass spectrometry (nTDMS). These data were used to determine the fragmentation propensities for 399 residue pairs. In comparison to denatured top-down mass spectrometry (dTDMS), the fragmentation pathways occurring either N-terminal to proline or C-terminal to aspartic acid were even more enhanced in nTDMS compared with other residues. More generally, 257/399 (64%) of the fragmentation propensities were significantly altered ( P ≤ 0.05) when using nTDMS compared with dTDMS, and of these, 123 were altered by 2-fold or greater. The most notable enhancements of fragmentation propensities for TDMS in native versus denatured mode occurred (1) C-terminal to aspartic acid, (2) between phenylalanine and tryptophan (F|W), and (3) between tryptophan and alanine (W|A). The fragmentation propensities presented here will be of high value in the development of tailored scoring systems used in nTDMS of both intact proteins and protein complexes. [Figure not available: see fulltext.

Substantiation of artificial composite-structure roof construction in top-down cut-and-fill stoping

NASA Astrophysics Data System (ADS)

Rukavishnikov, GD; Neverov, SA; Neverov, AA

2018-03-01

It has been found efficient and safe to use top-down cut-and-fill stoping with saving of the artificial backfill cost and material through the use of a solid nonuniform material composed of two components (layers). It is shown that the artificial roof can be advanced after a stope without essential change in the stope condition as compared with the classical top-down slice method, which provides higher safety of mining.

What is Bottom-Up and What is Top-Down in Predictive Coding?

PubMed Central

Rauss, Karsten; Pourtois, Gilles

2013-01-01

Everyone knows what bottom-up is, and how it is different from top-down. At least one is tempted to think so, given that both terms are ubiquitously used, but only rarely defined in the psychology and neuroscience literature. In this review, we highlight the problems and limitations of our current understanding of bottom-up and top-down processes, and we propose a reformulation of this distinction in terms of predictive coding. PMID:23730295

Density- and trait-mediated top-down effects modify bottom-up control of a highly endemic tropical aquatic food web

Treesearch

C. M. Dalton; A. Mokiao-Lee; T. S. Sakihara; M. G. Weber; C. A. Roco; Z. Han; B. Dudley; R. A. MacKenzie; N. G. Hairston Jr.

2013-01-01

Benthic invertebrates mediate bottom–up and top–down influences in aquatic food webs, and changes in the abundance or traits of invertebrates can alter the strength of top–down effects. Studies assessing the role of invertebrate abundance and behavior as controls on food web structure are rare at the whole ecosystem scale. Here we use a comparative approach to...

A Top-down versus a Bottom-up Hidden-variables Description of the Stern-Gerlach Experiment

NASA Astrophysics Data System (ADS)

Arsenijević, M.; Jeknić-Dugić, J.; Dugić, M.

We employ the Stern-Gerlach experiment to highlight the basics of a minimalist, non-interpretational top-down approach to quantum foundations. Certain benefits of the "quantum structural studies" (QSS) highlightedhere are detected and discussed. While the top-down approach can be described without making any reference to the fundamental structure of a closed system, the hidden variables (HV) theory á la Bohm proves to be more subtle than it is typically regarded.

On the unsupervised analysis of domain-specific Chinese texts

PubMed Central

Deng, Ke; Bol, Peter K.; Li, Kate J.; Liu, Jun S.

2016-01-01

With the growing availability of digitized text data both publicly and privately, there is a great need for effective computational tools to automatically extract information from texts. Because the Chinese language differs most significantly from alphabet-based languages in not specifying word boundaries, most existing Chinese text-mining methods require a prespecified vocabulary and/or a large relevant training corpus, which may not be available in some applications. We introduce an unsupervised method, top-down word discovery and segmentation (TopWORDS), for simultaneously discovering and segmenting words and phrases from large volumes of unstructured Chinese texts, and propose ways to order discovered words and conduct higher-level context analyses. TopWORDS is particularly useful for mining online and domain-specific texts where the underlying vocabulary is unknown or the texts of interest differ significantly from available training corpora. When outputs from TopWORDS are fed into context analysis tools such as topic modeling, word embedding, and association pattern finding, the results are as good as or better than that from using outputs of a supervised segmentation method. PMID:27185919

Basomedial amygdala mediates top-down control of anxiety and fear.

PubMed

Adhikari, Avishek; Lerner, Talia N; Finkelstein, Joel; Pak, Sally; Jennings, Joshua H; Davidson, Thomas J; Ferenczi, Emily; Gunaydin, Lisa A; Mirzabekov, Julie J; Ye, Li; Kim, Sung-Yon; Lei, Anna; Deisseroth, Karl

2015-11-12

Anxiety-related conditions are among the most difficult neuropsychiatric diseases to treat pharmacologically, but respond to cognitive therapies. There has therefore been interest in identifying relevant top-down pathways from cognitive control regions in medial prefrontal cortex (mPFC). Identification of such pathways could contribute to our understanding of the cognitive regulation of affect, and provide pathways for intervention. Previous studies have suggested that dorsal and ventral mPFC subregions exert opposing effects on fear, as do subregions of other structures. However, precise causal targets for top-down connections among these diverse possibilities have not been established. Here we show that the basomedial amygdala (BMA) represents the major target of ventral mPFC in amygdala in mice. Moreover, BMA neurons differentiate safe and aversive environments, and BMA activation decreases fear-related freezing and high-anxiety states. Lastly, we show that the ventral mPFC-BMA projection implements top-down control of anxiety state and learned freezing, both at baseline and in stress-induced anxiety, defining a broadly relevant new top-down behavioural regulation pathway.

The role of attention in subliminal semantic processing: A mouse tracking study

PubMed Central

Xiao, Kunchen; Yamauchi, Takashi

2017-01-01

Recent evidence suggests that top-down attention facilitates unconscious semantic processing. To clarify the role of attention in unconscious semantic processing, we traced trajectories of the computer mouse in a semantic priming task and scrutinized the extent to which top-down attention enhances unconscious semantic processing in four different stimulus-onset asynchrony (SOA: 50, 200, 500, or 1000ms) conditions. Participants judged whether a target digit (e.g., “6”) was larger or smaller than five, preceded by a masked priming digit (e.g., “9”). The pre-prime duration changed randomly from trial to trial to disrupt participants’ top-down attention in an uncued condition (in a cued condition, a green square cue was presented to facilitate participants’ top-down attention). The results show that top-down attention modifies the time course of subliminal semantic processing, and the temporal attention window lasts more than 1000ms; attention facilitated by the cue may amplify semantic priming to some extent, yet the amplification effect of attention is relatively minor. PMID:28609460

Dynamic ErbB4 Activity in Hippocampal-Prefrontal Synchrony and Top-Down Attention in Rodents.

PubMed

Tan, Zhibing; Robinson, Heath L; Yin, Dong-Min; Liu, Yu; Liu, Fang; Wang, Hongsheng; Lin, Thiri W; Xing, Guanglin; Gan, Lin; Xiong, Wen-Cheng; Mei, Lin

2018-04-18

Top-down attention is crucial for meaningful behaviors and impaired in various mental disorders. However, its underpinning regulatory mechanisms are poorly understood. We demonstrate that the hippocampal-prefrontal synchrony associates with levels of top-down attention. Both attention and synchrony are reduced in mutant mice of ErbB4, a receptor of neuregulin-1. We used chemical genetic and optogenetic approaches to inactivate ErbB4 kinase and ErbB4+ interneurons, respectively, both of which reduce gamma-aminobutyric acid (GABA) activity. Such inhibitions in the hippocampus impair both hippocampal-prefrontal synchrony and top-down attention, whereas those in the prefrontal cortex alter attention, but not synchrony. These observations identify a role of ErbB4-dependent GABA activity in the hippocampus in synchronizing the hippocampal-prefrontal pathway and demonstrate that acute, dynamic ErbB4 signaling is required to command top-down attention. Because both neuregulin-1 and ErbB4 are susceptibility genes of schizophrenia and major depression, our study contributes to a better understanding of these disorders. VIDEO ABSTRACT. Copyright © 2018 Elsevier Inc. All rights reserved.

Attention, working memory, and phenomenal experience of WM content: memory levels determined by different types of top-down modulation.

PubMed

Jacob, Jane; Jacobs, Christianne; Silvanto, Juha

2015-01-01

What is the role of top-down attentional modulation in consciously accessing working memory (WM) content? In influential WM models, information can exist in different states, determined by allocation of attention; placing the original memory representation in the center of focused attention gives rise to conscious access. Here we discuss various lines of evidence indicating that such attentional modulation is not sufficient for memory content to be phenomenally experienced. We propose that, in addition to attentional modulation of the memory representation, another type of top-down modulation is required: suppression of all incoming visual information, via inhibition of early visual cortex. In this view, there are three distinct memory levels, as a function of the top-down control associated with them: (1) Nonattended, nonconscious associated with no attentional modulation; (2) attended, phenomenally nonconscious memory, associated with attentional enhancement of the actual memory trace; (3) attended, phenomenally conscious memory content, associated with enhancement of the memory trace and top-down suppression of all incoming visual input.

Perceptual salience does not influence emotional arousal's impairing effects on top-down attention.

PubMed

Sutherland, Matthew R; McQuiggan, Douglas A; Ryan, Jennifer D; Mather, Mara

2017-06-01

Emotional arousal impairs top-down attentional control while strengthening bottom-up attentional biases. In this study, we examined whether top-down impairments due to arousal can be modulated by increasing the perceptual salience of the target stimulus. To examine this question, we briefly displayed positive and negative arousing images prior to the encoding of 2 emotionally neutral items, 1 of which was to be remembered and 1 of which was perceptually salient (the to-be-remembered and the salient items were either the same item or different items). Eye tracking was used to measure attention biases during the encoding of the 2 competing neutral items, as well as to measure pupillary responses to the preceding modulator image. Viewing emotional images, regardless of valence, impaired top-down attention to animate stimulus targets (i.e., animals), regardless of perceptual salience. However, these effects on encoding had no influence on recognition memory. Taken together, these findings reveal that exposure to emotionally arousing images impairs top-down attention to animate stimuli, regardless of whether that stimulus is perceptually salient. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Top-down Estimates of Isoprene Emissions in Australia Inferred from OMI Satellite Data.

NASA Astrophysics Data System (ADS)

Greenslade, J.; Fisher, J. A.; Surl, L.; Palmer, P. I.

2017-12-01

Australia is a global hotspot for biogenic isoprene emission factors predicted by process-based models such as the Model of Emissions of Gases and Aerosols from Nature (MEGAN). It is also prone to increasingly frequent temperature extremes that can drive episodically high emissions. Estimates of biogenic isoprene emissions from Australia are poorly constrained, with the frequently used MEGAN model overestimating emissions by a factor of 4-6 in some areas. Evaluating MEGAN and other models in Australia is difficult due to sparse measurements of emissions and their ensuing chemical products. In this talk, we will describe efforts to better quantify Australian isoprene emissions using top-down estimates based on formaldehyde (HCHO) observations from the OMI satellite instrument, combined with modelled isoprene to HCHO yields obtained from the GEOS-Chem chemical transport model. The OMI-based estimates are evaluated using in situ observations from field campaigns conducted in southeast Australia. We also investigate the impact on the inferred emission of horizontal resolution used for the yield calculations, particularly in regions on the boundary between low- and high-NOx chemistry. The prevalence of fire smoke plumes roughly halves the available satellite dataset over Australia for much of the year; however, seasonal averages remain robust. Preliminary results show that the top-down isoprene emissions are lower than MEGAN estimates by up to 90% in summer. The overestimates are greatest along the eastern coast, including areas surrounding Australia's major population centres in Sydney, Melbourne, and Brisbane. The coarse horizontal resolution of the model significantly affects the emissions estimates, as many biogenic emitting regions lie along narrow coastal stretches. Our results confirm previous findings that the MEGAN biogenic emission model is poorly calibrated for the Australian environment and suggests that chemical transport models driven by MEGAN are likely to overpredict ozone and secondary organic aerosols from biogenic sources in the Australian environment. Further measurements of biogenic gases are critical to improving biogenic emissions and follow-on chemical transport modelling, in this region. We hope to quantify this overestimation and its flow-on effects in future work.

Agricultural ammonia emissions in China: reconciling bottom-up and top-down estimates

NASA Astrophysics Data System (ADS)

Zhang, Lin; Chen, Youfan; Zhao, Yuanhong; Henze, Daven K.; Zhu, Liye; Song, Yu; Paulot, Fabien; Liu, Xuejun; Pan, Yuepeng; Lin, Yi; Huang, Binxiang

2018-01-01

Current estimates of agricultural ammonia (NH3) emissions in China differ by more than a factor of 2, hindering our understanding of their environmental consequences. Here we apply both bottom-up statistical and top-down inversion methods to quantify NH3 emissions from agriculture in China for the year 2008. We first assimilate satellite observations of NH3 column concentration from the Tropospheric Emission Spectrometer (TES) using the GEOS-Chem adjoint model to optimize Chinese anthropogenic NH3 emissions at the 1/2° × 2/3° horizontal resolution for March-October 2008. Optimized emissions show a strong summer peak, with emissions about 50 % higher in summer than spring and fall, which is underestimated in current bottom-up NH3 emission estimates. To reconcile the latter with the top-down results, we revisit the processes of agricultural NH3 emissions and develop an improved bottom-up inventory of Chinese NH3 emissions from fertilizer application and livestock waste at the 1/2° × 2/3° resolution. Our bottom-up emission inventory includes more detailed information on crop-specific fertilizer application practices and better accounts for meteorological modulation of NH3 emission factors in China. We find that annual anthropogenic NH3 emissions are 11.7 Tg for 2008, with 5.05 Tg from fertilizer application and 5.31 Tg from livestock waste. The two sources together account for 88 % of total anthropogenic NH3 emissions in China. Our bottom-up emission estimates also show a distinct seasonality peaking in summer, consistent with top-down results from the satellite-based inversion. Further evaluations using surface network measurements show that the model driven by our bottom-up emissions reproduces the observed spatial and seasonal variations of NH3 gas concentrations and ammonium (NH4+) wet deposition fluxes over China well, providing additional credibility to the improvements we have made to our agricultural NH3 emission inventory.

The emerging process of Top Down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput†

PubMed Central

Kellie, John F.; Tran, John C.; Lee, Ji Eun; Ahlf, Dorothy R.; Thomas, Haylee M.; Ntai, Ioanna; Catherman, Adam D.; Durbin, Kenneth R.; Zamdborg, Leonid; Vellaichamy, Adaikkalam; Thomas, Paul M.

2011-01-01

Top Down mass spectrometry (MS) has emerged as an alternative to common Bottom Up strategies for protein analysis. In the Top Down approach, intact proteins are fragmented directly in the mass spectrometer to achieve both protein identification and characterization, even capturing information on combinatorial post-translational modifications. Just in the past two years, Top Down MS has seen incremental advances in instrumentation and dedicated software, and has also experienced a major boost from refined separations of whole proteins in complex mixtures that have both high recovery and reproducibility. Combined with steadily advancing commercial MS instrumentation and data processing, a high-throughput workflow covering intact proteins and polypeptides up to 70 kDa is directly visible in the near future. PMID:20711533

Spatial and temporal disaggregation of the on-road vehicle emission inventory in a medium-sized Andean city. Comparison of GIS-based top-down methodologies

NASA Astrophysics Data System (ADS)

Gómez, C. D.; González, C. M.; Osses, M.; Aristizábal, B. H.

2018-04-01

Emission data is an essential tool for understanding environmental problems associated with sources and dynamics of air pollutants in urban environments, especially those emitted from vehicular sources. There is a lack of knowledge about the estimation of air pollutant emissions and particularly its spatial and temporal distribution in South America, mainly in medium-sized cities with population less than one million inhabitants. This work performed the spatial and temporal disaggregation of the on-road vehicle emission inventory (EI) in the medium-sized Andean city of Manizales, Colombia, with a spatial resolution of 1 km × 1 km and a temporal resolution of 1 h. A reported top-down methodology, based on the analysis of traffic flow levels and road network distribution, was applied. Results obtained allowed the identification of several hotspots of emission at the downtown zone and the residential and commercial area of Manizales. Downtown exhibited the highest percentage contribution of emissions normalized by its total area, with values equal to 6% and 5% of total CO and PM10 emissions per km2 respectively. These indexes were higher than those obtained in residential-commercial area with values of 2%/km2 for both pollutants. Temporal distribution showed strong relationship with driving patterns at rush hours, as well as an important influence of passenger cars and motorcycles in emissions of CO both at downtown and residential-commercial areas, and the impact of public transport in PM10 emissions in the residential-commercial zone. Considering that detailed information about traffic counts and road network distribution is not always available in medium-sized cities, this work compares other simplified top-down methods for spatially assessing the on-road vehicle EI. Results suggested that simplified methods could underestimate the spatial allocation of downtown emissions, a zone dominated by high traffic of vehicles. The comparison between simplified methods based on total traffic counts and road density distribution suggested that the use of total traffic counts in a simplified form could enhance higher uncertainties in the spatial disaggregation of emissions. Results obtained could add new information that help to improve the air pollution management system in the city and contribute to local public policy decisions. Additionally, this work provides appropriate resolution emission fluxes for ongoing research in atmospheric modeling in the city, with the aim to improve the understanding of transport, transformation and impacts of pollutant emissions in urban air quality.

Goal-directed control with cortical units that are gated by both top-down feedback and oscillatory coherence.

PubMed

Kerr, Robert R; Grayden, David B; Thomas, Doreen A; Gilson, Matthieu; Burkitt, Anthony N

2014-01-01

The brain is able to flexibly select behaviors that adapt to both its environment and its present goals. This cognitive control is understood to occur within the hierarchy of the cortex and relies strongly on the prefrontal and premotor cortices, which sit at the top of this hierarchy. Pyramidal neurons, the principal neurons in the cortex, have been observed to exhibit much stronger responses when they receive inputs at their soma/basal dendrites that are coincident with inputs at their apical dendrites. This corresponds to inputs from both lower-order regions (feedforward) and higher-order regions (feedback), respectively. In addition to this, coherence between oscillations, such as gamma oscillations, in different neuronal groups has been proposed to modulate and route communication in the brain. In this paper, we develop a simple, but novel, neural mass model in which cortical units (or ensembles) exhibit gamma oscillations when they receive coherent oscillatory inputs from both feedforward and feedback connections. By forming these units into circuits that can perform logic operations, we identify the different ways in which operations can be initiated and manipulated by top-down feedback. We demonstrate that more sophisticated and flexible top-down control is possible when the gain of units is modulated by not only top-down feedback but by coherence between the activities of the oscillating units. With these types of units, it is possible to not only add units to, or remove units from, a higher-level unit's logic operation using top-down feedback, but also to modify the type of role that a unit plays in the operation. Finally, we explore how different network properties affect top-down control and processing in large networks. Based on this, we make predictions about the likely connectivities between certain brain regions that have been experimentally observed to be involved in goal-directed behavior and top-down attention.

Goal-directed control with cortical units that are gated by both top-down feedback and oscillatory coherence

PubMed Central

Kerr, Robert R.; Grayden, David B.; Thomas, Doreen A.; Gilson, Matthieu; Burkitt, Anthony N.

2014-01-01

The brain is able to flexibly select behaviors that adapt to both its environment and its present goals. This cognitive control is understood to occur within the hierarchy of the cortex and relies strongly on the prefrontal and premotor cortices, which sit at the top of this hierarchy. Pyramidal neurons, the principal neurons in the cortex, have been observed to exhibit much stronger responses when they receive inputs at their soma/basal dendrites that are coincident with inputs at their apical dendrites. This corresponds to inputs from both lower-order regions (feedforward) and higher-order regions (feedback), respectively. In addition to this, coherence between oscillations, such as gamma oscillations, in different neuronal groups has been proposed to modulate and route communication in the brain. In this paper, we develop a simple, but novel, neural mass model in which cortical units (or ensembles) exhibit gamma oscillations when they receive coherent oscillatory inputs from both feedforward and feedback connections. By forming these units into circuits that can perform logic operations, we identify the different ways in which operations can be initiated and manipulated by top-down feedback. We demonstrate that more sophisticated and flexible top-down control is possible when the gain of units is modulated by not only top-down feedback but by coherence between the activities of the oscillating units. With these types of units, it is possible to not only add units to, or remove units from, a higher-level unit's logic operation using top-down feedback, but also to modify the type of role that a unit plays in the operation. Finally, we explore how different network properties affect top-down control and processing in large networks. Based on this, we make predictions about the likely connectivities between certain brain regions that have been experimentally observed to be involved in goal-directed behavior and top-down attention. PMID:25152715

Top-down approach for the direct characterization of low molecular weight heparins using LC-FT-MS.

PubMed

Li, Lingyun; Zhang, Fuming; Zaia, Joseph; Linhardt, Robert J

2012-10-16

Low molecular heparins (LMWHs) are structurally complex, heterogeneous, polydisperse, and highly negatively charged mixtures of polysaccharides. The direct characterization of LMWH is a major challenge for currently available analytical technologies. Electrospray ionization (ESI) liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for the characterization complex biological samples in the fields of proteomics, metabolomics, and glycomics. LC-MS has been applied to the analysis of heparin oligosaccharides, separated by size exclusion, reversed phase ion-pairing chromatography, and chip-based amide hydrophilic interaction chromatography (HILIC). However, there have been limited applications of ESI-LC-MS for the direct characterization of intact LMWHs (top-down analysis) due to their structural complexity, low ionization efficiency, and sulfate loss. Here we present a simple and reliable HILIC-Fourier transform (FT)-ESI-MS platform to characterize and compare two currently marketed LMWH products using the top-down approach requiring no special sample preparation steps. This HILIC system relies on cross-linked diol rather than amide chemistry, affording highly resolved chromatographic separations using a relatively high percentage of acetonitrile in the mobile phase, resulting in stable and high efficiency ionization. Bioinformatics software (GlycReSoft 1.0) was used to automatically assign structures within 5-ppm mass accuracy.

Inverse Estimation of California Methane Emissions and Their Uncertainties using FLEXPART-WRF

NASA Astrophysics Data System (ADS)

Cui, Y.; Brioude, J. F.; Angevine, W. M.; McKeen, S. A.; Peischl, J.; Nowak, J. B.; Henze, D. K.; Bousserez, N.; Fischer, M. L.; Jeong, S.; Liu, Z.; Michelsen, H. A.; Santoni, G.; Daube, B. C.; Kort, E. A.; Frost, G. J.; Ryerson, T. B.; Wofsy, S. C.; Trainer, M.

2015-12-01

Methane (CH4) has a large global warming potential and mediates global tropospheric chemistry. In California, CH4 emissions estimates derived from "top-down" methods based on atmospheric observations have been found to be greater than expected from "bottom-up" population-apportioned national and state inventories. Differences between bottom-up and top-down estimates suggest that the understanding of California's CH4 sources is incomplete, leading to uncertainty in the application of regulations to mitigate regional CH4 emissions. In this study, we use airborne measurements from the California research at the Nexus of Air Quality and Climate Change (CalNex) campaign in 2010 to estimate CH4 emissions in the South Coast Air Basin (SoCAB), which includes California's largest metropolitan area (Los Angeles), and in the Central Valley, California's main agricultural and livestock management area. Measurements from 12 daytime flights, prior information from national and regional official inventories (e.g. US EPA's National Emission Inventory, the California Air Resources Board inventories, the Liu et al. Hybrid Inventory, and the California Greenhouse Gas Emissions Measurement dataset), and the FLEXPART-WRF transport model are used in our mesoscale Bayesian inverse system. We compare our optimized posterior CH4 inventory to the prior bottom-up inventories in terms of total emissions (Mg CH4/hr) and the spatial distribution of the emissions (0.1 degree), and quantify uncertainties in our posterior estimates. Our inversions show that the oil and natural gas industry (extraction, processing and distribution) is the main source accounting for the gap between top-down and bottom-up inventories over the SoCAB, while dairy farms are the largest CH4 source in the Central Valley. CH4 emissions of dairy farms in the San Joaquin Valley and variations of CH4 emissions in the rice-growing regions of Sacramento Valley are quantified and discussed. We also estimate CO and NH3 surface fluxes and use their observed correlation with CH4 mixing ratio to further evaluate our CH4 total emission estimates, and understand the spatial distribution of CH4 emissions.

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra

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

Kou, Qiang; Wu, Si; Tolić, Nikola

Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a “bird’s eye view” of intact proteoforms. The combinatorial explosion of various alterations on a protein may result inmore » billions of possible proteoforms, making proteoform identification a challenging computational problem. Results: We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry data sets showed that TopMG outperformed existing methods in identifying complex proteoforms.« less

A Physical Mechanism for the Asymmetry in Top-Down and Bottom-Up Diffusion.

NASA Astrophysics Data System (ADS)

Wyngaard, J. C.

1987-04-01

Recent large-eddy simulations of the vertical diffusion of a passive, conservative scalar through the convective boundary layer (CBL) show strikingly different eddy diffusivity profiles in the `top-down' and `bottom-up' cases. These results indicate that for a given turbulent velocity field and associated scalar flux, the mean change in scalar mixing ratio across the CBL is several times larger if the flux originates at the top of the boundary layer (i.e., in top-down diffusion) rather than at the bottom. The large-eddy simulation (LES) data show that this asymmetry is due to a breakdown of the eddy-diffusion concept.A simple updraft-downdraft model of the CBL reveals a physical mechanism that could cause this unexpected behavior. The large, positive skewness of the convectively driven vertical velocity gives an appreciably higher probability of downdrafts than updrafts; this excess probability of downdrafts, interacting with the time changes of the mean mixing ratio caused by the nonstationarity of the bottom-up and top-down diffusion processes, decreases the equilibrium value of mean mixing-ratio jump across the mixed layer in the bottom-up case and increases it in the top-down case. The resulting diffusion asymmetry agrees qualitatively with that found through LES.

Consumer species richness and nutrients interact in determining producer diversity.

PubMed

Groendahl, Sophie; Fink, Patrick

2017-03-17

While it is crucial to understand the factors that determine the biodiversity of primary producer communities, the relative importance of bottom-up and top-down control factors is still poorly understood. Using freshwater benthic algal communities in the laboratory as a model system, we find an unimodal relationship between nutrient availability and producer diversity, and that increasing number of consumer species increases producer diversity, but overall grazing decreases algal biodiversity. Interestingly, these two factors interact strongly in determining producer diversity, as an increase in nutrient supply diminishes the positive effect of consumer species richness on producer biodiversity. This novel and thus-far overlooked interaction of bottom-up and top-down control mechanisms of biodiversity may have a pronounced impact on ecosystem functioning and thus have repercussions for the fields of biodiversity conservation and restoration.

Top-down constraints on methane and non-methane hydrocarbon emissions in the US Four Corners

NASA Astrophysics Data System (ADS)

Petron, G.; Miller, B. R.; Vaughn, B. H.; Kofler, J.; Mielke-Maday, I.; Sherwood, O.; Schwietzke, S.; Conley, S.; Sweeney, C.; Dlugokencky, E. J.; White, A. B.; Tans, P. P.; Schnell, R. C.

2017-12-01

A NASA and NOAA supported field campaign took place in the US Four Corners in April 2015 to further investigate a regional "methane hotspot" detected from space. The Four Corners region is home to the fossil fuel rich San Juan Basin, which extends between SE Colorado and NE New Mexico. The area has been extracting coal, oil and natural gas for decades. Degassing from the Fruitland coal outcrop on the Colorado side has also been reported. Instrumented aircraft, vans and ground based wind profilers were deployed for the campaign with the goal to quantify and attribute methane and non-methane hydrocarbon emissions in the region. A new comprehensive analysis of the campaign data sets will be presented and top-down emission estimates for methane and ozone precursors will be compared with available bottom-up estimates.

Consumer species richness and nutrients interact in determining producer diversity

PubMed Central

Groendahl, Sophie; Fink, Patrick

2017-01-01

While it is crucial to understand the factors that determine the biodiversity of primary producer communities, the relative importance of bottom-up and top-down control factors is still poorly understood. Using freshwater benthic algal communities in the laboratory as a model system, we find an unimodal relationship between nutrient availability and producer diversity, and that increasing number of consumer species increases producer diversity, but overall grazing decreases algal biodiversity. Interestingly, these two factors interact strongly in determining producer diversity, as an increase in nutrient supply diminishes the positive effect of consumer species richness on producer biodiversity. This novel and thus-far overlooked interaction of bottom-up and top-down control mechanisms of biodiversity may have a pronounced impact on ecosystem functioning and thus have repercussions for the fields of biodiversity conservation and restoration. PMID:28303953

Ultraviolet photodissociation enhances top-down mass spectrometry as demonstrated on green fluorescent protein variants.

PubMed

Dang, Xibei; Young, Nicolas L

2014-05-01

Ultraviolet photodissociation (UVPD) is a compelling fragmentation technique with great potential to enhance proteomics generally and top-down MS specifically. In this issue, Cannon et al. (Proteomics 2014, 14, XXXX-XXXX) use UVPD to perform top-down MS on several sequence variants of green fluorescent protein and compare the results to CID, higher energy collision induced dissociation, and electron transfer dissociation. As compared to the other techniques UVPD produces a wider variety of fragment ion types that are relatively evenly distributed across the protein sequences. Overall, their results demonstrate enhanced sequence coverage and higher confidence in sequence assignment via UVPD MS. Based on these and other recent results UVPD is certain to become an increasingly widespread and valuable tool for top-down proteomics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Top-down proteomic identification of Shiga toxin 2 subtypes from Shiga toxin-producing Escherichia coli by matrix-assisted laser desorption ionization-tandem time of flight mass spectrometry.

PubMed

Fagerquist, Clifton K; Zaragoza, William J; Sultan, Omar; Woo, Nathan; Quiñones, Beatriz; Cooley, Michael B; Mandrell, Robert E

2014-05-01

We have analyzed 26 Shiga toxin-producing Escherichia coli (STEC) strains for Shiga toxin 2 (Stx2) production using matrix-assisted laser desorption ionization (MALDI)-tandem time of flight (TOF-TOF) tandem mass spectrometry (MS/MS) and top-down proteomic analysis. STEC strains were induced to overexpress Stx2 by overnight culturing on solid agar supplemented with either ciprofloxacin or mitomycin C. Harvested cells were lysed by bead beating, and unfractionated bacterial cell lysates were ionized by MALDI. The A2 fragment of the A subunit and the mature B subunit of Stx2 were analyzed by MS/MS. Sequence-specific fragment ions were used to identify amino acid subtypes of Stx2 using top-down proteomic analysis using software developed in-house at the U.S. Department of Agriculture (USDA). Stx2 subtypes (a, c, d, f, and g) were identified on the basis of the mass of the A2 fragment and the B subunit as well as from their sequence-specific fragment ions by MS/MS (postsource decay). Top-down proteomic identification was in agreement with DNA sequencing of the full Stx2 operon (stx2) for all strains. Top-down results were also compared to a bioassay using a Vero-d2EGFP cell line. Our results suggest that top-down proteomic identification is a rapid, highly specific technique for distinguishing Stx2 subtypes.

Top-down guidance in visual search for facial expressions.

PubMed

Hahn, Sowon; Gronlund, Scott D

2007-02-01

Using a visual search paradigm, we investigated how a top-down goal modified attentional bias for threatening facial expressions. In two experiments, participants searched for a facial expression either based on stimulus characteristics or a top-down goal. In Experiment 1 participants searched for a discrepant facial expression in a homogenous crowd of faces. Consistent with previous research, we obtained a shallower response time (RT) slope when the target face was angry than when it was happy. In Experiment 2, participants searched for a specific type of facial expression (allowing a top-down goal). When the display included a target, we found a shallower RT slope for the angry than for the happy face search. However, when an angry or happy face was present in the display in opposition to the task goal, we obtained equivalent RT slopes, suggesting that the mere presence of an angry face in opposition to the task goal did not support the well-known angry face superiority effect. Furthermore, RT distribution analyses supported the special status of an angry face only when it was combined with the top-down goal. On the basis of these results, we suggest that a threatening facial expression may guide attention as a high-priority stimulus in the absence of a specific goal; however, in the presence of a specific goal, the efficiency of facial expression search is dependent on the combined influence of a top-down goal and the stimulus characteristics.

Ultra Rapid Object Categorization: Effects of Level, Animacy and Context

PubMed Central

Praß, Maren; Grimsen, Cathleen; König, Martina; Fahle, Manfred

2013-01-01

It is widely agreed that in object categorization bottom-up and top-down influences interact. How top-down processes affect categorization has been primarily investigated in isolation, with only one higher level process at a time being manipulated. Here, we investigate the combination of different top-down influences (by varying the level of category, the animacy and the background of the object) and their effect on rapid object categorization. Subjects participated in a two-alternative forced choice rapid categorization task, while we measured accuracy and reaction times. Subjects had to categorize objects on the superordinate, basic or subordinate level. Objects belonged to the category animal or vehicle and each object was presented on a gray, congruent (upright) or incongruent (inverted) background. The results show that each top-down manipulation impacts object categorization and that they interact strongly. The best categorization was achieved on the superordinate level, providing no advantage for basic level in rapid categorization. Categorization between vehicles was faster than between animals on the basic level and vice versa on the subordinate level. Objects in homogenous gray background (context) yielded better overall performance than objects embedded in complex scenes, an effect most prominent on the subordinate level. An inverted background had no negative effect on object categorization compared to upright scenes. These results show how different top-down manipulations, such as category level, category type and background information, are related. We discuss the implications of top-down interactions on the interpretation of categorization results. PMID:23840810

Ultra rapid object categorization: effects of level, animacy and context.

PubMed

Praß, Maren; Grimsen, Cathleen; König, Martina; Fahle, Manfred

2013-01-01

It is widely agreed that in object categorization bottom-up and top-down influences interact. How top-down processes affect categorization has been primarily investigated in isolation, with only one higher level process at a time being manipulated. Here, we investigate the combination of different top-down influences (by varying the level of category, the animacy and the background of the object) and their effect on rapid object categorization. Subjects participated in a two-alternative forced choice rapid categorization task, while we measured accuracy and reaction times. Subjects had to categorize objects on the superordinate, basic or subordinate level. Objects belonged to the category animal or vehicle and each object was presented on a gray, congruent (upright) or incongruent (inverted) background. The results show that each top-down manipulation impacts object categorization and that they interact strongly. The best categorization was achieved on the superordinate level, providing no advantage for basic level in rapid categorization. Categorization between vehicles was faster than between animals on the basic level and vice versa on the subordinate level. Objects in homogenous gray background (context) yielded better overall performance than objects embedded in complex scenes, an effect most prominent on the subordinate level. An inverted background had no negative effect on object categorization compared to upright scenes. These results show how different top-down manipulations, such as category level, category type and background information, are related. We discuss the implications of top-down interactions on the interpretation of categorization results.

Top-Down Proteomic Identification of Shiga Toxin 2 Subtypes from Shiga Toxin-Producing Escherichia coli by Matrix-Assisted Laser Desorption Ionization–Tandem Time of Flight Mass Spectrometry

PubMed Central

Zaragoza, William J.; Sultan, Omar; Woo, Nathan; Quiñones, Beatriz; Cooley, Michael B.; Mandrell, Robert E.

2014-01-01

We have analyzed 26 Shiga toxin-producing Escherichia coli (STEC) strains for Shiga toxin 2 (Stx2) production using matrix-assisted laser desorption ionization (MALDI)–tandem time of flight (TOF-TOF) tandem mass spectrometry (MS/MS) and top-down proteomic analysis. STEC strains were induced to overexpress Stx2 by overnight culturing on solid agar supplemented with either ciprofloxacin or mitomycin C. Harvested cells were lysed by bead beating, and unfractionated bacterial cell lysates were ionized by MALDI. The A2 fragment of the A subunit and the mature B subunit of Stx2 were analyzed by MS/MS. Sequence-specific fragment ions were used to identify amino acid subtypes of Stx2 using top-down proteomic analysis using software developed in-house at the U.S. Department of Agriculture (USDA). Stx2 subtypes (a, c, d, f, and g) were identified on the basis of the mass of the A2 fragment and the B subunit as well as from their sequence-specific fragment ions by MS/MS (postsource decay). Top-down proteomic identification was in agreement with DNA sequencing of the full Stx2 operon (stx2) for all strains. Top-down results were also compared to a bioassay using a Vero-d2EGFP cell line. Our results suggest that top-down proteomic identification is a rapid, highly specific technique for distinguishing Stx2 subtypes. PMID:24584253

Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics

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

Lopez-Ferrer, Daniel; Petritis, Konstantinos; Robinson, Errol W.

2011-02-01

Integrated top-down bottom-up proteomics combined with online digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to highthroughput proteomics experiments. Bottom-up proteomics ultimately provides the peptide sequences derived from the tandem MS analyses of peptides after the proteome has been digested. Top-down proteomics conversely entails the MS analyses of intact proteins for more effective characterization of genetic variations and/or post-translational modifications (PTMs). Herein, we describe recent efforts towards efficient integration of bottom-up and top-down LCMS based proteomic strategies. Since most proteomic platforms (i.e. LC systems) operate in acidic environments, we exploited themore » compatibility of the pepsin (i.e. the enzyme’s natural acidic activity) for the integration of bottom-up and top-down proteomics. Pressure enhanced pepsin digestions were successfully performed and characterized with several standard proteins in either an offline mode using a Barocycler or an online mode using a modified high pressure LC system referred to as a fast online digestion system (FOLDS). FOLDS was tested using pepsin and a whole microbial proteome, and the results compared against traditional trypsin digestions on the same platform. Additionally, FOLDS was integrated with a RePlay configuration to demonstrate an ultra-rapid integrated bottom-up top-down proteomic strategy employing a standard mixture of proteins and a monkey pox virus proteome.« less

Stimulation of subgenual cingulate area decreases limbic top-down effect on ventral visual stream: A DBS-EEG pilot study.

PubMed

Kibleur, Astrid; Polosan, Mircea; Favre, Pauline; Rudrauf, David; Bougerol, Thierry; Chabardès, Stéphan; David, Olivier

2017-02-01

Deep brain stimulation (DBS) of the subgenual cingulate gyrus (area CG25) is beneficial in treatment resistant depression. Though the mechanisms of action of Cg25 DBS remain largely unknown, it is commonly believed that Cg25 DBS modulates limbic activity of large networks to achieve thymic regulation of patients. To investigate how emotional attention is influenced by Cg25 DBS, we assessed behavioral and electroencephalographic (EEG) responses to an emotional Stroop task in 5 patients during ON and OFF stimulation conditions. Using EEG source localization, we found that the main effect of DBS was a reduction of neuronal responses in limbic regions (temporal pole, medial prefrontal and posterior cingulate cortices) and in ventral visual areas involved in face processing. In the dynamic causal modeling (DCM) approach, the changes of the evoked response amplitudes are assumed to be due to changes of long range connectivity induced by Cg25 DBS. Here, using a simplified neural mass model that did not take explicitly into account the cytoarchitecture of the considered brain regions, we showed that the remote action of Cg25 DBS could be explained by a reduced top-down effective connectivity of the amygdalo-temporo-polar complex. Overall, our results thus indicate that Cg25 DBS during the emotional Stroop task causes a decrease of top-down limbic influence on the ventral visual stream itself, rather than a modulation of prefrontal cognitive processes only. Tuning down limbic excitability in relation to sensory processing might be one of the biological mechanisms through which Cg25 DBS produces positive clinical outcome in the treatment of resistant depression. Copyright © 2016 Elsevier Inc. All rights reserved.

Sediment unmixing using detrital geochronology

NASA Astrophysics Data System (ADS)

Sharman, Glenn R.; Johnstone, Samuel A.

2017-11-01

Sediment mixing within sediment routing systems can exert a strong influence on the preservation of provenance signals that yield insight into the effect of environmental forcing (e.g., tectonism, climate) on the Earth's surface. Here, we discuss two approaches to unmixing detrital geochronologic data in an effort to characterize complex changes in the sedimentary record. First, we summarize 'top-down' mixing, which has been successfully employed in the past to characterize the different fractions of prescribed source distributions ('parents') that characterize a derived sample or set of samples ('daughters'). Second, we propose the use of 'bottom-up' methods, previously used primarily for grain size distributions, to model parent distributions and the abundances of these parents within a set of daughters. We demonstrate the utility of both top-down and bottom-up approaches to unmixing detrital geochronologic data within a well-constrained sediment routing system in central California. Use of a variety of goodness-of-fit metrics in top-down modeling reveals the importance of considering the range of allowable that is well mixed over any single best-fit mixture calculation. Bottom-up modeling of 12 daughter samples from beaches and submarine canyons yields modeled parent distributions that are remarkably similar to those expected from the geologic context of the sediment-routing system. In general, mixture modeling has the potential to supplement more widely applied approaches in comparing detrital geochronologic data by casting differences between samples as differing proportions of geologically meaningful end-member provenance categories.

What are the fluxes of greenhouse gases from the greater Los Angeles area as inferred from top-down remote sensing studies?

NASA Astrophysics Data System (ADS)

Hedelius, J.; Wennberg, P. O.; Wunch, D.; Roehl, C. M.; Podolske, J. R.; Hillyard, P.; Iraci, L. T.

2017-12-01

Greenhouse gas (GHG) emissions from California's South Coast Air Basin (SoCAB) have been studied extensively using a variety of tower, aircraft, remote sensing, emission inventory, and modeling studies. It is impractical to survey GHG fluxes from all urban areas and hot-spots to the extent the SoCAB has been studied, but it can serve as a test location for scaling methods globally. We use a combination of remote sensing measurements from ground (Total Carbon Column Observing Network, TCCON) and space-based (Observing Carbon Observatory-2, OCO-2) sensors in an inversion to obtain the carbon dioxide flux from the SoCAB. We also perform a variety of sensitivity tests to see how the inversion performs using different model parameterizations. Fluxes do not significantly depend on the mixed layer depth, but are sensitive to the model surface layers (<5 m). Carbon dioxide fluxes are larger than those from bottom-up inventories by about 20%, and along with CO has a significant weekend:weekday effect. Methane fluxes have little weekend changes. Results also include flux estimates from sub-regions of the SoCAB. Larger top-down than bottom-up fluxes highlight the need for additional work on both approaches. Higher top-down fluxes could arise from sampling bias, model bias, or may show bottom-up values underestimate sources. Lessons learned here may help in scaling up inversions to hundreds of urban systems using space-based observations.

Altered emotional interference processing in affective and cognitive-control brain circuitry in major depression

PubMed Central

Fales, Christina L.; Barch, Deanna M.; Rundle, Melissa M.; Mintun, Mark A.; Snyder, Abraham Z.; Cohen, Jonathan D.; Mathews, Jose; Sheline, Yvette I.

2008-01-01

Background Major depression is characterized by a negativity bias: an enhanced responsiveness to, and memory for, affectively negative stimuli. However it is not yet clear whether this bias represents (1) impaired top-down cognitive control over affective responses, potentially linked to deficits in dorsolateral prefrontal cortex function; or (2) enhanced bottom-up responses to affectively-laden stimuli that dysregulate cognitive control mechanisms, potentially linked to deficits in amygdala and anterior cingulate function. Methods We used an attentional interference task using emotional distracters to test for top-down versus bottom-up dysfunction in the interaction of cognitive-control circuitry and emotion-processing circuitry. A total of 27 patients with major depression and 24 controls were tested. Event-related functional magnetic resonance imaging was carried out as participants directly attended to, or attempted to ignore, fear-related stimuli. Results Compared to controls, patients with depression showed an enhanced amygdala response to unattended fear-related stimuli (relative to unattended neutral). By contrast, control participants showed increased activity in right dorsolateral prefrontal cortex (Brodmann areas 46/9) when ignoring fear stimuli (relative to neutral), which the patients with depression did not. In addition, the depressed participants failed to show evidence of error-related cognitive adjustments (increased activity in bilateral dorsolateral prefrontal cortex on post-error trials), but the control group did show them. Conclusions These results suggest multiple sources of dysregulation in emotional and cognitive control circuitry in depression, implicating both top-down and bottom-up dysfunction. PMID:17719567

Environmental impact of noise levels in and around opencast bauxite mine.

PubMed

Kisku, G C; Barman, S C; Kidwai, M M; Bhargava, S K

2002-01-01

Until recently, noise pollution has not been paid adequate attention as air, water and land pollution. In order to assess (predict) the impact of bauxite mine noise on employees health and in and around bauxite mine environment, general noise sources and equipment noise were monitored. All these noise sources were compared with prescribed standard noise levels laid down by Central Pollution Control Board (CPCB). Data has also been compared with reference site, north block hill top which is barren and virgin plateau/top covered with grass only and free from human interference. Equipment noise levels were much higher than the other zone of the mine which does not have the corresponding standards. Rock breaker recorded the highest noise level with 73.1 +/- 14.2 to 89.5 +/- 10.1 dB (A) while from ripper dozer it was least with 61.0 +/- 17.3 to 76.2 +/- 6.2 dB (A). Meteorological parameters did not have much influence upon equipment noise up to 100 feet from the source.

Resilience of Self-Organised and Top-Down Planned Cities—A Case Study on London and Beijing Street Networks

PubMed Central

Wang, Jiaqiu

2015-01-01

The success or failure of the street network depends on its reliability. In this article, using resilience analysis, the author studies how the shape and appearance of street networks in self-organised and top-down planned cities influences urban transport. Considering London and Beijing as proxies for self-organised and top-down planned cities, the structural properties of London and Beijing networks first are investigated based on their primal and dual representations of planar graphs. The robustness of street networks then is evaluated in primal space and dual space by deactivating road links under random and intentional attack scenarios. The results show that the reliability of London street network differs from that of Beijing, which seems to rely more on its architecture and connectivity. It is found that top-down planned Beijing with its higher average degree in the dual space and assortativity in the primal space is more robust than self-organised London using the measures of maximum and second largest cluster size and network efficiency. The article offers an insight, from a network perspective, into the reliability of street patterns in self-organised and top-down planned city systems. PMID:26682551

Premature asphalt concrete pavement cracking.

DOT National Transportation Integrated Search

2015-06-01

Recently, the Oregon Department of Transportation (ODOT) has identified hot mix asphalt concrete : (HMAC) pavements that have displayed top-down cracking within three years of construction. The objective of : the study was to evaluate the top-down cr...

A comparison of top-down and bottom-up carbon dioxide fluxes in the UK using a multi-platform measurement network.

NASA Astrophysics Data System (ADS)

White, Emily; Rigby, Matt; O'Doherty, Simon; Stavert, Ann; Lunt, Mark; Nemitz, Eiko; Helfter, Carole; Allen, Grant; Pitt, Joe; Bauguitte, Stéphane; Levy, Pete; van Oijen, Marcel; Williams, Mat; Smallman, Luke; Palmer, Paul

2016-04-01

Having a comprehensive understanding, on a countrywide scale, of both biogenic and anthropogenic CO2 emissions is essential for knowing how best to reduce anthropogenic emissions and for understanding how the terrestrial biosphere is responding to global fossil fuel emissions. Whilst anthropogenic CO2 flux estimates are fairly well constrained, fluxes from biogenic sources are not. This work will help to verify existing anthropogenic emissions inventories and give a better understanding of biosphere - atmosphere CO2 exchange. Using an innovative top-down inversion scheme; a hierarchical Bayesian Markov Chain Monte Carlo approach with reversible jump "trans-dimensional" basis function selection, we aim to find emissions estimates for biogenic and anthropogenic sources simultaneously. Our approach allows flux uncertainties to be derived more comprehensively than previous methods, and allows the resolved spatial scales in the solution to be determined using the data. We use atmospheric CO2 mole fraction data from the UK Deriving Emissions related to Climate Change (DECC) and Greenhouse gAs UK and Global Emissions (GAUGE) projects. The network comprises of 6 tall tower sites, flight campaigns and a ferry transect along the east coast, and enables us to derive high-resolution monthly flux estimates across the UK and Ireland for the period 2013-2015. We have derived UK total fluxes of 675 PIC 78 Tg/yr during January 2014 (seasonal maximum) and 23 PIC 96 Tg/yr during May 2014 (seasonal minimum). Our disaggregated anthropogenic and biogenic flux estimates are compared to a new high-resolution time resolved anthropogenic inventory that will underpin future UNFCCC reports by the UK, and to DALEC carbon cycle model. This allows us to identify where significant differences exist between these "bottom-up" and "top-down" flux estimates and suggest reasons for discrepancies. We will highlight the strengths and limitations of the UK's CO2 emissions verification infrastructure at present and outline improvements that could be made in the future.

Top down, bottom up structured programming and program structuring

NASA Technical Reports Server (NTRS)

Hamilton, M.; Zeldin, S.

1972-01-01

New design and programming techniques for shuttle software. Based on previous Apollo experience, recommendations are made to apply top-down structured programming techniques to shuttle software. New software verification techniques for large software systems are recommended. HAL, the higher order language selected for the shuttle flight code, is discussed and found to be adequate for implementing these techniques. Recommendations are made to apply the workable combination of top-down, bottom-up methods in the management of shuttle software. Program structuring is discussed relevant to both programming and management techniques.

Structural analysis of an intact monoclonal antibody by online electrochemical reduction of disulfide bonds and Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Nicolardi, Simone; Deelder, André M; Palmblad, Magnus; van der Burgt, Yuri E M

2014-06-03

Structural confirmation and quality control of recombinant monoclonal antibodies (mAbs) by top-down mass spectrometry is still challenging due to the size of the proteins, disulfide content, and post-translational modifications such as glycosylation. In this study we have applied electrochemistry (EC) to overcome disulfide bridge complexity in top-down analysis of mAbs. To this end, an electrochemical cell was coupled directly to an electrospray ionization (ESI) source and a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer (MS) equipped with a 15 T magnet. By performing online EC-assisted reduction of interchain disulfide bonds in an intact mAb, the released light chains could be selected for tandem mass spectrometry (MS/MS) analysis without interference from heavy-chain fragments. Moreover, the acquisition of full MS scans under denaturing conditions allowed profiling of all abundant mAb glycoforms. Ultrahigh-resolution FTICR-MS measurements provided fully resolved isotopic distributions of intact mAb and enabled the identification of the most abundant adducts and other interfering species. Furthermore, it was found that reduction of interchain disulfide bonds occurs in the ESI source dependent on capillary voltage and solvent composition. This phenomenon was systematically evaluated and compared with the results obtained from reduction in the electrochemical cell.

Top of well partially covered by boards, looking down to ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Top of well partially covered by boards, looking down to west - Neville-Kanode Farmstead, Well, East side of U.S. Highway 81, 2.5 miles south of Kansas-Nebraska state line, Munden, Republic County, KS

Heuristic for learning common emitter amplification with bipolar transistors

NASA Astrophysics Data System (ADS)

Staffas, Kjell

2017-11-01

Mathematics in engineering education causes many thresholds in the courses because of the demand of abstract conceptualisation. Electronics depend heavily on more or less complex mathematics. Therefore the concepts of analogue electronics are hard to learn since a great deal of students struggle with the calculations and procedures needed. A survey was done focusing on students' struggle to pass a course in analogue electronics by introducing a top-down perspective and the revised taxonomy of Bloom. From a top-down perspective you can create learning environments from any spot in the taxonomy using a step-by-step approach of the verbs understand and apply. Three textbooks with a top-down perspective on analogue electronics are analysed on the concept of amplifying with a transistor circuit. The study claims issues when losing the top-down perspective to present concepts and procedures of the content to be learned.

Bottom-up and top-down emotion generation: implications for emotion regulation

PubMed Central

Misra, Supriya; Prasad, Aditya K.; Pereira, Sean C.; Gross, James J.

2012-01-01

Emotion regulation plays a crucial role in adaptive functioning and mounting evidence suggests that some emotion regulation strategies are often more effective than others. However, little attention has been paid to the different ways emotions can be generated: from the ‘bottom-up’ (in response to inherently emotional perceptual properties of the stimulus) or ‘top-down’ (in response to cognitive evaluations). Based on a process priming principle, we hypothesized that mode of emotion generation would interact with subsequent emotion regulation. Specifically, we predicted that top-down emotions would be more successfully regulated by a top-down regulation strategy than bottom-up emotions. To test this hypothesis, we induced bottom-up and top-down emotions, and asked participants to decrease the negative impact of these emotions using cognitive reappraisal. We observed the predicted interaction between generation and regulation in two measures of emotional responding. As measured by self-reported affect, cognitive reappraisal was more successful on top-down generated emotions than bottom-up generated emotions. Neurally, reappraisal of bottom-up generated emotions resulted in a paradoxical increase of amygdala activity. This interaction between mode of emotion generation and subsequent regulation should be taken into account when comparing of the efficacy of different types of emotion regulation, as well as when reappraisal is used to treat different types of clinical disorders. PMID:21296865

Top-down control of visual perception: attention in natural vision.

PubMed

Rolls, Edmund T

2008-01-01

Top-down perceptual influences can bias (or pre-empt) perception. In natural scenes, the receptive fields of neurons in the inferior temporal visual cortex (IT) shrink to become close to the size of objects. This facilitates the read-out of information from the ventral visual system, because the information is primarily about the object at the fovea. Top-down attentional influences are much less evident in natural scenes than when objects are shown against blank backgrounds, though are still present. It is suggested that the reduced receptive-field size in natural scenes, and the effects of top-down attention contribute to change blindness. The receptive fields of IT neurons in complex scenes, though including the fovea, are frequently asymmetric around the fovea, and it is proposed that this is the solution the IT uses to represent multiple objects and their relative spatial positions in a scene. Networks that implement probabilistic decision-making are described, and it is suggested that, when in perceptual systems they take decisions (or 'test hypotheses'), they influence lower-level networks to bias visual perception. Finally, it is shown that similar processes extend to systems involved in the processing of emotion-provoking sensory stimuli, in that word-level cognitive states provide top-down biasing that reaches as far down as the orbitofrontal cortex, where, at the first stage of affective representations, olfactory, taste, flavour, and touch processing is biased (or pre-empted) in humans.

Use of Multichannel Near Infrared Spectroscopy to Study Relationships Between Brain Regions and Neurocognitive Tasks of Selective/Divided Attention and 2-Back Working Memory.

PubMed

Tomita, Nozomi; Imai, Shoji; Kanayama, Yusuke; Kawashima, Issaku; Kumano, Hiroaki

2017-06-01

While dichotic listening (DL) was originally intended to measure bottom-up selective attention, it has also become a tool for measuring top-down selective attention. This study investigated the brain regions related to top-down selective and divided attention DL tasks and a 2-back task using alphanumeric and Japanese numeric sounds. Thirty-six healthy participants underwent near-infrared spectroscopy scanning while performing a top-down selective attentional DL task, a top-down divided attentional DL task, and a 2-back task. Pearson's correlations were calculated to show relationships between oxy-Hb concentration in each brain region and the score of each cognitive task. Different brain regions were activated during the DL and 2-back tasks. Brain regions activated in the top-down selective attention DL task were the left inferior prefrontal gyrus and left pars opercularis. The left temporopolar area was activated in the top-down divided attention DL task, and the left frontopolar area and left dorsolateral prefrontal cortex were activated in the 2-back task. As further evidence for the finding that each task measured different cognitive and brain area functions, neither the percentages of correct answers for the three tasks nor the response times for the selective attentional task and the divided attentional task were correlated to one another. Thus, the DL and 2-back tasks used in this study can assess multiple areas of cognitive, brain-related dysfunction to explore their relationship to different psychiatric and neurodevelopmental disorders.

Trophic cascades of bottom-up and top-down forcing on nutrients and plankton in the Kattegat, evaluated by modelling

NASA Astrophysics Data System (ADS)

Petersen, Marcell Elo; Maar, Marie; Larsen, Janus; Møller, Eva Friis; Hansen, Per Juel

2017-05-01

The aim of the study was to investigate the relative importance of bottom-up and top-down forcing on trophic cascades in the pelagic food-web and the implications for water quality indicators (summer phytoplankton biomass and winter nutrients) in relation to management. The 3D ecological model ERGOM was validated and applied in a local set-up of the Kattegat, Denmark, using the off-line Flexsem framework. The model scenarios were conducted by changing the forcing by ± 20% of nutrient inputs (bottom-up) and mesozooplankton mortality (top-down), and both types of forcing combined. The model results showed that cascading effects operated differently depending on the forcing type. In the single-forcing bottom-up scenarios, the cascade directions were in the same direction as the forcing. For scenarios involving top-down, there was a skipped-level-transmission in the trophic responses that was either attenuated or amplified at different trophic levels. On a seasonal scale, bottom-up forcing showed strongest response during winter-spring for DIN and Chl a concentrations, whereas top-down forcing had the highest cascade strength during summer for Chl a concentrations and microzooplankton biomass. On annual basis, the system was more bottom-up than top-down controlled. Microzooplankton was found to play an important role in the pelagic food web as mediator of nutrient and energy fluxes. This study demonstrated that the best scenario for improved water quality was a combined reduction in nutrient input and mesozooplankton mortality calling for the need of an integrated management of marine areas exploited by human activities.

A layered abduction model of perception: Integrating bottom-up and top-down processing in a multi-sense agent

NASA Technical Reports Server (NTRS)

Josephson, John R.

1989-01-01

A layered-abduction model of perception is presented which unifies bottom-up and top-down processing in a single logical and information-processing framework. The process of interpreting the input from each sense is broken down into discrete layers of interpretation, where at each layer a best explanation hypothesis is formed of the data presented by the layer or layers below, with the help of information available laterally and from above. The formation of this hypothesis is treated as a problem of abductive inference, similar to diagnosis and theory formation. Thus this model brings a knowledge-based problem-solving approach to the analysis of perception, treating perception as a kind of compiled cognition. The bottom-up passing of information from layer to layer defines channels of information flow, which separate and converge in a specific way for any specific sense modality. Multi-modal perception occurs where channels converge from more than one sense. This model has not yet been implemented, though it is based on systems which have been successful in medical and mechanical diagnosis and medical test interpretation.

Site-specific effects on productivity of an upper trophic-level marine predator: Bottom-up, top-down, and mismatch effects on reproduction in a colonial seabird

USGS Publications Warehouse

Suryan, R.M.; Irons, D.B.; Brown, E.D.; Jodice, P.G.R.; Roby, D.D.

2006-01-01

We investigated the relative roles of bottom-up and top-down factors in limiting productivity of an upper trophic level marine predator. Our primary working hypothesis was that the reproductive success of black-legged kittiwakes (Rissa tridactyla) a piscivorous, colonial-nesting seabird, was most limited by the abundance, distribution, and species composition of surface-schooling forage fishes. A secondary working hypothesis was that reproductive loss to kittiwake nest predators was greatest during years of reduced prey availability. We report on a broad-scale, integrated study of kittiwakes and their prey in Prince William Sound, Alaska. Our study spanned five breeding seasons (1995-1999) and focused on three colonies that differed in size (ranging from ca. 220 to ca. 7000 breeding pairs) and proximity to each other (50-135 km apart). Kittiwakes in PWS encountered a variety of aquatic habitats, creating a complex foraging environment for breeding birds. We measured kittiwake reproductive success and foraging activities, while simultaneously measuring the abundance of surface schooling forage fishes throughout the foraging range of breeding kittiwakes. The abundance of primary prey species for kittiwakes (Pacific herring Clupea pallasi, Pacific sand lance Ammodytes hexapterus, and capelin Mallotus villosus) varied both annually and regionally, with no one region consistently having the greatest abundance of prey. Likewise, kittiwake reproductive success varied considerably among colonies and years. We found that bottom-up, top-down, timing mismatch, and colony-specific effects were all important to kittiwake productivity. Although bottom-up effects appeared to be strongest, they were not evident in some cases until other effects, such as geographic location (proximity of colony to prey concentrations) and top-down predation, were considered. Important bottom-up effects on kittiwake reproductive success were not only total prey abundance and distribution, but also species, age composition, and chronology of prey occurrence (match/mismatch of timing with critical brood-rearing periods); these effects varied by colony. Top-down effects of predation on kittiwake nest contents (independent of prey abundance) confounded seabird-forage fish relationships. Ultimately, when confounding factors were minimized, non-linear asymptotic relationships were identified between kittiwakes and their prey, with an asymptotic threshold of fish school surface area density of ca. 5 m2/km2, beyond which top-down, physiological, or phylogenetic constraints likely restrict further reproductive output. The integrated approach of our investigations provided a more thorough understanding of the mechanisms underlying predator-prey relationships in the complex marine environment. However, such mechanistic theories can only be tested and refined through long-term research and monitoring of much greater duration than the 5-year study reported herein. ?? 2006 Elsevier Ltd. All rights reserved.

Social anxiety and information processing biases: An integrated theoretical perspective.

PubMed

Peschard, Virginie; Philippot, Pierre

2016-01-01

Models of anxiety disorders posit that information processing biases towards threat may result from an imbalance between top-down attentional control processes and bottom-up attentional processes, such that anxiety could reduce the influence of the former and increase the influence of the latter. However, researchers have recently pointed to limitations of the top-down/bottom-up terminology and outlined the additional contribution of memory processes to attention guidance. The goal of this paper is to provide bridges between recent findings from cognitive psychology and anxiety disorders research. We first provide an integrative overview of the processes influencing the content of working memory, including the availability of attentional control, and the strengths of task goals, stimulus salience, selection history and long-term memory. We then illustrate the interest of this formulation to the study of information processing biases in anxiety disorders, with a specific focus on social anxiety.

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

Bogdanov, Bogdan; Smith, Richard D.

This review offers a broad overview of recent FTICR applications and technological developments in the field of proteomics, directed to a variety of people with different expertise and interests. Both the ''bottom-up'' (peptide level) and ''top-down'' (intact protein level) approaches will be covered and various related aspects will be discussed and illustrated with examples that are among the best available references in the literature. ''Bottom-up topics include peptide fragmentation, the AMT approach and DREAMS technology, quantitative proteomics, post-translational modifications, and special FTICR software focused on peptide and protein identification. Topics in the ''top-down'' part include various aspects of high-mass measurements,more » protein tandem mass spectrometry, protein confirmations, protein-protein complexes, as well as some esoteric applications that may become more practical in the coming years. Finally, examples of integrating both approaches and medical proteomics applications using FTICR will be provided, closing with an outlook of what may be coming our way sooner than later.« less

Perceptual and conceptual information processing in schizophrenia and depression.

PubMed

Dreben, E K; Fryer, J H; McNair, D M

1995-04-01

Schizophrenic patients (n = 20), depressive patients (n = 20), and normal adults (n = 20) were compared on global vs local analyses of perceptual information using tachistoscopic tasks and on top-down vs bottom-up conceptual processing using card-sort tasks. The schizophrenic group performed more poorly on tasks requiring either global analyses (counting lines when distracting circles were present) or top-down conceptual processing (rule learning) than they did on tasks requiring local analyses (counting heterogeneous lines) or bottom-up processing (attribute identification). The schizophrenic group appeared not to use conceptually guided processing. Normal adults showed the reverse pattern. The depressive group performed similarly to the schizophrenic group on perceptual tasks but closer to the normal group on conceptual tasks, thereby appearing to be less dependent on a particular information-processing strategy. These deficits in organizational strategy may be related to the use of available processing resources as well as the allocation of attention.

Semi top-down method combined with earth-bank, an effective method for basement construction.

NASA Astrophysics Data System (ADS)

Tuan, B. Q.; Tam, Ng M.

2018-04-01

Choosing an appropriate method of deep excavation not only plays a decisive role in technical success, but also in economics of the construction project. Presently, we mainly base on to key methods: “Bottom-up” and “Top-down” construction method. Right now, this paper presents an another method of construction that is “Semi Top-down method combining with earth-bank” in order to take the advantages and limit the weakness of the above methods. The Bottom-up method was improved by using the earth-bank to stabilize retaining walls instead of the bracing steel struts. The Top-down method was improved by using the open cut method for the half of the earthwork quantities.

Top-down control of methane emission and nitrogen cycling by waterfowl.

PubMed

Winton, R Scott; Richardson, Curtis J

2017-01-01

Aquatic herbivores impose top-down control on the structure of wetland ecosystems, but the biogeochemical consequences of herbivory on methane (CH 4 ) and nitrogen (N) are poorly known. To investigate the top-down effects of waterfowl on wetland biogeochemistry, we implemented exclosure experiments in a major waterfowl overwintering wetland in the southeastern United States over two growing seasons. We found that herbivory inhibited the oxidation of CH 4 , leading to a mean increase in emission by 230% over control plots, and prevented nitrification, as indicated by low nitrate availability and undetectable emissions of nitrous oxide. Herbivory reduced belowground biomass of macrophytes, retarding the subsequent spring emergence of aerenchymous stems, effectively starving wetland soils of oxygen necessary for CH 4 oxidation and nitrification. The recognition that important populations of aquatic herbivores may influence the capacity for wetlands to emit greenhouse gases and cycle N is particularly salient in the context of climate change and nutrient pollution mitigation goals. For example, our results suggest that (1) annual emissions of 23 Gg CH 4 /yr from ~57 000 ha of publicly owned waterfowl impoundments in the southeastern United States could be tripled by overgrazing and that (2) waterfowl impoundments may export as much N as agricultural fields. We discuss potential implications for habitat management in the context of historic wetland loss and waterfowl population recovery. © 2016 by the Ecological Society of America.

Basomedial amygdala mediates top–down control of anxiety and fear

PubMed Central

Adhikari, Avishek; Lerner, Talia N.; Finkelstein, Joel; Pak, Sally; Jennings, Joshua H.; Davidson, Thomas J.; Ferenczi, Emily; Gunaydin, Lisa A.; Mirzabekov, Julie J.; Ye, Li; Kim, Sung-Yon; Lei, Anna; Deisseroth, Karl

2016-01-01

Anxiety-related conditions are among the most difficult neuropsychiatric diseases to treat pharmacologically, but respond to cognitive therapies. There has therefore been interest in identifying relevant top-down pathways from cognitive control regions in medial prefrontal cortex (mPFC). Identification of such pathways could contribute to our understanding of the cognitive regulation of affect, and provide pathways for intervention. Previous studies have suggested that dorsal and ventral mPFC subregions exert opposing effects on fear, as do subregions of other structures. However, precise causal targets for top-down connections among these diverse possibilities have not been established. Here we show that the basomedial amygdala (BMA) represents the major target of ventral mPFC in amygdala in mice. Moreover, BMA neurons differentiate safe and aversive environments, and BMA activation decreases fear-related freezing and high-anxiety states. Lastly, we show that the ventral mPFC–BMA projection implements top-down control of anxiety state and learned freezing, both at baseline and in stress-induced anxiety, defining a broadly relevant new top-down behavioural regulation pathway. PMID:26536109

Bottom-up meets top-down: tailored raspberry-like Fe 3 O 4 –Pt nanocrystal superlattices

DOE PAGES

Qiu, Fen; Vervuurt, René H. J.; Verheijen, Marcel A.; ...

2018-01-01

Bottom up colloidal synthesis is combined with top down atomic layer deposition to achieve raspberry-like Pt-decorated Fe 3 O 4 nanoparticle superlattices with good metal–oxide–metal contact for photoelectrocatalysis.

Bottom-up meets top-down: tailored raspberry-like Fe 3 O 4 –Pt nanocrystal superlattices

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

Qiu, Fen; Vervuurt, René H. J.; Verheijen, Marcel A.

Bottom up colloidal synthesis is combined with top down atomic layer deposition to achieve raspberry-like Pt-decorated Fe 3 O 4 nanoparticle superlattices with good metal–oxide–metal contact for photoelectrocatalysis.

Decoding of top-down cognitive processing for SSVEP-controlled BMI

PubMed Central

Min, Byoung-Kyong; Dähne, Sven; Ahn, Min-Hee; Noh, Yung-Kyun; Müller, Klaus-Robert

2016-01-01

We present a fast and accurate non-invasive brain-machine interface (BMI) based on demodulating steady-state visual evoked potentials (SSVEPs) in electroencephalography (EEG). Our study reports an SSVEP-BMI that, for the first time, decodes primarily based on top-down and not bottom-up visual information processing. The experimental setup presents a grid-shaped flickering line array that the participants observe while intentionally attending to a subset of flickering lines representing the shape of a letter. While the flickering pixels stimulate the participant’s visual cortex uniformly with equal probability, the participant’s intention groups the strokes and thus perceives a ‘letter Gestalt’. We observed decoding accuracy of 35.81% (up to 65.83%) with a regularized linear discriminant analysis; on average 2.05-fold, and up to 3.77-fold greater than chance levels in multi-class classification. Compared to the EEG signals, an electrooculogram (EOG) did not significantly contribute to decoding accuracies. Further analysis reveals that the top-down SSVEP paradigm shows the most focalised activation pattern around occipital visual areas; Granger causality analysis consistently revealed prefrontal top-down control over early visual processing. Taken together, the present paradigm provides the first neurophysiological evidence for the top-down SSVEP BMI paradigm, which potentially enables multi-class intentional control of EEG-BMIs without using gaze-shifting. PMID:27808125

Heart rate variability indices as bio-markers of top-down self-regulatory mechanisms: A meta-analytic review.

PubMed

Holzman, Jacob B; Bridgett, David J

2017-03-01

Theoretical perspectives posit that heart-rate variability (HRV) reflects self-regulatory capacity and therefore can be employed as a bio-marker of top-down self-regulation (the ability to regulate behavioral, cognitive, and emotional processes). However, existing findings of relations between self-regulation and HRV indices are mixed. To clarify the nature of such relations, we conducted a meta-analysis of 123 studies (N=14,347) reporting relations between HRV indices and aspects of top-down self-regulation (e.g., executive functioning, emotion regulation, effortful control). A significant, albeit small, effect was observed (r=0.09) such that greater HRV was related to better top-down self-regulation. Differences in relations were negligible across aspects of self-regulation, self-regulation measurement methods, HRV computational techniques, at-risk compared with healthy samples, and the context of HRV measurement. Stronger relations were observed in older relative to younger samples and in published compared to unpublished studies. These findings generally support the notion that HRV indices can tentatively be employed as bio-markers of top-down self-regulation. Conceptual and theoretical implications, and critical gaps in current knowledge to be addressed by future work, are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Perceptual Learning via Modification of Cortical Top-Down Signals

PubMed Central

Schäfer, Roland; Vasilaki, Eleni; Senn, Walter

2007-01-01

The primary visual cortex (V1) is pre-wired to facilitate the extraction of behaviorally important visual features. Collinear edge detectors in V1, for instance, mutually enhance each other to improve the perception of lines against a noisy background. The same pre-wiring that facilitates line extraction, however, is detrimental when subjects have to discriminate the brightness of different line segments. How is it possible to improve in one task by unsupervised practicing, without getting worse in the other task? The classical view of perceptual learning is that practicing modulates the feedforward input stream through synaptic modifications onto or within V1. However, any rewiring of V1 would deteriorate other perceptual abilities different from the trained one. We propose a general neuronal model showing that perceptual learning can modulate top-down input to V1 in a task-specific way while feedforward and lateral pathways remain intact. Consistent with biological data, the model explains how context-dependent brightness discrimination is improved by a top-down recruitment of recurrent inhibition and a top-down induced increase of the neuronal gain within V1. Both the top-down modulation of inhibition and of neuronal gain are suggested to be universal features of cortical microcircuits which enable perceptual learning. PMID:17715996

Top-down models in biology: explanation and control of complex living systems above the molecular level.

PubMed

Pezzulo, Giovanni; Levin, Michael

2016-11-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. © 2016 The Author(s).

Decoding of top-down cognitive processing for SSVEP-controlled BMI

NASA Astrophysics Data System (ADS)

Min, Byoung-Kyong; Dähne, Sven; Ahn, Min-Hee; Noh, Yung-Kyun; Müller, Klaus-Robert

2016-11-01

We present a fast and accurate non-invasive brain-machine interface (BMI) based on demodulating steady-state visual evoked potentials (SSVEPs) in electroencephalography (EEG). Our study reports an SSVEP-BMI that, for the first time, decodes primarily based on top-down and not bottom-up visual information processing. The experimental setup presents a grid-shaped flickering line array that the participants observe while intentionally attending to a subset of flickering lines representing the shape of a letter. While the flickering pixels stimulate the participant’s visual cortex uniformly with equal probability, the participant’s intention groups the strokes and thus perceives a ‘letter Gestalt’. We observed decoding accuracy of 35.81% (up to 65.83%) with a regularized linear discriminant analysis; on average 2.05-fold, and up to 3.77-fold greater than chance levels in multi-class classification. Compared to the EEG signals, an electrooculogram (EOG) did not significantly contribute to decoding accuracies. Further analysis reveals that the top-down SSVEP paradigm shows the most focalised activation pattern around occipital visual areas; Granger causality analysis consistently revealed prefrontal top-down control over early visual processing. Taken together, the present paradigm provides the first neurophysiological evidence for the top-down SSVEP BMI paradigm, which potentially enables multi-class intentional control of EEG-BMIs without using gaze-shifting.

Top-down models in biology: explanation and control of complex living systems above the molecular level

PubMed Central

2016-01-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. PMID:27807271

Consideration on the health risk reduction related to attainment of the new particulate matter standards in Poland: A top-down policy risk assessment approach.

PubMed

Kobza, Joanna; Pastuszka, Józef S; Gulis, Gabriel

2016-01-01

Policies can influence health of a population in various ways. Numerous epidemiological studies supported by toxicological investigations demonstrate a positive association between ambient concentrations of airborne particulate matter and increased adverse cardio-respiratory events, including morbidity and mortality. The aim of this paper was to present the concept of the top-down health policy risk assessment approach model developed to estimate the expected health risk reduction associated with policy aiming at attaining the new particulate matter ≤ 10 μm in diameter (PM10) standards in Poland. The top-down approach guides the analysis of causal chains from the policy to health outcomes. In this case study we tried to estimate the predicted health effects of the policy change over the past 20 years. Since Polish annual standard for PM10 changed from 50 μg/m³ in 1990 to 40 μg/m³ in 2010, we calculated the relative risk associated with decreasing PM10 in diameter to 10 μg/m3 in the annual level of PM10 for 6 adverse health effects. The relative risk slightly decreased for almost all adverse health effects, which means that the relative decrease in the incidence of health effects from the baseline incidence should range from about 0.5-0.6% for heart disease admissions to > 1% for respiratory admissions. The obtained results indicate that implementation of the new ambient air standards could influence improvement of the health status of Polish population. A top-down policy health risk assessment model can be one of the main tools in this process, providing harmonized guidance how to seek evidence-based information, which could serve policy-makers. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

A Comparison of Techniques To Find Mirrored Hosts on the WWW.

ERIC Educational Resources Information Center

Bharat, Krishna; Broder, Andrei; Dean, Jefferey; Henzinger, Monika R.

2000-01-01

Compares several "top-down" algorithms for identifying mirrored hosts on the Web. The algorithms operate on the basis of URL strings and linkage data: the type of information about Web pages easily available from Web proxies and crawlers. Results reveal that the best approach is a combination of five algorithms: on test data this…

The changing contribution of top-down and bottom-up limitation of mesopredators during 220 years of land use and climate change.

PubMed

Pasanen-Mortensen, Marianne; Elmhagen, Bodil; Lindén, Harto; Bergström, Roger; Wallgren, Märtha; van der Velde, Ype; Cousins, Sara A O

2017-05-01

Apex predators may buffer bottom-up driven ecosystem change, as top-down suppression may dampen herbivore and mesopredator responses to increased resource availability. However, theory suggests that for this buffering capacity to be realized, the equilibrium abundance of apex predators must increase. This raises the question: will apex predators maintain herbivore/mesopredator limitation, if bottom-up change relaxes resource constraints? Here, we explore changes in mesopredator (red fox Vulpes vulpes) abundance over 220 years in response to eradication and recovery of an apex predator (Eurasian lynx Lynx lynx), and changes in land use and climate which are linked to resource availability. A three-step approach was used. First, recent data from Finland and Sweden were modelled to estimate linear effects of lynx density, land use and winter temperature on fox density. Second, lynx density, land use and winter temperature was estimated in a 22 650 km 2 focal area in boreal and boreo-nemoral Sweden in the years 1830, 1920, 2010 and 2050. Third, the models and estimates were used to project historic and future fox densities in the focal area. Projected fox density was lowest in 1830 when lynx density was high, winters cold and the proportion of cropland low. Fox density peaked in 1920 due to lynx eradication, a mesopredator release boosted by favourable bottom-up changes - milder winters and cropland expansion. By 2010, lynx recolonization had reduced fox density, but it remained higher than in 1830, partly due to the bottom-up changes. Comparing 1830 to 2010, the contribution of top-down limitation decreased, while environment enrichment relaxed bottom-up limitation. Future scenarios indicated that by 2050, lynx density would have to increase by 79% to compensate for a projected climate-driven increase in fox density. We highlight that although top-down limitation in theory can buffer bottom-up change, this requires compensatory changes in apex predator abundance. Hence apex predator recolonization/recovery to historical levels would not be sufficient to compensate for widespread changes in climate and land use, which have relaxed the resource constraints for many herbivores and mesopredators. Variation in bottom-up conditions may also contribute to context dependence in apex predator effects. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

A neural mechanism of dynamic gating of task-relevant information by top-down influence in primary visual cortex.

PubMed

Kamiyama, Akikazu; Fujita, Kazuhisa; Kashimori, Yoshiki

2016-12-01

Visual recognition involves bidirectional information flow, which consists of bottom-up information coding from retina and top-down information coding from higher visual areas. Recent studies have demonstrated the involvement of early visual areas such as primary visual area (V1) in recognition and memory formation. V1 neurons are not passive transformers of sensory inputs but work as adaptive processor, changing their function according to behavioral context. Top-down signals affect tuning property of V1 neurons and contribute to the gating of sensory information relevant to behavior. However, little is known about the neuronal mechanism underlying the gating of task-relevant information in V1. To address this issue, we focus on task-dependent tuning modulations of V1 neurons in two tasks of perceptual learning. We develop a model of the V1, which receives feedforward input from lateral geniculate nucleus and top-down input from a higher visual area. We show here that the change in a balance between excitation and inhibition in V1 connectivity is necessary for gating task-relevant information in V1. The balance change well accounts for the modulations of tuning characteristic and temporal properties of V1 neuronal responses. We also show that the balance change of V1 connectivity is shaped by top-down signals with temporal correlations reflecting the perceptual strategies of the two tasks. We propose a learning mechanism by which synaptic balance is modulated. To conclude, top-down signal changes the synaptic balance between excitation and inhibition in V1 connectivity, enabling early visual area such as V1 to gate context-dependent information under multiple task performances. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Top-down modulation of visual processing and knowledge after 250 ms supports object constancy of category decisions

PubMed Central

Schendan, Haline E.; Ganis, Giorgio

2015-01-01

People categorize objects more slowly when visual input is highly impoverished instead of optimal. While bottom-up models may explain a decision with optimal input, perceptual hypothesis testing (PHT) theories implicate top-down processes with impoverished input. Brain mechanisms and the time course of PHT are largely unknown. This event-related potential study used a neuroimaging paradigm that implicated prefrontal cortex in top-down modulation of occipitotemporal cortex. Subjects categorized more impoverished and less impoverished real and pseudo objects. PHT theories predict larger impoverishment effects for real than pseudo objects because top-down processes modulate knowledge only for real objects, but different PHT variants predict different timing. Consistent with parietal-prefrontal PHT variants, around 250 ms, the earliest impoverished real object interaction started on an N3 complex, which reflects interactive cortical activity for object cognition. N3 impoverishment effects localized to both prefrontal and occipitotemporal cortex for real objects only. The N3 also showed knowledge effects by 230 ms that localized to occipitotemporal cortex. Later effects reflected (a) word meaning in temporal cortex during the N400, (b) internal evaluation of prior decision and memory processes and secondary higher-order memory involving anterotemporal parts of a default mode network during posterior positivity (P600), and (c) response related activity in posterior cingulate during an anterior slow wave (SW) after 700 ms. Finally, response activity in supplementary motor area during a posterior SW after 900 ms showed impoverishment effects that correlated with RTs. Convergent evidence from studies of vision, memory, and mental imagery which reflects purely top-down inputs, indicates that the N3 reflects the critical top-down processes of PHT. A hybrid multiple-state interactive, PHT and decision theory best explains the visual constancy of object cognition. PMID:26441701

Top-down Versus Step-up Prescribing Strategies for Tumor Necrosis Factor Alpha Inhibitors in Children and Young Adults with Inflammatory Bowel Disease.

PubMed

Lee, Wan-Ju; Briars, Leslie; Lee, Todd A; Calip, Gregory S; Suda, Katie J; Schumock, Glen T

2016-10-01

Early initiation of tumor necrosis factor-alpha inhibitor (TNFI) therapy for children and young adults with inflammatory bowel disease (IBD) is not well described. We conducted a retrospective cohort study of children and young adults (≤24 yr) newly diagnosed with IBD using health insurance claims from 2009 to 2013. The conventional "step-up" approach was defined as TNFI initiation >30 days after first IBD medication prescription, whereas the "top-down" approach was defined as new TNFI prescription within 30 days of first IBD medication prescription. Switching rates, time to initiation, discontinuation, and adherence to TNFIs were compared between the 2 strategies. A total of 11,962 IBD patients were identified. Among 3300 TNFI users, 1298 (39.3%) were treated with the top-down approach, whereas 2002 (60.7%) were treated with the step-up approach. Top-down approach use increased from 31.4% to 49.8% during the 5-year period, and under this approach, most patients were treated with TNFIs alone. Time to TNFI initiation was shorter for patients diagnosed in more recent years. Patients treated with the top-down strategy had lower rates of corticosteroid use (32.5% versus 94.2%) compared with step-up treatment but presented a higher rate of TNFI discontinuation. The 2 strategies both exhibited high adherence (mean proportion of days covered: 83.7%-95.4%). Early TNFI initiation increased over time for children and young adults with IBD and was related to lower rates of corticosteroid use compared with the conventional approach. However, the higher rate of TNFI discontinuation under the top-down approach requires further examination.

Mixed method versus full top-down microcosting for organ recovery cost assessment in a French hospital group.

PubMed

Hrifach, Abdelbaste; Brault, Coralie; Couray-Targe, Sandrine; Badet, Lionel; Guerre, Pascale; Ganne, Christell; Serrier, Hassan; Labeye, Vanessa; Farge, Pierre; Colin, Cyrille

2016-12-01

The costing method used can change the results of economic evaluations. Choosing the appropriate method to assess the cost of organ recovery is an issue of considerable interest to health economists, hospitals, financial managers and policy makers in most developed countries. The main objective of this study was to compare a mixed method, combining top-down microcosting and bottom-up microcosting versus full top-down microcosting to assess the cost of organ recovery in a French hospital group. The secondary objective was to describe the cost of kidney, liver and pancreas recovery from French databases using the mixed method. The resources consumed for each donor were identified and valued using the proposed mixed method and compared to the full top-down microcosting approach. Data on kidney, liver and pancreas recovery were collected from a medico-administrative French database for the years 2010 and 2011. Related cost data were recovered from the hospital cost accounting system database for 2010 and 2011. Statistical significance was evaluated at P < 0.05. All the median costs for organ recovery differ significantly between the two costing methods (non-parametric test method; P < 0.01). Using the mixed method, the median cost for recovering kidneys was found to be €5155, liver recovery was €2528 and pancreas recovery was €1911. Using the full top-down microcosting method, median costs were found to be 21-36% lower than with the mixed method. The mixed method proposed appears to be a trade-off between feasibility and accuracy for the identification and valuation of cost components when calculating the cost of organ recovery in comparison to the full top-down microcosting approach.

Prefrontal inhibition of threat processing reduces working memory interference

PubMed Central

Clarke, Robert; Johnstone, Tom

2013-01-01

Bottom-up processes can interrupt ongoing cognitive processing in order to adaptively respond to emotional stimuli of high potential significance, such as those that threaten wellbeing. However it is vital that this interference can be modulated in certain contexts to focus on current tasks. Deficits in the ability to maintain the appropriate balance between cognitive and emotional demands can severely impact on day-to-day activities. This fMRI study examined this interaction between threat processing and cognition; 18 adult participants performed a visuospatial working memory (WM) task with two load conditions, in the presence and absence of anxiety induction by threat of electric shock. Threat of shock interfered with performance in the low cognitive load condition; however interference was eradicated under high load, consistent with engagement of emotion regulation mechanisms. Under low load the amygdala showed significant activation to threat of shock that was modulated by high cognitive load. A directed top-down control contrast identified two regions associated with top-down control; ventrolateral PFC and dorsal ACC. Dynamic causal modeling provided further evidence that under high cognitive load, top-down inhibition is exerted on the amygdala and its outputs to prefrontal regions. Additionally, we hypothesized that individual differences in a separate, non-emotional top-down control task would predict the recruitment of dorsal ACC and ventrolateral PFC during top-down control of threat. Consistent with this, performance on a separate dichotic listening task predicted dorsal ACC and ventrolateral PFC activation during high WM load under threat of shock, though activation in these regions did not directly correlate with WM performance. Together, the findings suggest that under high cognitive load and threat, top-down control is exerted by dACC and vlPFC to inhibit threat processing, thus enabling WM performance without threat-related interference. PMID:23750133

Auditory Hallucinations in Schizophrenia and Nonschizophrenia Populations: A Review and Integrated Model of Cognitive Mechanisms

PubMed Central

Waters, Flavie; Allen, Paul; Aleman, André; Fernyhough, Charles; Woodward, Todd S.; Badcock, Johanna C.; Barkus, Emma; Johns, Louise; Varese, Filippo; Menon, Mahesh; Vercammen, Ans; Larøi, Frank

2012-01-01

While the majority of cognitive studies on auditory hallucinations (AHs) have been conducted in schizophrenia (SZ), an increasing number of researchers are turning their attention to different clinical and nonclinical populations, often using SZ findings as a model for research. Recent advances derived from SZ studies can therefore be utilized to make substantial progress on AH research in other groups. The objectives of this article were to (1) present an up-to-date review regarding the cognitive mechanisms of AHs in SZ, (2) review findings from cognitive research conducted in other clinical and nonclinical groups, and (3) integrate these recent findings into a cohesive framework. First, SZ studies show that the cognitive underpinnings of AHs include self-source-monitoring deficits and executive and inhibitory control dysfunctions as well as distortions in top-down mechanisms, perceptual and linguistic processes, and emotional factors. Second, consistent with SZ studies, findings in other population groups point to the role of top-down processing, abnormalities in executive inhibition, and negative emotions. Finally, we put forward an integrated model of AHs that incorporates the above findings. We suggest that AHs arise from an interaction between abnormal neural activation patterns that produce salient auditory signals and top-down mechanisms that include signal detection errors, executive and inhibition deficits, a tapestry of expectations and memories, and state characteristics that influence how these experiences are interpreted. Emotional factors play a particular prominent role at all levels of this hierarchy. Our model is distinctively powerful in explaining a range of phenomenological characteristics of AH across a spectrum of disorders. PMID:22446568

Top-down methane emissions estimates for the San Francisco Bay Area from 1990 to 2012

DOE PAGES

Fairley, David; Fischer, Marc L.

2015-01-30

Methane is a potent greenhouse gas (GHG) that is now included in both California State and San Francisco Bay Area (SFBA) bottom-up emission inventories as part of California's effort to reduce anthropogenic GHG emissions. Here we provide a top-down estimate of methane (CH 4) emissions from the SFBA by combining atmospheric measurements with the comparatively better estimated emission inventory for carbon monoxide (CO). Local enhancements of CH 4 and CO are estimated using measurements from 14 air quality sites in the SFBA combined together with global background measurements. Mean annual CH 4 emissions are estimated from the product of Baymore » Area Air Quality Management District (BAAQMD) emission inventory CO and the slope of ambient local CH 4 to CO. The resulting top-down estimates of CH 4 emissions are found to decrease slightly from 1990 to 2012, with a mean value of 240 ± 60 GgCH 4 yr⁻¹ (at 95% confidence) in the most recent (2009–2012) period, and correspond to reasonably a constant factor of 1.5–2.0 (at 95% confidence) times larger than the BAAQMD CH 4 emission inventory. However, we note that uncertainty in these emission estimates is dominated by the variation in CH 4:CO enhancement ratios across the observing sites and we expect the estimates could represent a lower-limit on CH 4 emissions because BAAQMD monitoring sites focus on urban air quality and may be biased toward CO rather than CH 4 sources.« less

Trade Studies of Space Launch Architectures using Modular Probabilistic Risk Analysis

NASA Technical Reports Server (NTRS)

Mathias, Donovan L.; Go, Susie

2006-01-01

A top-down risk assessment in the early phases of space exploration architecture development can provide understanding and intuition of the potential risks associated with new designs and technologies. In this approach, risk analysts draw from their past experience and the heritage of similar existing systems as a source for reliability data. This top-down approach captures the complex interactions of the risk driving parts of the integrated system without requiring detailed knowledge of the parts themselves, which is often unavailable in the early design stages. Traditional probabilistic risk analysis (PRA) technologies, however, suffer several drawbacks that limit their timely application to complex technology development programs. The most restrictive of these is a dependence on static planning scenarios, expressed through fault and event trees. Fault trees incorporating comprehensive mission scenarios are routinely constructed for complex space systems, and several commercial software products are available for evaluating fault statistics. These static representations cannot capture the dynamic behavior of system failures without substantial modification of the initial tree. Consequently, the development of dynamic models using fault tree analysis has been an active area of research in recent years. This paper discusses the implementation and demonstration of dynamic, modular scenario modeling for integration of subsystem fault evaluation modules using the Space Architecture Failure Evaluation (SAFE) tool. SAFE is a C++ code that was originally developed to support NASA s Space Launch Initiative. It provides a flexible framework for system architecture definition and trade studies. SAFE supports extensible modeling of dynamic, time-dependent risk drivers of the system and functions at the level of fidelity for which design and failure data exists. The approach is scalable, allowing inclusion of additional information as detailed data becomes available. The tool performs a Monte Carlo analysis to provide statistical estimates. Example results of an architecture system reliability study are summarized for an exploration system concept using heritage data from liquid-fueled expendable Saturn V/Apollo launch vehicles.

Top-down causation by information control: from a philosophical problem to a scientific research programme

PubMed Central

Auletta, G; Ellis, G.F.R; Jaeger, L

2008-01-01

It has been claimed that different types of causes must be considered in biological systems, including top-down as well as same-level and bottom-up causation, thus enabling the top levels to be causally efficacious in their own right. To clarify this issue, the important distinctions between information and signs are introduced here and the concepts of information control and functional equivalence classes in those systems are rigorously defined and used to characterize when top-down causation by feedback control happens, in a way that is testable. The causally significant elements we consider are equivalence classes of lower level processes, realized in biological systems through different operations having the same outcome within the context of information control and networks. PMID:18319208

Evaluation of power block arrangements for 100MW scale concentrated solar thermal power generation using top-down design

NASA Astrophysics Data System (ADS)

Post, Alexander; Beath, Andrew; Sauret, Emilie; Persky, Rodney

2017-06-01

Concentrated solar thermal power generation poses a unique situation for power block selection, in which a capital intensive heat source is subject to daily and seasonal fluctuations in intensity. In this study, a method is developed to easily evaluate the favourability of different power blocks for converting the heat supplied by a concentrated solar thermal plant into power at the 100MWe scale based on several key parameters. The method is then applied to a range of commercially available power cycles that operate over different temperatures and efficiencies, and with differing capital costs, each with performance and economic parameters selected to be typical of their technology type, as reported in literature. Using this method, the power cycle is identified among those examined that is most likely to result in a minimum levelised cost of energy of a solar thermal plant.

Evaluation of improved operational standard tropospheric NO2 retrievals from Ozone Monitoring Instrument using in situ and surface-based NO2 observations

NASA Astrophysics Data System (ADS)

Celarier, E. A.; Lamsal, L.; Krotkov, N. A.; Bucsela, E. J.; Herman, J. R.; Dickerson, R. R.; He, H.; Brent, L. C.; Retscher, C.; Swartz, W. H.; Gleason, J. F.

2011-12-01

Nitrogen oxides are key actors in air quality and climate change. Column observations of tropospheric NO2 from the nadir-veiwing satellite sensors have been widely used to understand sources and chemistry of NOx. We have implemented several improvements to the operational algorithm developed at NASA GSFC and retrieved tropospheric NO2. Here we evaluate the new product using in situ surface measurements at the SEARCH, AQS/EPA, and NAPS networks, in situ aircraft (DISCOVER-AQ and RAMMPP), and ground-based PANDORA and DOAS measurements. The agreement among these data is within the uncertainty of measurements. The new OMI tropospheric NO2 product available at high spatial resolution is valuable to evaluate chemical transport models, to examine spatial and temporal pattern of NOx emissions, to provide top-down constraints to surface NOx emissions, and to estimate NOx lifetimes.

5. VIEW LOOKING DOWN ON TOP OF ELEVATOR CAR FROM ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

5. VIEW LOOKING DOWN ON TOP OF ELEVATOR CAR FROM THIRD FLOOR, SHOWING CROSSHEAD AND BROKEN ROPE SAFETY STOP MECHANISM INSIDE; GUIDES AT LOWER LEFT AND UPPER RIGHT; OPERATING ROPE AT LEFT - 72 Marlborough Street, Residential Hydraulic Elevator, Boston, Suffolk County, MA

4. VIEW EAST, PERSPECTIVE DOWN INCLINED PLANE FROM TOP OF ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. VIEW EAST, PERSPECTIVE DOWN INCLINED PLANE FROM TOP OF ABUTMENT TO CONEMAUGH RIVER AND AREA OF LOWER INCLINE - Laurel Hill Quarry, Incline Plane, Both sides of State Route 56, 2.4 miles East of State Route 711, Seward, Westmoreland County, PA

When Art Moves the Eyes: A Behavioral and Eye-Tracking Study

PubMed Central

Massaro, Davide; Savazzi, Federica; Di Dio, Cinzia; Freedberg, David; Gallese, Vittorio; Gilli, Gabriella; Marchetti, Antonella

2012-01-01

The aim of this study was to investigate, using eye-tracking technique, the influence of bottom-up and top-down processes on visual behavior while subjects, naïve to art criticism, were presented with representational paintings. Forty-two subjects viewed color and black and white paintings (Color) categorized as dynamic or static (Dynamism) (bottom-up processes). Half of the images represented natural environments and half human subjects (Content); all stimuli were displayed under aesthetic and movement judgment conditions (Task) (top-down processes). Results on gazing behavior showed that content-related top-down processes prevailed over low-level visually-driven bottom-up processes when a human subject is represented in the painting. On the contrary, bottom-up processes, mediated by low-level visual features, particularly affected gazing behavior when looking at nature-content images. We discuss our results proposing a reconsideration of the definition of content-related top-down processes in accordance with the concept of embodied simulation in art perception. PMID:22624007

Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin

NASA Astrophysics Data System (ADS)

Floris, Federico; Chiron, Lionel; Lynch, Alice M.; Barrow, Mark P.; Delsuc, Marc-André; O'Connor, Peter B.

2018-06-01

Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about 23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from 23% to 42%.

Effective connectivities of cortical regions for top-down face processing: A Dynamic Causal Modeling study

PubMed Central

Li, Jun; Liu, Jiangang; Liang, Jimin; Zhang, Hongchuan; Zhao, Jizheng; Rieth, Cory A.; Huber, David E.; Li, Wu; Shi, Guangming; Ai, Lin; Tian, Jie; Lee, Kang

2013-01-01

To study top-down face processing, the present study used an experimental paradigm in which participants detected non-existent faces in pure noise images. Conventional BOLD signal analysis identified three regions involved in this illusory face detection. These regions included the left orbitofrontal cortex (OFC) in addition to the right fusiform face area (FFA) and right occipital face area (OFA), both of which were previously known to be involved in both top-down and bottom-up processing of faces. We used Dynamic Causal Modeling (DCM) and Bayesian model selection to further analyze the data, revealing both intrinsic and modulatory effective connectivities among these three cortical regions. Specifically, our results support the claim that the orbitofrontal cortex plays a crucial role in the top-down processing of faces by regulating the activities of the occipital face area, and the occipital face area in turn detects the illusory face features in the visual stimuli and then provides this information to the fusiform face area for further analysis. PMID:20423709

When art moves the eyes: a behavioral and eye-tracking study.

PubMed

Massaro, Davide; Savazzi, Federica; Di Dio, Cinzia; Freedberg, David; Gallese, Vittorio; Gilli, Gabriella; Marchetti, Antonella

2012-01-01

The aim of this study was to investigate, using eye-tracking technique, the influence of bottom-up and top-down processes on visual behavior while subjects, naïve to art criticism, were presented with representational paintings. Forty-two subjects viewed color and black and white paintings (Color) categorized as dynamic or static (Dynamism) (bottom-up processes). Half of the images represented natural environments and half human subjects (Content); all stimuli were displayed under aesthetic and movement judgment conditions (Task) (top-down processes). Results on gazing behavior showed that content-related top-down processes prevailed over low-level visually-driven bottom-up processes when a human subject is represented in the painting. On the contrary, bottom-up processes, mediated by low-level visual features, particularly affected gazing behavior when looking at nature-content images. We discuss our results proposing a reconsideration of the definition of content-related top-down processes in accordance with the concept of embodied simulation in art perception.

Testing the nutritional-limitation, predator-avoidance, and storm-avoidance hypotheses for restricted sea otter habitat use in the Aleutian Islands, Alaska

USGS Publications Warehouse

Stewart, Nathan L.; Konar, Brenda; Tinker, M. Tim

2015-01-01

Sea otters (Enhydra lutris) inhabiting the Aleutian Islands have stabilized at low abundance levels following a decline and currently exhibit restricted habitat-utilization patterns. Possible explanations for restricted habitat use by sea otters can be classified into two fundamentally different processes, bottom-up and top-down forcing. Bottom-up hypotheses argue that changes in the availability or nutritional quality of prey resources have led to the selective use of habitats that support the highest quality prey. In contrast, top-down hypotheses argue that increases in predation pressure from killer whales have led to the selective use of habitats that provide the most effective refuge from killer whale predation. A third hypothesis suggests that current restricted habitat use is based on a need for protection from storms. We tested all three hypotheses for restricted habitat use by comparing currently used and historically used sea otter foraging locations for: (1) prey availability and quality, (2) structural habitat complexity, and (3) exposure to prevailing storms. Our findings suggest that current use is based on physical habitat complexity and not on prey availability, prey quality, or protection from storms, providing further evidence for killer whale predation as a cause for restricted sea otter habitat use in the Aleutian Islands.

Testing the nutritional-limitation, predator-avoidance, and storm-avoidance hypotheses for restricted sea otter habitat use in the Aleutian Islands, Alaska.

PubMed

Stewart, Nathan L; Konar, Brenda; Tinker, M Tim

2015-03-01

Sea otters (Enhydra lutris) inhabiting the Aleutian Islands have stabilized at low abundance levels following a decline and currently exhibit restricted habitat-utilization patterns. Possible explanations for restricted habitat use by sea otters can be classified into two fundamentally different processes, bottom-up and top-down forcing. Bottom-up hypotheses argue that changes in the availability or nutritional quality of prey resources have led to the selective use of habitats that support the highest quality prey. In contrast, top-down hypotheses argue that increases in predation pressure from killer whales have led to the selective use of habitats that provide the most effective refuge from killer whale predation. A third hypothesis suggests that current restricted habitat use is based on a need for protection from storms. We tested all three hypotheses for restricted habitat use by comparing currently used and historically used sea otter foraging locations for: (1) prey availability and quality, (2) structural habitat complexity, and (3) exposure to prevailing storms. Our findings suggest that current use is based on physical habitat complexity and not on prey availability, prey quality, or protection from storms, providing further evidence for killer whale predation as a cause for restricted sea otter habitat use in the Aleutian Islands.

Is top-down vs bottom-up radiological evaluation after febrile urinary tract infection really less stressful for the child and family? Challenging the dogma.

PubMed

Telli, Onur; Mermerkaya, Murat; Hajiyev, Perviz; Aydogdu, Ozgu; Afandiyev, Faraj; Suer, Evren; Soygur, Tarkan; Burgu, Berk

2015-03-01

We evaluated whether stress levels in children and parents during radiological evaluation after febrile urinary tract infection are really lower using the top-down approach, where (99m)technetium dimercaptosuccinic acid renal scintigraphy is used initially, than the bottom-up approach, where voiding cystourethrography is initially performed and repeated examinations are easier for all. We prospectively evaluated 120 children 3 to 8 years old. Pain ratings were obtained using the Faces Pain Scale-Revised, and conversation during the procedure was evaluated using the Child-Adult Medical Procedure Interaction Scale-Revised by 2 independent observers. To evaluate parental anxiety, the State-Trait Anxiety Inventory form was also completed. Following a documented febrile urinary tract infection children were randomized to the top-down or bottom-up group. A third group of 44 children undergoing repeat voiding cystourethrography and their parents were also evaluated. Child ratings of pain using the Faces Pain Scale-Revised were not significantly different between the top-down group following (99m)technetium dimercaptosuccinic acid renal scintigraphy (2.99 on a scale of 10) and the bottom-up group following voiding cystourethrography (3.21). Also the Faces Pain Scale-Revised was not significantly different in the repeat voiding cystourethrography group (3.35). On the Child-Adult Medical Procedure Interaction Scale-Revised there was negative correlation between child coping and child distress, as well as rate of child distress and adult coping promoting behavior. Parental state anxiety scores were significantly less in the top-down and repeat voiding cystourethrography groups than in the bottom-up group. Although the top-down approach and repeat voiding cystourethrography cause less anxiety for caregivers, these values do not correlate to pain scale in children. This finding might be due to lack of appropriate evaluation tools of pediatric pain and anxiety. However, the theory that the top-down approach is less invasive, and thus less stressful, requires further research. The Child-Adult Medical Procedure Interaction Scale-Revised data indicate that influences in adult-child interaction are bidirectional. Copyright © 2015 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry

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

Zhou, Mowei; Wu, Si; Stenoien, David L.

Top-down mass spectrometry is a valuable tool for charactering post-translational modifications on histones for understanding of gene control and expression. In this protocol, we describe a top-down workflow using liquid chromatography coupled to mass spectrometry for fast global profiling of changes in histone proteoforms between a wild-type and a mutant of a fungal species. The proteoforms exhibiting different abundances can be subjected to further targeted studies by other mass spectrometric or biochemical assays. This method can be generally adapted for preliminary screening for changes in histone modifications between samples such as wild-type vs. mutant, and control vs. disease.

Priors in perception: Top-down modulation, Bayesian perceptual learning rate, and prediction error minimization.

PubMed

Hohwy, Jakob

2017-01-01

I discuss top-down modulation of perception in terms of a variable Bayesian learning rate, revealing a wide range of prior hierarchical expectations that can modulate perception. I then switch to the prediction error minimization framework and seek to conceive cognitive penetration specifically as prediction error minimization deviations from a variable Bayesian learning rate. This approach retains cognitive penetration as a category somewhat distinct from other top-down effects, and carves a reasonable route between penetrability and impenetrability. It prevents rampant, relativistic cognitive penetration of perception and yet is consistent with the continuity of cognition and perception. Copyright © 2016 Elsevier Inc. All rights reserved.

Creation of Functional Micro/Nano Systems through Top-down and Bottom-up Approaches

PubMed Central

Wong, Tak-Sing; Brough, Branden; Ho, Chih-Ming

2009-01-01

Mimicking nature’s approach in creating devices with similar functional complexity is one of the ultimate goals of scientists and engineers. The remarkable elegance of these naturally evolved structures originates from bottom-up self-assembly processes. The seamless integration of top-down fabrication and bottom-up synthesis is the challenge for achieving intricate artificial systems. In this paper, technologies necessary for guided bottom-up assembly such as molecular manipulation, molecular binding, and the self assembling of molecules will be reviewed. In addition, the current progress of synthesizing mechanical devices through top-down and bottom-up approaches will be discussed. PMID:19382535

Top-down modulation: the crossroads of perception, attention and memory

NASA Astrophysics Data System (ADS)

Gazzaley, Adam

2010-02-01

Research in our laboratory focuses on understanding the neural mechanisms that serve at the crossroads of perception, memory and attention, specifically exploring how brain region interactions underlie these abilities. To accomplish this, we study top-down modulation, the process by which we enhance neural activity associated with relevant information and suppress activity for irrelevant information, thus establishing a neural basis for all higher-order cognitive operations. We also study alterations in top-down modulation that occur with normal aging. Our experiments are performed on human participants, using a multimodal approach that integrates functional MRI (fMRI), transcranial magnetic stimulation (TMS) and electroencephalography (EEG).

Stereotypes and prejudice affect the recognition of emotional body postures.

PubMed

Bijlstra, Gijsbert; Holland, Rob W; Dotsch, Ron; Wigboldus, Daniel H J

2018-03-26

Most research on emotion recognition focuses on facial expressions. However, people communicate emotional information through bodily cues as well. Prior research on facial expressions has demonstrated that emotion recognition is modulated by top-down processes. Here, we tested whether this top-down modulation generalizes to the recognition of emotions from body postures. We report three studies demonstrating that stereotypes and prejudice about men and women may affect how fast people classify various emotional body postures. Our results suggest that gender cues activate gender associations, which affect the recognition of emotions from body postures in a top-down fashion. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The effects of urbanization on trophic interactions in a desert landscape

USDA-ARS?s Scientific Manuscript database

Background/Question/Methods: Trophic systems can be affected through top-down (predators) and bottom-up (resources) impacts. Human activity can alter trophic systems by causing predators to avoid areas (top-down) or by providing increased resources through irrigation and decorative plants that attra...

Multilingual Crews: Communication and the Operations of Ships.

ERIC Educational Resources Information Center

Sampson, Helen; Zhao, Minghua

2003-01-01

Focuses on efforts to improve standards of English among seafarers, including a top-down approach to language learning utilized by industry regulators and training establishments. Considers the effectiveness of top-down approaches to language development, drawing on ethnographic research conducted aboard vessels with multilingual crews.…

A synthesis study of noncontact nondestructive evaluation of top-down cracking in asphalt pavements.

DOT National Transportation Integrated Search

2013-12-01

The primary objective of this research study was to conduct an extensive literature review on top-down : cracking evaluation studies, prepare a synthesis of findings, and recommend a follow up phase for a : pilot study in Mississippi with a candidate...

Achieving Campus Sustainability: Top-Down, Bottom-Up, or Neither?

ERIC Educational Resources Information Center

Brinkhurst, Marena; Rose, Peter; Maurice, Gillian; Ackerman, Josef Daniel

2011-01-01

Purpose: The dynamics of organizational change related to environmental sustainability on university campuses are examined in this article. Whereas case studies of campus sustainability efforts tend to classify leadership as either "top-down" or "bottom-up", this classification neglects consideration of the leadership roles of…

Deformation of Attractor Landscape via Cholinergic Presynaptic Modulations: A Computational Study Using a Phase Neuron Model

PubMed Central

Kanamaru, Takashi; Fujii, Hiroshi; Aihara, Kazuyuki

2013-01-01

Corticopetal acetylcholine (ACh) is released transiently from the nucleus basalis of Meynert (NBM) into the cortical layers and is associated with top-down attention. Recent experimental data suggest that this release of ACh disinhibits layer 2/3 pyramidal neurons (PYRs) via muscarinic presynaptic effects on inhibitory synapses. Together with other possible presynaptic cholinergic effects on excitatory synapses, this may result in dynamic and temporal modifications of synapses associated with top-down attention. However, the system-level consequences and cognitive relevance of such disinhibitions are poorly understood. Herein, we propose a theoretical possibility that such transient modifications of connectivity associated with ACh release, in addition to top-down glutamatergic input, may provide a neural mechanism for the temporal reactivation of attractors as neural correlates of memories. With baseline levels of ACh, the brain returns to quasi-attractor states, exhibiting transitive dynamics between several intrinsic internal states. This suggests that top-down attention may cause the attention-induced deformations between two types of attractor landscapes: the quasi-attractor landscape (Q-landscape, present under low-ACh, non-attentional conditions) and the attractor landscape (A-landscape, present under high-ACh, top-down attentional conditions). We present a conceptual computational model based on experimental knowledge of the structure of PYRs and interneurons (INs) in cortical layers 1 and 2/3 and discuss the possible physiological implications of our results. PMID:23326520

Pressurized Pepsin Digestion in Proteomics

PubMed Central

López-Ferrer, Daniel; Petritis, Konstantinos; Robinson, Errol W.; Hixson, Kim K.; Tian, Zhixin; Lee, Jung Hwa; Lee, Sang-Won; Tolić, Nikola; Weitz, Karl K.; Belov, Mikhail E.; Smith, Richard D.; Paša-Tolić, Ljiljana

2011-01-01

Integrated top-down bottom-up proteomics combined with on-line digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to high throughput proteomics experiments. Bottom-up proteomics ultimately provides the peptide sequences derived from the tandem MS analyses of peptides after the proteome has been digested. Top-down proteomics conversely entails the MS analyses of intact proteins for more effective characterization of genetic variations and/or post-translational modifications. Herein, we describe recent efforts toward efficient integration of bottom-up and top-down LC-MS-based proteomics strategies. Since most proteomics separations utilize acidic conditions, we exploited the compatibility of pepsin (where the optimal digestion conditions are at low pH) for integration into bottom-up and top-down proteomics work flows. Pressure-enhanced pepsin digestions were successfully performed and characterized with several standard proteins in either an off-line mode using a Barocycler or an on-line mode using a modified high pressure LC system referred to as a fast on-line digestion system (FOLDS). FOLDS was tested using pepsin and a whole microbial proteome, and the results were compared against traditional trypsin digestions on the same platform. Additionally, FOLDS was integrated with a RePlay configuration to demonstrate an ultrarapid integrated bottom-up top-down proteomics strategy using a standard mixture of proteins and a monkey pox virus proteome. PMID:20627868

Top-down modulation of visual and auditory cortical processing in aging.

PubMed

Guerreiro, Maria J S; Eck, Judith; Moerel, Michelle; Evers, Elisabeth A T; Van Gerven, Pascal W M

2015-02-01

Age-related cognitive decline has been accounted for by an age-related deficit in top-down attentional modulation of sensory cortical processing. In light of recent behavioral findings showing that age-related differences in selective attention are modality dependent, our goal was to investigate the role of sensory modality in age-related differences in top-down modulation of sensory cortical processing. This question was addressed by testing younger and older individuals in several memory tasks while undergoing fMRI. Throughout these tasks, perceptual features were kept constant while attentional instructions were varied, allowing us to devise all combinations of relevant and irrelevant, visual and auditory information. We found no top-down modulation of auditory sensory cortical processing in either age group. In contrast, we found top-down modulation of visual cortical processing in both age groups, and this effect did not differ between age groups. That is, older adults enhanced cortical processing of relevant visual information and suppressed cortical processing of visual distractors during auditory attention to the same extent as younger adults. The present results indicate that older adults are capable of suppressing irrelevant visual information in the context of cross-modal auditory attention, and thereby challenge the view that age-related attentional and cognitive decline is due to a general deficits in the ability to suppress irrelevant information. Copyright © 2014 Elsevier B.V. All rights reserved.

Nitrogen-Doped Mesoporous Carbon: A Top-Down Strategy to Promote Sulfur Immobilization for Lithium-Sulfur Batteries.

PubMed

Zhao, Xiaohui; Liu, Ying; Manuel, James; Chauhan, Ghanshyam S; Ahn, Hyo-Jun; Kim, Ki-Won; Cho, Kwon-Koo; Ahn, Jou-Hyeon

2015-10-12

The loss of active sulfur material is a challenge in the application of lithium-sulfur (Li-S) batteries. To immobilize sulfur, a nitrogen-doped mesoporous carbon (PMC) was synthesized with polyaniline (PANi) as the carbon source, which was used for development of Li-S batteries. The nitrogen content and pore system of the PMCs were modulated by varying the pyrolysis temperature to impart good electrochemical properties to the Li-S cells. As a result, the optimal capacity reversibility was obtained with the PMC synthesized at 700 °C that consisted of 12.8 % nitrogen. The enhanced cycle performance of Li-S cells was also validated at high sulfur contents up to 70 % and high C-rates up to 2 C. Furthermore, such sulfur/PMC cathodes could alleviate volume expansion during the discharge process. The results suggest that our synthesized nitrogen-doped PMCs prepared by this top-down strategy are promising materials to immobilize active sulfur in Li-S batteries. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integration of Pragmatic and Phonetic Cues in Spoken Word Recognition

PubMed Central

Rohde, Hannah; Ettlinger, Marc

2015-01-01

Although previous research has established that multiple top-down factors guide the identification of words during speech processing, the ultimate range of information sources that listeners integrate from different levels of linguistic structure is still unknown. In a set of experiments, we investigate whether comprehenders can integrate information from the two most disparate domains: pragmatic inference and phonetic perception. Using contexts that trigger pragmatic expectations regarding upcoming coreference (expectations for either he or she), we test listeners' identification of phonetic category boundaries (using acoustically ambiguous words on the/hi/∼/∫i/continuum). The results indicate that, in addition to phonetic cues, word recognition also reflects pragmatic inference. These findings are consistent with evidence for top-down contextual effects from lexical, syntactic, and semantic cues, but they extend this previous work by testing cues at the pragmatic level and by eliminating a statistical-frequency confound that might otherwise explain the previously reported results. We conclude by exploring the time-course of this interaction and discussing how different models of cue integration could be adapted to account for our results. PMID:22250908

Toward a trophic theory of species diversity

PubMed Central

Terborgh, John W.

2015-01-01

Efforts to understand the ecological regulation of species diversity via bottom-up approaches have failed to yield a consensus theory. Theories based on the alternative of top-down regulation have fared better. Paine’s discovery of keystone predation demonstrated that the regulation of diversity via top-down forcing could be simple, strong, and direct, yet ecologists have persistently failed to perceive generality in Paine’s result. Removing top predators destabilizes many systems and drives transitions to radically distinct alternative states. These transitions typically involve community reorganization and loss of diversity, implying that top-down forcing is crucial to diversity maintenance. Contrary to the expectations of bottom-up theories, many terrestrial herbivores and mesopredators are capable of sustained order-of-magnitude population increases following release from predation, negating the assumption that populations of primary consumers are resource limited and at or near carrying capacity. Predation sensu lato (to include Janzen–Connell mortality agents) has been shown to promote diversity in a wide range of ecosystems, including rocky intertidal shelves, coral reefs, the nearshore ocean, streams, lakes, temperate and tropical forests, and arctic tundra. The compelling variety of these ecosystems suggests that top-down forcing plays a universal role in regulating diversity. This conclusion is further supported by studies showing that the reduction or absence of predation leads to diversity loss and, in the more dramatic cases, to catastrophic regime change. Here, I expand on the thesis that diversity is maintained by the interaction between predation and competition, such that strong top-down forcing reduces competition, allowing coexistence. PMID:26374788

Developing and Benchmarking Native Linux Applications on Android

NASA Astrophysics Data System (ADS)

Batyuk, Leonid; Schmidt, Aubrey-Derrick; Schmidt, Hans-Gunther; Camtepe, Ahmet; Albayrak, Sahin

Smartphones get increasingly popular where more and more smartphone platforms emerge. Special attention was gained by the open source platform Android which was presented by the Open Handset Alliance (OHA) hosting members like Google, Motorola, and HTC. Android uses a Linux kernel and a stripped-down userland with a custom Java VM set on top. The resulting system joins the advantages of both environments, while third-parties are intended to develop only Java applications at the moment.

Analytics that Inform the University: Using Data You Already Have

ERIC Educational Resources Information Center

Dziuban, Charles; Moskal, Patsy; Cavanagh, Thomas; Watts, Andre

2012-01-01

The authors describe the University of Central Florida's top-down/bottom-up action analytics approach to using data to inform decision-making at the University of Central Florida. The top-down approach utilizes information about programs, modalities, and college implementation of Web initiatives. The bottom-up approach continuously monitors…

A Top Down Strategy To Enhance Information Technologies into Israeli Higher Education.

ERIC Educational Resources Information Center

Guri-Rosenblit, Sara

2002-01-01

The integration of information technologies (IT) into Israeli higher education through a top-down strategy has created systemic change. The use of IT in Israeli universities varies in terms of access-outreach, teaching-learning processes, study materials production, data and information retrieval, administrative functions, the creation of…

A "Top-Down" Analysis of High School Teacher Motivation

ERIC Educational Resources Information Center

Ciani, Keith D.; Summers, Jessica J.; Easter, Matthew A.

2008-01-01

Classroom instruction may be affected by school contexts that are increasingly performance-driven because of legislative demands. Interpreting this as a need to investigate the relationships between school context and classroom practice, this study took a "top-down" approach by examining contextual elements of school goal structure and teacher…

A top-down strategy to synthesize wurtzite Cu2ZnSnS4 nanocrystals by green chemistry.

PubMed

Sun, Yiwen; Hu, Zhengqiao; Zhang, Junjun; Wang, Li; Wu, Chunyan; Xu, Jun

2016-07-28

Green synthesis of metastable wurtzite Cu2ZnSnS4 nanocrystals through a top-down synthetic strategy is presented. Formation mechanisms associated with Kirkendall and etching effects are illustrated in detail. The nanocrystals exhibit remarkable photoluminescence properties at room temperature.

What Does Distractibility in ADHD Reveal about Mechanisms for Top-Down Attentional Control?

ERIC Educational Resources Information Center

Friedman-Hill, Stacia R.; Wagman, Meryl R.; Gex, Saskia E.; Pine, Daniel S.; Leibenluft, Ellen; Ungerleider, Leslie G.

2010-01-01

In this study, we attempted to clarify whether distractibility in ADHD might arise from increased sensory-driven interference or from inefficient top-down control. We employed an attentional filtering paradigm in which discrimination difficulty and distractor salience (amount of image "graying") were parametrically manipulated. Increased…

Pinning down the large- x gluon with NNLO top-quark pair differential distributions

NASA Astrophysics Data System (ADS)

Czakon, Michał; Hartland, Nathan P.; Mitov, Alexander; Nocera, Emanuele R.; Rojo, Juan

2017-04-01

Top-quark pair production at the LHC is directly sensitive to the gluon PDF at large x. While total cross-section data is already included in several PDF determinations, differential distributions are not, because the corresponding NNLO calculations have become available only recently. In this work we study the impact on the large- x gluon of top-quark pair differential distributions measured by ATLAS and CMS at √{s}=8 TeV. Our analysis, performed in the NNPDF3.0 framework at NNLO accuracy, allows us to identify the optimal combination of LHC top-quark pair measurements that maximize the constraints on the gluon, as well as to assess the compatibility between ATLAS and CMS data. We find that differential distributions from top-quark pair production provide significant constraints on the large- x gluon, comparable to those obtained from inclusive jet production data, and thus should become an important ingredient for the next generation of global PDF fits.

Effects of fish density and river fertilization on algal standing stocks, invertebrates communities, and fish production in an Arctic River

USGS Publications Warehouse

Deegan, Linda A.; Peterson, B.J.; Golden, H.; McIvor, C.C.; Miller, M.C.

1997-01-01

This study examined the relative importance of bottom-up and top-down controls of an arctic stream food web by simultaneous manipulation of the top predator and nutrient availability. We created a two-step trophic system (algae to insects) by removal of the top predator (Arctic grayling, Thymallus arcticus) in fertilized and control stream reaches. Fish abundance was also increased 10 times to examine the effect of high fish density on stream ecosystem dynamics and fish. We measured the response of epilithic algae, benthic and drifting insects, and fish to nutrient enrichment and to changes in fish density. Insect grazers had little effect on algae and fish had little effect on insects. In both the control and fertilized reaches, fish growth, energy storage, and reproductive response of females declined with increased fish density. Fish growth and energy storage were more closely correlated with per capita insect availability than with per capita algal standing stock

Global gridded anthropogenic emissions inventory of carbonyl sulfide

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

Zumkehr, Andrew; Hilton, Tim; Whelan, Mary

Atmospheric carbonyl sulfide (COS or OCS) is the most abundant sulfur containing gas in the troposphere and is an atmospheric tracer for the carbon cycle. Gridded inventories of global anthropogenic COS are used for interpreting global COS measurements. However, previous gridded anthropogenic data are a climatological estimate based on input data that is over three decades old and are not representative of current conditions. Here we develop a new gridded data set of global anthropogenic COS sources that includes more source sectors than previously available and uses the most current emissions factors and industry activity data as input. Additionally, themore » inventory is provided as annually varying estimates from years 1980–2012 and employs a source specific spatial scaling procedure. We estimate a global source in year 2012 of 406 Gg S y -1 (range of 223–586 Gg S y -1), which is highly concentrated in China and is twice as large as the previous gridded inventory. Our large upward revision in the bottom-up estimate of the source is consistent with a recent top-down estimate based on air-monitoring and Antarctic firn data. Furthermore, our inventory time trends, including a decline in the 1990's and growth after the year 2000, are qualitatively consistent with trends in atmospheric data. Lastly, similarities between the spatial distribution in this inventory and remote sensing data suggest that the anthropogenic source could potentially play a role in explaining a missing source in the global COS budget.« less

Global gridded anthropogenic emissions inventory of carbonyl sulfide

DOE PAGES

Zumkehr, Andrew; Hilton, Tim; Whelan, Mary; ...

2018-03-31

Atmospheric carbonyl sulfide (COS or OCS) is the most abundant sulfur containing gas in the troposphere and is an atmospheric tracer for the carbon cycle. Gridded inventories of global anthropogenic COS are used for interpreting global COS measurements. However, previous gridded anthropogenic data are a climatological estimate based on input data that is over three decades old and are not representative of current conditions. Here we develop a new gridded data set of global anthropogenic COS sources that includes more source sectors than previously available and uses the most current emissions factors and industry activity data as input. Additionally, themore » inventory is provided as annually varying estimates from years 1980–2012 and employs a source specific spatial scaling procedure. We estimate a global source in year 2012 of 406 Gg S y -1 (range of 223–586 Gg S y -1), which is highly concentrated in China and is twice as large as the previous gridded inventory. Our large upward revision in the bottom-up estimate of the source is consistent with a recent top-down estimate based on air-monitoring and Antarctic firn data. Furthermore, our inventory time trends, including a decline in the 1990's and growth after the year 2000, are qualitatively consistent with trends in atmospheric data. Lastly, similarities between the spatial distribution in this inventory and remote sensing data suggest that the anthropogenic source could potentially play a role in explaining a missing source in the global COS budget.« less

Global gridded anthropogenic emissions inventory of carbonyl sulfide

NASA Astrophysics Data System (ADS)

Zumkehr, Andrew; Hilton, Tim W.; Whelan, Mary; Smith, Steve; Kuai, Le; Worden, John; Campbell, J. Elliott

2018-06-01

Atmospheric carbonyl sulfide (COS or OCS) is the most abundant sulfur containing gas in the troposphere and is an atmospheric tracer for the carbon cycle. Gridded inventories of global anthropogenic COS are used for interpreting global COS measurements. However, previous gridded anthropogenic data are a climatological estimate based on input data that is over three decades old and are not representative of current conditions. Here we develop a new gridded data set of global anthropogenic COS sources that includes more source sectors than previously available and uses the most current emissions factors and industry activity data as input. Additionally, the inventory is provided as annually varying estimates from years 1980-2012 and employs a source specific spatial scaling procedure. We estimate a global source in year 2012 of 406 Gg S y-1 (range of 223-586 Gg S y-1), which is highly concentrated in China and is twice as large as the previous gridded inventory. Our large upward revision in the bottom-up estimate of the source is consistent with a recent top-down estimate based on air-monitoring and Antarctic firn data. Furthermore, our inventory time trends, including a decline in the 1990's and growth after the year 2000, are qualitatively consistent with trends in atmospheric data. Finally, similarities between the spatial distribution in this inventory and remote sensing data suggest that the anthropogenic source could potentially play a role in explaining a missing source in the global COS budget.

The Aliso Canyon Natural Gas Leak : Large Eddy Simulations for Modeling Atmospheric Dynamics and Interpretation of Observations.

NASA Astrophysics Data System (ADS)

Prasad, K.; Thorpe, A. K.; Duren, R. M.; Thompson, D. R.; Whetstone, J. R.

2016-12-01

The National Institute of Standards and Technology (NIST) has supported the development and demonstration of a measurement capability to accurately locate greenhouse gas sources and measure their flux to the atmosphere over urban domains. However, uncertainties in transport models which form the basis of all top-down approaches can significantly affect our capability to attribute sources and predict their flux to the atmosphere. Reducing uncertainties between bottom-up and top-down models will require high resolution transport models as well as validation and verification of dispersion models over an urban domain. Tracer experiments involving the release of Perfluorocarbon Tracers (PFTs) at known flow rates offer the best approach for validating dispersion / transport models. However, tracer experiments are limited by cost, ability to make continuous measurements, and environmental concerns. Natural tracer experiments, such as the leak from the Aliso Canyon underground storage facility offers a unique opportunity to improve and validate high resolution transport models, test leak hypothesis, and to estimate the amount of methane released.High spatial resolution (10 m) Large Eddy Simulations (LES) coupled with WRF atmospheric transport models were performed to simulate the dynamics of the Aliso Canyon methane plume and to quantify the source. High resolution forward simulation results were combined with aircraft and tower based in-situ measurements as well as data from NASA airborne imaging spectrometers. Comparison of simulation results with measurement data demonstrate the capability of the LES models to accurately model transport and dispersion of methane plumes over urban domains.

A top-down approach to fabrication of high quality vertical heterostructure nanowire arrays.

PubMed

Wang, Hua; Sun, Minghua; Ding, Kang; Hill, Martin T; Ning, Cun-Zheng

2011-04-13

We demonstrate a novel top-down approach for fabricating nanowires with unprecedented complexity and optical quality by taking advantage of a nanoscale self-masking effect. We realized vertical arrays of nanowires of 20-40 nm in diameter with 16 segments of complex longitudinal InGaAsP/InP structures. The unprecedented high quality of etched wires is evidenced by the narrowest photoluminescence linewidth ever produced in similar wavelengths, indistinguishable from that of the corresponding wafer. This top-down, mask-free, large scale approach is compatible with the established device fabrication processes and could serve as an important alternative to the bottom-up approach, significantly expanding ranges and varieties of applications of nanowire technology.

Neural Correlates of Top-Down Letter Processing

ERIC Educational Resources Information Center

Liu, Jiangang; Li, Jun; Zhang, Hongchuan; Rieth, Cory A.; Huber, David E.; Li, Wu; Lee, Kang; Tian, Jie

2010-01-01

This fMRI study investigated top-down letter processing with an illusory letter detection task. Participants responded whether one of a number of different possible letters was present in a very noisy image. After initial training that became increasingly difficult, they continued to detect letters even though the images consisted of pure noise,…

Theory and Practice of Community Development: A Case Study from the United Kingdom.

ERIC Educational Resources Information Center

Popple, Keith; Quinney, Anne

2002-01-01

A top-down approach to British community development is rooted in Victorian paternalism, a bottom-up approach in radical action. The case of ACHIEVE (Academic Centre for Health Improvement and Evidence of Effectiveness) shows how the current government's top-down approach is inadequate and potentially exploitive. It emphasizes development and…

TOP DOWN CONTROL OF THE MICROBIAL LOOP IN ESTUARINE PHYTOPLANKTON

EPA Science Inventory

Top Down Control of the Microbial Loop in Estuarine Plankton (Abstract). To be presented at the 16th Biennial Conference of the Estuarine Research Foundation, ERF 2001: An Estuarine Odyssey, 4-8 November 2001, St. Pete Beach, FL. 1 p. (ERL,GB R846).

We examined the effects...

The landscape of fear: The missing link to understand top-down and bottom-up controls of prey abundance?

USDA-ARS?s Scientific Manuscript database

Identifying factors that may be responsible for affecting and possibly regulating the size of animal populations is a cornerstone in understanding population ecology. The main factors that are thought to influence population size are either resources (bottom-up), predation, (top-down), or interspec...

Mass spectrometry: Raw protein from the top down

NASA Astrophysics Data System (ADS)

Breuker, Kathrin

2018-02-01

Mass spectrometry is a powerful technique for analysing proteins, yet linking higher-order protein structure to amino acid sequence and post-translational modifications is far from simple. Now, a native top-down method has been developed that can provide information on higher-order protein structure and different proteoforms at the same time.

Teachers' Perceptions of Teaching in Workplace Simulations in Vocational Education

ERIC Educational Resources Information Center

Jossberger, Helen; Brand-Gruwel, Saskia; van de Wiel, Margje W.; Boshuizen, Henny P.

2015-01-01

In a large-scale top-down innovation operation in the Netherlands, workplace simulations have been implemented in vocational schools, where students are required to work independently and self-direct their learning. However, research has shown that the success of such large-scale top-down innovations depends on how well their execution in schools…

Top Down versus Bottom Up: The Social Construction of the Health Literacy Movement

ERIC Educational Resources Information Center

Huber, Jeffrey T.; Shapiro, Robert M., II; Gillaspy, Mary L.

2012-01-01

The health literacy movement has been socially constructed over time. Unlike the consumer health information movement, which developed with broad public support, the health literacy movement has been fashioned primarily from the top down, initiated by policy makers and imposed on targeted populations. Interest in the health literacy movement has…

Comparing Top-Down with Bottom-Up Approaches: Teaching Data Modeling

ERIC Educational Resources Information Center

Kung, Hsiang-Jui; Kung, LeeAnn; Gardiner, Adrian

2013-01-01

Conceptual database design is a difficult task for novice database designers, such as students, and is also therefore particularly challenging for database educators to teach. In the teaching of database design, two general approaches are frequently emphasized: top-down and bottom-up. In this paper, we present an empirical comparison of students'…

A Dynamic Causal Modeling Analysis of the Effective Connectivities Underlying Top-Down Letter Processing

ERIC Educational Resources Information Center

Liu, Jiangang; Li, Jun; Rieth, Cory A.; Huber, David E.; Tian, Jie; Lee, Kang

2011-01-01

The present study employed dynamic causal modeling to investigate the effective functional connectivity between regions of the neural network involved in top-down letter processing. We used an illusory letter detection paradigm in which participants detected letters while viewing pure noise images. When participants detected letters, the response…

Compartment C1, engine room. View down compionway of top of ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Compartment C-1, engine room. View down compionway of top of engine cylinder heads; note slots in frame at left of photograph, slots hold steel bars which form a protective grating above the engines during battle. (081) - USS Olympia, Penn's Landing, 211 South Columbus Boulevard, Philadelphia, Philadelphia County, PA

Correction to: Top Down Tandem Mass Spectrometric Analysis of a Chemically Modified Rough-Type Lipopolysaccharide Vaccine Candidate

NASA Astrophysics Data System (ADS)

Oyler, Benjamin L.; Khan, Mohd M.; Smith, Donald F.; Harberts, Erin M.; Kilgour, David P. A.; Ernst, Robert K.; Cross, Alan S.; Goodlett, David R.

2018-04-01

In the preceding article "Top Down Tandem Mass Spectrometric Analysis of a Chemically Modified Rough-Type Lipopolysaccharide Vaccine Candidate" by Oyler et al., an error in the J5 E. coli LPS chemical structure (Figs. 2 and 4) was introduced and propagated into the final revision.

Lexical Expertise and Reading Skill: Bottom-Up and Top-Down Processing of Lexical Ambiguity

ERIC Educational Resources Information Center

Andrews, Sally; Bond, Rachel

2009-01-01

The lexical quality hypothesis assumes that skilled readers rely on high quality lexical representations that afford autonomous lexical retrieval and reduce the need to rely on top-down context. This experiment investigated this hypothesis by comparing the performance of adults classified on reading comprehension and spelling performance. "Lexical…

Contingent involuntary motoric inhibition: the involuntary inhibition of a motor response contingent on top-down goals.

PubMed

Anderson, Brian A; Folk, Charles L

2012-12-01

Effective motor control involves both the execution of appropriate responses and the inhibition of inappropriate responses that are evoked by response-associated stimuli. The inhibition of a motor response has traditionally been characterized as either a voluntary act of cognitive control or a low-level perceptual bias arising from processes such as inhibition of return and priming. Involuntary effects of top-down goals on motoric inhibition have been reported, but involve the perseveration of an inhibitory strategy. It is unknown whether the inhibition of a motor response can be selectively triggered by a goal-relevant stimulus, reflecting the automatic activation of a top-down inhibitory strategy. Here we show that irrelevant flankers that share the color of a no-go target elicit the inhibition of their associated motor response while other-colored flankers do not, even when participants have sufficient time to prepare for the upcoming target while ignoring the flankers. Our results demonstrate contingent involuntary motoric inhibition: motoric inhibition can be automatically triggered by a stimulus based on top-down goals.

Intact mass detection, interpretation, and visualization to automate Top-Down proteomics on a large scale

PubMed Central

Durbin, Kenneth R.; Tran, John C.; Zamdborg, Leonid; Sweet, Steve M. M.; Catherman, Adam D.; Lee, Ji Eun; Li, Mingxi; Kellie, John F.; Kelleher, Neil L.

2011-01-01

Applying high-throughput Top-Down MS to an entire proteome requires a yet-to-be-established model for data processing. Since Top-Down is becoming possible on a large scale, we report our latest software pipeline dedicated to capturing the full value of intact protein data in automated fashion. For intact mass detection, we combine algorithms for processing MS1 data from both isotopically resolved (FT) and charge-state resolved (ion trap) LC-MS data, which are then linked to their fragment ions for database searching using ProSight. Automated determination of human keratin and tubulin isoforms is one result. Optimized for the intricacies of whole proteins, new software modules visualize proteome-scale data based on the LC retention time and intensity of intact masses and enable selective detection of PTMs to automatically screen for acetylation, phosphorylation, and methylation. Software functionality was demonstrated using comparative LC-MS data from yeast strains in addition to human cells undergoing chemical stress. We further these advances as a key aspect of realizing Top-Down MS on a proteomic scale. PMID:20848673

A top-down design methodology and its implementation for VCSEL-based optical links design

NASA Astrophysics Data System (ADS)

Li, Jiguang; Cao, Mingcui; Cai, Zilong

2005-01-01

In order to find the optimal design for a given specification of an optical communication link, an integrated simulation of electronic, optoelectronic, and optical components of a complete system is required. It is very important to be able to simulate at both system level and detailed model level. This kind of model is feasible due to the high potential of Verilog-AMS language. In this paper, we propose an effective top-down design methodology and employ it in the development of a complete VCSEL-based optical links simulation. The principle of top-down methodology is that the development would proceed from the system to device level. To design a hierarchical model for VCSEL based optical links, the design framework is organized in three levels of hierarchy. The models are developed, and implemented in Verilog-AMS. Therefore, the model parameters are fitted to measured data. A sample transient simulation demonstrates the functioning of our implementation. Suggestions for future directions in top-down methodology used for optoelectronic systems technology are also presented.

Factors controlling bacteria and protists in selected Mazurian eutrophic lakes (North-Eastern Poland) during spring

PubMed Central

2013-01-01

Background The bottom-up (food resources) and top-down (grazing pressure) controls, with other environmental parameters (water temperature, pH) are the main factors regulating the abundance and structure of microbial communities in aquatic ecosystems. It is still not definitively decided which of the two control mechanisms is more important. The significance of bottom-up versus top-down controls may alter with lake productivity and season. In oligo- and/or mesotrophic environments, the bottom-up control is mostly important in regulating bacterial abundances, while in eutrophic systems, the top-down control may be more significant. Results The abundance of bacteria, heterotrophic (HNF) and autotrophic (ANF) nanoflagellates and ciliates, as well as bacterial production (BP) and metabolically active cells of bacteria (CTC, NuCC, EST) were studied in eutrophic lakes (Mazurian Lake District, Poland) during spring. The studied lakes were characterized by high nanoflagellate (mean 17.36 ± 8.57 × 103 cells ml-1) and ciliate abundances (mean 59.9 ± 22.4 ind. ml-1) that were higher in the euphotic zone than in the bottom waters, with relatively low bacterial densities (4.76 ± 2.08 × 106 cells ml-1) that were lower in the euphotic zone compared to the profundal zone. Oligotrichida (Rimostrombidium spp.), Prostomatida (Urotricha spp.) and Scuticociliatida (Histiobalantium bodamicum) dominated in the euphotic zone, whereas oligotrichs Tintinnidium sp. and prostomatids Urotricha spp. were most numerous in the bottom waters. Among the staining methods used to examine bacterial cellular metabolic activity, the lowest percentage of active cells was recorded with the CTC (1.5–15.4%) and EST (2.7–14.2%) assay in contrast to the NuCC (28.8–97.3%) method. Conclusions In the euphotic zone, the bottom-up factors (TP and DOC concentrations) played a more important role than top-down control (grazing by protists) in regulating bacterial numbers and activity. None of the single analyzed factors controlled bacterial abundance in the bottom waters. The results of this study suggest that both control mechanisms, bottom-up and top-down, simultaneously regulated bacterial community and their activity in the profundal zone of the studied lakes during spring. In both lake water layers, food availability (algae, nanoflagellates) was probably the major factor determining ciliate abundance and their composition. In the bottom waters, both groups of protists appeared to be also influenced by oxygen, temperature, and total phosphorus. PMID:23566491

A critical role of temporoparietal junction in the integration of top-down and bottom-up attentional control

PubMed Central

Wu, Qiong; Chang, Chi-Fu; Xi, Sisi; Huang, I-Wen; Liu, Zuxiang; Juan, Chi-Hung; Wu, Yanhong; Fan, Jin

2015-01-01

Information processing can be biased toward behaviorally relevant and salient stimuli by top-down (goal-directed) and bottom-up (stimulus-driven) attentional control processes. However, the neural basis underlying the integration of these processes is not well understood. We employed functional magnetic resonance imaging and transcranial direct-current stimulation (tDCS) in humans to examine the brain mechanisms underlying the interaction between these two processes. We manipulated the cognitive load involved in top-down processing and stimulus surprise involved in bottom-up processing in a factorial design by combining a majority function task and an oddball paradigm. We found that high cognitive load and high surprise level were associated with prolonged reaction time compared to low cognitive load and low surprise level, with a synergistic interaction effect which was accompanied by a greater deactivation of bilateral temporoparietal junction (TPJ). In addition, the TPJ displayed negative functional connectivity with right middle occipital gyrus involved in bottom-up processing (modulated by the interaction effect) and the right frontal eye field (FEF) involved in top-down control. The enhanced negative functional connectivity between the TPJ and right FEF was accompanied by a larger behavioral interaction effect across subjects. Application of cathodal tDCS over the right TPJ eliminated the interaction effect. These results suggest that the TPJ plays a critical role in processing bottom-up information for top-down control of attention. PMID:26308973

Indirect nitrous oxide emissions from streams within the US Corn Belt scale with stream order

PubMed Central

Turner, Peter A.; Griffis, Timothy J.; Lee, Xuhui; Baker, John M.; Venterea, Rodney T.; Wood, Jeffrey D.

2015-01-01

N2O is an important greenhouse gas and the primary stratospheric ozone depleting substance. Its deleterious effects on the environment have prompted appeals to regulate emissions from agriculture, which represents the primary anthropogenic source in the global N2O budget. Successful implementation of mitigation strategies requires robust bottom-up inventories that are based on emission factors (EFs), simulation models, or a combination of the two. Top-down emission estimates, based on tall-tower and aircraft observations, indicate that bottom-up inventories severely underestimate regional and continental scale N2O emissions, implying that EFs may be biased low. Here, we measured N2O emissions from streams within the US Corn Belt using a chamber-based approach and analyzed the data as a function of Strahler stream order (S). N2O fluxes from headwater streams often exceeded 29 nmol N2O-N m−2⋅s−1 and decreased exponentially as a function of S. This relation was used to scale up riverine emissions and to assess the differences between bottom-up and top-down emission inventories at the local to regional scale. We found that the Intergovernmental Panel on Climate Change (IPCC) indirect EF for rivers (EF5r) is underestimated up to ninefold in southern Minnesota, which translates to a total tier 1 agricultural underestimation of N2O emissions by 40%. We show that accounting for zero-order streams as potential N2O hotspots can more than double the agricultural budget. Applying the same analysis to the US Corn Belt demonstrates that the IPCC EF5r underestimation explains the large differences observed between top-down and bottom-up emission estimates. PMID:26216994

Evaluating trophic cascades as drivers of regime shifts in different ocean ecosystems

PubMed Central

Pershing, Andrew J.; Mills, Katherine E.; Record, Nicholas R.; Stamieszkin, Karen; Wurtzell, Katharine V.; Byron, Carrie J.; Fitzpatrick, Dominic; Golet, Walter J.; Koob, Elise

2015-01-01

In ecosystems that are strongly structured by predation, reducing top predator abundance can alter several lower trophic levels—a process known as a trophic cascade. A persistent trophic cascade also fits the definition of a regime shift. Such ‘trophic cascade regime shifts' have been reported in a few pelagic marine systems—notably the Black Sea, Baltic Sea and eastern Scotian Shelf—raising the question of how common this phenomenon is in the marine environment. We provide a general methodology for distinguishing top-down and bottom-up effects and apply this methodology to time series from these three ecosystems. We found evidence for top-down forcing in the Black Sea due primarily to gelatinous zooplankton. Changes in the Baltic Sea are primarily bottom-up, strongly structured by salinity, but top-down forcing related to changes in cod abundance also shapes the ecosystem. Changes in the eastern Scotian Shelf that were originally attributed to declines in groundfish are better explained by changes in stratification. Our review suggests that trophic cascade regime shifts are rare in open ocean ecosystems and that their likelihood increases as the residence time of water in the system increases. Our work challenges the assumption that negative correlation between consecutive trophic levels implies top-down forcing.

Top-down and bottom-up definitions of human failure events in human reliability analysis

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

Boring, Ronald Laurids

2014-10-01

In the probabilistic risk assessments (PRAs) used in the nuclear industry, human failure events (HFEs) are determined as a subset of hardware failures, namely those hardware failures that could be triggered by human action or inaction. This approach is top-down, starting with hardware faults and deducing human contributions to those faults. Elsewhere, more traditionally human factors driven approaches would tend to look at opportunities for human errors first in a task analysis and then identify which of those errors is risk significant. The intersection of top-down and bottom-up approaches to defining HFEs has not been carefully studied. Ideally, both approachesmore » should arrive at the same set of HFEs. This question is crucial, however, as human reliability analysis (HRA) methods are generalized to new domains like oil and gas. The HFEs used in nuclear PRAs tend to be top-down—defined as a subset of the PRA—whereas the HFEs used in petroleum quantitative risk assessments (QRAs) often tend to be bottom-up—derived from a task analysis conducted by human factors experts. The marriage of these approaches is necessary in order to ensure that HRA methods developed for top-down HFEs are also sufficient for bottom-up applications.« less

Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics*

PubMed Central

Vorontsov, Egor A.; Rensen, Elena; Prangishvili, David; Krupovic, Mart; Chamot-Rooke, Julia

2016-01-01

Protein post-translational methylation has been reported to occur in archaea, including members of the genus Sulfolobus, but has never been characterized on a proteome-wide scale. Among important Sulfolobus proteins carrying such modification are the chromatin proteins that have been described to be methylated on lysine side chains, resembling eukaryotic histones in that aspect. To get more insight into the extent of this modification and its dynamics during the different growth steps of the thermoacidophylic archaeon S. islandicus LAL14/1, we performed a global and deep proteomic analysis using a combination of high-throughput bottom-up and top-down approaches on a single high-resolution mass spectrometer. 1,931 methylation sites on 751 proteins were found by the bottom-up analysis, with methylation sites on 526 proteins monitored throughout three cell culture growth stages: early-exponential, mid-exponential, and stationary. The top-down analysis revealed 3,978 proteoforms arising from 681 proteins, including 292 methylated proteoforms, 85 of which were comprehensively characterized. Methylated proteoforms of the five chromatin proteins (Alba1, Alba2, Cren7, Sul7d1, Sul7d2) were fully characterized by a combination of bottom-up and top-down data. The top-down analysis also revealed an increase of methylation during cell growth for two chromatin proteins, which had not been evidenced by bottom-up. These results shed new light on the ubiquitous lysine methylation throughout the S. islandicus proteome. Furthermore, we found that S. islandicus proteins are frequently acetylated at the N terminus, following the removal of the N-terminal methionine. This study highlights the great value of combining bottom-up and top-down proteomics for obtaining an unprecedented level of accuracy in detecting differentially modified intact proteoforms. The data have been deposited to the ProteomeXchange with identifiers PXD003074 and PXD004179. PMID:27555370

Climate-mediated changes in marine ecosystem regulation during El Niño.

PubMed

Lindegren, Martin; Checkley, David M; Koslow, Julian A; Goericke, Ralf; Ohman, Mark D

2018-02-01

The degree to which ecosystems are regulated through bottom-up, top-down, or direct physical processes represents a long-standing issue in ecology, with important consequences for resource management and conservation. In marine ecosystems, the role of bottom-up and top-down forcing has been shown to vary over spatio-temporal scales, often linked to highly variable and heterogeneously distributed environmental conditions. Ecosystem dynamics in the Northeast Pacific have been suggested to be predominately bottom-up regulated. However, it remains unknown to what extent top-down regulation occurs, or whether the relative importance of bottom-up and top-down forcing may shift in response to climate change. In this study, we investigate the effects and relative importance of bottom-up, top-down, and physical forcing during changing climate conditions on ecosystem regulation in the Southern California Current System (SCCS) using a generalized food web model. This statistical approach is based on nonlinear threshold models and a long-term data set (~60 years) covering multiple trophic levels from phytoplankton to predatory fish. We found bottom-up control to be the primary mode of ecosystem regulation. However, our results also demonstrate an alternative mode of regulation represented by interacting bottom-up and top-down forcing, analogous to wasp-waist dynamics, but occurring across multiple trophic levels and only during periods of reduced bottom-up forcing (i.e., weak upwelling, low nutrient concentrations, and primary production). The shifts in ecosystem regulation are caused by changes in ocean-atmosphere forcing and triggered by highly variable climate conditions associated with El Niño. Furthermore, we show that biota respond differently to major El Niño events during positive or negative phases of the Pacific Decadal Oscillation (PDO), as well as highlight potential concerns for marine and fisheries management by demonstrating increased sensitivity of pelagic fish to exploitation during El Niño. © 2017 John Wiley & Sons Ltd.

Cascading top-down effects of changing oceanic predator abundances.

PubMed

Baum, Julia K; Worm, Boris

2009-07-01

1. Top-down control can be an important determinant of ecosystem structure and function, but in oceanic ecosystems, where cascading effects of predator depletions, recoveries, and invasions could be significant, such effects had rarely been demonstrated until recently. 2. Here we synthesize the evidence for oceanic top-down control that has emerged over the last decade, focusing on large, high trophic-level predators inhabiting continental shelves, seas, and the open ocean. 3. In these ecosystems, where controlled manipulations are largely infeasible, 'pseudo-experimental' analyses of predator-prey interactions that treat independent predator populations as 'replicates', and temporal or spatial contrasts in predator populations and climate as 'treatments', are increasingly employed to help disentangle predator effects from environmental variation and noise. 4. Substantial reductions in marine mammals, sharks, and piscivorous fishes have led to mesopredator and invertebrate predator increases. Conversely, abundant oceanic predators have suppressed prey abundances. Predation has also inhibited recovery of depleted species, sometimes through predator-prey role reversals. Trophic cascades have been initiated by oceanic predators linking to neritic food webs, but seem inconsistent in the pelagic realm with effects often attenuating at plankton. 5. Top-down control is not uniformly strong in the ocean, and appears contingent on the intensity and nature of perturbations to predator abundances. Predator diversity may dampen cascading effects except where nonselective fisheries deplete entire predator functional groups. In other cases, simultaneous exploitation of predator and prey can inhibit prey responses. Explicit consideration of anthropogenic modifications to oceanic foodwebs should help inform predictions about trophic control. 6. Synthesis and applications. Oceanic top-down control can have important socio-economic, conservation, and management implications as mesopredators and invertebrates assume dominance, and recovery of overexploited predators is impaired. Continued research aimed at integrating across trophic levels is needed to understand and forecast the ecosystem effects of changing oceanic predator abundances, the relative strength of top-down and bottom-up control, and interactions with intensifying anthropogenic stressors such as climate change.

Engineering neural systems for high-level problem solving.

PubMed

Sylvester, Jared; Reggia, James

2016-07-01

There is a long-standing, sometimes contentious debate in AI concerning the relative merits of a symbolic, top-down approach vs. a neural, bottom-up approach to engineering intelligent machine behaviors. While neurocomputational methods excel at lower-level cognitive tasks (incremental learning for pattern classification, low-level sensorimotor control, fault tolerance and processing of noisy data, etc.), they are largely non-competitive with top-down symbolic methods for tasks involving high-level cognitive problem solving (goal-directed reasoning, metacognition, planning, etc.). Here we take a step towards addressing this limitation by developing a purely neural framework named galis. Our goal in this work is to integrate top-down (non-symbolic) control of a neural network system with more traditional bottom-up neural computations. galis is based on attractor networks that can be "programmed" with temporal sequences of hand-crafted instructions that control problem solving by gating the activity retention of, communication between, and learning done by other neural networks. We demonstrate the effectiveness of this approach by showing that it can be applied successfully to solve sequential card matching problems, using both human performance and a top-down symbolic algorithm as experimental controls. Solving this kind of problem makes use of top-down attention control and the binding together of visual features in ways that are easy for symbolic AI systems but not for neural networks to achieve. Our model can not only be instructed on how to solve card matching problems successfully, but its performance also qualitatively (and sometimes quantitatively) matches the performance of both human subjects that we had perform the same task and the top-down symbolic algorithm that we used as an experimental control. We conclude that the core principles underlying the galis framework provide a promising approach to engineering purely neurocomputational systems for problem-solving tasks that in people require higher-level cognitive functions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comprehensive Identification of Proteins from MALDI Imaging*

PubMed Central

Maier, Stefan K.; Hahne, Hannes; Gholami, Amin Moghaddas; Balluff, Benjamin; Meding, Stephan; Schoene, Cédrik; Walch, Axel K.; Kuster, Bernhard

2013-01-01

Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful tool for the visualization of proteins in tissues and has demonstrated considerable diagnostic and prognostic value. One main challenge is that the molecular identity of such potential biomarkers mostly remains unknown. We introduce a generic method that removes this issue by systematically identifying the proteins embedded in the MALDI matrix using a combination of bottom-up and top-down proteomics. The analyses of ten human tissues lead to the identification of 1400 abundant and soluble proteins constituting the set of proteins detectable by MALDI IMS including >90% of all IMS biomarkers reported in the literature. Top-down analysis of the matrix proteome identified 124 mostly N- and C-terminally fragmented proteins indicating considerable protein processing activity in tissues. All protein identification data from this study as well as the IMS literature has been deposited into MaTisse, a new publically available database, which we anticipate will become a valuable resource for the IMS community. PMID:23782541

One Size Does Not Fit All: Human Failure Event Decomposition and Task Analysis

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

Ronald Laurids Boring, PhD

2014-09-01

In the probabilistic safety assessments (PSAs) used in the nuclear industry, human failure events (HFEs) are determined as a subset of hardware failures, namely those hardware failures that could be triggered or exacerbated by human action or inaction. This approach is top-down, starting with hardware faults and deducing human contributions to those faults. Elsewhere, more traditionally human factors driven approaches would tend to look at opportunities for human errors first in a task analysis and then identify which of those errors is risk significant. The intersection of top-down and bottom-up approaches to defining HFEs has not been carefully studied. Ideally,more » both approaches should arrive at the same set of HFEs. This question remains central as human reliability analysis (HRA) methods are generalized to new domains like oil and gas. The HFEs used in nuclear PSAs tend to be top-down—defined as a subset of the PSA—whereas the HFEs used in petroleum quantitative risk assessments (QRAs) are more likely to be bottom-up—derived from a task analysis conducted by human factors experts. The marriage of these approaches is necessary in order to ensure that HRA methods developed for top-down HFEs are also sufficient for bottom-up applications. In this paper, I first review top-down and bottom-up approaches for defining HFEs and then present a seven-step guideline to ensure a task analysis completed as part of human error identification decomposes to a level suitable for use as HFEs. This guideline illustrates an effective way to bridge the bottom-up approach with top-down requirements.« less

Top-down nanofabrication of silicon nanoribbon field effect transistor (Si-NR FET) for carcinoembryonic antigen detection.

PubMed

Bao, Zengtao; Sun, Jialin; Zhao, Xiaoqian; Li, Zengyao; Cui, Songkui; Meng, Qingyang; Zhang, Ye; Wang, Tong; Jiang, Yanfeng

2017-01-01

Sensitive and quantitative detection of tumor markers is highly required in the clinic for cancer diagnosis and consequent treatment. A field-effect transistor-based (FET-based) nanobiosensor emerges with characteristics of being label-free, real-time, having high sensitivity, and providing direct electrical readout for detection of biomarkers. In this paper, a top-down approach is proposed and implemented to fulfill a novel silicon nano-ribbon FET, which acts as biomarker sensor for future clinical application. Compared with the bottom-up approach, a top-down fabrication approach can confine width and length of the silicon FET precisely to control its electrical properties. The silicon nanoribbon (Si-NR) transistor is fabricated on a Silicon-on-Insulator (SOI) substrate by a top-down approach with complementary metal oxide semiconductor (CMOS)-compatible technology. After the preparation, the surface of Si-NR is functionalized with 3-aminopropyltriethoxysilane (APTES). Glutaraldehyde is utilized to bind the amino terminals of APTES and antibody on the surface. Finally, a microfluidic channel is integrated on the top of the device, acting as a flowing channel for the carcinoembryonic antigen (CEA) solution. The Si-NR FET is 120 nm in width and 25 nm in height, with ambipolar electrical characteristics. A logarithmic relationship between the changing ratio of the current and the CEA concentration is measured in the range of 0.1-100 ng/mL. The sensitivity of detection is measured as 10 pg/mL. The top-down fabricated biochip shows feasibility in direct detecting of CEA with the benefits of real-time, low cost, and high sensitivity as a promising biosensor for tumor early diagnosis.

Expeditionary Civilians: Creating a Viable Practice of Civilian Deployment Within the U.S. Interagency Community and Among Foreign Defense Organizations

DTIC Science & Technology

2016-01-01

study for the U.S. Department of Defense (DoD) that constituted an end-to-end review of guidance across the civilian deployment process , with the...end-to-end review of guidance across the civilian deployment process , with the ultimate aim of recommending guidelines for establishing and...follows: • Reactive internal sourcing. A requirement is identified through either a top-down or bottom-up process , triggering a recruitment process

Transmittal of Background Statement on Top-Down BACT

EPA Pesticide Factsheets

This document may be of assistance in applying the New Source Review (NSR) air permitting regulations including the Prevention of Significant Deterioration (PSD) requirements. This document is part of the NSR Policy and Guidance Database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Development and Optimization of a Positron Annihilation Lifetime Spectrometer to Measure Nanoscale Defects in Solids and Borane Cage Molecules in Aqueous Nitrate Solutions

DTIC Science & Technology

2008-03-01

will be accomplished by the day prior to the sample transfer operation. i. The radiation hood lab bench tops where radioactive material will be...source container to a sample container in a single syringe transfer. (All other non- radioactive solutions will have been previously added to this... radioactive spill. 4. Procedure Checklist: a. Setup □ Tape down plastic liner and locate absorbent □ Lay out sample container holder, sample

The ups and downs of trophic control in continental shelf ecosystems.

PubMed

Frank, Kenneth T; Petrie, Brian; Shackell, Nancy L

2007-05-01

Traditionally, marine ecosystem structure was thought to be determined by phytoplankton dynamics. However, an integrated view on the relative roles of top-down (consumer-driven) and bottom-up (resource-driven) forcing in large-scale, exploited marine ecosystems is emerging. Long time series of scientific survey data, underpinning the management of commercially exploited species such as cod, are being used to diagnose mechanisms that could affect the composition and relative abundance of species in marine food webs. By assembling published data from studies in exploited North Atlantic ecosystems, we found pronounced geographical variation in top-down and bottom-up trophic forcing. The data suggest that ecosystem susceptibility to top-down control and their resiliency to exploitation are related to species richness and oceanic temperature conditions. Such knowledge could be used to produce ecosystem guidelines to regulate and manage fisheries in a sustainable fashion.

Fabrication for Nanotechnology

DTIC Science & Technology

2007-03-01

could be divided into four groups as pictured in the following figure. Figure 1 : Nanotechnology fabrication methods Top-down nanofabrication...cooled) substrate on which a layer is formed. RTO-EN-AVT-129bis 2 - 1 van Heeren, H. (2007) Fabrication for Nanotechnology. In Nanotechnology...Aerospace Applications – 2006 (pp. 2- 1 – 2-4). Educational Notes RTO-EN-AVT-129bis, Paper 2. Neuilly-sur-Seine, France: RTO. Available from: http

Consequences of omnivory for trophic interactions on a salt marsh shrub.

PubMed

Ho, Chuan-Kai; Pennings, Steven C

2008-06-01

Although omnivory is common in nature, its impact on trophic interactions is variable. Predicting the food web consequences of omnivory is complicated because omnivores can simultaneously produce conflicting direct and indirect effects on the same species or trophic level. We conducted field and laboratory experiments testing the top-down impacts of an omnivorous salt marsh crab, Armases cinereum, on the shrub Iva frutescens and its herbivorous and predatory arthropod fauna. Armases is a "true omnivore," consuming both Iva and arthropods living on Iva. We hypothesized that Armases would benefit Iva through a top-down trophic cascade, and that this benefit would be stronger than the direct negative effect of Armases on Iva. A field experiment on Sapelo Island, Georgia (USA), supported this hypothesis. Although Armases suppressed predators (spiders), it also suppressed herbivores (aphids), and benefited Iva, increasing leaf number, and reducing the proportion of dead shoots. A one-month laboratory experiment, focusing on the most common species in the food web, also supported this hypothesis. Armases strongly suppressed aphids and consumed fewer Iva leaves if aphids were available as an alternate diet. Armases gained more body mass if they could feed on aphids as well as on Iva. Although Armases had a negative effect on Iva when aphids were not present, Armases benefited Iva if aphids were present, because Armases controlled aphid populations, releasing Iva from herbivory. Although Armases is an omnivore, it produced strong top-down forces and a trophic cascade because it fed preferentially on herbivores rather than plants when both were available. At the same time, the ability of Armases to subsist on a plant diet allows it to persist in the food web when animal food is not available. Because omnivores feed on multiple trophic levels, their effects on food webs may differ from those predicted by standard trophic models that assume that each species feeds only on a single trophic level. To better understand the complexity of real food webs, the variable feeding habits and feeding preferences of different omnivorous species must be taken into consideration.

Quantifying Molecular Hydrogen Emissions and an Industrial Leakage Rate for the South Coast Air Basin of California

NASA Astrophysics Data System (ADS)

Irish, M. C.; Schroeder, J.; Beyersdorf, A. J.; Blake, D. R.

2015-12-01

The poorly understood atmospheric budget and distribution of molecular hydrogen (H2) have invited further research since the discovery that emissions from a hydrogen-based economy could have negative impacts on the global climate system and stratospheric ozone. The burgeoning fuel cell electric vehicle industry in the South Coast Air Basin of California (SoCAB) presents an opportunity to observe and constrain urban anthropogenic H2 emissions. This work presents the first H2 emissions estimate for the SoCAB and calculates an upper limit for the current rate of leakage from production and distribution infrastructure within the region. A top-down method utilized whole air samples collected during the Student Airborne Research Program (SARP) onboard the NASA DC-8 research aircraft from 23-25 June 2015 to estimate H2 emissions from combustion and non-combustion sources. H2:carbon monoxide (CO) and H2:carbon dioxide ratios from airborne observations were compared with experimentally established ratios from pure combustion source ratios and scaled with the well-constrained CO emissions inventory to yield H2 emissions of 24.9 ± 3.6 Gg a-1 (1σ) from combustion engines and 8.2 ± 4.7 Gg a-1 from non-combustion sources. Total daily production of H2 in the SoCAB was compared with the top-down results to estimate an upper limit leakage rate (5%) where all emissions not accounted for by incomplete combustion in engines were assumed to be emitted from H2 infrastructure. For bottom-up validation, the NOAA Hybrid Single Particle Lagrangian Integrated Trajectory dispersion model was run iteratively with all known stationary sources in attempt to constrain emissions. While this investigation determined that H2 emissions from non-combustion sources in the SoCAB are likely significant, more in-depth analysis is required to better predict the atmospheric implications of a hydrogen economy.

Studies of Visual Attention in Physics Problem Solving

ERIC Educational Resources Information Center

Madsen, Adrian M.

2013-01-01

The work described here represents an effort to understand and influence visual attention while solving physics problems containing a diagram. Our visual system is guided by two types of processes--top-down and bottom-up. The top-down processes are internal and determined by ones prior knowledge and goals. The bottom-up processes are external and…

Trait- and density-mediated indirect interactions initiated by an exotic invasive plant autogenic ecosystem engineer

Treesearch

Dean E. Pearson

2010-01-01

Indirect interactions are important for structuring ecological systems. However, research on indirect effects has been heavily biased toward top-down trophic interactions, and less is known about other indirect-interaction pathways. As autogenic ecosystem engineers, plants can serve as initiators of nontrophic indirect interactions that, like top-down pathways, can...

Improving Reading Fluency and Comprehension in Adult ESL Learners Using Bottom-Up and Top-Down Vocabulary Training

ERIC Educational Resources Information Center

Oliver, Rhonda; Young, Shahreen

2016-01-01

The current research examines the effect of two methods of vocabulary training on reading fluency and comprehension of adult English as second language (ESL) tertiary-bound students. The methods used were isolated vocabulary training (bottom-up reading) and vocabulary training in context (top-down reading). The current exploratory and…

Attention and Cognitive Control Networks Assessed in a Dichotic Listening fMRI Study

ERIC Educational Resources Information Center

Falkenberg, Liv E.; Specht, Karsten; Westerhausen, Rene

2011-01-01

A meaningful interaction with our environment relies on the ability to focus on relevant sensory input and to ignore irrelevant information, i.e. top-down control and attention processes are employed to select from competing stimuli following internal goals. In this, the demands for the recruitment of top-down control processes depend on the…

The Effect of Non-Visual Working Memory Load on Top-Down Modulation of Visual Processing

ERIC Educational Resources Information Center

Rissman, Jesse; Gazzaley, Adam; D'Esposito, Mark

2009-01-01

While a core function of the working memory (WM) system is the active maintenance of behaviorally relevant sensory representations, it is also critical that distracting stimuli are appropriately ignored. We used functional magnetic resonance imaging to examine the role of domain-general WM resources in the top-down attentional modulation of…

Attentional Capture by Salient Color Singleton Distractors Is Modulated by Top-Down Dimensional Set

ERIC Educational Resources Information Center

Muller, Hermann J.; Geyer, Thomas; Zehetleitner, Michael; Krummenacher, Joseph

2009-01-01

Three experiments examined whether salient color singleton distractors automatically interfere with the detection singleton form targets in visual search (e.g., J. Theeuwes, 1992), or whether the degree of interference is top-down modulable. In Experiments 1 and 2, observers started with a pure block of trials, which contained either never a…

The Role of Teaching Experience in Language Teachers' Perceptions of a Top-Down Curriculum Change

ERIC Educational Resources Information Center

Rahimi, Mehrak; Alavi, Jalil

2017-01-01

The current study aimed to investigate the role of teaching experience in language teachers' perceptions of a top-down curriculum change. One hundred twenty-seven language teachers who have been experiencing the change for three years participated in the study. Their perceptions of change were quantitatively assessed by perceptions of change…

A Hierarchical and Contextual Model for Learning and Recognizing Highly Variant Visual Categories

DTIC Science & Technology

2010-01-01

neighboring pattern primitives, to create our model. We also present a minimax entropy framework for automatically learning which contextual constraints are...Grammars . . . . . . . . . . . . . . . . . . 19 3.2 Markov Random Fields . . . . . . . . . . . . . . . . . . . . . . . . 23 3.3 Creating a Contextual...Compositional Boosting. . . . . 119 7.8 Top-down hallucinations of missing objects. . . . . . . . . . . . . . . 121 7.9 The bottom-up to top-down

Thinking about the Weather: How Display Salience and Knowledge Affect Performance in a Graphic Inference Task

ERIC Educational Resources Information Center

Hegarty, Mary; Canham, Matt S.; Fabrikant, Sara I.

2010-01-01

Three experiments examined how bottom-up and top-down processes interact when people view and make inferences from complex visual displays (weather maps). Bottom-up effects of display design were investigated by manipulating the relative visual salience of task-relevant and task-irrelevant information across different maps. Top-down effects of…

49 CFR 537.7 - Pre-model year and mid-model year reports.

Code of Federal Regulations, 2014 CFR

2014-10-01

.... List the model types in order of increasing average inertia weight from top to bottom down the left... form. List the model types in order of increasing average inertia weight from top to bottom down the... trucks in your fleet that meet the mild and strong hybrid vehicle definitions. For each mild and strong...

49 CFR 537.7 - Pre-model year and mid-model year reports.

Code of Federal Regulations, 2013 CFR

2013-10-01

.... List the model types in order of increasing average inertia weight from top to bottom down the left... form. List the model types in order of increasing average inertia weight from top to bottom down the... trucks in your fleet that meet the mild and strong hybrid vehicle definitions. For each mild and strong...

A balance of bottom-up and top-down in linking climate policies

NASA Astrophysics Data System (ADS)

Green, Jessica F.; Sterner, Thomas; Wagner, Gernot

2014-12-01

Top-down climate negotiations embodied by the Kyoto Protocol have all but stalled, chiefly because of disagreements over targets and objections to financial transfers. To avoid those problems, many have shifted their focus to linkage of bottom-up climate policies such as regional carbon markets. This approach is appealing, but we identify four obstacles to successful linkage: different levels of ambition; competing domestic policy objectives; objections to financial transfers; and the difficulty of close regulatory coordination. Even with a more decentralized approach, overcoming the 'global warming gridlock' of the intergovernmental negotiations will require close international coordination. We demonstrate how a balance of bottom-up and top-down elements can create a path toward an effective global climate architecture.

Top-down search for color prevents voluntary directing of attention to informative singleton cues.

PubMed

Worschech, Franziska; Ansorge, Ulrich

2012-01-01

Visuo-spatial attention can be directed in a top-down controlled way to search for color targets and it can be captured by color contrasts, regardless of color identity. Here we tested whether participants can both search for a particular color target (e.g., red) and make use of a color-contrast cue that predicted the target's most likely position to direct their attention voluntarily. Our results show that this was impossible for the participants. Results support that top-down search for particular colors is incommensurate with directing attention to just any color contrast. The results are discussed in light of the current debates concerning the roles of color and color contrast for visuo-spatial attention.

Preserved feedforward but impaired top-down processes in the vegetative state.

PubMed

Boly, Melanie; Garrido, Marta Isabel; Gosseries, Olivia; Bruno, Marie-Aurélie; Boveroux, Pierre; Schnakers, Caroline; Massimini, Marcello; Litvak, Vladimir; Laureys, Steven; Friston, Karl

2011-05-13

Frontoparietal cortex is involved in the explicit processing (awareness) of stimuli. Frontoparietal activation has also been found in studies of subliminal stimulus processing. We hypothesized that an impairment of top-down processes, involved in recurrent neuronal message-passing and the generation of long-latency electrophysiological responses, might provide a more reliable correlate of consciousness in severely brain-damaged patients, than frontoparietal responses. We measured effective connectivity during a mismatch negativity paradigm and found that the only significant difference between patients in a vegetative state and controls was an impairment of backward connectivity from frontal to temporal cortices. This result emphasizes the importance of top-down projections in recurrent processing that involve high-order associative cortices for conscious perception.

Cognitive functions of the posterior parietal cortex: top-down and bottom-up attentional control

PubMed Central

Shomstein, Sarah

2012-01-01

Although much less is known about human parietal cortex than that of homologous monkey cortex, recent studies, employing neuroimaging, and neuropsychological methods, have begun to elucidate increasingly fine-grained functional and structural distinctions. This review is focused on recent neuroimaging and neuropsychological studies elucidating the cognitive roles of dorsal and ventral regions of parietal cortex in top-down and bottom-up attentional orienting, and on the interaction between the two attentional allocation mechanisms. Evidence is reviewed arguing that regions along the dorsal areas of the parietal cortex, including the superior parietal lobule (SPL) are involved in top-down attentional orienting, while ventral regions including the temporo-parietal junction (TPJ) are involved in bottom-up attentional orienting. PMID:22783174

Highlighting Uncertainty and Recommendations for Improvement of Black Carbon Biomass Fuel-Based Emission Inventories in the Indo-Gangetic Plain Region.

PubMed

Soneja, Sutyajeet I; Tielsch, James M; Khatry, Subarna K; Curriero, Frank C; Breysse, Patrick N

2016-03-01

Black carbon (BC) is a major contributor to hydrological cycle change and glacial retreat within the Indo-Gangetic Plain (IGP) and surrounding region. However, significant variability exists for estimates of BC regional concentration. Existing inventories within the IGP suffer from limited representation of rural sources, reliance on idealized point source estimates (e.g., utilization of emission factors or fuel-use estimates for cooking along with demographic information), and difficulty in distinguishing sources. Inventory development utilizes two approaches, termed top down and bottom up, which rely on various sources including transport models, emission factors, and remote sensing applications. Large discrepancies exist for BC source attribution throughout the IGP depending on the approach utilized. Cooking with biomass fuels, a major contributor to BC production has great source apportionment variability. Areas requiring attention tied to research of cookstove and biomass fuel use that have been recognized to improve emission inventory estimates include emission factors, particulate matter speciation, and better quantification of regional/economic sectors. However, limited attention has been given towards understanding ambient small-scale spatial variation of BC between cooking and non-cooking periods in low-resource environments. Understanding the indoor to outdoor relationship of BC emissions due to cooking at a local level is a top priority to improve emission inventories as many health and climate applications rely upon utilization of accurate emission inventories.

Effects of Recent Regional Soil Moisture Variability on Global Net Ecosystem CO2 Exchange

NASA Astrophysics Data System (ADS)

Jones, L. A.; Madani, N.; Kimball, J. S.; Reichle, R. H.; Colliander, A.

2017-12-01

Soil moisture exerts a major regional control on the inter-annual variability of the global land sink for atmospheric CO2. In semi-arid regions, annual biomass production is closely coupled to variability in soil moisture availability, while in cold-season-affected regions, summer drought offsets the effects of advancing spring phenology. Availability of satellite solar-induced fluorescence (SIF) observations and improvements in atmospheric inversions has led to unprecedented ability to monitor atmospheric sink strength. However, discrepancies still exist between such top-down estimates as atmospheric inversion and bottom-up process and satellite driven models, indicating that relative strength, mechanisms, and interaction of driving factors remain poorly understood. We use soil moisture fields informed by Soil Moisture Active Passive Mission (SMAP) observations to compare recent (2015-2017) and historic (2000-2014) variability in net ecosystem land-atmosphere CO2 exchange (NEE). The operational SMAP Level 4 Carbon (L4C) product relates ground-based flux tower measurements to other bottom-up and global top-down estimates to underlying soil moisture and other driving conditions using data-assimilation-based SMAP Level 4 Soil Moisture (L4SM). Droughts in coastal Brazil, South Africa, Eastern Africa, and an anomalous wet period in Eastern Australia were observed by L4C. A seasonal seesaw pattern of below-normal sink strength at high latitudes relative to slightly above-normal sink strength for mid-latitudes was also observed. Whereas SMAP-based soil moisture is relatively informative for short-term temporal variability, soil moisture biases that vary in space and with season constrain the ability of the L4C estimates to accurately resolve NEE. Such biases might be caused by irrigation and plant-accessible ground-water. Nevertheless, SMAP L4C daily NEE estimates connect top-down estimates to variability of effective driving factors for accurate estimates of regional-to-global land-atmosphere CO2 exchange.

Savanna tree density, herbivores, and the herbaceous community: bottom-up vs. top-down effects.

PubMed

Riginos, Corinna; Grace, James B

2008-08-01

Herbivores choose their habitats both to maximize forage intake and to minimize their risk of predation. For African savanna herbivores, the available habitats range in woody cover from open areas with few trees to dense, almost-closed woodlands. This variation in woody cover or density can have a number of consequences for herbaceous species composition, cover, and productivity, as well as for ease of predator detection and avoidance. Here, we consider two alternative possibilities: first, that tree density affects the herbaceous vegetation, with concomitant "bottom-up" effects on herbivore habitat preferences; or, second, that tree density affects predator visibility, mediating "top-down" effects of predators on herbivore habitat preferences. We sampled sites spanning a 10-fold range of tree densities in an Acacia drepanolobium-dominated savanna in Laikipia, Kenya, for variation in (1) herbaceous cover, composition, and species richness; (2) wild and domestic herbivore use; and (3) degree of visibility obstruction by the tree layer. We then used structural equation modeling to consider the potential influences that tree density may have on herbivores and herbaceous community properties. Tree density was associated with substantial variation in herbaceous species composition and richness. Cattle exhibited a fairly uniform use of the landscape, whereas wild herbivores, with the exception of elephants, exhibited a strong preference for areas of low tree density. Model results suggest that this was not a response to variation in herbaceous-community characteristics, but rather a response to the greater visibility associated with more open places. Elephants, in contrast, preferred areas with higher densities of trees, apparently because of greater forage availability. These results suggest that, for all but the largest species, top-down behavioral effects of predator avoidance on herbivores are mediated by tree density. This, in turn, appears to have cascading effects on the herbaceous vegetation. These results shed light on one of the major features of the "landscape of fear" in which African savanna herbivores exist.

Neotropical peatland methane emissions along a vegetation and biogeochemical gradient.

PubMed

Winton, R Scott; Flanagan, Neal; Richardson, Curtis J

2017-01-01

Tropical wetlands are thought to be the most important source of interannual variability in atmospheric methane (CH4) concentrations, yet sparse data prevents them from being incorporated into Earth system models. This problem is particularly pronounced in the neotropics where bottom-up models based on water table depth are incongruent with top-down inversion models suggesting unaccounted sinks or sources of CH4. The newly documented vast areas of peatlands in the Amazon basin may account for an important unrecognized CH4 source, but the hydrologic and biogeochemical controls of CH4 dynamics from these systems remain poorly understood. We studied three zones of a peatland in Madre de Dios, Peru, to test whether CH4 emissions and pore water concentrations varied with vegetation community, soil chemistry and proximity to groundwater sources. We found that the open-canopy herbaceous zone emitted roughly one-third as much CH4 as the Mauritia flexuosa palm-dominated areas (4.7 ± 0.9 and 14.0 ± 2.4 mg CH4 m-2 h-1, respectively). Emissions decreased with distance from groundwater discharge across the three sampling sites, and tracked changes in soil carbon chemistry, especially increased soil phenolics. Based on all available data, we calculate that neotropical peatlands contribute emissions of 43 ± 11.9 Tg CH4 y-1, however this estimate is subject to geographic bias and will need revision once additional studies are published.

Risk assessment strategies as a tool in the application of the Appropriate Level of Protection (ALOP) and Food Safety Objective (FSO) by risk managers.

PubMed

Gkogka, E; Reij, M W; Gorris, L G M; Zwietering, M H

2013-10-01

In the course of the last decade, the Appropriate Level of Protection (ALOP), the Food Safety Objective (FSO) and their associated metrics have been proposed by the World Trade Organization and Codex Alimentarius as a means for competent authorities to ultimately translate governmental public health policy regarding food safety into risk-based targets for the food industry. The industry needs to meet these targets through the effective choice of control measures that are part of its operational food safety management system. The aim of this study was to put the practical application of ALOP and FSO to the test in the case of Salmonella in chicken meat in the Netherlands. Two different risk assessment approaches were applied to derive potential ALOP and FSO values, a 'top-down' approach based on epidemiological data and a 'bottom-up' approach based on food supply chain data. To this end, two stochastic models specific to the Dutch situation were built. Comparisons between 23 countries in Europe were also made using the top-down model. The mean estimated current Level Of Protection values were similar for the two approaches applied, with the bottom-up model yielding 87 cases per 100,000 inhabitants per year (95% CI: 0.03, 904) and the top-down model 71 (95% CI: 9.9, 155). The estimated FSO values on the other hand were considerably different with the mean 'top down' FSO being -4.6 log CFU/g (95% CI: -5.4, -4.1) and the mean 'bottom-up' FSO -6.0 log CFU/g (95% CI: -8.1, -2.9) reflecting major differences in the output distributions of this parameter obtained with the two approaches. Significant differences were observed between current LOP values for different EU countries, although it was not clear whether this was due to actual differences in the factors influencing the risk of salmonellosis or due to the quality of the available data. Copyright © 2013 Elsevier B.V. All rights reserved.

Asymmetric top-down modulation of ascending visual pathways in pigeons.

PubMed

Freund, Nadja; Valencia-Alfonso, Carlos E; Kirsch, Janina; Brodmann, Katja; Manns, Martina; Güntürkün, Onur

2016-03-01

Cerebral asymmetries are a ubiquitous phenomenon evident in many species, incl. humans, and they display some similarities in their organization across vertebrates. In many species the left hemisphere is associated with the ability to categorize objects based on abstract or experience-based behaviors. Using the asymmetrically organized visual system of pigeons as an animal model, we show that descending forebrain pathways asymmetrically modulate visually evoked responses of single thalamic units. Activity patterns of neurons within the nucleus rotundus, the largest thalamic visual relay structure in birds, were differently modulated by left and right hemispheric descending systems. Thus, visual information ascending towards the left hemisphere was modulated by forebrain top-down systems at thalamic level, while right thalamic units were strikingly less modulated. This asymmetry of top-down control could promote experience-based processes within the left hemisphere, while biasing the right side towards stimulus-bound response patterns. In a subsequent behavioral task we tested the possible functional impact of this asymmetry. Under monocular conditions, pigeons learned to discriminate color pairs, so that each hemisphere was trained on one specific discrimination. Afterwards the animals were presented with stimuli that put the hemispheres in conflict. Response patterns on the conflicting stimuli revealed a clear dominance of the left hemisphere. Transient inactivation of left hemispheric top-down control reduced this dominance while inactivation of right hemispheric top-down control had no effect on response patterns. Functional asymmetries of descending systems that modify visual ascending pathways seem to play an important role in the superiority of the left hemisphere in experience-based visual tasks. Copyright © 2015. Published by Elsevier Ltd.

Comparative higher-order structure analysis of antibody biosimilars using combined bottom-up and top-down hydrogen-deuterium exchange mass spectrometry.

PubMed

Pan, Jingxi; Zhang, Suping; Borchers, Christoph H

2016-12-01

Hydrogen/deuterium exchange (HDX) coupled with mass spectrometry (MS) is a powerful technique for higher-order structural characterization of antibodies. Although the peptide-based bottom-up HDX approach and the protein-based top-down HDX approach have complementary advantages, the work done so far on biosimilars has involved only one or the other approach. Herein we have characterized the structures of two bevacizumab (BEV) biosimilars and compared them to the reference BEV using both methods. A sequence coverage of 87% was obtained for the heavy chain and 74% for the light chain in the bottom-up approach. The deuterium incorporation behavior of the peptic peptides from the three BEVs were compared side by side and showed no differences at various HDX time points. Top-down experiments were carried out using subzero temperature LC-MS, and the deuterium incorporation of the intact light chain and heavy chain were obtained. Top-down ETD was also performed to obtain amino acid-level HDX information that covered 100% of the light chain, but only 50% coverage is possible for the heavy chain. Consistent with the intact subunit level data, no differences were observed in the amino acid level HDX data. All these results indicate that there are no differences between the three BEV samples with respect to their high-order structures. The peptide level information from the bottom-up approach, and the residue level and intact subunit level information from the top-down approach were complementary and covered the entire antibody. Copyright © 2016 Elsevier B.V. All rights reserved.

The impact of top-down spatial attention on laterality and hemispheric asymmetry in the human parietal cortex

PubMed Central

Jeong, Su Keun; Xu, Yaoda

2016-01-01

The human parietal cortex exhibits a preference to contralaterally presented visual stimuli (i.e., laterality) as well as an asymmetry between the two hemispheres with the left parietal cortex showing greater laterality than the right. Using visual short-term memory and perceptual tasks and varying target location predictability, this study examined whether hemispheric laterality and asymmetry are fixed characteristics of the human parietal cortex or whether they are dynamic and modulated by the deployment of top-down attention to the target present hemifield. Two parietal regions were examined here that have previously been shown to be involved in visual object individuation and identification and are located in the inferior and superior intraparietal sulcus (IPS), respectively. Across three experiments, significant laterality was found in both parietal regions regardless of attentional modulation with laterality being greater in the inferior than superior IPS, consistent with their roles in object individuation and identification, respectively. Although the deployment of top-down attention had no effect on the superior IPS, it significantly increased laterality in the inferior IPS. The deployment of top-down spatial attention can thus amplify the strength of laterality in the inferior IPS. Hemispheric asymmetry, on the other hand, was absent in both brain regions and only emerged in the inferior but not the superior IPS with the deployment of top-down attention. Interestingly, the strength of hemispheric asymmetry significantly correlated with the strength of laterality in the inferior IPS. Hemispheric asymmetry thus seems to only emerge when there is a sufficient amount of laterality present in a brain region. PMID:27494544

The impact of top-down spatial attention on laterality and hemispheric asymmetry in the human parietal cortex.

PubMed

Jeong, Su Keun; Xu, Yaoda

2016-08-01

The human parietal cortex exhibits a preference to contralaterally presented visual stimuli (i.e., laterality) as well as an asymmetry between the two hemispheres with the left parietal cortex showing greater laterality than the right. Using visual short-term memory and perceptual tasks and varying target location predictability, this study examined whether hemispheric laterality and asymmetry are fixed characteristics of the human parietal cortex or whether they are dynamic and modulated by the deployment of top-down attention to the target present hemifield. Two parietal regions were examined here that have previously been shown to be involved in visual object individuation and identification and are located in the inferior and superior intraparietal sulcus (IPS), respectively. Across three experiments, significant laterality was found in both parietal regions regardless of attentional modulation with laterality being greater in the inferior than superior IPS, consistent with their roles in object individuation and identification, respectively. Although the deployment of top-down attention had no effect on the superior IPS, it significantly increased laterality in the inferior IPS. The deployment of top-down spatial attention can thus amplify the strength of laterality in the inferior IPS. Hemispheric asymmetry, on the other hand, was absent in both brain regions and only emerged in the inferior but not the superior IPS with the deployment of top-down attention. Interestingly, the strength of hemispheric asymmetry significantly correlated with the strength of laterality in the inferior IPS. Hemispheric asymmetry thus seems to only emerge when there is a sufficient amount of laterality present in a brain region.

Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions

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

Ansong, Charles; Wu, Si; Meng, Da

Characterization of the mature protein complement in cells is crucial for a better understanding of cellular processes on a systems-wide scale. Bottom-up proteomic approaches often lead to loss of critical information about an endogenous protein’s actual state due to post translational modifications (PTMs) and other processes. Top-down approaches that involve analysis of the intact protein can address this concern but present significant analytical challenges related to the separation quality needed, measurement sensitivity, and speed that result in low throughput and limited coverage. Here we used single-dimension ultra high pressure liquid chromatography mass spectrometry to investigate the comprehensive ‘intact’ proteome ofmore » the Gram negative bacterial pathogen Salmonella Typhimurium. Top-down proteomics analysis revealed 563 unique proteins including 1665 proteoforms generated by PTMs, representing the largest microbial top-down dataset reported to date. Our analysis not only confirmed several previously recognized aspects of Salmonella biology and bacterial PTMs in general, but also revealed several novel biological insights. Of particular interest was differential utilization of the protein S-thiolation forms S-glutathionylation and S-cysteinylation in response to infection-like conditions versus basal conditions, which was corroborated by changes in corresponding biosynthetic pathways. This differential utilization highlights underlying metabolic mechanisms that modulate changes in cellular signaling, and represents to our knowledge the first report of S-cysteinylation in Gram negative bacteria. The demonstrated utility of our simple proteome-wide intact protein level measurement strategy for gaining biological insight should promote broader adoption and applications of top-down proteomics approaches.« less

Dissociable effects of top-down and bottom-up attention during episodic encoding

PubMed Central

Uncapher, Melina R.; Hutchinson, J. Benjamin; Wagner, Anthony D.

2011-01-01

It is well established that the formation of memories for life’s experiences—episodic memory—is influenced by how we attend to those experiences, yet the neural mechanisms by which attention shapes episodic encoding are still unclear. We investigated how top-down and bottom-up attention contribute to memory encoding of visual objects in humans by manipulating both types of attention during functional magnetic resonance imaging (fMRI) of episodic memory formation. We show that dorsal parietal cortex—specifically, intraparietal sulcus (IPS)—was engaged during top-down attention and was also recruited during the successful formation of episodic memories. By contrast, bottom-up attention engaged ventral parietal cortex—specifically, temporoparietal junction (TPJ)—and was also more active during encoding failure. Functional connectivity analyses revealed further dissociations in how top-down and bottom-up attention influenced encoding: while both IPS and TPJ influenced activity in perceptual cortices thought to represent the information being encoded (fusiform/lateral occipital cortex), they each exerted opposite effects on memory encoding. Specifically, during a preparatory period preceding stimulus presentation, a stronger drive from IPS was associated with a higher likelihood that the subsequently attended stimulus would be encoded. By contrast, during stimulus processing, stronger connectivity with TPJ was associated with a lower likelihood the stimulus would be successfully encoded. These findings suggest that during encoding of visual objects into episodic memory, top-down and bottom-up attention can have opposite influences on perceptual areas that subserve visual object representation, suggesting that one manner in which attention modulates memory is by altering the perceptual processing of to-be-encoded stimuli. PMID:21880922

Selection history alters attentional filter settings persistently and beyond top-down control.

PubMed

Kadel, Hanna; Feldmann-Wüstefeld, Tobias; Schubö, Anna

2017-05-01

Visual selective attention is known to be guided by stimulus-based (bottom-up) and goal-oriented (top-down) control mechanisms. Recent work has pointed out that selection history (i.e., the bias to prioritize items that have been previously attended) can result in a learning experience that also has a substantial impact on subsequent attention guidance. The present study examined to what extent goal-oriented top-down control mechanisms interact with an observer's individual selection history in guiding attention. Selection history was manipulated in a categorization task in a between-subjects design, where participants learned that either color or shape was the response-relevant dimension. The impact of this experience was assessed in a compound visual search task with an additional color distractor. Top-down preparation for each search trial was enabled by a pretrial task cue (Experiment 1) or a fixed, predictable trial sequence (Experiment 2). Reaction times and ERPs served as indicators of attention deployment. Results showed that attention was captured by the color distractor when participants had learned that color predicted the correct response in the categorization learning task, suggesting that a bias for predictive stimulus features had developed. The possibility to prepare for the search task reduced the bias, but could not entirely overrule this selection history effect. In Experiment 3, both tasks were performed in separate sessions, and the bias still persisted. These results indicate that selection history considerably shapes selective attention and continues to do so persistently even when the task allowed for high top-down control. © 2017 Society for Psychophysiological Research.

The importance of an underestimated grazer under climate change: how crab density, consumer competition, and physical stress affect salt marsh resilience.

PubMed

Angelini, Christine; van Montfrans, Schuyler G; Hensel, Marc J S; He, Qiang; Silliman, Brian R

2018-05-01

Climate change and consumer outbreaks are driving ecosystem collapse worldwide. Although much research has demonstrated that these factors can interact, how heterogeneity in top-down control intensity and physical forcing modulates ecosystem resilience to climate stress remains poorly understood. Here, we explore whether the nocturnal herbivorous crab Sesarma reticulatum can control spatially dominant cordgrass (Spartina alterniflora) growth and how its top-down effects vary with crab density, drought stress, and large-scale disturbance in southeastern US salt marshes. In multiple field experiments and surveys, we show that Sesarma depresses cordgrass growth and that its effects increase in a saturating manner with increasing crab density, such that the highest naturally occurring densities of this consumer can trigger local cordgrass die-off. This top-down effect of Sesarma is similar in magnitude to what is thought to be the dominant grazer in the system, the marsh periwinkle snail Littoraria irrorata. In a drought stress by Sesarma density experiment, we further show that salinity stress and intensive crab herbivory additively suppress cordgrass drought resistance. After drought subsides, surveys and experiments reveal that Sesarma also stifles cordgrass re-growth into existing die-off areas. Together, these results show that multiple grazers powerfully regulate the productivity and drought resilience of these intertidal grasslands and that heterogeneity in physical stress and consumer density can dictate when and where top-down forcing is important. More generally, this work provides a rare, experimental demonstration of the critical role top-down control can play across the initiation and recovery stages of ecosystem die-off.

Deficits in Top-Down Sensory Prediction in Infants At Risk due to Premature Birth.

PubMed

Emberson, Lauren L; Boldin, Alex M; Riccio, Julie E; Guillet, Ronnie; Aslin, Richard N

2017-02-06

A prominent theoretical view is that the brain is inherently predictive [1, 2] and that prediction helps drive the engine of development [3, 4]. Although infants exhibit neural signatures of top-down sensory prediction [5, 6], in order to establish that prediction supports development, it must be established that deficits in early prediction abilities alter trajectories. We investigated prediction in infants born prematurely, a leading cause of neuro-cognitive impairment worldwide [7]. Prematurity, independent of medical complications, leads to developmental disturbances [8-12] and a broad range of developmental delays [13-17]. Is an alteration in early prediction abilities the common cause? Using functional near-infrared spectroscopy (fNIRS), we measured top-down sensory prediction in preterm infants (born <33 weeks gestation) before infants exhibited clinically identifiable developmental delays (6 months corrected age). Whereas preterm infants had typical neural responses to presented visual stimuli, they exhibited altered neural responses to predicted visual stimuli. Importantly, a separate behavioral control confirmed that preterm infants detect pattern violations at the same rate as full-terms, establishing selectivity of this response to top-down predictions (e.g., not in learning an audiovisual association). These findings suggest that top-down sensory prediction plays a crucial role in development and that deficits in this ability may be the reason why preterm infants experience altered developmental trajectories and are at risk for poor developmental outcomes. Moreover, this work presents an opportunity for establishing a neuro-biomarker for early identification of infants at risk and could guide early intervention regimens. Copyright © 2017 Elsevier Ltd. All rights reserved.

Large emissions from floodplain trees close the Amazon methane budget.

PubMed

Pangala, Sunitha R; Enrich-Prast, Alex; Basso, Luana S; Peixoto, Roberta Bittencourt; Bastviken, David; Hornibrook, Edward R C; Gatti, Luciana V; Marotta, Humberto; Calazans, Luana Silva Braucks; Sakuragui, Cassia Mônica; Bastos, Wanderley Rodrigues; Malm, Olaf; Gloor, Emanuel; Miller, John Bharat; Gauci, Vincent

2017-12-14

Wetlands are the largest global source of atmospheric methane (CH 4 ), a potent greenhouse gas. However, methane emission inventories from the Amazon floodplain, the largest natural geographic source of CH 4 in the tropics, consistently underestimate the atmospheric burden of CH 4 determined via remote sensing and inversion modelling, pointing to a major gap in our understanding of the contribution of these ecosystems to CH 4 emissions. Here we report CH 4 fluxes from the stems of 2,357 individual Amazonian floodplain trees from 13 locations across the central Amazon basin. We find that escape of soil gas through wetland trees is the dominant source of regional CH 4 emissions. Methane fluxes from Amazon tree stems were up to 200 times larger than emissions reported for temperate wet forests and tropical peat swamp forests, representing the largest non-ebullitive wetland fluxes observed. Emissions from trees had an average stable carbon isotope value (δ 13 C) of -66.2 ± 6.4 per mil, consistent with a soil biogenic origin. We estimate that floodplain trees emit 15.1 ± 1.8 to 21.2 ± 2.5 teragrams of CH 4 a year, in addition to the 20.5 ± 5.3 teragrams a year emitted regionally from other sources. Furthermore, we provide a 'top-down' regional estimate of CH 4 emissions of 42.7 ± 5.6 teragrams of CH 4 a year for the Amazon basin, based on regular vertical lower-troposphere CH 4 profiles covering the period 2010-2013. We find close agreement between our 'top-down' and combined 'bottom-up' estimates, indicating that large CH 4 emissions from trees adapted to permanent or seasonal inundation can account for the emission source that is required to close the Amazon CH 4 budget. Our findings demonstrate the importance of tree stem surfaces in mediating approximately half of all wetland CH 4 emissions in the Amazon floodplain, a region that represents up to one-third of the global wetland CH 4 source when trees are combined with other emission sources.

Introducing Electronic Textbooks as Daily-Use Technology in Schools: A Top-Down Adoption Process

ERIC Educational Resources Information Center

Chiu, Thomas K. F.

2017-01-01

This study took frequency of use and the adoption process into account to define the participants and external variables of the research model. School electronic textbooks are a daily-use technology and they are adopted in a compulsory, top-down way. Their introduction can evoke feelings of anxiety among teachers because of a possible increase in…

The Role of Bottom-Up Processing in Perceptual Categorization by 3- to 4-Month-Old Infants: Simulations and Data

ERIC Educational Resources Information Center

French, Robert M.; Mareschal, Denis; Mermillod, Martial; Quinn, Paul C.

2004-01-01

Disentangling bottom-up and top-down processing in adult category learning is notoriously difficult. Studying category learning in infancy provides a simple way of exploring category learning while minimizing the contribution of top-down information. Three- to 4-month-old infants presented with cat or dog images will form a perceptual category…

On the Temporal Relation of Top-Down and Bottom-Up Mechanisms during Guidance of Attention

ERIC Educational Resources Information Center

Wykowska, Agnieszka; Schubo, Anna

2010-01-01

Two mechanisms are said to be responsible for guiding focal attention in visual selection: bottom-up, saliency-driven capture and top-down control. These mechanisms were examined with a paradigm that combined a visual search task with postdisplay probe detection. Two SOAs between the search display and probe onsets were introduced to investigate…

What Would You Ideally Do if There Were No Targets? An Ethnographic Study of the Unintended Consequences of Top-Down Governance in Two Clinical Settings

ERIC Educational Resources Information Center

Allard, Jon; Bleakley, Alan

2016-01-01

Top-down policy directives, such as targets and their associated protocols, may be driven politically rather than clinically and can be described as macro-political texts. While targets supposedly provide incentives for healthcare services, they may unintentionally shape practices of accommodation rather than implementation, deflecting…

Incorporating anthropogenic effects into trophic ecology: predator-prey interactions in a human-dominated landscape.

PubMed

Dorresteijn, Ine; Schultner, Jannik; Nimmo, Dale G; Fischer, Joern; Hanspach, Jan; Kuemmerle, Tobias; Kehoe, Laura; Ritchie, Euan G

2015-09-07

Apex predators perform important functions that regulate ecosystems worldwide. However, little is known about how ecosystem regulation by predators is influenced by human activities. In particular, how important are top-down effects of predators relative to direct and indirect human-mediated bottom-up and top-down processes? Combining data on species' occurrence from camera traps and hunting records, we aimed to quantify the relative effects of top-down and bottom-up processes in shaping predator and prey distributions in a human-dominated landscape in Transylvania, Romania. By global standards this system is diverse, including apex predators (brown bear and wolf), mesopredators (red fox) and large herbivores (roe and red deer). Humans and free-ranging dogs represent additional predators in the system. Using structural equation modelling, we found that apex predators suppress lower trophic levels, especially herbivores. However, direct and indirect top-down effects of humans affected the ecosystem more strongly, influencing species at all trophic levels. Our study highlights the need to explicitly embed humans and their influences within trophic cascade theory. This will greatly expand our understanding of species interactions in human-modified landscapes, which compose the majority of the Earth's terrestrial surface. © 2015 The Author(s).

Interactive effects of trait and state affect on top-down control of attention

PubMed Central

Hur, Juyoen; Miller, Gregory A.; McDavitt, Jenika R.B.; Spielberg, Jeffrey M.; Crocker, Laura D.; Infantolino, Zachary P.; Towers, David N.; Warren, Stacie L.

2015-01-01

Few studies have investigated how attentional control is affected by transient affective states while taking individual differences in affective traits into consideration. In this study, participants completed a color-word Stroop task immediately after undergoing a positive, neutral or negative affective context manipulation (ACM). Behavioral performance was unaffected by any ACM considered in isolation. For individuals high in trait negative affect (NA), performance was impaired by the negative but not the positive or neutral ACM. Neuroimaging results indicate that activity in primarily top-down control regions of the brain (inferior frontal gyrus and dorsal anterior cingulate cortex) was suppressed in the presence of emotional arousal (both negative and positive ACMs). This effect appears to have been exacerbated or offset by co-occurring activity in other top-down control regions (parietal) and emotion processing regions (orbitofrontal cortex, amygdala and nucleus accumbens) as a function of the valence of state affect (positive or negative) and trait affect (trait NA or trait PA). Neuroimaging results are consistent with behavioral findings. In combination, they indicate both additive and interactive influences of trait and state affect on top-down control of attention. PMID:25556211

Controlled synthesis of organic single-crystalline nanowires via the synergy approach of the bottom-up/top-down processes.

PubMed

Zhuo, Ming-Peng; Zhang, Ye-Xin; Li, Zhi-Zhou; Shi, Ying-Li; Wang, Xue-Dong; Liao, Liang-Sheng

2018-03-15

The controlled fabrication of organic single-crystalline nanowires (OSCNWs) with a uniform diameter in the nanoscale via the bottom-up approach, which is just based on weak intermolecular interaction, is a great challenge. Herein, we utilize the synergy approach of the bottom-up and the top-down processes to fabricate OSCNWs with diameters of 120 ± 10 nm through stepwise evolution processes. Specifically, the evolution processes vary from the self-assembled organic micro-rods with a quadrangular pyramid-like end-structure bounded with {111}s and {11-1}s crystal planes to the "top-down" synthesized organic micro-rods with the flat cross-sectional {002}s plane, to the organic micro-tubes with a wall thickness of ∼115 nm, and finally to the organic nanowires. Notably, the anisotropic etching process caused by the protic solvent molecules (such as ethanol) is crucial for the evolution of the morphology throughout the whole top-down process. Therefore, our demonstration opens a new avenue for the controlled-fabrication of organic nanowires, and also contributes to the development of nanowire-based organic optoelectronics such as organic nanowire lasers.

Top-down Mass Spectrometry of Cardiac Myofilament Proteins in Health and Disease

PubMed Central

Ying, Peng; Serife, Ayaz-Guner; Deyang, Yu; Ying, Ge

2014-01-01

Myofilaments are composed of thin and thick filaments which coordinate with each other to regulate muscle contraction and relaxation. Posttranslational modifications (PTMs) together with genetic variations and alternative splicing of the myofilament proteins play essential roles in regulating cardiac contractility in health and disease. Therefore, a comprehensive characterization of the myofilament proteins in physiological and pathological conditions is essential for better understanding the molecular basis of cardiac function and dysfunction. Due to the vast complexity and dynamic nature of proteins, it is challenging to obtain a holistic view of myofilament protein modifications. In recent years, top-down mass spectrometry (MS) has emerged as a powerful approach to study isoform composition and PTMs of proteins owing to its advantage of complete sequence coverage and its ability to identify PTMs and sequence variants without a priori knowledge. In this review, we will discuss the application of top-down MS to study cardiac myofilaments and highlight the insights it provides into the understanding of molecular mechanisms in contractile dysfunction of heart failure. Particularly, recent results of cardiac troponin and tropomyosin modifications will be elaborated. The limitations and perspectives on the use of top-down MS for myofilament protein characterization will also be briefly discussed. PMID:24945106

Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation.

PubMed

Brodie, Nicholas I; Huguet, Romain; Zhang, Terry; Viner, Rosa; Zabrouskov, Vlad; Pan, Jingxi; Petrotchenko, Evgeniy V; Borchers, Christoph H

2018-03-06

Top-down hydrogen-deuterium exchange (HDX) analysis using electron capture or transfer dissociation Fourier transform mass spectrometry (FTMS) is a powerful method for the analysis of secondary structure of proteins in solution. The resolution of the method is a function of the degree of fragmentation of backbone bonds in the proteins. While fragmentation is usually extensive near the N- and C-termini, electron capture (ECD) or electron transfer dissociation (ETD) fragmentation methods sometimes lack good coverage of certain regions of the protein, most often in the middle of the sequence. Ultraviolet photodissociation (UVPD) is a recently developed fast-fragmentation technique, which provides extensive backbone fragmentation that can be complementary in sequence coverage to the aforementioned electron-based fragmentation techniques. Here, we explore the application of electrospray ionization (ESI)-UVPD FTMS on an Orbitrap Fusion Lumos Tribrid mass spectrometer to top-down HDX analysis of proteins. We have incorporated UVPD-specific fragment-ion types and fragment-ion mixtures into our isotopic envelope fitting software (HDX Match) for the top-down HDX analysis. We have shown that UVPD data is complementary to ETD, thus improving the overall resolution when used as a combined approach.

Top-down proteomics for the analysis of proteolytic events - Methods, applications and perspectives.

PubMed

Tholey, Andreas; Becker, Alexander

2017-11-01

Mass spectrometry based proteomics is an indispensable tool for almost all research areas relevant for the understanding of proteolytic processing, ranging from the identification of substrates, products and cleavage sites up to the analysis of structural features influencing protease activity. The majority of methods for these studies are based on bottom-up proteomics performing analysis at peptide level. As this approach is characterized by a number of pitfalls, e.g. loss of molecular information, there is an ongoing effort to establish top-down proteomics, performing separation and MS analysis both at intact protein level. We briefly introduce major approaches of bottom-up proteomics used in the field of protease research and highlight the shortcomings of these methods. We then discuss the present state-of-the-art of top-down proteomics. Together with the discussion of known challenges we show the potential of this approach and present a number of successful applications of top-down proteomics in protease research. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John. Copyright © 2017 Elsevier B.V. All rights reserved.

The Role of Competitive Inhibition and Top-Down Feedback in Binding during Object Recognition

PubMed Central

Wyatte, Dean; Herd, Seth; Mingus, Brian; O’Reilly, Randall

2012-01-01

How does the brain bind together visual features that are processed concurrently by different neurons into a unified percept suitable for processes such as object recognition? Here, we describe how simple, commonly accepted principles of neural processing can interact over time to solve the brain’s binding problem. We focus on mechanisms of neural inhibition and top-down feedback. Specifically, we describe how inhibition creates competition among neural populations that code different features, effectively suppressing irrelevant information, and thus minimizing illusory conjunctions. Top-down feedback contributes to binding in a similar manner, but by reinforcing relevant features. Together, inhibition and top-down feedback contribute to a competitive environment that ensures only the most appropriate features are bound together. We demonstrate this overall proposal using a biologically realistic neural model of vision that processes features across a hierarchy of interconnected brain areas. Finally, we argue that temporal synchrony plays only a limited role in binding – it does not simultaneously bind multiple objects, but does aid in creating additional contrast between relevant and irrelevant features. Thus, our overall theory constitutes a solution to the binding problem that relies only on simple neural principles without any binding-specific processes. PMID:22719733

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

Vyatkina, Kira; Wu, Si; Dekker, Lennard J. M.

De novo sequencing of proteins and peptides is one of the most important problems in mass spectrometry-driven proteomics. A variety of methods have been developed to accomplish this task from a set of bottom-up tandem (MS/MS) mass spectra. However, a more recently emerged top-down technology, now gaining more and more popularity, opens new perspectives for protein analysis and characterization, implying a need in efficient algorithms for processing this kind of MS/MS data. Here we describe a method that allows to retrieve from a set of top-down MS/MS spectra long and accurate sequence fragments of the proteins contained in a sample.more » To this end, we outline a strategy for generating high-quality sequence tags from top-down spectra, and introduce the concept of a T-Bruijn graph by adapting to the case of tags the notion of an A-Bruijn graph widely used in genomics. The output of the proposed approach represents the set of amino acid strings spelled out by optimal paths in the connected components of a T-Bruijn graph. We illustrate its performance on top-down datasets acquired from carbonic anhydrase 2 (CAH2) and the Fab region of alemtuzumab.« less

Incorporating anthropogenic effects into trophic ecology: predator–prey interactions in a human-dominated landscape

PubMed Central

Dorresteijn, Ine; Schultner, Jannik; Nimmo, Dale G.; Fischer, Joern; Hanspach, Jan; Kuemmerle, Tobias; Kehoe, Laura; Ritchie, Euan G.

2015-01-01

Apex predators perform important functions that regulate ecosystems worldwide. However, little is known about how ecosystem regulation by predators is influenced by human activities. In particular, how important are top-down effects of predators relative to direct and indirect human-mediated bottom-up and top-down processes? Combining data on species' occurrence from camera traps and hunting records, we aimed to quantify the relative effects of top-down and bottom-up processes in shaping predator and prey distributions in a human-dominated landscape in Transylvania, Romania. By global standards this system is diverse, including apex predators (brown bear and wolf), mesopredators (red fox) and large herbivores (roe and red deer). Humans and free-ranging dogs represent additional predators in the system. Using structural equation modelling, we found that apex predators suppress lower trophic levels, especially herbivores. However, direct and indirect top-down effects of humans affected the ecosystem more strongly, influencing species at all trophic levels. Our study highlights the need to explicitly embed humans and their influences within trophic cascade theory. This will greatly expand our understanding of species interactions in human-modified landscapes, which compose the majority of the Earth's terrestrial surface. PMID:26336169

Using response time distributions to examine top-down influences on attentional capture.

PubMed

Burnham, Bryan R

2013-02-01

Three experiments examined contingent attentional capture, which is the finding that cuing effects are larger when cues are perceptually similar to a target than when they are dissimilar to the target. This study also analyzed response times (RTs) in terms of the underlying distributions for valid cues and invalid cues. Specifically, an ex-Gaussian analysis and a vincentile analysis examined the influence of top-down attentional control settings on the shift and skew of RT distributions and how the shift and the skew contributed to the cuing effects in the mean RTs. The results showed that cue/target similarity influenced the size of cuing effects. The RT distribution analyses showed that the cuing effects reflected only a shifting effect, not a skewing effect, in the RT distribution between valid cues and invalid cues. That is, top-down attentional control moderated the cuing effects in the mean RTs through distribution shifting, not distribution skewing. The results support the contingent orienting hypothesis (Folk, Remington, & Johnston, Journal of Experimental Psychology: Human Perception and Performance, 18, 1030-1044, 1992) over the attentional disengagement account (Theeuwes, Atchley, & Kramer, 2000) as an explanation for when top-down attentional settings influence the selection of salient stimuli.

Top-Down Processes Override Bottom-Up Interference in the Flanker Task.

PubMed

Avital-Cohen, Rotem; Tsal, Yehoshua

2016-05-01

Distractor interference in the flanker task is commonly viewed as an outcome of unintentional, involuntary processing, a by-product of attention-controlled processing of the target. An important implication of this notion is that the distractors are not subjected to top-down processing of their own. We tested this idea in a modified version of the flanker task, in which letter targets (S or O) were sometimes flanked by ambiguous distractors (a character that could be S or 5 or one that could be O or 0). Distractor interference was dependent on participants' expectations regarding the category of the distractors (i.e., letters or digits). For example, the O-0 distractor interfered with responding to S when it was perceived as a letter, but not when it was perceived as a digit. Hence, participants applied top-down processing to the peripheral distractors independently of the top-down processing applied to the targets. The fact that to-be-ignored peripheral distractors were processed to such a high level raises questions regarding the fundamental differences between target and distractor processing, and the quality of attentional filtering. © The Author(s) 2016.

Sleep deprivation selectively disrupts top-down adaptation to cognitive conflict in the Stroop test.

PubMed

Gevers, Wim; Deliens, Gaetane; Hoffmann, Sophie; Notebaert, Wim; Peigneux, Philippe

2015-12-01

Sleep deprivation is known to exert detrimental effects on various cognitive domains, including attention, vigilance and working memory. Seemingly at odds with these findings, prior studies repeatedly failed to evidence an impact of prior sleep deprivation on cognitive interference in the Stroop test, a hallmark paradigm in the study of cognitive control abilities. The present study investigated further the effect of sleep deprivation on cognitive control using an adapted version of the Stroop test that allows to segregate top-down (attentional reconfiguration on incongruent items) and bottom-up (facilitated processing after repetitions in responses and/or features of stimuli) components of performance. Participants underwent a regular night of sleep or a night of total sleep deprivation before cognitive testing. Results disclosed that sleep deprivation selectively impairs top-down adaptation mechanisms: cognitive control no longer increased upon detection of response conflict at the preceding trial. In parallel, bottom-up abilities were found unaffected by sleep deprivation: beneficial effects of stimulus and response repetitions persisted. Changes in vigilance states due to sleep deprivation selectively impact on cognitive control in the Stroop test by affecting top-down, but not bottom-up, mechanisms that guide adaptive behaviours. © 2015 European Sleep Research Society.

Warming shifts top-down and bottom-up control of pond food web structure and function

PubMed Central

Shurin, Jonathan B.; Clasen, Jessica L.; Greig, Hamish S.; Kratina, Pavel; Thompson, Patrick L.

2012-01-01

The effects of global and local environmental changes are transmitted through networks of interacting organisms to shape the structure of communities and the dynamics of ecosystems. We tested the impact of elevated temperature on the top-down and bottom-up forces structuring experimental freshwater pond food webs in western Canada over 16 months. Experimental warming was crossed with treatments manipulating the presence of planktivorous fish and eutrophication through enhanced nutrient supply. We found that higher temperatures produced top-heavy food webs with lower biomass of benthic and pelagic producers, equivalent biomass of zooplankton, zoobenthos and pelagic bacteria, and more pelagic viruses. Eutrophication increased the biomass of all organisms studied, while fish had cascading positive effects on periphyton, phytoplankton and bacteria, and reduced biomass of invertebrates. Surprisingly, virus biomass was reduced in the presence of fish, suggesting the possibility for complex mechanisms of top-down control of the lytic cycle. Warming reduced the effects of eutrophication on periphyton, and magnified the already strong effects of fish on phytoplankton and bacteria. Warming, fish and nutrients all increased whole-system rates of net production despite their distinct impacts on the distribution of biomass between producers and consumers, plankton and benthos, and microbes and macrobes. Our results indicate that warming exerts a host of indirect effects on aquatic food webs mediated through shifts in the magnitudes of top-down and bottom-up forcing. PMID:23007089

Long-term tropospheric trend of octafluorocyclobutane (c-C4F8 or PFC-318)

NASA Astrophysics Data System (ADS)

Oram, D. E.; Mani, F. S.; Laube, J. C.; Newland, M. J.; Reeves, C. E.; Sturges, W. T.; Penkett, S. A.; Brenninkmeijer, C. A. M.; Röckmann, T.; Fraser, P. J.

2012-01-01

Air samples collected at Cape Grim, Tasmania between 1978 and 2008 and during a series of more recent aircraft sampling programmes have been analysed to determine the atmospheric abundance and trend of octafluorocyclobutane (c-C4F8 or PFC-318). c-C4F8 has an atmospheric lifetime in excess of 3000 yr and a global warming potential (GWP) of 10 300 (100 yr time horizon), making it one of the most potent greenhouse gases detected in the atmosphere to date. The abundance of c-C4F8 in the Southern Hemisphere has risen from 0.35 ppt in 1978 to 1.2 ppt in 2010, and is currently increasing at a rate of around 0.03 ppt yr-1. It is the third most abundant perfluorocarbon (PFC) in the present day atmosphere, behind CF4 (~75 ppt) and C2F6 (~4 ppt). Although a number of potential sources of c-C4F8 have been reported, including the electronics and semi-conductor industries, there remains a large discrepancy in the atmospheric budget. Using a 2-D global model to derive top-down global emissions based on the Cape Grim measurements yields a recent (2007) emission rate of around 1.1 Gg yr-1 and a cumulative emission up to and including 2007 of 38.1 Gg. Emissions reported on the EDGAR emissions database for the period 1986-2005 represent less than 1% of the top-down emissions for the same period, which suggests there is a large unaccounted for source of this compound. It is also apparent that the magnitude of this source has varied considerably over the past 30 yr, declining sharply in the late 1980s before increasing again in the mid-1990s.

Pneumatically Actuated Miniature Peristaltic Vacuum Pumps

NASA Technical Reports Server (NTRS)

Feldman, Sabrina; Feldman, Jason; Svehla, Danielle

2003-01-01

Pneumatically actuated miniature peristaltic vacuum pumps have been proposed for incorporation into advanced miniature versions of scientific instruments that depend on vacuum for proper operation. These pumps are expected to be capable of reaching vacuum-side pressures in the torr to millitorr range (from .133 down to .0.13 Pa). Vacuum pumps that operate in this range are often denoted roughing pumps. In comparison with previously available roughing pumps, these pumps are expected to be an order of magnitude less massive and less power-hungry. In addition, they would be extremely robust, and would operate with little or no maintenance and without need for oil or other lubricants. Portable mass spectrometers are typical examples of instruments that could incorporate the proposed pumps. In addition, the proposed pumps could be used as roughing pumps in general laboratory applications in which low pumping rates could be tolerated. The proposed pumps could be designed and fabricated in conventionally machined and micromachined versions. A typical micromachined version (see figure) would include a rigid glass, metal, or plastic substrate and two layers of silicone rubber. The bottom silicone layer would contain shallow pump channels covered by silicone arches that could be pushed down pneumatically to block the channels. The bottom silicone layer would be covered with a thin layer of material with very low gas permeability, and would be bonded to the substrate everywhere except in the channel areas. The top silicone layer would be attached to the bottom silicone layer and would contain pneumatic- actuation channels that would lie crosswise to the pump channels. This version is said to be micromachined because the two silicone layers containing the channels would be fabricated by casting silicone rubber on micromachined silicon molds. The pneumatic-actuation channels would be alternately connected to a compressed gas and (depending on pump design) either to atmospheric pressure or to a partial vacuum source. The design would be such that the higher pneumatic pressure would be sufficient to push the silicone arches down onto the substrates, blocking the channels. Thus, by connecting pneumatic- actuation channels to the two pneumatic sources in spatial and temporal alternation, waves of opening and closing, equivalent to peristalsis, could be made to move along the pump channels. A pump according to this concept could be manufactured inexpensively. Pneumatic sources (compressors and partial vacuum sources) similar those needed for actuation are commercially available; they typically have masses of .100 g and power demands of the order of several W. In a design-optimization effort, it should be possible to reduce masses and power demands below even these low levels and to integrate pneumatic sources along with the proposed pumps into miniature units with overall dimensions of no more than a few centimeters per side.

Top-down and Bottom-up aerosol-cloud-closure: towards understanding sources of unvertainty in deriving cloud radiative flux

NASA Astrophysics Data System (ADS)

Sanchez, K.; Roberts, G.; Calmer, R.; Nicoll, K.; Hashimshoni, E.; Rosenfeld, D.; Ovadnevaite, J.; Preissler, J.; Ceburnis, D.; O'Dowd, C. D. D.; Russell, L. M.

2017-12-01

Top-down and bottom-up aerosol-cloud shortwave radiative flux closures were conducted at the Mace Head atmospheric research station in Galway, Ireland in August 2015. Instrument platforms include ground-based, unmanned aerial vehicles (UAV), and satellite measurements of aerosols, clouds and meteorological variables. The ground-based and airborne measurements of aerosol size distributions and cloud condensation nuclei (CCN) concentration were used to initiate a 1D microphysical aerosol-cloud parcel model (ACPM). UAVs were equipped for a specific science mission, with an optical particle counter for aerosol distribution profiles, a cloud sensor to measure cloud extinction, or a 5-hole probe for 3D wind vectors. These are the first UAV measurements at Mace Head. ACPM simulations are compared to in-situ cloud extinction measurements from UAVs to quantify closure in terms of cloud shortwave radiative flux. Two out of seven cases exhibit sub-adiabatic vertical temperature profiles within the cloud, which suggests that entrainment processes affect cloud microphysical properties and lead to an overestimate of simulated cloud shortwave radiative flux. Including an entrainment parameterization and explicitly calculating the entrainment fraction in the ACPM simulations both improved cloud-top radiative closure. Entrainment reduced the difference between simulated and observation-derived cloud-top shortwave radiative flux (δRF) by between 25 W m-2 and 60 W m-2. After accounting for entrainment, satellite-derived cloud droplet number concentrations (CDNC) were within 30% of simulated CDNC. In cases with a well-mixed boundary layer, δRF is no greater than 20 W m-2 after accounting for cloud-top entrainment, and up to 50 W m-2 when entrainment is not taken into account. In cases with a decoupled boundary layer, cloud microphysical properties are inconsistent with ground-based aerosol measurements, as expected, and δRF is as high as 88 W m-2, even high (> 30 W m-2) after accounting for cloud-top entrainment. This work demonstrates the need to take in-situ measurements of aerosol properties for cases where the boundary layer is decoupled as well as consider cloud-top entrainment to accurately model stratocumulus cloud radiative flux.

Top-down and Bottom-up aerosol-cloud-closure: towards understanding sources of unvertainty in deriving cloud radiative flux

NASA Astrophysics Data System (ADS)

Sanchez, K.; Roberts, G.; Calmer, R.; Nicoll, K.; Hashimshoni, E.; Rosenfeld, D.; Ovadnevaite, J.; Preissler, J.; Ceburnis, D.; O'Dowd, C. D. D.; Russell, L. M.

2016-12-01

Top-down and bottom-up aerosol-cloud shortwave radiative flux closures were conducted at the Mace Head atmospheric research station in Galway, Ireland in August 2015. Instrument platforms include ground-based, unmanned aerial vehicles (UAV), and satellite measurements of aerosols, clouds and meteorological variables. The ground-based and airborne measurements of aerosol size distributions and cloud condensation nuclei (CCN) concentration were used to initiate a 1D microphysical aerosol-cloud parcel model (ACPM). UAVs were equipped for a specific science mission, with an optical particle counter for aerosol distribution profiles, a cloud sensor to measure cloud extinction, or a 5-hole probe for 3D wind vectors. These are the first UAV measurements at Mace Head. ACPM simulations are compared to in-situ cloud extinction measurements from UAVs to quantify closure in terms of cloud shortwave radiative flux. Two out of seven cases exhibit sub-adiabatic vertical temperature profiles within the cloud, which suggests that entrainment processes affect cloud microphysical properties and lead to an overestimate of simulated cloud shortwave radiative flux. Including an entrainment parameterization and explicitly calculating the entrainment fraction in the ACPM simulations both improved cloud-top radiative closure. Entrainment reduced the difference between simulated and observation-derived cloud-top shortwave radiative flux (δRF) by between 25 W m-2 and 60 W m-2. After accounting for entrainment, satellite-derived cloud droplet number concentrations (CDNC) were within 30% of simulated CDNC. In cases with a well-mixed boundary layer, δRF is no greater than 20 W m-2 after accounting for cloud-top entrainment, and up to 50 W m-2 when entrainment is not taken into account. In cases with a decoupled boundary layer, cloud microphysical properties are inconsistent with ground-based aerosol measurements, as expected, and δRF is as high as 88 W m-2, even high (> 30 W m-2) after accounting for cloud-top entrainment. This work demonstrates the need to take in-situ measurements of aerosol properties for cases where the boundary layer is decoupled as well as consider cloud-top entrainment to accurately model stratocumulus cloud radiative flux.

Estimating Anthropogenic Emissions of Hydrogen Chloride and Fine Particulate Chloride in China

NASA Astrophysics Data System (ADS)

Fu, X.; Wang, T.; Wang, S.; Zhang, L.

2017-12-01

Nitryl chloride (ClNO2) can significantly impact the atmospheric photochemistry via photolysis and subsequent reactions of chlorine radical with other gases. The formation of ClNO2 in the atmosphere is sensitive to the emissions of chlorine-containing particulates from oceanic and anthropogenic sources. For China, the only available anthropogenic chlorine emission inventory was compiled for the year 1990 with a coarse resolution of 1 degree. In this study, we developed an up-to-date anthropogenic inventory of hydrogen chloride (HCl) and fine particulate chloride (Cl-) emissions in China for the year 2014, including coal burning, industrial processes, biomass burning and waste burning. Bottom-up and top-down methodologies were combined. Detailed local data (e.g. Cl content in coal, control technologies, etc.) were collected and applied. In order to improve the spatial resolution of emissions, detailed point source information were collected for coal-fired power plants, cement factories, iron & steel factories and waste incineration factories. Uncertainties of this emission inventory and their major causes were analyzed using the Monte Carlo method. This work enables better quantification of the ClNO2 production and impact over China.

Predator transitory spillover induces trophic cascades in ecological sinks

PubMed Central

Casini, Michele; Blenckner, Thorsten; Möllmann, Christian; Gårdmark, Anna; Lindegren, Martin; Llope, Marcos; Kornilovs, Georgs; Plikshs, Maris; Stenseth, Nils Christian

2012-01-01

Understanding the effects of cross-system fluxes is fundamental in ecosystem ecology and biological conservation. Source-sink dynamics and spillover processes may link adjacent ecosystems by movement of organisms across system boundaries. However, effects of temporal variability in these cross-system fluxes on a whole marine ecosystem structure have not yet been presented. Here we show, using 35 y of multitrophic data series from the Baltic Sea, that transitory spillover of the top-predator cod from its main distribution area produces cascading effects in the whole food web of an adjacent and semi-isolated ecosystem. At varying population size, cod expand/contract their distribution range and invade/retreat from the neighboring Gulf of Riga, thereby affecting the local prey population of herring and, indirectly, zooplankton and phytoplankton via top-down control. The Gulf of Riga can be considered for cod a “true sink” habitat, where in the absence of immigration from the source areas of the central Baltic Sea the cod population goes extinct due to the absence of suitable spawning grounds. Our results add a metaecosystem perspective to the ongoing intense scientific debate on the key role of top predators in structuring natural systems. The integration of regional and local processes is central to predict species and ecosystem responses to future climate changes and ongoing anthropogenic disturbances. PMID:22505739

The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics.

PubMed

Lyon, Yana A; Riggs, Dylan; Fornelli, Luca; Compton, Philip D; Julian, Ryan R

2018-01-01

Analysis of whole proteins by mass spectrometry, or top-down proteomics, has several advantages over methods relying on proteolysis. For example, proteoforms can be unambiguously identified and examined. However, from a gas-phase ion-chemistry perspective, proteins are enormous molecules that present novel challenges relative to peptide analysis. Herein, the statistics of cleaving the peptide backbone multiple times are examined to evaluate the inherent propensity for generating internal versus terminal ions. The raw statistics reveal an inherent bias favoring production of terminal ions, which holds true regardless of protein size. Importantly, even if the full suite of internal ions is generated by statistical dissociation, terminal ions are predicted to account for at least 50% of the total ion current, regardless of protein size, if there are three backbone dissociations or fewer. Top-down analysis should therefore be a viable approach for examining proteins of significant size. Comparison of the purely statistical analysis with actual top-down data derived from ultraviolet photodissociation (UVPD) and higher-energy collisional dissociation (HCD) reveals that terminal ions account for much of the total ion current in both experiments. Terminal ion production is more favored in UVPD relative to HCD, which is likely due to differences in the mechanisms controlling fragmentation. Importantly, internal ions are not found to dominate from either the theoretical or experimental point of view. Graphical abstract ᅟ.

Scaled CMOS Reliability and Considerations for Spacecraft Systems: Bottom-Up and Top-Down Perspective

NASA Technical Reports Server (NTRS)

White, Mark

2012-01-01

New space missions will increasingly rely on more advanced technologies because of system requirements for higher performance, particularly in instruments and high-speed processing. Component-level reliability challenges with scaled CMOS in spacecraft systems from a bottom-up perspective have been presented. Fundamental Front-end and Back-end processing reliability issues with more aggressively scaled parts have been discussed. Effective thermal management from system-level to the componentlevel (top-down) is a key element in overall design of reliable systems. Thermal management in space systems must consider a wide range of issues, including thermal loading of many different components, and frequent temperature cycling of some systems. Both perspectives (top-down and bottom-up) play a large role in robust, reliable spacecraft system design.

Top-down and bottom-up: Front to back. Comment on "Move me, astonish me... delight my eyes and brain: The Vienna Integrated Model of top-down and bottom-up processes in Art Perception (VIMAP) and corresponding affective, evaluative, and neurophysiological correlates" by Matthew Pelowski et al.

NASA Astrophysics Data System (ADS)

Nadal, Marcos; Skov, Martin

2017-07-01

The model presented here [1] is the latest in an evolving series of psychological models aimed at explaining the experience of art, first proposed by Leder and colleagues [2]. The aim of this new version is to ;explicitly connect early bottom-up, artwork-derived processing sequence and outputs to top-down, viewer-derived contribution to the processing sequence; [1, p. 5f & 6]. The ;meeting; of these two processing sequences, the authors contend, is crucial to the understanding of people's responses to art [sections 3.6ff & 4], and therefore the new model's principal motivation.

[Empowerment and health promotion programming].

PubMed

Laverack, G

2008-12-01

Health promotion often presents a tension between "bottom up" and "top down" programming. "Bottom-up" is associated with community empowerment and begins on issues of concern to particular groups or individuals and regards an increase in overall control as an important element of the health outcome. "Top-down" is associated with disease prevention efforts and begins by seeking to involve beneficiaries on issues defined by health agencies. It regards improvements in health behaviours or bio-medical indicators as the important outcome and community empowerment is viewed simply as a means to the end of health behaviour change. The tension between these two approaches is not unresolvable, and this article presents a framework, the "parallel-track", intended to assist health promotion practitioners to systematically accommodate community empowerment goals within "top-down" health programming.

The need for harmonization of methods for finding locations and magnitudes of air pollution sources using observations of concentrations and wind fields

NASA Astrophysics Data System (ADS)

Hanna, Steven R.; Young, George S.

2017-01-01

What do the terms "top-down", "inverse", "backwards", "adjoint", "sensor data fusion", "receptor", "source term estimation (STE)", to name several appearing in the current literature, have in common? These varied terms are used by different disciplines to describe the same general methodology - the use of observations of air pollutant concentrations and knowledge of wind fields to identify air pollutant source locations and/or magnitudes. Academic journals are publishing increasing numbers of papers on this topic. Examples of scenarios related to this growing interest, ordered from small scale to large scale, are: use of real-time samplers to quickly estimate the location of a toxic gas release by a terrorist at a large public gathering (e.g., Haupt et al., 2009);

Top-Down Control of Visual Attention by the Prefrontal Cortex. Functional Specialization and Long-Range Interactions

PubMed Central

Paneri, Sofia; Gregoriou, Georgia G.

2017-01-01

The ability to select information that is relevant to current behavioral goals is the hallmark of voluntary attention and an essential part of our cognition. Attention tasks are a prime example to study at the neuronal level, how task related information can be selectively processed in the brain while irrelevant information is filtered out. Whereas, numerous studies have focused on elucidating the mechanisms of visual attention at the single neuron and population level in the visual cortices, considerably less work has been devoted to deciphering the distinct contribution of higher-order brain areas, which are known to be critical for the employment of attention. Among these areas, the prefrontal cortex (PFC) has long been considered a source of top-down signals that bias selection in early visual areas in favor of the attended features. Here, we review recent experimental data that support the role of PFC in attention. We examine the existing evidence for functional specialization within PFC and we discuss how long-range interactions between PFC subregions and posterior visual areas may be implemented in the brain and contribute to the attentional modulation of different measures of neural activity in visual cortices. PMID:29033784

Predictive coding in autism spectrum disorder and attention deficit hyperactivity disorder.

PubMed

Gonzalez-Gadea, Maria Luz; Chennu, Srivas; Bekinschtein, Tristan A; Rattazzi, Alexia; Beraudi, Ana; Tripicchio, Paula; Moyano, Beatriz; Soffita, Yamila; Steinberg, Laura; Adolfi, Federico; Sigman, Mariano; Marino, Julian; Manes, Facundo; Ibanez, Agustin

2015-11-01

Predictive coding has been proposed as a framework to understand neural processes in neuropsychiatric disorders. We used this approach to describe mechanisms responsible for attentional abnormalities in autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD). We monitored brain dynamics of 59 children (8-15 yr old) who had ASD or ADHD or who were control participants via high-density electroencephalography. We performed analysis at the scalp and source-space levels while participants listened to standard and deviant tone sequences. Through task instructions, we manipulated top-down expectation by presenting expected and unexpected deviant sequences. Children with ASD showed reduced superior frontal cortex (FC) responses to unexpected events but increased dorsolateral prefrontal cortex (PFC) activation to expected events. In contrast, children with ADHD exhibited reduced cortical responses in superior FC to expected events but strong PFC activation to unexpected events. Moreover, neural abnormalities were associated with specific control mechanisms, namely, inhibitory control in ASD and set-shifting in ADHD. Based on the predictive coding account, top-down expectation abnormalities could be attributed to a disproportionate reliance (precision) allocated to prior beliefs in ASD and to sensory input in ADHD. Copyright © 2015 the American Physiological Society.

Predictive coding in autism spectrum disorder and attention deficit hyperactivity disorder

PubMed Central

Gonzalez-Gadea, Maria Luz; Chennu, Srivas; Bekinschtein, Tristan A.; Rattazzi, Alexia; Beraudi, Ana; Tripicchio, Paula; Moyano, Beatriz; Soffita, Yamila; Steinberg, Laura; Adolfi, Federico; Sigman, Mariano; Marino, Julian; Manes, Facundo

2015-01-01

Predictive coding has been proposed as a framework to understand neural processes in neuropsychiatric disorders. We used this approach to describe mechanisms responsible for attentional abnormalities in autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD). We monitored brain dynamics of 59 children (8–15 yr old) who had ASD or ADHD or who were control participants via high-density electroencephalography. We performed analysis at the scalp and source-space levels while participants listened to standard and deviant tone sequences. Through task instructions, we manipulated top-down expectation by presenting expected and unexpected deviant sequences. Children with ASD showed reduced superior frontal cortex (FC) responses to unexpected events but increased dorsolateral prefrontal cortex (PFC) activation to expected events. In contrast, children with ADHD exhibited reduced cortical responses in superior FC to expected events but strong PFC activation to unexpected events. Moreover, neural abnormalities were associated with specific control mechanisms, namely, inhibitory control in ASD and set-shifting in ADHD. Based on the predictive coding account, top-down expectation abnormalities could be attributed to a disproportionate reliance (precision) allocated to prior beliefs in ASD and to sensory input in ADHD. PMID:26311184

Electrophysiological evidence for cognitive control during conflict processing in visual spatial attention.

PubMed

Kehrer, Stefanie; Kraft, Antje; Irlbacher, Kerstin; Koch, Stefan P; Hagendorf, Herbert; Kathmann, Norbert; Brandt, Stephan A

2009-11-01

Event-related potentials were measured to investigate the role of visual spatial attention mechanisms in conflict processing. We suggested that a more difficult target selection leads to stronger attentional top-down control, thereby reducing the effects of arising conflicts. This hypothesis was tested by varying the selection difficulty in a location negative priming (NP) paradigm. The difficult task resulted in prolonged responses as compared to the easy task. A behavioral NP effect was only evident in the easy task. Psychophysiologically the easy task was associated with reduced parietal N1, enhanced frontocentral N2 and N2pc components and a prolonged P3 latency for the conflict as compared to the control condition. The N2pc effect was also obvious in the difficult task. Additionally frontocentral N2 amplitudes increased and latencies of N2pc and P3 were delayed compared to the easy task. The differences at frontocentral and parietal electrodes are consistent with previous studies ascribing activity in the prefrontal and parietal cortex as the source of top-down attentional control. Thus, we propose that stronger cognitive control is involved in the difficult task, resulting in a reduced behavioral NP conflict.

Top-Down Control of Visual Attention by the Prefrontal Cortex. Functional Specialization and Long-Range Interactions.

PubMed

Paneri, Sofia; Gregoriou, Georgia G

2017-01-01

The ability to select information that is relevant to current behavioral goals is the hallmark of voluntary attention and an essential part of our cognition. Attention tasks are a prime example to study at the neuronal level, how task related information can be selectively processed in the brain while irrelevant information is filtered out. Whereas, numerous studies have focused on elucidating the mechanisms of visual attention at the single neuron and population level in the visual cortices, considerably less work has been devoted to deciphering the distinct contribution of higher-order brain areas, which are known to be critical for the employment of attention. Among these areas, the prefrontal cortex (PFC) has long been considered a source of top-down signals that bias selection in early visual areas in favor of the attended features. Here, we review recent experimental data that support the role of PFC in attention. We examine the existing evidence for functional specialization within PFC and we discuss how long-range interactions between PFC subregions and posterior visual areas may be implemented in the brain and contribute to the attentional modulation of different measures of neural activity in visual cortices.

Direct Top-down Estimates of Biomass Burning CO Emissions Using TES and MOPITT Versus Bottom-up GFED Inventory

NASA Technical Reports Server (NTRS)

Pechony, Olga; Shindell, Drew T.; Faluvegi, Greg

2013-01-01

In this study, we utilize near-simultaneous observations from two sets of multiple satellite sensors to segregate Tropospheric Emission Spectrometer (TES) and Measurements of Pollution in the Troposphere (MOPITT) CO observations over active fire sources from those made over clear background. Hence, we obtain direct estimates of biomass burning CO emissions without invoking inverse modeling as in traditional top-down methods. We find considerable differences between Global Fire Emissions Database (GFED) versions 2.1 and 3.1 and satellite-based emission estimates in many regions. Both inventories appear to greatly underestimate South and Southeast Asia emissions, for example. On global scales, however, CO emissions in both inventories and in the MOPITT-based analysis agree reasonably well, with the largest bias (30%) found in the Northern Hemisphere spring. In the Southern Hemisphere, there is a one-month shift between the GFED and MOPITT-based fire emissions peak. Afternoon tropical fire emissions retrieved from TES are about two times higher than the morning MOPITT retrievals. This appears to be both a real difference due to the diurnal fire activity variations, and a bias due to the scarcity of TES data.

Laboratory Formation of Fullerenes from PAHs: Top-down Interstellar Chemistry

NASA Astrophysics Data System (ADS)

Zhen, Junfeng; Castellanos, Pablo; Paardekooper, Daniel M.; Linnartz, Harold; Tielens, Alexander G. G. M.

2014-12-01

Interstellar molecules are thought to build up in the shielded environment of molecular clouds or in the envelope of evolved stars. This follows many sequential reaction steps of atoms and simple molecules in the gas phase and/or on (icy) grain surfaces. However, these chemical routes are highly inefficient for larger species in the tenuous environment of space as many steps are involved and, indeed, models fail to explain the observed high abundances. This is definitely the case for the C60 fullerene, recently identified as one of the most complex molecules in the interstellar medium. Observations have shown that, in some photodissociation regions, its abundance increases close to strong UV-sources. In this Letter we report laboratory findings in which C60 formation can be explained by characterizing the photochemical evolution of large polycyclic aromatic hydrocarbons (PAHs). Sequential H losses lead to fully dehydrogenated PAHs and subsequent losses of C2 units convert graphene into cages. Our results present for the first time experimental evidence that PAHs in excess of 60 C-atoms efficiently photo-isomerize to buckminsterfullerene, C60. These laboratory studies also attest to the importance of top-down synthesis routes for chemical complexity in space.

Large-scale inverse and forward modeling of adaptive resonance in the tinnitus decompensation.

PubMed

Low, Yin Fen; Trenado, Carlos; Delb, Wolfgang; D'Amelio, Roberto; Falkai, Peter; Strauss, Daniel J

2006-01-01

Neural correlates of psychophysiological tinnitus models in humans may be used for their neurophysiological validation as well as for their refinement and improvement to better understand the pathogenesis of the tinnitus decompensation and to develop new therapeutic approaches. In this paper we make use of neural correlates of top-down projections, particularly, a recently introduced synchronization stability measure, together with a multiscale evoked response potential (ERP) model in order to study and evaluate the tinnitus decompensation by using a hybrid inverse-forward mathematical methodology. The neural synchronization stability, which according to the underlying model is linked to the focus of attention on the tinnitus signal, follows the experimental and inverse way and allows to discriminate between a group of compensated and decompensated tinnitus patients. The multiscale ERP model, which works in the forward direction, is used to consolidate hypotheses which are derived from the experiments for a known neural source dynamics related to attention. It is concluded that both methodologies agree and support each other in the description of the discriminatory character of the neural correlate proposed, but also help to fill the gap between the top-down adaptive resonance theory and the Jastreboff model of tinnitus.

Protistan Predation Affects Trichloroethene Biodegradation in a Bedrock Aquifer▿

PubMed Central

Cunningham, Joseph J.; Kinner, Nancy E.; Lewis, Maureen

2009-01-01

Despite extensive research on the bottom-up force of resource availability (e.g., electron donors and acceptors), slow biodegradation rates and stalling at cis-dichloroethene (cDCE) and vinyl chloride continue to be observed in aquifers contaminated with trichloroethene (TCE). The objective of this research was to gauge the impact of the top-down force of protistan predation on TCE biodegradation in laboratory microcosms. When indigenous bacteria from an electron donor-limited TCE-contaminated bedrock aquifer were present, the indigenous protists inhibited reductive dechlorination altogether. The presence of protists during organic carbon-amended conditions caused the bacteria to elongate (length:width, ≥10:1), but reductive dechlorination was still inhibited. When a commercially available dechlorinating bacterial culture and an organic carbon amendment were added in he presence of protists, the elongated bacteria predominated and reductive dechlorination stalled at cDCE. When protists were removed under organic carbon-amended conditions, reductive dechlorination stalled at cDCE, whereas in the presence organic carbon and bacterial amendments, the total chlorinated ethene concentration decreased, indicating TCE was converted to ethene and/or CO2. The data suggested that indigenous protists grazed dechlorinators to extremely low levels, inhibiting dechlorination altogether. Hence, in situ bioremediation/bioaugmentation may not be successful in mineralizing TCE unless the top-down force of protistan predation is inhibited. PMID:19820148

Comparing bottom-up and top-down approaches at the landscape scale, including agricultural activities and water systems, at the Roskilde Fjord, Denmark

NASA Astrophysics Data System (ADS)

Lequy, Emeline; Ibrom, Andreas; Ambus, Per; Massad, Raia-Silvia; Markager, Stiig; Asmala, Eero; Garnier, Josette; Gabrielle, Benoit; Loubet, Benjamin

2015-04-01

The greenhouse gas nitrous oxide (N2O) mainly originates in direct emissions from agricultural soils due to microbial reactions stimulated by the use of nitrogen fertilisers. Indirect N2O emissions from water systems due to nitrogen leaching and deposition from crop fields range between 26 and 37% of direct agricultural emissions, indicating their potential importance and uncertainty (Reay et al. 2012). The study presented here couples a top-down approach with eddy covariance (EC) and a bottom-up approach using different models and measurements. A QCL sensor at 96-m height on a tall tower measures the emissions of N2O from 1100 ha of crop fields and from the south part of the Roskilde fjord, in a 5-km radius area around the tall tower at Roskilde, Denmark. The bottom-up approach includes ecosystem modelling with CERES-EGC for the crops and PaSIM for the grasslands, and the N2O fluxes from the Roskilde fjord are derived from N2O sea water concentration measurements. EC measurements are now available from July to December 2014, and indicate a magnitude of the emissions from the crop fields around 0.2 mg N2O-N m-2 day-1 (range -9 to 5) which is consistent with the CERES-EGC simulations and calculations using IPCC emission factors. N2O fluxes from the Roskilde fjord in May and July indicated quite constant N2O concentrations around 0.1 µg N L-1 despite variations of nitrate and ammonium in the fjord. The calculated fluxes from these concentrations and the tall tower measurements consistently ranged between -7 and 6 mg N2O-N m-2 day-1. The study site also contains a waste water treatment plant, whose direct emissions will be measured in early 2015 using a dynamic plume tracer dispersion method (Mønster et al. 2014). A refined source attribution methodology together with more measurements and simulations of the N2O fluxes from the different land uses in this study site will provide a clearer view of the dynamics and budgets of N2O at the regional scale. The complementarity between these bottom-up and top-down approaches and their usefulness to disentangle direct and indirect N2O fluxes will also be discussed. Acknowledgements: This work was funded by the EU-FP7 InGOS project. References: Mønster JG, Samuelsson J, Kjeldsen P, Rella CW, Scheutz C. Quantifying methane emission from fugitive sources by combining tracer release and downwind measurements - A sensitivity analysis based on multiple field surveys. Waste Management. 2014 Aug;34(8):1416-28. Reay DS, Davidson EA, Smith KA, Smith P, Melillo JM, Dentener F, et al. Global agriculture and nitrous oxide emissions. Nature Clim Change. 2012 Jun;2(6):410-6.

50. THIRD FLOOR, HALL, LOOKING SOUTH. Note ceiling extends down ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

50. THIRD FLOOR, HALL, LOOKING SOUTH. Note ceiling extends down over window case and exterior frieze extends halfway down top light of sash - Robinson-Aiken House, 48 Elizabeth Street, Charleston, Charleston County, SC

Top-down venomics of the East African green mamba, Dendroaspis angusticeps, and the black mamba, Dendroaspis polylepis, highlight the complexity of their toxin arsenals.

PubMed

Petras, Daniel; Heiss, Paul; Harrison, Robert A; Süssmuth, Roderich D; Calvete, Juan J

2016-09-02

We report the characterization, by combination of high-resolution on-line molecular mass and disulfide bond profiling and top-down MS/MS analysis, of the venom proteomes of two congeneric African snake species of medical importance, Dendroaspis angusticeps (green mamba) and D. polylepis (black mamba). Each of these mamba venoms comprised more than two-hundred polypeptides belonging to just a few toxin families. Both venom proteomes are overwhelmingly composed of post-synaptically-acting short- and long-chain neurotoxins that potently inhibit muscle- and neuronal-type nicotinic acetylcholine receptors; muscarinic cardiotoxins; and dendrotoxins, that block some of the Kv1, n-class of K+ channels. However, the identity of the major proteins and their relative abundances exhibit marked interspecific variation. In addition, the greater resolution of the top-down venomic analytical approach revealed previously undetected protein species, isoforms and proteoforms, including the identification and precise location of modified lysine residues in a number of proteins in both venoms, but particularly in green mamba toxins. This comparative top-down venomic analysis unveiled the untapped complexity of Dendroaspis venoms and lays the foundations for rationalizing the notably different potency of green and black mamba lethal arsenals at locus resolution. We report the characterization, by combination of high-resolution on-line molecular mass and disulfide bond profiling and top-down MS/MS analysis, of the venom proteomes of two congeneric African snake species of medical importance, Dendroaspis angusticeps (green mamba) and D. polylepis (black mamba). Each of these mamba venoms comprised more than two-hundred polypeptides belonging to just a few toxin families. Both venom proteomes are overwhelmingly composed of post-synaptically-acting short- and long-chain neurotoxins that potently inhibit muscle- and neuronal-type nicotinic acetylcholine receptors; muscarinic cardiotoxins; and dendrotoxins, that block some of the Kv1, n-class of K+ channels. However, the identity of the major proteins and their relative abundances exhibit marked interspecific variation. In addition, the greater resolution of the top-down venomic analytical approach revealed previously undetected protein species, isoforms and proteoforms, including the identification and precise location of modified lysine residues in a number of proteins in both venoms, but particularly in green mamba toxins. This comparative top-down venomic analysis unveiled the untapped complexity of Dendroaspis venoms and lays the foundations for rationalizing the notably different potency of green and black mamba lethal arsenals at locus resolution.

A study of the mechanical vibrations of a table-top extreme ultraviolet interference nanolithography tool.

PubMed

Prezioso, S; De Marco, P; Zuppella, P; Santucci, S; Ottaviano, L

2010-04-01

A prototype low cost table-top extreme ultraviolet (EUV) laser source (1.5 ns pulse duration, lambda=46.9 nm) was successfully employed as a laboratory scale interference nanolithography (INL) tool. Interference patterns were obtained with a simple Lloyd's mirror setup. Periodic structures on Polymethylmethacrylate/Si substrates were produced on large areas (8 mm(2)) with resolutions from 400 to 22.5 nm half pitch (the smallest resolution achieved so far with table-top EUV laser sources). The mechanical vibrations affecting both the laser source and Lloyd's setup were studied to determine if and how they affect the lateral resolution of the lithographic system. The vibration dynamics was described by a statistical model based on the assumption that the instantaneous position of the vibrating mechanical parts follows a normal distribution. An algorithm was developed to simulate the process of sample irradiation under different vibrations. The comparison between simulations and experiments allowed to estimate the characteristic amplitude of vibrations that was deduced to be lower than 50 nm. The same algorithm was used to reproduce the expected pattern profiles in the lambda/4 half pitch physical resolution limit. In that limit, a nonzero pattern modulation amplitude was obtained from the simulations, comparable to the peak-to-valley height (2-3 nm) measured for the 45 nm spaced fringes, indicating that the mechanical vibrations affecting the INL tool do not represent a limit in scaling down the resolution.

Effect of Light Availability on the Interaction between Maritime Pine and the Pine Weevil: Light Drives Insect Feeding Behavior But Also the Defensive Capabilities of the Host

PubMed Central

Suárez-Vidal, Estefanía; López-Goldar, Xosé; Sampedro, Luis; Zas, Rafael

2017-01-01

Light is a major environmental factor that may determine the interaction between plants and herbivores in several ways, including top-down effects through changes in herbivore behavior and bottom-up effects mediated by alterations of plant physiology. Here we explored the relative contribution of these two regulation processes to the outcome of the interaction of pine trees with a major forest pest, the pine weevil (Hylobius abietis). We studied to what extent light availability influence insect feeding behavior and/or the ability of pines to produce induced defenses in response to herbivory. For this purpose, 3-year old Pinus pinaster plants from three contrasting populations were subjected to 6 days of experimental herbivory by the pine weevil under two levels of light availability (complete darkness or natural sunlight) independently applied to the plant and to the insect in a fully factorial design. Light availability strongly affected the pine weevil feeding behavior. The pine weevil fed more and caused larger feeding scars in darkness than under natural sunlight. Besides, under the more intense levels of weevil damage (i.e., those registered with insects in darkness), light availability also affected the pine’s ability to respond to insect feeding by producing induced resin defenses. These results were consistent across the three studied populations despite they differed in weevil susceptibility and inducibility of defenses. Morocco was the most damaged population and the one that induced more defensive compounds. Overall, results indicate that light availability modulates the outcome of the pine–weevil interactions through both bottom-up and top-down regulation mechanisms. PMID:28912787

Congruency effects in the remote distractor paradigm: evidence for top-down modulation.

PubMed

Born, Sabine; Kerzel, Dirk

2009-08-10

In three experiments, we examined effects of target-distractor similarity in the remote distractor effect (RDE). Observers made saccades to peripheral targets that were either gray or green. Foveal or peripheral distractors were presented at the same time. The distractors could either share the target's defining property (congruent) or be different from the target (incongruent). Congruent distractors slowed down saccadic reaction times more than incongruent distractors. The increase of the RDE with target-distractor congruency depended on task demands. The more participants had to rely on the target property to locate the target, the larger the congruency effect. We conclude that the RDE can be modulated in a top-down manner. Alternative explanations such as persisting memory traces for the target property or differences in stimulus arrangement were considered but discarded. Our claim is in line with models of saccade generation which assume that the structures underlying the RDE (e.g. the superior colliculus) receive bottom-up as well as top-down information.

Bottom-up effects of host-plant species diversity and top-down effects of ants interactively increase plant performance

PubMed Central

Moreira, Xoaquín; Mooney, Kailen A.; Zas, Rafael; Sampedro, Luis

2012-01-01

While plant diversity is well known to increase primary productivity, whether these bottom-up effects are enhanced by reciprocal top-down effects from the third trophic level is unknown. We studied whether pine tree species diversity, aphid-tending ants and their interaction determined plant performance and arthropod community structure. Plant diversity had a positive effect on aphids, but only in the presence of mutualistic ants, leading to a threefold greater number of both groups in the tri-specific cultures than in monocultures. Plant diversity increased ant abundance not only by increasing aphid number, but also by increasing ant recruitment per aphid. The positive effect of diversity on ants in turn cascaded down to increase plant performance; diversity increased plant growth (but not biomass), and this effect was stronger in the presence of ants. Consequently, bottom-up effects of diversity within the same genus and guild of plants, and top-down effects from the third trophic level (predatory ants), interactively increased plant performance. PMID:22951745

Top-emitting white organic light-emitting devices with down-conversion phosphors: theory and experiment.

PubMed

Ji, Wenyu; Zhang, Letian; Gao, Ruixue; Zhang, Liming; Xie, Wenfa; Zhang, Hanzhuang; Li, Bin

2008-09-29

White top-emitting organic light-emitting devices (TEOLEDs) with down-conversion phosphors are investigated from theory and experiment. The theoretical simulation was described by combining the microcavity model with the down-conversion model. A White TEOLED by the combination of a blue TEOLED with organic down-conversion phosphor 3-(4-(diphenylamino)phenyl)-1-pheny1prop-2-en-1-one was fabricated to validate the simulated results. It is shown that this approach permits the generation of white light in TEOLEDs. The efficiency of the white TEOLED is twice over the corresponding blue TEOLED. The feasible methods to improve the performance of such white TEOLEDs are discussed.

A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom

PubMed Central

Trevisan-Silva, Dilza; Bednaski, Aline V.; Fischer, Juliana S.G.; Veiga, Silvio S.; Bandeira, Nuno; Guthals, Adrian; Marchini, Fabricio K.; Leprevost, Felipe V.; Barbosa, Valmir C.; Senff-Ribeiro, Andrea; Carvalho, Paulo C.

2017-01-01

Venoms are a rich source for the discovery of molecules with biotechnological applications, but their analysis is challenging even for state-of-the-art proteomics. Here we report on a large-scale proteomic assessment of the venom of Loxosceles intermedia, the so-called brown spider. Venom was extracted from 200 spiders and fractioned into two aliquots relative to a 10 kDa cutoff mass. Each of these was further fractioned and digested with trypsin (4 h), trypsin (18 h), pepsin (18 h), and chymotrypsin (18 h), then analyzed by MudPIT on an LTQ-Orbitrap XL ETD mass spectrometer fragmenting precursors by CID, HCD, and ETD. Aliquots of undigested samples were also analyzed. Our experimental design allowed us to apply spectral networks, thus enabling us to obtain meta-contig assemblies, and consequently de novo sequencing of practically complete proteins, culminating in a deep proteome assessment of the venom. Data are available via ProteomeXchange, with identifier PXD005523. PMID:28696408

A Preliminary Study of Perfectionism and Loneliness as Predictors of Depressive and Anxious Symptoms in Latinas: A Top-Down Test of a Model

ERIC Educational Resources Information Center

Chang, Edward C.; Hirsch, Jameson K.; Sanna, Lawrence J.; Jeglic, Elizabeth L.; Fabian, Cathryn G.

2011-01-01

In the present study, we used a top-down approach to examine perfectionism and loneliness as additive sociocognitive predictors of depressive and anxious symptoms in a sample of 121 Latina college students. Consistent with expectations, we found perfectionism and loneliness to be associated with both depressive and anxious symptoms. In addition,…

Top-down proteomic identification of Shiga toxin 2 subtypes from Shiga toxin-producing Escherichia coli by Matrix-Assisted Laser Desorption Ionization-Tandem Time of Flight mass spectrometry

USDA-ARS?s Scientific Manuscript database

We have analyzed 26 Shiga toxin-producing Escherichia coli (STEC) strains for Shiga toxin 2 (Stx2) production using matrix-assisted laser desorption/ionization time-of-flight-time-of-flight tandem mass spectrometry (MALDI-TOF-TOF-MS/MS) and top-down proteomic analysis. STEC strains were induced to ...

When Seeing Depends on Knowing: Adults with Autism Spectrum Conditions Show Diminished Top-Down Processes in the Visual Perception of Degraded Faces but Not Degraded Objects

ERIC Educational Resources Information Center

Loth, Eva; Gomez, Juan Carlos; Happe, Francesca

2010-01-01

Behavioural, neuroimaging and neurophysiological approaches emphasise the active and constructive nature of visual perception, determined not solely by the environmental input, but modulated top-down by prior knowledge. For example, degraded images, which at first appear as meaningless "blobs", can easily be recognized as, say, a face, after…

Sediment unmixing using detrital geochronology

USGS Publications Warehouse

Sharman, Glenn R.; Johnstone, Samuel

2017-01-01

Sediment mixing within sediment routing systems can exert a strong influence on the preservation of provenance signals that yield insight into the influence of environmental forcings (e.g., tectonism, climate) on the earth’s surface. Here we discuss two approaches to unmixing detrital geochronologic data in an effort to characterize complex changes in the sedimentary record. First we summarize ‘top-down’ mixing, which has been successfully employed in the past to characterize the different fractions of prescribed source distributions (‘parents’) that characterize a derived sample or set of samples (‘daughters’). Second we propose the use of ‘bottom-up’ methods, previously used primarily for grain size distributions, to model parent distributions and the abundances of these parents within a set of daughters. We demonstrate the utility of both top-down and bottom-up approaches to unmixing detrital geochronologic data within a well-constrained sediment routing system in central California. Use of a variety of goodness-of-fit metrics in top-down modeling reveals the importance of considering the range of allowable mixtures over any single best-fit mixture calculation. Bottom-up modeling of 12 daughter samples from beaches and submarine canyons yields modeled parent distributions that are remarkably similar to those expected from the geologic context of the sediment-routing system. In general, mixture modeling has potential to supplement more widely applied approaches in comparing detrital geochronologic data by casting differences between samples as differing proportions of geologically meaningful end-member provenance categories.

Bottom-up and top-down controls on picoplankton in the East China Sea

NASA Astrophysics Data System (ADS)

Guo, C.; Liu, H.; Zheng, L.; Song, S.; Chen, B.; Huang, B.

2013-05-01

Dynamics of picoplankton population distribution in the East China Sea (ECS), a marginal sea in the western North Pacific Ocean, were studied during two "CHOICE-C" cruises in August 2009 (summer) and January 2010 (winter). Dilution experiments were conducted during the two cruises to investigate the growth and grazing among picophytoplantkon populations. Picoplankton accounted for an average of ~29% (2% to 88%) of community carbon biomass in the ECS on average, with lower percentages in plume region than in shelf and kuroshio regions. Averaged growth rates (μ) for Prochlorococcus (Pro), Synechococcus (Syn) and picoeukaryotes (peuk) were 0.36, 0.89, 0.90 d-1, respectively, in summer, and 0.46, 0.58, 0.56 d-1, respectively, in winter. Seawater salinity and nutrient availability exerted significant controls on picoplankton growth rate. Averaged grazing mortality (m) were 0.46, 0.63, 0.68 d-1 in summer, and 0.22, 0.32, 0.22 d-1 in winter for Pro, Syn and peuk respectively. The three populations demonstrated very different distribution patterns regionally and seasonally affected by both bottom-up and top-down controls. In summer, Pro, Syn and peuk were dominant in Kuroshio, transitional and plume regions respectively. Protist grazing consumed 84%, 78%, 73% and 45%, 47%, 57% of production for Pro, Syn and peuk in summer and winter respectively, suggesting more significant top-down controls in summer. In winter, all three populations tended to distribute in offshore regions, although the area of coverage was different (peuk > Syn > Pro). Bottom-up factors can explain as much as 91.5%, 82% and 81.2% of Pro, Syn and peuk abundance variance in winter, while only 59.1% and 43.7% for Pro and peuk in summer. Regionally, Yangtze River discharge plays a significant role in affecting the intensity of top-down control, indicated by significant and negative association between salinity and grazing mortality of all three populations and higher grazing mortality to growth rate ratio (m / μ) in plume region than Kuroshio region in summer. The gradient of bottom-up factors caused by Yangtze River input and Kuroshio warm current intrusion also exerted important influence on picoplankton abundance evidenced by the significant correlations. Vertically, picoplankton exhibited highest abundance at subsurface layer around 20 m thick in summer, while at surface in winter. Both growth rate and grazing mortality were higher at surface than at the deep chlorophyll maximum (DCM) layer. Our study first systematically described the bottom-up and top-down regulations of different picoplankton populations between contrasting seasons, different depths, and among different regions in the ECS, which provide insights for better understanding the population dynamics of picoplankton and trophic transfer in microbial food web in highly dynamic shelf ecosystems and in general.

Triple dissociation of duration perception regulating mechanisms: Top-down attention is inherent.

PubMed

Lin, Yong-Jun; Shimojo, Shinsuke

2017-01-01

The brain constantly adjusts perceived duration based on the recent event history. One such lab phenomenon is subjective time expansion induced in an oddball paradigm ("oddball chronostasis"), where the duration of a distinct item (oddball) appears subjectively longer when embedded in a series of other repeated items (standards). Three hypotheses have been separately proposed but it remains unresolved which or all of them are true: 1) attention prolongs oddball duration, 2) repetition suppression reduces standards duration, and 3) accumulative temporal preparation (anticipation) expedites the perceived item onset so as to lengthen its duration. We thus conducted critical systematic experiments to dissociate the relative contribution of all hypotheses, by orthogonally manipulating sequences types (repeated, ordered, or random) and target serial positions. Participants' task was to judge whether a target lasts shorter or longer than its reference. The main finding was that a random item sequence still elicited significant chronostasis even though each item was odd. That is, simply being a target draws top-down attention and induces chronostasis. In Experiments 1 (digits) and 2 (orientations), top-down attention explained about half of the effect while saliency/adaptation explained the other half. Additionally, for non-repeated (ordered and random) sequence types, a target with later serial position still elicited stronger chronostasis, favoring a temporal preparation over a repetition suppression account. By contrast, in Experiment 3 (colors), top-down attention was likely the sole factor. Consequently, top-down attention is necessary and sometimes sufficient to explain oddball chronostasis; saliency/adaptation and temporal preparation are contingent factors. These critical boundary conditions revealed in our study serve as quantitative constraints for neural models of duration perception.

Optimization of synthesis process of thermally-responsive poly-n-isopropylacrylamide nanoparticles for controlled release of antimicrobial hydrophobic compounds

NASA Astrophysics Data System (ADS)

Hill, Laura E.; Gomes, Carmen L.

2014-12-01

The goal of this study was to develop an effective method to synthesize poly-n-isopropylacrylamide (PNIPAAM) nanoparticles with entrapped cinnamon bark extract (CBE) to improve its delivery to foodborne pathogens and control its release with temperature stimuli. CBE was used as a model for hydrophobic natural antimicrobials. A top-down procedure using crosslinked PNIPAAM was compared to a bottom-up procedure using NIPAAM monomer. Both processes relied on self-assembly of the molecules into micelles around the CBE at 40 °C. Processing conditions were compared including homogenization time of the polymer, hydration time prior to homogenization, lyophilization, and the effect of particle ultrafiltration. The top-down versus bottom-up synthesis methods yielded particles with significantly different characteristics, especially their release profiles and antimicrobial activities. The synthesis methods affected particle size, with the bottom-up procedure resulting in smaller (P < 0.05) diameters than the top-down procedure. The controlled release profile of CBE from nanoparticles was dependent on the release media temperature. A faster, burst release was observed at 40 °C and a slower, more sustained release was observed at lower temperatures. PNIPAAM particles containing CBE were analyzed for their antimicrobial activity against Salmonella enterica serovar Typhimurium LT2 and Listeria monocytogenes Scott A. The PNIPAAM particles synthesized via the top-down procedure had a much faster release, which led to a greater (P < 0.05) antimicrobial activity. Both of the top-down nanoparticles performed similarly, therefore the 7 min homogenization time nanoparticles would be the best for this application, as the process time is shorter and little improvement was seen by using a slightly longer homogenization.

The role of top-down spatial attention in contingent attentional capture.

PubMed

Huang, Wanyi; Su, Yuling; Zhen, Yanfen; Qu, Zhe

2016-05-01

It is well known that attentional capture by an irrelevant salient item is contingent on top-down feature selection, but whether attentional capture may be modulated by top-down spatial attention remains unclear. Here, we combined behavioral and ERP measurements to investigate the contribution of top-down spatial attention to attentional capture under modified spatial cueing paradigms. Each target stimulus was preceded by a peripheral circular cue array containing a spatially uninformative color singleton cue. We varied target sets but kept the cue array unchanged among different experimental conditions. When participants' task was to search for a colored letter in the target array that shared the same peripheral locations with the cue array, attentional capture by the peripheral color cue was reflected by both a behavioral spatial cueing effect and a cue-elicited N2pc component. When target arrays were presented more centrally, both the behavioral and N2pc effects were attenuated but still significant. The attenuated cue-elicited N2pc was found even when participants focused their attention on the fixed central location to identify a colored letter among an RSVP letter stream. By contrast, when participants were asked to identify an outlined or larger target, neither the behavioral spatial cueing effect nor the cue-elicited N2pc was observed, regardless of whether the target and cue arrays shared same locations or not. These results add to the evidence that attentional capture by salient stimuli is contingent upon feature-based task sets, and further indicate that top-down spatial attention is important but may not be necessary for contingent attentional capture. © 2016 Society for Psychophysiological Research.

Nano-LC FTICR tandem mass spectrometry for top-down proteomics: routine baseline unit mass resolution of whole cell lysate proteins up to 72 kDa.

PubMed

Tipton, Jeremiah D; Tran, John C; Catherman, Adam D; Ahlf, Dorothy R; Durbin, Kenneth R; Lee, Ji Eun; Kellie, John F; Kelleher, Neil L; Hendrickson, Christopher L; Marshall, Alan G

2012-03-06

Current high-throughput top-down proteomic platforms provide routine identification of proteins less than 25 kDa with 4-D separations. This short communication reports the application of technological developments over the past few years that improve protein identification and characterization for masses greater than 25 kDa. Advances in separation science have allowed increased numbers of proteins to be identified, especially by nanoliquid chromatography (nLC) prior to mass spectrometry (MS) analysis. Further, a goal of high-throughput top-down proteomics is to extend the mass range for routine nLC MS analysis up to 80 kDa because gene sequence analysis predicts that ~70% of the human proteome is transcribed to be less than 80 kDa. Normally, large proteins greater than 50 kDa are identified and characterized by top-down proteomics through fraction collection and direct infusion at relatively low throughput. Further, other MS-based techniques provide top-down protein characterization, however at low resolution for intact mass measurement. Here, we present analysis of standard (up to 78 kDa) and whole cell lysate proteins by Fourier transform ion cyclotron resonance mass spectrometry (nLC electrospray ionization (ESI) FTICR MS). The separation platform reduced the complexity of the protein matrix so that, at 14.5 T, proteins from whole cell lysate up to 72 kDa are baseline mass resolved on a nano-LC chromatographic time scale. Further, the results document routine identification of proteins at improved throughput based on accurate mass measurement (less than 10 ppm mass error) of precursor and fragment ions for proteins up to 50 kDa.

Top-Down Dysregulation—From ADHD to Emotional Instability

PubMed Central

Petrovic, Predrag; Castellanos, F. Xavier

2016-01-01

Deficient cognitive top-down executive control has long been hypothesized to underlie inattention and impulsivity in attention-deficit/hyperactivity disorder (ADHD). However, top-down cognitive dysfunction explains a modest proportion of the ADHD phenotype whereas the salience of emotional dysregulation is being noted increasingly. Together, these two types of dysfunction have the potential to account for more of the phenotypic variance in patients diagnosed with ADHD. We develop this idea and suggest that top-down dysregulation constitutes a gradient extending from mostly non-emotional top-down control processes (i.e., “cool” executive functions) to mainly emotional regulatory processes (including “hot” executive functions). While ADHD has been classically linked primarily to the former, conditions involving emotional instability such as borderline and antisocial personality disorder are closer to the other. In this model, emotional subtypes of ADHD are located at intermediate levels of this gradient. Neuroanatomically, gradations in “cool” processing appear to be related to prefrontal dysfunction involving dorsolateral prefrontal cortex (dlPFC) and caudal anterior cingulate cortex (cACC), while “hot” processing entails orbitofrontal cortex and rostral anterior cingulate cortex (rACC). A similar distinction between systems related to non-emotional and emotional processing appears to hold for the basal ganglia (BG) and the neuromodulatory effects of the dopamine system. Overall we suggest that these two systems could be divided according to whether they process non-emotional information related to the exteroceptive environment (associated with “cool” regulatory circuits) or emotional information related to the interoceptive environment (associated with “hot” regulatory circuits). We propose that this framework can integrate ADHD, emotional traits in ADHD, borderline and antisocial personality disorder into a related cluster of mental conditions. PMID:27242456

Developing a Comprehensive and Comparative Questionnaire for Measuring Personality in Chimpanzees Using a Simultaneous Top-Down/Bottom-Up Design

PubMed Central

Freeman, Hani D.; Brosnan, Sarah F.; Hopper, Lydia M.; Lambeth, Susan P.; Schapiro, Steven J.; Gosling, Samuel D.

2013-01-01

One effective method for measuring personality in primates is to use personality trait ratings to distill the experience of people familiar with the individual animals. Previous rating instruments were created using either top-down or bottom-up approaches. Top-down approaches, which essentially adapt instruments originally designed for use with another species, can unfortunately lead to the inclusion of traits irrelevant to chimpanzees or fail to include all relevant aspects of chimpanzee personality. Conversely, because bottom-up approaches derive traits specifically for chimpanzees, their unique items may impede comparisons with findings in other studies and other species. To address the limitations of each approach, we developed a new personality rating scale using a combined top-down/bottom-up design. Seventeen raters rated 99 chimpanzees on the new 41-item scale, with all but one item being rated reliably. Principal components analysis, using both varimax and direct oblimin rotations, identified six broad factors. Strong evidence was found for five of the factors (Reactivity/Undependability, Dominance, Openness, Extraversion, and Agreeableness). A sixth factor (Methodical) was offered provisionally until more data are collected. We validated the factors against behavioral data collected independently on the chimpanzees. The five factors demonstrated good evidence for convergent and predictive validity, thereby underscoring the robustness of the factors. Our combined top-down/ bottom-up approach provides the most extensive data to date to support the universal existence of these five personality factors in chimpanzees. This framework, which facilitates cross-species comparisons, can also play a vital role in understanding the evolution of personality and can assist with husbandry and welfare efforts. PMID:23733359

Don't be fooled! Attentional responses to social cues in a face-to-face and video magic trick reveals greater top-down control for overt than covert attention.

PubMed

Kuhn, Gustav; Teszka, Robert; Tenaw, Natalia; Kingstone, Alan

2016-01-01

People's attention is oriented towards faces, but the extent to which these social attention effects are under top down control is more ambiguous. Our first aim was to measure and compare, in real life and in the lab, people's top-down control over overt and covert shifts in reflexive social attention to the face of another. We employed a magic trick in which the magician used social cues (i.e. asking a question whilst establishing eye contact) to misdirect attention towards his face, and thus preventing participants from noticing a visible colour change to a playing card. Our results show that overall people spend more time looking at the magician's face when he is seen on video than in reality. Additionally, although most participants looked at the magician's face when misdirected, this tendency to look at the face was modulated by instruction (i.e., "keep your attention on the cards"), and therefore, by top down control. Moreover, while the card's colour change was fully visible, the majority of participants failed to notice the change, and critically, change detection (our measure of covert attention) was not affected by where people looked (overt attention). We conclude that there is a tendency to shift overt and covert attention reflexively to faces, but that people exert more top down control over this overt shift in attention. These finding are discussed within a new framework that focuses on the role of eye movements as an attentional process as well as a form of non-verbal communication. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantum optics with single nanodiamonds flying over gold films: Towards a Robust quantum plasmonics

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

Mollet, O.; Drezet, A.; Huant, S.

2013-12-04

A nanodiamond (ND) hosting nitrogen-vacancy (NV) color centers is attached on the apex of an optical tip for near-field microscopy. Its fluorescence is used to launch surface plasmon-polaritons (SPPs) in a thin polycrystalline gold film. It is shown that the quantum nature of the initial source of light is preserved after conversion to SPPs. This opens the way to a deterministic quantum plasmonics, where single SPPs can be injected at well-defined positions in a plasmonic device produced by top-down approaches.

Characterization of a low-level unknown isomeric degradation product using an integrated online-offline top-down tandem mass spectrometry platform.

PubMed

Yu, Xiang; Warme, Christopher; Lee, Dinah; Zhang, Jing; Zhong, Wendy

2013-10-01

An integrated online-offline platform was developed combining automated online LC-MS fraction collection, continuous accumulation of selected ions (CASI), and offline top-down electron capture dissociation (ECD) tandem mass spectrometry experiments to identify a low-level, unknown isomeric degradant in a formulated drug product during an accelerated stability study. By identifying the diagnostic ions of the isoaspartic acid (isoAsp), the top-down ECD experiment showed that the Asp9 in exenatide was converted to isoAsp9 to form the unknown isomeric degradant. The platform described here provides an accurate, straightforward, and low limit of detection method for the analysis of Asp isomerization as well as other potential low-level degradants in therapeutic polypeptides and proteins. It is especially useful for unstable and time-sensitive degradants and impurities.

Interpreting Chicken-Scratch: Lexical Access for Handwritten Words

PubMed Central

Barnhart, Anthony S.; Goldinger, Stephen D.

2014-01-01

Handwritten word recognition is a field of study that has largely been neglected in the psychological literature, despite its prevalence in society. Whereas studies of spoken word recognition almost exclusively employ natural, human voices as stimuli, studies of visual word recognition use synthetic typefaces, thus simplifying the process of word recognition. The current study examined the effects of handwriting on a series of lexical variables thought to influence bottom-up and top-down processing, including word frequency, regularity, bidirectional consistency, and imageability. The results suggest that the natural physical ambiguity of handwritten stimuli forces a greater reliance on top-down processes, because almost all effects were magnified, relative to conditions with computer print. These findings suggest that processes of word perception naturally adapt to handwriting, compensating for physical ambiguity by increasing top-down feedback. PMID:20695708

A top-down approach to heliostat cost reduction

NASA Astrophysics Data System (ADS)

Larmuth, James N.; Landamn, Willem A.; Gauché, Paul

2016-05-01

The Technology Innovation Agency (TIA) has funded a South African central receiver collector technology development project, called Helio100. The project aims to provide South Africa's first commercially viable heliostat technology, which is both low in cost and offers high local content potential. A top-down approach is employed for heliostat cost reduction. This approach incorporates interlinked tools which move from high level cost analyses based on qualitative data during early stages of conceptual design, to detailed quantitative analyses in the final stages of design. Low cost heliostat designs are realized by the incorporation of both a top-down and bottom-up method. The current H100 design results in heliostat costs of 155/m2 at 20 000 units p.a. while further industrialisation results in heliostat costs of 126/m2 at 20 000 units.

Scaled CMOS Reliability and Considerations for Spacecraft Systems : Bottom-Up and Top-Down Perspectives

NASA Technical Reports Server (NTRS)

White, Mark

2012-01-01

The recently launched Mars Science Laboratory (MSL) flagship mission, named Curiosity, is the most complex rover ever built by NASA and is scheduled to touch down on the red planet in August, 2012 in Gale Crater. The rover and its instruments will have to endure the harsh environments of the surface of Mars to fulfill its main science objectives. Such complex systems require reliable microelectronic components coupled with adequate component and system-level design margins. Reliability aspects of these elements of the spacecraft system are presented from bottom- up and top-down perspectives.

A community-based prevention program in western Norway. Organisation and progression model.

PubMed

Skutle, Arvid; Iversen, Erik; Bergan, Tone

2002-01-01

This paper presents the organisation, progression, and main findings from a community-based substance use prevention project in five municipalities in western Norway. At the central level, this project was organised with a steering committee and a principal project leader, who is situated at the Department of Health and Social Welfare at the county level. Locally, the way of organizing differed, as one would expect from the community-based model. Top-down/bottom-up strategies can apply both in the way a community organises its efforts, as well as in the relationship between the central project organisation and the participating local communities. It is argued that it can be beneficial for the success of community action programs if one attains a "good mix" between top-down and bottom-up strategies. Factors of importance for such "mix" in the Hordaland project were that the municipalities applied for participation, the availability of economic funding, the venues for meetings between central and local project management, the position of local coordinators, the possibilities for coupling project work to otherwise existing community planning, and the extent of formal bureaucracy.

Quasi-perfect FIFO: Synchronous or asynchronous with application in controller design for the UNICON laser memory. [digital memory and buffer storage

NASA Technical Reports Server (NTRS)

Lim, R. S.

1974-01-01

The first-in-first-out memory buffer (FIFO), is an elastic digital memory whose main application is in data buffering between devices operating at different rates. Data written into the top is moved autonomously down toward the bottom of the FIFO to the lowest unoccupied location, and data read from the bottom of the FIFO will cause data from the top to move autonomously down toward the bottom. The FIFO is available in MOS LSI asynchronous form with data rate in the 1 MHz region. The FIFO described yields a simple high-speed iterative implementation, either synchronous of asynchronous. Because of this simple iterative structure, the FIFO is expandable in both number of words and bits per word, and it is attractive from the viewpoint of integrated-circuit production. For the synchronous FIFO, a model was built and successfully used in the controller for the UNICON laser memory. For the asynchronous FIFO, a model was built and also successfully used in a high-performance magnetic tape controller.

Explaining Meiji Japans Top Down Revolution

DTIC Science & Technology

2017-12-01

enabled Japan to become a great power also provides insights into how Japan became what it is today—an economically strong but militarily weak country...top- down nature of the Japanese revolution allowed for effective decision-making that centralized domestic politics and boosted economic ...other road focuses on changes made to compete with the West in the economic and military realm. Since Meiji Japan began in reaction to hostile Western

Change Levers for Unifying Top-Down and Bottom-Up Approaches to the Adoption and Diffusion of e-Learning in Higher Education

ERIC Educational Resources Information Center

Singh, Gurmak; Hardaker, Glenn

2017-01-01

Using Giddens' theory of structuration as a theoretical framework, this paper outlines how five prominent United Kingdom universities aimed to integrate top-down and bottom-up approaches to the adoption and diffusion of e-learning. The aim of this paper is to examine the major challenges that arise from the convergence of bottom-up perspectives…

Large-Eddy Simulation in Planetary Boundary-Layer Research

NASA Technical Reports Server (NTRS)

Wyngaard, J. C.

1985-01-01

The structure and dynamics of the convective boundary layer are discussed. The vertical transport of a conservative, passive scalar was simulated. Also studied were the statistics by top-down and bottom-up scalar fields. Substantial differences were found between them due, presumably, to the asymmetry in the convective boundary layer. A generalization of mixed-layer scaling was developed which allows one to include the effects of top-down diffusion.

Sodium-cutting: a new top-down approach to cut open nanostructures on nonplanar surfaces on a large scale.

PubMed

Chen, Wei; Deng, Da

2014-11-11

We report a new, low-cost and simple top-down approach, "sodium-cutting", to cut and open nanostructures deposited on a nonplanar surface on a large scale. The feasibility of sodium-cutting was demonstrated with the successfully cutting open of ∼100% carbon nanospheres into nanobowls on a large scale from Sn@C nanospheres for the first time.

What Top-Down Task Sets Do for Us: An ERP Study on the Benefits of Advance Preparation in Visual Search

ERIC Educational Resources Information Center

Eimer, Martin; Kiss, Monika; Nicholas, Susan

2011-01-01

When target-defining features are specified in advance, attentional target selection in visual search is controlled by preparatory top-down task sets. We used ERP measures to study voluntary target selection in the absence of such feature-specific task sets, and to compare it to selection that is guided by advance knowledge about target features.…

Subjective Well-Being: The Constructionist Point of View. A Longitudinal Study to Verify the Predictive Power of Top-Down Effects and Bottom-Up Processes

ERIC Educational Resources Information Center

Leonardi, Fabio; Spazzafumo, Liana; Marcellini, Fiorella

2005-01-01

Based on the constructionist point of view applied to Subjective Well-Being (SWB), five hypotheses were advanced about the predictive power of the top-down effects and bottom-up processes over a five years period. The sample consisted of 297 respondents, which represent the Italian sample of a European longitudinal survey; the first phase was…

Methods, Tools, and Data for Coastal System Resilience Assessments

DTIC Science & Technology

2015-10-06

Baseline Resilience Indicators for Communities ( BRIC ) BUILDING STRONG® Innovative solutions for a safer, better world ► T: SoVI® – Social...address policy  Objective, although data may be arbitrarily weighted in an index Examples: Top-Down (T) and Bottom-Up (B) Bottom-UpTop-Down BRIC ...Coastal Resilience Index USACE’s Resilience Matrix ASCE’s Infrastructure Report Card T: Baseline Resilience Index for Communities ( BRIC

Controllable Fabrication of GeSi Nanowires in Diameter of About 10 nm Using the Top-Down Approach

NASA Astrophysics Data System (ADS)

Zeng, Cheng; Li, Yi; Xia, Jin-Song

2017-11-01

Not Available Supported by the State Key Program of the National Natural Science Foundation of China under Grant No 61335002, the National High Technology Research and Development Program of China under Grant No 2015AA016904, the National Natural Science Foundation of China under Grant No 11574102, and the National Basic Research Program of China under Grant Nos 2013CB933303 and 2013CB632104.

Monolithic multinozzle emitters for nanoelectrospray mass spectrometry

DOEpatents

Wang, Daojing [Daly City, CA; Yang, Peidong [Kensington, CA; Kim, Woong [Seoul, KR; Fan, Rong [Pasadena, CA

2011-09-20

Novel and significantly simplified procedures for fabrication of fully integrated nanoelectrospray emitters have been described. For nanofabricated monolithic multinozzle emitters (NM.sup.2 emitters), a bottom up approach using silicon nanowires on a silicon sliver is used. For microfabricated monolithic multinozzle emitters (M.sup.3 emitters), a top down approach using MEMS techniques on silicon wafers is used. The emitters have performance comparable to that of commercially-available silica capillary emitters for nanoelectrospray mass spectrometry.

The Primary Visual Cortex Is Differentially Modulated by Stimulus-Driven and Top-Down Attention

PubMed Central

Bekisz, Marek; Bogdan, Wojciech; Ghazaryan, Anaida; Waleszczyk, Wioletta J.; Kublik, Ewa; Wróbel, Andrzej

2016-01-01

Selective attention can be focused either volitionally, by top-down signals derived from task demands, or automatically, by bottom-up signals from salient stimuli. Because the brain mechanisms that underlie these two attention processes are poorly understood, we recorded local field potentials (LFPs) from primary visual cortical areas of cats as they performed stimulus-driven and anticipatory discrimination tasks. Consistent with our previous observations, in both tasks, we found enhanced beta activity, which we have postulated may serve as an attention carrier. We characterized the functional organization of task-related beta activity by (i) cortical responses (EPs) evoked by electrical stimulation of the optic chiasm and (ii) intracortical LFP correlations. During the anticipatory task, peripheral stimulation that was preceded by high-amplitude beta oscillations evoked large-amplitude EPs compared with EPs that followed low-amplitude beta. In contrast, during the stimulus-driven task, cortical EPs preceded by high-amplitude beta oscillations were, on average, smaller than those preceded by low-amplitude beta. Analysis of the correlations between the different recording sites revealed that beta activation maps were heterogeneous during the bottom-up task and homogeneous for the top-down task. We conclude that bottom-up attention activates cortical visual areas in a mosaic-like pattern, whereas top-down attentional modulation results in spatially homogeneous excitation. PMID:26730705

Validity of the top-down approach of inverse dynamics analysis in fast and large rotational trunk movements.

PubMed

Iino, Yoichi; Kojima, Takeji

2012-08-01

This study investigated the validity of the top-down approach of inverse dynamics analysis in fast and large rotational movements of the trunk about three orthogonal axes of the pelvis for nine male collegiate students. The maximum angles of the upper trunk relative to the pelvis were approximately 47°, 49°, 32°, and 55° for lateral bending, flexion, extension, and axial rotation, respectively, with maximum angular velocities of 209°/s, 201°/s, 145°/s, and 288°/s, respectively. The pelvic moments about the axes during the movements were determined using the top-down and bottom-up approaches of inverse dynamics and compared between the two approaches. Three body segment inertial parameter sets were estimated using anthropometric data sets (Ae et al., Biomechanism 11, 1992; De Leva, J Biomech, 1996; Dumas et al., J Biomech, 2007). The root-mean-square errors of the moments and the absolute errors of the peaks of the moments were generally smaller than 10 N·m. The results suggest that the pelvic moment in motions involving fast and large trunk movements can be determined with a certain level of validity using the top-down approach in which the trunk is modeled as two or three rigid-link segments.

Top-down dimensional weight set determines the capture of visual attention: evidence from the PCN component.

PubMed

Töllner, Thomas; Müller, Hermann J; Zehetleitner, Michael

2012-07-01

Visual search for feature singletons is slowed when a task-irrelevant, but more salient distracter singleton is concurrently presented. While there is a consensus that this distracter interference effect can be influenced by internal system settings, it remains controversial at what stage of processing this influence starts to affect visual coding. Advocates of the "stimulus-driven" view maintain that the initial sweep of visual processing is entirely driven by physical stimulus attributes and that top-down settings can bias visual processing only after selection of the most salient item. By contrast, opponents argue that top-down expectancies can alter the initial selection priority, so that focal attention is "not automatically" shifted to the location exhibiting the highest feature contrast. To precisely trace the allocation of focal attention, we analyzed the Posterior-Contralateral-Negativity (PCN) in a task in which the likelihood (expectancy) with which a distracter occurred was systematically varied. Our results show that both high (vs. low) distracter expectancy and experiencing a distracter on the previous trial speed up the timing of the target-elicited PCN. Importantly, there was no distracter-elicited PCN, indicating that participants did not shift attention to the distracter before selecting the target. This pattern unambiguously demonstrates that preattentive vision is top-down modifiable.

A Robust Two-Dimensional Separation for Top-Down Tandem Mass Spectrometry of the Low-Mass Proteome

PubMed Central

Lee, Ji Eun; Kellie, John F.; Tran, John C.; Tipton, Jeremiah D.; Catherman, Adam D.; Thomas, Haylee M.; Ahlf, Dorothy R.; Durbin, Kenneth R.; Vellaichamy, Adaikkalam; Ntai, Ioanna; Marshall, Alan G.; Kelleher, Neil L.

2010-01-01

For fractionation of intact proteins by molecular weight (MW), a sharply improved two-dimensional (2D) separation is presented to drive reproducible and robust fractionation before top-down mass spectrometry of complex mixtures. The “GELFrEE” (i.e., gel-eluted liquid fraction entrapment electrophoresis) approach is implemented by use of Tris-glycine and Tris-tricine gel systems applied to human cytosolic and nuclear extracts from HeLa S3 cells, to achieve a MW-based fractionation of proteins from 5 to >100 kDa in 1 h. For top-down tandem mass spectroscopy (MS/MS) of the low-mass proteome (5–25 kDa), between 5 and 8 gel-elution (GE) fractions are sampled by nanocapillary-LC-MS/MS with 12 or 14.5 tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers. Single injections give about 40 detectable proteins, about half of which yield automated ProSight identifications. Reproducibility metrics of the system are presented, along with comparative analysis of protein targets in mitotic versus asynchronous cells. We forward this basic 2D approach to facilitate wider implementation of top-down mass spectrometry and a variety of other protein separation and/or characterization approaches. PMID:19747844

Top Down Proteomics Reveals Mature Proteoforms Expressed in Subcellular Fractions of the Echinococcus granulosus Preadult Stage.

PubMed

Lorenzatto, Karina R; Kim, Kyunggon; Ntai, Ioanna; Paludo, Gabriela P; Camargo de Lima, Jeferson; Thomas, Paul M; Kelleher, Neil L; Ferreira, Henrique B

2015-11-06

Echinococcus granulosus is the causative agent of cystic hydatid disease, a neglected zoonosis responsible for high morbidity and mortality. Several molecular mechanisms underlying parasite biology remain poorly understood. Here, E. granulosus subcellular fractions were analyzed by top down and bottom up proteomics for protein identification and characterization of co-translational and post-translational modifications (CTMs and PTMs, respectively). Nuclear and cytosolic extracts of E. granulosus protoscoleces were fractionated by 10% GELFrEE and proteins under 30 kDa were analyzed by LC-MS/MS. By top down analysis, 186 proteins and 207 proteoforms were identified, of which 122 and 52 proteoforms were exclusively detected in nuclear and cytosolic fractions, respectively. CTMs were evident as 71% of the proteoforms had methionine excised and 47% were N-terminal acetylated. In addition, in silico internal acetylation prediction coupled with top down MS allowed the characterization of 9 proteins differentially acetylated, including histones. Bottom up analysis increased the overall number of identified proteins in nuclear and cytosolic fractions to 154 and 112, respectively. Overall, our results provided the first description of the low mass proteome of E. granulosus subcellular fractions and highlighted proteoforms with CTMs and PTMS whose characterization may lead to another level of understanding about molecular mechanisms controlling parasitic flatworm biology.

Interactive effects of trait and state affect on top-down control of attention.

PubMed

Hur, Juyoen; Miller, Gregory A; McDavitt, Jenika R B; Spielberg, Jeffrey M; Crocker, Laura D; Infantolino, Zachary P; Towers, David N; Warren, Stacie L; Heller, Wendy

2015-08-01

Few studies have investigated how attentional control is affected by transient affective states while taking individual differences in affective traits into consideration. In this study, participants completed a color-word Stroop task immediately after undergoing a positive, neutral or negative affective context manipulation (ACM). Behavioral performance was unaffected by any ACM considered in isolation. For individuals high in trait negative affect (NA), performance was impaired by the negative but not the positive or neutral ACM. Neuroimaging results indicate that activity in primarily top-down control regions of the brain (inferior frontal gyrus and dorsal anterior cingulate cortex) was suppressed in the presence of emotional arousal (both negative and positive ACMs). This effect appears to have been exacerbated or offset by co-occurring activity in other top-down control regions (parietal) and emotion processing regions (orbitofrontal cortex, amygdala and nucleus accumbens) as a function of the valence of state affect (positive or negative) and trait affect (trait NA or trait PA). Neuroimaging results are consistent with behavioral findings. In combination, they indicate both additive and interactive influences of trait and state affect on top-down control of attention. © The Author (2015). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Coupled wake boundary layer model of windfarms

NASA Astrophysics Data System (ADS)

Stevens, Richard; Gayme, Dennice; Meneveau, Charles

2014-11-01

We present a coupled wake boundary layer (CWBL) model that describes the distribution of the power output in a windfarm. The model couples the traditional, industry-standard wake expansion/superposition approach with a top-down model for the overall windfarm boundary layer structure. Wake models capture the effect of turbine positioning, while the top-down approach represents the interaction between the windturbine wakes and the atmospheric boundary layer. Each portion of the CWBL model requires specification of a parameter that is unknown a-priori. The wake model requires the wake expansion rate, whereas the top-down model requires the effective spanwise turbine spacing within which the model's momentum balance is relevant. The wake expansion rate is obtained by matching the mean velocity at the turbine from both approaches, while the effective spanwise turbine spacing is determined from the wake model. Coupling of the constitutive components of the CWBL model is achieved by iterating these parameters until convergence is reached. We show that the CWBL model predictions compare more favorably with large eddy simulation results than those made with either the wake or top-down model in isolation and that the model can be applied successfully to the Horns Rev and Nysted windfarms. The `Fellowships for Young Energy Scientists' (YES!) of the Foundation for Fundamental Research on Matter supported by NWO, and NSF Grant #1243482.

Top predators, mesopredators and their prey: interference ecosystems along bioclimatic productivity gradients.

PubMed

Elmhagen, B; Ludwig, G; Rushton, S P; Helle, P; Lindén, H

2010-07-01

1. The Mesopredator Release Hypothesis (MRH) suggests that top predator suppression of mesopredators is a key ecosystem function with cascading impacts on herbivore prey, but it remains to be shown that this top-down cascade impacts the large-scale structure of ecosystems. 2. The Exploitation Ecosystems Hypothesis (EEH) predicts that regional ecosystem structures are determined by top-down exploitation and bottom-up productivity. In contrast to MRH, EEH assumes that interference among predators has a negligible impact on the structure of ecosystems with three trophic levels. 3. We use the recolonization of a top predator in a three-level boreal ecosystem as a natural experiment to test if large-scale biomass distributions and population trends support MRH. Inspired by EEH, we also test if top-down interference and bottom-up productivity impact regional ecosystem structures. 4. We use data from the Finnish Wildlife Triangle Scheme which has monitored top predator (lynx, Lynx lynx), mesopredator (red fox, Vulpes vulpes) and prey (mountain hare, Lepus timidus) abundance for 17 years in a 200 000 km(2) study area which covers a distinct productivity gradient. 5. Fox biomass was lower than expected from productivity where lynx biomass was high, whilst hare biomass was lower than expected from productivity where fox biomass was high. Hence, where interference controlled fox abundance, lynx had an indirect positive impact on hare abundance as predicted by MRH. The rates of change indicated that lynx expansion gradually suppressed fox biomass. 6. Lynx status caused shifts between ecosystem structures. In the 'interference ecosystem', lynx and hare biomass increased with productivity whilst fox biomass did not. In the 'mesopredator release ecosystem', fox biomass increased with productivity but hare biomass did not. Thus, biomass controlled top-down did not respond to changes in productivity. This fulfils a critical prediction of EEH. 7. We conclude that the cascade involving top predators, mesopredators and their prey can determine large-scale biomass distribution patterns and regional ecosystem structures. Hence, interference within trophic levels has to be taken into account to understand how terrestrial ecosystem structures are shaped.

Determining the pattern of cementum annuli and relationship to reproduction in male sea otters

USGS Publications Warehouse

Proper, Josh; von Biela, Vanessa R.; Burns, Jennifer M.

2007-01-01

Since the early 1990s, the southwestern Alaskan sea otter (Enhydra lutris) population has declined dramatically and the cause has yet to be determined. Population trajectories of large mammals are determined by three factors: survival rate, reproduction rate, and age of first reproduction (AFR). Of these three, AFR should respond first to environmental change. Life history theory predicts that AFR will be older with bottom-up causes (ie, food limitation) and younger when the cause of the decline is top-down (ie, predation), as there is usually abundant resources in this scenario. Traditionally, determining AFR required lethal sampling, which may not always be possible. Work on many mammalian species suggests that the width of annual cementum layers in teeth may decline when breeding begins. If so, examining teeth annuli may provide a nonlethal alternative for determining AFR. Ongoing research has shown this relationship in female sea otters, but male sea otters have not been tested. Sea otter testes and premolar teeth slides were collected by subsistence hunters working with the US Fish and Wildlife Service and the Alaska Sea Otter and Steller Sea Lion Commission from Alaska (1994– 2005). We determined the pattern in cementum annuli thickness for male sea otters across age by measuring annuli at three sites on each of the two slide sections available. We found that cementum annuli layers decreased with age, but found no correlation between cementum annuli and sexual maturity in male sea otters. This lack of correlation may be due to sampling error or different energy expenditures during reproduction for each sex. Since females expend large amounts of energy through gestation and lactation, we hypothesize that the width of female cementum annuli decreases at a much sharper rate when they reach AFR.The southwest Alaskan sea otter population has plummeted up to 90% since the early 1990s and the reason is unknown.1 Declines may be due to a bottom-up source caused by lack of food and habitat that occurs when populations are dense, in which case we would expect reproduction rates to decrease and age of first reproduction (AFR) to increase. However, circumstantial evidence suggests that the decline may be due to a top-down source, ie, predation.2 In this case, we would expect reproduction rates to increase and AFR to decrease due to lowered densities that coincide with top-down declines.3 An ongoing study of female sea otters has shown that past reproduction can be determined by analysis of cementum annuli in the teeth, and used to calculate AFR.4 Cementum annuli are annual deposits of minerals that occur on the root of a tooth that correspond to the growth of the animal (Figure 1). During summer and spring, growth is fast which accounts for the white area, but during winter, growth slows down and the cementum is compressed which accounts for a darkened line. In females, the relationship between cementum width declines and reproduction likely reflects the large expenditure of energy that is required during gestation and lactation. However, male and female mammals expend energy for reproduction in very distinct ways,3 and the same pattern of cementum decline may not be present in males. Since shifts in the life history strategy of males are poorly understood, we are interested in testing the relationship between cementum declines and reproduction in male sea otters using cementum analysis.

Using the NAME Lagrangian Particle Dispersion model, and aircraft measurements to assess the accuracy of trace gas emission inventories from the U.K.

NASA Astrophysics Data System (ADS)

O'Sullivan, D. A.; Harrison, M.; Ploson, D.; Oram, D.; Reeves, C.

2007-12-01

A top-down approach using a combination of aircraft data and atmospheric dispersion modelling has been used to estimate emissions for 24 halogenated trace gases from the United Kingdom. This has been done using data collected during AMPEP/FLUXEX, a U.K based measurement campaign which took place between April and September 2005. The primary objective relating to this work was to make direct airborne measurements of concentration enhancements within the boundary layer arising from anthropogenic pollution events, and then to use mass balance methods to determine an emission flux. This was done by analysing Whole Air Samples (WAS) collected in the boundary layer upwind and downwind of the UK at frequent intervals around the coast using the technique of gas chromatography mass spectrometry (GCMS). Emissions were then calculated using a simple box-model approach and also using NAME (Numerical Atmospheric-dispersion Modelling Environment) which is a Lagrangian particle model using 3 hourly 3D meteorology fields from the Met Office Unified Model. By using such an approach it is also possible to identify the most likely main source regions in the UK for the compounds measured. Among the trace gases studied are many which through their effects on stratospheric ozone, and their large radiative forcing have a direct impact on global climate such as CFC's 11, 12, 113 and 114, HCFC's 21, 22, 141b and 142b, HFC's 134a and 152a, methyl chloroform, methyl bromide and carbon tetrachloride. Also the emissions of some short lived gases with have direct effects on human health, such as tetrachloroethene, and trichloroethene, have been derived. The UK emissions estimates calculated from this experimental and modelling work are compared with bottom-up and other top-down emission inventories for the UK and Europe. It was found that the estimates from this study were often higher than those in bottom-up emission inventories derived from industry. In addition for a number of trace gases, for example HCFC-21 and the HFC's, there are no accurate emissions estimates available due to privacy laws which in the UK restrict the availability of the production and sales data required to construct bottom-up emission inventories. Therefore for some of the compounds included in this study, this work provides the first available estimate of UK emissions.

Revised methane emissions factors and spatially distributed annual carbon fluxes for global livestock.

PubMed

Wolf, Julie; Asrar, Ghassem R; West, Tristram O

2017-09-29

Livestock play an important role in carbon cycling through consumption of biomass and emissions of methane. Recent research suggests that existing bottom-up inventories of livestock methane emissions in the US, such as those made using 2006 IPCC Tier 1 livestock emissions factors, are too low. This may be due to outdated information used to develop these emissions factors. In this study, we update information for cattle and swine by region, based on reported recent changes in animal body mass, feed quality and quantity, milk productivity, and management of animals and manure. We then use this updated information to calculate new livestock methane emissions factors for enteric fermentation in cattle, and for manure management in cattle and swine. Using the new emissions factors, we estimate global livestock emissions of 119.1 ± 18.2 Tg methane in 2011; this quantity is 11% greater than that obtained using the IPCC 2006 emissions factors, encompassing an 8.4% increase in enteric fermentation methane, a 36.7% increase in manure management methane, and notable variability among regions and sources. For example, revised manure management methane emissions for 2011 in the US increased by 71.8%. For years through 2013, we present (a) annual livestock methane emissions, (b) complete annual livestock carbon budgets, including carbon dioxide emissions, and (c) spatial distributions of livestock methane and other carbon fluxes, downscaled to 0.05 × 0.05 degree resolution. Our revised bottom-up estimates of global livestock methane emissions are comparable to recently reported top-down global estimates for recent years, and account for a significant part of the increase in annual methane emissions since 2007. Our results suggest that livestock methane emissions, while not the dominant overall source of global methane emissions, may be a major contributor to the observed annual emissions increases over the 2000s to 2010s. Differences at regional and local scales may help distinguish livestock methane emissions from those of other sectors in future top-down studies. The revised estimates allow improved reconciliation of top-down and bottom-up estimates of methane emissions, will facilitate the development and evaluation of Earth system models, and provide consistent regional and global Tier 1 estimates for environmental assessments.

Testing the Late Noachian Icy Highlands Model: Geological Observations, Processes and Origin of Fluvial and Lacustrine Features.

NASA Astrophysics Data System (ADS)

Head, James; Wordsworth, Robin; Forget, Francis; Madeleine, Jean-Baptiste; Halvey, Italy

2014-05-01

A new reconstruction of the Late Noachian Mars atmosphere and climate shows atmosphere-surface thermal coupling and an adiabatic cooling effect producing preferential distribution of snow and ice in the highlands. In this Late Noachian Icy Highlands (LNIH) scenario, snow and ice accumulate in the south circumpolar region and in the higher altitudes of the southern uplands, but the mean annual temperature is everywhere below freezing. How can the abundant evidence for water-related fluvial and lacustrine activity (valley networks, VN; open-basin lakes, OBL; closed-basin lakes; CBL) be reconciled with the icy highlands model? We investigate the nature of geologic processes operating in the icy highlands and use the Antarctic McMurdo Dry Valleys (MDV) as guidance in understanding and assessing how melting might be taking place. In the MDV, mean annual temperatures (MAT) are well below freezing. This results in a thick regional permafrost layer, the presence of an ice-table at shallow depths, and an overlying dry active layer. This configuration produces a perched aquifer and a horizontally stratified hydrologic system, where any melting results in local saturation of the dry active layer and channelized flow on top of the ice table. Top-down melting results in the dominance of lateral water transport, in contrast to temperate climates with vertical infiltration and transport to the groundwater table. Despite subzero MAT, MDV peak seasonal and peak daytime temperatures can exceed 273K and have a strong influence on the melting of available water ice. We present maps of the predicted distribution of LNIH snow and ice, compare these to the distribution of VN, OBL and CBL, and assess how top-down and bottom-up melting processes might explain the formation of these features in an otherwise cold and icy LN Mars. We assess the global near-surface water budget, analyze thickness estimates to distinguish areas of cold-based and wet-based glaciation, analyze the state of the ice cover and its susceptibility to melting and runoff, and describe top-down melting and fluvial channel formation processes in a LNIH environment. We find that: 1) episodic top-down melting of the LNIH is a robust mechanism to produce the observed fluvial and lacustrine features; 2) the characteristics and distribution of features in the Dorsa Argentea Formation are consistent with an extensive circum-polar ice cap during LNIH time; and 3) the nature of preserved LN impact craters is consistent with impact cratering processes in the LNIH environment. 393 words.

Bottom-up processes drive reproductive success in an apex predator.

PubMed

Schmidt, Joshua H; McIntyre, Carol L; Roland, Carl A; MacCluskie, Margaret C; Flamme, Melanie J

2018-02-01

One of the central goals of the field of population ecology is to identify the drivers of population dynamics, particularly in the context of predator-prey relationships. Understanding the relative role of top-down versus bottom-up drivers is of particular interest in understanding ecosystem dynamics. Our goal was to explore predator-prey relationships in a boreal ecosystem in interior Alaska through the use of multispecies long-term monitoring data. We used 29 years of field data and a dynamic multistate site occupancy modeling approach to explore the trophic relationships between an apex predator, the golden eagle, and cyclic populations of the two primary prey species available to eagles early in the breeding season, snowshoe hare and willow ptarmigan. We found that golden eagle reproductive success was reliant on prey numbers, but also responded prior to changes in the phase of the snowshoe hare population cycle and failed to respond to variation in hare cycle amplitude. There was no lagged response to ptarmigan populations, and ptarmigan populations recovered quickly from the low phase. Together, these results suggested that eagle reproduction is largely driven by bottom-up processes, with little evidence of top-down control of either ptarmigan or hare populations. Although the relationship between golden eagle reproductive success and prey abundance had been previously established, here we established prey populations are likely driving eagle dynamics through bottom-up processes. The key to this insight was our focus on golden eagle reproductive parameters rather than overall abundance. Although our inference is limited to the golden eagle-hare-ptarmigan relationships we studied, our results suggest caution in interpreting predator-prey abundance patterns among other species as strong evidence for top-down control.

Biased Competition in Visual Processing Hierarchies: A Learning Approach Using Multiple Cues.

PubMed

Gepperth, Alexander R T; Rebhan, Sven; Hasler, Stephan; Fritsch, Jannik

2011-03-01

In this contribution, we present a large-scale hierarchical system for object detection fusing bottom-up (signal-driven) processing results with top-down (model or task-driven) attentional modulation. Specifically, we focus on the question of how the autonomous learning of invariant models can be embedded into a performing system and how such models can be used to define object-specific attentional modulation signals. Our system implements bi-directional data flow in a processing hierarchy. The bottom-up data flow proceeds from a preprocessing level to the hypothesis level where object hypotheses created by exhaustive object detection algorithms are represented in a roughly retinotopic way. A competitive selection mechanism is used to determine the most confident hypotheses, which are used on the system level to train multimodal models that link object identity to invariant hypothesis properties. The top-down data flow originates at the system level, where the trained multimodal models are used to obtain space- and feature-based attentional modulation signals, providing biases for the competitive selection process at the hypothesis level. This results in object-specific hypothesis facilitation/suppression in certain image regions which we show to be applicable to different object detection mechanisms. In order to demonstrate the benefits of this approach, we apply the system to the detection of cars in a variety of challenging traffic videos. Evaluating our approach on a publicly available dataset containing approximately 3,500 annotated video images from more than 1 h of driving, we can show strong increases in performance and generalization when compared to object detection in isolation. Furthermore, we compare our results to a late hypothesis rejection approach, showing that early coupling of top-down and bottom-up information is a favorable approach especially when processing resources are constrained.

Comprehensive Characterization of Swine Cardiac Troponin T Proteoforms by Top-Down Mass Spectrometry

NASA Astrophysics Data System (ADS)

Lin, Ziqing; Guo, Fang; Gregorich, Zachery R.; Sun, Ruixiang; Zhang, Han; Hu, Yang; Shanmuganayagam, Dhanansayan; Ge, Ying

2018-04-01

Cardiac troponin T (cTnT) regulates the Ca2+-mediated interaction between myosin thick filaments and actin thin filaments during cardiac contraction and relaxation. cTnT is released into the blood following injury, and increased serum levels of the protein are used clinically as a biomarker for myocardial infarction. Moreover, mutations in cTnT are causative in a number of familial cardiomyopathies. With the increasing use of large animal (swine) model to recapitulate human diseases, it is essential to characterize species-dependent protein sequence variants, alternative RNA splicing, and post-translational modifications (PTMs), but challenges remain due to the incomplete database and lack of validation of the predicted splicing isoforms. Herein, we integrated top-down mass spectrometry (MS) with online liquid chromatography (LC) and immunoaffinity purification to comprehensively characterize miniature swine cTnT proteoforms, including those arising from alternative RNA splicing and PTMs. A total of seven alternative splicing isoforms of cTnT were identified by LC/MS from swine left ventricular tissue, with each isoform containing un-phosphorylated and mono-phosphorylated proteoforms. The phosphorylation site was localized to Ser1 for the mono-phosphorylated proteoforms of cTnT1, 3, 4, and 6 by online MS/MS combining collisionally activated dissociation (CAD) and electron transfer dissociation (ETD). Offline MS/MS on Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer with CAD and electron capture dissociation (ECD) was then utilized to achieve deep sequencing of mono-phosphorylated cTnT1 (35.2 kDa) with a high sequence coverage of 87%. Taken together, this study demonstrated the unique advantage of top-down MS in the comprehensive characterization of protein alternative splicing isoforms together with PTMs. [Figure not available: see fulltext.

Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation

NASA Astrophysics Data System (ADS)

Riley, Nicholas M.; Westphall, Michael S.; Coon, Joshua J.

2018-01-01

The analysis of intact proteins via mass spectrometry can offer several benefits to proteome characterization, although the majority of top-down experiments focus on proteoforms in a relatively low mass range (<30 kDa). Recent studies have focused on improving the analysis of larger intact proteins (up to 75 kDa), but they have also highlighted several challenges to be addressed. One major hurdle is the efficient dissociation of larger protein ions, which often to do not yield extensive fragmentation via conventional tandem MS methods. Here we describe the first application of activated ion electron transfer dissociation (AI-ETD) to proteins in the 30-70 kDa range. AI-ETD leverages infrared photo-activation concurrent to ETD reactions to improve sequence-informative product ion generation. This method generates more product ions and greater sequence coverage than conventional ETD, higher-energy collisional dissociation (HCD), and ETD combined with supplemental HCD activation (EThcD). Importantly, AI-ETD provides the most thorough protein characterization for every precursor ion charge state investigated in this study, making it suitable as a universal fragmentation method in top-down experiments. Additionally, we highlight several acquisition strategies that can benefit characterization of larger proteins with AI-ETD, including combination of spectra from multiple ETD reaction times for a given precursor ion, multiple spectral acquisitions of the same precursor ion, and combination of spectra from two different dissociation methods (e.g., AI-ETD and HCD). In all, AI-ETD shows great promise as a method for dissociating larger intact protein ions as top-down proteomics continues to advance into larger mass ranges. [Figure not available: see fulltext.

Top Down Tandem Mass Spectrometric Analysis of a Chemically Modified Rough-Type Lipopolysaccharide Vaccine Candidate

NASA Astrophysics Data System (ADS)

Oyler, Benjamin L.; Khan, Mohd M.; Smith, Donald F.; Harberts, Erin M.; Kilgour, David P. A.; Ernst, Robert K.; Cross, Alan S.; Goodlett, David R.

2018-02-01

Recent advances in lipopolysaccharide (LPS) biology have led to its use in drug discovery pipelines, including vaccine and vaccine adjuvant discovery. Desirable characteristics for LPS vaccine candidates include both the ability to produce a specific antibody titer in patients and a minimal host inflammatory response directed by the innate immune system. However, in-depth chemical characterization of most LPS extracts has not been performed; hence, biological activities of these extracts are unpredictable. Additionally, the most widely adopted workflow for LPS structure elucidation includes nonspecific chemical decomposition steps before analyses, making structures inferred and not necessarily biologically relevant. In this work, several different mass spectrometry workflows that have not been previously explored were employed to show proof-of-principle for top down LPS primary structure elucidation, specifically for a rough-type mutant (J5) E. coli-derived LPS component of a vaccine candidate. First, ion mobility filtered precursor ions were subjected to collision induced dissociation (CID) to define differences in native J5 LPS v. chemically detoxified J5 LPS (dLPS). Next, ultra-high mass resolving power, accurate mass spectrometry was employed for unequivocal precursor and product ion empirical formulae generation. Finally, MS3 analyses in an ion trap instrument showed that previous knowledge about dissociation of LPS components can be used to reconstruct and sequence LPS in a top down fashion. A structural rationale is also explained for differential inflammatory dose-response curves, in vitro, when HEK-Blue hTLR4 cells were administered increasing concentrations of native J5 LPS v. dLPS, which will be useful in future drug discovery efforts. [Figure not available: see fulltext.

Vista-LA: Mapping methane-emitting infrastructure in the Los Angeles megacity

NASA Astrophysics Data System (ADS)

Carranza, Valerie; Rafiq, Talha; Frausto-Vicencio, Isis; Hopkins, Francesca M.; Verhulst, Kristal R.; Rao, Preeti; Duren, Riley M.; Miller, Charles E.

2018-03-01

Methane (CH4) is a potent greenhouse gas (GHG) and a critical target of climate mitigation efforts. However, actionable emission reduction efforts are complicated by large uncertainties in the methane budget on relevant scales. Here, we present Vista, a Geographic Information System (GIS)-based approach to map potential methane emissions sources in the South Coast Air Basin (SoCAB) that encompasses Los Angeles, an area with a dense, complex mixture of methane sources. The goal of this work is to provide a database that, together with atmospheric observations, improves methane emissions estimates in urban areas with complex infrastructure. We aggregated methane source location information into three sectors (energy, agriculture, and waste) following the frameworks used by the State of California GHG Inventory and the Intergovernmental Panel on Climate Change (IPCC) Guidelines for GHG Reporting. Geospatial modeling was applied to publicly available datasets to precisely geolocate facilities and infrastructure comprising major anthropogenic methane source sectors. The final database, Vista-Los Angeles (Vista-LA), is presented as maps of infrastructure known or expected to emit CH4. Vista-LA contains over 33 000 features concentrated on < 1 % of land area in the region. Currently, Vista-LA is used as a planning and analysis tool for atmospheric measurement surveys of methane sources, particularly for airborne remote sensing, and methane hotspot detection using regional observations. This study represents a first step towards developing an accurate, spatially resolved methane flux estimate for point sources in SoCAB, with the potential to address discrepancies between bottom-up and top-down methane emissions accounting in this region. The Vista-LA datasets and associated metadata are available from the Oak Ridge National Laboratory Distributed Active Archive Center for Biogeochemical Dynamics (ORNL DAAC; https://doi.org/10.3334/ORNLDAAC/1525).

The influence of Cr and Al pack cementation on low carbon steel to improve oxidation resistance

NASA Astrophysics Data System (ADS)

Prasetya, Didik; Sugiarti, Eni; Destyorini, Fredina; Thosin, Kemas Ahmad Zaini

2012-06-01

Pack chromizing and aluminizing has been widely used for many years to improve hot temperature oxidation and corrosion resistance of metals. The coating process involves packing the steel in a powder mixture which contain aluminum and chromium source, and inert filler (usually alumina), and halide activator NH4Cl. Al and Cr were deposited onto carbon steel by pack cementation process using elemental Al and Cr powder as Al and Cr source, whereas NiCo alloys codeposited by electrodeposition. The position of Al and Cr could be under or over Ni-Co alloys deposited. Pack cementation was heated on dry inert gas at temperature 800 °C about 5 hours and 20 minute for Cr and Al respectively. Al and Cr was successfully deposited. Laying down effect of Al and Cr onto carbon steel whether up and down toward NiCo alloys coating have affected to oxidation resistance. The pack aluminizing as top layer given best resitance to restrain excessive oxide scale, in contrast pack chromizing reveal bad oxidation resistance, moreover occured spallation on layer.

REVIEWS OF TOPICAL PROBLEMS: Ultrahigh-energy neutrinos from astrophysical sources and superheavy particle decays

NASA Astrophysics Data System (ADS)

Ryabov, Vladimir A.

2006-09-01

Problems in the fields of neutrino astronomy and ultrahigh-energy astrophysics are reviewed. Neutrino fluxes produced in various astrophysical sources (bottom-up acceleration scenarios) and resulting from the decay of superheavy particles (top-down scenarios) are considered. Neutrino oscillation processes and the absorption and regeneration of neutrinos inside the earth are analyzed and some other factors affecting the intensity and flavor composition of astrophysical neutrino fluxes are discussed. Details of ultrahigh-energy neutrino interactions are discussed within the Standard Model, as well as using nonstandard scenarios predicting an anomalous increase in the inelastic neutrino-nucleon cross section. Ultrahigh-energy neutrino detection techniques currently in use in new-generation neutrino telescopes and cosmic ray detectors are also discussed.

Profiling of Histone Post-Translational Modifications in Mouse Brain with High-Resolution Top-Down Mass Spectrometry.

PubMed

Zhou, Mowei; Paša-Tolić, Ljiljana; Stenoien, David L

2017-02-03

As histones play central roles in most chromosomal functions including regulation of DNA replication, DNA damage repair, and gene transcription, both their basic biology and their roles in disease development have been the subject of intense study. Because multiple post-translational modifications (PTMs) along the entire protein sequence are potential regulators of histones, a top-down approach, where intact proteins are analyzed, is ultimately required for complete characterization of proteoforms. However, significant challenges remain for top-down histone analysis primarily because of deficiencies in separation/resolving power and effective identification algorithms. Here we used state-of-the-art mass spectrometry and a bioinformatics workflow for targeted data analysis and visualization. The workflow uses ProMex for intact mass deconvolution, MSPathFinder as a search engine, and LcMsSpectator as a data visualization tool. When complemented with the open-modification tool TopPIC, this workflow enabled identification of novel histone PTMs including tyrosine bromination on histone H4 and H2A, H3 glutathionylation, and mapping of conventional PTMs along the entire protein for many histone subunits.

Neotropical peatland methane emissions along a vegetation and biogeochemical gradient

PubMed Central

Flanagan, Neal; Richardson, Curtis J.

2017-01-01

Tropical wetlands are thought to be the most important source of interannual variability in atmospheric methane (CH4) concentrations, yet sparse data prevents them from being incorporated into Earth system models. This problem is particularly pronounced in the neotropics where bottom-up models based on water table depth are incongruent with top-down inversion models suggesting unaccounted sinks or sources of CH4. The newly documented vast areas of peatlands in the Amazon basin may account for an important unrecognized CH4 source, but the hydrologic and biogeochemical controls of CH4 dynamics from these systems remain poorly understood. We studied three zones of a peatland in Madre de Dios, Peru, to test whether CH4 emissions and pore water concentrations varied with vegetation community, soil chemistry and proximity to groundwater sources. We found that the open-canopy herbaceous zone emitted roughly one-third as much CH4 as the Mauritia flexuosa palm-dominated areas (4.7 ± 0.9 and 14.0 ± 2.4 mg CH4 m-2 h-1, respectively). Emissions decreased with distance from groundwater discharge across the three sampling sites, and tracked changes in soil carbon chemistry, especially increased soil phenolics. Based on all available data, we calculate that neotropical peatlands contribute emissions of 43 ± 11.9 Tg CH4 y-1, however this estimate is subject to geographic bias and will need revision once additional studies are published. PMID:29053738

44. Building 102, view from mezzanine looking down to first ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

44. Building 102, view from mezzanine looking down to first floor showing Klystron tube equipment vaults with dual waveguides leaving top of vaults through bifurcation combiner system at start of waveguides; note tops of capacitor vaults along photograph to left. - Clear Air Force Station, Ballistic Missile Early Warning System Site II, One mile west of mile marker 293.5 on Parks Highway, 5 miles southwest of Anderson, Anderson, Denali Borough, AK

Elucidating unconscious processing with instrumental hypnosis

PubMed Central

Landry, Mathieu; Appourchaux, Krystèle; Raz, Amir

2014-01-01

Most researchers leverage bottom-up suppression to unlock the underlying mechanisms of unconscious processing. However, a top-down approach – for example via hypnotic suggestion – paves the road to experimental innovation and complementary data that afford new scientific insights concerning attention and the unconscious. Drawing from a reliable taxonomy that differentiates subliminal and preconscious processing, we outline how an experimental trajectory that champions top-down suppression techniques, such as those practiced in hypnosis, is uniquely poised to further contextualize and refine our scientific understanding of unconscious processing. Examining subliminal and preconscious methods, we demonstrate how instrumental hypnosis provides a reliable adjunct that supplements contemporary approaches. Specifically, we provide an integrative synthesis of the advantages and shortcomings that accompany a top-down approach to probe the unconscious mind. Our account provides a larger framework for complementing the results from core studies involving prevailing subliminal and preconscious techniques. PMID:25120504

Does Top-Down Feedback Modulate the Encoding of Orthographic Representations During Visual-Word Recognition?

PubMed

Perea, Manuel; Marcet, Ana; Vergara-Martínez, Marta

2016-09-01

In masked priming lexical decision experiments, there is a matched-case identity advantage for nonwords, but not for words (e.g., ERTAR-ERTAR <  ertar-ERTAR; ALTAR-ALTAR = altar-ALTAR). This dissociation has been interpreted in terms of feedback from higher levels of processing during orthographic encoding. Here, we examined whether a matched-case identity advantage also occurs for words when top-down feedback is minimized. We employed a task that taps prelexical orthographic processes: the masked prime same-different task. For "same" trials, results showed faster response times for targets when preceded by a briefly presented matched-case identity prime than when preceded by a mismatched-case identity prime. Importantly, this advantage was similar in magnitude for nonwords and words. This finding constrains the interplay of bottom-up versus top-down mechanisms in models of visual-word identification.

The generation of myricetin-nicotinamide nanococrystals by top down and bottom up technologies

NASA Astrophysics Data System (ADS)

Liu, Mingyu; Hong, Chao; Li, Guowen; Ma, Ping; Xie, Yan

2016-09-01

Myricetin-nicotinamide (MYR-NIC) nanococrystal preparation methods were developed and optimized using both top down and bottom up approaches. The grinding (top down) method successfully achieved nanococrystals, but there were some micrometer range particles and aggregation. The key consideration of the grinding technology was to control the milling time to determine a balance between the particle size and distribution. In contrast, a modified bottom up approach based on a solution method in conjunction with sonochemistry resulted in a uniform MYR-NIC nanococrystal that was confirmed by powder x-ray diffraction, scanning electron microscopy, dynamic light scattering, and differential scanning calorimeter, and the particle dissolution rate and amount were significantly greater than that of MYR-NIC cocrystal. Notably, this was a simple method without the addition of any non-solvent. We anticipate our findings will provide some guidance for future nanococrystal preparation as well as its application in both chemical and pharmaceutical area.

The precedence of topological change over top-down attention in masked priming.

PubMed

Huang, Yan; Zhou, Tiangang; Chen, Lin

2011-10-14

Recent data indicate that unconscious masked priming can be mediated by top-down attentional set, so that priming effects of congruence between a masked prime and a subsequent probe vanish when the congruence ceases to be task relevant. Here, we show that, while the attentional set determines masked priming for color and orientation features, it does not fully determine priming based on the topological properties of stimuli. Specifically, across a series of different choice-RT tasks, we find that topological congruence between prime and probe stimuli affects RTs for the probes even when other stimulus information (e.g., color or orientation) is required for the response, whereas congruence priming effects of color or orientation occur only when these features are response relevant. Our results suggest that changes in topological properties take precedence over task-directed top-down attentional modulation in masked priming.

Enhanced stimulated emission in ZnO thin films using microdisk top-down structuring

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

Nomenyo, K.; Kostcheev, S.; Lérondel, G.

2014-05-05

Microdisks were fabricated in zinc oxide (ZnO) thin films using a top-down approach combining electron beam lithography and reactive ion etching. These microdisk structured thin films exhibit a stimulated surface emission between 3 and 7 times higher than that from a reference film depending on the excitation power density. Emission peak narrowing, reduction in lasing threshold and blue-shifting of the emission wavelength were observed along with enhancement in the emitted intensity. Results indicate that this enhancement is due to an increase in the internal quantum efficiency combined with an amplification of the stimulated emission. An analysis in terms of waveguidingmore » is presented in order to explain these effects. These results demonstrate that very significant gains in emission can be obtained through conventional microstructuration without the need for more onerous top-down nanostructuration techniques.« less

Top-down analysis of protein samples by de novo sequencing techniques

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

Vyatkina, Kira; Wu, Si; Dekker, Lennard J. M.

MOTIVATION: Recent technological advances have made high-resolution mass spectrometers affordable to many laboratories, thus boosting rapid development of top-down mass spectrometry, and implying a need in efficient methods for analyzing this kind of data. RESULTS: We describe a method for analysis of protein samples from top-down tandem mass spectrometry data, which capitalizes on de novo sequencing of fragments of the proteins present in the sample. Our algorithm takes as input a set of de novo amino acid strings derived from the given mass spectra using the recently proposed Twister approach, and combines them into aggregated strings endowed with offsets. Themore » former typically constitute accurate sequence fragments of sufficiently well-represented proteins from the sample being analyzed, while the latter indicate their location in the protein sequence, and also bear information on post-translational modifications and fragmentation patterns.« less

Top-down visual search in Wimmelbild

NASA Astrophysics Data System (ADS)

Bergbauer, Julia; Tari, Sibel

2013-03-01

Wimmelbild which means "teeming figure picture" is a popular genre of visual puzzles. Abundant masses of small figures are brought together in complex arrangements to make one scene in a Wimmelbild. It is picture hunt game. We discuss what type of computations/processes could possibly underlie the solution of the discovery of figures that are hidden due to a distractive influence of the context. One thing for sure is that the processes are unlikely to be purely bottom-up. One possibility is to re-arrange parts and see what happens. As this idea is linked to creativity, there are abundant examples of unconventional part re-organization in modern art. A second possibility is to define what to look for. That is to formulate the search as a top-down process. We address top-down visual search in Wimmelbild with the help of diffuse distance and curvature coding fields.

A single bout of meditation biases cognitive control but not attentional focusing: Evidence from the global-local task.

PubMed

Colzato, Lorenza S; van der Wel, Pauline; Sellaro, Roberta; Hommel, Bernhard

2016-01-01

Recent studies show that a single bout of meditation can impact information processing. We were interested to see whether this impact extends to attentional focusing and the top-down control over irrelevant information. Healthy adults underwent brief single bouts of either focused attention meditation (FAM), which is assumed to increase top-down control, or open monitoring meditation (OMM), which is assumed to weaken top-down control, before performing a global-local task. While the size of the global-precedence effect (reflecting attentional focusing) was unaffected by type of meditation, the congruency effect (indicating the failure to suppress task-irrelevant information) was considerably larger after OMM than after FAM. Our findings suggest that engaging in particular kinds of meditation creates particular cognitive-control states that bias the individual processing style toward either goal-persistence or cognitive flexibility. Copyright © 2015 Elsevier Inc. All rights reserved.

Learning to Link Visual Contours

PubMed Central

Li, Wu; Piëch, Valentin; Gilbert, Charles D.

2008-01-01

SUMMARY In complex visual scenes, linking related contour elements is important for object recognition. This process, thought to be stimulus driven and hard wired, has substrates in primary visual cortex (V1). Here, however, we find contour integration in V1 to depend strongly on perceptual learning and top-down influences that are specific to contour detection. In naive monkeys the information about contours embedded in complex backgrounds is absent in V1 neuronal responses, and is independent of the locus of spatial attention. Training animals to find embedded contours induces strong contour-related responses specific to the trained retinotopic region. These responses are most robust when animals perform the contour detection task, but disappear under anesthesia. Our findings suggest that top-down influences dynamically adapt neural circuits according to specific perceptual tasks. This may serve as a general neuronal mechanism of perceptual learning, and reflect top-down mediated changes in cortical states. PMID:18255036

Disentangling the Importance of Psychological Predispositions and Social Constructions in the Organization of American Political Ideology.

PubMed

Verhulst, Brad; Hatemi, Peter K; Eaves, Lindon J

2012-06-01

Ideological preferences within the American electorate are contingent on both the environmental conditions that provide the content of the contemporary political debate and internal predispositions that motivate people to hold liberal or conservative policy preferences. In this article we apply Jost, Federico, and Napier's (2009) top-down/bottom-up theory of political attitude formation to a genetically informative population sample. In doing so, we further develop the theory by operationalizing the top-down pathway to be a function of the social environment and the bottom-up pathway as a latent set of genetic factors. By merging insights from psychology, behavioral genetics, and political science, we find strong support for the top-down/bottom-up framework that segregates the two independent pathways in the formation of political attitudes and identifies a different pattern of relationships between political attitudes at each level of analysis.

Rigorous evaluation of chemical measurement uncertainty: liquid chromatographic analysis methods using detector response factor calibration

NASA Astrophysics Data System (ADS)

Toman, Blaza; Nelson, Michael A.; Bedner, Mary

2017-06-01

Chemical measurement methods are designed to promote accurate knowledge of a measurand or system. As such, these methods often allow elicitation of latent sources of variability and correlation in experimental data. They typically implement measurement equations that support quantification of effects associated with calibration standards and other known or observed parametric variables. Additionally, multiple samples and calibrants are usually analyzed to assess accuracy of the measurement procedure and repeatability by the analyst. Thus, a realistic assessment of uncertainty for most chemical measurement methods is not purely bottom-up (based on the measurement equation) or top-down (based on the experimental design), but inherently contains elements of both. Confidence in results must be rigorously evaluated for the sources of variability in all of the bottom-up and top-down elements. This type of analysis presents unique challenges due to various statistical correlations among the outputs of measurement equations. One approach is to use a Bayesian hierarchical (BH) model which is intrinsically rigorous, thus making it a straightforward method for use with complex experimental designs, particularly when correlations among data are numerous and difficult to elucidate or explicitly quantify. In simpler cases, careful analysis using GUM Supplement 1 (MC) methods augmented with random effects meta analysis yields similar results to a full BH model analysis. In this article we describe both approaches to rigorous uncertainty evaluation using as examples measurements of 25-hydroxyvitamin D3 in solution reference materials via liquid chromatography with UV absorbance detection (LC-UV) and liquid chromatography mass spectrometric detection using isotope dilution (LC-IDMS).

Synthesis of Remote Sensing and Field Observations to Model and Understand Disturbance and Climate Effects on the Carbon Balance of Oregon & Northern California

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

Beverly Law; David Turner; Warren Cohen

2008-05-22

The goal is to quantify and explain the carbon (C) budget for Oregon and N. California. The research compares "bottom -up" and "top-down" methods, and develops prototype analytical systems for regional analysis of the carbon balance that are potentially applicable to other continental regions, and that can be used to explore climate, disturbance and land-use effects on the carbon cycle. Objectives are: 1) Improve, test and apply a bottom up approach that synthesizes a spatially nested hierarchy of observations (multispectral remote sensing, inventories, flux and extensive sites), and the Biome-BGC model to quantify the C balance across the region; 2)more » Improve, test and apply a top down approach for regional and global C flux modeling that uses a model-data fusion scheme (MODIS products, AmeriFlux, atmospheric CO2 concentration network), and a boundary layer model to estimate net ecosystem production (NEP) across the region and partition it among GPP, R(a) and R(h). 3) Provide critical understanding of the controls on regional C balance (how NEP and carbon stocks are influenced by disturbance from fire and management, land use, and interannual climate variation). The key science questions are, "What are the magnitudes and distributions of C sources and sinks on seasonal to decadal time scales, and what processes are controlling their dynamics? What are regional spatial and temporal variations of C sources and sinks? What are the errors and uncertainties in the data products and results (i.e., in situ observations, remote sensing, models)?« less

Worldwide biogenic soil NOx emission estimates from OMI NO2 observations and the GEOS-Chem model

NASA Astrophysics Data System (ADS)

Vinken, Geert; Boersma, Folkert; Maasakkers, Bram; Martin, Randall

2014-05-01

Bacteria in soils are an important source of biogenic nitrogen oxides (NOx = NO + NO2), which are important precursors for ozone (O3) formation. Furthermore NOx emissions contribute to increased nitrogen deposition and particulate matter formation. Bottom-up estimates of global soil NOx emissions range from 4 to 27 Tg N / yr, reflecting our incomplete knowledge of emission factors and processes driving these emissions. In this study we used, for the first time, OMI NO2 columns on all continents to reduce the uncertainty in soil NOx emissions. Regions and months dominated by soil NOx emissions were identified using a filtering scheme in the GEOS-Chem chemistry transport model. Consequently, we compared OMI observed NO2 observed columns to GEOS-Chem simulated columns and provide constraints for these months in 11 regions. This allows us to provide a top-down emission inventory for 2005 for soil NOx emissions from all continents. Our total global soil NOx emission inventory amounts to 10 Tg N / yr. Our estimate is 4% higher than the GEOS-Chem a priori (Hudman et al., 2012), but substantial regional differences exist (e.g. +20% for Sahel and India; and -40% for mid-USA). We furthermore observed a stronger seasonal cycle in the Sahel region, indicating directions for possible future improvements to the parameterization currently used in GEOS-Chem. We validated NO2 concentrations simulated with this new top-down inventory against surface NO2 measurements from monitoring stations in Africa, the USA and Europe. On the whole, we conclude that simulations with our new top-down inventory better agree with measurements. Our work shows that satellite retrieved NO2 columns can improve estimates of soil NOx emissions over sparsely monitored remote rural areas. We show that the range in previous estimates of soil NOx emissions is too large, and global emissions are most likely around 10 Tg N/yr, in agreement with the most recent parameterizations.

PubMed Central

Castagnola, M.; Scarano, E.; Messana, I.; Cabras, T.; Iavarone, F.; Di Cintio, G.; Fiorita, A.; De Corso, E.; Paludetti, G.

2017-01-01

SUMMARY Saliva testing is a non-invasive and inexpensive test that can serve as a source of information useful for diagnosis of disease. As we enter the era of genomic technologies and –omic research, collection of saliva has increased. Recent proteomic platforms have analysed the human salivary proteome and characterised about 3000 differentially expressed proteins and peptides: in saliva, more than 90% of proteins in weight are derived from the secretion of three couples of "major" glands; all the other components are derived from minor glands, gingival crevicular fluid, mucosal exudates and oral microflora. The most common aim of proteomic analysis is to discriminate between physiological and pathological conditions. A proteomic protocol to analyze the whole saliva proteome is not currently available. It is possible distinguish two type of proteomic platforms: top-down proteomics investigates intact naturally-occurring structure of a protein under examination; bottom-up proteomics analyses peptide fragments after pre-digestion (typically with trypsin). Because of this heterogeneity, many different biomarkers may be proposed for the same pathology. The salivary proteome has been characterised in several diseases: oral squamous cell carcinoma and oral leukoplakia, chronic graft-versus-host disease Sjögren's syndrome and other autoimmune disorders such as SAPHO, schizophrenia and bipolar disorder, and genetic diseases like Down's Syndrome and Wilson disease. The results of research reported herein suggest that in the near future human saliva will be a relevant diagnostic fluid for clinical diagnosis and prognosis. PMID:28516971

Generative models for discovering sparse distributed representations.

PubMed Central

Hinton, G E; Ghahramani, Z

1997-01-01

We describe a hierarchical, generative model that can be viewed as a nonlinear generalization of factor analysis and can be implemented in a neural network. The model uses bottom-up, top-down and lateral connections to perform Bayesian perceptual inference correctly. Once perceptual inference has been performed the connection strengths can be updated using a very simple learning rule that only requires locally available information. We demonstrate that the network learns to extract sparse, distributed, hierarchical representations. PMID:9304685

Rethinking volitional control over task choice in multitask environments: use of a stimulus set selection strategy in voluntary task switching.

PubMed

Arrington, Catherine M; Weaver, Starla M

2015-01-01

Under conditions of volitional control in multitask environments, subjects may engage in a variety of strategies to guide task selection. The current research examines whether subjects may sometimes use a top-down control strategy of selecting a task-irrelevant stimulus dimension, such as location, to guide task selection. We term this approach a stimulus set selection strategy. Using a voluntary task switching procedure, subjects voluntarily switched between categorizing letter and number stimuli that appeared in two, four, or eight possible target locations. Effects of stimulus availability, manipulated by varying the stimulus onset asynchrony between the two target stimuli, and location repetition were analysed to assess the use of a stimulus set selection strategy. Considered across position condition, Experiment 1 showed effects of both stimulus availability and location repetition on task choice suggesting that only in the 2-position condition, where selection based on location always results in a target at the selected location, subjects may have been using a stimulus set selection strategy on some trials. Experiment 2 replicated and extended these findings in a visually more cluttered environment. These results indicate that, contrary to current models of task selection in voluntary task switching, the top-down control of task selection may occur in the absence of the formation of an intention to perform a particular task.

Factors shaping bacterial phylogenetic and functional diversity in coastal waters of the NW Mediterranean Sea

NASA Astrophysics Data System (ADS)

Boras, Julia A.; Vaqué, Dolors; Maynou, Francesc; Sà, Elisabet L.; Weinbauer, Markus G.; Sala, Maria Montserrat

2015-03-01

To evaluate the main factors shaping bacterioplankton phylogenetic and functional diversity in marine coastal waters, we carried out a two-year study based on a monthly sampling in Blanes Bay (NW Mediterranean). We expected the key factors driving bacterial diversity to be (1) temperature and nutrient concentration, together with chlorophyll a concentration as an indicator of phytoplankton biomass and, hence, a carbon source for bacteria (here called bottom-up factors), and (2) top-down pressure (virus- and protist-mediated mortality of bacteria). Phylogenetic diversity was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA. Functional diversity was assessed by using monomeric carbon sources in Biolog EcoPlates and by determining the activity of six extracellular enzymes. Our results indicate that the bacterial phylogenetic and functional diversity in this coastal system is shaped mainly by bottom-up factors. A dendrogram analysis of the DGGE banding patterns revealed three main sample clusters. Two clusters differed significantly in temperature, nitrate and chlorophyll a concentration, and the third was characterized by the highest losses of bacterial production due to viral lysis detected over the whole study period. Protistan grazing had no effect on bacterial functional diversity, since there were no correlations between protist-mediated mortality (PMM) and extracellular enzyme activities, and utilization of only two out of the 31 carbon sources (N-acetyl-D-glucosamine and α-cyclodextrin) was correlated with PMM. In contrast, virus-mediated mortality correlated with changes in the percentage of use of four carbon sources, and also with specific leu-aminopeptidase and β-glucosidase activity. This suggests that viral lysate provides a pool of labile carbon sources, presumably including amino acids and glucose, which may inhibit proteolytic and glucosidic activity. Our results indicate that bottom-up factors play a more important role than top-down factors (i.e. viral lysis and protistan grazing) in shaping bacterial community structure and activity. Furthermore, they suggest that viruses play a more important role than protists in modifying community structure and functional diversity of bacteria in oligotrophic marine coastal waters.

Intact and Top-Down Characterization of Biomolecules and Direct Analysis Using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Coupled to FT-ICR Mass Spectrometry

PubMed Central

Sampson, Jason S.; Murray, Kermit K.; Muddiman, David C.

2013-01-01

We report the implementation of an infrared laser onto our previously reported matrix-assisted laser desorption electrospray ionization (MALDESI) source with ESI post-ionization yielding multiply charged peptides and proteins. Infrared (IR)-MALDESI is demonstrated for atmospheric pressure desorption and ionization of biological molecules ranging in molecular weight from 1.2 to 17 kDa. High resolving power, high mass accuracy single-acquisition Fourier transform ion cyclotron resonance (FT-ICR) mass spectra were generated from liquid-and solid-state peptide and protein samples by desorption with an infrared laser (2.94 µm) followed by ESI post-ionization. Intact and top-down analysis of equine myoglobin (17 kDa) desorbed from the solid state with ESI post-ionization demonstrates the sequencing capabilities using IR-MALDESI coupled to FT-ICR mass spectrometry. Carbohydrates and lipids were detected through direct analysis of milk and egg yolk using both UV- and IR-MALDESI with minimal sample preparation. Three of the four classes of biological macromolecules (proteins, carbohydrates, and lipids) have been ionized and detected using MALDESI with minimal sample preparation. Sequencing of O-linked glycans, cleaved from mucin using reductive β-elimination chemistry, is also demonstrated. PMID:19185512

Hybrid Donor-Dot Devices made using Top-down Ion Implantation for Quantum Computing

NASA Astrophysics Data System (ADS)

Bielejec, Edward; Bishop, Nathan; Carroll, Malcolm

2012-02-01

We present progress towards fabricating hybrid donor -- quantum dots (QD) for quantum computing. These devices will exploit the long coherence time of the donor system and the surface state manipulation associated with a QD. Fabrication requires detection of single ions implanted with 10's of nanometer precision. We show in this talk, 100% detection efficiency for single ions using a single ion Geiger mode avalanche (SIGMA) detector integrated into a Si MOS QD process flow. The NanoImplanter (nI) a focused ion beam system is used for precision top-down placement of the implanted ion. This machine has a 10 nm resolution combined with a mass velocity filter, allowing for the use of multi-species liquid metal ion sources (LMIS) to implant P and Sb ions, and a fast blanking and chopping system for single ion implants. The combination of the nI and integration of the SIGMA with the MOS QD process flow establishes a path to fabricate hybrid single donor-dot devices. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Discrepancies and Uncertainties in Bottom-up Gridded Inventories of Livestock Methane Emissions for the Contiguous United States

NASA Astrophysics Data System (ADS)

Randles, C. A.; Hristov, A. N.; Harper, M.; Meinen, R.; Day, R.; Lopes, J.; Ott, T.; Venkatesh, A.

2017-12-01

In this analysis we used a spatially-explicit, bottom-up approach, based on animal inventories, feed intake, and feed intake-based emission factors to estimate county-level enteric (cattle) and manure (cattle, swine, and poultry) livestock methane emissions for the contiguous United States. Combined enteric and manure emissions were highest for counties in California's Central Valley. Overall, this analysis yielded total livestock methane emissions (8,916 Gg/yr; lower and upper bounds of 6,423 and 11,840 Gg/yr, respectively) for 2012 that are comparable to the current USEPA estimates for 2012 (9,295 Gg/yr) and to estimates from the global gridded Emission Database for Global Atmospheric Research (EDGAR) inventory (8,728 Gg/yr), used previously in a number of top-down studies. However, the spatial distribution of emissions developed in this analysis differed significantly from that of EDGAR. As an example, methane emissions from livestock in Texas and California (highest contributors to the national total) in this study were 36% lesser and 100% greater, respectively, than estimates by EDGAR. Thespatial distribution of emissions in gridded inventories (e.g., EDGAR) likely strongly impacts the conclusions of top-down approaches that use them, especially in the source attribution of resulting (posterior) emissions, and hence conclusions from such studies should be interpreted with caution.

Frequency modulation of neural oscillations according to visual task demands.

PubMed

Wutz, Andreas; Melcher, David; Samaha, Jason

2018-02-06

Temporal integration in visual perception is thought to occur within cycles of occipital alpha-band (8-12 Hz) oscillations. Successive stimuli may be integrated when they fall within the same alpha cycle and segregated for different alpha cycles. Consequently, the speed of alpha oscillations correlates with the temporal resolution of perception, such that lower alpha frequencies provide longer time windows for perceptual integration and higher alpha frequencies correspond to faster sampling and segregation. Can the brain's rhythmic activity be dynamically controlled to adjust its processing speed according to different visual task demands? We recorded magnetoencephalography (MEG) while participants switched between task instructions for temporal integration and segregation, holding stimuli and task difficulty constant. We found that the peak frequency of alpha oscillations decreased when visual task demands required temporal integration compared with segregation. Alpha frequency was strategically modulated immediately before and during stimulus processing, suggesting a preparatory top-down source of modulation. Its neural generators were located in occipital and inferotemporal cortex. The frequency modulation was specific to alpha oscillations and did not occur in the delta (1-3 Hz), theta (3-7 Hz), beta (15-30 Hz), or gamma (30-50 Hz) frequency range. These results show that alpha frequency is under top-down control to increase or decrease the temporal resolution of visual perception.

Dynamic Modulation of Sensory Cortex by Top-Down Spatial Attention

DTIC Science & Technology

2015-04-15

yet only in recent decades has the neural basis for these benefits begun to be studied. The studies presented here use EEG and MEG to identify patterns...presented here use EEG and MEG to identify patterns of neural activity related to the deployment of attention in extrapersonal space, and examine the...we use simultaneously recorded EEG/ MEG to examine the interaction of these top-down signals with neural responses evoked by attended and unattended

Profiling of integral membrane proteins and their post translational modifications using high-resolution mass spectrometry

PubMed Central

Souda, Puneet; Ryan, Christopher M.; Cramer, William A.; Whitelegge, Julian

2011-01-01

Integral membrane proteins pose challenges to traditional proteomics approaches due to unique physicochemical properties including hydrophobic transmembrane domains that limit solubility in aqueous solvents. A well resolved intact protein molecular mass profile defines a protein’s native covalent state including post-translational modifications, and is thus a vital measurement toward full structure determination. Both soluble loop regions and transmembrane regions potentially contain post-translational modifications that must be characterized if the covalent primary structure of a membrane protein is to be defined. This goal has been achieved using electrospray-ionization mass spectrometry (ESI-MS) with low-resolution mass analyzers for intact protein profiling, and high-resolution instruments for top-down experiments, toward complete covalent primary structure information. In top-down, the intact protein profile is supplemented by gas-phase fragmentation of the intact protein, including its transmembrane regions, using collisionally activated and/or electroncapture dissociation (CAD/ECD) to yield sequence-dependent high-resolution MS information. Dedicated liquid chromatography systems with aqueous/organic solvent mixtures were developed allowing us to demonstrate that polytopic integral membrane proteins are amenable to ESI-MS analysis, including top-down measurements. Covalent post-translational modifications are localized regardless of their position in transmembrane domains. Top-down measurements provide a more detail oriented high-resolution description of post-transcriptional and post-translational diversity for enhanced understanding beyond genomic translation. PMID:21982782

Spatial accuracy of a simplified disaggregation method for traffic emissions applied in seven mid-sized Chilean cities

NASA Astrophysics Data System (ADS)

Ossés de Eicker, Margarita; Zah, Rainer; Triviño, Rubén; Hurni, Hans

The spatial accuracy of top-down traffic emission inventory maps obtained with a simplified disaggregation method based on street density was assessed in seven mid-sized Chilean cities. Each top-down emission inventory map was compared against a reference, namely a more accurate bottom-up emission inventory map from the same study area. The comparison was carried out using a combination of numerical indicators and visual interpretation. Statistically significant differences were found between the seven cities with regard to the spatial accuracy of their top-down emission inventory maps. In compact cities with a simple street network and a single center, a good accuracy of the spatial distribution of emissions was achieved with correlation values>0.8 with respect to the bottom-up emission inventory of reference. In contrast, the simplified disaggregation method is not suitable for complex cities consisting of interconnected nuclei, resulting in correlation values<0.5. Although top-down disaggregation of traffic emissions generally exhibits low accuracy, the accuracy is significantly higher in compact cities and might be further improved by applying a correction factor for the city center. Therefore, the method can be used by local environmental authorities in cities with limited resources and with little knowledge on the pollution situation to get an overview on the spatial distribution of the emissions generated by traffic activities.

Top-down processing of symbolic meanings modulates the visual word form area.

PubMed

Song, Yiying; Tian, Moqian; Liu, Jia

2012-08-29

Functional magnetic resonance imaging (fMRI) studies on humans have identified a region in the left middle fusiform gyrus consistently activated by written words. This region is called the visual word form area (VWFA). Recently, a hypothesis, called the interactive account, is proposed that to effectively analyze the bottom-up visual properties of words, the VWFA receives predictive feedback from higher-order regions engaged in processing sounds, meanings, or actions associated with words. Further, this top-down influence on the VWFA is independent of stimulus formats. To test this hypothesis, we used fMRI to examine whether a symbolic nonword object (e.g., the Eiffel Tower) intended to represent something other than itself (i.e., Paris) could activate the VWFA. We found that scenes associated with symbolic meanings elicited a higher VWFA response than those not associated with symbolic meanings, and such top-down modulation on the VWFA can be established through short-term associative learning, even across modalities. In addition, the magnitude of the symbolic effect observed in the VWFA was positively correlated with the subjective experience on the strength of symbol-referent association across individuals. Therefore, the VWFA is likely a neural substrate for the interaction of the top-down processing of symbolic meanings with the analysis of bottom-up visual properties of sensory inputs, making the VWFA the location where the symbolic meaning of both words and nonword objects is represented.

Propulsion integration of hypersonic air-breathing vehicles utilizing a top-down design methodology

NASA Astrophysics Data System (ADS)

Kirkpatrick, Brad Kenneth

In recent years, a focus of aerospace engineering design has been the development of advanced design methodologies and frameworks to account for increasingly complex and integrated vehicles. Techniques such as parametric modeling, global vehicle analyses, and interdisciplinary data sharing have been employed in an attempt to improve the design process. The purpose of this study is to introduce a new approach to integrated vehicle design known as the top-down design methodology. In the top-down design methodology, the main idea is to relate design changes on the vehicle system and sub-system level to a set of over-arching performance and customer requirements. Rather than focusing on the performance of an individual system, the system is analyzed in terms of the net effect it has on the overall vehicle and other vehicle systems. This detailed level of analysis can only be accomplished through the use of high fidelity computational tools such as Computational Fluid Dynamics (CFD) or Finite Element Analysis (FEA). The utility of the top-down design methodology is investigated through its application to the conceptual and preliminary design of a long-range hypersonic air-breathing vehicle for a hypothetical next generation hypersonic vehicle (NHRV) program. System-level design is demonstrated through the development of the nozzle section of the propulsion system. From this demonstration of the methodology, conclusions are made about the benefits, drawbacks, and cost of using the methodology.

Profiling of integral membrane proteins and their post translational modifications using high-resolution mass spectrometry.

PubMed

Souda, Puneet; Ryan, Christopher M; Cramer, William A; Whitelegge, Julian

2011-12-01

Integral membrane proteins pose challenges to traditional proteomics approaches due to unique physicochemical properties including hydrophobic transmembrane domains that limit solubility in aqueous solvents. A well resolved intact protein molecular mass profile defines a protein's native covalent state including post-translational modifications, and is thus a vital measurement toward full structure determination. Both soluble loop regions and transmembrane regions potentially contain post-translational modifications that must be characterized if the covalent primary structure of a membrane protein is to be defined. This goal has been achieved using electrospray-ionization mass spectrometry (ESI-MS) with low-resolution mass analyzers for intact protein profiling, and high-resolution instruments for top-down experiments, toward complete covalent primary structure information. In top-down, the intact protein profile is supplemented by gas-phase fragmentation of the intact protein, including its transmembrane regions, using collisionally activated and/or electron-capture dissociation (CAD/ECD) to yield sequence-dependent high-resolution MS information. Dedicated liquid chromatography systems with aqueous/organic solvent mixtures were developed allowing us to demonstrate that polytopic integral membrane proteins are amenable to ESI-MS analysis, including top-down measurements. Covalent post-translational modifications are localized regardless of their position in transmembrane domains. Top-down measurements provide a more detail oriented high-resolution description of post-transcriptional and post-translational diversity for enhanced understanding beyond genomic translation. Copyright © 2011 Elsevier Inc. All rights reserved.

Impact of peripheral hearing loss on top-down auditory processing.

PubMed

Lesicko, Alexandria M H; Llano, Daniel A

2017-01-01

The auditory system consists of an intricate set of connections interposed between hierarchically arranged nuclei. The ascending pathways carrying sound information from the cochlea to the auditory cortex are, predictably, altered in instances of hearing loss resulting from blockage or damage to peripheral auditory structures. However, hearing loss-induced changes in descending connections that emanate from higher auditory centers and project back toward the periphery are still poorly understood. These pathways, which are the hypothesized substrate of high-level contextual and plasticity cues, are intimately linked to the ascending stream, and are thereby also likely to be influenced by auditory deprivation. In the current report, we review both the human and animal literature regarding changes in top-down modulation after peripheral hearing loss. Both aged humans and cochlear implant users are able to harness the power of top-down cues to disambiguate corrupted sounds and, in the case of aged listeners, may rely more heavily on these cues than non-aged listeners. The animal literature also reveals a plethora of structural and functional changes occurring in multiple descending projection systems after peripheral deafferentation. These data suggest that peripheral deafferentation induces a rebalancing of bottom-up and top-down controls, and that it will be necessary to understand the mechanisms underlying this rebalancing to develop better rehabilitation strategies for individuals with peripheral hearing loss. Copyright © 2016 Elsevier B.V. All rights reserved.

Bottom-up or top-down: unit cost estimation of tuberculosis diagnostic tests in India.

PubMed

Rupert, S; Vassall, A; Raizada, N; Khaparde, S D; Boehme, C; Salhotra, V S; Sachdeva, K S; Nair, S A; Hoog, A H Van't

2017-04-01

Of 18 sites that participated in an implementation study of the Xpert® MTB/RIF assay in India, we selected five microscopy centres and two reference laboratories. To obtain unit costs of diagnostic tests for tuberculosis (TB) and drug-resistant TB. Laboratories were purposely selected to capture regional variations and different laboratory types. Both bottom-up and the top-down methods were used to estimate unit costs. At the microscopy centres, mean bottom-up unit costs were respectively US$0.83 (range US$0.60-US$1.10) and US$12.29 (US$11.61-US$12.89) for sputum smear microscopy and Xpert. At the reference laboratories, mean unit costs were US$1.69 for the decontamination procedure, US$9.83 for a solid culture, US$11.06 for a liquid culture, US$29.88 for a drug susceptibility test, and US$18.18 for a line-probe assay. Top-down mean unit cost estimates were higher for all tests, and for sputum smear microscopy and Xpert these increased to respectively US$1.51 and US$13.58. The difference between bottom-up and top-down estimates was greatest for tests performed at the reference laboratories. These unit costs for TB diagnostics can be used to estimate resource requirements and cost-effectiveness in India, taking into account geographical location, laboratory type and capacity utilisation.

Global nitrogen budgets in cereals: A 50-year assessment for maize, rice, and wheat production systems.

PubMed

Ladha, J K; Tirol-Padre, A; Reddy, C K; Cassman, K G; Verma, Sudhir; Powlson, D S; van Kessel, C; de B Richter, Daniel; Chakraborty, Debashis; Pathak, Himanshu

2016-01-18

Industrially produced N-fertilizer is essential to the production of cereals that supports current and projected human populations. We constructed a top-down global N budget for maize, rice, and wheat for a 50-year period (1961 to 2010). Cereals harvested a total of 1551 Tg of N, of which 48% was supplied through fertilizer-N and 4% came from net soil depletion. An estimated 48% (737 Tg) of crop N, equal to 29, 38, and 25 kg ha(-1) yr(-1) for maize, rice, and wheat, respectively, is contributed by sources other than fertilizer- or soil-N. Non-symbiotic N2 fixation appears to be the major source of this N, which is 370 Tg or 24% of total N in the crop, corresponding to 13, 22, and 13 kg ha(-1) yr(-1) for maize, rice, and wheat, respectively. Manure (217 Tg or 14%) and atmospheric deposition (96 Tg or 6%) are the other sources of N. Crop residues and seed contribute marginally. Our scaling-down approach to estimate the contribution of non-symbiotic N2 fixation is robust because it focuses on global quantities of N in sources and sinks that are easier to estimate, in contrast to estimating N losses per se, because losses are highly soil-, climate-, and crop-specific.

Top-Down Versus Bottom-Up Estimative of CO2 and CO Vehicular Emission Contribution from the Megacity of SãO Paulo, Brazil

NASA Astrophysics Data System (ADS)

Andrade, M.; Nogueira, T.; Martínez, P. J.; Fornaro, A.; Miranda, R. M.; Ynoue, R.

2013-12-01

The Metropolitan Area of São Paulo (MASP) is composed by 39 municipalities with a population of 20 million inhabitants in an area of 8,511 km2. The main source of pollutants to the air is the vehicular emission: exhaust and evaporative fuel. The climate is influenced by the sea breeze from the Southeast direction - MASP is approximately 40 km far from the sea; and by the valley- mountain circulation, due to the presence of the Serra do Mar Mountains in the Northwest part of the city. This wind circulation suffers the influence of the heat island due to the high degree of urbanization. The MASP fleet is composed by approximately 7 million passenger cars and freight vehicles, with 85% light duty vehicles (LDVs), 3% heavy-duty diesel vehicles (HDVs, diesel + 5% bio-diesel) and 12% motorcycles. About 55% of LDVs burn a mixture of 78% gasoline and 22% ethanol (gasohol), 4% use hydrous ethanol (95% ethanol and 5% water), 38% are flex-fuel vehicles that are capable of burning both gasohol and hydrous ethanol and 2% use diesel (CETESB, 2013a). The use of gasohol or hydrous ethanol by the flex-fuel is determined by the price of the fuel. Vehicle traffic is the main source of regulated pollutants: carbon monoxide (CO), nitrogen oxides (NOx) and hydrocarbons (HC), and contributes to the formation of inhalable particulate matter emissions (PM10) as well as being the principal source of carbon dioxide (CO2). 97% of all CO emissions, 85% of HC, 82% of NOx, 36% of sulfur dioxide (SO2), and 36% of all PM10 emissions come from mobile sources (CETESB, 2013b). The official inventory is calculated with the botton-up methodology: calculation of the emission factors in dynamometer, estimation of the average distance each kind of vehicles drives per day and the total number of vehicles in circulation. The values considered a deterioration factor due to the vehicle aging. The top-down methodology was performed from measurements performed in experiments in traffic roads and tunnels. The data presented here compared tunnel measurements performed in 2004 and 2011. The official data estimate an emission of 15327 million tons per year of CO2eq (60% by LDV, 38% HDV and 2% motorcycles) and 128 million tons per year of CO. The top-down estimative based on tunnel measurements resulted in values approximately 5 times higher, being the difference more attributable to the estimative of the diesel emission factor. The uncertainties are related to the deterioration of the emission factor with time and the driving pattern. The diurnal variation of CO2 atmospheric concentration is characterized by the mobile source emission pattern. CETESB. Relatório Anual de Qualidade do Ar no Estado de São Paulo 2012. Companhia de Tecnologia de Saneamento Ambiental, São Paulo, Brazil, 2013a. CETESB. Plano de Controle de Poluição Veicular do Estado de São Paulo 2011 /2013. Companhia de Tecnologia de Saneamento Ambiental, São Paulo, Brazil, 2013b.

One decade of space-based isoprene emission estimates: Interannual variations and emission trends between 2005 and 2014

NASA Astrophysics Data System (ADS)

Bauwens, Maite; Stavrakou, Trissevgeni; Müller, Jean-François; De Smedt, Isabelle; Van Roozendael, Michel

2016-04-01

Isoprene is one of the most largely emitted hydrocarbons in the atmosphere, with global annual emissions estimated at about 500 Tg, but with large uncertainties (Arneth et al., 2011). Here we use the source inversion approach to derive top-down biogenic isoprene emission estimates for the period between 2005 and 2014 constrained by formaldehyde observations, a high-yield intermediate in the oxidation of isoprene in the atmosphere. Formaldehyde columns retrieved from the Ozone Monitoring Instrument (OMI) are used to constrain the IMAGESv2 global chemistry-transport model and its adjoint code (Stavrakou et al., 2009). The MEGAN-MOHYCAN isoprene emissions (Stavrakou et al., 2014) are used as bottom-up inventory in the model. The inversions are performed separately for each year of the study period, and monthly emissions are derived for every model grid cell. The inversion results are compared to independent isoprene emissions from GUESS-ES (Arneth et al., 2007) and MEGAN-MACC (Sinderalova et al., 2014) and to top-down fluxes based on GOME-2 formaldehyde columns (Bauwens et al., 2014; Stavrakou et al., 2015). The mean global annual OMI-based isoprene flux for the period 2005-2014 is estimated to be 270 Tg, with small interannual variation. This estimate is by 20% lower with regard to the a priori inventory on average, but on the regional scale strong emission updates are inferred. The OMI-based emissions are substantially lower than the MEGAN-MACC and the GUESS-ES inventory, but agree well with the isoprene fluxes constrained by GOME-2 formaldehyde columns. Strong emission reductions are derived over tropical regions. The seasonal pattern of isoprene emissions is generally well preserved after inversion and relatively consistent with other inventories, lending confidence to the MEGAN parameterization of the a priori inventory. In boreal regions the isoprene emission trend is positive and reinforced after inversion, whereas the inversion suggests negative trends in the rainforests of Equatorial Africa and South America. The top-down isoprene fluxes are available at a resolution of 0.5°x0.5° between 2005 and 2014 at the GlobEmission website (http://www.globemission.eu). References: Arneth, A., et al.: Process-based estimates of terrestrial ecosystem isoprene emissions: incorporating the effects of a direct CO 2-isoprene interaction, Atmos. Chem. Phys., 7(1), 31-53, 2007. Arneth, A., et al.: Global terrestrial isoprene emission models: sensitivity to variability in climate and vegetation, Atmos. Chem. Phys., 11(15), 8037-8052, 2011. Bauwens, M., et al.: Satellite-based isoprene emission estimates (2007-2012) from the GlobEmission project, in ACCENT-Plus Symposium 2013 Proceedings., 2014. Stavrakou, T., et al.: Isoprene emissions over Asia 1979 - 2012: impact of climate and land-use changes, Atmos. Chem. Phys., 14(9), 4587-4605, doi:10.5194/acp-14-4587-2014, 2014. Stavrakou, T., et al.: How consistent are top-down hydrocarbon emissions based on formaldehyde observations from GOME-2 and OMI?, Atmos. Chem. Phys., 15(20), 11861-11884, doi:10.5194/acp-15-11861-2015, 2015. Stavrakou, T., et al.: Evaluating the performance of pyrogenic and biogenic emission inventories against one decade of space-based formaldehyde columns, Atmos. Chem. Phys., 9(3), 1037-1060, doi:10.5194/acp-9-1037-2009, 2009.

Biotechnological Processes in Microbial Amylase Production

PubMed Central

Arshad, M. K. Md; Lakshmipriya, Thangavel; Hashim, Uda; Chinni, Suresh V.

2017-01-01

Amylase is an important and indispensable enzyme that plays a pivotal role in the field of biotechnology. It is produced mainly from microbial sources and is used in many industries. Industrial sectors with top-down and bottom-up approaches are currently focusing on improving microbial amylase production levels by implementing bioengineering technologies. The further support of energy consumption studies, such as those on thermodynamics, pinch technology, and environment-friendly technologies, has hastened the large-scale production of the enzyme. Herein, the importance of microbial (bacteria and fungi) amylase is discussed along with its production methods from the laboratory to industrial scales. PMID:28280725

Space station data system analysis/architecture study. Task 1: Functional requirements definition, DR-5. Appendix: Requirements data base

NASA Technical Reports Server (NTRS)

1985-01-01

Appendix A contains data that characterize the system functions in sufficient depth as to determine the requirements for the Space Station Data System (SSDS). This data is in the form of: (1) top down traceability report; (2) bottom up traceability report; (3) requirements data sheets; and (4) cross index of requirements paragraphs of the source documents and the requirements numbers. A data base users guide is included that interested parties can use to access the requirements data base and get up to date information about the functions.

Biotechnological Processes in Microbial Amylase Production.

PubMed

Gopinath, Subash C B; Anbu, Periasamy; Arshad, M K Md; Lakshmipriya, Thangavel; Voon, Chun Hong; Hashim, Uda; Chinni, Suresh V

2017-01-01

Amylase is an important and indispensable enzyme that plays a pivotal role in the field of biotechnology. It is produced mainly from microbial sources and is used in many industries. Industrial sectors with top-down and bottom-up approaches are currently focusing on improving microbial amylase production levels by implementing bioengineering technologies. The further support of energy consumption studies, such as those on thermodynamics, pinch technology, and environment-friendly technologies, has hastened the large-scale production of the enzyme. Herein, the importance of microbial (bacteria and fungi) amylase is discussed along with its production methods from the laboratory to industrial scales.

Elliptical quantum dots as on-demand single photons sources with deterministic polarization states

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

Teng, Chu-Hsiang; Demory, Brandon; Ku, Pei-Cheng, E-mail: peicheng@umich.edu

In quantum information, control of the single photon's polarization is essential. Here, we demonstrate single photon generation in a pre-programmed and deterministic polarization state, on a chip-scale platform, utilizing site-controlled elliptical quantum dots (QDs) synthesized by a top-down approach. The polarization from the QD emission is found to be linear with a high degree of linear polarization and parallel to the long axis of the ellipse. Single photon emission with orthogonal polarizations is achieved, and the dependence of the degree of linear polarization on the QD geometry is analyzed.

Evaluation of helicity generation in the tropical storm Gonu

NASA Astrophysics Data System (ADS)

Farahani, Majid M.; Khansalari, Sakineh; Azadi, Majid

2017-06-01

Helicity is a valuable dynamical concept for the study of rotating flows. Consequently helicity flux, indicative of the source or sink of helicity, owns comparable importance. In this study, while reviewing the existing methods, a mathematical relation between helicity and helicity-flux is introduced, discussed and examined. The computed values of helicity and helicity fluxes in an actual case, using the classical and this proposed method are compared. The down-stream helicity flux including sources and sinks of helicity is considered for the tropical storm Gonu that occurred over the coasts of Oman and Iran on June 2-7, 2007. Results show that the buoyancy, through the upper troposphere down to a height within boundary layer, is the main source in producing helicity, and surface friction from earth surface up to a height within boundary layer, is the main dissipating element of helicity. The dominance of buoyancy forcing over the dissipative friction forcing results in generation of vortex or enhancement of it after bouncing the land. Furthermore, the increase (decrease) of helicity results in an increase (decrease) in the height of the level in which maximum helicity flux occurs. It is suggested that the maximum helicity flux occurs at the top of the turbulent boundary layer, so that the height of boundary layer could be obtained.

Cognitive control, attention, and the other race effect in memory.

PubMed

Brown, Thackery I; Uncapher, Melina R; Chow, Tiffany E; Eberhardt, Jennifer L; Wagner, Anthony D

2017-01-01

People are better at remembering faces from their own race than other races-a phenomenon with significant societal implications. This Other Race Effect (ORE) in memory could arise from different attentional allocation to, and cognitive control over, same- and other-race faces during encoding. Deeper or more differentiated processing of same-race faces could yield more robust representations of same- vs. other-race faces that could support better recognition memory. Conversely, to the extent that other-race faces may be characterized by lower perceptual expertise, attention and cognitive control may be more important for successful encoding of robust, distinct representations of these stimuli. We tested a mechanistic model in which successful encoding of same- and other-race faces, indexed by subsequent memory performance, is differentially predicted by (a) engagement of frontoparietal networks subserving top-down attention and cognitive control, and (b) interactions between frontoparietal networks and fusiform cortex face processing. European American (EA) and African American (AA) participants underwent fMRI while intentionally encoding EA and AA faces, and ~24 hrs later performed an "old/new" recognition memory task. Univariate analyses revealed greater engagement of frontoparietal top-down attention and cognitive control networks during encoding for same- vs. other-race faces, stemming particularly from a failure to engage the cognitive control network during processing of other-race faces that were subsequently forgotten. Psychophysiological interaction (PPI) analyses further revealed that OREs were characterized by greater functional interaction between medial intraparietal sulcus, a component of the top-down attention network, and fusiform cortex during same- than other-race face encoding. Together, these results suggest that group-based face memory biases at least partially stem from differential allocation of cognitive control and top-down attention during encoding, such that same-race memory benefits from elevated top-down attentional engagement with face processing regions; conversely, reduced recruitment of cognitive control circuitry appears more predictive of memory failure when encoding out-group faces.

Cognitive control, attention, and the other race effect in memory

PubMed Central

Uncapher, Melina R.; Chow, Tiffany E.; Eberhardt, Jennifer L.; Wagner, Anthony D.

2017-01-01

People are better at remembering faces from their own race than other races–a phenomenon with significant societal implications. This Other Race Effect (ORE) in memory could arise from different attentional allocation to, and cognitive control over, same- and other-race faces during encoding. Deeper or more differentiated processing of same-race faces could yield more robust representations of same- vs. other-race faces that could support better recognition memory. Conversely, to the extent that other-race faces may be characterized by lower perceptual expertise, attention and cognitive control may be more important for successful encoding of robust, distinct representations of these stimuli. We tested a mechanistic model in which successful encoding of same- and other-race faces, indexed by subsequent memory performance, is differentially predicted by (a) engagement of frontoparietal networks subserving top-down attention and cognitive control, and (b) interactions between frontoparietal networks and fusiform cortex face processing. European American (EA) and African American (AA) participants underwent fMRI while intentionally encoding EA and AA faces, and ~24 hrs later performed an “old/new” recognition memory task. Univariate analyses revealed greater engagement of frontoparietal top-down attention and cognitive control networks during encoding for same- vs. other-race faces, stemming particularly from a failure to engage the cognitive control network during processing of other-race faces that were subsequently forgotten. Psychophysiological interaction (PPI) analyses further revealed that OREs were characterized by greater functional interaction between medial intraparietal sulcus, a component of the top-down attention network, and fusiform cortex during same- than other-race face encoding. Together, these results suggest that group-based face memory biases at least partially stem from differential allocation of cognitive control and top-down attention during encoding, such that same-race memory benefits from elevated top-down attentional engagement with face processing regions; conversely, reduced recruitment of cognitive control circuitry appears more predictive of memory failure when encoding out-group faces. PMID:28282414

Top-down and bottom-up lipidomic analysis of rabbit lipoproteins under different metabolic conditions using flow field-flow fractionation, nanoflow liquid chromatography and mass spectrometry.

PubMed

Byeon, Seul Kee; Kim, Jin Yong; Lee, Ju Yong; Chung, Bong Chul; Seo, Hong Seog; Moon, Myeong Hee

2015-07-31

This study demonstrated the performances of top-down and bottom-up approaches in lipidomic analysis of lipoproteins from rabbits raised under different metabolic conditions: healthy controls, carrageenan-induced inflammation, dehydration, high cholesterol (HC) diet, and highest cholesterol diet with inflammation (HCI). In the bottom-up approach, the high density lipoproteins (HDL) and the low density lipoproteins (LDL) were size-sorted and collected on a semi-preparative scale using a multiplexed hollow fiber flow field-flow fractionation (MxHF5), followed by nanoflow liquid chromatography-ESI-MS/MS (nLC-ESI-MS/MS) analysis of the lipids extracted from each lipoprotein fraction. In the top-down method, size-fractionated lipoproteins were directly infused to MS for quantitative analysis of targeted lipids using chip-type asymmetrical flow field-flow fractionation-electrospray ionization-tandem mass spectrometry (cAF4-ESI-MS/MS) in selected reaction monitoring (SRM) mode. The comprehensive bottom-up analysis yielded 122 and 104 lipids from HDL and LDL, respectively. Rabbits within the HC and HCI groups had lipid patterns that contrasted most substantially from those of controls, suggesting that HC diet significantly alters the lipid composition of lipoproteins. Among the identified lipids, 20 lipid species that exhibited large differences (>10-fold) were selected as targets for the top-down quantitative analysis in order to compare the results with those from the bottom-up method. Statistical comparison of the results from the two methods revealed that the results were not significantly different for most of the selected species, except for those species with only small differences in concentration between groups. The current study demonstrated that top-down lipid analysis using cAF4-ESI-MS/MS is a powerful high-speed analytical platform for targeted lipidomic analysis that does not require the extraction of lipids from blood samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Top-down and middle-down approach by fraction collection enrichment using off-line capillary electrophoresis - mass spectrometry coupling: Application to monoclonal antibody Fc/2 charge variants.

PubMed

Biacchi, Michael; Said, Nassur; Beck, Alain; Leize-Wagner, Emmanuelle; François, Yannis-Nicolas

2017-05-19

The characterization of complex protein mixtures represents one of the biggest challenge in many research fields such as biological or biopharmaceutical sciences. Out of all categories, monoclonal antibodies (mAbs) and related products drawn the most interest due to their strong therapeutic potency and specificity. Because of their intrinsic complexity due to a large number of micro-heterogeneities, there is a crucial need for analytical methods to provide comprehensive in-depth characterization of these proteins. In this work, we developed a methodology using CE-UV/MALDI-MS to perform top-down or middle-down characterization after fraction collection enrichment applied to intact protein and mAbs samples. The performance of the method was evaluated with the rapid separation of three intact protein mixture. Good robustness of CZE separation and quality of MALDI-MS spectra and MALDI-ISD spectra of each protein confirms the usefulness of sample enrichment to obtain adequate quantity of deposed protein for top-down analysis and the proof of principle of the method. In a second step, the method was applied to the middle-down characterization of Fc/2 cetuximab variants. Identification of around 9% sequence coverage of Fc/2 cetuximab fragments allows to conclude on the feasibility of the strategy for middle-down characterization of Fc/2 cetuximab variants using CE-UV/MALDI-MS. Moreover, MALDI-ISD fragmentation of Fc/2 cetuximab variants confirm separation phenomenon based on the formation of Fc/2 dimers with and without C-terminal truncation. Copyright © 2017 Elsevier B.V. All rights reserved.

Tropical forests are a net carbon source based on aboveground measurements of gain and loss

NASA Astrophysics Data System (ADS)

Baccini, A.; Walker, W.; Carvalho, L.; Farina, M.; Sulla-Menashe, D.; Houghton, R. A.

2017-10-01

The carbon balance of tropical ecosystems remains uncertain, with top-down atmospheric studies suggesting an overall sink and bottom-up ecological approaches indicating a modest net source. Here we use 12 years (2003 to 2014) of MODIS pantropical satellite data to quantify net annual changes in the aboveground carbon density of tropical woody live vegetation, providing direct, measurement-based evidence that the world’s tropical forests are a net carbon source of 425.2 ± 92.0 teragrams of carbon per year (Tg C year-1). This net release of carbon consists of losses of 861.7 ± 80.2 Tg C year-1 and gains of 436.5 ± 31.0 Tg C year-1. Gains result from forest growth; losses result from deforestation and from reductions in carbon density within standing forests (degradation or disturbance), with the latter accounting for 68.9% of overall losses.