Fast and behavior-selective exploitation of a marine fish targeted by anglers

NASA Astrophysics Data System (ADS)

Alós, Josep; Palmer, Miquel; Rosselló, Rosario; Arlinghaus, Robert

2016-12-01

Harvesting of wild-living animals is often intensive and may selectively target heritable behavioral traits. We studied the exploitation dynamics and the vulnerability consequences of individual heterogeneity in movement-related behaviors in free-ranging pearly razorfish (Xyrichthys novacula). Using underwater-video recording, we firstly document a fast and high exploitation rate of about 60% of the adult population removed in just few days after the opening of the season. Subsequently, we tagged a sample of individuals with acoustic transmitters and studied whether behavioral traits were significant predictors of the vulnerability to angling. Tagged individuals revealed repeatable behaviors in several home range-related traits, suggesting the presence of spatial behavioral types. The individuals surviving the experimental fishery showed only localized and low-intensity movement patterns. Our study provides new insights for understanding the harvesting pressures and selective properties acting on behavioral traits of recreational fishing. Many fish stocks around the globe are today predominantly exploited by recreational fisheries. The fisheries-induced change in fish behavior described here may be therefore widespread, and has the potential to alter food-webs, profitability of the fisheries and to affect stock assessment by eroding catchability in the long-term.

Integrating Climate Science, Marine Ecology, and Fisheries Economics to Predict the Effects of Climate Change on New England lobster Fisheries

NASA Astrophysics Data System (ADS)

Le Bris, A.; Pershing, A. J.; Holland, D. S.; Mills, K.; Sun, C. H. J.

2016-02-01

The Gulf of Maine and the northwest Atlantic shelf have experienced one of the fastest warming rates of the global ocean over the past decade, and concerns are growing about the long-term sustainability of the fishing industries in the region. The lucrative American lobster fishery occurs over a steep temperature gradient, providing a unique opportunity to evaluate the consequences of climate change and variability on marine socio-ecological systems. This study aims at developing an integrated climate, population dynamics, and fishery economics model to predict consequences of climate change on the American lobster fishery. In this talk, we first describe a mechanistic model that combines life-history theory and a size-spectrum approach to simulate the dynamics of the population. Results show that as temperature increases, early growth rate and predation on small individuals increases, while size-at-maturity, maximum length and predation on large individuals decreases, resulting in a lower recruitment in the southern New-England and higher recruitment in the northern Gulf of Maine. Second, we present an integrated fishery and economic module that links temperature to landings and price through its influence on catchability and abundance. Preliminary results show that temperature is positively correlated with landings and negatively correlated with price in the Gulf of Maine. Finally, we discuss how model simulations under various fishing effort, market and climate scenarios can be used to identify adaptation opportunities to improve the resilience of the fishery to climate change.

Development of working hypotheses linking management of the Missouri River to population dynamics of Scaphirhynchus albus (pallid sturgeon)

USGS Publications Warehouse

Jacobson, Robert B.; Parsley, Michael J.; Annis, Mandy L.; Colvin, Michael E.; Welker, Timothy L.; James, Daniel A.

2016-01-20

The initial set of candidate hypotheses provides a useful starting point for quantitative modeling and adaptive management of the river and species. We anticipate that hypotheses will change from the set of working management hypotheses as adaptive management progresses. More importantly, hypotheses that have been filtered out of our multistep process are still being considered. These filtered hypotheses are archived and if existing hypotheses are determined to be inadequate to explain observed population dynamics, new hypotheses can be created or filtered hypotheses can be reinstated.

Intercalibration of research survey vessels on Lake Erie

USGS Publications Warehouse

Tyson, J.T.; Johnson, T.B.; Knight, C.T.; Bur, M.T.

2006-01-01

Fish abundance indices obtained from annual research trawl surveys are an integral part of fisheries stock assessment and management in the Great Lakes. It is difficult, however, to administer trawl surveys using a single vessel-gear combination owing to the large size of these systems, the jurisdictional boundaries that bisect the Great Lakes, and changes in vessels as a result of fleet replacement. When trawl surveys are administered by multiple vessel-gear combinations, systematic error may be introduced in combining catch-per-unit-effort (CPUE) data across vessels. This bias is associated with relative differences in catchability among vessel-gear combinations. In Lake Erie, five different research vessels conduct seasonal trawl surveys in the western half of the lake. To eliminate this systematic bias, the Lake Erie agencies conducted a side-by-side trawling experiment in 2003 to develop correction factors for CPUE data associated with different vessel-gear combinations. Correcting for systematic bias in CPUE data should lead to more accurate and comparable estimates of species density and biomass. We estimated correction factors for the 10 most commonly collected species age-groups for each vessel during the experiment. Most of the correction factors (70%) ranged from 0.5 to 2.0, indicating that the systematic bias associated with different vessel-gear combinations was not large. Differences in CPUE were most evident for vessels using different sampling gears, although significant differences also existed for vessels using the same gears. These results suggest that standardizing gear is important for multiple-vessel surveys, but there will still be significant differences in catchability stemming from the vessel effects and agencies must correct for this. With standardized estimates of CPUE, the Lake Erie agencies will have the ability to directly compare and combine time series for species abundance. ?? Copyright by the American Fisheries Society 2006.

Effects of environmental covariates and density on the catchability of fish populations and interpretation of catch per unit effort trends

USGS Publications Warehouse

Korman, Josh; Yard, Mike

2017-01-01

Article for outlet: Fisheries Research. Abstract: Quantifying temporal and spatial trends in abundance or relative abundance is required to evaluate effects of harvest and changes in habitat for exploited and endangered fish populations. In many cases, the proportion of the population or stock that is captured (catchability or capture probability) is unknown but is often assumed to be constant over space and time. We used data from a large-scale mark-recapture study to evaluate the extent of spatial and temporal variation, and the effects of fish density, fish size, and environmental covariates, on the capture probability of rainbow trout (Oncorhynchus mykiss) in the Colorado River, AZ. Estimates of capture probability for boat electrofishing varied 5-fold across five reaches, 2.8-fold across the range of fish densities that were encountered, 2.1-fold over 19 trips, and 1.6-fold over five fish size classes. Shoreline angle and turbidity were the best covariates explaining variation in capture probability across reaches and trips. Patterns in capture probability were driven by changes in gear efficiency and spatial aggregation, but the latter was more important. Failure to account for effects of fish density on capture probability when translating a historical catch per unit effort time series into a time series of abundance, led to 2.5-fold underestimation of the maximum extent of variation in abundance over the period of record, and resulted in unreliable estimates of relative change in critical years. Catch per unit effort surveys have utility for monitoring long-term trends in relative abundance, but are too imprecise and potentially biased to evaluate population response to habitat changes or to modest changes in fishing effort.

The impact of chief executive officer personality on top management team dynamics:one mechanism by which leadership affects organizational performance.

PubMed

Peterson, Randall S; Smith, D Brent; Martorana, Paul V; Owens, Pamela D

2003-10-01

This article explores 1 mechanism by which leader personality affects organizational performance. The authors hypothesized and tested the effects of leader personality on the group dynamics of the top management team (TMT) and of TMT dynamics on organizational performance. To test their hypotheses, the authors used the group dynamics q-sort method, which is designed to permit rigorous, quantitative comparisons of data derived from qualitative sources. Results from independent observations of chief executive officer (CEO) personality and TMT dynamics for 17 CEOs supported the authors' hypothesized relationships both between CEO personality and TMT group dynamics and between TMT dynamics and organizational performance.

Toward Dynamic Ocean Management: Fisheries assessment and climate projections informed by community developed habitat models based on dynamic coastal oceanography

NASA Astrophysics Data System (ADS)

Kohut, J. T.; Manderson, J.; Palamara, L. J.; Saba, V. S.; Saba, G.; Hare, J. A.; Curchitser, E. N.; Moore, P.; Seibel, B.; DiDomenico, G.

2016-12-01

Through a multidisciplinary study group of experts in marine ecology, physical oceanography and stock assessment from the fishing industry, government and academia we developed a method to explicitly account for shifting habitat distributions in fish population assessments. We used data from field surveys throughout the Northwest Atlantic Ocean to develop a parametric thermal niche model for an important short-lived pelagic forage fish, Atlantic Butterfish. This niche model was coupled to a hindcast of daily bottom water temperature derived from a regional numerical ocean model in order to project daily thermal habitat suitability over the last 40 years. This ecological hindcast was used to estimate the proportion of thermal habitat suitability available on the U.S. Northeast Shelf that was sampled on fishery-independent surveys, accounting for the relative motions of thermal habitat and the trajectory of sampling on the survey. The method and habitat based estimates of availability was integrated into the catchability estimate used to scale population size in the butterfish stock assessment model accepted by the reviewers of the 59th NEFSC stock assessment review, as well as the mid-Atlantic Council's Scientific and Statistical Committee. The contribution of the availability estimate (along with an estimate of detectability) allowed for the development of fishery reference points, a change in stock status from unknown to known, and the establishment of a directed fishery with an allocation of 20,000 metric tons of quota. This presentation will describe how a community based workgroup utilized ocean observing technologies combined with ocean models to better understand the physical ocean that structures marine ecosystems. Using these approaches we will discuss opportunities to inform ecological hindcasts and climate projections with mechanistic models that link species-specific physiology to climate-based thermal scenarios.

Toward Dynamic Ocean Management: Fisheries assessment and climate projections informed by community developed habitat models based on dynamic coastal oceanography

NASA Astrophysics Data System (ADS)

Kohut, J. T.; Manderson, J.; Palamara, L. J.; Saba, V. S.; Saba, G.; Hare, J. A.; Curchitser, E. N.; Moore, P.; Seibel, B.; DiDomenico, G.

2016-02-01

Through a multidisciplinary study group of experts in marine ecology, physical oceanography and stock assessment from the fishing industry, government and academia we developed a method to explicitly account for shifting habitat distributions in fish population assessments. We used data from field surveys throughout the Northwest Atlantic Ocean to develop a parametric thermal niche model for an important short-lived pelagic forage fish, Atlantic Butterfish. This niche model was coupled to a hindcast of daily bottom water temperature derived from a regional numerical ocean model in order to project daily thermal habitat suitability over the last 40 years. This ecological hindcast was used to estimate the proportion of thermal habitat suitability available on the U.S. Northeast Shelf that was sampled on fishery-independent surveys, accounting for the relative motions of thermal habitat and the trajectory of sampling on the survey. The method and habitat based estimates of availability was integrated into the catchability estimate used to scale population size in the butterfish stock assessment model accepted by the reviewers of the 59th NEFSC stock assessment review, as well as the mid-Atlantic Council's Scientific and Statistical Committee. The contribution of the availability estimate (along with an estimate of detectability) allowed for the development of fishery reference points, a change in stock status from unknown to known, and the establishment of a directed fishery with an allocation of 20,000 metric tons of quota. This presentation will describe how a community based workgroup utilized ocean observing technologies combined with ocean models to better understand the physical ocean that structures marine ecosystems. Using these approaches we will discuss opportunities to inform ecological hindcasts and climate projections with mechanistic models that link species-specific physiology to climate-based thermal scenarios.

Environmental preferences of tuna and non-tuna species associated with drifting fish aggregating devices (DFADs) in the Atlantic Ocean, ascertained through fishers' echo-sounder buoys

NASA Astrophysics Data System (ADS)

Lopez, Jon; Moreno, Gala; Lennert-Cody, Cleridy; Maunder, Mark; Sancristobal, Igor; Caballero, Ainhoa; Dagorn, Laurent

2017-06-01

Understanding the relationship between environmental variables and pelagic species concentrations and dynamics is helpful to improve fishery management, especially in a changing environment. Drifting fish aggregating device (DFAD)-associated tuna and non-tuna biomass data from the fishers' echo-sounder buoys operating in the Atlantic Ocean have been modelled as functions of oceanographic (Sea Surface Temperature, Chlorophyll-a, Salinity, Sea Level Anomaly, Thermocline depth and gradient, Geostrophic current, Total Current, Depth) and DFAD variables (DFAD speed, bearing and soak time) using Generalized Additive Mixed Models (GAMMs). Biological interaction (presence of non-tuna species at DFADs) was also included in the tuna model, and found to be significant at this time scale. All variables were included in the analyses but only some of them were highly significant, and variable significance differed among fish groups. In general, most of the fish biomass distribution was explained by the ocean productivity and DFAD-variables. Indeed, this study revealed different environmental preferences for tunas and non-tuna species and suggested the existence of active habitat selection. This improved assessment of environmental and DFAD effects on tuna and non-tuna catchability in the purse seine tuna fishery will contribute to transfer of better scientific advice to regional tuna commissions for the management and conservation of exploited resources.

Standardization of a geo-referenced fishing data set for the Indian Ocean bigeye tuna, Thunnus obesus (1952-2014)

NASA Astrophysics Data System (ADS)

Wibawa, Teja A.; Lehodey, Patrick; Senina, Inna

2017-02-01

Geo-referenced catch and fishing effort data of the bigeye tuna fisheries in the Indian Ocean over 1952-2014 were analyzed and standardized to facilitate population dynamics modeling studies. During this 62-year historical period of exploitation, many changes occurred both in the fishing techniques and the monitoring of activity. This study includes a series of processing steps used for standardization of spatial resolution, conversion and standardization of catch and effort units, raising of geo-referenced catch into nominal catch level, screening and correction of outliers, and detection of major catchability changes over long time series of fishing data, i.e., the Japanese longline fleet operating in the tropical Indian Ocean. A total of 30 fisheries were finally determined from longline, purse seine and other-gears data sets, from which 10 longline and 4 purse seine fisheries represented 96 % of the whole historical geo-referenced catch. Nevertheless, one-third of total nominal catch is still not included due to a total lack of geo-referenced information and would need to be processed separately, accordingly to the requirements of the study. The geo-referenced records of catch, fishing effort and associated length frequency samples of all fisheries are available at doi:10.1594/PANGAEA.864154.

Fish and fisher behaviour influence the vulnerability of groupers (Epinephelidae) to fishing at a multispecies spawning aggregation site

NASA Astrophysics Data System (ADS)

Robinson, J.; Graham, N. A. J.; Cinner, J. E.; Almany, G. R.; Waldie, P.

2015-06-01

Targeted fishing of spawning aggregations is a major contributor to extinction risk in numerous species of grouper (Epinephelidae). Marine reserves are often used to protect spawning aggregation sites, including multispecies sites shared by several species of grouper. However, marine reserves may be biologically, socioeconomically or culturally unviable in some fisheries, and alternative management actions must be explored. Implementing effective management actions that control rather than prohibit fishing requires an improved understanding of how species vary in their vulnerability to fishing gears and respond to changes in fishing effort. To estimate sources of variability in vulnerability to fishing (i.e. catchability), catch-per-unit-effort (CPUE) and other fisheries data were collected in parallel with underwater visual census-derived estimates of aggregation size at a multispecies spawning site of Epinephelus fuscoguttatus and E. polyphekadion. Despite having similar abundances, E. polyphekadion was eightfold more vulnerable to capture by hook-and-line gear, clearly outcompeting its congener for bait. Contrasting with the common assumption of a proportional relationship, the CPUE of both species was unrelated to the size of their respective aggregations. Moreover, the CPUE of each species was unrelated to hook size and depth fished. However, E. polyphekadion CPUE declined as the density of fishing effort increased at the site, with gear saturation identified as the likely mechanism for this effect. E. fuscoguttatus CPUE was negatively related to the size of aggregations formed by its congener, stemming from the superior competitiveness and therefore higher selectivity of the gear for E. polyphekadion. Our findings demonstrate that CPUE is an unreliable indicator of spawning aggregation status. The other sources of variation in CPUE that we identify have implications for gear-based management, which must be based on understanding of gear selectivity for aggregating species, and fishing effort controls, which must consider the potential for effort-dependent patterns in catchability.

Growth, condition, diet, and consumption rates of northern pike in three Arizona reservoirs

USGS Publications Warehouse

Flinders, J.M.; Bonar, Scott A.

2008-01-01

Northern pike (Esox lucius L.) introductions are controversial in the western United States due to suspected impacts they might have on established sport fisheries and potential illegal introductions. Tbree Arizona reservoirs, Parker Canyon Lake, Upper Lake Mary and Long Lake were sampled to examine the diet, consumption dynamics, and growth of northern pike. Northern pike diets varied by season and reservoir. In Parker Canyon Lake, diets were dominated by rainbow trout in winter and spring and bluegill and green sunfish in the fall. In Long Lake the northern pike ate crayfish in spring and early summer and switched to young of the year common carp in summer and fall. Black crappie, golden shiners, and crayfish were the major prey in Upper Lake Mary during spring, but they switched to stocked rainbow trout in the fall. Northern pike growth was in the high range of growth reported throughout the United States. Estimated northern pike specific consumption rate (scr) of rainbow trout (g/g/d ?? 10-6) was greatest in Upper Lake Mary (scr = 329.1 ?? 23.7 g/g/d ?? 10-6) where stocked fingerling (280 mm TL) rainbow trout stocked in Long Lake (scr = 1.4 ?? 0.1 g/g/d ?? 10-6) and Parker Canyon Lake (scr = 287.2 ?? 15.1 g/g/d ?? 10-6) where catchable-sized rainbow trout were stocked. Managers should consider the cost-benefits of stocking fish >200 mm TL in lakes containing northern pike. ?? Copyright by the North American Lake Management Society 2008.

Spatial variability of Spanish sardine (Sardinella aurita) abundance as related to the upwelling cycle off the southeastern Caribbean Sea

PubMed Central

Cárdenas, Juan José; Achury, Alina; Astor, Yrene

2017-01-01

The Sardinella aurita fishery off northeastern Venezuela, region of seasonal wind-driven coastal-upwelling, accounts for 90% of the Caribbean Sea small pelagic catch. This law-protected artisanal fishery takes place up to ~10 km offshore. The spatial distribution, number of schools, and biomass of S. aurita were studied using eight hydro-acoustic surveys (1995–1998). The study included the analysis of satellite-derived sea surface temperature and chlorophyll-a. Surveys were grouped by strong, weak, and transitional upwelling seasons. Relationships between these observations were analyzed using Generalized Additive Models. Results show that during the primary upwelling season (January-May) sardines were widely distributed in upwelling plumes that extended up to 70 km offshore. In the other hand, during the weak upwelling season (September-October) higher sardine densities were found within 10 Km off the coastal upwelling foci. The number of small pelagic schools was directly correlated with small pelagic densities; however, regardless of the season, higher numbers of small pelagic schools were always closer to the shoreline, especially during warm conditions. These two behaviors increase the availability and catchability of sardines for the artisanal fishery during the warm season, regardless of the total stock size. Using this evidence, we pose the hypothesis that the collapse of the regional S. aurita fishery in 2005 was due to a combination of stressful habitat conditions sustained since 2004. These included bottom-up factors due to food scarcity caused by weak upwelling, combined with top-down stress due to overfishing, as sardines accumulated in narrow diminished upwelling plumes located close to the coast. The increased catchability within easily accessible upwelling foci led to the demise of this biological resource, which as of 2014 had not yet recovered. Environmental conditions affecting the sardine habitat needs to be taken into account for the management of this stock. For example, during years with weak upwelling, special measures should be taken during the warm season on the second half of the year to avoid further pressure on the stock. PMID:28654685

Assessing potential impacts of energized submarine power cables on crab harvests

NASA Astrophysics Data System (ADS)

Love, Milton S.; Nishimoto, Mary M.; Clark, Scott; McCrea, Merit; Bull, Ann Scarborough

2017-12-01

Offshore renewable energy facilities transmit electricity to shore through submarine power cables. Electromagnetic field emissions (EMFs) are generated from the transmission of electricity through these cables, such as the AC inter-array (between unit) and AC export (to shore) cables often used in offshore energy production. The EMF has both an electric component and a magnetic component. While sheathing can block the direct electric field, the magnetic field is not blocked. A concern raised by fishermen on the Pacific Coast of North America is that commercially important Dungeness crab (Metacarcinus magister Dana, 1852)) might not cross over an energized submarine power cable to enter a baited crab trap, thus potentially reducing their catch. The presence of operating energized cables off southern California and in Puget Sound (cables that are comparable to those within the arrays of existing offshore wind energy devices) allowed us to conduct experiments on how energized power cables might affect the harvesting of both M. magister and another commercially important crab species, Cancer productus Randall, 1839. In this study we tested the questions: 1) Is the catchability of crabs reduced if these animals must traverse an energized power cable to enter a trap and 2) if crabs preferentially do not cross an energized cable, is it the cable structure or the EMF emitted from that cable that deters crabs from crossing? In field experiments off southern California and in Puget Sound, crabs were given a choice of walking over an energized power cable to a baited trap or walking directly away from that cable to a second baited trap. Based on our research we found no evidence that the EMF emitted by energized submarine power cables influenced the catchability of these two species of commercially important crabs. In addition, there was no difference in the crabs' responses to lightly buried versus unburied cables. We did observe that, regardless of the position of the cable, Cancer productus in southern California tended to move to the west and Metacarcinus magister tended to move to the east.

Intercalibration of MOCNESS and Bongo nets: Assessing relative efficiency for ichthyoplankton

NASA Astrophysics Data System (ADS)

Johnson, Donna L.; Fogarty, Michael J.

2013-01-01

The evaluation of catchability of egg and larval fish with the 0.61-m Bongo and the 1-m2 Multiple Opening and Closing Net Environmental Sensing System (MOCNESS) was conducted as part of a paired station analysis. The two samplers were deployed on 331 stations on Georges Bank during the U.S. GLOBEC program from January through June for years 1996 and 1997. Significant differences were found when combined catches of all eggs and all larvae for each sampler were compared. Overall catches of larvae from the MOCNESS were 3-5 times greater than those from the Bongo. Gear effects were modeled and revealed that the catches in 14 of the 22 dominant taxa were significantly different between sampling gear. The differences between samplers during diel intervals for the taxa were not significantly different.

Climate Change in U.S. South Atlantic, Gulf of Mexico and Caribbean Fisheries Regions

NASA Astrophysics Data System (ADS)

Roffer, M. A.; Hernandez, D. L.; Lamkin, J. T.; Pugliese, R.; Reichert, M.; Hall, C.

2016-02-01

A review of the recent evidence that climate change is affecting marine ecosystems in the U.S. fishery management zones of the South Atlantic, Gulf of Mexico and Caribbean regions will be presented. This will include affects on the living marine resources (including fish, invertebrates, marine mammals and turtles), fisheries, habitat and people. Emphasis will be given on the effects that impact managed species and the likely new challenges that they present to fishery managers. The evidence is being derived from the results of the "Climate Variability and Fisheries Workshop: Setting Research Priorities for the Gulf of Mexico, South Atlantic, and Caribbean Regions," October 26-28, 2015 in St. Petersburg Beach, Florida. Commonalities and regional differences will be presented in terms of how climate variability is likely to impact distribution, catch, catchability, socioeconomics, and management.

Landscape prediction and mapping of game fish biomass, an ecosystem service of Michigan rivers

USGS Publications Warehouse

Esselman, Peter C.; Stevenson, R Jan; Lupi, Frank; Riseng, Catherine M.; Wiley, Michael J.

2015-01-01

The increased integration of ecosystem service concepts into natural resource management places renewed emphasis on prediction and mapping of fish biomass as a major provisioning service of rivers. The goals of this study were to predict and map patterns of fish biomass as a proxy for the availability of catchable fish for anglers in rivers and to identify the strongest landscape constraints on fish productivity. We examined hypotheses about fish responses to total phosphorus (TP), as TP is a growth-limiting nutrient known to cause increases (subsidy response) and/or decreases (stress response) in fish biomass depending on its concentration and the species being considered. Boosted regression trees were used to define nonlinear functions that predicted the standing crops of Brook Trout Salvelinus fontinalis, Brown Trout Salmo trutta, Smallmouth Bass Micropterus dolomieu, panfishes (seven centrarchid species), and Walleye Sander vitreus by using landscape and modeled local-scale predictors. Fitted models were highly significant and explained 22–56% of the variation in validation data sets. Nonlinear and threshold responses were apparent for numerous predictors, including TP concentration, which had significant effects on all except the Walleye fishery. Brook Trout and Smallmouth Bass exhibited both subsidy and stress responses, panfish biomass exhibited a subsidy response only, and Brown Trout exhibited a stress response. Maps of reach-specific standing crop predictions showed patterns of predicted fish biomass that corresponded to spatial patterns in catchment area, water temperature, land cover, and nutrient availability. Maps illustrated predictions of higher trout biomass in coldwater streams draining glacial till in northern Michigan, higher Smallmouth Bass and panfish biomasses in warmwater systems of southern Michigan, and high Walleye biomass in large main-stem rivers throughout the state. Our results allow fisheries managers to examine the biomass potential of streams, describe geographic patterns of fisheries, explore possible nutrient management targets, and identify habitats that are candidates for species management.

Fisheries conservation on the high seas: linking conservation physiology and fisheries ecology for the management of large pelagic fishes

PubMed Central

Horodysky, Andrij Z.; Cooke, Steven J.; Graves, John E.; Brill, Richard W.

2016-01-01

Populations of tunas, billfishes and pelagic sharks are fished at or over capacity in many regions of the world. They are captured by directed commercial and recreational fisheries (the latter of which often promote catch and release) or as incidental catch or bycatch in commercial fisheries. Population assessments of pelagic fishes typically incorporate catch-per-unit-effort time-series data from commercial and recreational fisheries; however, there have been notable changes in target species, areas fished and depth-specific gear deployments over the years that may have affected catchability. Some regional fisheries management organizations take into account the effects of time- and area-specific changes in the behaviours of fish and fishers, as well as fishing gear, to standardize catch-per-unit-effort indices and refine population estimates. However, estimates of changes in stock size over time may be very sensitive to underlying assumptions of the effects of oceanographic conditions and prey distribution on the horizontal and vertical movement patterns and distribution of pelagic fishes. Effective management and successful conservation of pelagic fishes requires a mechanistic understanding of their physiological and behavioural responses to environmental variability, potential for interaction with commercial and recreational fishing gear, and the capture process. The interdisciplinary field of conservation physiology can provide insights into pelagic fish demography and ecology (including environmental relationships and interspecific interactions) by uniting the complementary expertise and skills of fish physiologists and fisheries scientists. The iterative testing by one discipline of hypotheses generated by the other can span the fundamental–applied science continuum, leading to the development of robust insights supporting informed management. The resulting species-specific understanding of physiological abilities and tolerances can help to improve stock assessments, develop effective bycatch-reduction strategies, predict rates of post-release mortality, and forecast the population effects of environmental change. In this synthesis, we review several examples of these interdisciplinary collaborations that currently benefit pelagic fisheries management. PMID:27382467

Dynamic hypoxic zones in Lake Erie compress fish habitat, altering vulnerability to fishing gears

USGS Publications Warehouse

Kraus, Richard T.; Knight, Carey T.; Farmer, Troy M.; Gorman, Ann Marie; Collingsworth, Paris D.; Warren, Glenn J.; Kocovsky, Patrick M.; Conroy, Joseph D.

2015-01-01

Seasonal degradation of aquatic habitats from hypoxia occurs in numerous freshwater and coastal marine systems and can result in direct mortality or displacement of fish. Yet, fishery landings from these systems are frequently unresponsive to changes in the severity and extent of hypoxia, and population-scale effects have been difficult to measure except in extreme hypoxic conditions with hypoxia-sensitive species. We investigated fine-scale temporal and spatial variability in dissolved oxygen in Lake Erie as it related to fish distribution and catch efficiencies of both active (bottom trawls) and passive (trap nets) fishing gears. Temperature and dissolved oxygen loggers placed near the edge of the hypolimnion exhibited much higher than expected variability. Hypoxic episodes of variable durations were frequently punctuated by periods of normoxia, consistent with high-frequency internal waves. High-resolution interpolations of water quality and hydroacoustic surveys suggest that fish habitat is compressed during hypoxic episodes, resulting in higher fish densities near the edges of hypoxia. At fixed locations with passive commercial fishing gear, catches with the highest values occurred when bottom waters were hypoxic for intermediate proportions of time. Proximity to hypoxia explained significant variation in bottom trawl catches, with higher catch rates near the edge of hypoxia. These results emphasize how hypoxia may elevate catch rates in various types of fishing gears, leading to a lack of association between indices of hypoxia and fishery landings. Increased catch rates of fish at the edges of hypoxia have important implications for stock assessment models that assume catchability is spatially homogeneous.

Learning and robustness to catch-and-release fishing in a shark social network

PubMed Central

Brown, Culum; Planes, Serge

2017-01-01

Individuals can play different roles in maintaining connectivity and social cohesion in animal populations and thereby influence population robustness to perturbations. We performed a social network analysis in a reef shark population to assess the vulnerability of the global network to node removal under different scenarios. We found that the network was generally robust to the removal of nodes with high centrality. The network appeared also highly robust to experimental fishing. Individual shark catchability decreased as a function of experience, as revealed by comparing capture frequency and site presence. Altogether, these features suggest that individuals learnt to avoid capture, which ultimately increased network robustness to experimental catch-and-release. Our results also suggest that some caution must be taken when using capture–recapture models often used to assess population size as assumptions (such as equal probabilities of capture and recapture) may be violated by individual learning to escape recapture. PMID:28298593

Diffusion of innovations theory applied to global tobacco control treaty ratification.

PubMed

Valente, Thomas W; Dyal, Stephanie R; Chu, Kar-Hai; Wipfli, Heather; Fujimoto, Kayo

2015-11-01

This study applies diffusion of innovations theory to understand network influences on country ratification of an international health treaty, the Framework Convention for Tobacco Control (FCTC). From 2003 to 2014 approximately 90% of United Nations member countries ratified the FCTC. We hypothesized that communication between tobacco control advocates on GLOBALink, a 7000-member online communication forum in existence from 1992 to 2012, would be associated with the timing of treaty ratification. We further hypothesized dynamic network influences such that external influence decreased over time, internal influence increased over time, and the role of opinion leader countries varied over time. In addition we develop two concepts: Susceptibility and influence that uncover the micro-level dynamics of network influence. Statistical analyses lend support to the influence of co-subscriptions on GLOBALink providing a conduit for inter-country influences on treaty ratification and some support for the dynamic hypotheses. Analyses of susceptibility and infection indicated particularly influential countries. These results have implications for the study of policy diffusion as well as dynamic models of behavior change. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Model-Data Fusion to Test Hypothesized Drivers of Lake Carbon Cycling Reveals Importance of Physical Controls

NASA Astrophysics Data System (ADS)

Hararuk, Oleksandra; Zwart, Jacob A.; Jones, Stuart E.; Prairie, Yves; Solomon, Christopher T.

2018-03-01

Formal integration of models and data to test hypotheses about the processes controlling carbon dynamics in lakes is rare, despite the importance of lakes in the carbon cycle. We built a suite of models (n = 102) representing different hypotheses about lake carbon processing, fit these models to data from a north-temperate lake using data assimilation, and identified which processes were essential for adequately describing the observations. The hypotheses that we tested concerned organic matter lability and its variability through time, temperature dependence of biological decay, photooxidation, microbial dynamics, and vertical transport of water via hypolimnetic entrainment and inflowing density currents. The data included epilimnetic and hypolimnetic CO2 and dissolved organic carbon, hydrologic fluxes, carbon loads, gross primary production, temperature, and light conditions at high frequency for one calibration and one validation year. The best models explained 76-81% and 64-67% of the variability in observed epilimnetic CO2 and dissolved organic carbon content in the validation data. Accurately describing C dynamics required accounting for hypolimnetic entrainment and inflowing density currents, in addition to accounting for biological transformations. In contrast, neither photooxidation nor variable organic matter lability improved model performance. The temperature dependence of biological decay (Q10) was estimated at 1.45, significantly lower than the commonly assumed Q10 of 2. By confronting multiple models of lake C dynamics with observations, we identified processes essential for describing C dynamics in a temperate lake at daily to annual scales, while also providing a methodological roadmap for using data assimilation to further improve understanding of lake C cycling.

Spontaneous Facial Mimicry in Response to Dynamic Facial Expressions

ERIC Educational Resources Information Center

Sato, Wataru; Yoshikawa, Sakiko

2007-01-01

Based on previous neuroscientific evidence indicating activation of the mirror neuron system in response to dynamic facial actions, we hypothesized that facial mimicry would occur while subjects viewed dynamic facial expressions. To test this hypothesis, dynamic/static facial expressions of anger/happiness were presented using computer-morphing…

Formulation, General Features and Global Calibration of a Bioenergetically-Constrained Fishery Model

PubMed Central

Bianchi, Daniele; Galbraith, Eric D.

2017-01-01

Human exploitation of marine resources is profoundly altering marine ecosystems, while climate change is expected to further impact commercially-harvested fish and other species. Although the global fishery is a highly complex system with many unpredictable aspects, the bioenergetic limits on fish production and the response of fishing effort to profit are both relatively tractable, and are sure to play important roles. Here we describe a generalized, coupled biological-economic model of the global marine fishery that represents both of these aspects in a unified framework, the BiOeconomic mArine Trophic Size-spectrum (BOATS) model. BOATS predicts fish production according to size spectra as a function of net primary production and temperature, and dynamically determines harvest spectra from the biomass density and interactive, prognostic fishing effort. Within this framework, the equilibrium fish biomass is determined by the economic forcings of catchability, ex-vessel price and cost per unit effort, while the peak harvest depends on the ecosystem parameters. Comparison of a large ensemble of idealized simulations with observational databases, focusing on historical biomass and peak harvests, allows us to narrow the range of several uncertain ecosystem parameters, rule out most parameter combinations, and select an optimal ensemble of model variants. Compared to the prior distributions, model variants with lower values of the mortality rate, trophic efficiency, and allometric constant agree better with observations. For most acceptable parameter combinations, natural mortality rates are more strongly affected by temperature than growth rates, suggesting different sensitivities of these processes to climate change. These results highlight the utility of adopting large-scale, aggregated data constraints to reduce model parameter uncertainties and to better predict the response of fisheries to human behaviour and climate change. PMID:28103280

Formulation, General Features and Global Calibration of a Bioenergetically-Constrained Fishery Model.

PubMed

Carozza, David A; Bianchi, Daniele; Galbraith, Eric D

2017-01-01

Human exploitation of marine resources is profoundly altering marine ecosystems, while climate change is expected to further impact commercially-harvested fish and other species. Although the global fishery is a highly complex system with many unpredictable aspects, the bioenergetic limits on fish production and the response of fishing effort to profit are both relatively tractable, and are sure to play important roles. Here we describe a generalized, coupled biological-economic model of the global marine fishery that represents both of these aspects in a unified framework, the BiOeconomic mArine Trophic Size-spectrum (BOATS) model. BOATS predicts fish production according to size spectra as a function of net primary production and temperature, and dynamically determines harvest spectra from the biomass density and interactive, prognostic fishing effort. Within this framework, the equilibrium fish biomass is determined by the economic forcings of catchability, ex-vessel price and cost per unit effort, while the peak harvest depends on the ecosystem parameters. Comparison of a large ensemble of idealized simulations with observational databases, focusing on historical biomass and peak harvests, allows us to narrow the range of several uncertain ecosystem parameters, rule out most parameter combinations, and select an optimal ensemble of model variants. Compared to the prior distributions, model variants with lower values of the mortality rate, trophic efficiency, and allometric constant agree better with observations. For most acceptable parameter combinations, natural mortality rates are more strongly affected by temperature than growth rates, suggesting different sensitivities of these processes to climate change. These results highlight the utility of adopting large-scale, aggregated data constraints to reduce model parameter uncertainties and to better predict the response of fisheries to human behaviour and climate change.

Translational systems biology using an agent-based approach for dynamic knowledge representation: An evolutionary paradigm for biomedical research.

PubMed

An, Gary C

2010-01-01

The greatest challenge facing the biomedical research community is the effective translation of basic mechanistic knowledge into clinically effective therapeutics. This challenge is most evident in attempts to understand and modulate "systems" processes/disorders, such as sepsis, cancer, and wound healing. Formulating an investigatory strategy for these issues requires the recognition that these are dynamic processes. Representation of the dynamic behavior of biological systems can aid in the investigation of complex pathophysiological processes by augmenting existing discovery procedures by integrating disparate information sources and knowledge. This approach is termed Translational Systems Biology. Focusing on the development of computational models capturing the behavior of mechanistic hypotheses provides a tool that bridges gaps in the understanding of a disease process by visualizing "thought experiments" to fill those gaps. Agent-based modeling is a computational method particularly well suited to the translation of mechanistic knowledge into a computational framework. Utilizing agent-based models as a means of dynamic hypothesis representation will be a vital means of describing, communicating, and integrating community-wide knowledge. The transparent representation of hypotheses in this dynamic fashion can form the basis of "knowledge ecologies," where selection between competing hypotheses will apply an evolutionary paradigm to the development of community knowledge.

Shaping the Latitudinal Diversity Gradient: New Perspectives from a Synthesis of Paleobiology and Biogeography.

PubMed

Jablonski, David; Huang, Shan; Roy, Kaustuv; Valentine, James W

2017-01-01

An impediment to understanding the origin and dynamics of the latitudinal diversity gradient (LDG)-the most pervasive large-scale biotic pattern on Earth-has been the tendency to focus narrowly on a single causal factor when a more synthetic, integrative approach is needed. Using marine bivalves as a model system and drawing on other systems where possible, we review paleobiologic and biogeographic support for two supposedly opposing views, that the LDG is shaped primarily by (a) local environmental factors that determine the number of species and higher taxa at a given latitude (in situ hypotheses) or (b) the entry of lineages arising elsewhere into a focal region (spatial dynamics hypotheses). Support for in situ hypotheses includes the fit of present-day diversity trends in many clades to such environmental factors as temperature and the correlation of extinction intensities in Pliocene bivalve faunas with net regional temperature changes. Support for spatial dynamics hypotheses includes the age-frequency distribution of bivalve genera across latitudes, which is consistent with an out-of-the-tropics dynamic, as are the higher species diversities in temperate southeastern Australia and southeastern Japan than in the tropical Caribbean. Thus, both in situ and spatial dynamics processes must shape the bivalve LDG and are likely to operate in other groups as well. The relative strengths of the two processes may differ among groups showing similar LDGs, but dissecting their effects will require improved methods of integrating fossil data with molecular phylogenies. We highlight several potential research directions and argue that many of the most dramatic biotic patterns, past and present, are likely to have been generated by diverse, mutually reinforcing drivers.

Temporal Dynamics of Hypothesis Generation: The Influences of Data Serial Order, Data Consistency, and Elicitation Timing

PubMed Central

Lange, Nicholas D.; Thomas, Rick P.; Davelaar, Eddy J.

2012-01-01

The pre-decisional process of hypothesis generation is a ubiquitous cognitive faculty that we continually employ in an effort to understand our environment and thereby support appropriate judgments and decisions. Although we are beginning to understand the fundamental processes underlying hypothesis generation, little is known about how various temporal dynamics, inherent in real world generation tasks, influence the retrieval of hypotheses from long-term memory. This paper presents two experiments investigating three data acquisition dynamics in a simulated medical diagnosis task. The results indicate that the mere serial order of data, data consistency (with previously generated hypotheses), and mode of responding influence the hypothesis generation process. An extension of the HyGene computational model endowed with dynamic data acquisition processes is forwarded and explored to provide an account of the present data. PMID:22754547

Characterization of fish assemblages and population structure of freshwater fish in two Tunisian reservoirs: implications for fishery management.

PubMed

Mili, Sami; Ennouri, Rym; Dhib, Amel; Laouar, Houcine; Missaoui, Hechmi; Aleya, Lotfi

2016-06-01

To monitor and assess the state of Tunisian freshwater fisheries, two surveys were undertaken at Ghezala and Lahjar reservoirs. Samples were taken in April and May 2013, a period when the fish catchability is high. The selected reservoirs have different surface areas and bathymetries. Using multi-mesh gill nets (EN 14575 amended) designed for sampling fish in lakes, standard fishing methods were applied to estimate species composition, abundance, biomass, and size distribution. Four species were caught in the two reservoirs: barbel, mullet, pike-perch, and roach. Fish abundance showed significant change according to sampling sites, depth strata, and the different mesh sizes used. From the reservoir to the tributary, it was concluded that fish biomass distribution was governed by depth and was most abundant in the upper water layers. Species size distribution differed significantly between the two reservoirs, exceeding the length at first maturity. Species composition and abundance were greater in Lahjar reservoir than in Ghezala. Both reservoirs require support actions to improve fish productivity.

Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction.

PubMed

Velderraín, José Dávila; Martínez-García, Juan Carlos; Álvarez-Buylla, Elena R

2017-01-01

Mathematical models based on dynamical systems theory are well-suited tools for the integration of available molecular experimental data into coherent frameworks in order to propose hypotheses about the cooperative regulatory mechanisms driving developmental processes. Computational analysis of the proposed models using well-established methods enables testing the hypotheses by contrasting predictions with observations. Within such framework, Boolean gene regulatory network dynamical models have been extensively used in modeling plant development. Boolean models are simple and intuitively appealing, ideal tools for collaborative efforts between theorists and experimentalists. In this chapter we present protocols used in our group for the study of diverse plant developmental processes. We focus on conceptual clarity and practical implementation, providing directions to the corresponding technical literature.

Infant Externalizing Behavior as a Self-Organizing Construct

ERIC Educational Resources Information Center

Lorber, Michael F.; Del Vecchio, Tamara; Slep, Amy M. Smith

2014-01-01

We evaluated the extent to which the externalizing behavior construct is self-organizing in the first 2 years of life. Based on dynamic systems theory, we hypothesized that changes in physical aggression, defiance, activity level, and distress to limitations would each be predicted by earlier manifestations of one another. These hypotheses were…

Comparing models of Red Knot population dynamics

USGS Publications Warehouse

McGowan, Conor P.

2015-01-01

Predictive population modeling contributes to our basic scientific understanding of population dynamics, but can also inform management decisions by evaluating alternative actions in virtual environments. Quantitative models mathematically reflect scientific hypotheses about how a system functions. In Delaware Bay, mid-Atlantic Coast, USA, to more effectively manage horseshoe crab (Limulus polyphemus) harvests and protect Red Knot (Calidris canutus rufa) populations, models are used to compare harvest actions and predict the impacts on crab and knot populations. Management has been chiefly driven by the core hypothesis that horseshoe crab egg abundance governs the survival and reproduction of migrating Red Knots that stopover in the Bay during spring migration. However, recently, hypotheses proposing that knot dynamics are governed by cyclical lemming dynamics garnered some support in data analyses. In this paper, I present alternative models of Red Knot population dynamics to reflect alternative hypotheses. Using 2 models with different lemming population cycle lengths and 2 models with different horseshoe crab effects, I project the knot population into the future under environmental stochasticity and parametric uncertainty with each model. I then compare each model's predictions to 10 yr of population monitoring from Delaware Bay. Using Bayes' theorem and model weight updating, models can accrue weight or support for one or another hypothesis of population dynamics. With 4 models of Red Knot population dynamics and only 10 yr of data, no hypothesis clearly predicted population count data better than another. The collapsed lemming cycle model performed best, accruing ~35% of the model weight, followed closely by the horseshoe crab egg abundance model, which accrued ~30% of the weight. The models that predicted no decline or stable populations (i.e. the 4-yr lemming cycle model and the weak horseshoe crab effect model) were the most weakly supported.

GPS Spoofing Attack Characterization and Detection in Smart Grids

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

Blum, Rick S.; Pradhan, Parth; Nagananda, Kyatsandra

The problem of global positioning system (GPS) spoofing attacks on smart grids endowed with phasor measurement units (PMUs) is addressed, taking into account the dynamical behavior of the states of the system. First, it is shown how GPS spoofing introduces a timing synchronization error in the phasor readings recorded by the PMUs and alters the measurement matrix of the dynamical model. Then, a generalized likelihood ratio-based hypotheses testing procedure is devised to detect changes in the measurement matrix when the system is subjected to a spoofing attack. Monte Carlo simulations are performed on the 9-bus, 3-machine test grid to demonstratemore » the implication of the spoofing attack on dynamic state estimation and to analyze the performance of the proposed hypotheses test.« less

Landscape host abundance and configuration regulate periodic outbreak behavior in spruce budworm Choristoneura fumiferana

Treesearch

Louis-Etienne Robert; Brian R. Sturtevant; Barry J. Cooke; Patrick M. A. James; Marie-Josée Fortin; Philip A. Townsend; Peter T. Wolter; Daniel Kneeshaw

2018-01-01

Landscape-level forest management has long been hypothesized to affect forest insect outbreak dynamics, but empirical evidence remains elusive. We hypothesized that the combination of increased hardwood relative to host tree species, prevalence of younger forests, and fragmentation of those forests due to forest harvesting legacies would reduce outbreak intensity,...

Parsing in a Dynamical System: An Attractor-Based Account of the Interaction of Lexical and Structural Constraints in Sentence Processing.

ERIC Educational Resources Information Center

Tabor, Whitney; And Others

1997-01-01

Proposes a dynamical systems approach to parsing in which syntactic hypotheses are associated with attractors in a metric space. The experiments discussed documented various contingent frequency effects that cut across traditional linguistic grains, each of which was predicted by the dynamical systems model. (47 references) (Author/CK)

Chaos Versus Noisy Periodicity: Alternative Hypotheses for Childhood Epidemics

NASA Astrophysics Data System (ADS)

Olsen, L. F.; Schaffer, W. M.

1990-08-01

Whereas case rates for some childhood diseases (chickenpox) often vary according to an almost regular annual cycle, the incidence of more efficiently transmitted infections such as measles is more variable. Three hypotheses have been proposed to account for such fluctuations. (i) Irregular dynamics result from random shocks to systems with stable equilibria. (ii) The intrinsic dynamics correspond to biennial cycles that are subject to stochastic forcing. (iii) Aperiodic fluctuations are intrinsic to the epidemiology. Comparison of real world data and epidemiological models suggests that measles epidemics are inherently chaotic. Conversely, the extent to which chickenpox outbreaks approximate a yearly cycle depends inversely on the population size.

SUSTAINABILITY, OPTION, THEORY, AND QUALITY CONTROL

EPA Science Inventory

Recently, Cabezas and Fath (2000) hypothesized that constant Fisher Information is a necessary condition for the persistence, i.e., sustainability of a dynamic regime of a system. A sustainable dynamic regime is one that persists and an unsustainable regime is one that does not ...

Regime shifts in the Humboldt Current ecosystem [review article

NASA Astrophysics Data System (ADS)

Alheit, Jürgen; Niquen, Miguel

2004-02-01

Of the four major eastern boundary currents, the Humboldt Current (HC) stands out because it is extremely productive, dominated by anchovy dynamics and subject to frequent direct environmental perturbations of the El Niño Southern Oscillation (ENSO). The long-term dynamics of the HC ecosystem are controlled by shifts between alternating anchovy and sardine regimes that restructure the entire ecosystem from phytoplankton to the top predators. These regime shifts are caused by lasting periods of warm or cold temperature anomalies related to the approach or retreat of warm subtropical oceanic waters to the coast of Peru and Chile. Phases with mainly negative temperature anomalies parallel anchovy regimes (1950-1970; 1985 to the present) and the rather warm period from 1970 to 1985 was characterized by sardine dominance. The transition periods (turning points) from one regime to the other were 1968-1970 and 1984-1986. Like an El Nino, the warm periods drastically change trophic relationships in the entire HC ecosystem, exposing the Peruvian anchovy to a multitude of adverse conditions. Positive temperature anomalies off Peru drive the anchovy population close to the coast as the coastal upwelling cells usually offer the coolest environment, thereby substantially decreasing the extent of the areas of anchovy distribution and spawning. This enhances the effects of negative density-dependent processes such as egg and larval cannibalism and dramatically increases its catchability. Increased spatial overlap between anchovies and the warmer water preferring sardines intensifies anchovy egg mortality further as sardines feed heavily on anchovy eggs. Food sources for juvenile and adult anchovies which prey on a mixed diet of phyto- and zooplankton are drastically reduced because of decreased plankton production due to restricted upwelling in warm years, as demonstrated by lower zooplankton and phytoplankton volumes and the diminution of the fraction of large copepods, their main food source. Horse mackerel and mackerel, the main predators of anchovy, increase predation pressure on juvenile and adult anchovies due to extended invasion into the anchovy habitat in warmer years. In contrast to these periods of warm and cold temperature anomalies on the decadal scale, ENSO events do not play an important role for long-term anchovy dynamics, as the anchovy can recover even from strong ENSO events within 1-2 years. Consequently, the strong 1972-1973 ENSO event (in combination with overfishing) was not the cause of the famous crash of the Peruvian anchovy fishery in the 1970s.

Temporal carbon dynamics of forests in Washington, US: implications for ecological theory and carbon management

Treesearch

Crystal L. Raymond; Donald McKenzie

2014-01-01

We quantified carbon (C) dynamics of forests in Washington, US using theoretical models of C dynamics as a function of forest age. We fit empirical models to chronosequences of forest inventory data at two scales: a coarse-scale ecosystem classification (ecosections) and forest types (potential vegetation) within ecosections. We hypothesized that analysis at the finer...

Biology of Consciousness

PubMed Central

Edelman, Gerald M.; Gally, Joseph A.; Baars, Bernard J.

2010-01-01

The Dynamic Core and Global Workspace hypotheses were independently put forward to provide mechanistic and biologically plausible accounts of how brains generate conscious mental content. The Dynamic Core proposes that reentrant neural activity in the thalamocortical system gives rise to conscious experience. Global Workspace reconciles the limited capacity of momentary conscious content with the vast repertoire of long-term memory. In this paper we show the close relationship between the two hypotheses. This relationship allows for a strictly biological account of phenomenal experience and subjectivity that is consistent with mounting experimental evidence. We examine the constraints on causal analyses of consciousness and suggest that there is now sufficient evidence to consider the design and construction of a conscious artifact. PMID:21713129

A dynamical system view of cerebellar function

NASA Astrophysics Data System (ADS)

Keeler, James D.

1990-06-01

First some previous theories of cerebellar function are reviewed, and deficiencies in how they map onto the neurophysiological structure are pointed out. I hypothesize that the cerebellar cortex builds an internal model, or prediction, of the dynamics of the animal. A class of algorithms for doing prediction based on local reconstruction of attractors are described, and it is shown how this class maps very well onto the structure of the cerebellar cortex. I hypothesize that the climbing fibers multiplex between different trajectories corresponding to different modes of operation. Then the vestibulo-ocular reflex is examined, and experiments to test the proposed model are suggested. The purpose of the presentation here is twofold: (1) To enlighten physiologists to the mathematics of a class of prediction algorithms that map well onto cerebellar architecture. (2) To enlighten dynamical system theorists to the physiological and anatomical details of the cerebellum.

Can MOND type hypotheses be tested in a free fall laboratory environment?

NASA Astrophysics Data System (ADS)

Das, Saurya; Patitsas, S. N.

2013-05-01

The extremely small accelerations of objects required for the onset of modified Newtonian dynamics, or modified Newtonian dynamics (MOND), makes testing the hypothesis in conventional terrestrial laboratories virtually impossible. This is due to the large background acceleration of Earth, which is transmitted to the acceleration of test objects within an apparatus. We show, however, that it may be possible to test MOND-type hypotheses with experiments using a conventional apparatus capable of tracking very small accelerations of its components but performed in locally inertial frames such as artificial satellites and other freely falling laboratories. For example, experiments involving an optical interferometer or a torsion balance in these laboratories would show nonlinear dynamics and displacement amplitudes larger than expected. These experiments may also be able to test potential violations of the strong equivalence principle by MOND and to distinguish between its two possible interpretations (modified inertia and modified gravity).

Robust operative diagnosis as problem solving in a hypothesis space

NASA Technical Reports Server (NTRS)

Abbott, Kathy H.

1988-01-01

This paper describes an approach that formulates diagnosis of physical systems in operation as problem solving in a hypothesis space. Such a formulation increases robustness by: (1) incremental hypotheses construction via dynamic inputs, (2) reasoning at a higher level of abstraction to construct hypotheses, and (3) partitioning the space by grouping fault hypotheses according to the type of physical system representation and problem solving techniques used in their construction. It was implemented for a turbofan engine and hydraulic subsystem. Evaluation of the implementation on eight actual aircraft accident cases involving engine faults provided very promising results.

A Decentralized Approach to the Formulation of Hypotheses: A Hierarchical Structural Model for a Prion Self-Assembled System

NASA Astrophysics Data System (ADS)

Wang, Mingyang; Zhang, Feifei; Song, Chao; Shi, Pengfei; Zhu, Jin

2016-07-01

Innovation in hypotheses is a key transformative driver for scientific development. The conventional centralized hypothesis formulation approach, where a dominant hypothesis is typically derived from a primary phenomenon, can, inevitably, impose restriction on the range of conceivable experiments and legitimate hypotheses, and ultimately impede understanding of the system of interest. We report herein the proposal of a decentralized approach for the formulation of hypotheses, through initial preconception-free phenomenon accumulation and subsequent reticular logical reasoning processes. The two-step approach can provide an unbiased, panoramic view of the system and as such should enable the generation of a set of more coherent and therefore plausible hypotheses. As a proof-of-concept demonstration of the utility of this open-ended approach, a hierarchical model has been developed for a prion self-assembled system, allowing insight into hitherto elusive static and dynamic features associated with this intriguing structure.

Double Trouble at High Density: Cross-Level Test of Resource-Related Adaptive Plasticity and Crowding-Related Fitness

PubMed Central

Gergs, André; Preuss, Thomas G.; Palmqvist, Annemette

2014-01-01

Population size is often regulated by negative feedback between population density and individual fitness. At high population densities, animals run into double trouble: they might concurrently suffer from overexploitation of resources and also from negative interference among individuals regardless of resource availability, referred to as crowding. Animals are able to adapt to resource shortages by exhibiting a repertoire of life history and physiological plasticities. In addition to resource-related plasticity, crowding might lead to reduced fitness, with consequences for individual life history. We explored how different mechanisms behind resource-related plasticity and crowding-related fitness act independently or together, using the water flea Daphnia magna as a case study. For testing hypotheses related to mechanisms of plasticity and crowding stress across different biological levels, we used an individual-based population model that is based on dynamic energy budget theory. Each of the hypotheses, represented by a sub-model, is based on specific assumptions on how the uptake and allocation of energy are altered under conditions of resource shortage or crowding. For cross-level testing of different hypotheses, we explored how well the sub-models fit individual level data and also how well they predict population dynamics under different conditions of resource availability. Only operating resource-related and crowding-related hypotheses together enabled accurate model predictions of D. magna population dynamics and size structure. Whereas this study showed that various mechanisms might play a role in the negative feedback between population density and individual life history, it also indicated that different density levels might instigate the onset of the different mechanisms. This study provides an example of how the integration of dynamic energy budget theory and individual-based modelling can facilitate the exploration of mechanisms behind the regulation of population size. Such understanding is important for assessment, management and the conservation of populations and thereby biodiversity in ecosystems. PMID:24626228

Hypothesizing the body's genius to trigger and self-organize its healing: 25 years using a standardized neurophysics therapy

PubMed Central

Ross, Sara N.; Ware, Ken

2013-01-01

We aim for this contribution to operate bi-directionally, both as a “bedside to bench” reverse-translational fractal physiological hypothesis and as a methodological innovation to inform clinical practice. In 25 years using gym equipment therapeutically in non-research settings, the standardized therapy is consistently observed to trigger universal responses of micro to macro waves of system transition dynamics in the human nervous system. These are associated with observably desirable impacts on disorders, injuries, diseases, and athletic performance. Requisite conditions are therapeutic coaching, erect posture, extremely slow movements in mild resistance exercises, and executive control over arousal and attention. To motivate research into the physiological improvements and in validation studies, we integrate from across disciplines to hypothesize explanations for the relationships among the methods, the system dynamics, and evident results. Key hypotheses include: (1) Correctly-directed system efforts may reverse a system's heretofore misdirected efforts, restoring healthier neurophysiology. (2) The enhanced information processing accompanying good posture is an essential initial condition. (3) Behaviors accompanying exercises performed with few degrees of freedom amplify information processing, triggering destabilization and transition dynamics. (4) Executive control over arousal and attention is essential to release system constraints, amplifying and complexifying information. (5) The dynamics create necessary and in many cases evidently sufficient conditions for the body to resolve or improve its own conditions within often short time periods. Literature indicates how the human system possesses material self-awareness. A broad explanation for the nature and effects of the therapy appears rooted in the cascading recursions of the systems' dynamics, which appear to trigger health-fostering self-reorganizing processes when this therapy provides catalytic initial conditions. PMID:24312056

FORUM: Dynamics and Causation of Environmental Equity, Locally Unwanted Land Uses, and Neighborhood Changes

PubMed

Liu

1997-09-01

/ Why are some environmental risks distributed disproportionately in the neighborhoods of the minorities and the poor? A hypothesis was proposed in a recent study that market dynamics contributed to the current environmental inequity. That is, locally unwanted land uses (LULUs) make the host communities home to more poor people and people of color. This hypothesis was allegedly supported by a Houston case study, whereby its author analyzed the postsiting changes of the socioeconomic characteristics of the neighborhoods surrounding solid waste facilities. I argue that such an analysis of postsiting changes alone is insufficient to test the causation hypothesis. Instead, I propose a conceptual framework for analysis of environmental equity dynamics and causation. I suggest that the presiting neighborhood dynamics and the characteristics of control neighborhoods be analyzed as the first test for the causation hypothesis. Furthermore, I present theories of neighborhood change and then examine alternative hypotheses that these theories offer for explaining neighborhood changes and for the roles of LULUs in neighborhood changes. These alternative hypotheses should be examined when analyzing the relationship between LULUs and neighborhood changes in a metropolitan area. Using this framework of analysis, I revisited the Houston case. First, I found no evidence that provided support for the hypothesis that the presence of LULUs made the neighborhoods home to more blacks and poor people, contrary to the conclusion made by the previous study. Second, I examined alternative hypotheses for explaining neighborhood changes-invasion-succession, other push forces, and neighborhood life-cycle; the former two might offer better explanation.KEY WORDS: Environmental equity and justice; Locally unwanted lane uses; Siting; Market dynamics; Invasion-succession; Neighborhood changes

Structure theorems and the dynamics of nitrogen catabolite repression in yeast

PubMed Central

Boczko, Erik M.; Cooper, Terrance G.; Gedeon, Tomas; Mischaikow, Konstantin; Murdock, Deborah G.; Pratap, Siddharth; Wells, K. Sam

2005-01-01

By using current biological understanding, a conceptually simple, but mathematically complex, model is proposed for the dynamics of the gene circuit responsible for regulating nitrogen catabolite repression (NCR) in yeast. A variety of mathematical “structure” theorems are described that allow one to determine the asymptotic dynamics of complicated systems under very weak hypotheses. It is shown that these theorems apply to several subcircuits of the full NCR circuit, most importantly to the URE2–GLN3 subcircuit that is independent of the other constituents but governs the switching behavior of the full NCR circuit under changes in nitrogen source. Under hypotheses that are fully consistent with biological data, it is proven that the dynamics of this subcircuit is simple periodic behavior in synchrony with the cell cycle. Although the current mathematical structure theorems do not apply to the full NCR circuit, extensive simulations suggest that the dynamics is constrained in much the same way as that of the URE2–GLN3 subcircuit. This finding leads to the proposal that mathematicians study genetic circuits to find new geometries for which structure theorems may exist. PMID:15814615

Parasite transmission among relatives halts Red Queen dynamics.

PubMed

Greenspoon, Philip B; Mideo, Nicole

2017-03-01

The theory that coevolving hosts and parasites create a fluctuating selective environment for one another (i.e., produce Red Queen dynamics) has deep roots in evolutionary biology; yet empirical evidence for Red Queen dynamics remains scarce. Fluctuating coevolutionary dynamics underpin the Red Queen hypothesis for the evolution of sex, as well as hypotheses explaining the persistence of genetic variation under sexual selection, local parasite adaptation, the evolution of mutation rate, and the evolution of nonrandom mating. Coevolutionary models that exhibit Red Queen dynamics typically assume that hosts and parasites encounter one another randomly. However, if related individuals aggregate into family groups or are clustered spatially, related hosts will be more likely to encounter parasites transmitted by genetically similar individuals. Using a model that incorporates familial parasite transmission, we show that a slight degree of familial parasite transmission is sufficient to halt coevolutionary fluctuations. Our results predict that evidence for Red Queen dynamics, and its evolutionary consequences, are most likely to be found in biological systems in which hosts and parasites mix mainly at random, and are less likely to be found in systems with familial aggregation. This presents a challenge to the Red Queen hypothesis and other hypotheses that depend on coevolutionary cycling. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Source-sink dynamics sustain central stonerollers (Campostoma anomalum) in a heavily urbanized catchment

Treesearch

Eric R. Waits; Mark J. Bagley; Michael J. Blum; Frank H. McCormick; James M. Lazorchak

2008-01-01

Relating local demographic processes to spatial structure (e.g. habitat heterogeneity) is essential for understanding population and species persistence (Hanski & Gilpin, 1997; Fagan, 2002). Yet few studies have tested general hypotheses about the importance of spatial patterns in determining population dynamics within river­stream networks (Lowe, Likens &...

Social Dynamics of a University Weight Room: A Microethnography.

ERIC Educational Resources Information Center

Ittenbach, Richard F.; Chissom, Brad S.

The purpose of this investigation was to describe and explain the social dynamics of America's second most popular recreational sport, weight lifting, as performed on a university campus. Data were collected and analyzed using the participant observation approach to grounded theory research. Several hypotheses evolved from this analysis: (1) it is…

Dynamic Redox Regulation of IL-4 Signaling.

PubMed

Dwivedi, Gaurav; Gran, Margaret A; Bagchi, Pritha; Kemp, Melissa L

2015-11-01

Quantifying the magnitude and dynamics of protein oxidation during cell signaling is technically challenging. Computational modeling provides tractable, quantitative methods to test hypotheses of redox mechanisms that may be simultaneously operative during signal transduction. The interleukin-4 (IL-4) pathway, which has previously been reported to induce reactive oxygen species and oxidation of PTP1B, may be controlled by several other putative mechanisms of redox regulation; widespread proteomic thiol oxidation observed via 2D redox differential gel electrophoresis upon IL-4 treatment suggests more than one redox-sensitive protein implicated in this pathway. Through computational modeling and a model selection strategy that relied on characteristic STAT6 phosphorylation dynamics of IL-4 signaling, we identified reversible protein tyrosine phosphatase (PTP) oxidation as the primary redox regulatory mechanism in the pathway. A systems-level model of IL-4 signaling was developed that integrates synchronous pan-PTP oxidation with ROS-independent mechanisms. The model quantitatively predicts the dynamics of IL-4 signaling over a broad range of new redox conditions, offers novel hypotheses about regulation of JAK/STAT signaling, and provides a framework for interrogating putative mechanisms involving receptor-initiated oxidation.

Dynamic Redox Regulation of IL-4 Signaling

PubMed Central

Dwivedi, Gaurav; Gran, Margaret A.; Bagchi, Pritha; Kemp, Melissa L.

2015-01-01

Quantifying the magnitude and dynamics of protein oxidation during cell signaling is technically challenging. Computational modeling provides tractable, quantitative methods to test hypotheses of redox mechanisms that may be simultaneously operative during signal transduction. The interleukin-4 (IL-4) pathway, which has previously been reported to induce reactive oxygen species and oxidation of PTP1B, may be controlled by several other putative mechanisms of redox regulation; widespread proteomic thiol oxidation observed via 2D redox differential gel electrophoresis upon IL-4 treatment suggests more than one redox-sensitive protein implicated in this pathway. Through computational modeling and a model selection strategy that relied on characteristic STAT6 phosphorylation dynamics of IL-4 signaling, we identified reversible protein tyrosine phosphatase (PTP) oxidation as the primary redox regulatory mechanism in the pathway. A systems-level model of IL-4 signaling was developed that integrates synchronous pan-PTP oxidation with ROS-independent mechanisms. The model quantitatively predicts the dynamics of IL-4 signaling over a broad range of new redox conditions, offers novel hypotheses about regulation of JAK/STAT signaling, and provides a framework for interrogating putative mechanisms involving receptor-initiated oxidation. PMID:26562652

The dynamics of radical right-wing populist party preferences and perceived group threat: A comparative panel analysis of three competing hypotheses in the Netherlands and Germany.

PubMed

Berning, Carl C; Schlueter, Elmar

2016-01-01

Existing cross-sectional research considers citizens' preferences for radical right-wing populist (RRP) parties to be centrally driven by their perception that immigrants threaten the well-being of the national ingroup. However, longitudinal evidence for this relationship is largely missing. To remedy this gap in the literature, we developed three competing hypotheses to investigate: (a) whether perceived group threat is temporally prior to RRP party preferences, (b) whether RRP party preferences are temporally prior to perceived group threat, or (c) whether the relation between perceived group threat and RRP party preferences is bidirectional. Based on multiwave panel data from the Netherlands for the years 2008-2013 and from Germany spanning the period 1994-2002, we examined the merits of these hypotheses using autoregressive cross-lagged structural equation models. The results show that perceptions of threatened group interests precipitate rather than follow citizens' preferences for RRP parties. These findings help to clarify our knowledge of the dynamic structure underlying RRP party preferences. Copyright © 2015 Elsevier Inc. All rights reserved.

Dynamic Pedagogy for Effective Training of Youths in Cell Phone Maintenance

ERIC Educational Resources Information Center

Ogbuanya, T. C.; Jimoh, Bakare

2015-01-01

The study determined dynamic pedagogies for effective training of youths in cell phone maintenance. The study was conducted in Enugu State of Nigeria. Four research questions were developed while four null hypotheses formulated were tested at 0.05 level of significance. A survey research design was adopted for the study. The population for the…

Effortful Pitch Glide: A Potential New Exercise Evaluated by Dynamic MRI

ERIC Educational Resources Information Center

Miloro, Keri Vasquez; Pearson, William G., Jr.; Langmore, Susan E.

2014-01-01

Purpose: The purpose of this study was to compare the biomechanics of the effortful pitch glide (EPG) with swallowing using dynamic MRI. The EPG is a combination of a pitch glide and a pharyngeal squeeze maneuver for targeting laryngeal and pharyngeal muscles. The authors hypothesized that the EPG would elicit significantly greater structural…

Can Dynamic Visualizations with Variable Control Enhance the Acquisition of Intuitive Knowledge?

ERIC Educational Resources Information Center

Wichmann, Astrid; Timpe, Sebastian

2015-01-01

An important feature of inquiry learning is to take part in science practices including exploring variables and testing hypotheses. Computer-based dynamic visualizations have the potential to open up various exploration possibilities depending on the level of learner control. It is assumed that variable control, e.g., by changing parameters of a…

Functional connectivity dynamics during film viewing reveal common networks for different emotional experiences.

PubMed

Raz, Gal; Touroutoglou, Alexandra; Wilson-Mendenhall, Christine; Gilam, Gadi; Lin, Tamar; Gonen, Tal; Jacob, Yael; Atzil, Shir; Admon, Roee; Bleich-Cohen, Maya; Maron-Katz, Adi; Hendler, Talma; Barrett, Lisa Feldman

2016-08-01

Recent theoretical and empirical work has highlighted the role of domain-general, large-scale brain networks in generating emotional experiences. These networks are hypothesized to process aspects of emotional experiences that are not unique to a specific emotional category (e.g., "sadness," "happiness"), but rather that generalize across categories. In this article, we examined the dynamic interactions (i.e., changing cohesiveness) between specific domain-general networks across time while participants experienced various instances of sadness, fear, and anger. We used a novel method for probing the network connectivity dynamics between two salience networks and three amygdala-based networks. We hypothesized, and found, that the functional connectivity between these networks covaried with the intensity of different emotional experiences. Stronger connectivity between the dorsal salience network and the medial amygdala network was associated with more intense ratings of emotional experience across six different instances of the three emotion categories examined. Also, stronger connectivity between the dorsal salience network and the ventrolateral amygdala network was associated with more intense ratings of emotional experience across five out of the six different instances. Our findings demonstrate that a variety of emotional experiences are associated with dynamic interactions of domain-general neural systems.

Developmental metaplasticity in neural circuit codes of firing and structure.

PubMed

Baram, Yoram

2017-01-01

Firing-rate dynamics have been hypothesized to mediate inter-neural information transfer in the brain. While the Hebbian paradigm, relating learning and memory to firing activity, has put synaptic efficacy variation at the center of cortical plasticity, we suggest that the external expression of plasticity by changes in the firing-rate dynamics represents a more general notion of plasticity. Hypothesizing that time constants of plasticity and firing dynamics increase with age, and employing the filtering property of the neuron, we obtain the elementary code of global attractors associated with the firing-rate dynamics in each developmental stage. We define a neural circuit connectivity code as an indivisible set of circuit structures generated by membrane and synapse activation and silencing. Synchronous firing patterns under parameter uniformity, and asynchronous circuit firing are shown to be driven, respectively, by membrane and synapse silencing and reactivation, and maintained by the neuronal filtering property. Analytic, graphical and simulation representation of the discrete iteration maps and of the global attractor codes of neural firing rate are found to be consistent with previous empirical neurobiological findings, which have lacked, however, a specific correspondence between firing modes, time constants, circuit connectivity and cortical developmental stages. Copyright © 2016 Elsevier Ltd. All rights reserved.

What do predators really want? The role of gerbil energetic state in determining prey choice by Barn Owls.

PubMed

Embar, Keren; Mukherjee, Shomen; Kotler, Burt P

2014-02-01

In predator-prey foraging games, predators should respond to variations in prey state. The value of energy for the prey changes depending on season. Prey in a low energetic state and/or in a reproductive state should invest more in foraging and tolerate higher predation risk. This should make the prey more catchable, and thereby, more preferable to predators. We ask, can predators respond to prey state? How does season and state affect the foraging game from the predator's perspective? By letting owls choose between gerbils whose states we experimentally manipulated, we could demonstrate predator sensitivity to prey state and predator selectivity that otherwise may be obscured by the foraging game. During spring, owls invested more time and attacks in the patch with well-fed gerbils. During summer, owls attacked both patches equally, yet allocated more time to the patch with hungry gerbils. Energetic state per se does not seem to be the basis of owl choice. The owls strongly responded to these subtle differences. In summer, gerbils managed their behavior primarily for survival, and the owls equalized capture opportunities by attacking both patches equally.

Addressing the translational dilemma: dynamic knowledge representation of inflammation using agent-based modeling.

PubMed

An, Gary; Christley, Scott

2012-01-01

Given the panoply of system-level diseases that result from disordered inflammation, such as sepsis, atherosclerosis, cancer, and autoimmune disorders, understanding and characterizing the inflammatory response is a key target of biomedical research. Untangling the complex behavioral configurations associated with a process as ubiquitous as inflammation represents a prototype of the translational dilemma: the ability to translate mechanistic knowledge into effective therapeutics. A critical failure point in the current research environment is a throughput bottleneck at the level of evaluating hypotheses of mechanistic causality; these hypotheses represent the key step toward the application of knowledge for therapy development and design. Addressing the translational dilemma will require utilizing the ever-increasing power of computers and computational modeling to increase the efficiency of the scientific method in the identification and evaluation of hypotheses of mechanistic causality. More specifically, development needs to focus on facilitating the ability of non-computer trained biomedical researchers to utilize and instantiate their knowledge in dynamic computational models. This is termed "dynamic knowledge representation." Agent-based modeling is an object-oriented, discrete-event, rule-based simulation method that is well suited for biomedical dynamic knowledge representation. Agent-based modeling has been used in the study of inflammation at multiple scales. The ability of agent-based modeling to encompass multiple scales of biological process as well as spatial considerations, coupled with an intuitive modeling paradigm, suggest that this modeling framework is well suited for addressing the translational dilemma. This review describes agent-based modeling, gives examples of its applications in the study of inflammation, and introduces a proposed general expansion of the use of modeling and simulation to augment the generation and evaluation of knowledge by the biomedical research community at large.

Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach.

PubMed

Blazquez-Navarro, Arturo; Schachtner, Thomas; Stervbo, Ulrik; Sefrin, Anett; Stein, Maik; Westhoff, Timm H; Reinke, Petra; Klipp, Edda; Babel, Nina; Neumann, Avidan U; Or-Guil, Michal

2018-05-01

BK virus (BKV) associated nephropathy affects 1-10% of kidney transplant recipients, leading to graft failure in about 50% of cases. Immune responses against different BKV antigens have been shown to have a prognostic value for disease development. Data currently suggest that the structural antigens and regulatory antigens of BKV might each trigger a different mode of action of the immune response. To study the influence of different modes of action of the cellular immune response on BKV clearance dynamics, we have analysed the kinetics of BKV plasma load and anti-BKV T cell response (Elispot) in six patients with BKV associated nephropathy using ODE modelling. The results show that only a small number of hypotheses on the mode of action are compatible with the empirical data. The hypothesis with the highest empirical support is that structural antigens trigger blocking of virus production from infected cells, whereas regulatory antigens trigger an acceleration of death of infected cells. These differential modes of action could be important for our understanding of BKV resolution, as according to the hypothesis, only regulatory antigens would trigger a fast and continuous clearance of the viral load. Other hypotheses showed a lower degree of empirical support, but could potentially explain the clearing mechanisms of individual patients. Our results highlight the heterogeneity of the dynamics, including the delay between immune response against structural versus regulatory antigens, and its relevance for BKV clearance. Our modelling approach is the first that studies the process of BKV clearance by bringing together viral and immune kinetics and can provide a framework for personalised hypotheses generation on the interrelations between cellular immunity and viral dynamics.

Emotional intelligence and job performance: The mediating role of work-family balance.

PubMed

Weinzimmer, Laurence G; Baumann, Heidi M; Gullifor, Daniel P; Koubova, Veronika

2017-01-01

In this study, we examine the dynamics between emotional intelligence, work-family balance, and job performance. A review of the literature to date has shown distinct relationships between emotional intelligence to job performance and work-family balance to job performance. We utilize a sample of 233 respondents to empirically test our set of hypotheses that contend work-family balance mediates the relationship between emotional intelligence and job performance. Our results support these hypotheses. Practical implications and directions for future research are discussed.

Assessing hypotheses about nesting site occupancy dynamics

USGS Publications Warehouse

Bled, Florent; Royle, J. Andrew; Cam, Emmanuelle

2011-01-01

Hypotheses about habitat selection developed in the evolutionary ecology framework assume that individuals, under some conditions, select breeding habitat based on expected fitness in different habitat. The relationship between habitat quality and fitness may be reflected by breeding success of individuals, which may in turn be used to assess habitat quality. Habitat quality may also be assessed via local density: if high-quality sites are preferentially used, high density may reflect high-quality habitat. Here we assessed whether site occupancy dynamics vary with site surrogates for habitat quality. We modeled nest site use probability in a seabird subcolony (the Black-legged Kittiwake, Rissa tridactyla) over a 20-year period. We estimated site persistence (an occupied site remains occupied from time t to t + 1) and colonization through two subprocesses: first colonization (site creation at the timescale of the study) and recolonization (a site is colonized again after being deserted). Our model explicitly incorporated site-specific and neighboring breeding success and conspecific density in the neighborhood. Our results provided evidence that reproductively "successful'' sites have a higher persistence probability than "unsuccessful'' ones. Analyses of site fidelity in marked birds and of survival probability showed that high site persistence predominantly reflects site fidelity, not immediate colonization by new owners after emigration or death of previous owners. There is a negative quadratic relationship between local density and persistence probability. First colonization probability decreases with density, whereas recolonization probability is constant. This highlights the importance of distinguishing initial colonization and recolonization to understand site occupancy. All dynamics varied positively with neighboring breeding success. We found evidence of a positive interaction between site-specific and neighboring breeding success. We addressed local population dynamics using a site occupancy approach integrating hypotheses developed in behavioral ecology to account for individual decisions. This allows development of models of population and metapopulation dynamics that explicitly incorporate ecological and evolutionary processes.

Relationships between substrate, surface characteristics, and vegetation in an initial ecosystem

NASA Astrophysics Data System (ADS)

Biber, P.; Seifert, S.; Zaplata, M. K.; Schaaf, W.; Pretzsch, H.; Fischer, A.

2013-12-01

We investigated surface and vegetation dynamics in the artificial initial ecosystem "Chicken Creek" (Lusatia, Germany) in the years 2006-2011 across a wide spectrum of empirical data. We scrutinized three overarching hypotheses concerning (1) the relations between initial geomorphological and substrate characteristics with surface structure and terrain properties, (2) the effects of the latter on the occurrence of grouped plant species, and (3) vegetation density effects on terrain surface change. Our data comprise and conflate annual vegetation monitoring results, biennial terrestrial laser scans (starting in 2008), annual groundwater levels, and initially measured soil characteristics. The empirical evidence mostly confirms the hypotheses, revealing statistically significant relations for several goal variables: (1) the surface structure properties, local rill density, local relief energy and terrain surface height change; (2) the cover of different plant groups (annual, herbaceous, grass-like, woody, Fabaceae), and local vegetation height; and (3) terrain surface height change showed significant time-dependent relations with a variable that proxies local plant biomass. Additionally, period specific effects (like a calendar-year optimum effect for the occurrence of Fabaceae) were proven. Further and beyond the hypotheses, our findings on the spatiotemporal dynamics during the system's early development grasp processes which generally mark the transition from a geo-hydro-system towards a bio-geo-hydro system (weakening geomorphology effects on substrate surface dynamics, while vegetation effects intensify with time), where pure geomorphology or substrate feedbacks are changing into vegetation-substrate feedback processes.

Comparisons of Social Competence in Young Children with and without Hearing Loss: A Dynamic Systems Framework

ERIC Educational Resources Information Center

Hoffman, Michael F.; Quittner, Alexandra L.; Cejas, Ivette

2015-01-01

This study compared levels of social competence and language development in 74 young children with hearing loss and 38 hearing peers aged 2.5-5.3 years. This study was the first to examine the relationship between oral language and social competence using a dynamic systems framework in children with and without hearing loss. We hypothesized that,…

Using computational fluid dynamics to test functional and ecological hypotheses in fossil taxa

NASA Astrophysics Data System (ADS)

Rahman, Imran

2016-04-01

Reconstructing how ancient organisms moved and fed is a major focus of study in palaeontology. Traditionally, this has been hampered by a lack of objective data on the functional morphology of extinct species, especially those without a clear modern analogue. However, cutting-edge techniques for characterizing specimens digitally and in three dimensions, coupled with state-of-the-art computer models, now provide a robust framework for testing functional and ecological hypotheses even in problematic fossil taxa. One such approach is computational fluid dynamics (CFD), a method for simulating fluid flows around objects that has primarily been applied to complex engineering-design problems. Here, I will present three case studies of CFD applied to fossil taxa, spanning a range of specimen sizes, taxonomic groups and geological ages. First, I will show how CFD enabled a rigorous test of hypothesized feeding modes in an enigmatic Ediacaran organism with three-fold symmetry, revealing previously unappreciated complexity of pre-Cambrian ecosystems. Second, I will show how CFD was used to evaluate hydrodynamic performance and feeding in Cambrian stem-group echinoderms, shedding light on the probable feeding strategy of the latest common ancestor of all deuterostomes. Third, I will show how CFD allowed us to explore the link between form and function in Mesozoic ichthyosaurs. These case studies serve to demonstrate the enormous potential of CFD for addressing long-standing hypotheses for a variety of fossil taxa, opening up an exciting new avenue in palaeontological studies of functional morphology.

Toward the Darwinian transition: Switching between distributed and speciated states in a simple model of early life.

PubMed

Arnoldt, Hinrich; Strogatz, Steven H; Timme, Marc

2015-01-01

It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for stochastic processes potentially contributing to this hypothesized "Darwinian transition." The model suggests that HGT-dominated dynamics may have been intermittently interrupted by selection-driven processes during which genotypes became fitter and decreased their inclination toward HGT. Stochastic switching in the population dynamics with three-point (hypernetwork) interactions may have destabilized the HGT-dominated collective state and essentially contributed to the emergence of vertical descent and the first well-defined species in early evolution. A systematic nonlinear analysis of the stochastic model dynamics covering key features of evolutionary processes (such as selection, mutation, drift and HGT) supports this view. Our findings thus suggest a viable direction out of early collective evolution, potentially enabling the start of individuality and vertical Darwinian evolution.

Some anticipated contributions to core fluid dynamics from the GRM

NASA Technical Reports Server (NTRS)

Vanvorhies, C.

1985-01-01

It is broadly maintained that the secular variation (SV) of the large scale geomagnetic field contains information on the fluid dynamics of Earth's electrically conducting outer core. The electromagnetic theory appropriate to a simple Earth model has recently been combined with reduced geomagnetic data in order to extract some of this information and ascertain its significance. The simple Earth model consists of a rigid, electrically insulating mantle surrounding a spherical, inviscid, and perfectly conducting liquid outer core. This model was tested against seismology by using truncated spherical harmonic models of the observed geomagnetic field to locate Earth's core-mantle boundary, CMB. Further electromagnetic theory has been developed and applied to the problem of estimating the horizontal fluid motion just beneath CMB. Of particular geophysical interest are the hypotheses that these motions: (1) include appreciable surface divergence indicative of vertical motion at depth, and (2) are steady for time intervals of a decade or more. In addition to the extended testing of the basic Earth model, the proposed GRM provides a unique opportunity to test these dynamical hypotheses.

The Creative Chaos: Speculations on the Connection Between Non-Linear Dynamics and the Creative Process

NASA Astrophysics Data System (ADS)

Zausner, Tobi

Chaos theory may provide models for creativity and for the personality of the artist. A collection of speculative hypotheses examines the connection between art and such fundamentals of non-linear dynamics as iteration, dissipative processes, open systems, entropy, sensitivity to stimuli, autocatalysis, subsystems, bifurcations, randomness, unpredictability, irreversibility, increasing levels of organization, far-from-equilibrium conditions, strange attractors, period doubling, intermittency and self-similar fractal organization. Non-linear dynamics may also explain why certain individuals suffer mental disorders while others remain intact during a lifetime of sustained creative output.

Using Dynamic Time Warping and Data Forensics to Examine Tradeoffs among Land-Energy-Water Networks Across the Conterminous United States

NASA Astrophysics Data System (ADS)

McManamay, R.; Allen, M. R.; Piburn, J.; Sanyal, J.; Stewart, R.; Bhaduri, B. L.

2017-12-01

Characterizing interdependencies among land-energy-water sectors, their vulnerabilities, and tipping points, is challenging, especially if all sectors are simultaneously considered. Because such holistic system behavior is uncertain, largely unmodeled, and in need of testable hypotheses of system drivers, these dynamics are conducive to exploratory analytics of spatiotemporal patterns, powered by tools, such as Dynamic Time Warping (DTW). Here, we conduct a retrospective analysis (1950 - 2010) of temporal trends in land use, energy use, and water use within US counties to identify commonalities in resource consumption and adaptation strategies to resource limitations. We combine existing and derived data from statistical downscaling to synthesize a temporally comprehensive land-energy-water dataset at the US county level and apply DTW and subsequent hierarchical clustering to examine similar temporal trends in resource typologies for land, energy, and water sectors. As expected, we observed tradeoffs among water uses (e.g., public supply vs irrigation) and land uses (e.g., urban vs ag). Strong associations between clusters amongst sectors reveal tight system interdependencies, whereas weak associations suggest unique behaviors and potential for human adaptations towards disruptive technologies and less resource-dependent population growth. Our framework is useful for exploring complex human-environmental system dynamics and generating hypotheses to guide subsequent energy-water-nexus research.

Neural Dynamics Underlying Event-Related Potentials

NASA Technical Reports Server (NTRS)

Shah, Ankoor S.; Bressler, Steven L.; Knuth, Kevin H.; Ding, Ming-Zhou; Mehta, Ashesh D.; Ulbert, Istvan; Schroeder, Charles E.

2003-01-01

There are two opposing hypotheses about the brain mechanisms underlying sensory event-related potentials (ERPs). One holds that sensory ERPs are generated by phase resetting of ongoing electroencephalographic (EEG) activity, and the other that they result from signal averaging of stimulus-evoked neural responses. We tested several contrasting predictions of these hypotheses by direct intracortical analysis of neural activity in monkeys. Our findings clearly demonstrate evoked response contributions to the sensory ERP in the monkey, and they suggest the likelihood that a mixed (Evoked/Phase Resetting) model may account for the generation of scalp ERPs in humans.

Combining Theory-Driven Evaluation and Causal Loop Diagramming for Opening the 'Black Box' of an Intervention in the Health Sector: A Case of Performance-Based Financing in Western Uganda.

PubMed

Renmans, Dimitri; Holvoet, Nathalie; Criel, Bart

2017-09-03

Increased attention on "complexity" in health systems evaluation has resulted in many different methodological responses. Theory-driven evaluations and systems thinking are two such responses that aim for better understanding of the mechanisms underlying given outcomes. Here, we studied the implementation of a performance-based financing intervention by the Belgian Technical Cooperation in Western Uganda to illustrate a methodological strategy of combining these two approaches. We utilized a systems dynamics tool called causal loop diagramming (CLD) to generate hypotheses feeding into a theory-driven evaluation. Semi-structured interviews were conducted with 30 health workers from two districts (Kasese and Kyenjojo) and with 16 key informants. After CLD, we identified three relevant hypotheses: "success to the successful", "growth and underinvestment", and "supervision conundrum". The first hypothesis leads to increasing improvements in performance, as better performance leads to more incentives, which in turn leads to better performance. The latter two hypotheses point to potential bottlenecks. Thus, the proposed methodological strategy was a useful tool for identifying hypotheses that can inform a theory-driven evaluation. The hypotheses are represented in a comprehensible way while highlighting the underlying assumptions, and are more easily falsifiable than hypotheses identified without using CLD.

Using body mass dynamics to examine long-term habitat shifts of arctic-molting geese: Evidence for ecological change

USGS Publications Warehouse

Lewis, Tyler L.; Flint, Paul L.; Derksen, Dirk V.; Schmutz, Joel A.; Taylor, Eric J.; Bollinger, Karen S.

2011-01-01

From 1976 onward, molting brant geese (Branta bernicla) within the Teshekpuk Lake Special Area, Alaska, shifted from inland, freshwater lakes toward coastal wetlands. Two hypotheses explained this redistribution: (1) ecological change: redistribution of molting brant reflects improvements in coastal foraging habitats, which have undergone a succession toward salt-tolerant plants due to increased coastal erosion and saltwater intrusion as induced by climate change or (2) interspecific competition: greater white-fronted geese (Anser albifrons) populations increased 12-fold at inland lakes, limiting food availability and forcing brant into coastal habitats. Both hypotheses presume that brant redistributions were driven by food availability; thus, body mass dynamics may provide insight into the relevance of these hypotheses. We compared body mass dynamics of molting brant across decades (1978, 1987–1992, 2005–2007) and, during 2005–2007, across habitats (coastal vs. inland). Brant lost body mass during molt in all three decades. At inland habitats, rates of mass loss progressively decreased by decade despite the increased number of greater white-fronted geese. These results do not support an interspecific competition hypothesis, instead suggesting that ecological change enhanced foraging habitats for brant. During 2005–2007, rates of mass loss did not vary by habitat. Thus, while habitats have improved from earlier decades, our results cannot distinguish between ecological changes at inland versus coastal habitats. However, we speculate that coastal forage quality has improved beyond that of inland habitats and that the body mass benefits of these higher quality foods are offset by the disproportionate number of brant now molting coastally.

Diagnosing and Reconstructing Real-World Hydroclimatic Dynamics from Time Sequenced Data: The Case of Saltwater Intrusion into Coastal Wetlands in Everglades National Park

NASA Astrophysics Data System (ADS)

Huffaker, R.; Munoz-Carpena, R.

2016-12-01

There are increasing calls to audit decision-support models used for environmental policy to ensure that they correspond with the reality facing policy makers. Modelers can establish correspondence by providing empirical evidence of real-world dynamic behavior that their models skillfully simulate. We present a pre-modeling diagnostic framework—based on nonlinear dynamic analysis—for detecting and reconstructing real-world environmental dynamics from observed time-sequenced data. Phenomenological (data-driven) modeling—based on machine learning regression techniques—extracts a set of ordinary differential equations governing empirically-diagnosed system dynamics from a single time series, or from multiple time series on causally-interacting variables. We apply the framework to investigate saltwater intrusion into coastal wetlands in Everglades National Park, Florida, USA. We test the following hypotheses posed in the literature linking regional hydrologic variables with global climatic teleconnections: (1) Sea level in Florida Bay drives well level and well salinity in the coastal Everglades; (2) Atlantic Multidecadal Oscillation (AMO) drives sea level, well level and well salinity; and (3) AMO and (El Niño Southern Oscillation) ENSO bi-causally interact. The thinking is that salt water intrusion links ocean-surface salinity with salinity of inland water sources, and sea level with inland water; that AMO and ENSO share a teleconnective relationship (perhaps through the atmosphere); and that AMO and ENSO both influence inland precipitation and thus well levels. Our results support these hypotheses, and we successfully construct a parsimonious phenomenological model that reproduces diagnosed nonlinear dynamics and system interactions. We propose that reconstructed data dynamics be used, along with other expert information, as a rigorous benchmark to guide specification and testing of hydrologic decision support models corresponding with real-world behavior.

OBSERVING LYAPUNOV EXPONENTS OF INFINITE-DIMENSIONAL DYNAMICAL SYSTEMS

PubMed Central

OTT, WILLIAM; RIVAS, MAURICIO A.; WEST, JAMES

2016-01-01

Can Lyapunov exponents of infinite-dimensional dynamical systems be observed by projecting the dynamics into ℝN using a ‘typical’ nonlinear projection map? We answer this question affirmatively by developing embedding theorems for compact invariant sets associated with C1 maps on Hilbert spaces. Examples of such discrete-time dynamical systems include time-T maps and Poincaré return maps generated by the solution semigroups of evolution partial differential equations. We make every effort to place hypotheses on the projected dynamics rather than on the underlying infinite-dimensional dynamical system. In so doing, we adopt an empirical approach and formulate checkable conditions under which a Lyapunov exponent computed from experimental data will be a Lyapunov exponent of the infinite-dimensional dynamical system under study (provided the nonlinear projection map producing the data is typical in the sense of prevalence). PMID:28066028

OBSERVING LYAPUNOV EXPONENTS OF INFINITE-DIMENSIONAL DYNAMICAL SYSTEMS.

PubMed

Ott, William; Rivas, Mauricio A; West, James

2015-12-01

Can Lyapunov exponents of infinite-dimensional dynamical systems be observed by projecting the dynamics into ℝ N using a 'typical' nonlinear projection map? We answer this question affirmatively by developing embedding theorems for compact invariant sets associated with C 1 maps on Hilbert spaces. Examples of such discrete-time dynamical systems include time- T maps and Poincaré return maps generated by the solution semigroups of evolution partial differential equations. We make every effort to place hypotheses on the projected dynamics rather than on the underlying infinite-dimensional dynamical system. In so doing, we adopt an empirical approach and formulate checkable conditions under which a Lyapunov exponent computed from experimental data will be a Lyapunov exponent of the infinite-dimensional dynamical system under study (provided the nonlinear projection map producing the data is typical in the sense of prevalence).

Dynamic augmentation restores anterior tibial translation in ACL suture repair: a biomechanical comparison of non-, static and dynamic augmentation techniques.

PubMed

Hoogeslag, Roy A G; Brouwer, Reinoud W; Huis In 't Veld, Rianne; Stephen, Joanna M; Amis, Andrew A

2018-02-03

There is a lack of objective evidence investigating how previous non-augmented ACL suture repair techniques and contemporary augmentation techniques in ACL suture repair restrain anterior tibial translation (ATT) across the arc of flexion, and after cyclic loading of the knee. The purpose of this work was to test the null hypotheses that there would be no statistically significant difference in ATT after non-, static- and dynamic-augmented ACL suture repair, and they will not restore ATT to normal values across the arc of flexion of the knee after cyclic loading. Eleven human cadaveric knees were mounted in a test rig, and knee kinematics from 0° to 90° of flexion were recorded by use of an optical tracking system. Measurements were recorded without load and with 89-N tibial anterior force. The knees were tested in the following states: ACL-intact, ACL-deficient, non-augmented suture repair, static tape augmentation and dynamic augmentation after 10 and 300 loading cycles. Only static tape augmentation and dynamic augmentation restored ATT to values similar to the ACL-intact state directly postoperation, and maintained this after cyclic loading. However, contrary to dynamic augmentation, the ATT after static tape augmentation failed to remain statistically less than for the ACL-deficient state after cyclic loading. Moreover, after cyclic loading, ATT was significantly less with dynamic augmentation when compared to static tape augmentation. In contrast to non-augmented ACL suture repair and static tape augmentation, only dynamic augmentation resulted in restoration of ATT values similar to the ACL-intact knee and decreased ATT values when compared to the ACL-deficient knee immediately post-operation and also after cyclic loading, across the arc of flexion, thus allowing the null hypotheses to be rejected. This may assist healing of the ruptured ACL. Therefore, this study would support further clinical evaluation of dynamic augmentation of ACL repair.

DISTURBANCE PATTERNS IN A SOCIO-ECOLOGICAL SYSTEM AT MULTIPLE SCALES

EPA Science Inventory

Ecological systems with hierarchical organization and non-equilibrium dynamics require multiple-scale analyses to comprehend how a system is structured and to formulate hypotheses about regulatory mechanisms. Characteristic scales in real landscapes are determined by, or at least...

Diel shifts in the structure and function of nearshore estuarine fish communities.

PubMed

Yeoh, D E; Valesini, F J; Hallett, C S; Abdo, D A; Williams, J

2017-04-01

Day-night shifts in the nearshore fish fauna of a temperate microtidal estuary were assessed using a holistic suite of structural and functional community attributes. Mean fish species richness and diversity (taxonomic distinctness) were higher at night across all regions of the estuary and seasons, concurring with the findings of numerous comparable studies reviewed worldwide, while the diel period in which mean abundance was higher varied among seasons. Likewise, species and functional guild compositions (the latter based on feeding modes and habitat use) both differed significantly between day and night, with the extent of the diel shift again varying seasonally. Daytime fish communities were characterized by higher abundances of Atherinidae, Sillaginidae and Mugilidae, while Gobiidae were far more abundant at night. Marked shifts in size composition were also evident, with smaller fishes (<100 mm total length, L T ) being more prevalent during the day and larger fishes (≥200 mm L T ) proportionally more abundant at night. The above diel shifts were feasibly related to a range of predator-prey interactions and feeding-related movements, namely a nocturnal decrease in top-order avian piscivory coupled with an increase in invertebrate prey availability, resulting in changes in the presence and catchability of certain fish species in shallow estuarine waters. © 2016 The Fisheries Society of the British Isles.

Evaluating sampling strategies for larval cisco (Coregonus artedi)

USGS Publications Warehouse

Myers, J.T.; Stockwell, J.D.; Yule, D.L.; Black, J.A.

2008-01-01

To improve our ability to assess larval cisco (Coregonus artedi) populations in Lake Superior, we conducted a study to compare several sampling strategies. First, we compared density estimates of larval cisco concurrently captured in surface waters with a 2 x 1-m paired neuston net and a 0.5-m (diameter) conical net. Density estimates obtained from the two gear types were not significantly different, suggesting that the conical net is a reasonable alternative to the more cumbersome and costly neuston net. Next, we assessed the effect of tow pattern (sinusoidal versus straight tows) to examine if propeller wash affected larval density. We found no effect of propeller wash on the catchability of larval cisco. Given the availability of global positioning systems, we recommend sampling larval cisco using straight tows to simplify protocols and facilitate straightforward measurements of volume filtered. Finally, we investigated potential trends in larval cisco density estimates by sampling four time periods during the light period of a day at individual sites. Our results indicate no significant trends in larval density estimates during the day. We conclude estimates of larval cisco density across space are not confounded by time at a daily timescale. Well-designed, cost effective surveys of larval cisco abundance will help to further our understanding of this important Great Lakes forage species.

Late Miocene Pacific plate kinematic change explained with coupled global models of mantle and lithosphere dynamics

NASA Astrophysics Data System (ADS)

Stotz, I. L.; Iaffaldano, G.; Davies, D. R.

2017-07-01

The timing and magnitude of a Pacific plate motion change within the past 10 Ma remains enigmatic, due to the noise associated with finite-rotation data. Nonetheless, it has been hypothesized that this change was driven by the arrival of the Ontong Java Plateau (OJP) at the Melanesian arc and the consequent subduction polarity reversal. The uncertainties associated with the timing of this event, however, make it difficult to quantitatively demonstrate a dynamical association. Here, we first reconstruct the Pacific plate's absolute motion since the mid-Miocene (15 Ma), at high-temporal resolution, building on previous efforts to mitigate the impact of finite-rotation data noise. We find that the largest change in Pacific plate-motion direction occurred between 10 and 5 Ma, with the plate rotating clockwise. We subsequently develop and use coupled global numerical models of the mantle/lithosphere system to test hypotheses on the dynamics driving this change. These indicate that the arrival of the OJP at the Melanesian arc, between 10 and 5 Ma, followed by a subduction polarity reversal that marked the initiation of subduction of the Australian plate underneath the Pacific realm, were the key drivers of this kinematic change.

Fish population dynamics in a seasonally varying wetland

USGS Publications Warehouse

DeAngelis, Donald L.; Trexler, Joel C.; Cosner, Chris; Obaza, Adam; Jopp, Fred

2010-01-01

Small fishes in seasonally flooded environments such as the Everglades are capable of spreading into newly flooded areas and building up substantial biomass. Passive drift cannot account for the rapidity of observed population expansions. To test the reaction-diffusion mechanism for spread of the fish, we estimated their diffusion coefficient and applied a reaction-diffusion model. This mechanism was also too weak to account for the spatial dynamics. Two other hypotheses were tested through modeling. The first--the 'refuge mechanism--hypothesizes that small remnant populations of small fishes survive the dry season in small permanent bodies of water (refugia), sites where the water level is otherwise below the surface. The second mechanism, which we call the 'dynamic ideal free distribution mechanism' is that consumption by the fish creates a prey density gradient and that fish taxis along this gradient can lead to rapid population expansion in space. We examined the two alternatives and concluded that although refugia may play an important role in recolonization by the fish population during reflooding, only the second, taxis in the direction of the flooding front, seems capable of matching empirical observations. This study has important implications for management of wetlands, as fish biomass is an essential support of higher trophic levels.

Enol tautomers of Watson-Crick base pair models are metastable because of nuclear quantum effects.

PubMed

Pérez, Alejandro; Tuckerman, Mark E; Hjalmarson, Harold P; von Lilienfeld, O Anatole

2010-08-25

Intermolecular enol tautomers of Watson-Crick base pairs could emerge spontaneously via interbase double proton transfer. It has been hypothesized that their formation could be facilitated by thermal fluctuations and proton tunneling, and possibly be relevant to DNA damage. Theoretical and computational studies, assuming classical nuclei, have confirmed the dynamic stability of these rare tautomers. However, by accounting for nuclear quantum effects explicitly through Car-Parrinello path integral molecular dynamics calculations, we find the tautomeric enol form to be dynamically metastable, with lifetimes too insignificant to be implicated in DNA damage.

Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis.

PubMed

Seal, John B; Alverdy, John C; Zaborina, Olga; An, Gary

2011-09-19

There is a growing realization that alterations in host-pathogen interactions (HPI) can generate disease phenotypes without pathogen invasion. The gut represents a prime region where such HPI can arise and manifest. Under normal conditions intestinal microbial communities maintain a stable, mutually beneficial ecosystem. However, host stress can lead to changes in environmental conditions that shift the nature of the host-microbe dialogue, resulting in escalation of virulence expression, immune activation and ultimately systemic disease. Effective modulation of these dynamics requires the ability to characterize the complexity of the HPI, and dynamic computational modeling can aid in this task. Agent-based modeling is a computational method that is suited to representing spatially diverse, dynamical systems. We propose that dynamic knowledge representation of gut HPI with agent-based modeling will aid in the investigation of the pathogenesis of gut-derived sepsis. An agent-based model (ABM) of virulence regulation in Pseudomonas aeruginosa was developed by translating bacterial and host cell sense-and-response mechanisms into behavioral rules for computational agents and integrated into a virtual environment representing the host-microbe interface in the gut. The resulting gut milieu ABM (GMABM) was used to: 1) investigate a potential clinically relevant laboratory experimental condition not yet developed--i.e. non-lethal transient segmental intestinal ischemia, 2) examine the sufficiency of existing hypotheses to explain experimental data--i.e. lethality in a model of major surgical insult and stress, and 3) produce behavior to potentially guide future experimental design--i.e. suggested sample points for a potential laboratory model of non-lethal transient intestinal ischemia. Furthermore, hypotheses were generated to explain certain discrepancies between the behaviors of the GMABM and biological experiments, and new investigatory avenues proposed to test those hypotheses. Agent-based modeling can account for the spatio-temporal dynamics of an HPI, and, even when carried out with a relatively high degree of abstraction, can be useful in the investigation of system-level consequences of putative mechanisms operating at the individual agent level. We suggest that an integrated and iterative heuristic relationship between computational modeling and more traditional laboratory and clinical investigations, with a focus on identifying useful and sufficient degrees of abstraction, will enhance the efficiency and translational productivity of biomedical research.

Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis

PubMed Central

2011-01-01

Background There is a growing realization that alterations in host-pathogen interactions (HPI) can generate disease phenotypes without pathogen invasion. The gut represents a prime region where such HPI can arise and manifest. Under normal conditions intestinal microbial communities maintain a stable, mutually beneficial ecosystem. However, host stress can lead to changes in environmental conditions that shift the nature of the host-microbe dialogue, resulting in escalation of virulence expression, immune activation and ultimately systemic disease. Effective modulation of these dynamics requires the ability to characterize the complexity of the HPI, and dynamic computational modeling can aid in this task. Agent-based modeling is a computational method that is suited to representing spatially diverse, dynamical systems. We propose that dynamic knowledge representation of gut HPI with agent-based modeling will aid in the investigation of the pathogenesis of gut-derived sepsis. Methodology/Principal Findings An agent-based model (ABM) of virulence regulation in Pseudomonas aeruginosa was developed by translating bacterial and host cell sense-and-response mechanisms into behavioral rules for computational agents and integrated into a virtual environment representing the host-microbe interface in the gut. The resulting gut milieu ABM (GMABM) was used to: 1) investigate a potential clinically relevant laboratory experimental condition not yet developed - i.e. non-lethal transient segmental intestinal ischemia, 2) examine the sufficiency of existing hypotheses to explain experimental data - i.e. lethality in a model of major surgical insult and stress, and 3) produce behavior to potentially guide future experimental design - i.e. suggested sample points for a potential laboratory model of non-lethal transient intestinal ischemia. Furthermore, hypotheses were generated to explain certain discrepancies between the behaviors of the GMABM and biological experiments, and new investigatory avenues proposed to test those hypotheses. Conclusions/Significance Agent-based modeling can account for the spatio-temporal dynamics of an HPI, and, even when carried out with a relatively high degree of abstraction, can be useful in the investigation of system-level consequences of putative mechanisms operating at the individual agent level. We suggest that an integrated and iterative heuristic relationship between computational modeling and more traditional laboratory and clinical investigations, with a focus on identifying useful and sufficient degrees of abstraction, will enhance the efficiency and translational productivity of biomedical research. PMID:21929759

A hypothesis for delayed dynamic earthquake triggering

USGS Publications Warehouse

Parsons, T.

2005-01-01

It's uncertain whether more near-field earthquakes are triggered by static or dynamic stress changes. This ratio matters because static earthquake interactions are increasingly incorporated into probabilistic forecasts. Recent studies were unable to demonstrate all predictions from the static-stress-change hypothesis, particularly seismicity rate reductions. However, current dynamic stress change hypotheses do not explain delayed earthquake triggering and Omori's law. Here I show numerically that if seismic waves can alter some frictional contacts in neighboring fault zones, then dynamic triggering might cause delayed triggering and an Omori-law response. The hypothesis depends on faults following a rate/state friction law, and on seismic waves changing the mean critical slip distance (Dc) at nucleation zones.

Dynamics of Inhomogeneous Shell Systems Under Non-Stationary Loading (Survey)

NASA Astrophysics Data System (ADS)

Lugovoi, P. Z.; Meish, V. F.

2017-09-01

Experimental works on the determination of dynamics of smooth and stiffened cylindrical shells contacting with a soil medium under various non-stationary loading are reviewed. The results of studying three-layer shells of revolution whose motion equations are obtained within the framework of the hypotheses of the Timoshenko geometrically nonlinear theory are stated. The numerical results for shells with a piecewise or discrete filler enable the analysis of estimation of the influence of geometrical and physical-mechanical parameters of structures on their dynamics and reveal new mechanical effects. Basing on the classical theory of shells and rods, the effect of the discrete arrangement of ribs and coefficients of the Winkler or Pasternak elastic foundation on the normal frequencies and modes of rectangular planar cylindrical and spherical shells is studied. The number and shape of dispersion curves for longitudinal harmonic waves in a stiffened cylindrical shell are determined. The equations of vibrations of ribbed shells of revolution on Winkler or Pasternak elastic foundation are obtained using the geometrically nonlinear theory and the Timoshenko hypotheses. On applying the integral-interpolational method, numerical algorithms are developed and the corresponding non-stationary problems are solved. The special attention is paid to the statement and solution of coupled problems on the dynamical interaction of cylindrical or spherical shells with the soil water-saturated medium of different structure.

Modeling temperature and humidity profiles within forest canopies

USDA-ARS?s Scientific Manuscript database

Physically-based models are a powerful tool to help understand interactions of vegetation, atmospheric dynamics, and hydrology, and to test hypotheses regarding the effects of land cover, management, hydrometeorology, and climate variability on ecosystem processes. The purpose of this paper is to f...

The Dynamics of Perceptual Learning: An Incremental Reweighting Model

ERIC Educational Resources Information Center

Petrov, Alexander A.; Dosher, Barbara Anne; Lu, Zhong-Lin

2005-01-01

The mechanisms of perceptual learning are analyzed theoretically, probed in an orientation-discrimination experiment involving a novel nonstationary context manipulation, and instantiated in a detailed computational model. Two hypotheses are examined: modification of early cortical representations versus task-specific selective reweighting.…

Combining Theory-Driven Evaluation and Causal Loop Diagramming for Opening the ‘Black Box’ of an Intervention in the Health Sector: A Case of Performance-Based Financing in Western Uganda

PubMed Central

Holvoet, Nathalie; Criel, Bart

2017-01-01

Increased attention on “complexity” in health systems evaluation has resulted in many different methodological responses. Theory-driven evaluations and systems thinking are two such responses that aim for better understanding of the mechanisms underlying given outcomes. Here, we studied the implementation of a performance-based financing intervention by the Belgian Technical Cooperation in Western Uganda to illustrate a methodological strategy of combining these two approaches. We utilized a systems dynamics tool called causal loop diagramming (CLD) to generate hypotheses feeding into a theory-driven evaluation. Semi-structured interviews were conducted with 30 health workers from two districts (Kasese and Kyenjojo) and with 16 key informants. After CLD, we identified three relevant hypotheses: “success to the successful”, “growth and underinvestment”, and “supervision conundrum”. The first hypothesis leads to increasing improvements in performance, as better performance leads to more incentives, which in turn leads to better performance. The latter two hypotheses point to potential bottlenecks. Thus, the proposed methodological strategy was a useful tool for identifying hypotheses that can inform a theory-driven evaluation. The hypotheses are represented in a comprehensible way while highlighting the underlying assumptions, and are more easily falsifiable than hypotheses identified without using CLD. PMID:28869518

ClueNet: Clustering a temporal network based on topological similarity rather than denseness.

PubMed

Crawford, Joseph; Milenković, Tijana

2018-01-01

Network clustering is a very popular topic in the network science field. Its goal is to divide (partition) the network into groups (clusters or communities) of "topologically related" nodes, where the resulting topology-based clusters are expected to "correlate" well with node label information, i.e., metadata, such as cellular functions of genes/proteins in biological networks, or age or gender of people in social networks. Even for static data, the problem of network clustering is complex. For dynamic data, the problem is even more complex, due to an additional dimension of the data-their temporal (evolving) nature. Since the problem is computationally intractable, heuristic approaches need to be sought. Existing approaches for dynamic network clustering (DNC) have drawbacks. First, they assume that nodes should be in the same cluster if they are densely interconnected within the network. We hypothesize that in some applications, it might be of interest to cluster nodes that are topologically similar to each other instead of or in addition to requiring the nodes to be densely interconnected. Second, they ignore temporal information in their early steps, and when they do consider this information later on, they do so implicitly. We hypothesize that capturing temporal information earlier in the clustering process and doing so explicitly will improve results. We test these two hypotheses via our new approach called ClueNet. We evaluate ClueNet against six existing DNC methods on both social networks capturing evolving interactions between individuals (such as interactions between students in a high school) and biological networks capturing interactions between biomolecules in the cell at different ages. We find that ClueNet is superior in over 83% of all evaluation tests. As more real-world dynamic data are becoming available, DNC and thus ClueNet will only continue to gain importance.

The auditory dynamic attending theory revisited: A closer look at the pitch comparison task.

PubMed

Bauer, Anna-Katharina R; Jaeger, Manuela; Thorne, Jeremy D; Bendixen, Alexandra; Debener, Stefan

2015-11-11

The dynamic attending theory as originally proposed by Jones, 1976. Psychol. Rev. 83(5), 323-355 posits that tone sequences presented at a regular rhythm entrain attentional oscillations and thereby facilitate the processing of sounds presented in phase with this rhythm. The increased interest in neural correlates of dynamic attending requires robust behavioral indicators of the phenomenon. Here we aimed to replicate and complement the most prominent experimental implementation of dynamic attending (Jones et al., 2002. Psychol. Sci. 13(4), 313-319). The paradigm uses a pitch comparison task in which two tones, the initial and the last of a longer series, have to be compared. In-between the two, distractor tones with variable pitch are presented, at a regular pace. A comparison tone presented in phase with the entrained rhythm is hypothesized to lead to better behavioral performance. Aiming for a conceptual replication, four different variations of the original paradigm were created which were followed by an exact replication attempt. Across all five experiments, only 40 of the 140 tested participants showed the hypothesized pattern of an inverted U-shaped profile in task accuracy, and the group average effects did not replicate the pattern reported by Jones et al., 2002. Psychol. Sci. 13(4), 313-319 in any of the five experiments. However, clear evidence for a relationship between musicality and overall behavioral performance was found. This study casts doubt on the suitability of the pitch comparison task for demonstrating auditory dynamic attending. We discuss alternative tasks that have been shown to support dynamic attending theory, thus lending themselves more readily to studying its neural correlates. This article is part of a Special Issue entitled SI: Prediction and Attention. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Contagion of Cooperation in Static and Fluid Social Networks.

PubMed

Jordan, Jillian J; Rand, David G; Arbesman, Samuel; Fowler, James H; Christakis, Nicholas A

2013-01-01

Cooperation is essential for successful human societies. Thus, understanding how cooperative and selfish behaviors spread from person to person is a topic of theoretical and practical importance. Previous laboratory experiments provide clear evidence of social contagion in the domain of cooperation, both in fixed networks and in randomly shuffled networks, but leave open the possibility of asymmetries in the spread of cooperative and selfish behaviors. Additionally, many real human interaction structures are dynamic: we often have control over whom we interact with. Dynamic networks may differ importantly in the goals and strategic considerations they promote, and thus the question of how cooperative and selfish behaviors spread in dynamic networks remains open. Here, we address these questions with data from a social dilemma laboratory experiment. We measure the contagion of both cooperative and selfish behavior over time across three different network structures that vary in the extent to which they afford individuals control over their network ties. We find that in relatively fixed networks, both cooperative and selfish behaviors are contagious. In contrast, in more dynamic networks, selfish behavior is contagious, but cooperative behavior is not: subjects are fairly likely to switch to cooperation regardless of the behavior of their neighbors. We hypothesize that this insensitivity to the behavior of neighbors in dynamic networks is the result of subjects' desire to attract new cooperative partners: even if many of one's current neighbors are defectors, it may still make sense to switch to cooperation. We further hypothesize that selfishness remains contagious in dynamic networks because of the well-documented willingness of cooperators to retaliate against selfishness, even when doing so is costly. These results shed light on the contagion of cooperative behavior in fixed and fluid networks, and have implications for influence-based interventions aiming at increasing cooperative behavior.

Dynamical Resilience Indicators in Time Series of Self-Rated Health Correspond to Frailty Levels in Older Adults.

PubMed

Gijzel, Sanne M W; van de Leemput, Ingrid A; Scheffer, Marten; Roppolo, Mattia; Olde Rikkert, Marcel G M; Melis, René J F

2017-07-01

We currently still lack valid methods to dynamically measure resilience for stressors before the appearance of adverse health outcomes that hamper well-being. Quantifying an older adult's resilience in an early stage would aid complex decision-making in health care. Translating complex dynamical systems theory to humans, we hypothesized that three dynamical indicators of resilience (variance, temporal autocorrelation, and cross-correlation) in time series of self-rated physical, mental, and social health were associated with frailty levels in older adults. We monitored self-rated physical, mental, and social health during 100 days using daily visual analogue scale questions in 22 institutionalized older adults (mean age 84.0, SD: 5.9 years). Frailty was determined by the Survey of Health, Ageing and Retirement in Europe (SHARE) frailty index. The resilience indicators (variance, temporal autocorrelation, and cross-correlation) were calculated using multilevel models. The self-rated health time series of frail elderly exhibited significantly elevated variance in the physical, mental, and social domain, as well as significantly stronger cross-correlations between all three domains, as compared to the nonfrail group (all P < 0.001). Temporal autocorrelation was not significantly associated with frailty. We found supporting evidence for two out of three hypothesized resilience indicators to be related to frailty levels in older adults. By mirroring the dynamical resilience indicators to a frailty index, we delivered a first empirical base to validate and quantify the construct of systemic resilience in older adults in a dynamic way. © The Author 2017. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Coordination Dynamics in Cognitive Neuroscience

PubMed Central

Bressler, Steven L.; Kelso, J. A. Scott

2016-01-01

Many researchers and clinicians in cognitive neuroscience hold to a modular view of cognitive function in which the cerebral cortex operates by the activation of areas with circumscribed elementary cognitive functions. Yet an ongoing paradigm shift to a dynamic network perspective is underway. This new viewpoint treats cortical function as arising from the coordination dynamics within and between cortical regions. Cortical coordination dynamics arises due to the unidirectional influences imposed on a cortical area by inputs from other areas that project to it, combined with the projection reciprocity that characterizes cortical connectivity and gives rise to reentrant processing. As a result, cortical dynamics exhibits both segregative and integrative tendencies and gives rise to both cooperative and competitive relations within and between cortical areas that are hypothesized to underlie the emergence of cognition in brains. PMID:27695395

Developing research competencies through a project-based tissue-engineering module in the biomedical engineering undergraduate curriculum.

PubMed

Wallen, M; Pandit, A

2009-05-01

In addressing the task of developing an undergraduate module in the field of tissue engineering, the greatest challenge lies in managing to capture what is a growing and rapidly changing field. Acknowledging the call for the development of greater critical thinking and interpersonal skills among the next generation of engineers as well as encouraging students to engage actively with the dynamic nature of research in the field, the module was developed to include both project-based and cooperative-learning experiences. These learning activities include developing hypotheses for the application of newly introduced laboratory procedures, a collaborative mock grant submission, and debates on ethical issues in which students are assigned roles as various stakeholders. Feedback from module evaluations has indicated that, while students find the expectations challenging, they are able to gain an advanced insight into a dynamic field. More importantly, students develop research competencies by engaging in activities that require them to link current research directions with their own development of hypotheses for future tissue-engineering applications.

Navigating the cancer information environment: The reciprocal relationship between patient-clinician information engagement and information seeking from nonmedical sources.

PubMed

Moldovan-Johnson, Mihaela; Tan, Andy S L; Hornik, Robert C

2014-01-01

Prior theory has argued and empirical studies have shown that cancer patients rely on information from their health care providers as well as lay sources to understand and make decisions about their disease. However, research on the dynamic and interdependent nature of cancer patients' engagement with different information sources is lacking. This study tested the hypotheses that patient-clinician information engagement and information seeking from nonmedical sources influence one another longitudinally among a representative cohort of 1,293 cancer survivors in Pennsylvania. The study hypotheses were supported in a series of lagged multiple regression analyses. Baseline seeking information from nonmedical sources positively predicted subsequent patient-clinician information engagement at 1-year follow-up. The reverse relationship was also statistically significant; baseline patient-clinician information engagement positively predicted information seeking from nonmedical sources at follow-up. These findings suggest that cancer survivors move between nonmedical and clinician sources in a dynamic way to learn about their disease.

Innovation implementation in the public sector: an integration of institutional and collective dynamics.

PubMed

Choi, Jin Nam; Chang, Jae Yoon

2009-01-01

The present study integrates institutional factors and employee-based collective processes as predictors of 2 key implementation outcomes: implementation effectiveness and innovation effectiveness (Klein, Conn, & Sorra, 2001). Specifically, the authors proposed that institutional factors shape employees' collective implementation efficacy and innovation acceptance. The authors further hypothesized that these employee-based collective processes mediate the effects of institutional factors on implementation outcomes. This integrative framework was examined in the context of 47 agencies and ministries of the Korean Government that were implementing a process innovation called E-Government. Three-wave longitudinal data were collected from 60 external experts and 1,732 government employees. The results reveal the importance of management support for collective implementation efficacy, which affected employees' collective acceptance of the innovation. As hypothesized, these collective employee dynamics mediated the effects of institutional enablers on successful implementation as well as the amount of long-term benefit that accrued to the agencies and ministries. (PsycINFO Database Record (c) 2009 APA, all rights reserved).

Navigating the cancer information environment: The reciprocal relationship between patient-clinician information engagement and information seeking from nonmedical sources

PubMed Central

Moldovan-Johnson, Mihaela; Tan, Andy SL; Hornik, Robert C

2014-01-01

Prior theory has argued and empirical studies have shown that cancer patients rely on information from their health care providers as well as lay sources to understand and make decisions about their disease. However, research on the dynamic and interdependent nature of cancer patients’ engagement with different information sources is lacking. This study tested the hypotheses that patient-clinician information engagement and information seeking from nonmedical sources influence one another longitudinally among a representative cohort of 1,293 cancer survivors in Pennsylvania. The study hypotheses were supported in a series of lagged multiple regression analyses. Baseline seeking information from nonmedical sources positively predicted subsequent patient-clinician information engagement at one-year follow-up. The reverse relationship was also statistically significant; baseline patient-clinician information engagement positively predicted information seeking from nonmedical sources at follow-up. These findings suggest that cancer survivors move between nonmedical to clinician sources in a dynamic way to learn about their disease. PMID:24359259

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

DOE PAGES

Kim, Young-Mo; Nowack, Shane; Olsen, Millie; ...

2015-04-17

Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptative and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number ofmore » predominant taxa inhabiting this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate) and fermentation (e.g. acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2) Synechococcus spp. produce CH4 via metabolism of phosphonates, and photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4) fluctuations in many metabolite pools (e.g. wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.« less

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

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

Kim, Young-Mo; Nowack, Shane; Olsen, Millie

Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptative and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number ofmore » predominant taxa inhabiting this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate) and fermentation (e.g. acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2) Synechococcus spp. produce CH4 via metabolism of phosphonates, and photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4) fluctuations in many metabolite pools (e.g. wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.« less

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

PubMed Central

Kim, Young-Mo; Nowack, Shane; Olsen, Millie T.; Becraft, Eric D.; Wood, Jason M.; Thiel, Vera; Klapper, Isaac; Kühl, Michael; Fredrickson, James K.; Bryant, Donald A.; Ward, David M.; Metz, Thomas O.

2015-01-01

Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g., glycolate) and fermentation (e.g., acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gasses (e.g., H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and (4) fluctuations in many metabolite pools (e.g., wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches. PMID:25941514

Qualitative simulation of bathymetric changes due to reservoir sedimentation: A Japanese case study

PubMed Central

Dai, Wenhong; Larson, Magnus; Beebo, Qaid Naamo; Xie, Qiancheng

2017-01-01

Sediment-dynamics modeling is a useful tool for estimating a dam’s lifespan and its cost–benefit analysis. Collecting real data for sediment-dynamics analysis from conventional field survey methods is both tedious and expensive. Therefore, for most rivers, the historical record of data is either missing or not very detailed. Available data and existing tools have much potential and may be used for qualitative prediction of future bathymetric change trend. This study shows that proxy approaches may be used to increase the spatiotemporal resolution of flow data, and hypothesize the river cross-sections and sediment data. Sediment-dynamics analysis of the reach of the Tenryu River upstream of Sakuma Dam in Japan was performed to predict its future bathymetric changes using a 1D numerical model (HEC-RAS). In this case study, only annually-averaged flow data and the river’s longitudinal bed profile at 5-year intervals were available. Therefore, the other required data, including river cross-section and geometry and sediment inflow grain sizes, had to be hypothesized or assimilated indirectly. The model yielded a good qualitative agreement, with an R2 (coefficient of determination) of 0.8 for the observed and simulated bed profiles. A predictive simulation demonstrated that the useful life of the dam would end after the year 2035 (±5 years), which is in conformity with initial detailed estimates. The study indicates that a sediment-dynamic analysis can be performed even with a limited amount of data. However, such studies may only assess the qualitative trends of sediment dynamics. PMID:28384361

Qualitative simulation of bathymetric changes due to reservoir sedimentation: A Japanese case study.

PubMed

Bilal, Ahmed; Dai, Wenhong; Larson, Magnus; Beebo, Qaid Naamo; Xie, Qiancheng

2017-01-01

Sediment-dynamics modeling is a useful tool for estimating a dam's lifespan and its cost-benefit analysis. Collecting real data for sediment-dynamics analysis from conventional field survey methods is both tedious and expensive. Therefore, for most rivers, the historical record of data is either missing or not very detailed. Available data and existing tools have much potential and may be used for qualitative prediction of future bathymetric change trend. This study shows that proxy approaches may be used to increase the spatiotemporal resolution of flow data, and hypothesize the river cross-sections and sediment data. Sediment-dynamics analysis of the reach of the Tenryu River upstream of Sakuma Dam in Japan was performed to predict its future bathymetric changes using a 1D numerical model (HEC-RAS). In this case study, only annually-averaged flow data and the river's longitudinal bed profile at 5-year intervals were available. Therefore, the other required data, including river cross-section and geometry and sediment inflow grain sizes, had to be hypothesized or assimilated indirectly. The model yielded a good qualitative agreement, with an R2 (coefficient of determination) of 0.8 for the observed and simulated bed profiles. A predictive simulation demonstrated that the useful life of the dam would end after the year 2035 (±5 years), which is in conformity with initial detailed estimates. The study indicates that a sediment-dynamic analysis can be performed even with a limited amount of data. However, such studies may only assess the qualitative trends of sediment dynamics.

Kinome rewiring reveals AURKA is a molecular barrier to the efficacy of PI3K/mTOR-pathway inhibitors in breast cancer | Office of Cancer Genomics

Cancer.gov

Dysregulation of the PI3K-AKT-mTOR signaling network is a prominent feature of breast cancers. However, clinical responses to drugs targeting this pathway have been modest. We hypothesized that dynamic changes in signaling, including adaptation and feedback, limit drug efficacy. Using a quantitative chemoproteomics approach we mapped dynamic changes in the kinome in response to various agents and identified signaling changes that correlate with drug sensitivity.

Topics in Microeconometrics: Estimation of a Dynamic Model of Occupational Transitions, Wage and Non-Wage Benefits Cross Validation Bandwidth Selection for Derivatives of Various Dimensional Densities Testing the Additive Separability of the Teacher Value Added Effect Semiparametrically

ERIC Educational Resources Information Center

Baird, Matthew David

2012-01-01

I study three separate questions in this dissertation. In Chapter 1, I develop and estimate a structural dynamic model of occupation and job choice to test hypotheses of the importance of wages and non-wages and learning in occupational transitions, and find that wages are approximately 3 times as important as non-wage benefits in decisions and…

Interplay of Noisy Gene Expression and Dynamics Explains Patterns of Bacterial Operon Organization

NASA Astrophysics Data System (ADS)

Igoshin, Oleg

2011-03-01

Bacterial chromosomes are organized into operons -- sets of genes co-transcribed into polycistronic messenger RNA. Hypotheses explaining the emergence and maintenance of operons include proportional co-regulation, horizontal transfer of intact ``selfish'' operons, emergence via gene duplication, and co-production of physically interacting proteins to speed their association. We hypothesized an alternative: operons can reduce or increase intrinsic gene expression noise in a manner dependent on the post-translational interactions, thereby resulting in selection for or against operons in depending on the network architecture. We devised five classes of two-gene network modules and show that the effects of operons on intrinsic noise depend on class membership. Two classes exhibit decreased noise with co-transcription, two others reveal increased noise, and the remaining one does not show a significant difference. To test our modeling predictions we employed bioinformatic analysis to determine the relationship gene expression noise and operon organization. The results confirm the overrepresentation of noise-minimizing operon architectures and provide evidence against other hypotheses. Our results thereby suggest a central role for gene expression noise in selecting for or maintaining operons in bacterial chromosomes. This demonstrates how post-translational network dynamics may provide selective pressure for organizing bacterial chromosomes, and has practical consequences for designing synthetic gene networks. This work is supported by National Institutes of Health grant 1R01GM096189-01.

Skin Stem Cell Hypotheses and Long Term Clone Survival – Explored Using Agent-based Modelling

PubMed Central

Li, X.; Upadhyay, A. K.; Bullock, A. J.; Dicolandrea, T.; Xu, J.; Binder, R. L.; Robinson, M. K.; Finlay, D. R.; Mills, K. J.; Bascom, C. C.; Kelling, C. K.; Isfort, R. J.; Haycock, J. W.; MacNeil, S.; Smallwood, R. H.

2013-01-01

Epithelial renewal in skin is achieved by the constant turnover and differentiation of keratinocytes. Three popular hypotheses have been proposed to explain basal keratinocyte regeneration and epidermal homeostasis: 1) asymmetric division (stem-transit amplifying cell); 2) populational asymmetry (progenitor cell with stochastic fate); and 3) populational asymmetry with stem cells. In this study, we investigated lineage dynamics using these hypotheses with a 3D agent-based model of the epidermis. The model simulated the growth and maintenance of the epidermis over three years. The offspring of each proliferative cell was traced. While all lineages were preserved in asymmetric division, the vast majority were lost when assuming populational asymmetry. The third hypothesis provided the most reliable mechanism for self-renewal by preserving genetic heterogeneity in quiescent stem cells, and also inherent mechanisms for skin ageing and the accumulation of genetic mutation. PMID:23712735

Skin stem cell hypotheses and long term clone survival--explored using agent-based modelling.

PubMed

Li, X; Upadhyay, A K; Bullock, A J; Dicolandrea, T; Xu, J; Binder, R L; Robinson, M K; Finlay, D R; Mills, K J; Bascom, C C; Kelling, C K; Isfort, R J; Haycock, J W; MacNeil, S; Smallwood, R H

2013-01-01

Epithelial renewal in skin is achieved by the constant turnover and differentiation of keratinocytes. Three popular hypotheses have been proposed to explain basal keratinocyte regeneration and epidermal homeostasis: 1) asymmetric division (stem-transit amplifying cell); 2) populational asymmetry (progenitor cell with stochastic fate); and 3) populational asymmetry with stem cells. In this study, we investigated lineage dynamics using these hypotheses with a 3D agent-based model of the epidermis. The model simulated the growth and maintenance of the epidermis over three years. The offspring of each proliferative cell was traced. While all lineages were preserved in asymmetric division, the vast majority were lost when assuming populational asymmetry. The third hypothesis provided the most reliable mechanism for self-renewal by preserving genetic heterogeneity in quiescent stem cells, and also inherent mechanisms for skin ageing and the accumulation of genetic mutation.

Towards understanding the dynamical evolution of asteroid 25143 Itokawa: constraints from sample analysis

NASA Astrophysics Data System (ADS)

Connolly, Harold C.; Lauretta, Dante S.; Walsh, Kevin J.; Tachibana, Shogo; Bottke, William F.

2015-01-01

The data from the analysis of samples returned by Hayabusa from asteroid 25143 Itokawa are used to constrain the preaccretion history, the geological activity that occurred after accretion, and the dynamical history of the asteroid from the main belt to near-Earth space. We synthesize existing data to pose hypotheses to be tested by dynamical modeling and the analyses of future samples returned by Hayabusa 2 and OSIRIS-REx. Specifically, we argue that the Yarkosky-O'Keefe-Radzievskii-Paddack (YORP) effect may be responsible for producing geologically high-energy environments on Itokawa and other asteroids that process regolith and essentially affect regolith gardening.

You Be the Chemist [Multimedia Kit].

ERIC Educational Resources Information Center

National Association of Chemical Distributors, Arlington, VA. Educational Foundation.

This multimedia kit includes a teacher's manual, video, and activity packet. The unique interactive course uses safe, controlled dynamic experiments to teach kids about chemistry, the proper handling of chemicals, and responsible product stewardship. Students are asked to hypothesize about chemical substances, collect and analyze data, and share…

Missouri River Scaphirhynchus albus (pallid sturgeon) effects analysis—Integrative report 2016

USGS Publications Warehouse

Jacobson, Robert B.; Annis, Mandy L.; Colvin, Michael E.; James, Daniel A.; Welker, Timothy L.; Parsley, Michael J.

2016-07-15

The Missouri River Pallid Sturgeon Effects Analysis was designed to carry out three components of an assessment of how Missouri River management has affected, and will affect, population dynamics of endangered Scaphirhynchus albus (pallid sturgeon): (1) collection of reliable scientific information, (2) critical assessment and synthesis of available data and analyses, and (3) analysis of the effects of actions on listed species and their habitats. This report is a synthesis of the three components emphasizing development of lines of evidence relating potential future management actions to pallid sturgeon population dynamics. We address 21 working management hypotheses that emerged from an expert opinion-based filtering process.The ability to quantify linkages from abiotic changes to pallid sturgeon population dynamics is compromised by fundamental information gaps. Although a substantial foundation of pallid sturgeon science has been developed during the past 20 years, our efforts attempt to push beyond that understanding to provide predictions of how future management actions may affect pallid sturgeon responses. For some of the 21 hypotheses, lines of evidence are limited to theoretical deduction, inference from sparse empirical datasets, or expert opinion. Useful simulation models have been developed to predict the effects of management actions on survival of drifting pallid sturgeon free embryos in the Yellowstone and Upper Missouri River complex (hereafter referred to as the “upper river”), and to assess the effects of flow and channel reconfigurations on habitat availability in the Lower Missouri River, tributaries, and Mississippi River downstream of Gavins Point Dam (hereafter referred to as the “lower river”). A population model also has been developed that can be used to assess sensitivity of the population to survival of specific life stages, assess some hypotheses related to stocking decisions, and explore a limited number of management scenarios.Consideration of lines of evidence for each of the 21 hypotheses includes a discussion of how the degree of uncertainty and risk associated with each hypothesis may guide science and implementation strategies. Implementation strategies include full implementation in the field, limited implementations as field-scale experiments, or (in the case of greatest uncertainty) implementation as learning actions, including research and opportunistic experiments or field-based gradient studies. Given the substantive uncertainties associated with pallid sturgeon population dynamics and the need to continually assimilate and assess new information, we proposed that an Effects Analysis-like process should be considered an integral part of ongoing Missouri River adaptive management.

Immunotherapy for pancreatic cancer: present and future.

PubMed

Aroldi, Francesca; Zaniboni, Alberto

2017-06-01

Despite the identification of some efficient drugs for the treatment of metastatic pancreatic cancer, this tumor remains one of the most lethal cancers and is characterized by a strong resistance to therapies. Pancreatic cancer has some unique features including the presence of a microenvironment filled with immunosuppressive mediators and a dense stroma, which is both a physical barrier to drug penetration and a dynamic entity involved in immune system control. Therefore, the immune system has been hypothesized to play an important role in pancreatic cancer. Thus, therapies acting on innate or adaptive immunity are being investigated. Here, we review the literature, report the most interesting results and hypothesize future treatment directions.

Enhanced subliminal emotional responses to dynamic facial expressions.

PubMed

Sato, Wataru; Kubota, Yasutaka; Toichi, Motomi

2014-01-01

Emotional processing without conscious awareness plays an important role in human social interaction. Several behavioral studies reported that subliminal presentation of photographs of emotional facial expressions induces unconscious emotional processing. However, it was difficult to elicit strong and robust effects using this method. We hypothesized that dynamic presentations of facial expressions would enhance subliminal emotional effects and tested this hypothesis with two experiments. Fearful or happy facial expressions were presented dynamically or statically in either the left or the right visual field for 20 (Experiment 1) and 30 (Experiment 2) ms. Nonsense target ideographs were then presented, and participants reported their preference for them. The results consistently showed that dynamic presentations of emotional facial expressions induced more evident emotional biases toward subsequent targets than did static ones. These results indicate that dynamic presentations of emotional facial expressions induce more evident unconscious emotional processing.

Eavesdropping on altered cell-to-cell signaling in cancer by secretome profiling.

PubMed

Klinke, David J

2016-01-01

In the past decade, cumulative clinical experiences with molecular targeted therapies and immunotherapies for cancer have promoted a shift in our conceptual understanding of cancer. This view shifted from viewing solid tumors as a homogeneous mass of malignant cells to viewing tumors as heterogeneous structures that are dynamically shaped by intercellular interactions among the variety of stromal, immune, and malignant cells present within the tumor microenvironment. As in any dynamic system, identifying how cells communicate to maintain homeostasis and how this communication is altered during oncogenesis are key hurdles for developing therapies to restore normal tissue homeostasis. Here, I discuss tissues as dynamic systems, using the mammary gland as an example, and the evolutionary concepts applied to oncogenesis. Drawing from these concepts, I present 2 competing hypotheses for how intercellular communication might be altered during oncogenesis. As an initial test of these competing hypotheses, a recent secretome comparison between normal human mammary and HER2+ breast cancer cell lines suggested that the particular proteins secreted by the malignant cells reflect a convergent evolutionary path associated with oncogenesis in a specific anatomical niche, despite arising in different individuals. Overall, this study illustrates the emerging power of secretome proteomics to probe, in an unbiased way, how intercellular communication changes during oncogenesis.

Eavesdropping on altered cell-to-cell signaling in cancer by secretome profiling

PubMed Central

Klinke, David J

2016-01-01

In the past decade, cumulative clinical experiences with molecular targeted therapies and immunotherapies for cancer have promoted a shift in our conceptual understanding of cancer. This view shifted from viewing solid tumors as a homogeneous mass of malignant cells to viewing tumors as heterogeneous structures that are dynamically shaped by intercellular interactions among the variety of stromal, immune, and malignant cells present within the tumor microenvironment. As in any dynamic system, identifying how cells communicate to maintain homeostasis and how this communication is altered during oncogenesis are key hurdles for developing therapies to restore normal tissue homeostasis. Here, I discuss tissues as dynamic systems, using the mammary gland as an example, and the evolutionary concepts applied to oncogenesis. Drawing from these concepts, I present 2 competing hypotheses for how intercellular communication might be altered during oncogenesis. As an initial test of these competing hypotheses, a recent secretome comparison between normal human mammary and HER2+ breast cancer cell lines suggested that the particular proteins secreted by the malignant cells reflect a convergent evolutionary path associated with oncogenesis in a specific anatomical niche, despite arising in different individuals. Overall, this study illustrates the emerging power of secretome proteomics to probe, in an unbiased way, how intercellular communication changes during oncogenesis. PMID:27308541

Perfusion information extracted from resting state functional magnetic resonance imaging.

PubMed

Tong, Yunjie; Lindsey, Kimberly P; Hocke, Lia M; Vitaliano, Gordana; Mintzopoulos, Dionyssios; Frederick, Blaise deB

2017-02-01

It is widely known that blood oxygenation level dependent (BOLD) contrast in functional magnetic resonance imaging (fMRI) is an indirect measure for neuronal activations through neurovascular coupling. The BOLD signal is also influenced by many non-neuronal physiological fluctuations. In previous resting state (RS) fMRI studies, we have identified a moving systemic low frequency oscillation (sLFO) in BOLD signal and were able to track its passage through the brain. We hypothesized that this seemingly intrinsic signal moves with the blood, and therefore, its dynamic patterns represent cerebral blood flow. In this study, we tested this hypothesis by performing Dynamic Susceptibility Contrast (DSC) MRI scans (i.e. bolus tracking) following the RS scans on eight healthy subjects. The dynamic patterns of sLFO derived from RS data were compared with the bolus flow visually and quantitatively. We found that the flow of sLFO derived from RS fMRI does to a large extent represent the blood flow measured with DSC. The small differences, we hypothesize, are largely due to the difference between the methods in their sensitivity to different vessel types. We conclude that the flow of sLFO in RS visualized by our time delay method represents the blood flow in the capillaries and veins in the brain.

The importance of within-system spatial variation in drivers of marine ecosystem regime shifts

PubMed Central

Fisher, J. A. D.; Casini, M.; Frank, K. T.; Möllmann, C.; Leggett, W. C.; Daskalov, G.

2015-01-01

Comparative analyses of the dynamics of exploited marine ecosystems have led to differing hypotheses regarding the primary causes of observed regime shifts, while many ecosystems have apparently not undergone regime shifts. These varied responses may be partly explained by the decade-old recognition that within-system spatial heterogeneity in key climate and anthropogenic drivers may be important, as recent theoretical examinations have concluded that spatial heterogeneity in environmental characteristics may diminish the tendency for regime shifts. Here, we synthesize recent, empirical within-system spatio-temporal analyses of some temperate and subarctic large marine ecosystems in which regime shifts have (and have not) occurred. Examples from the Baltic Sea, Black Sea, Bengula Current, North Sea, Barents Sea and Eastern Scotian Shelf reveal the largely neglected importance of considering spatial variability in key biotic and abiotic influences and species movements in the context of evaluating and predicting regime shifts. We highlight both the importance of understanding the scale-dependent spatial dynamics of climate influences and key predator–prey interactions to unravel the dynamics of regime shifts, and the utility of spatial downscaling of proposed mechanisms (as evident in the North Sea and Barents Sea) as a means of evaluating hypotheses originally derived from among-system comparisons.

Predicting dynamic range and intensity discrimination for electrical pulse-train stimuli using a stochastic auditory nerve model: the effects of stimulus noise.

PubMed

Xu, Yifang; Collins, Leslie M

2005-06-01

This work investigates dynamic range and intensity discrimination for electrical pulse-train stimuli that are modulated by noise using a stochastic auditory nerve model. Based on a hypothesized monotonic relationship between loudness and the number of spikes elicited by a stimulus, theoretical prediction of the uncomfortable level has previously been determined by comparing spike counts to a fixed threshold, Nucl. However, no specific rule for determining Nucl has been suggested. Our work determines the uncomfortable level based on the excitation pattern of the neural response in a normal ear. The number of fibers corresponding to the portion of the basilar membrane driven by a stimulus at an uncomfortable level in a normal ear is related to Nucl at an uncomfortable level of the electrical stimulus. Intensity discrimination limens are predicted using signal detection theory via the probability mass function of the neural response and via experimental simulations. The results show that the uncomfortable level for pulse-train stimuli increases slightly as noise level increases. Combining this with our previous threshold predictions, we hypothesize that the dynamic range for noise-modulated pulse-train stimuli should increase with additive noise. However, since our predictions indicate that intensity discrimination under noise degrades, overall intensity coding performance may not improve significantly.

A Longitudinal Investigation of Commitment Dynamics in Cohabiting Relationships

ERIC Educational Resources Information Center

Rhoades, Galena K.; Stanley, Scott M.; Markman, Howard J.

2012-01-01

This longitudinal study followed 120 cohabiting, opposite-sex couples over 8 months to test hypotheses derived from commitment theory about how two types of commitment (dedication and constraint) operate during cohabitation. In nearly half the couples, there were large differences between partners in terms of dedication. These differences were…

Identification of pilot-vehicle dynamics from simulation and flight test

NASA Technical Reports Server (NTRS)

Hess, Ronald A.

1990-01-01

The paper discusses an identification problem in which a basic feedback control structure, or pilot control strategy, is hypothesized. Identification algorithms are employed to determine the particular form of pilot equalization in each feedback loop. It was found that both frequency- and time-domain identification techniques provide useful information.

Elevated enzyme activities in soils under the invasive nitrogen-fixing tree Falcataria moluccana

Treesearch

Steven D. Allison; Caroline Nielsen; R. Flint Hughes

2006-01-01

Like other N-fixing invasive species in Hawaii, Falcataria moluccana dramatically alters forest structure, litterfall quality and quantity, and nutrient dynamics. We hypothesized that these biogeochemical changes would also affect the soil microbial community and the extracellular enzymes responsible for carbon and nutrient mineralization. Across...

How Augmented Reality Enables Conceptual Understanding of Challenging Science Content

ERIC Educational Resources Information Center

Yoon, Susan; Anderson, Emma; Lin, Joyce; Elinich, Karen

2017-01-01

Research on learning about science has revealed that students often hold robust misconceptions about a number of scientific ideas. Digital simulation and dynamic visualization tools have helped to ameliorate these learning challenges by providing scaffolding to understand various aspects of the phenomenon. In this study we hypothesize that…

Influences of environment and disturbance on forest patterns in coastal Oregon watersheds.

Treesearch

Michael C. Wimberly; Thomas A. Spies

2001-01-01

Modern ecology often emphasizes the distinction between traditional theories of stable, environmentally structured communities and a new paradigm of disturbance driven, nonequilibrium dynamics. However, multiple hypotheses for observed vegetation patterns have seldom been explicitly tested. We used multivariate statistics and variation partitioning methods to assess...

Mechanisms driving postfire abundance of a generalist mammal

Treesearch

R. Zwolak; D. E. Pearson; Y. K. Ortega; E. E. Crone

2012-01-01

Changes in vertebrate abundance following disturbance are commonly attributed to shifts in food resources or predation pressure, but underlying mechanisms have rarely been tested. We examined four hypotheses for the commonly reported increase in abundance of deer mouse (Peromyscus maniculatus (Wagner, 1845)) following forest fires: source-sink dynamics, decreased...

ELEVATED CO2 AND ELEVATED TEMPERATURE HAVE NO EFFECT ON DOUGLAS-FIR FINE-ROOT DYNAMICS IN NITROGEN-POOR SOIL

EPA Science Inventory

Here, we investigate fine-root production, mortality and standing crop of Douglas-fir (Pseudotsuga menziesii) seedlings exposed to elevated atmospheric CO2 and elevated air temperature. We hypothesized that these treatments would increase fine-root production, but that mortality ...

The Intrapsychics of Gender: A Model of Self-Socialization

ERIC Educational Resources Information Center

Tobin, Desiree D.; Menon, Meenakshi; Menon, Madhavi; Spatta, Brooke C.; Hodges, Ernest V. E.; Perry, David G.

2010-01-01

This article outlines a model of the structure and the dynamics of gender cognition in childhood. The model incorporates 3 hypotheses featured in different contemporary theories of childhood gender cognition and unites them under a single theoretical framework. Adapted from Greenwald et al. (2002), the model distinguishes three constructs: gender…

Climate variability drives population cycling and synchrony

Treesearch

Lars Y. Pomara; Benjamin Zuckerberg

2017-01-01

Aim There is mounting concern that climate change will lead to the collapse of cyclic population dynamics, yet the influence of climate variability on population cycling remains poorly understood. We hypothesized that variability in survival and fecundity, driven by climate variability at different points in the life cycle, scales up from...

Integrating social science into empirical models of coupled human and natural systems

Treesearch

Jeffrey D. Kline; Eric M. White; A Paige Fischer; Michelle M. Steen-Adams; Susan Charnley; Christine S. Olsen; Thomas A. Spies; John D. Bailey

2017-01-01

Coupled human and natural systems (CHANS) research highlights reciprocal interactions (or feedbacks) between biophysical and socioeconomic variables to explain system dynamics and resilience. Empirical models often are used to test hypotheses and apply theory that represent human behavior. Parameterizing reciprocal interactions presents two challenges for social...

Orbital Dynamics, Environmental Heterogeneity, and the Evolution of the Human Brain

ERIC Educational Resources Information Center

Grove, Matt

2012-01-01

Many explanations have been proposed for the evolution of our anomalously large brains, including social, ecological, and epiphenomenal hypotheses. Recently, an additional hypothesis has emerged, suggesting that advanced cognition and, by inference, increases in brain size, have been driven over evolutionary time by the need to deal with…

Genetic Algorithm Approaches to Prebiobiotic Chemistry Modeling

NASA Technical Reports Server (NTRS)

Lohn, Jason; Colombano, Silvano

1997-01-01

We model an artificial chemistry comprised of interacting polymers by specifying two initial conditions: a distribution of polymers and a fixed set of reversible catalytic reactions. A genetic algorithm is used to find a set of reactions that exhibit a desired dynamical behavior. Such a technique is useful because it allows an investigator to determine whether a specific pattern of dynamics can be produced, and if it can, the reaction network found can be then analyzed. We present our results in the context of studying simplified chemical dynamics in theorized protocells - hypothesized precursors of the first living organisms. Our results show that given a small sample of plausible protocell reaction dynamics, catalytic reaction sets can be found. We present cases where this is not possible and also analyze the evolved reaction sets.

Dynamics of Long-period Comets

NASA Technical Reports Server (NTRS)

Weissman, P. R.

1985-01-01

Dynamical studies of the origin and evolution of long period comets in the Oort cloud during the past year have concentrated on four areas: (1) interpretation of IRAS observations of dust shells around Vega and some 40 other main sequence stars as evidence for cometary clouds around each of these stars; (2) the dynamical plausibility of an unseen solar companion star orbiting in the Oort cloud and causing periodic cometary showers which result in biological extinction events on the earth; (3) a review of the current hypotheses for cometary formation with particular attention to how each mechanism supplies the required mass of comets to the Oort cloud; and (4) development of new dynamics software to simulate the passage of individual stars directly through the Oort cloud. Each of these efforts is described in detail.

Dynamics of place, boundary and object encoding in rat anterior claustrum

PubMed Central

Jankowski, Maciej M.; O’Mara, Shane M.

2015-01-01

Discrete populations of brain cells signal differing types of spatial information. These “spatial cells” are largely confined to a closely-connected network of sites. We describe here, for the first time, cells in the anterior claustrum of the freely-moving rat encoding place, boundary and object information. This novel claustral spatial signal potentially directly modulates a wide variety of anterior cortical regions. We hypothesize that one of the functions of the claustrum is to provide information about body position, boundaries and landmark information, enabling dynamic control of behavior. PMID:26557060

Catch rates relative to angler party size with implications for monitoring angler success

USGS Publications Warehouse

Miranda, L.E.

2005-01-01

Angler catch rates often are used to monitor angler success, assess the need for additional management actions, and evaluate the effectiveness of management practices. Potential linkages between catch rate and angler party size were examined to assess how party size might affect the use of catch rate as an index of angler success in recreational fisheries. Data representing 22,355 completed interviews conducted at access points in lakes and reservoirs throughout Mississippi during 1987-2003 were analyzed. Total party catch was not proportional to total party effort; thus, catch rate decreased as party size increased. Depending on the taxa targeted, the average catch rate per angler decreased 40-50% between parties of one and parties of two, although subsequent decreases were less substantial. Because party size accounted for a considerable portion of the variability in catch rate over time and space, failure to remove this variability weakens the manager's ability to detect differences or changes in catch rates. Therefore, the use of catch rates to monitor fisheries may be inappropriate unless party size is taken into account. Party size may influence the angler's ability to catch fish through a variety of processes, including partitioning a limited number of catchable fish among members of a party and party composition. When catch rates are used to estimate total catch rather than to index angler success, party size is not a concern.

Spatial distribution patterns and movements of Holothuria arguinensis in the Ria Formosa (Portugal)

NASA Astrophysics Data System (ADS)

Siegenthaler, Andjin; Cánovas, Fernando; González-Wangüemert, Mercedes

2015-08-01

Holothurian populations are under pressure worldwide because of increasing demand for beche-de-mer, mainly for Asian consumption. Importations to this area from new temperate fishing grounds provide economic opportunities but also raise concerns regarding future over-exploitation. Studies on the habitat preferences and movements of sea cucumbers are important for the management of sea cucumber stocks and sizing of no-take zones, but information on the ecology and behavior of temperate sea cucumbers is scarce. This study describes the small-scale distribution and movement patterns of Holothuria arguinensis in the intertidal zone of the Ria Formosa national park (Portugal). Mark/recapture studies were performed to record their movements over time on different habitats (sand and seagrass). H. arguinensis preferred seagrass habitats and did not show a size or life stage-related spatial segregation. Its density was 563 ind. ha- 1 and mean movement speed was 10 m per day. Movement speed did not differ between habitats and the direction of movement was offshore during the day and shoreward during the night. Median home range size was 35 m2 and overlap among home ranges was 84%. H. arguinensis' high abundance, close association with seagrass and easy catchability in the intertidal zone, indicate the importance of including intertidal lagoons in future studies on temperate sea cucumber ecology since those systems might require different management strategies than fully submerged habitats.

Toward an Integration of Deep Learning and Neuroscience

PubMed Central

Marblestone, Adam H.; Wayne, Greg; Kording, Konrad P.

2016-01-01

Neuroscience has focused on the detailed implementation of computation, studying neural codes, dynamics and circuits. In machine learning, however, artificial neural networks tend to eschew precisely designed codes, dynamics or circuits in favor of brute force optimization of a cost function, often using simple and relatively uniform initial architectures. Two recent developments have emerged within machine learning that create an opportunity to connect these seemingly divergent perspectives. First, structured architectures are used, including dedicated systems for attention, recursion and various forms of short- and long-term memory storage. Second, cost functions and training procedures have become more complex and are varied across layers and over time. Here we think about the brain in terms of these ideas. We hypothesize that (1) the brain optimizes cost functions, (2) the cost functions are diverse and differ across brain locations and over development, and (3) optimization operates within a pre-structured architecture matched to the computational problems posed by behavior. In support of these hypotheses, we argue that a range of implementations of credit assignment through multiple layers of neurons are compatible with our current knowledge of neural circuitry, and that the brain's specialized systems can be interpreted as enabling efficient optimization for specific problem classes. Such a heterogeneously optimized system, enabled by a series of interacting cost functions, serves to make learning data-efficient and precisely targeted to the needs of the organism. We suggest directions by which neuroscience could seek to refine and test these hypotheses. PMID:27683554

Progress in violence risk assessment and communication: hypothesis versus evidence.

PubMed

Harris, Grant T; Rice, Marnie E

2015-02-01

We draw a distinction between hypothesis and evidence with respect to the assessment and communication of the risk of violent recidivism. We suggest that some authorities in the field have proposed quite valid and reasonable hypotheses with respect to several issues. Among these are the following: that accuracy will be improved by the adjustment or moderation of numerical scores based on clinical opinions about rare risk factors or other considerations pertaining to the applicability to the case at hand; that there is something fundamentally distinct about protective factors so that they are not merely the obverse of risk factors, such that optimal accuracy cannot be achieved without consideration of such protective factors; and that assessment of dynamic factors is required for optimal accuracy and furthermore interventions aimed at such dynamic factors can be expected to cause reductions in violence risk. We suggest here that, while these are generally reasonable hypotheses, they have been inappropriately presented to practitioners as empirically supported facts, and that practitioners' assessment and communication about violence risk run beyond that supported by the available evidence as a result. We further suggest that this represents harm, especially in impeding scientific progress. Nothing here justifies stasis or simply surrendering to authoritarian custody with somatic treatment. Theoretically motivated and clearly articulated assessment and intervention should be provided for offenders, but in a manner that moves the field more firmly from hypotheses to evidence. Copyright © 2015 John Wiley & Sons, Ltd.

Retardation of Bulk Water Dynamics by Disaccharide Osmolytes

NASA Astrophysics Data System (ADS)

Shukla, Nimesh; Chen, Lee; Pomarico, Enrico; Chergui, Majed; Othon, Christina

Bioprotective nature of disaccharides is hypothesized to derive from the modification of the hydrogen bonding network of water which protects biomolecules through lowered water activity at the protein interface. Using ultrafast fluorescence spectroscopy, we measured the relaxation of bulk water dynamics around the induced dipole moment of two fluorescent probes (Lucifer Yellow Ethylenediamine and Tryptophan). Our results indicate a reduction in bulk water reorganization rate of approximately 30%. We observe this retardation in the low concentration regime measured at 0.1 and 0.25 M, far below the onset of glassy dynamics. This water structuring should be significant in crowded biological systems, contributing to a global change in protein energy landscape, resulting in a significant enhancement of protein stability under environmental stress. We observed similar dynamic reduction for two disaccharide osmolytes, sucrose and trehalose, with trehalose being the more effective in reducing solvation dynamics.

Shear-banding and superdiffusivity in entangled polymer solutions

NASA Astrophysics Data System (ADS)

Shin, Seunghwan; Dorfman, Kevin D.; Cheng, Xiang

2017-12-01

Using high-resolution confocal rheometry, we study the shear profiles of well-entangled DNA solutions under large-amplitude oscillatory shear in a rectilinear planar shear cell. With increasing Weissenberg number (Wi), we observe successive transitions from normal Newtonian linear shear profiles to wall-slip dominant shear profiles and, finally, to shear-banding profiles at high Wi. To investigate the microscopic origin of the observed shear banding, we study the dynamics of micron-sized tracers embedded in DNA solutions. Surprisingly, tracer particles in the shear frame exhibit transient superdiffusivity and strong dynamic heterogeneity. The probability distribution functions of particle displacements follow a power-law scaling at large displacements, indicating a Lévy-walk-type motion, reminiscent of tracer dynamics in entangled wormlike micelle solutions and sheared colloidal glasses. We further characterize the length and time scales associated with the abnormal dynamics of tracer particles. We hypothesize that the unusual particle dynamics arise from localized shear-induced chain disentanglement.

More Gamma More Predictions: Gamma-Synchronization as a Key Mechanism for Efficient Integration of Classical Receptive Field Inputs with Surround Predictions

PubMed Central

Vinck, Martin; Bosman, Conrado A.

2016-01-01

During visual stimulation, neurons in visual cortex often exhibit rhythmic and synchronous firing in the gamma-frequency (30–90 Hz) band. Whether this phenomenon plays a functional role during visual processing is not fully clear and remains heavily debated. In this article, we explore the function of gamma-synchronization in the context of predictive and efficient coding theories. These theories hold that sensory neurons utilize the statistical regularities in the natural world in order to improve the efficiency of the neural code, and to optimize the inference of the stimulus causes of the sensory data. In visual cortex, this relies on the integration of classical receptive field (CRF) data with predictions from the surround. Here we outline two main hypotheses about gamma-synchronization in visual cortex. First, we hypothesize that the precision of gamma-synchronization reflects the extent to which CRF data can be accurately predicted by the surround. Second, we hypothesize that different cortical columns synchronize to the extent that they accurately predict each other’s CRF visual input. We argue that these two hypotheses can account for a large number of empirical observations made on the stimulus dependencies of gamma-synchronization. Furthermore, we show that they are consistent with the known laminar dependencies of gamma-synchronization and the spatial profile of intercolumnar gamma-synchronization, as well as the dependence of gamma-synchronization on experience and development. Based on our two main hypotheses, we outline two additional hypotheses. First, we hypothesize that the precision of gamma-synchronization shows, in general, a negative dependence on RF size. In support, we review evidence showing that gamma-synchronization decreases in strength along the visual hierarchy, and tends to be more prominent in species with small V1 RFs. Second, we hypothesize that gamma-synchronized network dynamics facilitate the emergence of spiking output that is particularly information-rich and sparse. PMID:27199684

Microbial infection affects egg viability and incubation behavior in a tropical passerine.

Treesearch

Mark I. Cook; Steven R. Beissinger; Gary A. Toranzos; Roberto A. Arendt Rodriguez

2004-01-01

Many avian species initiate incubation before clutch completion, which causes eggs to hatch asynchronously. This influences brood competitive dynamics and often results in nestling mortality. The prevailing hypotheses contend that parents incubate early because asynchronous hatching provides fitness benefits to parents or surviving offspring. An alternative idea is...

Linkages between large-scale climate patterns and the dynamics of Alaskan caribou populations

Treesearch

Kyle Joly; David R. Klein; David L. Verbyla; T. Scott Rupp; F. Stuart Chapin

2011-01-01

Recent research has linked climate warming to global declines in caribou and reindeer (both Rangifer tarandus) populations. We hypothesize large-scale climate patterns are a contributing factor explaining why these declines are not universal. To test our hypothesis for such relationships among Alaska caribou herds, we calculated the population growth...

Modelling Relations between Sensory Processing, Speech Perception, Orthographic and Phonological Ability, and Literacy Achievement

ERIC Educational Resources Information Center

Boets, Bart; Wouters, Jan; van Wieringen, Astrid; De Smedt, Bert; Ghesquiere, Pol

2008-01-01

The general magnocellular theory postulates that dyslexia is the consequence of a multimodal deficit in the processing of transient and dynamic stimuli. In the auditory modality, this deficit has been hypothesized to interfere with accurate speech perception, and subsequently disrupt the development of phonological and later reading and spelling…

Disturbance patterns in a socio-ecological system at multiple scales

Treesearch

G. Zurlini; Kurt H. Riitters; N. Zaccarelli; I. Petrosillo; K.B. Jones; L. Rossi

2006-01-01

Ecological systems with hierarchical organization and non-equilibrium dynamics require multiple-scale analyses to comprehend how a system is structured and to formulate hypotheses about regulatory mechanisms. Characteristic scales in real landscapes are determined by, or at least reflect, the spatial patterns and scales of constraining human interactions with the...

Fixation and Commitment while Designing and Its Measurement

ERIC Educational Resources Information Center

Gero, John S.

2011-01-01

This paper introduces the notion that fixation and commitment while designing can be measured by studying the protocol of the design session. It is hypothesized that the dynamic entropy of the linkograph of the protocol provides the basis for such a measurement. The hypothesis is empirically tested using a design protocol and the results…

Perceptual Veridicality in Esthetic Communication: A Model, General Procedure, and Illustration.

ERIC Educational Resources Information Center

Holbrook, Morris B.; Bertges, Stephen A.

1981-01-01

Developed a model and tested the following hypotheses: (1) esthetic features--tempo, rhythm, dynamics, and phrasing in piano performance--are accurately perceived by audience members and (2) such perceptual veridicality does not depend upon one's degree of education/training and is therefore shared by critics and audience members. (PD)

Intimate Homicide between Asians and Non-Asians: The Impact of Community Context

ERIC Educational Resources Information Center

Wu, Bohsiu

2009-01-01

This study tests two competing hypotheses regarding the social structural dynamics of intimate homicide: backlash versus collective efficacy. This study also examines the role of race in how social factors specified in each hypothesis affect intimate homicide. Data are from the California Vital Statistics and Homicide Data, 1990-1999. Results from…

Vocalization Subsystem Responses to a Temporarily Induced Unilateral Vocal Fold Paralysis

ERIC Educational Resources Information Center

Croake, Daniel J.; Andreatta, Richard D.; Stemple, Joseph C.

2018-01-01

Purpose: The purpose of this study is to quantify the interactions of the 3 vocalization subsystems of respiration, phonation, and resonance before, during, and after a perturbation to the larynx (temporarily induced unilateral vocal fold paralysis) in 10 vocally healthy participants. Using dynamic systems theory as a guide, we hypothesized that…

Self-Disclosure in Youth at Different Stages of Development of Interpersonal Relationships.

ERIC Educational Resources Information Center

Niebrzydowski, Leon

This study investigated the connection between self-disclosure and stages in development of interpersonal relationships. It hypothesized that self-disclosure in relationships is of a dynamic character which works in two directions: towards the interaction partner, and in the opposite direction. The study proposed three stages in the development of…

Context-dependent dynamic processes in attention deficit/hyperactivity disorder: differentiating common and unique effects of state regulation deficits and delay aversion.

PubMed

Sonuga-Barke, Edmund J S; Wiersema, Jan R; van der Meere, Jacob J; Roeyers, Herbert

2010-03-01

The ability to specify differential predictions is a mark of a scientific models' value. State regulation deficits (SRD) and delay aversion (DAv) have both been hypothesized as context-dependent dynamic dysfunctions in ADHD. However, to date there has been no systematic comparison of their common and unique elements. Here we review these hypotheses-and describe the core and secondary manifestations of the two constructs and review evidence in support of them. Second, we focus on what are seen as the hallmark indicators of the two deficits-preference of small immediate over large delayed rewards for DAv and the slow event rate effect for SRD. We describe the overlap between these two manifestations and then explore how experimental manipulations and the analysis of neuropsychological and physiological mediators of effects can allow us to differentiate these two patterns of neuropsychological dysfunction on the basis of specific predictions. Finally, we highlight the implications of neuropsychological heterogeneity for the practical implementation of tests of DAv and SRD.

Understanding the heavy-tailed dynamics in human behavior

NASA Astrophysics Data System (ADS)

Ross, Gordon J.; Jones, Tim

2015-06-01

The recent availability of electronic data sets containing large volumes of communication data has made it possible to study human behavior on a larger scale than ever before. From this, it has been discovered that across a diverse range of data sets, the interevent times between consecutive communication events obey heavy-tailed power law dynamics. Explaining this has proved controversial, and two distinct hypotheses have emerged. The first holds that these power laws are fundamental, and arise from the mechanisms such as priority queuing that humans use to schedule tasks. The second holds that they are statistical artifacts which only occur in aggregated data when features such as circadian rhythms and burstiness are ignored. We use a large social media data set to test these hypotheses, and find that although models that incorporate circadian rhythms and burstiness do explain part of the observed heavy tails, there is residual unexplained heavy-tail behavior which suggests a more fundamental cause. Based on this, we develop a quantitative model of human behavior which improves on existing approaches and gives insight into the mechanisms underlying human interactions.

New Evidence for Strategic Differences between Static and Dynamic Search Tasks: An Individual Observer Analysis of Eye Movements

PubMed Central

Dickinson, Christopher A.; Zelinsky, Gregory J.

2013-01-01

Two experiments are reported that further explore the processes underlying dynamic search. In Experiment 1, observers’ oculomotor behavior was monitored while they searched for a randomly oriented T among oriented L distractors under static and dynamic viewing conditions. Despite similar search slopes, eye movements were less frequent and more spatially constrained under dynamic viewing relative to static, with misses also increasing more with target eccentricity in the dynamic condition. These patterns suggest that dynamic search involves a form of sit-and-wait strategy in which search is restricted to a small group of items surrounding fixation. To evaluate this interpretation, we developed a computational model of a sit-and-wait process hypothesized to underlie dynamic search. In Experiment 2 we tested this model by varying fixation position in the display and found that display positions optimized for a sit-and-wait strategy resulted in higher d′ values relative to a less optimal location. We conclude that different strategies, and therefore underlying processes, are used to search static and dynamic displays. PMID:23372555

Dynamic Triggering of Seismic Events and Their Relation to Slow Slip in Interior Alaska

NASA Astrophysics Data System (ADS)

Sims, N. E.; Holtkamp, S. G.

2017-12-01

We conduct a search for dynamically triggered events in the Minto Flats Fault Zone (MFFZ), a left-lateral strike-slip zone expressed as multiple, partially overlapping faults, in central Alaska. We focus on the MFFZ because we have observed slow slip processes (earthquake swarms and Very Low Frequency Earthquakes) and interaction between earthquake swarms and larger main-shock (MS) events in this area before. We utilize the Alaska Earthquake Center catalog to identify potential earthquake swarms and dynamically triggered foreshock and mainshock events along the fault zone. We find 30 swarms occurring in the last two decades, five of which we classify as foreshock (FS) swarms due to their close proximity in both time and space to MS events. Many of the earthquake swarms cluster around 15-20 km depth, which is near the seismic-aseismic transition along this fault zone. Additionally, we observe instances of large teleseismic events such as the M8.6 2012 Sumatra earthquake and M7.4 2012 Guatemala earthquake triggering seismic events within the MFFZ, with the Sumatra earthquake triggering a mainshock event that was preceded by an ongoing earthquake swarm and the Guatemala event triggering earthquake swarms that subsequently transition into a larger mainshock event. In both cases an earthquake swarm transitioned into a mainshock-aftershock event and activity continued for several days after the teleseismic waves had passed, lending some evidence to delayed dynamic triggering of seismic events. We hypothesize that large dynamic transient strain associated with the passage of teleseismic surface waves is triggering slow slip processes near the base of the seismogenic zone. These triggered aseismic transient events result in earthquake swarms, which sometimes lead to the nucleation of larger earthquakes. We utilize network matched filtering to build more robust catalogs of swarm earthquake families in this region to search for additional swarm-like or triggered activity in response to teleseismic surface waves, and to test dynamic triggering hypotheses.

Ecological optimality in water-limited natural soil-vegetation systems. I - Theory and hypothesis

NASA Technical Reports Server (NTRS)

Eagleson, P. S.

1982-01-01

The solution space of an approximate statistical-dynamic model of the average annual water balance is explored with respect to the hydrologic parameters of both soil and vegetation. Within the accuracy of this model it is shown that water-limited natural vegetation systems are in stable equilibrium with their climatic and pedologic environments when the canopy density and species act to minimize average water demand stress. Theory shows a climatic limit to this equilibrium above which it is hypothesized that ecological pressure is toward maximization of biomass productivity. It is further hypothesized that natural soil-vegetation systems will develop gradually and synergistically, through vegetation-induced changes in soil structure, toward a set of hydraulic soil properties for which the minimum stress canopy density of a given species is maximum in a given climate. Using these hypotheses, only the soil effective porosity need be known to determine the optimum soil and vegetation parameters in a given climate.

ClueNet: Clustering a temporal network based on topological similarity rather than denseness

PubMed Central

Milenković, Tijana

2018-01-01

Network clustering is a very popular topic in the network science field. Its goal is to divide (partition) the network into groups (clusters or communities) of “topologically related” nodes, where the resulting topology-based clusters are expected to “correlate” well with node label information, i.e., metadata, such as cellular functions of genes/proteins in biological networks, or age or gender of people in social networks. Even for static data, the problem of network clustering is complex. For dynamic data, the problem is even more complex, due to an additional dimension of the data—their temporal (evolving) nature. Since the problem is computationally intractable, heuristic approaches need to be sought. Existing approaches for dynamic network clustering (DNC) have drawbacks. First, they assume that nodes should be in the same cluster if they are densely interconnected within the network. We hypothesize that in some applications, it might be of interest to cluster nodes that are topologically similar to each other instead of or in addition to requiring the nodes to be densely interconnected. Second, they ignore temporal information in their early steps, and when they do consider this information later on, they do so implicitly. We hypothesize that capturing temporal information earlier in the clustering process and doing so explicitly will improve results. We test these two hypotheses via our new approach called ClueNet. We evaluate ClueNet against six existing DNC methods on both social networks capturing evolving interactions between individuals (such as interactions between students in a high school) and biological networks capturing interactions between biomolecules in the cell at different ages. We find that ClueNet is superior in over 83% of all evaluation tests. As more real-world dynamic data are becoming available, DNC and thus ClueNet will only continue to gain importance. PMID:29738568

Effects of national culture on human failures in container shipping: the moderating role of Confucian dynamism.

PubMed

Lu, Chin-Shan; Lai, Kee-hung; Lun, Y H Venus; Cheng, T C E

2012-11-01

Recent reports on work safety in container shipping operations highlight high frequencies of human failures. In this study, we empirically examine the effects of seafarers' perceptions of national culture on the occurrence of human failures affecting work safety in shipping operations. We develop a model adopting Hofstede's national culture construct, which comprises five dimensions, namely power distance, collectivism/individualism, uncertainty avoidance, masculinity/femininity, and Confucian dynamism. We then formulate research hypotheses from theory and test the hypotheses using survey data collected from 608 seafarers who work on global container carriers. Using a point scale for evaluating seafarers' perception of the five national culture dimensions, we find that Filipino seafarers score highest on collectivism, whereas Chinese and Taiwanese seafarers score highest on Confucian dynamism, followed by collectivism, masculinity, power distance, and uncertainty avoidance. The results also indicate that Taiwanese seafarers have a propensity for uncertainty avoidance and masculinity, whereas Filipino seafarers lean more towards power distance, masculinity, and collectivism, which are consistent with the findings of Hofstede and Bond (1988). The results suggest that there will be fewer human failures in container shipping operations when power distance is low, and collectivism and uncertainty avoidance are high. Specifically, this study finds that Confucian dynamism plays an important moderating role as it affects the strength of associations between some national culture dimensions and human failures. Finally, we discuss our findings' contribution to the development of national culture theory and their managerial implications for reducing the occurrence of human failures in shipping operations. Copyright © 2012 Elsevier Ltd. All rights reserved.

"Is political behavior a viable coping strategy to perceived organizational politics? Unveiling the underlying resource dynamics": Correction to Sun and Chen (2017).

PubMed

2017-10-01

Reports an error in "Is Political Behavior a Viable Coping Strategy to Perceived Organizational Politics? Unveiling the Underlying Resource Dynamics" by Shuhua Sun and Huaizhong Chen ( Journal of Applied Psychology , Advanced Online Publication, May 22, 2017, np). In the article, Table 1 contained a formatting error. Correlation coefficient values in the last four cells of column 6 were misplaced with correlation coefficient values in the last four cells of column 7. All versions of this article have been corrected. (The following abstract of the original article appeared in record 2017-22542-001.) We conduct a theory-driven empirical investigation on whether political behavior, as a coping strategy to perceived organizational politics, creates resource trade-offs in moderating the relationship between perceived organizational politics and task performance. Drawing on conservation of resources theory, we hypothesize that political behavior mitigates the adverse effect of perceived organizational politics on task performance via psychological empowerment, yet exacerbates its adverse effect on task performance via emotional exhaustion. Three-wave multisource data from a sample of 222 employees and their 75 supervisors were collected for hypothesis testing. Findings supported our hypotheses. Our study enhances understandings of the complex resource dynamics of using political behavior to cope with perceived organizational politics and highlights the need to move stress-coping research from a focus on the stress-buffering effect of coping on outcomes to a focus on the underlying competing resource dynamics. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Firm Size, a Self-Organized Critical Phenomenon: Evidence from the Dynamical Systems Theory

NASA Astrophysics Data System (ADS)

Chandra, Akhilesh

This research draws upon a recent innovation in the dynamical systems literature called the theory of self -organized criticality (SOC) (Bak, Tang, and Wiesenfeld 1988) to develop a computational model of a firm's size by relating its internal and the external sub-systems. As a holistic paradigm, the theory of SOC implies that a firm as a composite system of many degrees of freedom naturally evolves to a critical state in which a minor event starts a chain reaction that can affect either a part or the system as a whole. Thus, the global features of a firm cannot be understood by analyzing its individual parts separately. The causal framework builds upon a constant capital resource to support a volume of production at the existing level of efficiency. The critical size is defined as the production level at which the average product of a firm's factors of production attains its maximum value. The non -linearity is inferred by a change in the nature of relations at the border of criticality, between size and the two performance variables, viz., the operating efficiency and the financial efficiency. The effect of breaching the critical size is examined on the stock price reactions. Consistent with the theory of SOC, it is hypothesized that the temporal response of a firm breaching the level of critical size should behave as a flicker noise (1/f) process. The flicker noise is characterized by correlations extended over a wide range of time scales, indicating some sort of cooperative effect among a firm's degrees of freedom. It is further hypothesized that a firm's size evolves to a spatial structure with scale-invariant, self-similar (fractal) properties. The system is said to be self-organized inasmuch as it naturally evolves to the state of criticality without any detailed specifications of the initial conditions. In this respect, the critical state is an attractor of the firm's dynamics. Another set of hypotheses examines the relations between the size and the performance variables during the sub-critical (below the critical size) and the supra-critical (above the critical size) states. Since the dynamics of any two firms is likely to be different, the analysis is performed individually for each company within the Pharmaceuticals and the Perfume industries. The statistical results of this study provide evidence in support of the hypotheses. The size of a firm is found to be a self-organized critical phenomenon. The presence of 1/f noise and the spatial power-law behavior is taken as an evidence of the firm's size as a self-organized critical phenomenon. (Abstract shortened by UMI.).

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

PubMed Central

Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R.

2015-01-01

Motivation: Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters. Results: In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: julio@iim.csic.es or saezrodriguez@ebi.ac.uk PMID:26002881

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

PubMed

Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R

2015-09-15

Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters. In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. Supplementary data are available at Bioinformatics online. julio@iim.csic.es or saezrodriguez@ebi.ac.uk. © The Author 2015. Published by Oxford University Press.

Wood and Sediment Dynamics in River Corridors

NASA Astrophysics Data System (ADS)

Wohl, E.; Scott, D.

2015-12-01

Large wood along rivers influences entrainment, transport, and storage of mineral sediment and particulate organic matter. We review how wood alters sediment dynamics and explore patterns among volumes of instream wood, sediment storage, and residual pools for dispersed pieces of wood, logjams, and beaver dams. We hypothesized that: volume of sediment per unit area of channel stored in association with wood is inversely proportional to drainage area; the form of sediment storage changes downstream; sediment storage correlates most strongly with wood load; and volume of sediment stored behind beaver dams correlates with pond area. Lack of data from larger drainage areas limits tests of these hypotheses, but analyses suggest a negative correlation between sediment volume and drainage area and a positive correlation between wood and sediment volume. The form of sediment storage in relation to wood changes downstream, with wedges of sediment upstream from jammed steps most prevalent in small, steep channels and more dispersed sediment storage in lower gradient channels. Use of a published relation between sediment volume, channel width, and gradient predicted about half of the variation in sediment stored upstream from jammed steps. Sediment volume correlates well with beaver pond area. Historically more abundant instream wood and beaver populations likely equated to greater sediment storage within river corridors. This review of the existing literature on wood and sediment dynamics highlights the lack of studies on larger rivers.

Is political behavior a viable coping strategy to perceived organizational politics? Unveiling the underlying resource dynamics.

PubMed

Sun, Shuhua; Chen, Huaizhong

2017-10-01

[Correction Notice: An Erratum for this article was reported in Vol 102(10) of Journal of Applied Psychology (see record 2017-34254-001). In the article, Table 1 contained a formatting error. Correlation coefficient values in the last four cells of column 6 were misplaced with correlation coefficient values in the last four cells of column 7. All versions of this article have been corrected.] We conduct a theory-driven empirical investigation on whether political behavior, as a coping strategy to perceived organizational politics, creates resource trade-offs in moderating the relationship between perceived organizational politics and task performance. Drawing on conservation of resources theory, we hypothesize that political behavior mitigates the adverse effect of perceived organizational politics on task performance via psychological empowerment, yet exacerbates its adverse effect on task performance via emotional exhaustion. Three-wave multisource data from a sample of 222 employees and their 75 supervisors were collected for hypothesis testing. Findings supported our hypotheses. Our study enhances understandings of the complex resource dynamics of using political behavior to cope with perceived organizational politics and highlights the need to move stress-coping research from a focus on the stress-buffering effect of coping on outcomes to a focus on the underlying competing resource dynamics. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Predictability in community dynamics.

PubMed

Blonder, Benjamin; Moulton, Derek E; Blois, Jessica; Enquist, Brian J; Graae, Bente J; Macias-Fauria, Marc; McGill, Brian; Nogué, Sandra; Ordonez, Alejandro; Sandel, Brody; Svenning, Jens-Christian

2017-03-01

The coupling between community composition and climate change spans a gradient from no lags to strong lags. The no-lag hypothesis is the foundation of many ecophysiological models, correlative species distribution modelling and climate reconstruction approaches. Simple lag hypotheses have become prominent in disequilibrium ecology, proposing that communities track climate change following a fixed function or with a time delay. However, more complex dynamics are possible and may lead to memory effects and alternate unstable states. We develop graphical and analytic methods for assessing these scenarios and show that these dynamics can appear in even simple models. The overall implications are that (1) complex community dynamics may be common and (2) detailed knowledge of past climate change and community states will often be necessary yet sometimes insufficient to make predictions of a community's future state. © 2017 John Wiley & Sons Ltd/CNRS.

Universal Critical Dynamics in High Resolution Neuronal Avalanche Data

NASA Astrophysics Data System (ADS)

Friedman, Nir; Ito, Shinya; Brinkman, Braden A. W.; Shimono, Masanori; DeVille, R. E. Lee; Dahmen, Karin A.; Beggs, John M.; Butler, Thomas C.

2012-05-01

The tasks of neural computation are remarkably diverse. To function optimally, neuronal networks have been hypothesized to operate near a nonequilibrium critical point. However, experimental evidence for critical dynamics has been inconclusive. Here, we show that the dynamics of cultured cortical networks are critical. We analyze neuronal network data collected at the individual neuron level using the framework of nonequilibrium phase transitions. Among the most striking predictions confirmed is that the mean temporal profiles of avalanches of widely varying durations are quantitatively described by a single universal scaling function. We also show that the data have three additional features predicted by critical phenomena: approximate power law distributions of avalanche sizes and durations, samples in subcritical and supercritical phases, and scaling laws between anomalous exponents.

Identity Processes and Coping Strategies in College Students: Short-Term Longitudinal Dynamics and the Role of Personality

ERIC Educational Resources Information Center

Luyckx, Koen; Klimstra, Theo A.; Duriez, Bart; Schwartz, Seth J.; Vanhalst, Janne

2012-01-01

Coping strategies and identity processes are hypothesized to influence one another over time. This three-wave longitudinal study ("N" = 458; 84.9% women) examined, for the first time, how and to what extent identity processes (i.e., commitment making, identification with commitment, exploration in breadth, exploration in depth, and ruminative…

Primary School Science: Implementation of Domain-General Strategies into Teaching Didactics

ERIC Educational Resources Information Center

Dejonckheere, Peter J. N.; Van de Keere, Kristof; Tallir, Isabel; Vervaet, Stephanie

2013-01-01

In the present study we present a didactic method to help children aged 11 and 12 learn science in such a way as to enable a dynamic interaction between domain general strategies and the development of conceptual knowledge, whilst each type of scientific process has been considered (forming of hypotheses, experimenting and evaluating). We have…

Parasitism and generation cycles in a salt-marsh planthopper

Treesearch

John D. Reeve; James T. Cronin; Donald R. Strong

1994-01-01

1. In warm climates many insects exhibit discrete generations, in the absence of obvious factors that could synchronize their age structure.It has been hypothesized that parasitoid wasps might be responsible for these oscillations in the host age structure, known as generation cycles. 2. We examine the role of the parasitoid Anagrus delicatus in the dynamics of the...

Dynamic Models of Learning That Characterize Parent-Child Exchanges Predict Vocabulary Growth

ERIC Educational Resources Information Center

Ober, David R.; Beekman, John A.

2016-01-01

Cumulative vocabulary models for infants and toddlers were developed from models of learning that predict trajectories associated with low, average, and high vocabulary growth rates (14 to 46 months). It was hypothesized that models derived from rates of learning mirror the type of exchanges provided to infants and toddlers by parents and…

Can Landscape-scale management influence insect outbreak dynamics? A natural experiment for eastern spruce budworm

Treesearch

Brian R. Sturtevant; V. Quinn; L.E. Robert; D. Kneeshaw; P. James; M.-J. Fortin; P. Wolter; P. Townsend; B. Cooke; D. Anderson

2010-01-01

The balance of evidence suggests forest insect outbreaks today are more damaging than ever because of changes in forest composition and structure induced by fire suppression and post-harvest proliferation of tree species intolerant to herbivory. We hypothesized that landscape connectivity of acceptable host trees increases defoliator population connectivity, altering...

Perceived Discrimination and Psychological Well-Being: The Mediating and Moderating Role of Sense of Control

ERIC Educational Resources Information Center

Jang, Yuri; Chiriboga, David A.; Small, Brent J.

2008-01-01

Being discriminated against is an unpleasant and stressful experience, and its connection to reduced psychological well-being is well-documented. The present study hypothesized that a sense of control would serve as both mediator and moderator in the dynamics of perceived discrimination and psychological well-being. In addition, variations by age,…

Comment on "Social Contagion, Adolescent Sexual Behavior, and Pregnancy: A Nonlinear Dynamic EMOSA Model."

ERIC Educational Resources Information Center

Stoolmiller, Mike

1998-01-01

Examines the Rodgers, Rowe, and Buster (1998) epidemic model of the onset of social activities for adolescent sexuality. Maintains that its strengths include its theoretical potential to generate new hypotheses for further testing at the individual level. Asserts that its limitations include the lack of a well-developed statistical framework and…

Adolescents' School Enrollment and Employment: Effect of State Welfare Policies. JCPR Working Paper.

ERIC Educational Resources Information Center

Hao, Lingxin; Astone, Nan M.; Cherlin, Andrew J.

This study hypothesizes that stringent welfare policies may promote school enrollment and reduce employment among adolescents from low-income, single parent, and welfare families. Using data from the National Longitudinal Survey of Youth, 1997 cohort, combined with state-level data sources, this analysis uses a dynamic model to study school and…

Mutational Dynamics of Aroid Chloroplast Genomes

PubMed Central

Ahmed, Ibrar; Biggs, Patrick J.; Matthews, Peter J.; Collins, Lesley J.; Hendy, Michael D.; Lockhart, Peter J.

2012-01-01

A characteristic feature of eukaryote and prokaryote genomes is the co-occurrence of nucleotide substitution and insertion/deletion (indel) mutations. Although similar observations have also been made for chloroplast DNA, genome-wide associations have not been reported. We determined the chloroplast genome sequences for two morphotypes of taro (Colocasia esculenta; family Araceae) and compared these with four publicly available aroid chloroplast genomes. Here, we report the extent of genome-wide association between direct and inverted repeats, indels, and substitutions in these aroid chloroplast genomes. We suggest that alternative but not mutually exclusive hypotheses explain the mutational dynamics of chloroplast genome evolution. PMID:23204304

Self-induced stretch syncope of adolescence: a video-EEG documentation.

PubMed

Mazzuca, Michel; Thomas, Pierre

2007-12-01

We present the first video-EEG documentation, with ECG and EMG features, of stretch syncope of adolescence in a young, healthy 16-year-old boy. Stretch syncope of adolescence is a rarely reported, benign cause of fainting in young patients, which can be confused with epileptic seizures. In our patient, syncopes were self-induced to avoid school. Dynamic transcranial Doppler showed evidence of blood flow decrease in both posterior cerebral arteries mimicking effects of a Valsalva manoeuvre. Dynamic angiogram of the vertebral arteries was normal. Hypotheses concerning the physiopathology are discussed. [Published with video sequences].

Vertebrate gravity sensors as dynamic systems

NASA Technical Reports Server (NTRS)

Ross, M. D.

1985-01-01

This paper considers verterbrate gravity receptors as dynamic sensors. That is, it is hypothesized that gravity is a constant force to which an acceleration-sensing system would readily adapt. Premises are considered in light of the presence of kinocilia on hair cells of vertebrate gravity sensors; differences in loading of the sensors among species; and of possible reduction in loading by inclusion of much organic material in otoconia. Moreover, organic-inorganic interfaces may confer a piezoelectric property upon otoconia, which increase the sensitivity of the sensory system to small accelerations. Comparisons with man-made accelerometers are briefly taken up.

Core-satellite species hypothesis and native versus exotic species in secondary succession

USGS Publications Warehouse

Martinez, Kelsey A.; Gibson, David J.; Middleton, Beth A.

2015-01-01

A number of hypotheses exist to explain species’ distributions in a landscape, but these hypotheses are not frequently utilized to explain the differences in native and exotic species distributions. The core-satellite species (CSS) hypothesis predicts species occupancy will be bimodally distributed, i.e., many species will be common and many species will be rare, but does not explicitly consider exotic species distributions. The parallel dynamics (PD) hypothesis predicts that regional occurrence patterns of exotic species will be similar to native species. Together, the CSS and PD hypotheses may increase our understanding of exotic species’ distribution relative to natives. We selected an old field undergoing secondary succession to study the CSS and PD hypotheses in conjunction with each other. The ratio of exotic to native species (richness and abundance) was observed through 17 years of secondary succession. We predicted species would be bimodally distributed and that exotic:native species ratios would remain steady or decrease through time under frequent disturbance. In contrast to the CSS and PD hypotheses, native species occupancies were not bimodally distributed at the site, but exotic species were. The exotic:native species ratios for both richness (E:Nrichness) and abundance (E:Ncover) generally decreased or remained constant throughout supporting the PD hypothesis. Our results suggest exotic species exhibit metapopulation structure in old field landscapes, but that metapopulation structures of native species are disrupted, perhaps because these species are dispersal limited in the fragmented landscape.

The impact of alternative trait-scaling hypotheses for the maximum photosynthetic carboxylation rate ( V cmax) on global gross primary production [The impact of alternative V cmax trait-scaling hypotheses on global gross primary production

DOE PAGES

Walker, Anthony P.; Quaife, Tristan; van Bodegom, Peter M.; ...

2017-06-23

Here, the maximum photosynthetic carboxylation rate (V cmax) is an influential plant trait that has multiple scaling hypotheses, which is a source of uncertainty in predictive understanding of global gross primary production (GPP). Four trait-scaling hypotheses (plant functional type, nutrient limitation, environmental filtering, and plant plasticity) with nine specific implementations were used to predict global V cmax distributions and their impact on global GPP in the Sheffield Dynamic Global Vegetation Model (SDGVM). Global GPP varied from 108.1 to 128.2 PgC yr –1, 65% of the range of a recent model intercomparison of global GPP. The variation in GPP propagated throughmore » to a 27% coefficient of variation in net biome productivity (NBP). All hypotheses produced global GPP that was highly correlated ( r = 0.85–0.91) with three proxies of global GPP. Plant functional type-based nutrient limitation, underpinned by a core SDGVM hypothesis that plant nitrogen (N) status is inversely related to increasing costs of N acquisition with increasing soil carbon, adequately reproduced global GPP distributions. Further improvement could be achieved with accurate representation of water sensitivity and agriculture in SDGVM. Mismatch between environmental filtering (the most data-driven hypothesis) and GPP suggested that greater effort is needed understand V cmax variation in the field, particularly in northern latitudes.« less

The impact of alternative trait-scaling hypotheses for the maximum photosynthetic carboxylation rate ( V cmax) on global gross primary production [The impact of alternative V cmax trait-scaling hypotheses on global gross primary production

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

Walker, Anthony P.; Quaife, Tristan; van Bodegom, Peter M.

Here, the maximum photosynthetic carboxylation rate (V cmax) is an influential plant trait that has multiple scaling hypotheses, which is a source of uncertainty in predictive understanding of global gross primary production (GPP). Four trait-scaling hypotheses (plant functional type, nutrient limitation, environmental filtering, and plant plasticity) with nine specific implementations were used to predict global V cmax distributions and their impact on global GPP in the Sheffield Dynamic Global Vegetation Model (SDGVM). Global GPP varied from 108.1 to 128.2 PgC yr –1, 65% of the range of a recent model intercomparison of global GPP. The variation in GPP propagated throughmore » to a 27% coefficient of variation in net biome productivity (NBP). All hypotheses produced global GPP that was highly correlated ( r = 0.85–0.91) with three proxies of global GPP. Plant functional type-based nutrient limitation, underpinned by a core SDGVM hypothesis that plant nitrogen (N) status is inversely related to increasing costs of N acquisition with increasing soil carbon, adequately reproduced global GPP distributions. Further improvement could be achieved with accurate representation of water sensitivity and agriculture in SDGVM. Mismatch between environmental filtering (the most data-driven hypothesis) and GPP suggested that greater effort is needed understand V cmax variation in the field, particularly in northern latitudes.« less

Effects of spatial structure of population size on the population dynamics of barnacles across their elevational range.

PubMed

Fukaya, Keiichi; Okuda, Takehiro; Nakaoka, Masahiro; Noda, Takashi

2014-11-01

Explanations for why population dynamics vary across the range of a species reflect two contrasting hypotheses: (i) temporal variability of populations is larger in the centre of the range compared to the margins because overcompensatory density dependence destabilizes population dynamics and (ii) population variability is larger near the margins, where populations are more susceptible to environmental fluctuations. In both of these hypotheses, positions within the range are assumed to affect population variability. In contrast, the fact that population variability is often related to mean population size implies that the spatial structure of the population size within the range of a species may also be a useful predictor of the spatial variation in temporal variability of population size over the range of the species. To explore how population temporal variability varies spatially and the underlying processes responsible for the spatial variation, we focused on the intertidal barnacle Chthamalus dalli and examined differences in its population dynamics along the tidal levels it inhabits. Changes in coverage of barnacle populations were monitored for 10.5 years at 25 plots spanning the elevational range of this species. Data were analysed by fitting a population dynamics model to estimate the effects of density-dependent and density-independent processes on population growth. We also examined the temporal mean-variance relationship of population size with parameters estimated from the population dynamics model. We found that the relative variability of populations tended to increase from the centre of the elevational range towards the margins because of an increase in the magnitude of stochastic fluctuations of growth rates. Thus, our results supported hypothesis (2). We also found that spatial variations in temporal population variability were well characterized by Taylor's power law, the relative population variability being inversely related to the mean population size. Results suggest that understanding the population dynamics of a species over its range may be facilitated by taking the spatial structure of population size into account as well as by considering changes in population processes as a function of position within the range of the species. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

A juvenile-adult population model: climate change, cannibalism, reproductive synchrony, and strong Allee effects.

PubMed

Veprauskas, Amy; Cushing, J M

2017-03-01

We study a discrete time, structured population dynamic model that is motivated by recent field observations concerning certain life history strategies of colonial-nesting gulls, specifically the glaucous-winged gull (Larus glaucescens). The model focuses on mechanisms hypothesized to play key roles in a population's response to degraded environment resources, namely, increased cannibalism and adjustments in reproductive timing. We explore the dynamic consequences of these mechanics using a juvenile-adult structure model. Mathematically, the model is unusual in that it involves a high co-dimension bifurcation at [Formula: see text] which, in turn, leads to a dynamic dichotomy between equilibrium states and synchronized oscillatory states. We give diagnostic criteria that determine which dynamic is stable. We also explore strong Allee effects caused by positive feedback mechanisms in the model and the possible consequence that a cannibalistic population can survive when a non-cannibalistic population cannot.

How to turn a genetic circuit into a synthetic tunable oscillator, or a bistable switch.

PubMed

Marucci, Lucia; Barton, David A W; Cantone, Irene; Ricci, Maria Aurelia; Cosma, Maria Pia; Santini, Stefania; di Bernardo, Diego; di Bernardo, Mario

2009-12-07

Systems and Synthetic Biology use computational models of biological pathways in order to study in silico the behaviour of biological pathways. Mathematical models allow to verify biological hypotheses and to predict new possible dynamical behaviours. Here we use the tools of non-linear analysis to understand how to change the dynamics of the genes composing a novel synthetic network recently constructed in the yeast Saccharomyces cerevisiae for In-vivo Reverse-engineering and Modelling Assessment (IRMA). Guided by previous theoretical results that make the dynamics of a biological network depend on its topological properties, through the use of simulation and continuation techniques, we found that the network can be easily turned into a robust and tunable synthetic oscillator or a bistable switch. Our results provide guidelines to properly re-engineering in vivo the network in order to tune its dynamics.

Evolutionary game theory for physical and biological scientists. I. Training and validating population dynamics equations.

PubMed

Liao, David; Tlsty, Thea D

2014-08-06

Failure to understand evolutionary dynamics has been hypothesized as limiting our ability to control biological systems. An increasing awareness of similarities between macroscopic ecosystems and cellular tissues has inspired optimism that game theory will provide insights into the progression and control of cancer. To realize this potential, the ability to compare game theoretic models and experimental measurements of population dynamics should be broadly disseminated. In this tutorial, we present an analysis method that can be used to train parameters in game theoretic dynamics equations, used to validate the resulting equations, and used to make predictions to challenge these equations and to design treatment strategies. The data analysis techniques in this tutorial are adapted from the analysis of reaction kinetics using the method of initial rates taught in undergraduate general chemistry courses. Reliance on computer programming is avoided to encourage the adoption of these methods as routine bench activities.

Autumn leaf subsidies influence spring dynamics of freshwater plankton communities.

PubMed

Fey, Samuel B; Mertens, Andrew N; Cottingham, Kathryn L

2015-07-01

While ecologists primarily focus on the immediate impact of ecological subsidies, understanding the importance of ecological subsidies requires quantifying the long-term temporal dynamics of subsidies on recipient ecosystems. Deciduous leaf litter transferred from terrestrial to aquatic ecosystems exerts both immediate and lasting effects on stream food webs. Recently, deciduous leaf additions have also been shown to be important subsidies for planktonic food webs in ponds during autumn; however, the inter-seasonal effects of autumn leaf subsidies on planktonic food webs have not been studied. We hypothesized that autumn leaf drop will affect the spring dynamics of freshwater pond food webs by altering the availability of resources, water transparency, and the metabolic state of ponds. We created leaf-added and no-leaf-added field mesocosms in autumn 2012, allowed mesocosms to ice-over for the winter, and began sampling the physical, chemical, and biological properties of mesocosms immediately following ice-off in spring 2013. At ice-off, leaf additions reduced dissolved oxygen, elevated total phosphorus concentrations and dissolved materials, and did not alter temperature or total nitrogen. These initial abiotic effects contributed to higher bacterial densities and lower chlorophyll concentrations, but by the end of spring, the abiotic environment, chlorophyll and bacterial densities converged. By contrast, zooplankton densities diverged between treatments during the spring, with leaf additions stimulating copepods but inhibiting cladocerans. We hypothesized that these differences between zooplankton orders resulted from resource shifts following leaf additions. These results suggest that leaf subsidies can alter both the short- and long-term dynamics of planktonic food webs, and highlight the importance of fully understanding how ecological subsidies are integrated into recipient food webs.

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction.

PubMed

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Gihring, Thomas; Zhang, Gengxin; Schadt, Chris W; Watson, David; Jardine, Phil; Criddle, Craig S; Brooks, Scott; Marsh, Terence L; Tiedje, James M; Arkin, Adam P; Zhou, Jizhong

2015-06-15

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO3 (-), Mn(IV), Fe(III), U(VI), and SO4 (2-) significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO3 (-), Mn(II), Fe(II), U(VI), and SO4 (2-). Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

PubMed Central

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D.; Deng, Ye; He, Zhili; Gihring, Thomas; Zhang, Gengxin; Schadt, Chris W.; Watson, David; Jardine, Phil; Criddle, Craig S.; Brooks, Scott; Marsh, Terence L.; Tiedje, James M.; Arkin, Adam P.

2015-01-01

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO3−, Mn(IV), Fe(III), U(VI), and SO42− significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO3−, Mn(II), Fe(II), U(VI), and SO42−. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction. PMID:25862231

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

DOE PAGES

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D.; ...

2015-04-10

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this paper, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using amore » comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO 3 -, Mn(IV), Fe(III), U(VI), and SO 4 2- significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO 3 -, Mn(II), Fe(II), U(VI), and SO 4 2-. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. Finally, this study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction.« less

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

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

Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D.

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this paper, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using amore » comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO 3 -, Mn(IV), Fe(III), U(VI), and SO 4 2- significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO 3 -, Mn(II), Fe(II), U(VI), and SO 4 2-. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. Finally, this study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction.« less

Dynamics of social behaviour at parturition in a gregarious ungulate.

PubMed

Pérez-Barbería, F J; Walker, D M

2018-05-01

Group living is the behavioural response that results when individuals assess the costs vs benefits of sociality, and these trade-offs vary across an animal's life. Here we quantitatively assess how periparturient condition (mother/non-mother) and births affect the dynamics of social interactions of a gregarious ungulate, and how such can help to explain evolutionary hypotheses of the mother-offspring bond. To achieve this we used data of the individual movement of a group of Scottish blackface sheep (Ovis aries) marked with GPS collars and properties of mathematical graphs (networks). Euclidean pair-wise distance between sheep were threshold at different percentiles to determine network links, and these thresholds have a profound effect on the connectivity of the resulting network. Births increased the average pair-wise distance between mothers, and between mothers and non-mothers, with less effect on the distance between non-mothers. Mothers occupied peripheral positions within the flock, more evident following births. Associations between individuals (i.e. network community change) were highly dynamic, though mothers were less likely to change community than non-mothers, especially after births. Births hampered individual communication within the flock (assessed via network closeness centrality), especially in mothers. Overall leadership (lead positioning relative to flock movement) was not associated to reproductive condition, and individual leadership rank was not affected by births. A ten minute GPS acquisition time was adequate to capture complex social dynamics in sheep movement. The results on mother's isolation behaviour support the hypotheses of selection for maternal imprint facilitation, reducing risks to nursing alien offspring, and group/multilevel selection on group formation. Copyright © 2018 Elsevier B.V. All rights reserved.

Potentiation of the NO-cGMP pathway and blood flow responses during dynamic exercise in healthy humans

PubMed Central

Limberg, Jacqueline K.; Malterer, Katherine R.; Kellawan, J. Mikhail; Schrage, William G.; Wilkins, Brad W.; Nicholson, Wayne T.; Eisenach, John H.; Joyner, Michael J.; Curry, Timothy B.

2017-01-01

Purpose Previous work has shown nitric oxide (NO) contributes to ~15% of the hyperemic response to dynamic exercise in healthy humans. This NO-mediated vasodilation occurs, in part, via increases in intracellular cyclic guanosine monophosphate (cGMP), which is catabolized by phosphodiesterase. We sought to examine the effect of phosphodiesterase-5 (PDE-5) inhibition on forearm blood flow (FBF responses to dynamic handgrip exercise in healthy humans and the role of NO. We hypothesized exercise hyperemia would be augmented by sildenafil citrate (SDF, PDE-5 inhibitor). We further hypothesized any effect of SDF on exercise hyperemia would be abolished with intra-arterial infusion of the NO synthase (NOS) inhibitor L-NG-monomethyl arginine (L-NMMA). Methods FBF (Doppler ultrasound) was assessed at rest and during 5 minutes of dynamic forearm handgrip exercise at 15% of maximal voluntary contraction under control (saline) conditions and during 3 experimental protocols: 1) oral SDF (n=10), 2) intra-arterial L-NMMA (n=20), 3) SDF and L-NMMA (n=10). FBF responses to intra-arterial sodium nitroprusside (NTP, NO donor) were also assessed. Results FBF increased with exercise (p<0.01). Intra-arterial infusion of L-NMMA resulted in a reduction in exercise hyperemia (17±1 to 15±1 mL/dL/min, p<0.01). Although the hyperemic response to NTP was augmented by SDF (Area under the curve: 41±7 vs 61±11 AU, p<0.01), there was no effect of SDF on exercise hyperemia (p=0.33). Conclusions Despite improving NTP-mediated vasodilation, oral SDF failed to augment exercise hyperemia in young, healthy adults. These observations reflect a minor contribution of NO and the cGMP pathway during exercise hyperemia in healthy young humans. PMID:28013386

Dynamic phase coexistence in glass-forming liquids.

PubMed

Pastore, Raffaele; Coniglio, Antonio; Ciamarra, Massimo Pica

2015-07-09

One of the most controversial hypotheses for explaining the heterogeneous dynamics of glasses postulates the temporary coexistence of two phases characterized by a high and by a low diffusivity. In this scenario, two phases with different diffusivities coexist for a time of the order of the relaxation time and mix afterwards. Unfortunately, it is difficult to measure the single-particle diffusivities to test this hypothesis. Indeed, although the non-Gaussian shape of the van-Hove distribution suggests the transient existence of a diffusivity distribution, it is not possible to infer from this quantity whether two or more dynamical phases coexist. Here we provide the first direct observation of the dynamical coexistence of two phases with different diffusivities, by showing that in the deeply supercooled regime the distribution of the single-particle diffusivities acquires a transient bimodal shape. We relate this distribution to the heterogeneity of the dynamics and to the breakdown of the Stokes-Einstein relation, and we show that the coexistence of two dynamical phases occurs up to a timescale growing faster than the relaxation time on cooling, for some of the considered models. Our work offers a basis for rationalizing the dynamics of supercooled liquids and for relating their structural and dynamical properties.

When prey provide more than food: mammalian predators appropriating the refugia of their prey

Treesearch

Bill Zielinski

2015-01-01

Some mammalian predators acquire both food and shelter from their prey, by eating them and using the refugia the prey construct. I searched the literature for examples of predators that exhibit this behavior and summarize their taxonomic affiliations, relative sizes, and distributions. I hypothesized that size ratios of species involved in this dynamic would be near 1....

Mother-Child Conflict and Sibling Relatedness: A Test of Hypotheses from Parent-Offspring Conflict Theory

ERIC Educational Resources Information Center

Schlomer, Gabriel L.; Ellis, Bruce J.; Garber, Judy

2010-01-01

Parent-offspring conflict theory (POCT) has been underutilized in studies of human family dynamics. An implication of POCT is that the presence of siblings will increase conflict in biological parent-child dyads, and that half siblings will increase that conflict more than full siblings. Evidence consistent with this prediction was found in a…

Inferring controls on the epidemiology of beech bark disease from spatial patterning of disease organisms

Treesearch

Jeffrey R. Garnas; David R. Houston; Mark J. Twery; Matthew P. Ayres; Celia Evans

2013-01-01

Spatial pattern in the distribution and abundance of organisms is an emergent property of collective rates of reproduction, survival and movement of individuals in a heterogeneous environment. The form, intensity and scale of spatial patterning can be used to test hypotheses regarding the relative importance of candidate processes to population dynamics. Using 84 plots...

The herb community of a tropical forest in central Panama: dynamics and impact of mammalian herbivores

Treesearch

Alejandro A. Royo; Walter P. Carson

2005-01-01

Mammals are hypothesized to either promote plant diversity by preventing competitive exclusion or limit diversity by reducing the abundance of sensitive plant species through their activities as browsers or disturbance agents. Previous studies of herbivore impacts in plant communities have focused on tree species and ignored the herbaceous community. In an experiment...

Abundance and productivity of warbling vireos across an elevational gradient in the Sierra Nevada

Treesearch

Kathryn L. Purcell

2006-01-01

Recent studies have shown that Warbling Vireos (Vireo gilvus) are declining in California and that these trends are due to low reproductive success. Brood parasitism by Brown-headed Cowbirds (Molothrus ater) has been implicated in the low productivity. I explored two hypotheses related to population dynamics of Warbling Vireos along an elevational gradient: (1)...

Observed diurnal variations in Mars Science Laboratory Dynamic Albedo of Neutrons passive mode data

NASA Astrophysics Data System (ADS)

Tate, C. G.; Moersch, J.; Jun, I.; Mitrofanov, I.; Litvak, M.; Boynton, W. V.; Drake, D.; Fedosov, F.; Golovin, D.; Hardgrove, C.; Harshman, K.; Kozyrev, A. S.; Kuzmin, R.; Lisov, D.; Maclennan, E.; Malakhov, A.; Mischna, M.; Mokrousov, M.; Nikiforov, S.; Sanin, A. B.; Starr, R.; Vostrukhin, A.

2018-06-01

The Mars Science Laboratory Dynamic Albedo of Neutrons (DAN) experiment measures the martian neutron leakage flux in order to estimate the amount of water equivalent hydrogen present in the shallow regolith. When DAN is operating in passive mode, it is sensitive to neutrons produced through the interactions of galactic cosmic rays (GCR) with the regolith and atmosphere and neutrons produced by the rover's Multi-Mission Radioisotope Thermoelectric Generator (MMRTG). During the mission, DAN passive mode data were collected over the full diurnal cycle at the locations known as Rocknest (sols 60-100) and John Klein (sols 166-272). A weak, but unexpected, diurnal variation was observed in the neutron count rates reported at these locations. We investigate different hypotheses that could be causing these observed variations. These hypotheses are variations in subsurface temperature, atmospheric pressure, the exchange of water vapor between the atmosphere and regolith, and instrumental effects on the neutron count rates. Our investigation suggests the most likely factors contributing to the observed diurnal variations in DAN passive data are instrumental effects and time-variable preferential shielding of alpha particles, with other environmental effects only having small contributions.

Mathematical modeling of the female reproductive system: from oocyte to delivery.

PubMed

Clark, Alys R; Kruger, Jennifer A

2017-01-01

From ovulation to delivery, and through the menstrual cycle, the female reproductive system undergoes many dynamic changes to provide an optimal environment for the embryo to implant, and to develop successfully. It is difficult ethically and practically to observe the system over the timescales involved in growth and development (often hours to days). Even in carefully monitored conditions clinicians and biologists can only see snapshots of the development process. Mathematical models are emerging as a key means to supplement our knowledge of the reproductive process, and to tease apart complexity in the reproductive system. These models have been used successfully to test existing hypotheses regarding the mechanisms of female infertility and pathological fetal development, and also to provide new experimentally testable hypotheses regarding the process of development. This new knowledge has allowed for improvements in assisted reproductive technologies and is moving toward translation to clinical practice via multiscale assessments of the dynamics of ovulation, development in pregnancy, and the timing and mechanics of delivery. WIREs Syst Biol Med 2017, 9:e1353. doi: 10.1002/wsbm.1353 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

Market reaction to a bid-ask spread change: A power-law relaxation dynamics

NASA Astrophysics Data System (ADS)

Ponzi, Adam; Lillo, Fabrizio; Mantegna, Rosario N.

2009-07-01

We study the relaxation dynamics of the bid-ask spread and of the midprice after a sudden variation of the spread in a double auction financial market. We find that the spread decays as a power law to its normal value. We measure the price reversion dynamics and the permanent impact, i.e., the long-time effect on price, of a generic event altering the spread and we find an approximately linear relation between immediate and permanent impact. We hypothesize that the power-law decay of the spread is a consequence of the strategic limit order placement of liquidity providers. We support this hypothesis by investigating several quantities, such as order placement rates and distribution of prices and times of submitted orders, which affect the decay of the spread.

Structural network heterogeneities and network dynamics: a possible dynamical mechanism for hippocampal memory reactivation.

NASA Astrophysics Data System (ADS)

Jablonski, Piotr; Poe, Gina; Zochowski, Michal

2007-03-01

The hippocampus has the capacity for reactivating recently acquired memories and it is hypothesized that one of the functions of sleep reactivation is the facilitation of consolidation of novel memory traces. The dynamic and network processes underlying such a reactivation remain, however, unknown. We show that such a reactivation characterized by local, self-sustained activity of a network region may be an inherent property of the recurrent excitatory-inhibitory network with a heterogeneous structure. The entry into the reactivation phase is mediated through a physiologically feasible regulation of global excitability and external input sources, while the reactivated component of the network is formed through induced network heterogeneities during learning. We show that structural changes needed for robust reactivation of a given network region are well within known physiological parameters.

Structural network heterogeneities and network dynamics: A possible dynamical mechanism for hippocampal memory reactivation

NASA Astrophysics Data System (ADS)

Jablonski, Piotr; Poe, Gina R.; Zochowski, Michal

2007-01-01

The hippocampus has the capacity for reactivating recently acquired memories and it is hypothesized that one of the functions of sleep reactivation is the facilitation of consolidation of novel memory traces. The dynamic and network processes underlying such a reactivation remain, however, unknown. We show that such a reactivation characterized by local, self-sustained activity of a network region may be an inherent property of the recurrent excitatory-inhibitory network with a heterogeneous structure. The entry into the reactivation phase is mediated through a physiologically feasible regulation of global excitability and external input sources, while the reactivated component of the network is formed through induced network heterogeneities during learning. We show that structural changes needed for robust reactivation of a given network region are well within known physiological parameters.

Mitochondrial morphology transitions and functions: implications for retrograde signaling?

PubMed Central

Picard, Martin; Shirihai, Orian S.; Gentil, Benoit J.

2013-01-01

In response to cellular and environmental stresses, mitochondria undergo morphology transitions regulated by dynamic processes of membrane fusion and fission. These events of mitochondrial dynamics are central regulators of cellular activity, but the mechanisms linking mitochondrial shape to cell function remain unclear. One possibility evaluated in this review is that mitochondrial morphological transitions (from elongated to fragmented, and vice-versa) directly modify canonical aspects of the organelle's function, including susceptibility to mitochondrial permeability transition, respiratory properties of the electron transport chain, and reactive oxygen species production. Because outputs derived from mitochondrial metabolism are linked to defined cellular signaling pathways, fusion/fission morphology transitions could regulate mitochondrial function and retrograde signaling. This is hypothesized to provide a dynamic interface between the cell, its genome, and the fluctuating metabolic environment. PMID:23364527

Ontogenetic scaling of hydrostatic skeletons: geometric, static stress and dynamic stress scaling of the earthworm lumbricus terrestris

PubMed

Quillin

1998-05-21

Soft-bodied organisms with hydrostatic skeletons range enormously in body size, both during the growth of individuals and in the comparison of species. Therefore, body size is an important consideration in an examination of the mechanical function of hydrostatic skeletons. The scaling of hydrostatic skeletons cannot be inferred from existing studies of the lever-like skeletons of vertebrates and arthropods because the two skeleton types function by different mechanisms. Hydrostats are constructed of an extensible body wall in tension surrounding a fluid or deformable tissue under compression. It is the pressurized internal fluid (rather than the rigid levers of vertebrates and arthropods) that enables the maintenance of posture, antagonism of muscles and transfer of muscle forces to the environment. The objectives of the present study were (1) to define the geometric, static stress and dynamic stress similarity scaling hypotheses for hydrostatic skeletons on the basis of their generalized form and function, and (2) to apply these similarity hypotheses in a study of the ontogenetic scaling of earthworms, Lumbricus terrestris, to determine which parameters of skeletal function are conserved or changed as a function of body mass during growth (from 0.01 to 8 g). Morphometric measurements on anesthetized earthworms revealed that the earthworms grew isometrically; the external proportions and number of segments were constant as a function of body size. Calculations of static stresses (forces per cross-sectional area in the body wall) during rest and dynamic stresses during peristaltic crawling (calculated from measurements of internal pressure and body wall geometry) revealed that the earthworms also maintained static and dynamic stress similarity, despite a slight increase in body wall thickness in segment 50 (but not in segment 15). In summary, the hydrostatic skeletons of earthworms differ fundamentally from the rigid, lever-like skeletons of their terrestrial counterparts in their ability to grow isometrically while maintaining similarity in both static and dynamic stresses.

Modelling the Course of an HIV Infection: Insights from Ecology and Evolution

PubMed Central

Alizon, Samuel; Magnus, Carsten

2012-01-01

The Human Immunodeficiency Virus (HIV) is one of the most threatening viral agents. This virus infects approximately 33 million people, many of whom are unaware of their status because, except for flu-like symptoms right at the beginning of the infection during the acute phase, the disease progresses more or less symptom-free for 5 to 10 years. During this asymptomatic phase, the virus slowly destroys the immune system until the onset of AIDS when opportunistic infections like pneumonia or Kaposi’s sarcoma can overcome immune defenses. Mathematical models have played a decisive role in estimating important parameters (e.g., virion clearance rate or life-span of infected cells). However, most models only account for the acute and asymptomatic latency phase and cannot explain the progression to AIDS. Models that account for the whole course of the infection rely on different hypotheses to explain the progression to AIDS. The aim of this study is to review these models, present their technical approaches and discuss the robustness of their biological hypotheses. Among the few models capturing all three phases of an HIV infection, we can distinguish between those that mainly rely on population dynamics and those that involve virus evolution. Overall, the modeling quest to capture the dynamics of an HIV infection has improved our understanding of the progression to AIDS but, more generally, it has also led to the insight that population dynamics and evolutionary processes can be necessary to explain the course of an infection. PMID:23202449

Transfer of movement sequences: bigger is better.

PubMed

Dean, Noah J; Kovacs, Attila J; Shea, Charles H

2008-02-01

Experiment 1 was conducted to determine if proportional transfer from "small to large" scale movements is as effective as transferring from "large to small." We hypothesize that the learning of larger scale movement will require the participant to learn to manage the generation, storage, and dissipation of forces better than when practicing smaller scale movements. Thus, we predict an advantage for transfer of larger scale movements to smaller scale movements relative to transfer from smaller to larger scale movements. Experiment 2 was conducted to determine if adding a load to a smaller scale movement would enhance later transfer to a larger scale movement sequence. It was hypothesized that the added load would require the participants to consider the dynamics of the movement to a greater extent than without the load. The results replicated earlier findings of effective transfer from large to small movements, but consistent with our hypothesis, transfer was less effective from small to large (Experiment 1). However, when a load was added during acquisition transfer from small to large was enhanced even though the load was removed during the transfer test. These results are consistent with the notion that the transfer asymmetry noted in Experiment 1 was due to factors related to movement dynamics that were enhanced during practice of the larger scale movement sequence, but not during the practice of the smaller scale movement sequence. The findings that the movement structure is unaffected by transfer direction but the movement dynamics are influenced by transfer direction is consistent with hierarchal models of sequence production.

Method and system for detecting a failure or performance degradation in a dynamic system such as a flight vehicle

NASA Technical Reports Server (NTRS)

Miller, Robert H. (Inventor); Ribbens, William B. (Inventor)

2003-01-01

A method and system for detecting a failure or performance degradation in a dynamic system having sensors for measuring state variables and providing corresponding output signals in response to one or more system input signals are provided. The method includes calculating estimated gains of a filter and selecting an appropriate linear model for processing the output signals based on the input signals. The step of calculating utilizes one or more models of the dynamic system to obtain estimated signals. The method further includes calculating output error residuals based on the output signals and the estimated signals. The method also includes detecting one or more hypothesized failures or performance degradations of a component or subsystem of the dynamic system based on the error residuals. The step of calculating the estimated values is performed optimally with respect to one or more of: noise, uncertainty of parameters of the models and un-modeled dynamics of the dynamic system which may be a flight vehicle or financial market or modeled financial system.

Results of the Utah-Arizona stage-by-stage migrations

USGS Publications Warehouse

Ellis, D.H.; Mellon, C.; Kinloch, M.; Dolbeare, T.; Ossi, D.P.

2001-01-01

In an effort to find a safer means of teaching cranes new migration routes, each year (in 1998 and 1999) we transported a group of greater sandhill cranes (Grus canadensis tabida) stage-by-stage, in a horse trailer, with stops for brief flights at about 30-km intervals, along a 1300-1400-km fall migration route from Fish Springs National Wildlife Refuge (Fish Springs) in west-central Utah to the vicinity of Gila Bend, Arizona. Thereafter, we released them into a wild flock of sandhill cranes. All stage-by-stage birds were hand-reared with both a plastic crane decoy (to encourage them to roost in water) and a costume-draped humanoid form (called a scare-eagle and used for its namesake purpose). When these 2 teaching aids were placed in water, our cranes readily roosted nearby. All but 4 of our cranes proved cooperative (i.e., catchable at each of the ca 25-36 stops) during the migration. All were efficiently released into a wild flock and experienced good survival. The stage-by-stage method proved to be a safe means of transporting cranes south and giving them experience along the route. Some cranes apparently learned their route from the limited experience afforded by releasing them at intervals, and the 1999 cranes have made repealed migrations to or near our chosen northern terminus. However, after 1 winter in our chosen area, the birds have moved elsewhere to winter.

Application of a Delay-difference model for the stock assessment of southern Atlantic albacore ( Thunnus alalunga)

NASA Astrophysics Data System (ADS)

Zhang, Kui; Liu, Qun; Kalhoro, Muhsan Ali

2015-06-01

Delay-difference models are intermediate between simple surplus-production models and complicated age-structured models. Such intermediate models are more efficient and require less data than age-structured models. In this study, a delay-difference model was applied to fit catch and catch per unit effort (CPUE) data (1975-2011) of the southern Atlantic albacore ( Thunnus alalunga) stock. The proposed delay-difference model captures annual fluctuations in predicted CPUE data better than Fox model. In a Monte Carlo simulation, white noises (CVs) were superimposed on the observed CPUE data at four levels. Relative estimate error was then calculated to compare the estimated results with the true values of parameters α and β in Ricker stock-recruitment model and the catchability coefficient q. a is more sensitive to CV than β and q. We also calculated an 80% percentile confidence interval of the maximum sustainable yield (MSY, 21756 t to 23408 t; median 22490 t) with the delay-difference model. The yield of the southern Atlantic albacore stock in 2011 was 24122 t, and the estimated ratios of catch against MSY for the past seven years were approximately 1.0. We suggest that care should be taken to protect the albacore fishery in the southern Atlantic Ocean. The proposed delay-difference model provides a good fit to the data of southern Atlantic albacore stock and may be a useful choice for the assessment of regional albacore stock.

An equivalent potential vorticity theory applied to the analysis and prediction of severe storm dynamics

NASA Technical Reports Server (NTRS)

Paine, D. A.; Kaplan, M. L.

1976-01-01

Potential vorticity theory is developed in a description of an equivalent potential temperature topography, and a new theory suited to the description of scale interaction is elaborated. Macroscale triggering of ageostrophic flow fields at the mesoscale, in turn leading to release of convective instability along narrow zones at the microscale, is examined. Correlation of appreciable decrease in potential vorticity with such phenomena as cumulonimbi, tornados, and duststorms is examined. The relevance of a multiscale energy-momentum cascade in numerical prediction of severe mesoscale and microscale phenomena from radiosonde data is reviewed. Hypotheses for mesoscale dynamics are constructed.

Introduction of a Framework for Dynamic Knowledge Representation of the Control Structure of Transplant Immunology: Employing the Power of Abstraction with a Solid Organ Transplant Agent-Based Model

PubMed Central

An, Gary

2015-01-01

Agent-based modeling has been used to characterize the nested control loops and non-linear dynamics associated with inflammatory and immune responses, particularly as a means of visualizing putative mechanistic hypotheses. This process is termed dynamic knowledge representation and serves a critical role in facilitating the ability to test and potentially falsify hypotheses in the current data- and hypothesis-rich biomedical research environment. Importantly, dynamic computational modeling aids in identifying useful abstractions, a fundamental scientific principle that pervades the physical sciences. Recognizing the critical scientific role of abstraction provides an intellectual and methodological counterweight to the tendency in biology to emphasize comprehensive description as the primary manifestation of biological knowledge. Transplant immunology represents yet another example of the challenge of identifying sufficient understanding of the inflammatory/immune response in order to develop and refine clinically effective interventions. Advances in immunosuppressive therapies have greatly improved solid organ transplant (SOT) outcomes, most notably by reducing and treating acute rejection. The end goal of these transplant immune strategies is to facilitate effective control of the balance between regulatory T cells and the effector/cytotoxic T-cell populations in order to generate, and ideally maintain, a tolerant phenotype. Characterizing the dynamics of immune cell populations and the interactive feedback loops that lead to graft rejection or tolerance is extremely challenging, but is necessary if rational modulation to induce transplant tolerance is to be accomplished. Herein is presented the solid organ agent-based model (SOTABM) as an initial example of an agent-based model (ABM) that abstractly reproduces the cellular and molecular components of the immune response to SOT. Despite its abstract nature, the SOTABM is able to qualitatively reproduce acute rejection and the suppression of acute rejection by immunosuppression to generate transplant tolerance. The SOTABM is intended as an initial example of how ABMs can be used to dynamically represent mechanistic knowledge concerning transplant immunology in a scalable and expandable form and can thus potentially serve as useful adjuncts to the investigation and development of control strategies to induce transplant tolerance. PMID:26594211

Introduction of a Framework for Dynamic Knowledge Representation of the Control Structure of Transplant Immunology: Employing the Power of Abstraction with a Solid Organ Transplant Agent-Based Model.

PubMed

An, Gary

2015-01-01

Agent-based modeling has been used to characterize the nested control loops and non-linear dynamics associated with inflammatory and immune responses, particularly as a means of visualizing putative mechanistic hypotheses. This process is termed dynamic knowledge representation and serves a critical role in facilitating the ability to test and potentially falsify hypotheses in the current data- and hypothesis-rich biomedical research environment. Importantly, dynamic computational modeling aids in identifying useful abstractions, a fundamental scientific principle that pervades the physical sciences. Recognizing the critical scientific role of abstraction provides an intellectual and methodological counterweight to the tendency in biology to emphasize comprehensive description as the primary manifestation of biological knowledge. Transplant immunology represents yet another example of the challenge of identifying sufficient understanding of the inflammatory/immune response in order to develop and refine clinically effective interventions. Advances in immunosuppressive therapies have greatly improved solid organ transplant (SOT) outcomes, most notably by reducing and treating acute rejection. The end goal of these transplant immune strategies is to facilitate effective control of the balance between regulatory T cells and the effector/cytotoxic T-cell populations in order to generate, and ideally maintain, a tolerant phenotype. Characterizing the dynamics of immune cell populations and the interactive feedback loops that lead to graft rejection or tolerance is extremely challenging, but is necessary if rational modulation to induce transplant tolerance is to be accomplished. Herein is presented the solid organ agent-based model (SOTABM) as an initial example of an agent-based model (ABM) that abstractly reproduces the cellular and molecular components of the immune response to SOT. Despite its abstract nature, the SOTABM is able to qualitatively reproduce acute rejection and the suppression of acute rejection by immunosuppression to generate transplant tolerance. The SOTABM is intended as an initial example of how ABMs can be used to dynamically represent mechanistic knowledge concerning transplant immunology in a scalable and expandable form and can thus potentially serve as useful adjuncts to the investigation and development of control strategies to induce transplant tolerance.

Dynamic Density: An Air Traffic Management Metric

NASA Technical Reports Server (NTRS)

Laudeman, I. V.; Shelden, S. G.; Branstrom, R.; Brasil, C. L.

1998-01-01

The definition of a metric of air traffic controller workload based on air traffic characteristics is essential to the development of both air traffic management automation and air traffic procedures. Dynamic density is a proposed concept for a metric that includes both traffic density (a count of aircraft in a volume of airspace) and traffic complexity (a measure of the complexity of the air traffic in a volume of airspace). It was hypothesized that a metric that includes terms that capture air traffic complexity will be a better measure of air traffic controller workload than current measures based only on traffic density. A weighted linear dynamic density function was developed and validated operationally. The proposed dynamic density function includes a traffic density term and eight traffic complexity terms. A unit-weighted dynamic density function was able to account for an average of 22% of the variance in observed controller activity not accounted for by traffic density alone. A comparative analysis of unit weights, subjective weights, and regression weights for the terms in the dynamic density equation was conducted. The best predictor of controller activity was the dynamic density equation with regression-weighted complexity terms.

Social Dominance Orientation Relates to Believing Men Should Dominate Sexually, Sexual Self-Efficacy, and Taking Free Female Condoms Among Undergraduate Women and Men

PubMed Central

Levy, Sheri R.; Earnshaw, Valerie A.

2014-01-01

Gendered-based power affects heterosexual relationships, with beliefs in the U.S. prescribing that men dominate women sexually. We draw on social dominance theory to examine whether women’s and men’s level of support for group-based hierarchy (i.e., social dominance orientation; SDO) helps explain gender-based power beliefs and dynamics in heterosexual relationships. We conducted a laboratory study at a Northeastern U.S. university among 357 women and 126 men undergraduates who reported being heterosexual and sexually active, testing three sets of hypotheses. First, as hypothesized, women endorsed SDO and the belief that men should dominate sexually less than men did. Second, as hypothesized, among women and men, SDO was positively correlated with the belief that men should dominate sexually, and negatively correlated with sexual self-efficacy (confidence in sexual situations) and number of female condoms (a woman-controlled source of protection) taken. Third, structural equation modeling, controlling for age, family income, number of sexual partners in the past month, and perceived HIV/AIDS risk, supported the hypothesis that among women and men, the belief that men should dominate sexually mediates SDO’s association with sexual self-efficacy. The hypothesis that the belief that men should dominate sexually mediates SDO’s association with number of female condoms taken was supported for women only. The hypothesis that sexual self-efficacy mediates SDO’s association with number of female condoms taken was not supported. Results suggest SDO influences power beliefs and dynamics in heterosexual relationships. Although female condoms are an important woman-controlled source of protection, power-related beliefs may pose a challenge to their use. PMID:24482555

Landscape genetics of high mountain frog metapopulations

USGS Publications Warehouse

Murphy, M.A.; Dezzani, R.; Pilliod, D.S.; Storfer, A.

2010-01-01

Explaining functional connectivity among occupied habitats is crucial for understanding metapopulation dynamics and species ecology. Landscape genetics has primarily focused on elucidating how ecological features between observations influence gene flow. Functional connectivity, however, may be the result of both these between-site (landscape resistance) landscape characteristics and at-site (patch quality) landscape processes that can be captured using network based models. We test hypotheses of functional connectivity that include both between-site and at-site landscape processes in metapopulations of Columbia spotted frogs (Rana luteiventris) by employing a novel justification of gravity models for landscape genetics (eight microsatellite loci, 37 sites, n = 441). Primarily used in transportation and economic geography, gravity models are a unique approach as flow (e.g. gene flow) is explained as a function of three basic components: distance between sites, production/attraction (e.g. at-site landscape process) and resistance (e.g. between-site landscape process). The study system contains a network of nutrient poor high mountain lakes where we hypothesized a short growing season and complex topography between sites limit R. luteiventris gene flow. In addition, we hypothesized production of offspring is limited by breeding site characteristics such as the introduction of predatory fish and inherent site productivity. We found that R. luteiventris connectivity was negatively correlated with distance between sites, presence of predatory fish (at-site) and topographic complexity (between-site). Conversely, site productivity (as measured by heat load index, at-site) and growing season (as measured by frost-free period between-sites) were positively correlated with gene flow. The negative effect of predation and positive effect of site productivity, in concert with bottleneck tests, support the presence of source-sink dynamics. In conclusion, gravity models provide a powerful new modelling approach for examining a wide range of both basic and applied questions in landscape genetics.

A collection of sprouting parameters for simulating regeneration establishment in the Missouri Ozarks

Treesearch

Lance A. Vickers; David R. Larsen; John M. Kabrick; Daniel C. Dey; Benjamin O. Knapp

2016-01-01

Predicting the effects of silvicultural choices on tree regeneration has traditionally been difficult with the tools currently available to foresters. In an effort to improve this, we have developed a simulation framework based on hypotheses of stand dynamics for several species found in the Missouri Ozarks. This framework includes separate modules for establishment,...

Defining Early Markers of Neurodevelopmental Disorders in Infants With TSC

DTIC Science & Technology

2013-10-01

in (1) children with autism and tuberous sclerosis complex and (2) children with temporal lobe tubers. This study is the first to quantify atypical...Furthermore, we hypothesize that it is the dynamic interplay between aberrant functional connectivity and physiological stressors, such as epilepsy ...neurodevelopmental disorders in children with TSC, particularly the interaction between clinical factors (such as epilepsy or tuber burden) and cognitive and

Soil organic matter dynamics under decaying wood in a subtropical wet forest: effect of tree species and decay stage.

Treesearch

Marcela Zalamea; Grizelle Gonzalez; Chien-Lu Ping; Gary Michaelson

2007-01-01

Decaying wood is an important structural and functional component of forests: it contributes to generate habitat diversity, acts as either sink or source of nutrients, and plays a preponderant role in soil formation. Thus, decaying wood might likely have measurable effects on chemical properties of the underlying soil.We hypothesized that decaying wood would have a...

Adolescent Deviant Peer Clustering as an Amplifying Mechanism Underlying the Progression from Early Substance Use to Late Adolescent Dependence

ERIC Educational Resources Information Center

Van Ryzin, Mark J.; Dishion, Thomas J.

2014-01-01

Background: Early substance use co-occurs with youths' self-organization into deviant peer groups in which substance use is central to social interaction. We hypothesized that the social dynamics of deviant peer groups amplify the risk of progressing from early use to later dependence, and that this influence occurs over and above escalations…

Impaired Object Recognition but Normal Social Behavior and Ultrasonic Communication in Cofilin1 Mutant Mice

PubMed Central

Sungur, A. Özge; Stemmler, Lea; Wöhr, Markus; Rust, Marco B.

2018-01-01

Autism spectrum disorder (ASD), schizophrenia (SCZ) and intellectual disability (ID) show a remarkable overlap in symptoms, including impairments in cognition, social behavior and communication. Human genetic studies revealed an enrichment of mutations in actin-related genes for these disorders, and some of the strongest candidate genes control actin dynamics. These findings led to the hypotheses: (i) that ASD, SCZ and ID share common disease mechanisms; and (ii) that, at least in a subgroup of affected individuals, defects in the actin cytoskeleton cause or contribute to their pathologies. Cofilin1 emerged as a key regulator of actin dynamics and we previously demonstrated its critical role for synaptic plasticity and associative learning. Notably, recent studies revealed an over-activation of cofilin1 in mutant mice displaying ASD- or SCZ-like behavioral phenotypes, suggesting that dysregulated cofilin1-dependent actin dynamics contribute to their behavioral abnormalities, such as deficits in social behavior. These findings let us hypothesize: (i) that, apart from cognitive impairments, cofilin1 mutants display additional behavioral deficits with relevance to ASD or SCZ; and (ii) that our cofilin1 mutants represent a valuable tool to study the underlying disease mechanisms. To test our hypotheses, we compared social behavior and ultrasonic communication of juvenile mutants to control littermates, and we did not obtain evidence for impaired direct reciprocal social interaction, social approach or social memory. Moreover, concomitant emission of ultrasonic vocalizations was not affected and time-locked to social activity, supporting the notion that ultrasonic vocalizations serve a pro-social communicative function as social contact calls maintaining social proximity. Finally, cofilin1 mutants did not display abnormal repetitive behaviors. Instead, they performed weaker in novel object recognition, thereby demonstrating that cofilin1 is relevant not only for associative learning, but also for “non-matching-to-sample” learning. Here we report the absence of an ASD- or a SCZ-like phenotype in cofilin1 mutants, and we conclude that cofilin1 is relevant specifically for non-social cognition. PMID:29515378

The impact of alternative trait-scaling hypotheses for the maximum photosynthetic carboxylation rate (Vcmax ) on global gross primary production.

PubMed

Walker, Anthony P; Quaife, Tristan; van Bodegom, Peter M; De Kauwe, Martin G; Keenan, Trevor F; Joiner, Joanna; Lomas, Mark R; MacBean, Natasha; Xu, Chongang; Yang, Xiaojuan; Woodward, F Ian

2017-09-01

The maximum photosynthetic carboxylation rate (V cmax ) is an influential plant trait that has multiple scaling hypotheses, which is a source of uncertainty in predictive understanding of global gross primary production (GPP). Four trait-scaling hypotheses (plant functional type, nutrient limitation, environmental filtering, and plant plasticity) with nine specific implementations were used to predict global V cmax distributions and their impact on global GPP in the Sheffield Dynamic Global Vegetation Model (SDGVM). Global GPP varied from 108.1 to 128.2 PgC yr -1 , 65% of the range of a recent model intercomparison of global GPP. The variation in GPP propagated through to a 27% coefficient of variation in net biome productivity (NBP). All hypotheses produced global GPP that was highly correlated (r = 0.85-0.91) with three proxies of global GPP. Plant functional type-based nutrient limitation, underpinned by a core SDGVM hypothesis that plant nitrogen (N) status is inversely related to increasing costs of N acquisition with increasing soil carbon, adequately reproduced global GPP distributions. Further improvement could be achieved with accurate representation of water sensitivity and agriculture in SDGVM. Mismatch between environmental filtering (the most data-driven hypothesis) and GPP suggested that greater effort is needed understand V cmax variation in the field, particularly in northern latitudes. © 2017 UT-Battelle LLC. New Phytologist © 2017 New Phytologist Trust.

The Impact of Alternative Trait-Scaling Hypotheses for the Maximum Photosynthetic Carboxylation Rate (V (sub cmax)) on Global Gross Primary Production

NASA Technical Reports Server (NTRS)

Walker, Anthony P.; Quaife, Tristan; Van Bodegom, Peter M.; De Kauwe, Martin G.; Keenan, Trevor F.; Joiner, Joanna; Lomas, Mark R.; MacBean, Natasha; Xu, Chongang; Yang, Xiaojuan;

Nonlinear Dynamics of Biofilm Growth on Sediment Surfaces

NASA Astrophysics Data System (ADS)

Molz, F. J.; Murdoch, L. C.; Faybishenko, B.

2013-12-01

Bioclogging often begins with the establishment of small colonies (microcolonies), which then form biofilms on the surfaces of a porous medium. These biofilm-porous media surfaces are not simple coatings of single microbes, but complex assemblages of cooperative and competing microbes, interacting with their chemical environment. This leads one to ask: what are the underlying dynamics involved with biofilm growth? To begin answering this question, we have extended the work of Kot et al. (1992, Bull. Mathematical Bio.) from a fully mixed chemostat to an idealized, one-dimensional, biofilm environment, taking into account a simple predator-prey microbial competition, with the prey feeding on a specified food source. With a variable (periodic) food source, Kot et al. (1992) were able to demonstrate chaotic dynamics in the coupled substrate-prey-predator system. Initially, deterministic chaos was thought by many to be mainly a mathematical phenomenon. However, several recent publications (e.g., Becks et al, 2005, Nature Letters; Graham et al. 2007, Int. Soc Microb. Eco. J.; Beninca et al., 2008, Nature Letters; Saleh, 2011, IJBAS) have brought together, using experimental studies and relevant mathematics, a breakthrough discovery that deterministic chaos is present in relatively simple biochemical systems. Two of us (Faybishenko and Molz, 2013, Procedia Environ. Sci)) have numerically analyzed a mathematical model of rhizosphere dynamics (Kravchenko et al., 2004, Microbiology) and detected patterns of nonlinear dynamical interactions supporting evidence of synchronized synergetic oscillations of microbial populations, carbon and oxygen concentrations driven by root exudation into a fully mixed system. In this study, we have extended the application of the Kot et al. model to investigate a spatially-dependent biofilm system. We will present the results of numerical simulations obtained using COMSOL Multi-Physics software, which we used to determine the nature of the complex dynamics. We found that complex dynamics occur even with a constant food supply maintained at the upstream boundary of the biofilm. Results will be presented along with a description of the model, including 3 coupled partial differential equations and examples of the localized and propagating nonlinear dynamics inherent in the system. Contrary to a common opinion that chaos in many mechanical systems is a type of instability, appearing when energy is added, we hypothesize, based on the results of our modeling, that chaos in biofilm dynamics and other microbial ecosystems is driven by a competitive decrease in the food supply (i.e., chemical energy). We also hypothesize that, somewhat paradoxically, this, in turn, may support a long-term system stability that could cause bioclogging in porous media.

Novel insight into the origin of the growth dynamics of sauropod dinosaurs.

PubMed

Cerda, Ignacio Alejandro; Chinsamy, Anusuya; Pol, Diego; Apaldetti, Cecilia; Otero, Alejandro; Powell, Jaime Eduardo; Martínez, Ricardo Nestor

2017-01-01

Sauropod dinosaurs include the largest terrestrial animals and are considered to have uninterrupted rapid rates of growth, which differs from their more basal relatives, which have a slower cyclical growth. Here we examine the bone microstructure of several sauropodomorph dinosaurs, including basal taxa, as well as the more derived sauropods. Although our results agree that the plesiomorphic condition for Sauropodomorpha is cyclical growth dynamics, we found that the hypothesized dichotomy between the growth patterns of basal and more derived sauropodomorphs is not supported. Here, we show that sauropod-like growth dynamics of uninterrupted rapid growth also occurred in some basal sauropodomorphs, and that some basal sauropods retained the plesiomorphic cyclical growth patterns. Among the sauropodomorpha it appears that the basal taxa exploited different growth strategies, but the more derived Eusauropoda successfully utilized rapid, uninterrupted growth strategies.

Novel insight into the origin of the growth dynamics of sauropod dinosaurs

PubMed Central

Cerda, Ignacio Alejandro; Chinsamy, Anusuya; Pol, Diego; Apaldetti, Cecilia; Otero, Alejandro; Martínez, Ricardo Nestor

2017-01-01

Sauropod dinosaurs include the largest terrestrial animals and are considered to have uninterrupted rapid rates of growth, which differs from their more basal relatives, which have a slower cyclical growth. Here we examine the bone microstructure of several sauropodomorph dinosaurs, including basal taxa, as well as the more derived sauropods. Although our results agree that the plesiomorphic condition for Sauropodomorpha is cyclical growth dynamics, we found that the hypothesized dichotomy between the growth patterns of basal and more derived sauropodomorphs is not supported. Here, we show that sauropod-like growth dynamics of uninterrupted rapid growth also occurred in some basal sauropodomorphs, and that some basal sauropods retained the plesiomorphic cyclical growth patterns. Among the sauropodomorpha it appears that the basal taxa exploited different growth strategies, but the more derived Eusauropoda successfully utilized rapid, uninterrupted growth strategies. PMID:28654696

Emotional inertia and psychological maladjustment.

PubMed

Kuppens, Peter; Allen, Nicholas B; Sheeber, Lisa B

2010-07-01

In this article, we examine the concept of emotional inertia as a fundamental property of the emotion dynamics that characterize psychological maladjustment. Emotional inertia refers to the degree to which emotional states are resistant to change. Because psychological maladjustment has been associated with both emotional underreactivity and ineffective emotion-regulation skills, we hypothesized that its overall emotion dynamics would be characterized by high levels of inertia. We provide evidence from two naturalistic studies that, using different methods, showed that the emotional fluctuations of individuals who exhibited low self-esteem (Study 1) and depression (Study 2) were characterized by higher levels of inertia in both positive and negative emotions than the emotional fluctuations of people who did not exhibit low self-esteem and depression. We also discuss the usefulness of the concept of emotional inertia as a hallmark of maladaptive emotion dynamics.

ACF7 regulates colonic permeability.

PubMed

Liang, Yong; Shi, Chenzhang; Yang, Jun; Chen, Hongqi; Xia, Yang; Zhang, Peng; Wang, Feng; Han, Huazhong; Qin, Huanlong

2013-04-01

Colonic paracellular permeability is regulated by various factors, including dynamics of the cytoskeleton. Recently, ACF7 has been found to play a critical role in cytoskeletal dynamics as an essential integrator. To elucidate the physiological importance of ACF7 and paracellular permeability, we conditionally knocked out ACF7 in the intestinal mucosa of mice. Histopathological findings indicated that ACF7 deficiency resulted in significant interstitial proliferation and columnar epithelial cell rearrangement. Decreased colonic paracellular permeability was detected using a Ussing chamber and the FITC-inulin method. In order to clarify the underlying mechanism, we further analyzed the expression levels of three important tight junction proteins. Downregulation of ZO-1, occludin and claudin-1 was identified. Immunofluorescence provided strong evidence that ZO-1, occludin and claudin-1 were weakly stained. We hypothesized that ACF7 regulates cytoskeleton dynamics to alter mucosal epithelial arrangement and colonic paracellular permeability.

The role of feedback information for calibration and attunement in perceiving length by dynamic touch.

PubMed

Withagen, Rob; Michaels, Claire F

2005-12-01

Two processes have been hypothesized to underlie improvement in perception: attunement and calibration. These processes were examined in a dynamic touch paradigm in which participants were asked to report the lengths of unseen, wielded rods differing in length, diameter, and material. Two experiments addressed whether feedback informs about the need for reattunement and recalibration. Feedback indicating actual length induced both recalibration and reattunement. Recalibration did not occur when feedback indicated only whether 2 rods were of the same length or of different lengths. Such feedback, however, did induce reattunement. These results suggest that attunement and calibration are dissociable processes and that feedback informs which is needed. The observed change in variable use has implications also for research on what mechanical variables underlie length perception by dynamic touch. (c) 2005 APA, all rights reserved.

CASSIA--a dynamic model for predicting intra-annual sink demand and interannual growth variation in Scots pine.

PubMed

Schiestl-Aalto, Pauliina; Kulmala, Liisa; Mäkinen, Harri; Nikinmaa, Eero; Mäkelä, Annikki

2015-04-01

The control of tree growth vs environment by carbon sources or sinks remains unresolved although it is widely studied. This study investigates growth of tree components and carbon sink-source dynamics at different temporal scales. We constructed a dynamic growth model 'carbon allocation sink source interaction' (CASSIA) that calculates tree-level carbon balance from photosynthesis, respiration, phenology and temperature-driven potential structural growth of tree organs and dynamics of stored nonstructural carbon (NSC) and their modifying influence on growth. With the model, we tested hypotheses that sink demand explains the intra-annual growth dynamics of the meristems, and that the source supply is further needed to explain year-to-year growth variation. The predicted intra-annual dimensional growth of shoots and needles and the number of cells in xylogenesis phases corresponded with measurements, whereas NSC hardly limited the growth, supporting the first hypothesis. Delayed GPP influence on potential growth was necessary for simulating the yearly growth variation, indicating also at least an indirect source limitation. CASSIA combines seasonal growth and carbon balance dynamics with long-term source dynamics affecting growth and thus provides a first step to understanding the complex processes regulating intra- and interannual growth and sink-source dynamics. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Self similarities in desalination dynamics and performance using capacitive deionization.

PubMed

Ramachandran, Ashwin; Hemmatifar, Ali; Hawks, Steven A; Stadermann, Michael; Santiago, Juan G

2018-09-01

Charge transfer and mass transport are two underlying mechanisms which are coupled in desalination dynamics using capacitive deionization (CDI). We developed simple reduced-order models based on a mixed reactor volume principle which capture the coupled dynamics of CDI operation using closed-form semi-analytical and analytical solutions. We use the models to identify and explore self-similarities in the dynamics among flow rate, current, and voltage for CDI cell operation including both charging and discharging cycles. The similarity approach identifies the specific combination of cell (e.g. capacitance, resistance) and operational parameters (e.g. flow rate, current) which determine a unique effluent dynamic response. We here demonstrate self-similarity using a conventional flow between CDI (fbCDI) architecture, and we hypothesize that our similarity approach has potential application to a wide range of designs. We performed an experimental study of these dynamics and used well-controlled experiments of CDI cell operation to validate and explore limits of the model. For experiments, we used a CDI cell with five electrode pairs and a standard flow between (electrodes) architecture. Guided by the model, we performed a series of experiments that demonstrate natural response of the CDI system. We also identify cell parameters and operation conditions which lead to self-similar dynamics under a constant current forcing function and perform a series of experiments by varying flowrate, currents, and voltage thresholds to demonstrate self-similarity. Based on this study, we hypothesize that the average differential electric double layer (EDL) efficiency (a measure of ion adsorption rate to EDL charging rate) is mainly dependent on user-defined voltage thresholds, whereas flow efficiency (measure of how well desalinated water is recovered from inside the cell) depends on cell volumes flowed during charging, which is determined by flowrate, current and voltage thresholds. Results of experiments strongly support this hypothesis. Results show that cycle efficiency and salt removal for a given flowrate and current are maximum when average EDL and flow efficiencies are approximately equal. We further explored a range of CC operations with varying flowrates, currents, and voltage thresholds using our similarity variables to highlight trade-offs among salt removal, energy, and throughput performance. Copyright © 2018 Elsevier Ltd. All rights reserved.

Size-Energy Relationships in Ecological Communities

PubMed Central

Sewall, Brent J.; Freestone, Amy L.; Hawes, Joseph E.; Andriamanarina, Ernest

2013-01-01

Hypotheses that relate body size to energy use are of particular interest in community ecology and macroecology because of their potential to facilitate quantitative predictions about species interactions and to clarify complex ecological patterns. One prominent size-energy hypothesis, the energetic equivalence hypothesis, proposes that energy use from shared, limiting resources by populations or size classes of foragers will be independent of body size. Alternative hypotheses propose that energy use will increase with body size, decrease with body size, or peak at an intermediate body size. Despite extensive study, however, size-energy hypotheses remain controversial, due to a lack of directly-measured data on energy use, a tendency to confound distinct scaling relationships, and insufficient attention to the ecological contexts in which predicted relationships are likely to occur. Our goal, therefore, was to directly evaluate size-energy hypotheses while clarifying how results would differ with alternate methods and assumptions. We comprehensively tested size-energy hypotheses in a vertebrate frugivore guild in a tropical forest in Madagascar. Our test of size-energy hypotheses, which is the first to examine energy intake directly, was consistent with the energetic equivalence hypothesis. This finding corresponds with predictions of metabolic theory and models of energy distribution in ecological communities, which imply that body size does not confer an advantage in competition for energy among populations or size classes of foragers. This result was robust to different assumptions about energy regulation. Our results from direct energy measurement, however, contrasted with those obtained with conventional methods of indirect inference from size-density relationships, suggesting that size-density relationships do not provide an appropriate proxy for size-energy relationships as has commonly been assumed. Our research also provides insights into mechanisms underlying local size-energy relationships and has important implications for predicting species interactions and for understanding the structure and dynamics of ecological communities. PMID:23950873

A New Role for Attentional Corticopetal Acetylcholine in Cortical Memory Dynamics

NASA Astrophysics Data System (ADS)

Fujii, Hiroshi; Kanamaru, Takashi; Aihara, Kazuyuki; Tsuda, Ichiro

2011-09-01

Although the role of corticopetal acetylcholine (ACh) in higher cognitive functions is increasingly recognized, the questions as (1) how ACh works in attention(s), memory dynamics and cortical state transitions, and also (2) why and how loss of ACh is involved in dysfunctions such as visual hallucinations in dementia with Lewy bodies and deficit of attention(s), are not well understood. From the perspective of a dynamical systems viewpoint, we hypothesize that transient ACh released under top-down attention serves to temporarily invoke attractor-like memories, while a background level of ACh reverses this process returning the dynamical nature of the memory structure back to attractor ruins (quasi-attractors). In fact, transient ACh loosens inhibitions of py ramidal neurons (PYRs) by P V+ fas t spiking (FS) i nterneurons, while a baseline ACh recovers inhibitory actions of P V+ FS. Attentional A Ch thus dynamically modifies brain's connectivity. Th e core of this process is in the depression of GABAergic inhibitory currents in PYRs due to muscarinic (probably M2 subtype) presyn aptic effects on GABAergic synapses of PV+ FS neurons

Cross-national comparisons of complex problem-solving strategies in two microworlds.

PubMed

Güss, C Dominik; Tuason, Ma Teresa; Gerhard, Christiane

2010-04-01

Research in the fields of complex problem solving (CPS) and dynamic decision making using microworlds has been mainly conducted in Western industrialized countries. This study analyzes the CPS process by investigating thinking-aloud protocols in five countries. Participants were 511 students from Brazil, Germany, India, the Philippines, and the United States who worked on two microworlds. On the basis of cultural-psychological theories, specific cross-national differences in CPS strategies were hypothesized. Following theories of situatedness of cognition, hypotheses about the specific frequency of problem-solving strategies in the two microworlds were developed. Results of the verbal protocols showed (a) modification of the theoretical CPS model, (b) task dependence of CPS strategies, and (c) cross-national differences in CPS strategies. Participants' CPS processes were particularly influenced by country-specific problem-solving strategies. Copyright © 2009 Cognitive Science Society, Inc.

Human Cognition and a Pile of Sand: A Discussion on Serial Correlations and Self-Organized Criticality

PubMed Central

Wagenmakers, Eric-Jan; Farrell, Simon; Ratcliff, Roger

2005-01-01

Recently, G. C. Van Orden, J. G. Holden, and M. T. Turvey (2003) proposed to abandon the conventional framework of cognitive psychology in favor of the framework of nonlinear dynamical systems theory. Van Orden et al. presented evidence that “purposive behavior originates in self-organized criticality” (p. 333). Here, the authors show that Van Orden et al.’s analyses do not test their hypotheses. Further, the authors argue that a confirmation of Van Orden et al.’s hypotheses would not have constituted firm evidence in support of their framework. Finally, the absence of a specific model for how self-organized criticality produces the observed behavior makes it very difficult to derive testable predictions. The authors conclude that the proposed paradigm shift is presently unwarranted. PMID:15702966

The intrapsychics of gender: a model of self-socialization.

PubMed

Tobin, Desiree D; Menon, Meenakshi; Menon, Madhavi; Spatta, Brooke C; Hodges, Ernest V E; Perry, David G

2010-04-01

This article outlines a model of the structure and the dynamics of gender cognition in childhood. The model incorporates 3 hypotheses featured in different contemporary theories of childhood gender cognition and unites them under a single theoretical framework. Adapted from Greenwald et al. (2002), the model distinguishes three constructs: gender identity, gender stereotypes, and attribute self-perceptions. The model specifies 3 causal processes among the constructs: Gender identity and stereotypes interactively influence attribute self-perceptions (stereotype emulation hypothesis); gender identity and attribute self-perceptions interactively influence gender stereotypes (stereotype construction hypothesis); and gender stereotypes and attribute self-perceptions interactively influence identity (identity construction hypothesis). The model resolves nagging ambiguities in terminology, organizes diverse hypotheses and empirical findings under a unifying conceptual umbrella, and stimulates many new research directions. PsycINFO Database Record (c) 2010 APA, all rights reserved.

MD Simulations of P-Type ATPases in a Lipid Bilayer System.

PubMed

Autzen, Henriette Elisabeth; Musgaard, Maria

2016-01-01

Molecular dynamics (MD) simulation is a computational method which provides insight on protein dynamics with high resolution in both space and time, in contrast to many experimental techniques. MD simulations can be used as a stand-alone method to study P-type ATPases as well as a complementary method aiding experimental studies. In particular, MD simulations have proved valuable in generating and confirming hypotheses relating to the structure and function of P-type ATPases. In the following, we describe a detailed practical procedure on how to set up and run a MD simulation of a P-type ATPase embedded in a lipid bilayer using software free of use for academics. We emphasize general considerations and problems typically encountered when setting up simulations. While full coverage of all possible procedures is beyond the scope of this chapter, we have chosen to illustrate the MD procedure with the Nanoscale Molecular Dynamics (NAMD) and the Visual Molecular Dynamics (VMD) software suites.

Emotion unfolded by motion: a role for parietal lobe in decoding dynamic facial expressions.

PubMed

Sarkheil, Pegah; Goebel, Rainer; Schneider, Frank; Mathiak, Klaus

2013-12-01

Facial expressions convey important emotional and social information and are frequently applied in investigations of human affective processing. Dynamic faces may provide higher ecological validity to examine perceptual and cognitive processing of facial expressions. Higher order processing of emotional faces was addressed by varying the task and virtual face models systematically. Blood oxygenation level-dependent activation was assessed using functional magnetic resonance imaging in 20 healthy volunteers while viewing and evaluating either emotion or gender intensity of dynamic face stimuli. A general linear model analysis revealed that high valence activated a network of motion-responsive areas, indicating that visual motion areas support perceptual coding for the motion-based intensity of facial expressions. The comparison of emotion with gender discrimination task revealed increased activation of inferior parietal lobule, which highlights the involvement of parietal areas in processing of high level features of faces. Dynamic emotional stimuli may help to emphasize functions of the hypothesized 'extended' over the 'core' system for face processing.

Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics

PubMed Central

Goldbogen, Jeremy A.

2017-01-01

Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct species, we show that mysticetes underwent a clade-wide shift in their mode of body size evolution during the Plio-Pleistocene. This transition, from Brownian motion-like dynamics to a trended random walk towards larger size, is temporally linked to the onset of seasonally intensified upwelling along coastal ecosystems. High prey densities resulting from wind-driven upwelling, rather than abundant resources alone, are the primary determinant of efficient foraging in extant mysticetes and Late Pliocene changes in ocean dynamics may have provided an ecological pathway to gigantism in multiple independent lineages. PMID:28539520

Modulation of Active Site Electronic Structure by the Protein Matrix to Control [NiFe] Hydrogenase Reactivity

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

Smith, Dayle MA; Raugei, Simone; Squier, Thomas C.

2014-09-30

Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere ligands that act to modify the geometry and physical properties of the active site metal centers. We carried out a combined set of classical molecular dynamics and quantum/classical mechanics calculations to provide quantitative estimates of how dynamic fluctuations of the active site within the protein matrix modulate the electronic structure at the catalytic center. Specifically we focused on the dynamics of the inner and outer coordination spheres of the cysteinate-bound Ni–Fe cluster in the catalytically active Ni-C state. There aremore » correlated movements of the cysteinate ligands and the surrounding hydrogen-bonding network, which modulate the electron affinity at the active site and the proton affinity of a terminal cysteinate. On the basis of these findings, we hypothesize a coupling between protein dynamics and electron and proton transfer reactions critical to dihydrogen production.« less

Modulation of active site electronic structure by the protein matrix to control [NiFe] hydrogenase reactivity.

PubMed

Smith, Dayle M A; Raugei, Simone; Squier, Thomas C

2014-11-21

Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere ligands that act to modify the geometry and physical properties of the active site metal centers. We carried out a combined set of classical molecular dynamics and quantum/classical mechanics calculations to provide quantitative estimates of how dynamic fluctuations of the active site within the protein matrix modulate the electronic structure at the catalytic center. Specifically we focused on the dynamics of the inner and outer coordination spheres of the cysteinate-bound Ni-Fe cluster in the catalytically active Ni-C state. There are correlated movements of the cysteinate ligands and the surrounding hydrogen-bonding network, which modulate the electron affinity at the active site and the proton affinity of a terminal cysteinate. On the basis of these findings, we hypothesize a coupling between protein dynamics and electron and proton transfer reactions critical to dihydrogen production.

Working memory dynamics bias the generation of beliefs: the influence of data presentation rate on hypothesis generation.

PubMed

Lange, Nicholas D; Thomas, Rick P; Buttaccio, Daniel R; Illingworth, David A; Davelaar, Eddy J

2013-02-01

Although temporal dynamics are inherent aspects of diagnostic tasks, few studies have investigated how various aspects of time course influence hypothesis generation. An experiment is reported that demonstrates that working memory dynamics operating during serial data acquisition bias hypothesis generation. The presentation rate (and order) of a sequence of serially presented symptoms was manipulated to be either fast (180 ms per symptom) or slow (1,500 ms per symptom) in a simulated medical diagnosis task. When the presentation rate was slow, participants chose the disease hypothesis consistent with the symptoms appearing later in the sequence. When the presentation rate was fast, however, participants chose the disease hypothesis consistent with the symptoms appearing earlier in the sequence, therefore representing a novel primacy effect. We predicted and account for this effect through competitive working memory dynamics governing information acquisition and the contribution of maintained information to the retrieval of hypotheses from long-term memory.

A prototypic mathematical model of the human hair cycle.

PubMed

Al-Nuaimi, Yusur; Goodfellow, Marc; Paus, Ralf; Baier, Gerold

2012-10-07

The human hair cycle is a complex, dynamic organ-transformation process during which the hair follicle repetitively progresses from a growth phase (anagen) to a rapid apoptosis-driven involution (catagen) and finally a relative quiescent phase (telogen) before returning to anagen. At present no theory satisfactorily explains the origin of the hair cycle rhythm. Based on experimental evidence we propose a prototypic model that focuses on the dynamics of hair matrix keratinocytes. We argue that a plausible feedback-control structure between two key compartments (matrix keratinocytes and dermal papilla) leads to dynamic instabilities in the population dynamics resulting in rhythmic hair growth. The underlying oscillation consists of an autonomous switching between two quasi-steady states. Additional features of the model, namely bistability and excitability, lead to new hypotheses about the impact of interventions on hair growth. We show how in silico testing may facilitate testing of candidate hair growth modulatory agents in human HF organ culture or in clinical trials. Copyright © 2012 Elsevier Ltd. All rights reserved.

Nonlinear vibrations and dynamic stability of viscoelastic orthotropic rectangular plates

NASA Astrophysics Data System (ADS)

Eshmatov, B. Kh.

2007-03-01

This paper describes the analyses of the nonlinear vibrations and dynamic stability of viscoelastic orthotropic plates. The models are based on the Kirchhoff-Love (K.L.) hypothesis and Reissner-Mindlin (R.M.) generalized theory (with the incorporation of shear deformation and rotatory inertia) in geometrically nonlinear statements. It provides justification for the choice of the weakly singular Koltunov-Rzhanitsyn type kernel, with three rheological parameters. In addition, the implication of each relaxation kernel parameter has been studied. To solve problems of viscoelastic systems with weakly singular kernels of relaxation, a numerical method has been used, based on quadrature formulae. With a combination of the Bubnov-Galerkin and the presented method, problems of nonlinear vibrations and dynamic stability in viscoelastic orthotropic rectangular plates have been solved, according to the K.L. and R.M. hypotheses. A comparison of the results obtained via these theories is also presented. In all problems, the convergence of the Bubnov-Galerkin method has been investigated. The implications of material viscoelasticity on vibration and dynamic stability are presented graphically.

Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics.

PubMed

Slater, Graham J; Goldbogen, Jeremy A; Pyenson, Nicholas D

2017-05-31

Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct species, we show that mysticetes underwent a clade-wide shift in their mode of body size evolution during the Plio-Pleistocene. This transition, from Brownian motion-like dynamics to a trended random walk towards larger size, is temporally linked to the onset of seasonally intensified upwelling along coastal ecosystems. High prey densities resulting from wind-driven upwelling, rather than abundant resources alone, are the primary determinant of efficient foraging in extant mysticetes and Late Pliocene changes in ocean dynamics may have provided an ecological pathway to gigantism in multiple independent lineages. © 2017 The Author(s).

Dynamic range adaptation in primary motor cortical populations

PubMed Central

Rasmussen, Robert G; Schwartz, Andrew; Chase, Steven M

2017-01-01

Neural populations from various sensory regions demonstrate dynamic range adaptation in response to changes in the statistical distribution of their input stimuli. These adaptations help optimize the transmission of information about sensory inputs. Here, we show a similar effect in the firing rates of primary motor cortical cells. We trained monkeys to operate a brain-computer interface in both two- and three-dimensional virtual environments. We found that neurons in primary motor cortex exhibited a change in the amplitude of their directional tuning curves between the two tasks. We then leveraged the simultaneous nature of the recordings to test several hypotheses about the population-based mechanisms driving these changes and found that the results are most consistent with dynamic range adaptation. Our results demonstrate that dynamic range adaptation is neither limited to sensory regions nor to rescaling of monotonic stimulus intensity tuning curves, but may rather represent a canonical feature of neural encoding. DOI: http://dx.doi.org/10.7554/eLife.21409.001 PMID:28417848

Coherence and population dynamics of chlorophyll excitations in FCP complex: Two-dimensional spectroscopy study

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

Butkus, Vytautas; Gelzinis, Andrius; Valkunas, Leonas

2015-06-07

Energy transfer processes and coherent phenomena in the fucoxanthin–chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of Q{sub y} transitions of chlorophylls a and c. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) a and fucoxanthin intramolecular vibrations dominating over the first few picoseconds. Closer inspection of the spectral region of the Q{submore » y} transition of Chl c revealed previously not identified, mutually non-interacting chlorophyll c states participating in femtosecond or picosecond energy transfer to the Chl a molecules. Consideration of separated coherent and incoherent dynamics allowed us to hypothesize the vibrations-assisted coherent energy transfer between Chl c and Chl a and the overall spatial arrangement of chlorophyll molecules.« less

Influence of static habitat attributes on local and regional Rocky intertidal community structure

USGS Publications Warehouse

Konar, B.; Iken, K.; Coletti, H.; Monson, Daniel H.; Weitzman, Ben P.

2016-01-01

Rocky intertidal communities are structured by local environmental drivers, which can be dynamic, fluctuating on various temporal scales, or static and not greatly varying across years. We examined the role of six static drivers (distance to freshwater, tidewater glacial presence, wave exposure, fetch, beach slope, and substrate composition) on intertidal community structure across the northern Gulf of Alaska. We hypothesized that community structure is less similar at the local scale compared with the regional scale, coinciding with static drivers being less similar on smaller than larger scales. We also hypothesized that static attributes mainly drive local biological community structure. For this, we surveyed five to six sites in each of the six regions in the mid and low intertidal strata. Across regions, static attributes were not consistently different and only small clusters of sites had similar attributes. Additionally, intertidal communities were less similar on the site compared with the region level. These results suggest that these biological communities are not strongly influenced by the local static attributes measured in this study. An alternative explanation is that static attributes among our regions are not different enough to influence the biological communities. This lack of evidence for a strong static driver may be a result of our site selection, which targeted rocky sheltered communities. This suggests that this habitat may be ideal to examine the influence of dynamic drivers. We recommend that future analyses of dynamic attributes may best be performed after analyses have demonstrated that sites do not differ in static attributes.

Non-degradative Ubiquitination of Protein Kinases

PubMed Central

Ball, K. Aurelia; Johnson, Jeffrey R.; Lewinski, Mary K.; Guatelli, John; Verschueren, Erik; Krogan, Nevan J.; Jacobson, Matthew P.

2016-01-01

Growing evidence supports other regulatory roles for protein ubiquitination in addition to serving as a tag for proteasomal degradation. In contrast to other common post-translational modifications, such as phosphorylation, little is known about how non-degradative ubiquitination modulates protein structure, dynamics, and function. Due to the wealth of knowledge concerning protein kinase structure and regulation, we examined kinase ubiquitination using ubiquitin remnant immunoaffinity enrichment and quantitative mass spectrometry to identify ubiquitinated kinases and the sites of ubiquitination in Jurkat and HEK293 cells. We find that, unlike phosphorylation, ubiquitination most commonly occurs in structured domains, and on the kinase domain, ubiquitination is concentrated in regions known to be important for regulating activity. We hypothesized that ubiquitination, like other post-translational modifications, may alter the conformational equilibrium of the modified protein. We chose one human kinase, ZAP-70, to simulate using molecular dynamics with and without a monoubiquitin modification. In Jurkat cells, ZAP-70 is ubiquitinated at several sites that are not sensitive to proteasome inhibition and thus may have other regulatory roles. Our simulations show that ubiquitination influences the conformational ensemble of ZAP-70 in a site-dependent manner. When monoubiquitinated at K377, near the C-helix, the active conformation of the ZAP-70 C-helix is disrupted. In contrast, when monoubiquitinated at K476, near the kinase hinge region, an active-like ZAP-70 C-helix conformation is stabilized. These results lead to testable hypotheses that ubiquitination directly modulates kinase activity, and that ubiquitination is likely to alter structure, dynamics, and function in other protein classes as well. PMID:27253329

Potential of new machine learning methods for understanding long-term interannual variability of carbon and energy fluxes and states from site to global scale

NASA Astrophysics Data System (ADS)

Reichstein, M.; Jung, M.; Bodesheim, P.; Mahecha, M. D.; Gans, F.; Rodner, E.; Camps-Valls, G.; Papale, D.; Tramontana, G.; Denzler, J.; Baldocchi, D. D.

2016-12-01

Machine learning tools have been very successful in describing and predicting instantaneous climatic influences on the spatial and seasonal variability of biosphere-atmosphere exchange, while interannual variability is harder to model (e.g. Jung et al. 2011, JGR Biogeosciences). Here we hypothesize that innterannual variability is harder to describe for two reasons. 1) The signal-to-noise ratio in both, predictors (e.g. remote sensing) and target variables (e.g. net ecosystem exchange) is relatively weak, 2) The employed machine learning methods do not sufficiently account for dynamic lag and carry-over effects. In this presentation we can largely confirm both hypotheses: 1) We show that based on FLUXNET data and an ensemble of machine learning methods we can arrive at estimates of global NEE that correlate well with the residual land sink overall and CO2 flux inversions over latitudinal bands. Furthermore these results highlight the importance of variations in water availability for variations in carbon fluxes locally, while globally, as a scale-emergent property, tropical temperatures correlate well with the atmospheric CO2 growth rate, because of spatial anticorrelation and compensation of water availability. 2) We evidence with synthetic and real data that machine learning methods with embed dynamic memory effects of the system such as recurrent neural networks (RNNs) are able to better capture lag and carry-over effect which are caused by dynamic carbon pools in vegetation and soils. For these methods, long-term replicate observations are an essential asset.

Bone laminarity in the avian forelimb skeleton and its relationship to flight mode: testing functional interpretations.

PubMed

Simons, Erin L R; O'connor, Patrick M

2012-03-01

Wing bone histology in three species of birds was characterized in order to test hypotheses related to the relationship between skeletal microstructure and inferred wing loading during flight. Data on the degree of laminarity (the proportion of circular vascular canals) and the occurrence of secondary osteons were obtained from three species that utilize different primary flight modes: the Double-crested cormorant, a continuous flapper; the Brown pelican, a static soarer; and the Laysan albatross, a dynamic soarer. Laminarity indices were calculated for four quadrants for each of the three main wing elements. Ulnae and carpometacarpi were predicted to exhibit quadrant specific patterns of laminarity due to hypothesized differences in locally applied loads related to the attachment of flight feathers. However, few differences among the quadrants were identified. No significant differences were identified among the three elements, which is notable as different bones are likely experiencing different loading conditions. These results do not support the concept of bone functional adaptation in the primary structure of the wing elements. Significant differences in laminarity were found among the three primary flight modes. The dynamic soaring birds exhibited significantly lower laminarity than the flapping and static soaring birds. These results support the proposed hypothesis that laminarity is an adaptation for resisting torsional loading. This may be explained by overall wing shape: whereas dynamic soaring birds have long slender wings, flappers and static soaring birds have broader wings with a larger wing chord that would necessarily impart a higher torsional moment on the feather-bearing bones. Copyright © 2012 Wiley Periodicals, Inc.

Influences of climate, fire, and topography on contemporary age structure patterns of Douglas-fir at 205 old forest sites in western Oregon

Treesearch

Nathan J. Poage; Peter J. Weisberg; Peter C. Impara; John C. Tappeiner; Thomas S. Sensenig

2009-01-01

Knowledge of forest development is basic to understanding the ecology, dynamics, and management of forest ecosystems. We hypothesized that the age structure patterns of Douglas-fir at 205 old forest sites in western Oregon are extremely variable with long and (or) multiple establishment periods common, and that these patterns reflect variation in regional-scale climate...

Identification of the feedforward component in manual control with predictable target signals.

PubMed

Drop, Frank M; Pool, Daan M; Damveld, Herman J; van Paassen, Marinus M; Mulder, Max

2013-12-01

In the manual control of a dynamic system, the human controller (HC) often follows a visible and predictable reference path. Compared with a purely feedback control strategy, performance can be improved by making use of this knowledge of the reference. The operator could effectively introduce feedforward control in conjunction with a feedback path to compensate for errors, as hypothesized in literature. However, feedforward behavior has never been identified from experimental data, nor have the hypothesized models been validated. This paper investigates human control behavior in pursuit tracking of a predictable reference signal while being perturbed by a quasi-random multisine disturbance signal. An experiment was done in which the relative strength of the target and disturbance signals were systematically varied. The anticipated changes in control behavior were studied by means of an ARX model analysis and by fitting three parametric HC models: two different feedback models and a combined feedforward and feedback model. The ARX analysis shows that the experiment participants employed control action on both the error and the target signal. The control action on the target was similar to the inverse of the system dynamics. Model fits show that this behavior can be modeled best by the combined feedforward and feedback model.

Convection and Dynamo Action in Ice Giant Dynamo Models with Electrical Conductivity Stratification

NASA Astrophysics Data System (ADS)

Soderlund, K. M.; Featherstone, N. A.; Heimpel, M. H.; Aurnou, J. M.

2017-12-01

Uranus and Neptune are relatively unexplored, yet critical for understanding the physical and chemical processes that control the behavior and evolution of giant planets. Because their multipolar magnetic fields, three-jet zonal winds, and extreme energy balances are distinct from other planets in our Solar System, the ice giants provide a unique opportunity to test hypotheses for internal dynamics and magnetic field generation. While it is generally agreed that dynamo action in the ionic ocean generates their magnetic fields, the mechanisms that control the morphology, strength, and evolution of the dynamos - which are likely distinct from those in the gas giants and terrestrial planets - are not well understood. We hypothesize that the dynamos and zonal winds are dynamically coupled and argue that their characteristics are a consequence of quasi-three-dimensional turbulence in their interiors. Here, we will present new dynamo simulations with an inner electrically conducting region and outer electrically insulating layer to self-consistently couple the ionic oceans and molecular envelopes of these planets. For each simulation, the magnetic field morphology and amplitude, zonal flow profile, and internal heat flux pattern will be compared against corresponding observations of Uranus and Neptune. We will also highlight how these simulations will both contribute to and benefit from a future ice giant mission.

Inter-subject phase synchronization for exploratory analysis of task-fMRI.

PubMed

Bolt, Taylor; Nomi, Jason S; Vij, Shruti G; Chang, Catie; Uddin, Lucina Q

2018-08-01

Analysis of task-based fMRI data is conventionally carried out using a hypothesis-driven approach, where blood-oxygen-level dependent (BOLD) time courses are correlated with a hypothesized temporal structure. In some experimental designs, this temporal structure can be difficult to define. In other cases, experimenters may wish to take a more exploratory, data-driven approach to detecting task-driven BOLD activity. In this study, we demonstrate the efficiency and power of an inter-subject synchronization approach for exploratory analysis of task-based fMRI data. Combining the tools of instantaneous phase synchronization and independent component analysis, we characterize whole-brain task-driven responses in terms of group-wise similarity in temporal signal dynamics of brain networks. We applied this framework to fMRI data collected during performance of a simple motor task and a social cognitive task. Analyses using an inter-subject phase synchronization approach revealed a large number of brain networks that dynamically synchronized to various features of the task, often not predicted by the hypothesized temporal structure of the task. We suggest that this methodological framework, along with readily available tools in the fMRI community, provides a powerful exploratory, data-driven approach for analysis of task-driven BOLD activity. Copyright © 2018 Elsevier Inc. All rights reserved.

A new perspective on the growth pattern of the Wandering Albatross (Diomedea exulans) through DEB theory

NASA Astrophysics Data System (ADS)

Teixeira, Carlos M. G. L.; Sousa, Tânia; Marques, Gonçalo M.; Domingos, Tiago; Kooijman, Sebastiaan A. L. M.

2014-11-01

The Wandering Albatross (Diomedea exulans) and other seabirds exhibit a growing pattern that includes a period of body mass decrease before fledging. Several hypotheses have been suggested to explain it without success. We hypothesized that: 1) chicks and adults have similar metabolic traits regulating assimilation, growth and maturation; 2) there is a difference in locomotion effort between chicks and adults, and 3) chicks are exposed to a decline in food availability before fledging. This set of hypotheses allows for an energy surplus to be available and stored in reserve during the first months of development, explaining the mass recession that starts before fledging and the fact that adults keep a lower weight than fledglings, throughout the rest of their life span. To test this set of hypotheses we applied the Dynamic Energy Budget (DEB) theory. Using a small set of life-history traits and growth curves we parameterized the DEB standard model. We confirmed this set of hypotheses and estimated the pattern of decline in food availability that explains mass recession. An assessment of the daily energy intake was also performed. The implications related to that energy flux and diet composition are discussed based on current knowledge. The DEB model for the Wandering Albatross also provided estimates for the adult daily food ingested by adults (464.06 kJ kg- 1 d- 1), fasting capacity (25 d), Field Metabolic Rate (4.29 W kg- 1) and resting metabolic rate (2.87 W kg- 1). These values are consistent with the averages obtained in the field, suggesting that DEB may be useful to provide good estimations on a broader scale.

Recruitment processes in Baltic sprat - A re-evaluation of GLOBEC Germany hypotheses

NASA Astrophysics Data System (ADS)

Voss, Rüdiger; Peck, Myron A.; Hinrichsen, Hans-Harald; Clemmesen, Catriona; Baumann, Hannes; Stepputtis, Daniel; Bernreuther, Matthias; Schmidt, Jörn O.; Temming, Axel; Köster, Fritz W.

2012-12-01

The GLOBEC Germany program (2002-2007) had the ambitious goal to resolve the processes impacting the recruitment dynamics of Baltic sprat (Sprattus sprattus L.) by examining various factors affecting early life history stages. At the start of the research program, a number of general recruitment hypotheses were formulated, i.e. focusing on (1) predation, (2) food availability, (3) physical parameters, (4) the impact of current systems, and finally (5) the importance of top-down vs bottom-up effects. The present study synthesizes the results of field sampling (2002 and 2003), laboratory experiments, and modeling studies to re-evaluate these hypotheses for the Baltic sprat stock. Recruitment success was quite different in the 2 years investigated. Despite a lower spawning stock biomass in 2003, the total number of recruits was almost 2-fold higher that year compared to 2002. The higher recruitment success in 2003 could be attributed to enhanced survival success during the post-larval/juvenile stage, a life phase that appears to be critical for recruitment dynamics. In the state of the Baltic ecosystem during the period of investigation, we consider bottom-up control (e.g. temperature, prey abundance) to be more important than top-down control (predation mortality). This ranking in importance does not vary seasonally. Prevailing water circulation patterns and the transport dynamics of larval cohorts have a strong influence on sprat recruitment success. Pronounced transport to coastal areas is detrimental for year-class strength particularly at high sprat stock sizes. A suggested mechanism is density-dependant regulation of survival via intra- and inter-specific competition for prey in coastal areas. A documented change in larval vertical migration behavior between the early 1990s and early 2000s increased the transport potential to the coast, strengthening the coupling between inter-annual differences in the magnitude and direction of wind-driven surface currents and year-to-year changes in reproductive success. However, due to the strong linkages and feed-back loops in the Baltic Sea food web, the most robust projections of the future strength of the Baltic sprat stock will need to take into account climate-driven changes in both abiotic (e.g., drift trajectories) and biotic (trophodynamic) factors. Although our understanding of processes affecting pre-recruit (larval) growth and survival has been advanced by the integrated research conducted within the GLOBEC Germany program, key mechanisms potentially affecting life stages outside of the spawning basins remain to be explored including the dynamics of coastal habitats of juveniles and the feeding and overwintering grounds of adults.

Coagulation of particles in Saturn's rings - Measurements of the cohesive force of water frost

NASA Technical Reports Server (NTRS)

Hatzes, A. P.; Bridges, F.; Lin, D. N. C.; Sachtjen, S.

1991-01-01

Experimental data are presented on the sticking force of water ice particles which are indicative of the role that the cohesive properties of such particles could play in the dynamics of Saturn ring particles. Sticking forces are dependent on particle impact velocities; a 'Velcro' model is devised to describe the surface structure involved in sticking. The data indicate that below the critical impact velocity of about 0.03 cm/sec, particle cohesion always occurs. Due to the optical depth of micron-sized grains in the Saturn rings, particles are hypothesized to be coated with a layer of frost which will render cohesion an important ring-dynamics process.

Creativity, information, and consciousness: The information dynamics of thinking.

PubMed

Wiggins, Geraint A

2018-05-07

This paper presents a theory of the basic operation of mind, Information Dynamics of Thinking, which is intended for computational implementation and thence empirical testing. It is based on the information theory of Shannon, and treats the mind/brain as an information processing organ that aims to be information-efficient, in that it predicts its world, so as to use information efficiently, and regularly re-represents it, so as to store information efficiently. The theory is presented in context of a background review of various research areas that impinge upon its development. Consequences of the theory and testable hypotheses arising from it are discussed. Copyright © 2018. Published by Elsevier B.V.

Complex dynamics at the interface between wild and domestic viruses of finfish

USGS Publications Warehouse

Kurath, G.; Winton, J.

2011-01-01

Viral traffic occurs readily between wild and domesticated stocks of finfish because aquatic environments have greater connectivity than their terrestrial counterparts and because the global expansion and dynamic nature of intensive aquaculture provide multiple pathways of transmission and unique drivers of virus adaptation. Supported by examples from the literature, we provide reasons why viruses move from wild fish reservoirs to infect domestic fish in aquaculture more readily than 'domestic' viruses move across the interface to infect wild stocks. We also hypothesize that 'wild' viruses moving across the interface to domestic populations of finfish are more frequently associated with disease outbreaks and host switches compared to domestic viruses that cross the interface to infect wild fish.

Intracellular calcium dynamics permit a Purkinje neuron model to perform toggle and gain computations upon its inputs

PubMed Central

Forrest, Michael D.

2014-01-01

Without synaptic input, Purkinje neurons can spontaneously fire in a repeating trimodal pattern that consists of tonic spiking, bursting and quiescence. Climbing fiber input (CF) switches Purkinje neurons out of the trimodal firing pattern and toggles them between a tonic firing and a quiescent state, while setting the gain of their response to Parallel Fiber (PF) input. The basis to this transition is unclear. We investigate it using a biophysical Purkinje cell model under conditions of CF and PF input. The model can replicate these toggle and gain functions, dependent upon a novel account of intracellular calcium dynamics that we hypothesize to be applicable in real Purkinje cells. PMID:25191262

Neuromodulation, Emotional Feelings and Affective Disorders

PubMed Central

Wang, Fushun; Pereira, Alfredo

2016-01-01

Affective disorders such as anxiety, phobia and depression are a leading cause of disabilities worldwide. Monoamine neuromodulators are used to treat most of them, with variable degrees of efficacy. Here, we review and interpret experimental findings about the relation of neuromodulation and emotional feelings, in pursuit of two goals: (a) to improve the conceptualisation of affective/emotional states, and (b) to develop a descriptive model of basic emotional feelings related to the actions of neuromodulators. In this model, we hypothesize that specific neuromodulators are effective for basic emotions. The model can be helpful for mental health professionals to better understand the affective dynamics of persons and the actions of neuromodulators - and respective psychoactive drugs - on this dynamics. PMID:28031622

Evidence of Chinese income dynamics and its effects on income scaling law

NASA Astrophysics Data System (ADS)

Xu, Yan; Wang, Yougui; Tao, Xiaobo; Ližbetinová, Lenka

2017-12-01

With personal annual income data of 5 consecutive years (1998-2002) from CHIPS, dynamic characteristics of Chinese income are studied, especially two hypotheses of time reversal symmetry and independent growth rate are tested. In high income regions, an increasing trend of the standard deviation of income growth rate is observed, which means independent growth rate hypothesis fails to hold. This empirical finding is designed as a new mechanism and added into Gibrat's model, which yields a distribution with a power-law tail. Our model's simulation result shows that increasing variance of income growth rates for higher income regions is the key ingredient to get the power-law tail.

Isotrope und homogene Materie - Kosmen; On Dynamics and Thermodynamics of Isotropic Matter-Universes

NASA Astrophysics Data System (ADS)

Treder, H.-J.

Die Dynamik und Thermodynamik großer kosmischer Systeme ist fast unabhängig von den besonderen Theorien über die Gravitation. Nur die Feinstruktur der Kosmologie und Kosmonogie reflektiert die speziellen Hypothesen. Diese Neutralität gegenüber den konkreten Gravodynamiken ist die Konsequenz der fundamentalen Eigenschaften der Gravitation: Der Prinzipien der Äquivalenz von Trägheit und Schwere. The dynamics and thermodynamics of great cosmical systems are nearly independent of the theory of gravitation and only the fine-structure of cosmogony and cosmology reflects the special hypotheses.The neutrality against the concret gravodynamics is a consequence of the fundamental properties of gravitation: the principlies of equivalence of gravity and inertia.

Engineering dynamical control of cell fate switching using synthetic phospho-regulons

PubMed Central

Gordley, Russell M.; Williams, Reid E.; Bashor, Caleb J.; Toettcher, Jared E.; Yan, Shude; Lim, Wendell A.

2016-01-01

Many cells can sense and respond to time-varying stimuli, selectively triggering changes in cell fate only in response to inputs of a particular duration or frequency. A common motif in dynamically controlled cells is a dual-timescale regulatory network: although long-term fate decisions are ultimately controlled by a slow-timescale switch (e.g., gene expression), input signals are first processed by a fast-timescale signaling layer, which is hypothesized to filter what dynamic information is efficiently relayed downstream. Directly testing the design principles of how dual-timescale circuits control dynamic sensing, however, has been challenging, because most synthetic biology methods have focused solely on rewiring transcriptional circuits, which operate at a single slow timescale. Here, we report the development of a modular approach for flexibly engineering phosphorylation circuits using designed phospho-regulon motifs. By then linking rapid phospho-feedback with slower downstream transcription-based bistable switches, we can construct synthetic dual-timescale circuits in yeast in which the triggering dynamics and the end-state properties of the ON state can be selectively tuned. These phospho-regulon tools thus open up the possibility to engineer cells with customized dynamical control. PMID:27821768

Dealing with Organizational Double Binds: Three-way Interactive Effects of Role Stressors and Coping on Worker Exhaustion.

PubMed

Hornung, Severin; Lampert, Bettina; Glaser, Jürgen

2016-04-01

Based on theory regarding the dynamics of organizational double binds, hypotheses were developed about interactive effects of role conflict, role ambiguity, and coping on psychological exhaustion. Hypotheses were tested in a sample of 948 civil servants employed by a government administration in Germany. The sample included 250 (26.4%) women (M age = 43.6 year, SD = 8.3) and average organizational tenure was 17.1 year (SD = 10.0). Moderated multiple regression supported the two hypothesized three-way interactions. Under conditions of high role conflict and high role ambiguity, exhaustion was lower in workers reporting high control coping than in workers reporting low control coping. Under conditions of high role conflict and high role ambiguity, worker exhaustion was more pronounced when support coping was high than when it was low. Problem-focused control coping seems crucial to maintain mental health in dealing with contradictory and unclear work role expectations. Emotion-focused support coping appears symptomatic of prolonged involvement in psychologically dysfunctional work situations that cannot otherwise be addressed. Implications are discussed in the context of growing awareness of the contradictory demands organizations impose on employees. © The Author(s) 2016.

When seeking influences believing and promotes posttraumatic adaptation.

PubMed

Smith, Andrew J; Donlon, Katharine; Anderson, Scott R; Hughes, Michael; Jones, Russell T

2015-01-01

Theory and evidence link social support processes and self-efficacy appraisals in the promotion of adaptation following traumatic events. Dynamic causal processes, however, have not been examined longitudinally or in the context of mass-violence. This study tested whether quantity of social support seeking indirectly reduced distress severity among student survivors of mass university shootings. Hypotheses specified that the indirect effects of social support seeking on distress severity would occur through positively influencing perceived social support and self-efficacy, and that these effects would emerge and become stronger as posttraumatic stress symptom severity increased. Path analysis via Mplus 7.2 was used to test the hypothesized moderated-serial-mediation model (conditional indirect effects). The sample (N=1191) consisted of students enrolled at Virginia Tech during the 16 April 2007 shootings. Data were collected via online surveys at two time points, 3-4 months and 1-year post-shootings. Hypotheses were supported, showing that the indirect effects of social support seeking on distress reduction occurred through perceived social support, which in turn influenced self-efficacy. These effects emerged and grew in strength as PTS severity increased. Clinical implications, including the need to consider contextual determinants of posttraumatic recovery, are discussed.

Impaired social brain network for processing dynamic facial expressions in autism spectrum disorders.

PubMed

Sato, Wataru; Toichi, Motomi; Uono, Shota; Kochiyama, Takanori

2012-08-13

Impairment of social interaction via facial expressions represents a core clinical feature of autism spectrum disorders (ASD). However, the neural correlates of this dysfunction remain unidentified. Because this dysfunction is manifested in real-life situations, we hypothesized that the observation of dynamic, compared with static, facial expressions would reveal abnormal brain functioning in individuals with ASD.We presented dynamic and static facial expressions of fear and happiness to individuals with high-functioning ASD and to age- and sex-matched typically developing controls and recorded their brain activities using functional magnetic resonance imaging (fMRI). Regional analysis revealed reduced activation of several brain regions in the ASD group compared with controls in response to dynamic versus static facial expressions, including the middle temporal gyrus (MTG), fusiform gyrus, amygdala, medial prefrontal cortex, and inferior frontal gyrus (IFG). Dynamic causal modeling analyses revealed that bi-directional effective connectivity involving the primary visual cortex-MTG-IFG circuit was enhanced in response to dynamic as compared with static facial expressions in the control group. Group comparisons revealed that all these modulatory effects were weaker in the ASD group than in the control group. These results suggest that weak activity and connectivity of the social brain network underlie the impairment in social interaction involving dynamic facial expressions in individuals with ASD.

Dynamics of safety performance and culture: a group model building approach.

PubMed

Goh, Yang Miang; Love, Peter E D; Stagbouer, Greg; Annesley, Chris

2012-09-01

The management of occupational health and safety (OHS) including safety culture interventions is comprised of complex problems that are often hard to scope and define. Due to the dynamic nature and complexity of OHS management, the concept of system dynamics (SD) is used to analyze accident prevention. In this paper, a system dynamics group model building (GMB) approach is used to create a causal loop diagram of the underlying factors influencing the OHS performance of a major drilling and mining contractor in Australia. While the organization has invested considerable resources into OHS their disabling injury frequency rate (DIFR) has not been decreasing. With this in mind, rich individualistic knowledge about the dynamics influencing the DIFR was acquired from experienced employees with operations, health and safety and training background using a GMB workshop. Findings derived from the workshop were used to develop a series of causal loop diagrams that includes a wide range of dynamics that can assist in better understanding the causal influences OHS performance. The causal loop diagram provides a tool for organizations to hypothesize the dynamics influencing effectiveness of OHS management, particularly the impact on DIFR. In addition the paper demonstrates that the SD GMB approach has significant potential in understanding and improving OHS management. Copyright © 2011 Elsevier Ltd. All rights reserved.

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq

PubMed Central

Ramsköld, Daniel; Deng, Qiaolin; Johnsson, Per; Michaëlsson, Jakob; Frisén, Jonas; Sandberg, Rickard

2016-01-01

Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vivo. Here, we used allele-sensitive single-cell RNA-seq on clonal primary mouse fibroblasts and in vivo human CD8+ T-cells to dissect clonal and dynamic monoallelic expression patterns. Dynamic aRME affected a considerable portion of the cells’ transcriptomes, with levels dependent on the cells’ transcriptional activity. Importantly, clonal aRME was detected but was surprisingly scarce (<1% of genes) and affected mainly the most low-expressed genes. Consequently, the overwhelming portion of aRME occurs transiently within individual cells and patterns of aRME are thus primarily scattered throughout somatic cell populations rather than, as previously hypothesized, confined to patches of clonally related cells. PMID:27668657

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.

PubMed

Reinius, Björn; Mold, Jeff E; Ramsköld, Daniel; Deng, Qiaolin; Johnsson, Per; Michaëlsson, Jakob; Frisén, Jonas; Sandberg, Rickard

2016-11-01

Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vivo. Here we used allele-sensitive single-cell RNA-seq on clonal primary mouse fibroblasts and freshly isolated human CD8 + T cells to dissect clonal and dynamic monoallelic expression patterns. Dynamic aRME affected a considerable portion of the cells' transcriptomes, with levels dependent on the cells' transcriptional activity. Notably, clonal aRME was detected, but it was surprisingly scarce (<1% of genes) and mainly affected the most weakly expressed genes. Consequently, the overwhelming majority of aRME occurs transiently within individual cells, and patterns of aRME are thus primarily scattered throughout somatic cell populations rather than, as previously hypothesized, confined to patches of clonally related cells.

Effects of Dynamic Topography on the Cenozoic Carbonate Compensation Depth

NASA Astrophysics Data System (ADS)

Campbell, Siobhan M.; Moucha, Robert; Derry, Louis A.; Raymo, Maureen E.

2018-04-01

Reconstructions of the carbonate compensation depth (CCD) in the past have been used to inform hypotheses about the nature of weathering, tectonics, climate change, and the major ion content of the world's oceans over the Cenozoic. These reconstructions are sensitive to uncertainties in the input data, in particular, the paleodepth estimates of sediment cores. Here we propose that a significant, previously unconsidered contributor to uncertainties in paleodepth estimates is from dynamic topography produced by radial stresses exerted on the Earth's surface by the convecting mantle; these stresses can warp the ocean floor by hundreds of meters over broad regions and also vary significantly over millions of years. We present new reconstructions of the equatorial Pacific and Indian Ocean CCDs over the last 30 and 23 Myr, respectively, which demonstrate an overall deepening trend since the Miocene, and illustrate the possible effect of long-term changes in dynamic topography on these reconstructions.

Intramolecular Hydrogen Bonding Restricts Gd-Aqua-Ligand Dynamics [The Day the Water Stood Still: Intramolecular Hydrogen Bonding to Restrict Gd-Aqua Ligand Dynamics

DOE PAGES

Boros, Eszter; Srinivas, Raja; Kim, Hee -Kyung; ...

2017-04-11

Aqua ligands can undergo rapid internal rotation about the M-O bond. For magnetic resonance contrast agents, this rotation results in diminished relaxivity. Herein, we show that an intramolecular hydrogen bond to the aqua ligand can reduce this internal rotation and increase relaxivity. Molecular modeling was used to design a series of four Gd complexes capable of forming an intramolecular H-bond to the coordinated water ligand, and these complexes had anomalously high relaxivities compared to similar complexes lacking a H-bond acceptor. Molecular dynamics simulations supported the formation of a stable intramolecular H-bond, while alternative hypotheses that could explain the higher relaxivitymore » were systematically ruled out. Finally, intramolecular H-bonding represents a useful strategy to limit internal water rotational motion and increase relaxivity of Gd complexes.« less

A quantitative model of honey bee colony population dynamics.

PubMed

Khoury, David S; Myerscough, Mary R; Barron, Andrew B

2011-04-18

Since 2006 the rate of honey bee colony failure has increased significantly. As an aid to testing hypotheses for the causes of colony failure we have developed a compartment model of honey bee colony population dynamics to explore the impact of different death rates of forager bees on colony growth and development. The model predicts a critical threshold forager death rate beneath which colonies regulate a stable population size. If death rates are sustained higher than this threshold rapid population decline is predicted and colony failure is inevitable. The model also predicts that high forager death rates draw hive bees into the foraging population at much younger ages than normal, which acts to accelerate colony failure. The model suggests that colony failure can be understood in terms of observed principles of honey bee population dynamics, and provides a theoretical framework for experimental investigation of the problem.

Inferring collective dynamical states from widely unobserved systems.

PubMed

Wilting, Jens; Priesemann, Viola

2018-06-13

When assessing spatially extended complex systems, one can rarely sample the states of all components. We show that this spatial subsampling typically leads to severe underestimation of the risk of instability in systems with propagating events. We derive a subsampling-invariant estimator, and demonstrate that it correctly infers the infectiousness of various diseases under subsampling, making it particularly useful in countries with unreliable case reports. In neuroscience, recordings are strongly limited by subsampling. Here, the subsampling-invariant estimator allows to revisit two prominent hypotheses about the brain's collective spiking dynamics: asynchronous-irregular or critical. We identify consistently for rat, cat, and monkey a state that combines features of both and allows input to reverberate in the network for hundreds of milliseconds. Overall, owing to its ready applicability, the novel estimator paves the way to novel insight for the study of spatially extended dynamical systems.

Characterizing RNA ensembles from NMR data with kinematic models

PubMed Central

Fonseca, Rasmus; Pachov, Dimitar V.; Bernauer, Julie; van den Bedem, Henry

2014-01-01

Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention. PMID:25114056

Mitochondrial Fusion/Fission, Transport and Autophagy in Parkinson's Disease: When Mitochondria Get Nasty

PubMed Central

Arduíno, Daniela M.; Esteves, A. Raquel; Cardoso, Sandra M.

2011-01-01

Understanding the molecular basis of Parkinson's disease (PD) has proven to be a major challenge in the field of neurodegenerative diseases. Although several hypotheses have been proposed to explain the molecular mechanisms underlying the pathogenesis of PD, a growing body of evidence has highlighted the role of mitochondrial dysfunction and the disruption of the mechanisms of mitochondrial dynamics in PD and other parkinsonian disorders. In this paper, we comment on the recent advances in how changes in the mitochondrial function and mitochondrial dynamics (fusion/fission, transport, and clearance) contribute to neurodegeneration, specifically focusing on PD. We also evaluate the current controversies in those issues and discuss the role of fusion/fission dynamics in the mitochondrial lifecycle and maintenance. We propose that cellular demise and neurodegeneration in PD are due to the interplay between mitochondrial dysfunction, mitochondrial trafficking disruption, and impaired autophagic clearance. PMID:21403911

Mitochondrial fusion/fission, transport and autophagy in Parkinson's disease: when mitochondria get nasty.

PubMed

Arduíno, Daniela M; Esteves, A Raquel; Cardoso, Sandra M

2011-02-20

Understanding the molecular basis of Parkinson's disease (PD) has proven to be a major challenge in the field of neurodegenerative diseases. Although several hypotheses have been proposed to explain the molecular mechanisms underlying the pathogenesis of PD, a growing body of evidence has highlighted the role of mitochondrial dysfunction and the disruption of the mechanisms of mitochondrial dynamics in PD and other parkinsonian disorders. In this paper, we comment on the recent advances in how changes in the mitochondrial function and mitochondrial dynamics (fusion/fission, transport, and clearance) contribute to neurodegeneration, specifically focusing on PD. We also evaluate the current controversies in those issues and discuss the role of fusion/fission dynamics in the mitochondrial lifecycle and maintenance. We propose that cellular demise and neurodegeneration in PD are due to the interplay between mitochondrial dysfunction, mitochondrial trafficking disruption, and impaired autophagic clearance.

Dynamic Reciprocity in the Wound Microenvironment

PubMed Central

Schultz, Gregory S.; Davidson, Jeffrey M.; Kirsner, Robert S.; Bornstein, Paul; Herman, Ira M.

2011-01-01

Here, we define dynamic reciprocity (DR) as an ongoing, bidirectional interaction amongst cells and their surrounding microenvironment. In the review, we posit that DR is especially meaningful during wound healing as the DR-driven biochemical, biophysical and cellular responses to injury play pivotal roles in regulating tissue regenerative responses. Such cell-extracellular matrix interactions not only guide and regulate cellular morphology, but cellular differentiation, migration, proliferation, and survival during tissue development, including e.g. embryogenesis, angiogenesis, as well as during pathologic processes including cancer diabetes, hypertension and chronic wound healing. Herein, we examine DR within the wound microenvironment while considering specific examples across acute and chronic wound healing. This review also considers how a number of hypotheses that attempt to explain chronic wound pathophysiology, which may be understood within the DR framework. The implications of applying the principles of dynamic reciprocity to optimize wound care practice and future development of innovative wound healing therapeutics are also briefly considered. PMID:21362080

Network Dynamics Underlying Speed-Accuracy Trade-Offs in Response to Errors

PubMed Central

Agam, Yigal; Carey, Caitlin; Barton, Jason J. S.; Dyckman, Kara A.; Lee, Adrian K. C.; Vangel, Mark; Manoach, Dara S.

2013-01-01

The ability to dynamically and rapidly adjust task performance based on its outcome is fundamental to adaptive, flexible behavior. Over trials of a task, responses speed up until an error is committed and after the error responses slow down. These dynamic adjustments serve to optimize performance and are well-described by the speed-accuracy trade-off (SATO) function. We hypothesized that SATOs based on outcomes reflect reciprocal changes in the allocation of attention between the internal milieu and the task-at-hand, as indexed by reciprocal changes in activity between the default and dorsal attention brain networks. We tested this hypothesis using functional MRI to examine the pattern of network activation over a series of trials surrounding and including an error. We further hypothesized that these reciprocal changes in network activity are coordinated by the posterior cingulate cortex (PCC) and would rely on the structural integrity of its white matter connections. Using diffusion tensor imaging, we examined whether fractional anisotropy of the posterior cingulum bundle correlated with the magnitude of reciprocal changes in network activation around errors. As expected, reaction time (RT) in trials surrounding errors was consistent with predictions from the SATO function. Activation in the default network was: (i) inversely correlated with RT, (ii) greater on trials before than after an error and (iii) maximal at the error. In contrast, activation in the right intraparietal sulcus of the dorsal attention network was (i) positively correlated with RT and showed the opposite pattern: (ii) less activation before than after an error and (iii) the least activation on the error. Greater integrity of the posterior cingulum bundle was associated with greater reciprocity in network activation around errors. These findings suggest that dynamic changes in attention to the internal versus external milieu in response to errors underlie SATOs in RT and are mediated by the PCC. PMID:24069223

Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery.

PubMed

Bosl, William J

2007-02-15

Expert knowledge in journal articles is an important source of data for reconstructing biological pathways and creating new hypotheses. An important need for medical research is to integrate this data with high throughput sources to build useful models that span several scales. Researchers traditionally use mental models of pathways to integrate information and development new hypotheses. Unfortunately, the amount of information is often overwhelming and these are inadequate for predicting the dynamic response of complex pathways. Hierarchical computational models that allow exploration of semi-quantitative dynamics are useful systems biology tools for theoreticians, experimentalists and clinicians and may provide a means for cross-communication. A novel approach for biological pathway modeling based on hybrid intelligent systems or soft computing technologies is presented here. Intelligent hybrid systems, which refers to several related computing methods such as fuzzy logic, neural nets, genetic algorithms, and statistical analysis, has become ubiquitous in engineering applications for complex control system modeling and design. Biological pathways may be considered to be complex control systems, which medicine tries to manipulate to achieve desired results. Thus, hybrid intelligent systems may provide a useful tool for modeling biological system dynamics and computational exploration of new drug targets. A new modeling approach based on these methods is presented in the context of hedgehog regulation of the cell cycle in granule cells. Code and input files can be found at the Bionet website: www.chip.ord/~wbosl/Software/Bionet. This paper presents the algorithmic methods needed for modeling complicated biochemical dynamics using rule-based models to represent expert knowledge in the context of cell cycle regulation and tumor growth. A notable feature of this modeling approach is that it allows biologists to build complex models from their knowledge base without the need to translate that knowledge into mathematical form. Dynamics on several levels, from molecular pathways to tissue growth, are seamlessly integrated. A number of common network motifs are examined and used to build a model of hedgehog regulation of the cell cycle in cerebellar neurons, which is believed to play a key role in the etiology of medulloblastoma, a devastating childhood brain cancer.

The co-definition of self: conversations in virtual reality.

PubMed

Cantamesse, Matteo

2009-01-01

Conversation analysis can take the form of a qualitative methodology for the exploration of discursive productions, whose main goal is the formulation of hypotheses for reading psychosocial interaction through descriptive models of interlocution. Therefore, in this study, conversations in a shared Virtual Environment have been analyzed in order to understand the specific structure, dynamics, and phenomenology of Virtual Reality effects on the "interactive micro-chains" that constitute the communicative thread of daily experience.

Sampling bees in tropical forests and agroecosystems: A review

USGS Publications Warehouse

Prado, Sara G.; Ngo, Hien T.; Florez, Jaime A.; Collazo, Jaime A.

2017-01-01

Bees are the predominant pollinating taxa, providing a critical ecosystem service upon which many angiosperms rely for successful reproduction. Available data suggests that bee populations worldwide are declining, but scarce data in tropical regions precludes assessing their status and distribution, impact on ecological services, and response to management actions. Herein, we reviewed >150 papers that used six common sampling methods (pan traps, baits, Malaise traps, sweep nets, timed observations and aspirators) to better understand their strengths and weaknesses, and help guide method selection to meet research objectives and development of multi-species monitoring approaches. Several studies evaluated the effectiveness of sweep nets, pan traps, and malaise traps, but only one evaluated timed observations, and none evaluated aspirators. Only five studies compared two or more of the remaining four sampling methods to each other. There was little consensus regarding which method would be most reliable for sampling multiple species. However, we recommend that if the objective of the study is to estimate abundance or species richness, malaise traps, pan traps and sweep nets are the most effective sampling protocols in open tropical systems; conversely, malaise traps, nets and baits may be the most effective in forests. Declining bee populations emphasize the critical need in method standardization and reporting precision. Moreover, we recommend reporting a catchability coefficient, a measure of the interaction between the resource (bee) abundance and catching effort. Melittologists could also consider existing methods, such as occupancy models, to quantify changes in distribution and abundance after modeling heterogeneity in trapping probability, and consider the possibility of developing monitoring frameworks that draw from multiple sources of data.

Fewer but not smaller schools in declining fish and krill populations.

PubMed

Brierley, Andrew S; Cox, Martin J

2015-01-05

Many pelagic species (species that live in the water column), including herring and krill, aggregate to form schools, shoals, or swarms (hereafter simply "schools," although the words are not synonyms). Schools provide benefits to individual members, including locomotory economy and protection from predators that prey on individuals, but paradoxically make schooling species energetically viable and commercially attractive targets for predators of groups and for fishers. Large schools are easier to find and yield greater prey/catch than small schools, and there is a requirement from fields as diverse as theoretical ecology and fisheries management to understand whether and how aggregation sizes change with changing population size. We collated data from vertical echosounder surveys of taxonomically diverse pelagic stocks from geographically diverse ecosystems. The data contain common significant positive linear stock-biomass to school-number relationships. They show that the numbers of schools in the stocks change with changing stock biomass and suggest that the distributions of school sizes do not change with stock biomass. New data that we collected using a multibeam sonar, which can image entire schools, contained the same stock-biomass to school-number relationship and confirm that the distribution of school sizes is not related to changing stock size: put simply, as stocks decline, individuals are distributed among fewer schools, not smaller schools. Since school characteristics affect catchability (the ease or difficulty with which fishers can capture target species) and availability of prey to predators, our findings have commercial and ecological implications, particularly within the aspirational framework of ecosystem-based management of marine systems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impacts of Daily Bag Limit Reductions on Angler Effort in Wisconsin Walleye Lakes

USGS Publications Warehouse

Beard, T.D.; Cox, S.P.; Carpenter, S.R.

2003-01-01

Angler effort is an important factor affecting recreational fisheries. However, angler responses are rarely incorporated into recreational fisheries regulations or predictions. Few have attempted to examine how daily bag limit regulations affect total angling pressure and subsequent stock densities. Our paper develops a theoretical basis for predicting angler effort and harvest rate based on stock densities and bag limit regulations. We examined data from a management system that controls the total exploitation of walleyes Sander vitreus (formerly Stizostedion vitreum) in northern Wisconsin lakes and compared these empirical results with the predictions from a theoretical effort and harvest rate response model. The data indicated that higher general angler effort occurs on lakes regulated with a 5-walleye daily limit than on lakes regulated with either a 2- or 3-walleye daily limit. General walleye catch rates were lower on lakes with a 5-walleye limit than on lakes with either a 2- or 3-walleye daily limit. An effort response model predicted a logarithmic relationship between angler effort and adult walleye density and that an index of attractiveness would be greater on lakes with high bag limits. Predictions from the harvest rate model with constant walleye catchability indicated that harvest rates increased nonlinearly with increasing density. When the effort model was fitted to data from northern Wisconsin, we found higher lake attractiveness at 5-walleye-limit lakes. We conclude that different groups of anglers respond differently to bag limit changes and that reliance on daily bag limits may not be sufficient to maintain high walleye densities in some lakes in this region.

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

PubMed Central

Warshel, Arieh; Bora, Ram Prasad

2016-01-01

Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme’s conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions. PMID:27179464

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.

PubMed

Warshel, Arieh; Bora, Ram Prasad

2016-05-14

Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme's conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions.

A prospective study of the motivational and health dynamics of Internet Gaming Disorder.

PubMed

Weinstein, Netta; Przybylski, Andrew K; Murayama, Kou

2017-01-01

The American Psychiatric Association has identified Internet Gaming Disorder (IGD) as a potential psychiatric condition and called for research to investigate its etiology, stability, and impacts on health and behavior. The present study recruited 5,777 American adults and applied self-determination theory to examine how motivational factors influence, and are influenced by, IGD and health across a six month period. Following a preregistered analysis plan, results confirmed our hypotheses that IGD criteria are moderately stable and that they and basic psychological need satisfaction have a reciprocal relationship over time. Results also showed need satisfaction promoted health and served as a protective factor against IGD. Contrary to what was hypothesized, results provided no evidence directly linking IGD to health over time. Exploratory analyses suggested that IGD may have indirect effects on health by way of its impact on basic needs. Implications are discussed in terms of existing gaming addiction and motivational frameworks.

Integrated PK-PD and agent-based modeling in oncology.

PubMed

Wang, Zhihui; Butner, Joseph D; Cristini, Vittorio; Deisboeck, Thomas S

2015-04-01

Mathematical modeling has become a valuable tool that strives to complement conventional biomedical research modalities in order to predict experimental outcome, generate new medical hypotheses, and optimize clinical therapies. Two specific approaches, pharmacokinetic-pharmacodynamic (PK-PD) modeling, and agent-based modeling (ABM), have been widely applied in cancer research. While they have made important contributions on their own (e.g., PK-PD in examining chemotherapy drug efficacy and resistance, and ABM in describing and predicting tumor growth and metastasis), only a few groups have started to combine both approaches together in an effort to gain more insights into the details of drug dynamics and the resulting impact on tumor growth. In this review, we focus our discussion on some of the most recent modeling studies building on a combined PK-PD and ABM approach that have generated experimentally testable hypotheses. Some future directions are also discussed.

Integrated PK-PD and Agent-Based Modeling in Oncology

PubMed Central

Wang, Zhihui; Butner, Joseph D.; Cristini, Vittorio

2016-01-01

Mathematical modeling has become a valuable tool that strives to complement conventional biomedical research modalities in order to predict experimental outcome, generate new medical hypotheses, and optimize clinical therapies. Two specific approaches, pharmacokinetic-pharmacodynamic (PK-PD) modeling, and agent-based modeling (ABM), have been widely applied in cancer research. While they have made important contributions on their own (e.g., PK-PD in examining chemotherapy drug efficacy and resistance, and ABM in describing and predicting tumor growth and metastasis), only a few groups have started to combine both approaches together in an effort to gain more insights into the details of drug dynamics and the resulting impact on tumor growth. In this review, we focus our discussion on some of the most recent modeling studies building on a combined PK-PD and ABM approach that have generated experimentally testable hypotheses. Some future directions are also discussed. PMID:25588379

Complexity matching in dyadic conversation.

PubMed

Abney, Drew H; Paxton, Alexandra; Dale, Rick; Kello, Christopher T

2014-12-01

Recent studies of dyadic interaction have examined phenomena of synchronization, entrainment, alignment, and convergence. All these forms of behavioral matching have been hypothesized to play a supportive role in establishing coordination and common ground between interlocutors. In the present study, evidence is found for a new kind of coordination termed complexity matching. Temporal dynamics in conversational speech signals were analyzed through time series of acoustic onset events. Timing in periods of acoustic energy was found to exhibit behavioral matching that reflects complementary timing in turn-taking. In addition, acoustic onset times were found to exhibit power law clustering across a range of timescales, and these power law functions were found to exhibit complexity matching that is distinct from behavioral matching. Complexity matching is discussed in terms of interactive alignment and other theoretical principles that lead to new hypotheses about information exchange in dyadic conversation and interaction in general. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Gravity and lithospheric stress on the terrestrial planets with reference to the Tharsis region of Mars

NASA Technical Reports Server (NTRS)

Sleep, N. H.; Phillips, R. J.

1985-01-01

On Mars and Venus, a strong positive correlation is found between geoid height and topography. The Tharsis region of Mars provides an exhibition of this correlation. Several hypotheses have been proposed regarding the origin of Tharsis. For purposes of explanation, three end-member dynamic hypotheses are considered. A hypothesis that the flexural doming of Tharsis resulted from uplift caused by some force acting on the base of the lithosphere can be rejected. According to another hypothesis, Tharsis is associated with a lithospheric load, while a third one considers that Tharsis is primarily isostatically compensated. In the present study, improved stress models for isostatic compensation on Mars are obtained. The strains inferred from fracture patterns on Mars are compared with the stresses predicted by the isostatic theory. It is found that the computed stresses are in reasonable agreement with tectonic features on Mars.

A prospective study of the motivational and health dynamics of Internet Gaming Disorder

PubMed Central

Przybylski, Andrew K.; Murayama, Kou

2017-01-01

The American Psychiatric Association has identified Internet Gaming Disorder (IGD) as a potential psychiatric condition and called for research to investigate its etiology, stability, and impacts on health and behavior. The present study recruited 5,777 American adults and applied self-determination theory to examine how motivational factors influence, and are influenced by, IGD and health across a six month period. Following a preregistered analysis plan, results confirmed our hypotheses that IGD criteria are moderately stable and that they and basic psychological need satisfaction have a reciprocal relationship over time. Results also showed need satisfaction promoted health and served as a protective factor against IGD. Contrary to what was hypothesized, results provided no evidence directly linking IGD to health over time. Exploratory analyses suggested that IGD may have indirect effects on health by way of its impact on basic needs. Implications are discussed in terms of existing gaming addiction and motivational frameworks. PMID:28975056

Developing spatial inequalities in carbon appropriation: a sociological analysis of changing local emissions across the United States.

PubMed

Elliott, James R; Clement, Matthew Thomas

2015-05-01

This study examines an overlooked dynamic in sociological research on greenhouse gas emissions: how local areas appropriate the global carbon cycle for use and exchange purposes as they develop. Drawing on theories of place and space, we hypothesize that development differentially drives and spatially decouples use- and exchange-oriented emissions at the local level. To test our hypotheses, we integrate longitudinal, county-level data on residential and industrial emissions from the Vulcan Project with demographic, economic and environmental data from the U.S. Census Bureau and National Land Change Database. Results from spatial regression models with two-way fixed-effects indicate that alongside innovations and efficiencies capable of reducing environmentally harmful effects of development comes a spatial disarticulation between carbon-intensive production and consumption within as well as across societies. Implications for existing theory, methods and policy are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Action perception as hypothesis testing.

PubMed

Donnarumma, Francesco; Costantini, Marcello; Ambrosini, Ettore; Friston, Karl; Pezzulo, Giovanni

2017-04-01

We present a novel computational model that describes action perception as an active inferential process that combines motor prediction (the reuse of our own motor system to predict perceived movements) and hypothesis testing (the use of eye movements to disambiguate amongst hypotheses). The system uses a generative model of how (arm and hand) actions are performed to generate hypothesis-specific visual predictions, and directs saccades to the most informative places of the visual scene to test these predictions - and underlying hypotheses. We test the model using eye movement data from a human action observation study. In both the human study and our model, saccades are proactive whenever context affords accurate action prediction; but uncertainty induces a more reactive gaze strategy, via tracking the observed movements. Our model offers a novel perspective on action observation that highlights its active nature based on prediction dynamics and hypothesis testing. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Authoritarianism, conservatism, racial diversity threat, and the state distribution of hate groups.

PubMed

McCann, Stewart J H

2010-01-01

On the basis of K. Stenner's (2005) authoritarian dynamic theory, the author hypothesized that there is an interaction between U.S. state conservatism-liberalism and state racial heterogeneity threat, such that greater diversity threat tends to be associated with more hate groups in more conservative states and fewer hate groups in more liberal states. State aggregates of the conservative-liberal ideological preferences of 141,798 participants from 122 CBS News/New York Times national telephone polls conducted between 1976 and 1988 (R. S. Erikson, G. C. Wright, & J. P. McIver, 1993) served as proxies for authoritarian-nonauthoritarian dispositions. For the 47 states with complete data, the hypothesized interaction was tested for 2000, 2005, and 2006 with hierarchical multiple regression strategies and supported. The author's hypothesis was also affirmed with SES and the interaction of SES and diversity threat controlled for. In contrast, SES entirely accounted for simple relationships between threat and hate group frequency.

Nonstructural carbon dynamics are best predicted by the combination of photosynthesis and plant hydraulics during both bark beetle induced mortality and herbaceous plant response to drought

NASA Astrophysics Data System (ADS)

Ewers, B. E.; Mackay, D. S.; Guadagno, C.; Peckham, S. D.; Pendall, E.; Borkhuu, B.; Aston, T.; Frank, J. M.; Massman, W. J.; Reed, D. E.; Yarkhunova, Y.; Weinig, C.

2012-12-01

Recent work has shown that nonstructural carbon (NSC) provides both a signal and consequence of water stress in plants. The dynamics of NSC are likely not solely a result of the balance of photosynthesis and respiration (carbon starvation hypothesis) but also the availability of NSC for plant functions due to hydraulic condition. Further, plant hydraulics regulates photosynthesis both directly through stomatal conductance and indirectly through leaf water status control over leaf biochemistry. To test these hypotheses concerning NSC in response to a wide variety of plant perturbations, we used a model that combines leaf biochemical controls over photosynthesis (Farquhar model) with dynamic plant hydraulic conductance (Sperry model). This model (Terrestrial Regional Ecosystem Exchange Simulator; TREES) simulates the dynamics of NSC through a carbon budget approach that responds to plant hydraulic status. We tested TREES on two dramatically different datasets. The first dataset is from lodgepole pine and Engelmann spruce trees dying from bark beetles that carry blue-stain fungi which block xylem and cause hydraulic failure. The second data set is from Brassica rapa, a small herbaceous plant whose accessions are used in a variety of crops. The Brassica rapa plants include two parents whose circadian clock periods are different; NSC is known to provide inputs to the circadian clock likely modified by drought. Thus, drought may interact with clock control to constrain how NSC changes over the day. The Brassica rapa plants were grown in growth chamber conditions where drought was precisely controlled. The connection between these datasets is that both provide rigorous tests of our understanding of plant NSC dynamics and use similar leaf and whole plant gas exchange and NSC laboratory methods. Our results show that NSC decline (<10% in the whole plant) is less precipitous than expected from carbon starvation alone because both C uptake and use are impacted by water stress. The model is able to capture this relatively small decline in NSC by limiting NSC utilization through loss of plant hydraulic conductance. Our findings imply that NSC dynamics in plants undergoing water stress cannot be explained solely by carbon starvation or hydraulic failure but rather from the combination of both hypotheses. Our future work will determine whether additional environmental factors such as seasonality and plant developmental state alter the response of NSC to water stress.

Emergence of nutrient limitation in tropical dry forests: hypotheses from simulation models

NASA Astrophysics Data System (ADS)

Medvigy, D.; Waring, B. G.; Xu, X.; Trierweiler, A.; Werden, L. K.; Wang, G.; Zhu, Q.; Powers, J. S.

2017-12-01

It is unclear to what extent tropical dry forest productivity may be limited by nutrients. Direct assessment of nutrient limitation through fertilization experiments has been rare, and paradigms pertaining to other ecosystems may not extend to tropical dry forests. For example, because dry tropical forests have a lower water supply than moist tropical forests, dry forests can have lower decomposition rates, higher soil carbon and nitrogen concentrations, and a more open nitrogen cycle than moist forests. We used a mechanistic, numerical model to generate hypotheses about nutrient limitation in tropical dry forests. The model dynamically couples ED2 (vegetation dynamics), MEND (biogeochemistry), and N-COM (plant-microbe competition for nutrients). Here, the MEND-component of the model has been extended to include nitrogen (N) and phosphorus (P) cycles. We focus on simulation of sixteen 25m x 25m plots in Costa Rica where a fertilization experiment has been underway since 2015. Baseline simulations are characterized by both nitrogen and phosphorus limitation of vegetation. Fertilization with N and P increased vegetation biomass, with N fertilization having a somewhat stronger effect. Nutrient limitation was also sensitive to climate and was more pronounced during drought periods. Overflow respiration was identified as a key process that mitigated nutrient limitation. These results suggest that, despite often having richer soils than tropical moist forests, tropical dry forests can also become nutrient-limited. If the climate becomes drier in the next century, as is expected for Central America, drier soils may decrease microbial activity and exacerbate nutrient limitation. The importance of overflow respiration underscores the need for appropriate treatment of microbial dynamics in ecosystem models. Ongoing and new nutrient fertilization experiments will present opportunities for testing whether, and how, nutrient limitation may indeed be emerging in tropical dry forests.

Defining and Identifying Functional Habitat to Inform Species Recovery on a Large Regulated River

NASA Astrophysics Data System (ADS)

Erwin, S.; Jacobson, R. B.; Elliott, C. M.; Gemeinhardt, T.; Welker, T.; DeLonay, A. J.; Chojnacki, K.

2014-12-01

Goals and objectives for the restoration of aquatic ecosystems often focus on species recovery, but often the primary tools available to managers involve the manipulation of flow regime and physical habitat. Management decisions thus rely on hypotheses about the links between management actions, the response of physical habitat, and the assumed response of a target organism. Ongoing efforts to inform management of the Missouri River as part of Missouri River Restoration Project are focused on the recovery of three endangered species, including the pallid sturgeon (Scaphirhynchus albus), which is endemic to the Mississippi River basin. Recovery of the pallid sturgeon is hampered by uncertainties surrounding the definition and dynamics of ecologically significant habitats for the fish across a range of life stages. Of special interest are constructed side-channel chutes. Construction of these features has emerged as one of the primary restoration techniques used on the Lower Missouri River, yet much remains to be learned about the effectiveness of these chutes in the effort to recover pallid sturgeon. It remains unclear whether these constructed features provide habitat that may be beneficial to the species and for which life stages. Biologists hypothesize that these areas may be critical for larval retention, refugia, food production, foraging, or spawning. We present the integration of a suite of data - high-resolution hydroacoustic data, hydrodynamic modeling, biotic inventories, and laboratory experiments - designed to refine our understanding of habitat dynamics critical during the early life stages of the pallid sturgeon. We present our findings in the context of ongoing restoration activities in the basin and describe how fundamental science exploring habitat dynamics may be incorporated within the existing adaptive management framework.

The Importance of Large-Diameter Trees to Forest Structural Heterogeneity

PubMed Central

Lutz, James A.; Larson, Andrew J.; Freund, James A.; Swanson, Mark E.; Bible, Kenneth J.

2013-01-01

Large-diameter trees dominate the structure, dynamics and function of many temperate and tropical forests. However, their attendant contributions to forest heterogeneity are rarely addressed. We established the Wind River Forest Dynamics Plot, a 25.6 ha permanent plot within which we tagged and mapped all 30,973 woody stems ≥1 cm dbh, all 1,966 snags ≥10 cm dbh, and all shrub patches ≥2 m2. Basal area of the 26 woody species was 62.18 m2/ha, of which 61.60 m2/ha was trees and 0.58 m2/ha was tall shrubs. Large-diameter trees (≥100 cm dbh) comprised 1.5% of stems, 31.8% of basal area, and 17.6% of the heterogeneity of basal area, with basal area dominated by Tsuga heterophylla and Pseudotsuga menziesii. Small-diameter subpopulations of Pseudotsuga menziesii, Tsuga heterophylla and Thuja plicata, as well as all tree species combined, exhibited significant aggregation relative to the null model of complete spatial randomness (CSR) up to 9 m (P≤0.001). Patterns of large-diameter trees were either not different from CSR (Tsuga heterophylla), or exhibited slight aggregation (Pseudotsuga menziesii and Thuja plicata). Significant spatial repulsion between large-diameter and small-diameter Tsuga heterophylla suggests that large-diameter Tsuga heterophylla function as organizers of tree demography over decadal timescales through competitive interactions. Comparison among two forest dynamics plots suggests that forest structural diversity responds to intermediate-scale environmental heterogeneity and disturbances, similar to hypotheses about patterns of species richness, and richness- ecosystem function. Large mapped plots with detailed within-plot environmental spatial covariates will be required to test these hypotheses. PMID:24376579

The importance of large-diameter trees to forest structural heterogeneity.

PubMed

Lutz, James A; Larson, Andrew J; Freund, James A; Swanson, Mark E; Bible, Kenneth J

2013-01-01

Large-diameter trees dominate the structure, dynamics and function of many temperate and tropical forests. However, their attendant contributions to forest heterogeneity are rarely addressed. We established the Wind River Forest Dynamics Plot, a 25.6 ha permanent plot within which we tagged and mapped all 30,973 woody stems ≥ 1 cm dbh, all 1,966 snags ≥ 10 cm dbh, and all shrub patches ≥ 2 m(2). Basal area of the 26 woody species was 62.18 m(2)/ha, of which 61.60 m(2)/ha was trees and 0.58 m(2)/ha was tall shrubs. Large-diameter trees (≥ 100 cm dbh) comprised 1.5% of stems, 31.8% of basal area, and 17.6% of the heterogeneity of basal area, with basal area dominated by Tsuga heterophylla and Pseudotsuga menziesii. Small-diameter subpopulations of Pseudotsuga menziesii, Tsuga heterophylla and Thuja plicata, as well as all tree species combined, exhibited significant aggregation relative to the null model of complete spatial randomness (CSR) up to 9 m (P ≤ 0.001). Patterns of large-diameter trees were either not different from CSR (Tsuga heterophylla), or exhibited slight aggregation (Pseudotsuga menziesii and Thuja plicata). Significant spatial repulsion between large-diameter and small-diameter Tsuga heterophylla suggests that large-diameter Tsuga heterophylla function as organizers of tree demography over decadal timescales through competitive interactions. Comparison among two forest dynamics plots suggests that forest structural diversity responds to intermediate-scale environmental heterogeneity and disturbances, similar to hypotheses about patterns of species richness, and richness- ecosystem function. Large mapped plots with detailed within-plot environmental spatial covariates will be required to test these hypotheses.

A model for simulating adaptive, dynamic flows on networks: Application to petroleum infrastructure

DOE PAGES

Corbet, Thomas F.; Beyeler, Walt; Wilson, Michael L.; ...

2017-10-03

Simulation models can greatly improve decisions meant to control the consequences of disruptions to critical infrastructures. We describe a dynamic flow model on networks purposed to inform analyses by those concerned about consequences of disruptions to infrastructures and to help policy makers design robust mitigations. We conceptualize the adaptive responses of infrastructure networks to perturbations as market transactions and business decisions of operators. We approximate commodity flows in these networks by a diffusion equation, with nonlinearities introduced to model capacity limits. To illustrate the behavior and scalability of the model, we show its application first on two simple networks, thenmore » on petroleum infrastructure in the United States, where we analyze the effects of a hypothesized earthquake.« less

Dynamical emergence of the Universe into the false vacuum

NASA Astrophysics Data System (ADS)

Rafelski, Johann; Birrell, Jeremiah

2015-11-01

We study how the hot Universe evolves and acquires the prevailing vacuum state, demonstrating that in specific conditions which are believed to apply, the Universe becomes frozen into the state with the smallest value of Higgs vacuum field v=langle hrangle, even if this is not the state of lowest energy. This supports the false vacuum dark energy Λ-model. Under several likely hypotheses we determine the temperature in the evolution of the Universe at which two vacuua v1, v2 can swap between being true and false. We evaluate the dynamical surface pressure on domain walls between low and high mass vaccua due to the presence of matter and show that the low mass state remains the preferred vacuum of the Universe.

A model for simulating adaptive, dynamic flows on networks: Application to petroleum infrastructure

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

Corbet, Thomas F.; Beyeler, Walt; Wilson, Michael L.

Simulation models can greatly improve decisions meant to control the consequences of disruptions to critical infrastructures. We describe a dynamic flow model on networks purposed to inform analyses by those concerned about consequences of disruptions to infrastructures and to help policy makers design robust mitigations. We conceptualize the adaptive responses of infrastructure networks to perturbations as market transactions and business decisions of operators. We approximate commodity flows in these networks by a diffusion equation, with nonlinearities introduced to model capacity limits. To illustrate the behavior and scalability of the model, we show its application first on two simple networks, thenmore » on petroleum infrastructure in the United States, where we analyze the effects of a hypothesized earthquake.« less

Oxytocin receptor dynamics in the brain across development and species.

PubMed

Vaidyanathan, Radhika; Hammock, Elizabeth A D

2017-02-01

Oxytocin (OXT) signaling through the OXT receptor plays a significant role in a variety of physiological processes throughout the lifespan. OXT's effects depend on the tissue distribution of the receptor. This tissue specificity is dynamic and changes across development, and also varies with sex, experience, and species. The purpose of this review is to highlight these themes with examples from several life stages and several species. Important knowledge gaps will also be emphasized. Understanding the effective sites of action for OXT via its receptor will help refine hypotheses about the roles of this important neuropeptide in the experience-dependent development and expression of species-typical social behavior. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 143-157, 2017. © 2016 Wiley Periodicals, Inc.

Comment on “The reduction of friction in long-runout landslides as an emergent phenomenon” by Brandon C. Johnson et al.

USGS Publications Warehouse

Iverson, Richard M.

2016-01-01

Results from a highly idealized, 2-D computational model indicate that dynamic normal-stress rarefactions might cause friction reduction in long-runout landslides, but the physical relevance of the idealized dynamics has not been confirmed by experimental tests. More importantly, the model results provide no evidence that refutes alternative hypotheses about friction reduction mechanisms. One alternative hypothesis, which is strongly supported by field evidence, experimental data, and the predictions of a well-constrained computational model, involves development of high pore fluid pressures in deforming landslide material or overridden bed material. However, no scientific basis exists for concluding that a universal mechanism is responsible for friction reduction in all long-runout landslides.

One-Shot Decoupling and Page Curves from a Dynamical Model for Black Hole Evaporation.

PubMed

Brádler, Kamil; Adami, Christoph

2016-03-11

One-shot decoupling is a powerful primitive in quantum information theory and was hypothesized to play a role in the black hole information paradox. We study black hole dynamics modeled by a trilinear Hamiltonian whose semiclassical limit gives rise to Hawking radiation. An explicit numerical calculation of the discretized path integral of the S matrix shows that decoupling is exact in the continuous limit, implying that quantum information is perfectly transferred from the black hole to radiation. A striking consequence of decoupling is the emergence of an output radiation entropy profile that follows Page's prediction. We argue that information transfer and the emergence of Page curves is a robust feature of any multilinear interaction Hamiltonian with a bounded spectrum.

The role of the CN vibration in the activated dynamics of LiNC<−>LiCN isomerization in an argon solvent at high temperatures.

PubMed

Garcia-Muller, Pablo L; Hernandez, Rigoberto; Benito, R M; Borondo, F

2014-08-21

The isomerization between CN-Li and Li-CN in an argon bath provides a paradigmatic example of a reaction in a solvent with tunable coupling. In previous work, we found that the rates exhibited a turnover with the density of the argon bath in the limit that the CN bond was held fixed [P. L. Garcia-Muller, R. Hernandez, R. M. Benito, and F. Borondo, J. Chem. Phys. 137, 204301 (2012)]. Here, we report the effect of the CN bond vibration on the dynamics and the persistence of the turnover. As hypothesized earlier, the CN bond is indeed weakly coupled with the reaction path despite the presence of the argon cage.

A survey of automated methods for sensemaking support

NASA Astrophysics Data System (ADS)

Llinas, James

2014-05-01

Complex, dynamic problems in general present a challenge for the design of analysis support systems and tools largely because there is limited reliable a priori procedural knowledge descriptive of the dynamic processes in the environment. Problem domains that are non-cooperative or adversarial impute added difficulties involving suboptimal observational data and/or data containing the effects of deception or covertness. The fundamental nature of analysis in these environments is based on composite approaches involving mining or foraging over the evidence, discovery and learning processes, and the synthesis of fragmented hypotheses; together, these can be labeled as sensemaking procedures. This paper reviews and analyzes the features, benefits, and limitations of a variety of automated techniques that offer possible support to sensemaking processes in these problem domains.

Optimal exploitation strategies for an animal population in a Markovian environment: A theory and an example

USGS Publications Warehouse

Anderson, D.R.

1975-01-01

Optimal exploitation strategies were studied for an animal population in a Markovian (stochastic, serially correlated) environment. This is a general case and encompasses a number of important special cases as simplifications. Extensive empirical data on the Mallard (Anas platyrhynchos) were used as an example of general theory. The number of small ponds on the central breeding grounds was used as an index to the state of the environment. A general mathematical model was formulated to provide a synthesis of the existing literature, estimates of parameters developed from an analysis of data, and hypotheses regarding the specific effect of exploitation on total survival. The literature and analysis of data were inconclusive concerning the effect of exploitation on survival. Therefore, two hypotheses were explored: (1) exploitation mortality represents a largely additive form of mortality, and (2) exploitation mortality is compensatory with other forms of mortality, at least to some threshold level. Models incorporating these two hypotheses were formulated as stochastic dynamic programming models and optimal exploitation strategies were derived numerically on a digital computer. Optimal exploitation strategies were found to exist under the rather general conditions. Direct feedback control was an integral component in the optimal decision-making process. Optimal exploitation was found to be substantially different depending upon the hypothesis regarding the effect of exploitation on the population. If we assume that exploitation is largely an additive force of mortality in Mallards, then optimal exploitation decisions are a convex function of the size of the breeding population and a linear or slight concave function of the environmental conditions. Under the hypothesis of compensatory mortality forces, optimal exploitation decisions are approximately linearly related to the size of the Mallard breeding population. Dynamic programming is suggested as a very general formulation for realistic solutions to the general optimal exploitation problem. The concepts of state vectors and stage transformations are completely general. Populations can be modeled stochastically and the objective function can include extra-biological factors. The optimal level of exploitation in year t must be based on the observed size of the population and the state of the environment in year t unless the dynamics of the population, the state of the environment, and the result of the exploitation decisions are completely deterministic. Exploitation based on an average harvest, or harvest rate, or designed to maintain a constant breeding population size is inefficient.

From phase transitions to the topological renaissance. Comment on "Topodynamics of metastable brains" by Arturo Tozzi et al.

NASA Astrophysics Data System (ADS)

Somogyvári, Zoltán; Érdi, Péter

2017-07-01

The neural topodynamics theory of Tozzi et al. [13] has two main foci: metastable brain dynamics and the topological approach based on the Borsuk-Ulam theorem (BUT). Briefly, metastable brain dynamics theory hypothesizes that temporary stable synchronization and desynchronization of large number of individual dynamical systems, formed by local neural circuits, are responsible for coding of complex concepts in the brain and sudden changes of these synchronization patterns correspond to operational steps. But what dynamical network could form the substrate for this metastable dynamics, capable of entering into a combinatorially high number of metastable synchronization patterns and exhibit rapid transient changes between them? The general problem is related to the discrimination between ;Black Swans; and ;Dragon Kings;. While BSs are related to the theory of self-organized criticality, and suggests that high-impact extreme events are unpredictable, Dragon-kings are associated with the occurrence of a phase transition, whose emergent organization is based on intermittent criticality [9]. Widening the limits of predictability is one of the big open problems in the theory and practice of complex systems (Sect. 9.3 of Érdi [2]).

Pore dynamics in lipid membranes

NASA Astrophysics Data System (ADS)

Gozen, I.; Dommersnes, P.

2014-09-01

Transient circular pores can open in plasma membrane of cells due to mechanical stress, and failure to repair such pores lead to cell death. Similar pores in the form of defects also exist among smectic membranes, such as in myelin sheaths or mitochondrial membranes. The formation and growth of membrane defects are associated with diseases, for example multiple sclerosis. A deeper understanding of membrane pore dynamics can provide a more refined picture of membrane integrity-related disease development, and possibly also treatment options and strategies. Pore dynamics is also of great importance regarding healthcare applications such as drug delivery, gene or as recently been implied, cancer therapy. The dynamics of pores significantly differ in stacks which are confined in 2D compared to those in cells or vesicles. In this short review, we will summarize the dynamics of different types of pores that can be observed in biological membranes, which include circular transient, fusion and hemi-fusion pores. We will dedicate a section to floral and fractal pores which were discovered a few years ago and have highly peculiar characteristics. Finally, we will discuss the repair mechanisms of large area pores in conjunction with the current cell membrane repair hypotheses.

Structural model for fluctuations in financial markets

NASA Astrophysics Data System (ADS)

Anand, Kartik; Khedair, Jonathan; Kühn, Reimer

2018-05-01

In this paper we provide a comprehensive analysis of a structural model for the dynamics of prices of assets traded in a market which takes the form of an interacting generalization of the geometric Brownian motion model. It is formally equivalent to a model describing the stochastic dynamics of a system of analog neurons, which is expected to exhibit glassy properties and thus many metastable states in a large portion of its parameter space. We perform a generating functional analysis, introducing a slow driving of the dynamics to mimic the effect of slowly varying macroeconomic conditions. Distributions of asset returns over various time separations are evaluated analytically and are found to be fat-tailed in a manner broadly in line with empirical observations. Our model also allows us to identify collective, interaction-mediated properties of pricing distributions and it predicts pricing distributions which are significantly broader than their noninteracting counterparts, if interactions between prices in the model contain a ferromagnetic bias. Using simulations, we are able to substantiate one of the main hypotheses underlying the original modeling, viz., that the phenomenon of volatility clustering can be rationalized in terms of an interplay between the dynamics within metastable states and the dynamics of occasional transitions between them.

Dynamic inverse models in human-cyber-physical systems

NASA Astrophysics Data System (ADS)

Robinson, Ryan M.; Scobee, Dexter R. R.; Burden, Samuel A.; Sastry, S. Shankar

2016-05-01

Human interaction with the physical world is increasingly mediated by automation. This interaction is characterized by dynamic coupling between robotic (i.e. cyber) and neuromechanical (i.e. human) decision-making agents. Guaranteeing performance of such human-cyber-physical systems will require predictive mathematical models of this dynamic coupling. Toward this end, we propose a rapprochement between robotics and neuromechanics premised on the existence of internal forward and inverse models in the human agent. We hypothesize that, in tele-robotic applications of interest, a human operator learns to invert automation dynamics, directly translating from desired task to required control input. By formulating the model inversion problem in the context of a tracking task for a nonlinear control system in control-a_ne form, we derive criteria for exponential tracking and show that the resulting dynamic inverse model generally renders a portion of the physical system state (i.e., the internal dynamics) unobservable from the human operator's perspective. Under stability conditions, we show that the human can achieve exponential tracking without formulating an estimate of the system's state so long as they possess an accurate model of the system's dynamics. These theoretical results are illustrated using a planar quadrotor example. We then demonstrate that the automation can intervene to improve performance of the tracking task by solving an optimal control problem. Performance is guaranteed to improve under the assumption that the human learns and inverts the dynamic model of the altered system. We conclude with a discussion of practical limitations that may hinder exact dynamic model inversion.

Reduced Nucleus Pulposus Glycosaminoglycan Content Alters Intervertebral Disc Dynamic Viscoelastic Mechanics

PubMed Central

Boxberger, John I.; Orlansky, Amy S.; Sen, Sounok; Elliott, Dawn M.

2009-01-01

The intervertebral disc functions over a range of dynamic loading regimes including axial loads applied across a spectrum of frequencies at varying compressive loads. Biochemical changes occurring in early degeneration, including reduced nucleus pulposus glycosaminoglycan content, may alter disc mechanical behavior and thus may contribute to the progression of degeneration. The objective of this study was to determine disc dynamic viscoelastic properties under several equilibrium loads and loading frequencies, and further, to determine how reduced nucleus glycosaminglycan content alters dynamic mechanics. We hypothesized (1) that dynamic stiffness would be elevated with increasing equilibrium load and increasing frequency, (2) that the disc would behave more elastically at higher frequencies, and finally, (3) that dynamic stiffness would be reduced at low equilibrium loads under all frequencies due to nucleus glycosaminoglycan loss. We mechanically tested control and chondroitinase-ABC injected rat lumbar motion segments at several equilibrium loads using oscillatory loading at frequencies ranging from 0.05 to 5 Hz. The rat lumbar disc behaved non-linearly with higher dynamic stiffness at elevated compressive loads irrespective of frequency. Phase angle was not affected by equilibrium load, although it decreased as frequency was increased. Reduced glycosaminoglycan decreased dynamic stiffness at low loads but not at high equilibrium loads and led to increased phase angle at all loads and frequencies. The findings of this study demonstrate the effect of equilibrium load and loading frequencies on dynamic disc mechanics and indicate possible mechanical mechanisms through which disc degeneration can progress. PMID:19539936

Modeling the impacts of two age-related portfolio effects on recruitment variability with and without a marine reserve.

PubMed

McGilliard, Carey R; Punt, André E; Hilborn, Ray; Essington, Tim

2017-10-01

Many rockfish species are long-lived and thought to be susceptible to being overfished. Hypotheses about the importance of older female rockfish to population persistence have led to arguments that marine reserves are needed to ensure the sustainability of rockfish populations. However, the implications of these hypotheses for rockfish population dynamics are still unclear. We modeled two mechanisms by which reducing the proportion of older fish in a population has been hypothesized to influence sustainability, and explored whether these mechanisms influenced mean population dynamics and recruitment variability. We explored whether populations with these mechanisms could be managed more sustainably with a marine reserve in addition to a constant fishing mortality rate (F) than with a constant F alone. Both hypotheses can be seen as portfolio effects whereby risk of recruitment failure is spread over a "portfolio" of maternal ages. First, we modeled a spawning window effect whereby mothers of different ages spawned in different times or locations (windows) with local environmental conditions. Second, we modeled an offspring size effect whereby older mothers produced larger offspring than younger mothers, where length of a starvation period over which offspring could survive increased with maternal age. Recruitment variability resulting from both models was 55-65% lower than for models without maternal age-related portfolio effects in the absence of fishing and increased with increases in Fs for both models. An offspring size effect caused lower output reproductive rates such that the specified reproductive rate input as a model parameter was no longer the realized rate measured as the reproductive rate observed in model results; this quirk is not addressed in previous analyses of offspring size effects. We conducted a standardization such that offspring size effect and control models had the same observed reproductive rates. A comparison of long-term catch, the probability of falling below a biomass threshold, and recruitment variability over a range of exploitation rates for models with an age-related portfolio effect showed no benefit of a marine reserve implemented in addition to a constant F (as compared to a constant F alone) for populations with sedentary adults and sedentary or mobile larvae. © 2017 by the Ecological Society of America.

Holocene expansions of Fagus silvatica and Abies alba in Central Europe: where are we after eight decades of debate?

NASA Astrophysics Data System (ADS)

Tinner, Willy; Lotter, André F.

2006-03-01

During the past eight decades contrasting hypotheses have been put forward to explain the Holocene expansions of Fagus silvatica (beech) and Abies alba (fir) in Central Europe. The hypotheses can be referred to as: (1) climatic change; (2) migrational lag; (3) delay in population increase; (4) human disturbance; and (5) fire disturbance. High-resolution pollen and charcoal records from three sites in lowland Switzerland and southern Germany allow testing the human vs. fire-disturbance hypotheses by means of time-series analysis. Cross-correlations between pairs of pollen as well as between microscopic charcoal and pollen suggest that neither human nor fire disturbance substantially promoted the expansion of Fagus and Abies. We address the remaining hypotheses (climatic change, migrational lag, delay of population increase) by a combined interpretation of our data with independent climatic records and other evidence of past environmental dynamics (e.g. dynamic vegetation modelling) for southern Central Europe. Rapid population expansions in response to cooling and precipitation increase suggest that climatic change was the main forcing factor and that migrational lags were not effective since at least 8200 cal. yr ago. On the basis of this conclusion we propose an explanatory model for the Holocene expansion of Fagus and Abies in Central Europe: Both trees expanded stepwise across the continent during favourable 8200-type events, which were characterized by changes towards wetter and cooler conditions and corresponded to previously recognized Holocene cold phases in Central Europe as well as in the North Atlantic realm. Asynchronous expansions across continental Europe are explained by analogy to today's precipitation gradients resulting from orographic effects. Response lags of Fagus and Abies to climatic change reached a few decades at most, whereas population expansion in response to climatic change lasted for several centuries, probably as a consequence of intrinsic rates of population increase as well as competition with previously established forest communities. This model is in agreement with recent data from northern Central Europe, where large-scale expansion pulses of Fagus coincided with 8200-type events (e.g. 3800-3400 and 2750-2350 cal. BP). In addition to climatic change, human impact influenced the expansions of Fagus in northern Central Europe. We suggest that Abies expansions across Europe after 5000 cal. BP were inhibited by human and/or fire disturbance.

From the big five to the general factor of personality: a dynamic approach.

PubMed

Micó, Joan C; Amigó, Salvador; Caselles, Antonio

2014-10-28

An integrating and dynamic model of personality that allows predicting the response of the basic factors of personality, such as the Big Five Factors (B5F) or the general factor of personality (GFP) to acute doses of drug is presented in this paper. Personality has a dynamic nature, i.e., as a consequence of a stimulus, the GFP dynamics as well as each one of the B5F of personality dynamics can be explained by the same model (a system of three coupled differential equations). From this invariance hypothesis, a partial differential equation, whose solution relates the GFP with each one of the B5F, is deduced. From this dynamic approach, a co-evolution of the GFP and each one of the B5F occurs, rather than an unconnected evolution, as a consequence of the same stimulus. The hypotheses and deductions are validated through an experimental design centered on the individual, where caffeine is the considered stimulus. Thus, as much from a theoretical point of view as from an applied one, the models here proposed open a new perspective in the understanding and study of personality like a global system that interacts intimately with the environment, being a clear bet for the high level inter-disciplinary research.

Abnormal dynamics of language in schizophrenia.

PubMed

Stephane, Massoud; Kuskowski, Michael; Gundel, Jeanette

2014-05-30

Language could be conceptualized as a dynamic system that includes multiple interactive levels (sub-lexical, lexical, sentence, and discourse) and components (phonology, semantics, and syntax). In schizophrenia, abnormalities are observed at all language elements (levels and components) but the dynamic between these elements remains unclear. We hypothesize that the dynamics between language elements in schizophrenia is abnormal and explore how this dynamic is altered. We, first, investigated language elements with comparable procedures in patients and healthy controls. Second, using measures of reaction time, we performed multiple linear regression analyses to evaluate the inter-relationships among language elements and the effect of group on these relationships. Patients significantly differed from controls with respect to sub-lexical/lexical, lexical/sentence, and sentence/discourse regression coefficients. The intercepts of the regression slopes increased in the same order above (from lower to higher levels) in patients but not in controls. Regression coefficients between syntax and both sentence level and discourse level semantics did not differentiate patients from controls. This study indicates that the dynamics between language elements is abnormal in schizophrenia. In patients, top-down flow of linguistic information might be reduced, and the relationship between phonology and semantics but not between syntax and semantics appears to be altered. Published by Elsevier Ireland Ltd.

Effect of HSP27 on Human Breast Tumor Cell Growth and Motility.

DTIC Science & Technology

1997-09-01

the small heat shock protein, Hsp27 , on growth and motility characteristics of human mammary tumor cell lines. Since Hsp27 regulates actin...microfilament dynamics, we hypothesize that cells expressing high levels of Hsp27 will show increased motility and altered chemotactic properties, in addition to...significantly elevated levels of Hsp27 has proven to be daunting. Down regulation of Hsp27 levels in MCF7 cells using antisense technology has also

Linking micro- and macroevolutionary perspectives to evaluate the role of Quaternary sea-level oscillations in island diversification.

PubMed

Papadopoulou, Anna; Knowles, L Lacey

2017-12-01

With shifts in island area, isolation, and cycles of island fusion-fission, the role of Quaternary sea-level oscillations as drivers of diversification is complex and not well understood. Here, we conduct parallel comparisons of population and species divergence between two island areas of equivalent size that have been affected differently by sea-level oscillations, with the aim to understand the micro- and macroevolutionary dynamics associated with sea-level change. Using genome-wide datasets for a clade of seven Amphiacusta ground cricket species endemic to the Puerto Rico Bank (PRB), we found consistently deeper interspecific divergences and higher population differentiation across the unfragmented Western PRB, in comparison to the currently fragmented Eastern PRB that has experienced extreme changes in island area and connectivity during the Quaternary. We evaluate alternative hypotheses related to the microevolutionary processes (population splitting, extinction, and merging) that regulate the frequency of completed speciation across the PRB. Our results suggest that under certain combinations of archipelago characteristics and taxon traits, the repeated changes in island area and connectivity may create an opposite effect to the hypothesized "species pump" action of oscillating sea levels. Our study highlights how a microevolutionary perspective can complement current macroecological work on the Quaternary dynamics of island biodiversity. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Complex Dynamics in the Basal Ganglia: Health and Disease Beyond the Motor System.

PubMed

Andres, Daniela S; Darbin, Olivier

2018-01-01

The rate and oscillatory hypotheses are the two main current frameworks of basal ganglia pathophysiology. Both hypotheses have emerged from research on movement disorders sharing similar conceptualizations. These pathological conditions are classified either as hypokinetic or hyperkinetic, and the electrophysiological hallmarks of basal ganglia dysfunction are categorized as prokinetic or antikinetic. Although nonmotor symptoms, including neurobehavioral symptoms, are a key manifestation of basal ganglia dysfunction, they are uncommonly accounted for in these models. In patients with Parkinson's disease, the broad spectrum of motor symptoms and neurobehavioral symptoms challenges the concept that basal ganglia disorders can be classified into two categories. The profile of symptoms of basal ganglia dysfunction is best characterized by a breakdown of information processing, accompanied at an electrophysiological level by complex alterations of spiking activity from basal ganglia neurons. The authors argue that the dynamics of the basal ganglia circuit cannot be fully characterized by linear properties such as the firing rate or oscillatory activity. In fact, the neuronal spiking stream of the basal ganglia circuit is irregular but has temporal structure. In this context, entropy was introduced as a measure of probabilistic irregularity in the temporal organization of neuronal activity of the basal ganglia, giving place to the entropy hypothesis of basal ganglia pathology. Obtaining a quantitative characterization of irregularity of spike trains from basal ganglia neurons is key to elaborating a new framework of basal ganglia pathophysiology.

Exaggerated perception of facial expressions is increased in individuals with schizotypal traits

PubMed Central

Uono, Shota; Sato, Wataru; Toichi, Motomi

2015-01-01

Emotional facial expressions are indispensable communicative tools, and social interactions involving facial expressions are impaired in some psychiatric disorders. Recent studies revealed that the perception of dynamic facial expressions was exaggerated in normal participants, and this exaggerated perception is weakened in autism spectrum disorder (ASD). Based on the notion that ASD and schizophrenia spectrum disorder are at two extremes of the continuum with respect to social impairment, we hypothesized that schizophrenic characteristics would strengthen the exaggerated perception of dynamic facial expressions. To test this hypothesis, we investigated the relationship between the perception of facial expressions and schizotypal traits in a normal population. We presented dynamic and static facial expressions, and asked participants to change an emotional face display to match the perceived final image. The presence of schizotypal traits was positively correlated with the degree of exaggeration for dynamic, as well as static, facial expressions. Among its subscales, the paranoia trait was positively correlated with the exaggerated perception of facial expressions. These results suggest that schizotypal traits, specifically the tendency to over-attribute mental states to others, exaggerate the perception of emotional facial expressions. PMID:26135081

Exaggerated perception of facial expressions is increased in individuals with schizotypal traits.

PubMed

Uono, Shota; Sato, Wataru; Toichi, Motomi

2015-07-02

Emotional facial expressions are indispensable communicative tools, and social interactions involving facial expressions are impaired in some psychiatric disorders. Recent studies revealed that the perception of dynamic facial expressions was exaggerated in normal participants, and this exaggerated perception is weakened in autism spectrum disorder (ASD). Based on the notion that ASD and schizophrenia spectrum disorder are at two extremes of the continuum with respect to social impairment, we hypothesized that schizophrenic characteristics would strengthen the exaggerated perception of dynamic facial expressions. To test this hypothesis, we investigated the relationship between the perception of facial expressions and schizotypal traits in a normal population. We presented dynamic and static facial expressions, and asked participants to change an emotional face display to match the perceived final image. The presence of schizotypal traits was positively correlated with the degree of exaggeration for dynamic, as well as static, facial expressions. Among its subscales, the paranoia trait was positively correlated with the exaggerated perception of facial expressions. These results suggest that schizotypal traits, specifically the tendency to over-attribute mental states to others, exaggerate the perception of emotional facial expressions.

Micron-scale coherence in interphase chromatin dynamics

PubMed Central

Zidovska, Alexandra; Weitz, David A.; Mitchison, Timothy J.

2013-01-01

Chromatin structure and dynamics control all aspects of DNA biology yet are poorly understood, especially at large length scales. We developed an approach, displacement correlation spectroscopy based on time-resolved image correlation analysis, to map chromatin dynamics simultaneously across the whole nucleus in cultured human cells. This method revealed that chromatin movement was coherent across large regions (4–5 µm) for several seconds. Regions of coherent motion extended beyond the boundaries of single-chromosome territories, suggesting elastic coupling of motion over length scales much larger than those of genes. These large-scale, coupled motions were ATP dependent and unidirectional for several seconds, perhaps accounting for ATP-dependent directed movement of single genes. Perturbation of major nuclear ATPases such as DNA polymerase, RNA polymerase II, and topoisomerase II eliminated micron-scale coherence, while causing rapid, local movement to increase; i.e., local motions accelerated but became uncoupled from their neighbors. We observe similar trends in chromatin dynamics upon inducing a direct DNA damage; thus we hypothesize that this may be due to DNA damage responses that physically relax chromatin and block long-distance communication of forces. PMID:24019504

Pou5f1-dependent EGF expression controls E-cad endocytosis, cell adhesion, and zebrafish epiboly movements

PubMed Central

Song, Sungmin; Eckerle, Stephanie; Onichtchouk, Daria; Marrs, James A.; Nitschke, Roland; Driever, Wolfgang

2013-01-01

Summary Initiation of motile cell behavior in embryonic development occurs during late blastula stages when gastrulation begins. At this stage, the strong adhesion of blastomeres has to be modulated to enable dynamic behavior, similar to epithelial-to-mesenchymal transitions. We show that in zebrafish MZspg embryos mutant for the stem cell transcription factor Pou5f1/Oct4, which are severely delayed in the epiboly gastrulation movement, all blastomeres are defective in E-cad endosomal trafficking and E-cad accumulates at the plasma membrane. We find that Pou5f1-dependent control of EGF expression regulates endosomal E-cad trafficking. EGFR may act via modulation of p120 activity. Loss of E-cad dynamics reduces cohesion of cells in reaggregation assays. Quantitative analysis of cell behavior indicates that dynamic E-cad endosomal trafficking is required for epiboly cell movements. We hypothesize that dynamic control of E-cad trafficking is essential to effectively generate new adhesion sites when cells move relative to each other. PMID:23484854

The impact of intraglottal vortices on vocal fold dynamics

NASA Astrophysics Data System (ADS)

Erath, Byron; Pirnia, Alireza; Peterson, Sean

2016-11-01

During voiced speech a critical pressure is produced in the lungs that separates the vocal folds and creates a passage (the glottis) for airflow. As air passes through the vocal folds the resulting aerodynamic loading, coupled with the tissue properties of the vocal folds, produces self-sustained oscillations. Throughout each cycle a complex flow field develops, characterized by a plethora of viscous flow phenomena. Air passing through the glottis creates a jet, with periodically-shed vortices developing due to flow separation and the Kelvin-Helmholtz instability in the shear layer. These vortices have been hypothesized to be a crucial mechanism for producing vocal fold vibrations. In this study the effect of vortices on the vocal fold dynamics is investigated experimentally by passing a vortex ring over a flexible beam with the same non-dimensional mechanical properties as the vocal folds. Synchronized particle image velocimetry data are acquired in tandem with the beam dynamics. The resulting impact of the vortex ring loading on vocal fold dynamics is discussed in detail. This work was supported by the National Science Foundation Grant CBET #1511761.

Rethinking intractable conflict: the perspective of dynamical systems.

PubMed

Vallacher, Robin R; Coleman, Peter T; Nowak, Andrzej; Bui-Wrzosinska, Lan

2010-01-01

Intractable conflicts are demoralizing. Beyond destabilizing the families, communities, or international regions in which they occur, they tend to perpetuate the very conditions of misery and hate that contributed to them in the first place. Although the common factors and processes associated with intractable conflicts have been identified through research, they represent an embarrassment of riches for theory construction. Thus, the current task in this area is integrating these diverse factors into an account that provides a coherent perspective yet allows for prediction and a basis for conflict resolution in specific conflict settings. We suggest that the perspective of dynamical systems provides such an account. This article outlines the key concepts and hypotheses associated with this approach. It is organized around a set of basic questions concerning intractable conflict for which the dynamical perspective offers fresh insight and testable propositions. The questions and answers are intended to provide readers with basic concepts and principles of complexity and dynamical systems that are useful for rethinking the nature of intractable conflict and the means by which such conflict can be transformed. Copyright 2010 APA, all rights reserved.

Data collapse and critical dynamics in neuronal avalanche data

NASA Astrophysics Data System (ADS)

Butler, Thomas; Friedman, Nir; Dahmen, Karin; Beggs, John; Deville, Lee; Ito, Shinya

2012-02-01

The tasks of information processing, computation, and response to stimuli require neural computation to be remarkably flexible and diverse. To optimally satisfy the demands of neural computation, neuronal networks have been hypothesized to operate near a non-equilibrium critical point. In spite of their importance for neural dynamics, experimental evidence for critical dynamics has been primarily limited to power law statistics that can also emerge from non-critical mechanisms. By tracking the firing of large numbers of synaptically connected cortical neurons and comparing the resulting data to the predictions of critical phenomena, we show that cortical tissues in vitro can function near criticality. Among the most striking predictions of critical dynamics is that the mean temporal profiles of avalanches of widely varying durations are quantitatively described by a single universal scaling function (data collapse). We show for the first time that this prediction is confirmed in neuronal networks. We also show that the data have three additional features predicted by critical phenomena: approximate power law distributions of avalanche sizes and durations, samples in subcritical and supercritical phases, and scaling laws between anomalous exponents.

A wet-geology and cold-climate Mars model: Punctuation of a slow dynamic approach to equilibrium

NASA Technical Reports Server (NTRS)

Kargel, J. S.

1993-01-01

It was suggested that Mars may have possessed a relatively warm humid climate and a vigorous hydrological cycle involving meteoric precipitation, oceans, and continental ice sheets. Baker hypothesized that these geologically active conditions may have been repeated several times; each of these dynamic epochs was followed by a collapse of the climate and hydrologic cycle of Mars into essentially current conditions, completing what is termed a 'Baker cycle'. The purpose is to present an endmember possibility that Martian glacial landscapes, including some that were previously considered to have formed under warm climatic conditions, might be explained by processes compatible with an extremely cold surface. Two aspects of hypothesized Martian glacial terrains were cited as favoring a warm climate during Baker cycles: (1) the formation of some landscapes, including possible eskers, tunnel channels, drumlins, and outwash plains, appears to have required liquid water, and (2) a liquid-surfaced ocean was probably necessary to feed the glaciers. The requirement for liquid water, if these features were correctly interpreted, is difficult to avoid; it is entirely possible that a comparatively warm climate was involved, but it is not clear that formation of landforms by wet-based glaciers actually requires a warm climate. Even less certain is the supposed requirement for liquid oceans. Formation of glaciers only requires a source of water or ice to supply an amount of precipitation that exceeds losses due to melting and sublimation. At Martian temperatures precipitation is very low, but so are melting and sublimation, so a large body of ice that is unstable with respect to sublimation may take the role of Earth's oceans in feeding the glaciers. Recent models suggest that even current Martian polar caps, long thought to be static bodies of ice and dust, might actually be slow-moving, cryogenic continental glaciers. Is it possible that subglacial processes beneath cryogenic (but wetbased) ice sheets formed the hypothesized Martian glacial landscapes?

Narrow Scale Flow and a Weak Field by the Top of Earth's Core: Evidence from Orsted, Magsat and Secular Variation

NASA Technical Reports Server (NTRS)

Voorhies, Coerte V.

2004-01-01

As Earth's main magnetic field weakens, our magnetic shield against the onslaught of the solar wind thins. And the field strength needed to fend off battering by solar coronal mass ejections is decreasing, just when the delicate complexity of modem, vulnerable, electro-technological systems is increasing at an unprecedented rate. Recently, a working group of distinguished scientist from across the nation has asked NASA's Solid Earth and Natural Hazards program a key question: What are the dynamics of Earth s magnetic field and its interactions with the Earth system? Paleomagnetic studies of crustal rocks magnetized in the geologic past reveal that polarity reversals have occurred many times during Earth s history. Networked super-computer simulations of core field and flow, including effects of gravitational, pressure, rotational Coriolis, magnetic and viscous forces, suggest how this might happen in detail. And space-based measurements of the real, time-varying magnetic field help constrain estimates of the speed and direction of fluid iron flowing near the top of the core and enable tests of some hypotheses about such flow. Now scientists at NASA s Goddard Space Flight Center have developed and applied methods to test the hypotheses of narrow scale flow and of a dynamically weak magnetic field near the top of Earth s core. Using two completely different methods, C. V. Voorhies has shown these hypotheses lead to specific theoretical forms for the "spectrum" of Earth s main magnetic field and the spectrum of its rate of change. Much as solar physicists use a prism to separate sunlight into its spectrum, from long wavelength red to short wavelength blue light, geophysicists use a digital prism, spherical harmonic analysis, to separate the measured geomagnetic field into its spectrum, from long to short wavelength fields. They do this for the rate of change of the field as well.

Voltage Imaging of Waking Mouse Cortex Reveals Emergence of Critical Neuronal Dynamics

PubMed Central

Scott, Gregory; Fagerholm, Erik D.; Mutoh, Hiroki; Leech, Robert; Sharp, David J.; Shew, Woodrow L.

2014-01-01

Complex cognitive processes require neuronal activity to be coordinated across multiple scales, ranging from local microcircuits to cortex-wide networks. However, multiscale cortical dynamics are not well understood because few experimental approaches have provided sufficient support for hypotheses involving multiscale interactions. To address these limitations, we used, in experiments involving mice, genetically encoded voltage indicator imaging, which measures cortex-wide electrical activity at high spatiotemporal resolution. Here we show that, as mice recovered from anesthesia, scale-invariant spatiotemporal patterns of neuronal activity gradually emerge. We show for the first time that this scale-invariant activity spans four orders of magnitude in awake mice. In contrast, we found that the cortical dynamics of anesthetized mice were not scale invariant. Our results bridge empirical evidence from disparate scales and support theoretical predictions that the awake cortex operates in a dynamical regime known as criticality. The criticality hypothesis predicts that small-scale cortical dynamics are governed by the same principles as those governing larger-scale dynamics. Importantly, these scale-invariant principles also optimize certain aspects of information processing. Our results suggest that during the emergence from anesthesia, criticality arises as information processing demands increase. We expect that, as measurement tools advance toward larger scales and greater resolution, the multiscale framework offered by criticality will continue to provide quantitative predictions and insight on how neurons, microcircuits, and large-scale networks are dynamically coordinated in the brain. PMID:25505314

Impaired social brain network for processing dynamic facial expressions in autism spectrum disorders

PubMed Central

2012-01-01

Background Impairment of social interaction via facial expressions represents a core clinical feature of autism spectrum disorders (ASD). However, the neural correlates of this dysfunction remain unidentified. Because this dysfunction is manifested in real-life situations, we hypothesized that the observation of dynamic, compared with static, facial expressions would reveal abnormal brain functioning in individuals with ASD. We presented dynamic and static facial expressions of fear and happiness to individuals with high-functioning ASD and to age- and sex-matched typically developing controls and recorded their brain activities using functional magnetic resonance imaging (fMRI). Result Regional analysis revealed reduced activation of several brain regions in the ASD group compared with controls in response to dynamic versus static facial expressions, including the middle temporal gyrus (MTG), fusiform gyrus, amygdala, medial prefrontal cortex, and inferior frontal gyrus (IFG). Dynamic causal modeling analyses revealed that bi-directional effective connectivity involving the primary visual cortex–MTG–IFG circuit was enhanced in response to dynamic as compared with static facial expressions in the control group. Group comparisons revealed that all these modulatory effects were weaker in the ASD group than in the control group. Conclusions These results suggest that weak activity and connectivity of the social brain network underlie the impairment in social interaction involving dynamic facial expressions in individuals with ASD. PMID:22889284

Mitochondria: A Connecting Link In The Major Depressive Disorder Jigsaw.

PubMed

Sharma, Shilpa; Akundi, Ravi Shankar

2018-03-02

Depression is a widespread phenomenon with varying degrees of pathology in different patients. Various hypotheses have been proposed for the cause and continuance of depression. Some of these include, but not limited to, the monoamine hypothesis, the neuroendocrine hypothesis, and the more recent epigenetic and inflammatory hypotheses. In this article, we review all the above hypotheses with a focus on the role of mitochondria as the connecting link. Oxidative stress, respiratory activity, mitochondrial dynamics and metabolism are some of the mitochondria-dependent factors which are affected during depression. We also propose exogenous ATP as a contributing factor to depression. Literature review shows that pro-inflammatory markers are elevated in depressive individuals. The cause for elevated levels of cytokines in depression is not completely understood. We propose exogenous ATP activates purinergic receptors which in turn increase the levels of various pro-inflammatory factors in the pathophysiology of depression. Mitochondria are integral to the function of neurons and undergo dysfunction in major depressive disorder patients. This dysfunction is reflected in all the various hypotheses that have been proposed for depression. Among the newer targets identified, which also involve mitochondria, includes the role of exogenous ATP. The diversity of purinergic receptors, and their differential expression among various individuals in the population, due to genetic and environmental (prenatal) influences, may influence the susceptibility and severity of depression. Identifying specific receptors involved and using patient-specific purinergic receptor antagonist may be an appropriate therapeutic course in the future. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Motor control theories and their applications.

PubMed

Latash, Mark L; Levin, Mindy F; Scholz, John P; Schöner, Gregor

2010-01-01

We describe several influential hypotheses in the field of motor control including the equilibrium-point (referent configuration) hypothesis, the uncontrolled manifold hypothesis, and the idea of synergies based on the principle of motor abundance. The equilibrium-point hypothesis is based on the idea of control with thresholds for activation of neuronal pools; it provides a framework for analysis of both voluntary and involuntary movements. In particular, control of a single muscle can be adequately described with changes in the threshold of motor unit recruitment during slow muscle stretch (threshold of the tonic stretch reflex). Unlike the ideas of internal models, the equilibrium-point hypothesis does not assume neural computations of mechanical variables. The uncontrolled manifold hypothesis is based on the dynamic system approach to movements; it offers a toolbox to analyze synergic changes within redundant sets of elements related to stabilization of potentially important performance variables. The referent configuration hypothesis and the principle of abundance can be naturally combined into a single coherent scheme of control of multi-element systems. A body of experimental data on healthy persons and patients with movement disorders are reviewed in support of the mentioned hypotheses. In particular, movement disorders associated with spasticity are considered as consequences of an impaired ability to shift threshold of the tonic stretch reflex within the whole normal range. Technical details and applications of the mentioned hypo-theses to studies of motor learning are described. We view the mentioned hypotheses as the most promising ones in the field of motor control, based on a solid physical and neurophysiological foundation.

It matters how old you feel: Antecedents and performance consequences of average relative subjective age in organizations.

PubMed

Kunze, Florian; Raes, Anneloes M L; Bruch, Heike

2015-09-01

This article extends the conceptual knowledge of average relative subjective age in organizations by exploring organizational-level antecedents and consequences of employees, on average, feeling younger than their chronological age. We draw from the theories of selection-optimization-compensation and socioemotional selectivity to build a theoretical framework for relative subjective age in organizations. We hypothesize that companies in which employees, on average, perceive themselves to be younger than they actually are have a higher average individual goal accomplishment and, in turn, experience higher company performance. We further hypothesize that employees' average experience of high work-related meaning relates to a lower subjective age in organizations. In addition, we assess the role of environmental dynamism and age-inclusive human resource management as moderators in this theoretical model. Through empirically testing this model in a multisource dataset, including 107 companies with 15,164 participating employees, we received support for the hypothesized relationships. Our results contribute to current debates in the scientific literature on age and have important practical implications in light of the demographic changes faced by many companies. This research indicates to both researchers and practitioners that it is not employees' chronological age but their subjective age, a factor that can be influenced, which drives organizational performance outcomes. (c) 2015 APA, all rights reserved).

Capitalizing on Citizen Science Data for Validating Models and Generating Hypotheses Describing Meteorological Drivers of Mosquito-Borne Disease Risk

NASA Astrophysics Data System (ADS)

Boger, R. A.; Low, R.; Paull, S.; Anyamba, A.; Soebiyanto, R. P.

2017-12-01

Temperature and precipitation are important drivers of mosquito population dynamics, and a growing set of models have been proposed to characterize these relationships. Validation of these models, and development of broader theories across mosquito species and regions could nonetheless be improved by comparing observations from a global dataset of mosquito larvae with satellite-based measurements of meteorological variables. Citizen science data can be particularly useful for two such aspects of research into the meteorological drivers of mosquito populations: i) Broad-scale validation of mosquito distribution models and ii) Generation of quantitative hypotheses regarding changes to mosquito abundance and phenology across scales. The recently released GLOBE Observer Mosquito Habitat Mapper (GO-MHM) app engages citizen scientists in identifying vector taxa, mapping breeding sites and decommissioning non-natural habitats, and provides a potentially useful new tool for validating mosquito ubiquity projections based on the analysis of remotely sensed environmental data. Our early work with GO-MHM data focuses on two objectives: validating citizen science reports of Aedes aegypti distribution through comparison with accepted scientific data sources, and exploring the relationship between extreme temperature and precipitation events and subsequent observations of mosquito larvae. Ultimately the goal is to develop testable hypotheses regarding the shape and character of this relationship between mosquito species and regions.

A clinical data validated mathematical model of prostate cancer growth under intermittent androgen suppression therapy

NASA Astrophysics Data System (ADS)

Portz, Travis; Kuang, Yang; Nagy, John D.

2012-03-01

Prostate cancer is commonly treated by a form of hormone therapy called androgen suppression. This form of treatment, while successful at reducing the cancer cell population, adversely affects quality of life and typically leads to a recurrence of the cancer in an androgen-independent form. Intermittent androgen suppression aims to alleviate some of these adverse affects by cycling the patient on and off treatment. Clinical studies have suggested that intermittent therapy is capable of maintaining androgen dependence over multiple treatment cycles while increasing quality of life during off-treatment periods. This paper presents a mathematical model of prostate cancer to study the dynamics of androgen suppression therapy and the production of prostate-specific antigen (PSA), a clinical marker for prostate cancer. Preliminary models were based on the assumption of an androgen-independent (AI) cell population with constant net growth rate. These models gave poor accuracy when fitting clinical data during simulation. The final model presented hypothesizes an AI population with increased sensitivity to low levels of androgen. It also hypothesizes that PSA production is heavily dependent on androgen. The high level of accuracy in fitting clinical data with this model appears to confirm these hypotheses, which are also consistent with biological evidence.

Gas Replacements for GFP to Track Microbial Dynamics in Soils and Sediments

NASA Astrophysics Data System (ADS)

Cheng, Hsiao-Ying; Silberg, Jonathan; Masiello, Caroline

2016-04-01

Metagenomic analyses offer unprecedented views of soil microbial communities, and additionally provide a host of testable hypotheses about the biological mechanisms driving global biogeochemical fluxes. Outside the biogeosciences, hypotheses generated by metagenomics are often tested using biosensors, microbes programmed to respond in a detectable way to either changes in their metabolism or changes in the environment. A very large number of microbial behaviors can be monitored using biosensors, but these sensors typically report in ways that are undetectable in soils, e.g. by releasing green fluorescent protein (GFP). We are building a new class of biosensors that report by releasing easily-detected gases. We will provide an overview of the potential uses of gas-reporting biosensors in geobiology, and will report the current development these sensors. One goal in the development of these sensors is to make tractable the testing of gene expression hypotheses derived from metagenomics data. Examples of processes that could be tracked non-invasively with gas sensors include coordination of biofilm formation, nitrification, rhizobial infection of plant roots, and at least some forms of methanogenesis, all of which are managed by the easily-engineered acyl homoserine lactone cell-cell communication system. Another relatively simple process to track with gas sensors is horizontal gene transfer. We will report on the progress of these proof-of-concept examples.

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

Walker, Anthony P.; Quaife, Tristan; van Bodegom, Peter M.

Here, the maximum photosynthetic carboxylation rate (V cmax) is an influential plant trait that has multiple scaling hypotheses, which is a source of uncertainty in predictive understanding of global gross primary production (GPP). Four trait-scaling hypotheses (plant functional type, nutrient limitation, environmental filtering, and plant plasticity) with nine specific implementations were used to predict global V cmax distributions and their impact on global GPP in the Sheffield Dynamic Global Vegetation Model (SDGVM). Global GPP varied from 108.1 to 128.2 PgC yr –1, 65% of the range of a recent model intercomparison of global GPP. The variation in GPP propagated throughmore » to a 27% coefficient of variation in net biome productivity (NBP). All hypotheses produced global GPP that was highly correlated ( r = 0.85–0.91) with three proxies of global GPP. Plant functional type-based nutrient limitation, underpinned by a core SDGVM hypothesis that plant nitrogen (N) status is inversely related to increasing costs of N acquisition with increasing soil carbon, adequately reproduced global GPP distributions. Further improvement could be achieved with accurate representation of water sensitivity and agriculture in SDGVM. Mismatch between environmental filtering (the most data-driven hypothesis) and GPP suggested that greater effort is needed understand V cmax variation in the field, particularly in northern latitudes.« less

Resting-State Functional Connectivity Emerges from Structurally and Dynamically Shaped Slow Linear Fluctuations

PubMed Central

Deco, Gustavo; Mantini, Dante; Romani, Gian Luca; Hagmann, Patric; Corbetta, Maurizio

2013-01-01

Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure–function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure–function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications. PMID:23825427

Resting-state functional connectivity emerges from structurally and dynamically shaped slow linear fluctuations.

PubMed

Deco, Gustavo; Ponce-Alvarez, Adrián; Mantini, Dante; Romani, Gian Luca; Hagmann, Patric; Corbetta, Maurizio

2013-07-03

Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure-function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure-function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications.

High-Throughput Sequencing: A Roadmap Toward Community Ecology

PubMed Central

Poisot, Timothée; Péquin, Bérangère; Gravel, Dominique

2013-01-01

High-throughput sequencing is becoming increasingly important in microbial ecology, yet it is surprisingly under-used to generate or test biogeographic hypotheses. In this contribution, we highlight how adding these methods to the ecologist toolbox will allow the detection of new patterns, and will help our understanding of the structure and dynamics of diversity. Starting with a review of ecological questions that can be addressed, we move on to the technical and analytical issues that will benefit from an increased collaboration between different disciplines. PMID:23610649

Energy and institution size

PubMed Central

2017-01-01

Why do institutions grow? Despite nearly a century of scientific effort, there remains little consensus on this topic. This paper offers a new approach that focuses on energy consumption. A systematic relation exists between institution size and energy consumption per capita: as energy consumption increases, institutions become larger. I hypothesize that this relation results from the interplay between technological scale and human biological limitations. I also show how a simple stochastic model can be used to link energy consumption with firm dynamics. PMID:28178339

Impact of hyperbolicity on chimera states in ensembles of nonlocally coupled chaotic oscillators

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

Semenova, N.; Anishchenko, V.; Zakharova, A.

2016-06-08

In this work we analyse nonlocally coupled networks of identical chaotic oscillators. We study both time-discrete and time-continuous systems (Henon map, Lozi map, Lorenz system). We hypothesize that chimera states, in which spatial domains of coherent (synchronous) and incoherent (desynchronized) dynamics coexist, can be obtained only in networks of chaotic non-hyperbolic systems and cannot be found in networks of hyperbolic systems. This hypothesis is supported by numerical simulations for hyperbolic and non-hyperbolic cases.

Impact of Ultraviolet Light on Vitiligo.

PubMed

Singh, Rasnik K

2017-01-01

Vitiligo is a disorder of the melanocytes that results in a dynamic spectrum of skin depigmentation. Its etiology is complex and multifactorial, with data supporting several different hypotheses. Given its prominent phenotype, vitiligo has a significant negative impact on quality of life. Coupled with the chronic and incurable nature of the disease, this presents a formidable treatment challenge. Several treatment modalities have been instituted over the years, with varying efficacy. This chapter focuses on the use of ultraviolet light in vitiligo as an established therapeutic option.

Dynamical emergence of the Universe into the false vacuum

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

Rafelski, Johann; Birrell, Jeremiah, E-mail: rafelski@physics.arizona.edu, E-mail: jbirrell@email.arizona.edu

We study how the hot Universe evolves and acquires the prevailing vacuum state, demonstrating that in specific conditions which are believed to apply, the Universe becomes frozen into the state with the smallest value of Higgs vacuum field v=( h), even if this is not the state of lowest energy. This supports the false vacuum dark energy Λ-model. Under several likely hypotheses we determine the temperature in the evolution of the Universe at which two vacuua v{sub 1}, v{sub 2} can swap between being true and false. We evaluate the dynamical surface pressure on domain walls between low and high mass vaccuamore » due to the presence of matter and show that the low mass state remains the preferred vacuum of the Universe.« less

Auditory sensitivity may require dynamically unstable spike generators: evidence from a model of electrical stimulation.

PubMed

O'Gorman, David E; Colburn, H Steven; Shera, Christopher A

2010-11-01

The response of the auditory nerve to electrical stimulation is highly sensitive to small modulations (<0.5%). This report demonstrates that dynamical instability (i.e., a positive Lyapunov exponent) can account for this sensitivity in a modified FitzHugh-Nagumo model of spike generation, so long as the input noise is not too large. This finding suggests both that spike generator instability is necessary to account for auditory nerve sensitivity and that the amplitude of physiological noise, such as that produced by the random behavior of voltage-gated sodium channels, is small. Based on these results with direct electrical stimulation, it is hypothesized that spike generator instability may be the mechanism that reconciles high sensitivity with the cross-fiber independence observed under acoustic stimulation.

Gravitational dynamics of biosystems - Some speculations

NASA Technical Reports Server (NTRS)

Kessler, J. O.; Bier, M.

1976-01-01

The response of organisms to gravity is generally discussed in terms of hypotheses involving sedimentation and other static effects. This paper considers several complex, inhomogeneous fluid-containing systems that are intended to model some possible dynamic effects of gravity on biosystems. It is shown that the presence of gravity may result in modified long range transport, concentration oscillations, and broken symmetries. The magnitude of density-gradient-driven convective transport times, and their ratios to diffusive transport times, are calculated for cell dimensions of six different plant varieties. The results indicate that further investigation of gravitational convection effects may be realistic in some cases and is definitely not in others. The results of this paper should aid in the planning of 'zero-gravity' experiments concerning plant geotropism and bio-materials processing.

Compact structure and non-Gaussian dynamics of ring polymer melts.

PubMed

Brás, Ana R; Goossen, Sebastian; Krutyeva, Margarita; Radulescu, Aurel; Farago, Bela; Allgaier, Jürgen; Pyckhout-Hintzen, Wim; Wischnewski, Andreas; Richter, Dieter

2014-05-28

We present a neutron scattering analysis of the structure and dynamics of PEO polymer rings with a molecular weight 2.5 times higher than the entanglement mass. The melt structure was found to be more compact than a Gaussian model would suggest. With increasing time the center of mass (c.o.m.) diffusion undergoes a transition from sub-diffusive to diffusive behavior. The transition time agrees well with the decorrelation time predicted by a mode coupling approach. As a novel feature well pronounced non-Gaussian behavior of the c.o.m. diffusion was found that shows surprising analogies to the cage effect known from glassy systems. Finally, the longest wavelength Rouse modes are suppressed possibly as a consequence of an onset of lattice animal features as hypothesized in theoretical approaches.

A case of mental nerve paresthesia due to dynamic compression of alveolar inferior nerve along an elongated styloid process.

PubMed

Gooris, Peter J J; Zijlmans, Jan C M; Bergsma, J Eelco; Mensink, Gertjan

2014-07-01

Spontaneous paresthesia of the mental nerve is considered an ominous clinical sign. Mental nerve paresthesia has also been referred to as numb chin syndrome. Several potentially different factors have been investigated for their role in interfering with the inferior alveolar nerve (IAN) and causing mental nerve neuropathy. In the present case, the patient had an elongated calcified styloid process that we hypothesized had caused IAN irritation during mandibular movement. This eventually resulted in progressive loss of sensation in the mental nerve region. To our knowledge, this dynamic irritation, with complete recovery after resection of the styloid process, has not been previously reported. Copyright © 2014 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Reverse Launch Abort System Parachute Architecture Trade Study

NASA Technical Reports Server (NTRS)

Litton, Daniel K.; O'Keefe, Stephen A.; Winski, Richard G.

2011-01-01

This study investigated a potential Launch Abort System (LAS) Concept of Operations and abort parachute architecture. The purpose of the study was to look at the concept of jettisoning the LAS tower forward (Reverse LAS or RLAS) into the free-stream flow rather than after reorienting to a heatshield forward orientation. A hypothesized benefit was that due to the compressed timeline the dynamic pressure at main line stretch would be substantially less. This would enable the entry parachutes to be designed and sized based on entry loading conditions rather than the current stressing case of a Pad Abort. Ultimately, concerns about the highly dynamic reorientation of the CM via parachutes, and the additional requirement of a triple bridle attachment for the RLAS parachute system, overshadowed the potential benefits and ended this effort.

Parametric and non-parametric modeling of short-term synaptic plasticity. Part I: computational study

PubMed Central

Marmarelis, Vasilis Z.; Berger, Theodore W.

2009-01-01

Parametric and non-parametric modeling methods are combined to study the short-term plasticity (STP) of synapses in the central nervous system (CNS). The nonlinear dynamics of STP are modeled by means: (1) previously proposed parametric models based on mechanistic hypotheses and/or specific dynamical processes, and (2) non-parametric models (in the form of Volterra kernels) that transforms the presynaptic signals into postsynaptic signals. In order to synergistically use the two approaches, we estimate the Volterra kernels of the parametric models of STP for four types of synapses using synthetic broadband input–output data. Results show that the non-parametric models accurately and efficiently replicate the input–output transformations of the parametric models. Volterra kernels provide a general and quantitative representation of the STP. PMID:18506609

Experimental evidence for the effect of habitat loss on the dynamics of migratory networks.

PubMed

Betini, Gustavo S; Fitzpatrick, Mark J; Norris, D Ryan

2015-06-01

Migratory animals present a unique challenge for understanding the consequences of habitat loss on population dynamics because individuals are typically distributed over a series of interconnected breeding and non-breeding sites (termed migratory network). Using replicated breeding and non-breeding populations of Drosophila melanogaster and a mathematical model, we investigated three hypotheses to explain how habitat loss influenced the dynamics of populations in networks with different degrees of connectivity between breeding and non-breeding seasons. We found that habitat loss increased the degree of connectivity in the network and influenced population size at sites that were not directly connected to the site where habitat loss occurred. However, connected networks only buffered global population declines at high levels of habitat loss. Our results demonstrate why knowledge of the patterns of connectivity across a species range is critical for predicting the effects of environmental change and provide empirical evidence for why connected migratory networks are commonly found in nature. © 2015 John Wiley & Sons Ltd/CNRS.

Dual-loop model of the human controller

NASA Technical Reports Server (NTRS)

Hess, R. A.

1978-01-01

A dual-loop model of the human controller in single-axis compensatory tracking tasks is introduced. This model possesses an inner-loop closure that involves feeding back that portion of controlled element output rate that is due to control activity. A novel feature of the model is the explicit appearance of the human's internal representation of the manipulator-controlled element dynamics in the inner loop. The sensor inputs to the human controller are assumed to be system error and control force. The former can be sensed via visual, aural, or tactile displays, whereas the latter is assumed to be sensed in kinesthetic fashion. A set of general adaptive characteristics for the model is hypothesized, including a method for selecting simplified internal models of the manipulator-controlled element dynamics. It is demonstrated that the model can produce controller describing functions that closely approximate those measured in four laboratory tracking tasks in which the controlled element dynamics vary considerably in terms of ease of control. An empirically derived expression for the normalized injected error remnant spectrum is introduced.

Negative mood and mind wandering increase long-range temporal correlations in attention fluctuations.

PubMed

Irrmischer, Mona; van der Wal, C Natalie; Mansvelder, Huibert D; Linkenkaer-Hansen, Klaus

2018-01-01

There is growing evidence that the intermittent nature of mind wandering episodes and mood have a pronounced influence on trial-to-trial variability in performance. Nevertheless, the temporal dynamics and significance of such lapses in attention remains inadequately understood. Here, we hypothesize that the dynamics of fluctuations in sustained attention between external and internal sources of information obey so-called critical-state dynamics, characterized by trial-to-trial dependencies with long-range temporal correlations. To test this, we performed behavioral investigations measuring reaction times in a visual sustained attention task and cued introspection in probe-caught reports of mind wandering. We show that trial-to-trial variability in reaction times exhibit long-range temporal correlations in agreement with the criticality hypothesis. Interestingly, we observed the fastest responses in subjects with the weakest long-range temporal correlations and show the vital effect of mind wandering and bad mood on this response variability. The implications of these results stress the importance of future research to increase focus on behavioral variability.

Use of CFD for static sampling hood design: An example for methane flux assessment on landfill surfaces.

PubMed

Lucernoni, Federico; Rizzotto, Matteo; Tapparo, Federica; Capelli, Laura; Sironi, Selena; Busini, Valentina

2016-11-01

The work focuses on the principles for the design of a specific static hood and on the definition of an optimal sampling procedure for the assessment of landfill gas (LFG) surface emissions. This is carried out by means of computational fluid dynamics (CFD) simulations to investigate the fluid dynamics conditions of the hood. The study proves that understanding the fluid dynamic conditions is fundamental in order to understand the sampling results and correctly interpret the measured concentration values by relating them to a suitable LFG emission model, and therefore to estimate emission rates. For this reason, CFD is a useful tool for the design and evaluation of sampling systems, among others, to verify the fundamental hypotheses on which the mass balance for the sampling hood is defined. The procedure here discussed, which is specific for the case of the investigated landfill, can be generalized to be applied also to different scenarios, where hood sampling is involved. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tipping point analysis of ocean acoustic noise

NASA Astrophysics Data System (ADS)

Livina, Valerie N.; Brouwer, Albert; Harris, Peter; Wang, Lian; Sotirakopoulos, Kostas; Robinson, Stephen

2018-02-01

We apply tipping point analysis to a large record of ocean acoustic data to identify the main components of the acoustic dynamical system and study possible bifurcations and transitions of the system. The analysis is based on a statistical physics framework with stochastic modelling, where we represent the observed data as a composition of deterministic and stochastic components estimated from the data using time-series techniques. We analyse long-term and seasonal trends, system states and acoustic fluctuations to reconstruct a one-dimensional stochastic equation to approximate the acoustic dynamical system. We apply potential analysis to acoustic fluctuations and detect several changes in the system states in the past 14 years. These are most likely caused by climatic phenomena. We analyse trends in sound pressure level within different frequency bands and hypothesize a possible anthropogenic impact on the acoustic environment. The tipping point analysis framework provides insight into the structure of the acoustic data and helps identify its dynamic phenomena, correctly reproducing the probability distribution and scaling properties (power-law correlations) of the time series.

Agent-based modeling in ecological economics.

PubMed

Heckbert, Scott; Baynes, Tim; Reeson, Andrew

2010-01-01

Interconnected social and environmental systems are the domain of ecological economics, and models can be used to explore feedbacks and adaptations inherent in these systems. Agent-based modeling (ABM) represents autonomous entities, each with dynamic behavior and heterogeneous characteristics. Agents interact with each other and their environment, resulting in emergent outcomes at the macroscale that can be used to quantitatively analyze complex systems. ABM is contributing to research questions in ecological economics in the areas of natural resource management and land-use change, urban systems modeling, market dynamics, changes in consumer attitudes, innovation, and diffusion of technology and management practices, commons dilemmas and self-governance, and psychological aspects to human decision making and behavior change. Frontiers for ABM research in ecological economics involve advancing the empirical calibration and validation of models through mixed methods, including surveys, interviews, participatory modeling, and, notably, experimental economics to test specific decision-making hypotheses. Linking ABM with other modeling techniques at the level of emergent properties will further advance efforts to understand dynamics of social-environmental systems.

Limited and time-delayed internal resource allocation generates oscillations and chaos in the dynamics of citrus crops

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

Ye, Xujun, E-mail: yexujun@cc.hirosaki-u.ac.jp; Faculty of Agriculture and Life Sciences, Hirosaki University, Aomori 036-8561; Sakai, Kenshi, E-mail: ken@cc.tuat.ac.jp

Alternate bearing or masting is a yield variability phenomenon in perennial crops. The complex dynamics in this phenomenon have stimulated much ecological research. Motivated by data from an eight-year experiment with forty-eight individual trees, we explored the mechanism inherent to these dynamics in Satsuma mandarin (Citrus unshiu Marc.). By integrating high-resolution imaging technology, we found that the canopy structure and reproduction output of individual citrus crops are mutually dependent on each other. Furthermore, it was revealed that the mature leaves in early season contribute their energy to the fruiting of the current growing season, whereas the younger leaves show amore » delayed contribution to the next growing season. We thus hypothesized that the annual yield variability might be caused by the limited and time-delayed resource allocation in individual plants. A novel lattice model based on this hypothesis demonstrates that this pattern of resource allocation will generate oscillations and chaos in citrus yield.« less

Three parameters optimizing closed-loop control in sequential segmental neuromuscular stimulation.

PubMed

Zonnevijlle, E D; Somia, N N; Perez Abadia, G; Stremel, R W; Maldonado, C J; Werker, P M; Kon, M; Barker, J H

1999-05-01

In conventional dynamic myoplasties, the force generation is poorly controlled. This causes unnecessary fatigue of the transposed/transplanted electrically stimulated muscles and causes damage to the involved tissues. We introduced sequential segmental neuromuscular stimulation (SSNS) to reduce muscle fatigue by allowing part of the muscle to rest periodically while the other parts work. Despite this improvement, we hypothesize that fatigue could be further reduced in some applications of dynamic myoplasty if the muscles were made to contract according to need. The first necessary step is to gain appropriate control over the contractile activity of the dynamic myoplasty. Therefore, closed-loop control was tested on a sequentially stimulated neosphincter to strive for the best possible control over the amount of generated pressure. A selection of parameters was validated for optimizing control. We concluded that the frequency of corrections, the threshold for corrections, and the transition time are meaningful parameters in the controlling algorithm of the closed-loop control in a sequentially stimulated myoplasty.

The Dynamics of Neurosteroids and Sex-Related Hormones in the Pathogenesis of Alzheimer's Disease.

PubMed

Hasanpour, Milad; Nourazarian, Alireza; Geranmayeh, Mohammad Hossein; Nikanfar, Masoud; Khaki-Khatibi, Fatemeh; Rahbarghazi, Reza

2018-05-04

Alzheimer's disease (AD) is commonly diagnosed by vast extracellular amyloid deposits and existence of intracellular neurofibrillary tangles. In accordance with the literature, age-related loss of sex steroid hormones in either males or females was found in relation to AD subjects. The dynamics of these hormones have been previously described in both physiological and pathological conditions with the evidence of changes in various intracellular signalings regarding the neurodegenerative disease. The potent protective effects of sex steroid hormones and their synthetic analogs are indicative of the decrease in the accumulated levels of intercellular beta-amyloid (Aβ) protein and an increase of specific proteases activity, resulting in the improvement of pathological features. In the current review, we focused on the dynamic of signaling pathway related to sex steroid hormones. It is logical to hypothesize that androgen hormones have regulatory actions on the kinetics of Aβ which make them as a promising preventive approach for neurodegenerative diseases in the near future.

Modeling T-cell activation using gene expression profiling and state-space models.

PubMed

Rangel, Claudia; Angus, John; Ghahramani, Zoubin; Lioumi, Maria; Sotheran, Elizabeth; Gaiba, Alessia; Wild, David L; Falciani, Francesco

2004-06-12

We have used state-space models to reverse engineer transcriptional networks from highly replicated gene expression profiling time series data obtained from a well-established model of T-cell activation. State space models are a class of dynamic Bayesian networks that assume that the observed measurements depend on some hidden state variables that evolve according to Markovian dynamics. These hidden variables can capture effects that cannot be measured in a gene expression profiling experiment, e.g. genes that have not been included in the microarray, levels of regulatory proteins, the effects of messenger RNA and protein degradation, etc. Bootstrap confidence intervals are developed for parameters representing 'gene-gene' interactions over time. Our models represent the dynamics of T-cell activation and provide a methodology for the development of rational and experimentally testable hypotheses. Supplementary data and Matlab computer source code will be made available on the web at the URL given below. http://public.kgi.edu/~wild/LDS/index.htm

Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation.

PubMed

Zhang, Fan; Liu, Runsheng; Zheng, Jie

2016-12-23

Linking computational models of signaling pathways to predicted cellular responses such as gene expression regulation is a major challenge in computational systems biology. In this work, we present Sig2GRN, a Cytoscape plugin that is able to simulate time-course gene expression data given the user-defined external stimuli to the signaling pathways. A generalized logical model is used in modeling the upstream signaling pathways. Then a Boolean model and a thermodynamics-based model are employed to predict the downstream changes in gene expression based on the simulated dynamics of transcription factors in signaling pathways. Our empirical case studies show that the simulation of Sig2GRN can predict changes in gene expression patterns induced by DNA damage signals and drug treatments. As a software tool for modeling cellular dynamics, Sig2GRN can facilitate studies in systems biology by hypotheses generation and wet-lab experimental design. http://histone.scse.ntu.edu.sg/Sig2GRN/.

A modeling approach for reposition dynamics of litter composition in coastal areas of the city of Santos, Sao Paulo, Brazil.

PubMed

Cordeiro, Taynara Cristina; Barrella, Walter; Butturi-Gomes, Davi; Petrere Júnior, Miguel

2018-03-01

Given the complexity of the dynamics in litter reposition, our objective was modeling the possible main and interaction effects of tidal oscillations, seasons of the year and the moon phases over the solid waste in Santos beaches. A total of 80 collections were carried out using quadrat sampling, from which we classified, counted and weighed all residue items. We fitted mixed Hurdle models to the output datasets and performed hypotheses tests based on this framework. We found plastic to be the most abundant residue in all seasons, moon phases and tides, followed by Styrofoam and wood. Our models suggest the strongest effect was due to seasonal variations, which, in turn, may be related to different human activities. Although the dynamics of different components showed independency of all interaction structures, plastics depended on the interaction of tide and season, whose impact over estuarine life and ecosystem services shall be further investigated. Copyright © 2018 Elsevier Ltd. All rights reserved.

Negative mood and mind wandering increase long-range temporal correlations in attention fluctuations

PubMed Central

van der Wal, C. Natalie; Mansvelder, Huibert D.; Linkenkaer-Hansen, Klaus

2018-01-01

There is growing evidence that the intermittent nature of mind wandering episodes and mood have a pronounced influence on trial-to-trial variability in performance. Nevertheless, the temporal dynamics and significance of such lapses in attention remains inadequately understood. Here, we hypothesize that the dynamics of fluctuations in sustained attention between external and internal sources of information obey so-called critical-state dynamics, characterized by trial-to-trial dependencies with long-range temporal correlations. To test this, we performed behavioral investigations measuring reaction times in a visual sustained attention task and cued introspection in probe-caught reports of mind wandering. We show that trial-to-trial variability in reaction times exhibit long-range temporal correlations in agreement with the criticality hypothesis. Interestingly, we observed the fastest responses in subjects with the weakest long-range temporal correlations and show the vital effect of mind wandering and bad mood on this response variability. The implications of these results stress the importance of future research to increase focus on behavioral variability. PMID:29746529

Tracking ongoing cognition in individuals using brief, whole-brain functional connectivity patterns

PubMed Central

Gonzalez-Castillo, Javier; Hoy, Colin W.; Handwerker, Daniel A.; Robinson, Meghan E.; Buchanan, Laura C.; Saad, Ziad S.; Bandettini, Peter A.

2015-01-01

Functional connectivity (FC) patterns in functional MRI exhibit dynamic behavior on the scale of seconds, with rich spatiotemporal structure and limited sets of whole-brain, quasi-stable FC configurations (FC states) recurring across time and subjects. Based on previous evidence linking various aspects of cognition to group-level, minute-to-minute FC changes in localized connections, we hypothesized that whole-brain FC states may reflect the global, orchestrated dynamics of cognitive processing on the scale of seconds. To test this hypothesis, subjects were continuously scanned as they engaged in and transitioned between mental states dictated by tasks. FC states computed within windows as short as 22.5 s permitted robust tracking of cognition in single subjects with near perfect accuracy. Accuracy dropped markedly for subjects with the lowest task performance. Spatially restricting FC information decreased accuracy at short time scales, emphasizing the distributed nature of whole-brain FC dynamics, beyond univariate magnitude changes, as valuable markers of cognition. PMID:26124112

Oak Grove Fork Habitat Improvement Project, 1988 Annual Report.

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

Bettin, Scott

The Lower Oak Grove Fork of the Clackamas River is a fifth-order tributary of the Clackamas River drainage supporting depressed runs of coho and chinook salmon, and summer and winter steelhead. Habitat condition rating for the Lower Oak Grove is good, but smelt production estimates are below the average for Clackamas River tributaries. Limiting factors in the 3.8 miles of the Lower Oak Grove supporting anadromous fish include an overall lack of quality spawning and rearing habitat. Beginning in 1986. measures to improve fish habitat in the Lower Oak Grove were developed in coordination with the Oregon Department of Fishmore » and Wildlife (ODF&W) and Portland General Electric (PGE) fisheries biologists. Prior to 1986, no measures had been applied to the stream to mitigate for PGE's storage and regulation of flows in the Oak Grove Fork (Timothy Lake, Harriet Lake). Catchable rainbow trout are stocked by ODF&W two or three times a year during the trout fishing season in the lowermost portion of the Oak Grove Fork near two Forest Service campgrounds (Ripplebrook and Rainbow). The 1987 field season marked the third year of efforts to improve fish habitat of the Lower Oak Grove Fork and restore anadromous fish production. The efforts included the development of an implementation plan for habitat improvement activities in the Lower Oak Grove Fork. post-project monitoring. and maintenance of the 1986 improvement structures. No new structures were constructed or placed in 1987. Fiscal year 1988 brought a multitude of changes which delayed implementation of plans developed in 1987. The most prominent change was the withdrawal of the proposed Spotted Owl Habitat Area (SOHA) which overlapped the Oak Grove project implementation area. Another was the change in the Forest Service biologist responsible for implementation and design of this project.« less

Are most samples of animals systematically biased? Consistent individual trait differences bias samples despite random sampling.

PubMed

Biro, Peter A

2013-02-01

Sampling animals from the wild for study is something nearly every biologist has done, but despite our best efforts to obtain random samples of animals, 'hidden' trait biases may still exist. For example, consistent behavioral traits can affect trappability/catchability, independent of obvious factors such as size and gender, and these traits are often correlated with other repeatable physiological and/or life history traits. If so, systematic sampling bias may exist for any of these traits. The extent to which this is a problem, of course, depends on the magnitude of bias, which is presently unknown because the underlying trait distributions in populations are usually unknown, or unknowable. Indeed, our present knowledge about sampling bias comes from samples (not complete population censuses), which can possess bias to begin with. I had the unique opportunity to create naturalized populations of fish by seeding each of four small fishless lakes with equal densities of slow-, intermediate-, and fast-growing fish. Using sampling methods that are not size-selective, I observed that fast-growing fish were up to two-times more likely to be sampled than slower-growing fish. This indicates substantial and systematic bias with respect to an important life history trait (growth rate). If correlations between behavioral, physiological and life-history traits are as widespread as the literature suggests, then many animal samples may be systematically biased with respect to these traits (e.g., when collecting animals for laboratory use), and affect our inferences about population structure and abundance. I conclude with a discussion on ways to minimize sampling bias for particular physiological/behavioral/life-history types within animal populations.

Impacts of Northern Pike on stocked Rainbow Trout in Pactola Reservoir, South Dakota

USGS Publications Warehouse

Scheibel, Natalie C.; Dembkowski, Daniel J.; Davis, Jacob L.; Chipps, Steven R.

2016-01-01

Establishment of nonnative Northern Pike Esox lucius in Pactola Reservoir, South Dakota, has prompted concern among biologists about the influence of this species on the lake’s intensively managed salmonid fisheries. Ancedotal information suggests that catch rates of Rainbow Trout Oncorhynchus mykiss have declined while mean size and abundance of Northern Pike has increased, although quantitative information on diet and growth of the Northern Pike population is lacking. To address potential interactions between Northern Pike and Rainbow Trout, we assessed size-dependent predation by Northern Pike on Rainbow Trout and determined the relative energetic contribution of stocked Rainbow Trout to Northern Pike growth using bioenergetics modeling. Stable isotopes combined with traditional diet analyses revealed that smaller Northern Pike (<600 mm TL) consumed primarily centrarchids and Rainbow Smelt Osmerus mordax, and Rainbow Trout contributed less than 10% to their annual energy consumption. In contrast, larger Northern Pike (≥600 mm TL) consumed primarily Rainbow Trout, which accounted for 56% of their annual energy consumption. Combining estimates of Northern Pike predation with production costs of catchable-size Rainbow Trout revealed that annual economic losses ranged from US$15,259 to $24,801 per year. Over its lifespan, an age-10 Northern Pike was estimated to consume ~117 Rainbow Trout worth approximately $340. Thus, Northern Pike predation substantially influences salmonid management initiatives and is likely a primary factor contributing to reduced Rainbow Trout abundance and return to anglers in Pactola Reservoir. Strategies for reducing Northern Pike predation on Rainbow Trout include increasing the size of stocked fish or altering the timing and spatial distribution of stocking events.

Efficiency of baited hoop nets for sampling catfish in southeastern U.S. small impoundments

USGS Publications Warehouse

Wallace, Benjamin C.; Weaver, Daniel M.; Kwak, Thomas J.

2011-01-01

Many U.S. natural resource agencies stock catfish (Ictaluridae) into small impoundments to provide recreational fishing opportunities. However, effective standardized methods for sampling catfish in small impoundments have not been developed for wide application, particularly in the southeastern United States. We evaluated the efficiency of three bait treatments (i.e., soybean cake, sunflower cake, and no bait) of tandem hoop nets in two North Carolina small impoundments during the fall of 2008 and spring of 2009 in a factorial experimental design. The impoundments were stocked with catchable-size channel catfish Ictalurus punctatus at contrastingly low (5.5 fi sh/ha) and high (90.0 fi sh/ha) rates prior to our sampling. Nets baited with soybean cake consistently sampled more channel catfish than any other treatment. Channel catfish catch ranged as high as 3,251 fi sh per net series during the fall in nets baited with soybean cake in the intensively stocked impoundment and was up to 8.5 and 15.3 times higher during the fall than in the spring in each impoundment. Nets baited with soybean cake sampled significantly (12 and 24 times) more channel catfish than those with no bait in the two impoundments. These trends did not occur among other catfish species. Nonictalurid fish and turtle catch was higher during spring compared to that of fall, corresponding with low channel catfish catches. Our results indicate that tandem hoop nets baited with soybean cake during the fall is a more efficient method for sampling channel catfish compared to nets baited with sunflower cake or no bait in spring or fall. Our findings validate this technique for application in southeastern U.S. small impoundments to assess catfish abundance to guide management and evaluate the success of catfish stocking programs.

Effects of Climate Change and Fisheries Bycatch on Shy Albatross (Thalassarche cauta) in Southern Australia

PubMed Central

2015-01-01

The impacts of climate change on marine species are often compounded by other stressors that make direct attribution and prediction difficult. Shy albatrosses (Thalassarche cauta) breeding on Albatross Island, Tasmania, show an unusually restricted foraging range, allowing easier discrimination between the influence of non-climate stressors (fisheries bycatch) and environmental variation. Local environmental conditions (rainfall, air temperature, and sea-surface height, an indicator of upwelling) during the vulnerable chick-rearing stage, have been correlated with breeding success of shy albatrosses. We use an age-, stage- and sex-structured population model to explore potential relationships between local environmental factors and albatross breeding success while accounting for fisheries bycatch by trawl and longline fisheries. The model uses time-series of observed breeding population counts, breeding success, adult and juvenile survival rates and a bycatch mortality observation for trawl fishing to estimate fisheries catchability, environmental influence, natural mortality rate, density dependence, and productivity. Observed at-sea distributions for adult and juvenile birds were coupled with reported fishing effort to estimate vulnerability to incidental bycatch. The inclusion of rainfall, temperature and sea-surface height as explanatory variables for annual chick mortality rate was statistically significant. Global climate models predict little change in future local average rainfall, however, increases are forecast in both temperatures and upwelling, which are predicted to have detrimental and beneficial effects, respectively, on breeding success. The model shows that mitigation of at least 50% of present bycatch is required to offset losses due to future temperature changes, even if upwelling increases substantially. Our results highlight the benefits of using an integrated modeling approach, which uses available demographic as well as environmental data within a single estimation framework, to provide future predictions. Such predictions inform the development of management options in the face of climate change. PMID:26057739

Utility of Capture-Recapture Methodology to Estimate Prevalence of Congenital Heart Defects Among Adolescents in 11 New York State Counties: 2008 to 2010.

PubMed

Akkaya-Hocagil, Tugba; Hsu, Wan-Hsiang; Sommerhalter, Kristin; McGarry, Claire; Van Zutphen, Alissa

2017-11-01

Congenital heart defects (CHDs) are the most common birth defects in the United States, and the population of individuals living with CHDs is growing. Though CHD prevalence in infancy has been well characterized, better prevalence estimates among children and adolescents in the United States are still needed. We used capture-recapture methods to estimate CHD prevalence among adolescents residing in 11 New York counties. The three data sources used for analysis included Statewide Planning and Research Cooperative System (SPARCS) hospital inpatient records, SPARCS outpatient records, and medical records provided by seven pediatric congenital cardiac clinics from 2008 to 2010. Bayesian log-linear models were fit using the R package Conting to account for dataset dependencies and heterogeneous catchability. A total of 2537 adolescent CHD cases were captured in our three data sources. Forty-four cases were identified in all data sources, 283 cases were identified in two of three data sources, and 2210 cases were identified in a single data source. The final model yielded an estimated total adolescent CHD population of 3845, indicating that 66% of the cases in the catchment area were identified in the case-identifying data sources. Based on 2010 Census estimates, we estimated adolescent CHD prevalence as 6.4 CHD cases per 1000 adolescents (95% confidence interval: 6.2-6.6). We used capture-recapture methodology with a population-based surveillance system in New York to estimate CHD prevalence among adolescents. Future research incorporating additional data sources may improve prevalence estimates in this population. Birth Defects Research 109:1423-1429, 2017.© 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Duck Valley Resident Fish Stocking Program, 2000 Final Annual Report.

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

Dodson, Guy; Pero, Vincent

The Shoshone-Paiute Tribes fish-stocking program was begun in 1988 and is intended to provide a subsistence fishery for the tribal members. The program stocks catchable and fingerling size trout in Mt. View and Sheep Creek Reservoirs. Rainbow trout are purchased from only certified disease-free facilities to be stocked in our reservoirs. This project will help restore a fishery for tribal members that historically depended on wild salmon and steelhead in the Owyhee and Bruneau Rivers and their tributaries for their culture as well as for subsistence. This project is partial substitution for loss of anadromous fish production due to constructionmore » and operation of hydroelectric dams on the Columbia and Snake Rivers. Until anadromous fish can be returned to the Owyhee and Bruneau Rivers this project will continue indefinitely. As part of this project the Shoshone-Paiute Tribes will also receive income in the form of fees from non-tribal members who come to fish these reservoirs. Regular monitoring and evaluation of the fishery will include sampling for length/weight/condition and for signs of disease. A detailed Monitoring and evaluation plan has been put in place for this project. However due to budget limitations on this project only the fishery surveys and limited water quality work can be completed. A creel survey was initiated in 1998 and we are following the monitoring and evaluation schedule for this program (as budget allows) as well as managing the budget and personnel. This program has been very successful in the past decade and has provided enjoyment and sustenance for both tribal and non-tribal members. All biological data and stocking rates will be including in the Annual reports to Bonneville Power Administration (BPA).« less

Effects of Climate Change and Fisheries Bycatch on Shy Albatross (Thalassarche cauta) in Southern Australia.

PubMed

Thomson, Robin B; Alderman, Rachael L; Tuck, Geoffrey N; Hobday, Alistair J

2015-01-01

The impacts of climate change on marine species are often compounded by other stressors that make direct attribution and prediction difficult. Shy albatrosses (Thalassarche cauta) breeding on Albatross Island, Tasmania, show an unusually restricted foraging range, allowing easier discrimination between the influence of non-climate stressors (fisheries bycatch) and environmental variation. Local environmental conditions (rainfall, air temperature, and sea-surface height, an indicator of upwelling) during the vulnerable chick-rearing stage, have been correlated with breeding success of shy albatrosses. We use an age-, stage- and sex-structured population model to explore potential relationships between local environmental factors and albatross breeding success while accounting for fisheries bycatch by trawl and longline fisheries. The model uses time-series of observed breeding population counts, breeding success, adult and juvenile survival rates and a bycatch mortality observation for trawl fishing to estimate fisheries catchability, environmental influence, natural mortality rate, density dependence, and productivity. Observed at-sea distributions for adult and juvenile birds were coupled with reported fishing effort to estimate vulnerability to incidental bycatch. The inclusion of rainfall, temperature and sea-surface height as explanatory variables for annual chick mortality rate was statistically significant. Global climate models predict little change in future local average rainfall, however, increases are forecast in both temperatures and upwelling, which are predicted to have detrimental and beneficial effects, respectively, on breeding success. The model shows that mitigation of at least 50% of present bycatch is required to offset losses due to future temperature changes, even if upwelling increases substantially. Our results highlight the benefits of using an integrated modeling approach, which uses available demographic as well as environmental data within a single estimation framework, to provide future predictions. Such predictions inform the development of management options in the face of climate change.

Observing Clonal Dynamics across Spatiotemporal Axes: A Prelude to Quantitative Fitness Models for Cancer.

PubMed

McPherson, Andrew W; Chan, Fong Chun; Shah, Sohrab P

2018-02-01

The ability to accurately model evolutionary dynamics in cancer would allow for prediction of progression and response to therapy. As a prelude to quantitative understanding of evolutionary dynamics, researchers must gather observations of in vivo tumor evolution. High-throughput genome sequencing now provides the means to profile the mutational content of evolving tumor clones from patient biopsies. Together with the development of models of tumor evolution, reconstructing evolutionary histories of individual tumors generates hypotheses about the dynamics of evolution that produced the observed clones. In this review, we provide a brief overview of the concepts involved in predicting evolutionary histories, and provide a workflow based on bulk and targeted-genome sequencing. We then describe the application of this workflow to time series data obtained for transformed and progressed follicular lymphomas (FL), and contrast the observed evolutionary dynamics between these two subtypes. We next describe results from a spatial sampling study of high-grade serous (HGS) ovarian cancer, propose mechanisms of disease spread based on the observed clonal mixtures, and provide examples of diversification through subclonal acquisition of driver mutations and convergent evolution. Finally, we state implications of the techniques discussed in this review as a necessary but insufficient step on the path to predictive modelling of disease dynamics. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

A pediatric correlational study of stride interval dynamics, energy expenditure and activity level.

PubMed

Ellis, Denine; Sejdic, Ervin; Zabjek, Karl; Chau, Tom

2014-08-01

The strength of time-dependent correlations known as stride interval (SI) dynamics has been proposed as an indicator of neurologically healthy gait. Most recently, it has been hypothesized that these dynamics may be necessary for gait efficiency although the supporting evidence to date is scant. The current study examines over-ground SI dynamics, and their relationship with the cost of walking and physical activity levels in neurologically healthy children aged nine to 15 years. Twenty participants completed a single experimental session consisting of three phases: 10 min resting, 15 min walking and 10 min recovery. The scaling exponent (α) was used to characterize SI dynamics while net energy cost was measured using a portable metabolic cart, and physical activity levels were determined based on a 7-day recall questionnaire. No significant linear relationships were found between a and the net energy cost measures (r < .07; p > .25) or between α and physical activity levels (r = .01, p = .62). However, there was a marked reduction in the variance of α as activity levels increased. Over-ground stride dynamics do not appear to directly reflect energy conservation of gait in neurologically healthy youth. However, the reduction in the variance of α with increasing physical activity suggests a potential exercise-moderated convergence toward a level of stride interval persistence for able-bodied youth reported in the literature. This latter finding warrants further investigation.

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

NASA Astrophysics Data System (ADS)

Naritomi, Yusuke; Fuchigami, Sotaro

2013-12-01

We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of Cα atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

Earthquake triggering by seismic waves following the landers and hector mine earthquakes

USGS Publications Warehouse

Gomberg, J.; Reasenberg, P.A.; Bodin, P.; Harris, R.A.

2001-01-01

The proximity and similarity of the 1992, magnitude 7.3 Landers and 1999, magnitude 7.1 Hector Mine earthquakes in California permit testing of earthquake triggering hypotheses not previously possible. The Hector Mine earthquake confirmed inferences that transient, oscillatory 'dynamic' deformations radiated as seismic waves can trigger seismicity rate increases, as proposed for the Landers earthquake1-6. Here we quantify the spatial and temporal patterns of the seismicity rate changes7. The seismicity rate increase was to the north for the Landers earthquake and primarily to the south for the Hector Mine earthquake. We suggest that rupture directivity results in elevated dynamic deformations north and south of the Landers and Hector Mine faults, respectively, as evident in the asymmetry of the recorded seismic velocity fields. Both dynamic and static stress changes seem important for triggering in the near field with dynamic stress changes dominating at greater distances. Peak seismic velocities recorded for each earthquake suggest the existence of, and place bounds on, dynamic triggering thresholds. These thresholds vary from a few tenths to a few MPa in most places, depend on local conditions, and exceed inferred static thresholds by more than an order of magnitude. At some sites, the onset of triggering was delayed until after the dynamic deformations subsided. Physical mechanisms consistent with all these observations may be similar to those that give rise to liquefaction or cyclic fatigue.

Modelling and Simulation of the Dynamics of the Antigen-Specific T Cell Response Using Variable Structure Control Theory.

PubMed

Anelone, Anet J N; Spurgeon, Sarah K

2016-01-01

Experimental and mathematical studies in immunology have revealed that the dynamics of the programmed T cell response to vigorous infection can be conveniently modelled using a sigmoidal or a discontinuous immune response function. This paper hypothesizes strong synergies between this existing work and the dynamical behaviour of engineering systems with a variable structure control (VSC) law. These findings motivate the interpretation of the immune system as a variable structure control system. It is shown that dynamical properties as well as conditions to analytically assess the transition from health to disease can be developed for the specific T cell response from the theory of variable structure control. In particular, it is shown that the robustness properties of the specific T cell response as observed in experiments can be explained analytically using a VSC perspective. Further, the predictive capacity of the VSC framework to determine the T cell help required to overcome chronic Lymphocytic Choriomeningitis Virus (LCMV) infection is demonstrated. The findings demonstrate that studying the immune system using variable structure control theory provides a new framework for evaluating immunological dynamics and experimental observations. A modelling and simulation tool results with predictive capacity to determine how to modify the immune response to achieve healthy outcomes which may have application in drug development and vaccine design.

The effects of a dynamic graphical model during simulation-based training of console operation skill

NASA Technical Reports Server (NTRS)

Farquhar, John D.; Regian, J. Wesley

1993-01-01

LOADER is a Windows-based simulation of a complex procedural task. The task requires subjects to execute long sequences of console-operation actions (e.g., button presses, switch actuations, dial rotations) to accomplish specific goals. The LOADER interface is a graphical computer-simulated console which controls railroad cars, tracks, and cranes in a fictitious railroad yard. We hypothesized that acquisition of LOADER performance skill would be supported by the representation of a dynamic graphical model linking console actions to goal and goal states in the 'railroad yard'. Twenty-nine subjects were randomly assigned to one of two treatments (i.e., dynamic model or no model). During training, both groups received identical text-based instruction in an instructional-window above the LOADER interface. One group, however, additionally saw a dynamic version of the bird's-eye view of the railroad yard. After training, both groups were tested under identical conditions. They were asked to perform the complete procedure without guidance and without access to either type of railroad yard representation. Results indicate that rather than becoming dependent on the animated rail yard model, subjects in the dynamic model condition apparently internalized the model, as evidenced by their performance after the model was removed.

Species interactions may help explain the erratic periodicity of whooping cough dynamics.

PubMed

Bhattacharyya, Samit; Ferrari, Matthew J; Bjørnstad, Ottar N

2017-12-14

Incidence of whooping cough exhibits variable dynamics across time and space. The periodicity of this disease varies from annual to five years in different geographic regions in both developing and developed countries. Many hypotheses have been put forward to explain this variability such as nonlinearity and seasonality, stochasticity, variable recruitment of susceptible individuals via birth, immunization, and immune boosting. We propose an alternative hypothesis to describe the variability in periodicity - the intricate dynamical variability of whooping cough may arise from interactions between its dominant etiological agents of Bordetella pertussis and Bordetella parapertussis. We develop a two-species age-structured model, where two pathogens are allowed to interact by age-dependent convalescence of individuals with severe illness from infections. With moderate strength of interactions, the model exhibits multi-annual coexisting attractors that depend on the R 0 of the two pathogens. We also examine how perturbation from case importation and noise in transmission may push the system from one dynamical regime to another. The coexistence of multi-annual cycles and the behavior of switching between attractors suggest that variable dynamics of whopping cough could be an emergent property of its multi-agent etiology. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Extra permeability is required to model dynamic oxygen measurements: evidence for functional recruitment?

PubMed Central

Barrett, Matthew JP; Suresh, Vinod

2013-01-01

Neural activation triggers a rapid, focal increase in blood flow and thus oxygen delivery. Local oxygen consumption also increases, although not to the same extent as oxygen delivery. This ‘uncoupling' enables a number of widely-used functional neuroimaging techniques; however, the physiologic mechanisms that govern oxygen transport under these conditions remain unclear. Here, we explore this dynamic process using a new mathematical model. Motivated by experimental observations and previous modeling, we hypothesized that functional recruitment of capillaries has an important role during neural activation. Using conventional mechanisms alone, the model predictions were inconsistent with in vivo measurements of oxygen partial pressure. However, dynamically increasing net capillary permeability, a simple description of functional recruitment, led to predictions consistent with the data. Increasing permeability in all vessel types had the same effect, but two alternative mechanisms were unable to produce predictions consistent with the data. These results are further evidence that conventional models of oxygen transport are not sufficient to predict dynamic experimental data. The data and modeling suggest that it is necessary to include a mechanism that dynamically increases net vascular permeability. While the model cannot distinguish between the different possibilities, we speculate that functional recruitment could have this effect in vivo. PMID:23673433

Monkeys preferentially process body information while viewing affective displays.

PubMed

Bliss-Moreau, Eliza; Moadab, Gilda; Machado, Christopher J

2017-08-01

Despite evolutionary claims about the function of facial behaviors across phylogeny, rarely are those hypotheses tested in a comparative context-that is, by evaluating how nonhuman animals process such behaviors. Further, while increasing evidence indicates that humans make meaning of faces by integrating contextual information, including that from the body, the extent to which nonhuman animals process contextual information during affective displays is unknown. In the present study, we evaluated the extent to which rhesus macaques (Macaca mulatta) process dynamic affective displays of conspecifics that included both facial and body behaviors. Contrary to hypotheses that they would preferentially attend to faces during affective displays, monkeys looked for longest, most frequently, and first at conspecifics' bodies rather than their heads. These findings indicate that macaques, like humans, attend to available contextual information during the processing of affective displays, and that the body may also be providing unique information about affective states. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Chaotic attractors of relaxation oscillators

NASA Astrophysics Data System (ADS)

Guckenheimer, John; Wechselberger, Martin; Young, Lai-Sang

2006-03-01

We develop a general technique for proving the existence of chaotic attractors for three-dimensional vector fields with two time scales. Our results connect two important areas of dynamical systems: the theory of chaotic attractors for discrete two-dimensional Henon-like maps and geometric singular perturbation theory. Two-dimensional Henon-like maps are diffeomorphisms that limit on non-invertible one-dimensional maps. Wang and Young formulated hypotheses that suffice to prove the existence of chaotic attractors in these families. Three-dimensional singularly perturbed vector fields have return maps that are also two-dimensional diffeomorphisms limiting on one-dimensional maps. We describe a generic mechanism that produces folds in these return maps and demonstrate that the Wang-Young hypotheses are satisfied. Our analysis requires a careful study of the convergence of the return maps to their singular limits in the Ck topology for k >= 3. The theoretical results are illustrated with a numerical study of a variant of the forced van der Pol oscillator.

Adaptive significance of natural variations in maternal care in rats: a translational perspective

PubMed Central

Beery, Annaliese K.; Francis, Darlene D.

2011-01-01

A wealth of data from the last fifty years documents the potency of early life experiences including maternal care on developing offspring. A majority of this research has focused on the developing stress axis and stress-sensitive behaviors in hopes of identifying factors impacting resilience and risk-sensitivity. The power of early life experience to shape later development is profound and has the potential to increase fitness of individuals for their environments. Current findings in a rat maternal care paradigm highlight the complex and dynamic relation between early experiences and a variety of outcomes. In this review we propose adaptive hypotheses for alternate maternal strategies and resulting offspring phenotypes, and ways to distinguish between these hypotheses. We also provide evidence underscoring the critical role of context in interpreting the adaptive significance of early experiences. If our goal is to identify risk-factors relevant to humans, we must better explore the role of the social and physical environment in our basic animal models. PMID:21458485

Immunological self-tolerance: Lessons from mathematical modeling

NASA Astrophysics Data System (ADS)

Carneiro, Jorge; Paixao, Tiago; Milutinovic, Dejan; Sousa, Joao; Leon, Kalet; Gardner, Rui; Faro, Jose

2005-12-01

One of the fundamental properties of the immune system is its capacity to avoid autoimmune diseases. The mechanism underlying this process, known as self-tolerance, is hitherto unresolved but seems to involve the control of clonal expansion of autoreactive lymphocytes. This article reviews mathematical modeling of self-tolerance, addressing two specific hypotheses. The first hypothesis posits that self-tolerance is mediated by tuning of activation thresholds, which makes autoreactive T lymphocytes reversibly "anergic" and unable to proliferate. The second hypothesis posits that the proliferation of autoreactive T lymphocytes is instead controlled by specific regulatory T lymphocytes. Models representing the population dynamics of autoreactive T lymphocytes according to these two hypotheses were derived. For each model we identified how cell density affects tolerance, and predicted the corresponding phase spaces and bifurcations. We show that the simple induction of proliferative anergy, as modeled here, has a density dependence that is only partially compatible with adoptive transfers of tolerance, and that the models of tolerance mediated by specific regulatory T cells are closer to the observations.

SSME fault monitoring and diagnosis expert system

NASA Technical Reports Server (NTRS)

Ali, Moonis; Norman, Arnold M.; Gupta, U. K.

1989-01-01

An expert system, called LEADER, has been designed and implemented for automatic learning, detection, identification, verification, and correction of anomalous propulsion system operations in real time. LEADER employs a set of sensors to monitor engine component performance and to detect, identify, and validate abnormalities with respect to varying engine dynamics and behavior. Two diagnostic approaches are adopted in the architecture of LEADER. In the first approach fault diagnosis is performed through learning and identifying engine behavior patterns. LEADER, utilizing this approach, generates few hypotheses about the possible abnormalities. These hypotheses are then validated based on the SSME design and functional knowledge. The second approach directs the processing of engine sensory data and performs reasoning based on the SSME design, functional knowledge, and the deep-level knowledge, i.e., the first principles (physics and mechanics) of SSME subsystems and components. This paper describes LEADER's architecture which integrates a design based reasoning approach with neural network-based fault pattern matching techniques. The fault diagnosis results obtained through the analyses of SSME ground test data are presented and discussed.

A mathematical tool to generate complex whole body motor tasks and test hypotheses on underlying motor planning.

PubMed

Tagliabue, Michele; Pedrocchi, Alessandra; Pozzo, Thierry; Ferrigno, Giancarlo

2008-01-01

In spite of the complexity of human motor behavior, difficulties in mathematical modeling have restricted to rather simple movements attempts to identify the motor planning criterion used by the central nervous system. This paper presents a novel-simulation technique able to predict the "desired trajectory" corresponding to a wide range of kinematic and kinetic optimality criteria for tasks involving many degrees of freedom and the coordination between goal achievement and balance maintenance. Employment of proper time discretization, inverse dynamic methods and constrained optimization technique are combined. The application of this simulator to a planar whole body pointing movement shows its effectiveness in managing system nonlinearities and instability as well as in ensuring the anatomo-physiological feasibility of predicted motor plans. In addition, the simulator's capability to simultaneously optimize competing movement aspects represents an interesting opportunity for the motor control community, in which the coexistence of several controlled variables has been hypothesized.

Timescales and Mechanisms of Sigh-Like Bursting and Spiking in Models of Rhythmic Respiratory Neurons.

PubMed

Wang, Yangyang; Rubin, Jonathan E

2017-12-01

Neural networks generate a variety of rhythmic activity patterns, often involving different timescales. One example arises in the respiratory network in the pre-Bötzinger complex of the mammalian brainstem, which can generate the eupneic rhythm associated with normal respiration as well as recurrent low-frequency, large-amplitude bursts associated with sighing. Two competing hypotheses have been proposed to explain sigh generation: the recruitment of a neuronal population distinct from the eupneic rhythm-generating subpopulation or the reconfiguration of activity within a single population. Here, we consider two recent computational models, one of which represents each of the hypotheses. We use methods of dynamical systems theory, such as fast-slow decomposition, averaging, and bifurcation analysis, to understand the multiple-timescale mechanisms underlying sigh generation in each model. In the course of our analysis, we discover that a third timescale is required to generate sighs in both models. Furthermore, we identify the similarities of the underlying mechanisms in the two models and the aspects in which they differ.

Milk bioactives may manipulate microbes to mediate parent–offspring conflict

PubMed Central

Allen-Blevins, Cary R.; Sela, David A.; Hinde, Katie

2015-01-01

Among mammals, milk constituents directly influence the ecology of the infant’s commensal microbiota. The immunological and nutritional impacts of breast milk and microbiota are increasingly well understood; less clear are the consequences for infant behavior. Here, we propose that interactions among bioactives in mother’s milk and microbes in the infant gut contribute to infant behavioral phenotype and, in part, have the potential to mediate parent–offspring conflict. We hypothesize that infant behavior likely varies as a function of their mother’s milk composition interacting with the infant’s neurobiology directly and indirectly through the commensal gut bacteria. In this article, we will explore our hypothesis of a milk-microbiota-brain-behavior dynamic in the context of the coevolution between human milk oligosaccharides, bacteria, the gut–brain axis and behavior. Integrating established features of these systems allows us to generate novel hypotheses to motivate future research and consider potential implications of current and emerging clinical treatments. PMID:25835022

A boreal invasion in response to climate change? Range shifts and community effects in the borderland between forest and tundra.

PubMed

Elmhagen, Bodil; Kindberg, Jonas; Hellström, Peter; Angerbjörn, Anders

2015-01-01

It has been hypothesized that climate warming will allow southern species to advance north and invade northern ecosystems. We review the changes in the Swedish mammal and bird community in boreal forest and alpine tundra since the nineteenth century, as well as suggested drivers of change. Observed changes include (1) range expansion and increased abundance in southern birds, ungulates, and carnivores; (2) range contraction and decline in northern birds and carnivores; and (3) abundance decline or periodically disrupted dynamics in cyclic populations of small and medium-sized mammals and birds. The first warm spell, 1930-1960, stands out as a period of substantial faunal change. However, in addition to climate warming, suggested drivers of change include land use and other anthropogenic factors. We hypothesize all these drivers interacted, primarily favoring southern generalists. Future research should aim to distinguish between effects of climate and land-use change in boreal and tundra ecosystems.

Explicitly searching for useful inventions: dynamic relatedness and the costs of connecting versus synthesizing

PubMed Central

2010-01-01

Inventions combine technological features. When features are barely related, burdensomely broad knowledge is required to identify the situations that they share. When features are overly related, burdensomely broad knowledge is required to identify the situations that distinguish them. Thus, according to my first hypothesis, when features are moderately related, the costs of connecting and costs of synthesizing are cumulatively minimized, and the most useful inventions emerge. I also hypothesize that continued experimentation with a specific set of features is likely to lead to the discovery of decreasingly useful inventions; the earlier-identified connections reflect the more common consumer situations. Covering data from all industries, the empirical analysis provides broad support for the first hypothesis. Regressions to test the second hypothesis are inconclusive when examining industry types individually. Yet, this study represents an exploratory investigation, and future research should test refined hypotheses with more sophisticated data, such as that found in literature-based discovery research. PMID:21297855

Adaptive management for soil ecosystem services

USGS Publications Warehouse

Birge, Hannah E.; Bevans, Rebecca A.; Allen, Craig R.; Angeler, David G.; Baer, Sara G.; Wall, Diana H.

2016-01-01

Ecosystem services provided by soil include regulation of the atmosphere and climate, primary (including agricultural) production, waste processing, decomposition, nutrient conservation, water purification, erosion control, medical resources, pest control, and disease mitigation. The simultaneous production of these multiple services arises from complex interactions among diverse aboveground and belowground communities across multiple scales. When a system is mismanaged, non-linear and persistent losses in ecosystem services can arise. Adaptive management is an approach to management designed to reduce uncertainty as management proceeds. By developing alternative hypotheses, testing these hypotheses and adjusting management in response to outcomes, managers can probe dynamic mechanistic relationships among aboveground and belowground soil system components. In doing so, soil ecosystem services can be preserved and critical ecological thresholds avoided. Here, we present an adaptive management framework designed to reduce uncertainty surrounding the soil system, even when soil ecosystem services production is not the explicit management objective, so that managers can reach their management goals without undermining soil multifunctionality or contributing to an irreversible loss of soil ecosystem services.

A social identity analysis of responses to economic inequality.

PubMed

Jetten, Jolanda; Wang, Zhechen; Steffens, Niklas K; Mols, Frank; Peters, Kim; Verkuyten, Maykel

2017-12-01

Even though there is growing awareness that economic inequality is harmful for people's health, the way that such inequality affects social behavior and political attitudes remains poorly understood. Moving beyond a focus on the health and well-being costs of income inequality, we review research that examines how economic inequality shapes dynamics between groups within societies, addressing the questions why, when, and for whom inequality affects social behavior and political attitudes. On the basis of classic social identity theorizing, we develop five hypotheses that focus on the way inequality shapes the fit of wealth categorizations (H1), intergroup relations (H2), and stereotypes about wealth groups (H3). We also theorize how the effects of inequality are moderated by socio-structural conditions (H4) and socio-economic status (H5). Together, these hypotheses provide a theoretically informed account of the way in which inequality undermines the social fabric of society and negatively affects citizen's social and political behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

Differential association of family subsystem negativity on siblings' maladjustment: using behavior genetic methods to test process theory.

PubMed

Feinberg, Mark E; Reiss, David; Neiderhiser, Jenae M; Hetherington, E Mavis

2005-12-01

This study investigated the family context of adolescent sibling similarity and differentiation in maladjustment (antisocial behavior and depression) by examining negativity in different subsystems. Two hypotheses were proposed: (1) Parental and sibling negativity tends to diffuse through the family system, especially because of the high level of reciprocity in sibling relationships, leading to sibling similarity; and (2) interparental (coparenting) conflict disrupts cohesive functioning and thereby motivates and facilitates sibling differentiation and niche picking. To control for the effects of similar genes between siblings, the authors used behavioral genetic models with a genetically informed sample of 720 two-parent families, each with at least 2 adolescent siblings. Results for the differences in shared environmental influences across groups high and low in each of the domains of family negativity provided partial support for the hypotheses. The results further understanding of influences on individual differences and support a theory of how parent-child and interparental relationships intersect with sibling relationship dynamics. Copyright 2006 APA, all rights reserved).

Predicting short-term positive affect in individuals with social anxiety disorder: The role of selected personality traits and emotion regulation strategies.

PubMed

Weisman, Jaclyn S; Rodebaugh, Thomas L; Lim, Michelle H; Fernandez, Katya C

2015-08-01

Recently, research has provided support for a moderate, inverse relationship between social anxiety and dispositional positive affect. However, the dynamics of this relationship remain poorly understood. The present study evaluates whether certain personality traits and emotion regulation variables predict short-term positive affect for individuals with social anxiety disorder and healthy controls. Positive affect as measured by two self-report instruments was assessed before and after two tasks in which the participant conversed with either a friend or a romantic partner. Tests of models examining the hypothesized prospective predictors revealed that the paths did not differ significantly across diagnostic group and both groups showed the hypothesized patterns of endorsement for the emotion regulation variables. Further, a variable reflecting difficulty redirecting oneself when distressed prospectively predicted one measure of positive affect. Additional research is needed to explore further the role of emotion regulation strategies on positive emotions for individuals higher in social anxiety. Copyright © 2015 Elsevier Ltd. All rights reserved.

Incidence of workers compensation indemnity claims across socio-demographic and job characteristics.

PubMed

Du, Juan; Leigh, J Paul

2011-10-01

We hypothesized that low socioeconomic status, employer-provided health insurance, low wages, and overtime were predictors of reporting workers compensation indemnity claims. We also tested for gender and race disparities. Responses from 17,190 (person-years) Americans participating in the Panel Study of Income Dynamics, 1997-2005, were analyzed with logistic regressions. The dependent variable indicated whether the subject collected benefits from a claim. Odds ratios for men and African-Americans were relatively large and strongly significant predictors of claims; significance for Hispanics was moderate and confounded by education. Odds ratios for variables measuring education were the largest for all statistically significant covariates. Neither low wages nor employer-provided health insurance was a consistent predictor. Due to confounding from the "not salaried" variable, overtime was not a consistently significant predictor. Few studies use nationally representative longitudinal data to consider which demographic and job characteristics predict reporting workers compensation indemnity cases. This study did and tested some common hypotheses about predictors. Copyright © 2011 Wiley-Liss, Inc.

Bayesian inference of the lung alveolar spatial model for the identification of alveolar mechanics associated with acute respiratory distress syndrome

NASA Astrophysics Data System (ADS)

Christley, Scott; Emr, Bryanna; Ghosh, Auyon; Satalin, Josh; Gatto, Louis; Vodovotz, Yoram; Nieman, Gary F.; An, Gary

2013-06-01

Acute respiratory distress syndrome (ARDS) is acute lung failure secondary to severe systemic inflammation, resulting in a derangement of alveolar mechanics (i.e. the dynamic change in alveolar size and shape during tidal ventilation), leading to alveolar instability that can cause further damage to the pulmonary parenchyma. Mechanical ventilation is a mainstay in the treatment of ARDS, but may induce mechano-physical stresses on unstable alveoli, which can paradoxically propagate the cellular and molecular processes exacerbating ARDS pathology. This phenomenon is called ventilator induced lung injury (VILI), and plays a significant role in morbidity and mortality associated with ARDS. In order to identify optimal ventilation strategies to limit VILI and treat ARDS, it is necessary to understand the complex interplay between biological and physical mechanisms of VILI, first at the alveolar level, and then in aggregate at the whole-lung level. Since there is no current consensus about the underlying dynamics of alveolar mechanics, as an initial step we investigate the ventilatory dynamics of an alveolar sac (AS) with the lung alveolar spatial model (LASM), a 3D spatial biomechanical representation of the AS and its interaction with airflow pressure and the surface tension effects of pulmonary surfactant. We use the LASM to identify the mechanical ramifications of alveolar dynamics associated with ARDS. Using graphical processing unit parallel algorithms, we perform Bayesian inference on the model parameters using experimental data from rat lung under control and Tween-induced ARDS conditions. Our results provide two plausible models that recapitulate two fundamental hypotheses about volume change at the alveolar level: (1) increase in alveolar size through isotropic volume change, or (2) minimal change in AS radius with primary expansion of the mouth of the AS, with the implication that the majority of change in lung volume during the respiratory cycle occurs in the alveolar ducts. These two model solutions correspond to significantly different mechanical properties of the tissue, and we discuss the implications of these different properties and the requirements for new experimental data to discriminate between the hypotheses.

Landslides and Volcanoes: Fingerprinting Erosional Processes on a tropical island, Dominica, Lesser Antilles

NASA Astrophysics Data System (ADS)

Tomenchok, K.; Hill, M.; Jimerson, C.; Talbot-Wendlandt, , H.; Schmidt, A.; Frey, H. M.

2017-12-01

With 9 active volcanic centers, frequent tropical storms, and widespread landslides, the topography of Dominica is rugged and dynamic. This study aims to fingerprint sediment source dynamics in this relatively unstudied region with fallout radionuclides, clay mineralogy, and acid-extractable grain coating concentration measured in detrital sediments. We also aim to measure basin average erosion rates and determine river incision rates into the underlying ignimbrites. Baseline data on the effects of volcanoes, landslides, land use, and topography in setting erosional dynamics will be established. We sampled outlets of 20 large (>10 km2) rivers as well as 11 points in the Roseau River watershed for a network analysis. Block and ash flows and ignimbrites underlie 89% of the study area. Steep topography (mean slope = 19.6˚) and high levels of rainfall (mean annual rainfall = 1981.41 mm) are consistent throughout the 89% forested island. 934 landslides affect 13% of the study area. We hypothesize that basin average parameters and landslide frequency will correlate with erosion rates and fallout radionuclide activities. In addition, we used topographic data and published ignimbrite ages to calculate river incision rates that ranged from 0.448 - 113.9 mm/yr in the north and 0.86 - 44 mm/yr in the south. Basin average erosion rates will be compared to incision rates to quantify differences between basin wide erosional and river incision processes. We will fingerprint sediment sources with 7Be, 210Pbex, and 137Cs, concentration of grain coatings, and clay mineralogy. We hypothesize that watersheds with erosion from stabilizing landslide scars will have high 7Be, low 210Pbex and 137Cs, low concentrations of grain coatings, and less weathered clays. Watersheds with river bank/scarp erosion or active landslides will have little 7Be, 210Pbex, and 137Cs, less weathered clays, and low concentrations of grain coatings. Watersheds with widespread surface erosion will have high activities, weathered clays, and high concentrations of grain coatings. We will correlate basin average statistics with measured fingerprints to provide a better understanding of sediment source dynamics in an understudied region of the world. With the potential for future landslides, further information will advance hazard mitigation in Dominica.

Dispersal, niche breadth and population extinction: colonization ratios predict range size in North American dragonflies.

PubMed

McCauley, Shannon J; Davis, Christopher J; Werner, Earl E; Robeson, Michael S

2014-07-01

Species' range sizes are shaped by fundamental differences in species' ecological and evolutionary characteristics, and understanding the mechanisms determining range size can shed light on the factors responsible for generating and structuring biological diversity. Moreover, because geographic range size is associated with a species' risk of extinction and their ability to respond to global changes in climate and land use, understanding these mechanisms has important conservation implications. Despite the hypotheses that dispersal behaviour is a strong determinant of species range areas, few data are available to directly compare the relationship between dispersal behaviour and range size. Here, we overcome this limitation by combining data from a multispecies dispersal experiment with additional species-level trait data that are commonly hypothesized to affect range size (e.g. niche breadth, local abundance and body size.). This enables us to examine the relationship between these species-level traits and range size across North America for fifteen dragonfly species. Ten models based on a priori predictions about the relationship between species traits and range size were evaluated and two models were identified as good predictors of species range size. These models indicated that only two species' level traits, dispersal behaviour and niche breadth were strongly related to range size. The evidence from these two models indicated that dragonfly species that disperse more often and further had larger North American ranges. Extinction and colonization dynamics are expected to be a key linkage between dispersal behaviour and range size in dragonflies. To evaluate how extinction and colonization dynamics among dragonflies were related to range size we used an independent data set of extinction and colonization rates for eleven dragonfly species and assessed the relationship between these populations rates and North American range areas for these species. We found a negative relationship between North American range size and species' extinction-to-colonization ratios. Our results indicate that metapopulation dynamics act to shape the extent of species' continental distributions. These population dynamics are likely to interact with dispersal behaviour, particularly at species range margins, to determine range limits and ultimately species range sizes. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Using global, quantitative models of the coupled plates/mantle system to understand Late Miocene dynamics of the Pacific plate

NASA Astrophysics Data System (ADS)

Stotz, Ingo; Iaffaldano, Giampiero; Rhodri Davies, D.

2017-04-01

Knowledge of the evolution of continents, inferred from a variety of geological data, as well as observations of the ocean-floor magnetization pattern provide an increasingly-detailed picture of past and present-day plate motions. These are key to study the evolving balance of shallow- and deep-rooted forces acting upon plates and to unravel the dynamics of the coupled plates/mantle system. Here we focus on the clockwise rotation of the Pacific plate motion relative to the hotspots reference frame between 10 and 5 Ma, which is evidenced by a bend in the Hawaiian sea mount chain (Cox & Engebretson, 1985) as well as by marine magnetic and bathymetric data along the Pacific/Antarctica Ridge (Croon et al., 2008). It has been suggested that such a kinematic change owes to the arrival of the Ontong-Java plateau, the biggest oceanic plateau on the Pacific plate, at the Australia/Pacific subducting margin between 10 and 5 Ma, and to its collision with the Melanesian arc. This could have changed the local buoyancy forces and/or sparked a redistribution of the forces already acting within the Pacific realm, causing the Pacific plate to rotate clockwise. Such hypotheses have never been tested explicitly against the available kinematic reconstructions. We do so by using global numerical models of the coupled plates/mantle system. Our models build on the available codes Terra and Shells. Terra is a global, spherical finite-element code for mantle convection, developed by Baumgardner (1985) and Bunge et al. (1996), and further advanced by Yang (1997; 2000) and Davies et al. (2013), among others. Shells is a thin-sheet, finite-element code for lithosphere dynamics (e.g., Bird, 1998). By merging these two independent models we are able to simulate the rheological behavior of the brittle lithosphere and viscous mantle. We compare the plate velocities output by our models with the available kinematic reconstructions to test the above-mentioned hypotheses, and simulate the impact of the evolving mantle buoyancy-field and plate-boundary forces on the Pacific plate motion. Our approach allows linking geodynamical models and observations on the recent dynamics of the Pacific plate.

Alignment of dynamic networks.

PubMed

Vijayan, V; Critchlow, D; Milenkovic, T

2017-07-15

Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems' static network representations, as is currently done. For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. http://nd.edu/∼cone/DynaMAGNA++/ . tmilenko@nd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Alignment of dynamic networks

PubMed Central

Vijayan, V.; Critchlow, D.; Milenković, T.

2017-01-01

Abstract Motivation: Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems’ static network representations, as is currently done. Results: For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. Availability and implementation: http://nd.edu/∼cone/DynaMAGNA++/. Contact: tmilenko@nd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881980

Experimental Beetle Metapopulations Respond Positively to Dynamic Landscapes and Reduced Connectivity

PubMed Central

Govindan, Byju N.; Swihart, Robert K.

2012-01-01

Interactive effects of multiple environmental factors on metapopulation dynamics have received scant attention. We designed a laboratory study to test hypotheses regarding interactive effects of factors affecting the metapopulation dynamics of red flour beetle, Tribolium castaneum. Within a four-patch landscape we modified resource level (constant and diminishing), patch connectivity (high and low) and patch configuration (static and dynamic) to conduct a 23 factorial experiment, consisting of 8 metapopulations, each with 3 replicates. For comparison, two control populations consisting of isolated and static subpopulations were provided with resources at constant or diminishing levels. Longitudinal data from 22 tri-weekly counts of beetle abundance were analyzed using Bayesian Poisson generalized linear mixed models to estimate additive and interactive effects of factors affecting abundance. Constant resource levels, low connectivity and dynamic patches yielded greater levels of adult beetle abundance. For a given resource level, frequency of colonization exceeded extinction in landscapes with dynamic patches when connectivity was low, thereby promoting greater patch occupancy. Negative density dependence of pupae on adults occurred and was stronger in landscapes with low connectivity and constant resources; these metapopulations also demonstrated greatest stability. Metapopulations in control landscapes went extinct quickly, denoting lower persistence than comparable landscapes with low connectivity. When landscape carrying capacity was constant, habitat destruction coupled with low connectivity created asynchronous local dynamics and refugia within which cannibalism of pupae was reduced. Increasing connectivity may be counter-productive and habitat destruction/recreation may be beneficial to species in some contexts. PMID:22509314

Reduced Perceptual Exclusivity during Object and Grating Rivalry in Autism

PubMed Central

Freyberg, J.; Robertson, C.E.; Baron-Cohen, S.

2015-01-01

Background The dynamics of binocular rivalry may be a behavioural footprint of excitatory and inhibitory neural transmission in visual cortex. Given the presence of atypical visual features in Autism Spectrum Conditions (ASC), and evidence in support of the idea of an imbalance in excitatory/inhibitory neural transmission in ASC, we hypothesized that binocular rivalry might prove a simple behavioural marker of such a transmission imbalance in the autistic brain. In support of this hypothesis, we previously reported a slower rate of rivalry in ASC, driven by reduced perceptual exclusivity. Methods We tested whether atypical dynamics of binocular rivalry in ASC are specific to certain stimulus features. 53 participants (26 with ASC, matched for age, sex and IQ) participated in binocular rivalry experiments in which the dynamics of rivalry were measured at two levels of stimulus complexity, low (grayscale gratings) and high (coloured objects). Results Individuals with ASC experienced a slower rate of rivalry, driven by longer transitional states between dominant percepts. These exaggerated transitional states were present at both low and high levels of stimulus complexity, suggesting that atypical rivalry dynamics in autism are robust with respect to stimulus choice. Interactions between stimulus properties and rivalry dynamics in autism indicate that achromatic grating stimuli produce stronger group differences. Conclusion These results confirm the finding of atypical dynamics of binocular rivalry in ASC. These dynamics were present for stimuli of both low and high levels of visual complexity, suggesting an imbalance in competitive interactions throughout the visual system of individuals with ASC. PMID:26382002

Computational analysis of nonlinearities within dynamics of cable-based driving systems

NASA Astrophysics Data System (ADS)

Anghelache, G. D.; Nastac, S.

2017-08-01

This paper deals with computational nonlinear dynamics of mechanical systems containing some flexural parts within the actuating scheme, and, especially, the situations of the cable-based driving systems were treated. It was supposed both functional nonlinearities and the real characteristic of the power supply, in order to obtain a realistically computer simulation model being able to provide very feasible results regarding the system dynamics. It was taken into account the transitory and stable regimes during a regular exploitation cycle. The authors present a particular case of a lift system, supposed to be representatively for the objective of this study. The simulations were made based on the values of the essential parameters acquired from the experimental tests and/or the regular practice in the field. The results analysis and the final discussions reveal the correlated dynamic aspects within the mechanical parts, the driving system, and the power supply, whole of these supplying potential sources of particular resonances, within some transitory phases of the working cycle, and which can affect structural and functional dynamics. In addition, it was underlines the influences of computational hypotheses on the both quantitative and qualitative behaviour of the system. Obviously, the most significant consequence of this theoretical and computational research consist by developing an unitary and feasible model, useful to dignify the nonlinear dynamic effects into the systems with cable-based driving scheme, and hereby to help an optimization of the exploitation regime including a dynamics control measures.

Connecting Amazonian, Cerrado, and Atlantic Forest histories: Paraphyly, old divergences, and modern population dynamics in tyrant-manakins (Neopelma/Tyranneutes, Aves: Pipridae).

PubMed

Capurucho, João Marcos Guimarães; Ashley, Mary V; Ribas, Camila C; Bates, John M

2018-06-11

Several biogeographic hypotheses have been proposed to explain connections between Amazonian and Atlantic forest biotas. These hypotheses are related to the timing of the connections and their geographic patterns. We performed a phylogeographic investigation of Tyrant-manakins (Aves: Pipridae, Neopelma/Tyranneutes) which include species inhabiting the Amazon and Atlantic forests, as well as gallery forests of the Cerrado. Using DNA sequence data, we determined phylogenetic relationships, temporal and geographic patterns of diversification, and recent intraspecific population genetic patterns, relative to the history of these biomes. We found Neopelma to be a paraphyletic genus, as N. chrysolophum is sister to Neopelma + Tyranneutes, with an estimated divergence of approximately 18 Myrs BP, within the oldest estimated divergence times of other Amazonian and Atlantic forest avian taxa. Subsequent divergences in the group occurred from Mid Miocene to Early Pliocene and involved mainly the Amazonian species, with an expansion into and subsequent speciation in the Cerrado gallery forests by N. pallescens. We found additional structure within N. chrysocephalum and N. sulphureiventer. Analysis of recent population dynamics in N. chrysocephalum, N. sulphureiventer, and N. pallescens revealed recent demographic fluctuations and restrictions to gene flow related to environmental changes since the last glacial cycle. No genetic structure was detected across the Amazon River in N. pallescens. The tyrant-manakins represent an old historical connection between the Amazon and Atlantic Forest. Copyright © 2018. Published by Elsevier Inc.

Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator).

PubMed

Godwin, Ryan C; Melvin, Ryan L; Gmeiner, William H; Salsbury, Freddie R

2017-01-31

Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations. Consistent with experimental evidence, the zinc ion is essential for mechanical stabilization of the functional, folded conformation. Hydrogen bond motifs are unique for deprotonated configurations yet overlap in protonated cases. Correlated motions and principal component analysis corroborate the similarity of the protonated configurations and highlight unique relationships of the zinc-bound configuration. We hypothesize a potential mechanism for zinc binding from results of the thiol configurations. The deprotonated, zinc-bound configuration alone predominantly maintains its tertiary structure throughout all 5 μs and alludes rare conformations potentially important for (im)proper zinc-finger-related protein-protein or protein-DNA interactions.

Dynamic markers of altered gait rhythm in amyotrophic lateral sclerosis

NASA Technical Reports Server (NTRS)

Hausdorff, J. M.; Lertratanakul, A.; Cudkowicz, M. E.; Peterson, A. L.; Kaliton, D.; Goldberger, A. L.

2000-01-01

Amyotrophic lateral sclerosis (ALS) is a disorder marked by loss of motoneurons. We hypothesized that subjects with ALS would have an altered gait rhythm, with an increase in both the magnitude of the stride-to-stride fluctuations and perturbations in the fluctuation dynamics. To test for this locomotor instability, we quantitatively compared the gait rhythm of subjects with ALS with that of normal controls and with that of subjects with Parkinson's disease (PD) and Huntington's disease (HD), pathologies of the basal ganglia. Subjects walked for 5 min at their usual pace wearing an ankle-worn recorder that enabled determination of the duration of each stride and of stride-to-stride fluctuations. We found that the gait of patients with ALS is less steady and more temporally disorganized compared with that of healthy controls. In addition, advanced ALS, HD, and PD were associated with certain common, as well as apparently distinct, features of altered stride dynamics. Thus stride-to-stride control of gait rhythm is apparently compromised with ALS. Moreover, a matrix of markers based on gait dynamics may be useful in characterizing certain pathologies of motor control and, possibly, in quantitatively monitoring disease progression and evaluating therapeutic interventions.

Inattentional Blindness and Individual Differences in Cognitive Abilities.

PubMed

Kreitz, Carina; Furley, Philip; Memmert, Daniel; Simons, Daniel J

2015-01-01

People sometimes fail to notice salient unexpected objects when their attention is otherwise occupied, a phenomenon known as inattentional blindness. To explore individual differences in inattentional blindness, we employed both static and dynamic tasks that either presented the unexpected object away from the focus of attention (spatial) or near the focus of attention (central). We hypothesized that noticing in central tasks might be driven by the availability of cognitive resources like working memory, and that noticing in spatial tasks might be driven by the limits on spatial attention like attention breadth. However, none of the cognitive measures predicted noticing in the dynamic central task or in either the static or dynamic spatial task. Only in the central static task did working memory capacity predict noticing, and that relationship was fairly weak. Furthermore, whether or not participants noticed an unexpected object in a static task was only weakly associated with their odds of noticing an unexpected object in a dynamic task. Taken together, our results are largely consistent with the notion that noticing unexpected objects is driven more by stochastic processes common to all people than by stable individual differences in cognitive abilities.

Inattentional Blindness and Individual Differences in Cognitive Abilities

PubMed Central

Kreitz, Carina; Furley, Philip; Memmert, Daniel; Simons, Daniel J.

2015-01-01

People sometimes fail to notice salient unexpected objects when their attention is otherwise occupied, a phenomenon known as inattentional blindness. To explore individual differences in inattentional blindness, we employed both static and dynamic tasks that either presented the unexpected object away from the focus of attention (spatial) or near the focus of attention (central). We hypothesized that noticing in central tasks might be driven by the availability of cognitive resources like working memory, and that noticing in spatial tasks might be driven by the limits on spatial attention like attention breadth. However, none of the cognitive measures predicted noticing in the dynamic central task or in either the static or dynamic spatial task. Only in the central static task did working memory capacity predict noticing, and that relationship was fairly weak. Furthermore, whether or not participants noticed an unexpected object in a static task was only weakly associated with their odds of noticing an unexpected object in a dynamic task. Taken together, our results are largely consistent with the notion that noticing unexpected objects is driven more by stochastic processes common to all people than by stable individual differences in cognitive abilities. PMID:26258545

Design of a dynamic sensor inspired by bat ears

NASA Astrophysics Data System (ADS)

Müller, Rolf; Pannala, Mittu; Reddy, O. Praveen K.; Meymand, Sajjad Z.

2012-09-01

In bats, the outer ear shapes act as beamforming baffles that create a spatial sensitivity pattern for the reception of the biosonar signals. Whereas technical receivers for wave-based signals usually have rigid geometries, the outer ears of some bat species, such as horseshoe bats, can undergo non-rigid deformations as a result of muscular actuation. It is hypothesized that these deformations provide the animals with a mechanism to adapt their spatial hearing sensitivity on short, sub-second time scales. This biological approach could be of interest to engineering as an inspiration for the design of beamforming devices that combine flexibility with parsimonious implementation. To explore this possibility, a biomimetic dynamic baffle was designed based on a simple shape overall geometry based on an average bat ear. This shape was augmented with three different biomimetic local shape features, a ridge on its exposed surface as well as a flap and an incision along its rim. Dynamic non-rigid deformations of the shape were accomplished through a simple actuation mechanism based on linear actuation inserted at a single point. Despite its simplicity, the prototype device was able to reproduce the dynamic functional characteristics that have been predicted for its biological paragon in a qualitative fashion.

Dynamics and kinetics of narrow dusty ringlets

NASA Astrophysics Data System (ADS)

Sun, K. L.; Spahn, F.; Schmidt, J.

2011-10-01

Several narrow dusty rings have been discovered in the Saturn system, such as the F ring, ringlets in the C Ring, the Cassini division, and the Encke Gap [1] [2]. The kinky and clumpy structures in the F ring are considered as the result of embedded moonlets which are dynamically dominated by shepherding moons [3]. Similar features are found in Encke ringlets which we hypothesize to be associated with embedded moonlets [4] [5]. On the other hand, these ringlets are believed to be composed of micron-sized particles [6], which are strongly perturbed by solar radiation pressure and their lifetime is restricted. Therefore mechanisms must be at work to replenish these ringlets. We develop a model for the kinetic balance of dust production, dynamical evolution, and sinks by assuming that dust is freed and annihilated by moonlets embedded in the ringlet. The dynamics of particles ejected from these putative moonlets is explored and the contribution of impact-ejecta to the ringlet is estimated [7] [8]. We found that the optical depth sustained by embedded moonlets is too low (orders of magnitude), indicating that other sources or processes should be responsible for supporting the Encke ringlet.

On the hydration of subnanometric antifouling organosilane adlayers: a molecular dynamics simulation.

PubMed

Sheikh, Sonia; Blaszykowski, Christophe; Nolan, Robert; Thompson, Damien; Thompson, Michael

2015-01-01

The connection between antifouling and surface hydration is a fascinating but daunting question to answer. Herein, we use molecular dynamics (MD) computer simulations to gain further insight into the role of surface functionalities in the molecular-level structuration of water (surface kosmotropicity)--within and atop subnanometric organosilane adlayers that were shown in previous experimental work to display varied antifouling behavior. Our simulations support the hypothesized intimate link between surface hydration and antifouling, in particular the importance of both internal and interfacial hydrophilicity and kosmotropicity. The antifouling mechanism is also discussed in terms of surface dehydration energy and water dynamicity (lability and mobility), notably the crucial requirement for clustered water molecules to remain tightly bound for extensive periods of time--i.e. exhibit slow exchange dynamics. A substrate effect on surface hydration, which would also participate in endowing antifouling adlayers with hydrogel-like characteristics, is also proposed. In contrast, the role of adlayer flexibility, if any, is assigned a secondary role in these ultrathin structures made of short building blocks. The conclusions from this work are well in line with those previously drawn in the literature. Copyright © 2014 Elsevier Inc. All rights reserved.

Non-Newtonian blood flow dynamics in a right internal carotid artery with a saccular aneurysm

NASA Astrophysics Data System (ADS)

Valencia, Alvaro; Zarate, Alvaro; Galvez, Marcelo; Badilla, Lautaro

2006-02-01

Flow dynamics plays an important role in the pathogenesis and treatment of cerebral aneurysms. The temporal and spatial variations of wall shear stress in the aneurysm are hypothesized to be correlated with its growth and rupture. In addition, the assessment of the velocity field in the aneurysm dome and neck is important for the correct placement of endovascular coils. This work describes the flow dynamics in a patient-specific model of carotid artery with a saccular aneurysm under Newtonian and non-Newtonian fluid assumptions. The model was obtained from three-dimensional rotational angiography image data and blood flow dynamics was studied under physiologically representative waveform of inflow. The three-dimensional continuity and momentum equations for incompressible and unsteady laminar flow were solved with a commercial software using non-structured fine grid with 283 115 tetrahedral elements. The intra-aneurysmal flow shows complex vortex structure that change during one pulsatile cycle. The effect of the non-Newtonian properties of blood on the wall shear stress was important only in the arterial regions with high velocity gradients, on the aneurysmal wall the predictions with the Newtonian and non-Newtonian blood models were similar.

Engineering large cartilage tissues using dynamic bioreactor culture at defined oxygen conditions.

PubMed

Daly, Andrew C; Sathy, Binulal N; Kelly, Daniel J

2018-01-01

Mesenchymal stem cells maintained in appropriate culture conditions are capable of producing robust cartilage tissue. However, gradients in nutrient availability that arise during three-dimensional culture can result in the development of spatially inhomogeneous cartilage tissues with core regions devoid of matrix. Previous attempts at developing dynamic culture systems to overcome these limitations have reported suppression of mesenchymal stem cell chondrogenesis compared to static conditions. We hypothesize that by modulating oxygen availability during bioreactor culture, it is possible to engineer cartilage tissues of scale. The objective of this study was to determine whether dynamic bioreactor culture, at defined oxygen conditions, could facilitate the development of large, spatially homogeneous cartilage tissues using mesenchymal stem cell laden hydrogels. A dynamic culture regime was directly compared to static conditions for its capacity to support chondrogenesis of mesenchymal stem cells in both small and large alginate hydrogels. The influence of external oxygen tension on the response to the dynamic culture conditions was explored by performing the experiment at 20% O 2 and 3% O 2 . At 20% O 2 , dynamic culture significantly suppressed chondrogenesis in engineered tissues of all sizes. In contrast, at 3% O 2 dynamic culture significantly enhanced the distribution and amount of cartilage matrix components (sulphated glycosaminoglycan and collagen II) in larger constructs compared to static conditions. Taken together, these results demonstrate that dynamic culture regimes that provide adequate nutrient availability and a low oxygen environment can be employed to engineer large homogeneous cartilage tissues. Such culture systems could facilitate the scaling up of cartilage tissue engineering strategies towards clinically relevant dimensions.

Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks.

PubMed

Rumschinski, Philipp; Borchers, Steffen; Bosio, Sandro; Weismantel, Robert; Findeisen, Rolf

2010-05-25

Mathematical modeling and analysis have become, for the study of biological and cellular processes, an important complement to experimental research. However, the structural and quantitative knowledge available for such processes is frequently limited, and measurements are often subject to inherent and possibly large uncertainties. This results in competing model hypotheses, whose kinetic parameters may not be experimentally determinable. Discriminating among these alternatives and estimating their kinetic parameters is crucial to improve the understanding of the considered process, and to benefit from the analytical tools at hand. In this work we present a set-based framework that allows to discriminate between competing model hypotheses and to provide guaranteed outer estimates on the model parameters that are consistent with the (possibly sparse and uncertain) experimental measurements. This is obtained by means of exact proofs of model invalidity that exploit the polynomial/rational structure of biochemical reaction networks, and by making use of an efficient strategy to balance solution accuracy and computational effort. The practicability of our approach is illustrated with two case studies. The first study shows that our approach allows to conclusively rule out wrong model hypotheses. The second study focuses on parameter estimation, and shows that the proposed method allows to evaluate the global influence of measurement sparsity, uncertainty, and prior knowledge on the parameter estimates. This can help in designing further experiments leading to improved parameter estimates.

Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks

PubMed Central

2010-01-01

Background Mathematical modeling and analysis have become, for the study of biological and cellular processes, an important complement to experimental research. However, the structural and quantitative knowledge available for such processes is frequently limited, and measurements are often subject to inherent and possibly large uncertainties. This results in competing model hypotheses, whose kinetic parameters may not be experimentally determinable. Discriminating among these alternatives and estimating their kinetic parameters is crucial to improve the understanding of the considered process, and to benefit from the analytical tools at hand. Results In this work we present a set-based framework that allows to discriminate between competing model hypotheses and to provide guaranteed outer estimates on the model parameters that are consistent with the (possibly sparse and uncertain) experimental measurements. This is obtained by means of exact proofs of model invalidity that exploit the polynomial/rational structure of biochemical reaction networks, and by making use of an efficient strategy to balance solution accuracy and computational effort. Conclusions The practicability of our approach is illustrated with two case studies. The first study shows that our approach allows to conclusively rule out wrong model hypotheses. The second study focuses on parameter estimation, and shows that the proposed method allows to evaluate the global influence of measurement sparsity, uncertainty, and prior knowledge on the parameter estimates. This can help in designing further experiments leading to improved parameter estimates. PMID:20500862

Explicit tests of palaeodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia).

PubMed

Bossu, Christen M; Beaulieu, Jeremy M; Ceas, Patrick A; Near, Thomas J

2013-11-01

The alteration in palaeodrainage river connections has shaped patterns of speciation, genetic diversity and the geographical distribution of the species-rich freshwater fauna of North America. The integration of ancestral range reconstruction methods and divergence time estimates provides an opportunity to infer palaeodrainage connectivity and test alternative palaeodrainage hypotheses. Members of the Orangethroat Darter clade, Ceasia, are endemic to southeastern North America and occur north and south of the Pleistocene glacial front, a distributional pattern that makes this clade of closely related species an ideal system to investigate the number and location of glacial refugia and compare alternative hypotheses regarding the proposed evolution of the Teays-Mahomet palaeodrainage. This study utilized time-calibrated mitochondrial and nuclear gene phylogenies and present-day geographical distributions to investigate hypothesized Teays-Mahomet River connections through time using a dispersal-extinction-cladogenesis (DEC) framework. Results of DEC ancestral area reconstructions indicate that the Teays-Mahomet River was a key dispersal route between disjunct highland regions connecting the Mississippi River tributaries to the Old-Ohio Drainage minimally at two separate occasions during the Pleistocene. There was a dynamic interplay between palaeodrainage connections through time and postglacial range expansion from three glacial refugia that shaped the current genetic structure and geographical distributions of the species that comprise Ceasia. © 2013 John Wiley & Sons Ltd.

Attachment insecurity and psychological resources associated with adjustment disorders.

PubMed

Ponizovsky, Alexander M; Levov, Kathy; Schultz, Yakov; Radomislensky, Ira

2011-04-01

This study examined the adult attachment styles, interpersonal distance from potential attachment figures and strangers, coping strategies, perceived social support, and stress-related self-variables among patients diagnosed with adjustment disorders (AJD). Seventy patients at an outpatient clinic and 61 matched controls completed a battery of standardized questionnaires. Univariate and multivariate statistical analyses were used to evaluate the parameters of interest. Using attachment theory (J. Bowlby, 1988) and the dynamic stress-vulnerability model of depressive disorder (G. W. Brown & T. O. Harris, 1989) as the analytical frameworks, the authors hypothesized that participants with AJD would: (a) display more insecure attachment styles, (b) be less tolerant of close interpersonal proximity, (c) use more emotion-oriented coping strategies, (d) display lower self-efficacy and self-esteem, and (e) perceive less social support from family, friends, and significant others. We further hypothesized that these variables would be predictive of depressive symptoms. All of the hypotheses were confirmed. The results suggest that the insecure fearful-avoidant attachment style is associated with severe depressive symptoms in patients with AJD. However, other psychosocial factors, such as low self-esteem and poor social support from friends, were more predictive of AJD symptoms. The findings warrant further studies on the risk and protective effects of these factors in the development of AJD and other stress-induced disorders. © 2011 American Orthopsychiatric Association.

Dynamic test input generation for multiple-fault isolation

NASA Technical Reports Server (NTRS)

Schaefer, Phil

1990-01-01

Recent work is Causal Reasoning has provided practical techniques for multiple fault diagnosis. These techniques provide a hypothesis/measurement diagnosis cycle. Using probabilistic methods, they choose the best measurements to make, then update fault hypotheses in response. For many applications such as computers and spacecraft, few measurement points may be accessible, or values may change quickly as the system under diagnosis operates. In these cases, a hypothesis/measurement cycle is insufficient. A technique is presented for a hypothesis/test-input/measurement diagnosis cycle. In contrast to generating tests a priori for determining device functionality, it dynamically generates tests in response to current knowledge about fault probabilities. It is shown how the mathematics previously used for measurement specification can be applied to the test input generation process. An example from an efficient implementation called Multi-Purpose Causal (MPC) is presented.

Modeling the Ebola zoonotic dynamics: Interplay between enviroclimatic factors and bat ecology

PubMed Central

Johnson, Kaylynn

2017-01-01

Understanding Ebola necessarily requires the characterization of the ecology of its main enzootic reservoir, i.e. bats, and its interplay with seasonal and enviroclimatic factors. Here we present a SIR compartmental model where we implement a bidirectional coupling between the available resources and the dynamics of the bat population in order to understand their migration patterns. Our compartmental modeling approach and simulations include transport terms to account for bats mobility and spatiotemporal climate variability. We hypothesize that environmental pressure is the main driving force for bats’ migration and our results reveal the appearance of sustained migratory waves of Ebola virus infected bats coupled to resources availability. Ultimately, our study can be relevant to predict hot spots of Ebola outbreaks in space and time and suggest conservation policies to mitigate the risk of spillovers. PMID:28604813

The effect of a robot-assisted surgical system on the kinematics of user movements.

PubMed

Nisky, Ilana; Hsieh, Michael H; Okamura, Allison M

2013-01-01

Teleoperated robot-assisted surgery (RAS) offers many advantages over traditional minimally invasive surgery. However, RAS has not yet realized its full potential, and it is not clear how to optimally train surgeons to use these systems. We hypothesize that the dynamics of the master manipulator impact the ability of users to make desired movements with the robot. We compared freehand and teleoperated movements of novices and experienced surgeons. To isolate the effects of dynamics from procedural knowledge, we chose simple movements rather than surgical tasks. We found statistically significant effects of teleoperation and user expertise in several aspects of motion, including target acquisition error, movement speed, and movement smoothness. Such quantitative assessment of human motor performance in RAS can impact the design of surgical robots, their control, and surgeon training methods, and eventually, improve patient outcomes.

Why the long hours? Job demands and social exchange dynamics.

PubMed

Genin, Emilie; Haines, Victor Y; Pelletier, David; Rousseau, Vincent; Marchand, Alain

2016-11-22

This study investigates the determinants of long working hours from the perspectives of the demand-control model [Karasek, 1979] and social exchange theory [Blau, 1964; Goulder, 1960]. These two theoretical perspectives are tested to understand why individuals work longer (or shorter) hours. The hypotheses are tested with a representative sample of 1,604 employed Canadians. In line with Karasek's model, the results support that high job demands are positively associated with longer work hours. The social exchange perspective would predict a positive association between skill discretion and work hours. This hypothesis was supported for individuals with a higher education degree. Finally, the results support a positive association between active jobs and longer work hours. Our research suggests that job demands and social exchange dynamics need to be considered together in the explanation of longer (or shorter) work hours.

Social Ecology, Genomics, and African American Health: A Nonlinear Dynamical Perspective

PubMed Central

Madhere, Serge; Harrell, Jules; Royal, Charmaine D. M.

2009-01-01

This article offers a model that clarifies the degree of interdependence between social ecology and genomic processes. Drawing on principles from nonlinear dynamics, the model delineates major lines of bifurcation involving people's habitat, their family health history, and collective catastrophes experienced by their community. It shows how mechanisms of resource acquisition, depletion, and preservation can lead to disruptions in basic metabolism and in the activity of cytokines, neurotransmitters, and protein kinases, thus giving impetus to epigenetic changes. The hypotheses generated from the model are discussed throughout the article for their relevance to health problems among African Americans. Where appropriate, they are examined in light of data from the National Vital Statistics System. Multiple health outcomes are considered. For any one of them, the model makes clear the unique and converging contributions of multiple antecedent factors. PMID:19672481

Dynamic Social Networks and Physical Aggression: The Moderating Role of Gender and Social Status Among Peers

PubMed Central

Rulison, Kelly L.; Gest, Scott D.; Loken, Eric

2013-01-01

We examined three interrelated questions: (1) Who selects physically aggressive friends?; (2) Are physically aggressive adolescents influential?; and (3) Who is susceptible to influence from these friends? Using stochastic actor-based modeling, we tested our hypotheses using a sample of 480 adolescents (ages 11–13) who were followed across four assessments (fall and spring of 6th and 7th grade). After controlling for other factors that drive network and behavioral dynamics, we found that physically aggressive adolescents were attractive as friends, physically aggressive adolescents and girls were more likely to select physically aggressive friends, and peer-rejected adolescents were less likely to select physically aggressive friends. There was an overall peer influence effect, but gender and social status were not significant moderators of influence. PMID:24068860

The biology and polymer physics underlying large‐scale chromosome organization

PubMed Central

2017-01-01

Chromosome large‐scale organization is a beautiful example of the interplay between physics and biology. DNA molecules are polymers and thus belong to the class of molecules for which physicists have developed models and formulated testable hypotheses to understand their arrangement and dynamic properties in solution, based on the principles of polymer physics. Biologists documented and discovered the biochemical basis for the structure, function and dynamic spatial organization of chromosomes in cells. The underlying principles of chromosome organization have recently been revealed in unprecedented detail using high‐resolution chromosome capture technology that can simultaneously detect chromosome contact sites throughout the genome. These independent lines of investigation have now converged on a model in which DNA loops, generated by the loop extrusion mechanism, are the basic organizational and functional units of the chromosome. PMID:29105235

Virus-host interactions and their roles in coral reef health and disease.

PubMed

Thurber, Rebecca Vega; Payet, Jérôme P; Thurber, Andrew R; Correa, Adrienne M S

2017-04-01

Coral reefs occur in nutrient-poor shallow waters, constitute biodiversity and productivity hotspots, and are threatened by anthropogenic disturbance. This Review provides an introduction to coral reef virology and emphasizes the links between viruses, coral mortality and reef ecosystem decline. We describe the distinctive benthic-associated and water-column- associated viromes that are unique to coral reefs, which have received less attention than viruses in open-ocean systems. We hypothesize that viruses of bacteria and eukaryotes dynamically interact with their hosts in the water column and with scleractinian (stony) corals to influence microbial community dynamics, coral bleaching and disease, and reef biogeochemical cycling. Last, we outline how marine viruses are an integral part of the reef system and suggest that the influence of viruses on reef function is an essential component of these globally important environments.

Exploring bacterial infections: theoretical and experimental studies of the bacterial population dynamics and antibiotic treatment

NASA Astrophysics Data System (ADS)

Shao, Xinxian

Bacterial infections are very common in human society. Thus extensive research has been conducted to reveal the molecular mechanisms of the pathogenesis and to evaluate the antibiotics' efficacy against bacteria. Little is known, however, about the population dynamics of bacterial populations and their interactions with the host's immune system. In this dissertation, a stochatic model is developed featuring stochastic phenotypic switching of bacterial individuals to explain the single-variant bottleneck discovered in multi strain bacterial infections. I explored early events in a bacterial infection establishment using classical experiments of Moxon and Murphy on neonatal rats. I showed that the minimal model and its simple variants do not work. I proposed modifications to the model that could explain the data quantitatively. The bacterial infections are also commonly established in physical structures, as biofilms or 3-d colonies. In contrast, most research on antibiotic treatment of bacterial infections has been conducted in well-mixed liquid cultures. I explored the efficacy of antibiotics to treat such bacterial colonies, a broadly applicable method is designed and evaluated where discrete bacterial colonies on 2-d surfaces were exposed to antibiotics. I discuss possible explanations and hypotheses for the experimental results. To verify these hypotheses, we investigated the dynamics of bacterial population as 3-d colonies. We showed that a minimal mathematical model of bacterial colony growth in 3-d was able to account for the experimentally observed presence of a diffusion-limited regime. The model further revealed highly loose packing of the cells in 3-d colonies and smaller cell sizes in colonies than plancktonic cells in corresponding liquid culture. Further experimental tests of the model predictions have revealed that the ratio of the cell size in liquid culture to that in colony cultures was consistent with the model prediction, that the dead cells emerged randomly in a colony, and that the cells packed heterogeneously in the outer part of a colony, possibly explaining the loose packing.

Sexual Segregation in Juvenile New Zealand Sea Lion Foraging Ranges: Implications for Intraspecific Competition, Population Dynamics and Conservation

PubMed Central

Leung, Elaine S.; Chilvers, B. Louise; Nakagawa, Shinichi; Moore, Antoni B.; Robertson, Bruce C.

2012-01-01

Sexual segregation (sex differences in spatial organisation and resource use) is observed in a large range of taxa. Investigating causes for sexual segregation is vital for understanding population dynamics and has important conservation implications, as sex differences in foraging ecology may affect vulnerability to area-specific human activities. Although behavioural ecologists have proposed numerous hypotheses for this phenomenon, the underlying causes of sexual segregation are poorly understood. We examined the size-dimorphism and niche divergence hypotheses as potential explanations for sexual segregation in the New Zealand (NZ) sea lion (Phocarctos hookeri), a nationally critical, declining species impacted by trawl fisheries. We used satellite telemetry and linear mixed effects models to investigate sex differences in the foraging ranges of juvenile NZ sea lions. Male trip distances and durations were almost twice as long as female trips, with males foraging over the Auckland Island shelf and in further locations than females. Sex was the most important variable in trip distance, maximum distance travelled from study site, foraging cycle duration and percent time at sea whereas mass and age had small effects on these characteristics. Our findings support the predictions of the niche divergence hypothesis, which suggests that sexual segregation acts to decrease intraspecific resource competition. As a consequence of sexual segregation in foraging ranges, female foraging grounds had proportionally double the overlap with fisheries operations than males. This distribution exposes female juvenile NZ sea lions to a greater risk of resource competition and bycatch from fisheries than males, which can result in higher female mortality. Such sex-biased mortality could impact population dynamics, because female population decline can lead to decreased population fecundity. Thus, effective conservation and management strategies must take into account sex differences in foraging behaviour, as well as differential threat-risk to external impacts such as fisheries bycatch. PMID:23028978

Evaluating mallard adaptive management models with time series

USGS Publications Warehouse

Conn, P.B.; Kendall, W.L.

2004-01-01

Wildlife practitioners concerned with midcontinent mallard (Anas platyrhynchos) management in the United States have instituted a system of adaptive harvest management (AHM) as an objective format for setting harvest regulations. Under the AHM paradigm, predictions from a set of models that reflect key uncertainties about processes underlying population dynamics are used in coordination with optimization software to determine an optimal set of harvest decisions. Managers use comparisons of the predictive abilities of these models to gauge the relative truth of different hypotheses about density-dependent recruitment and survival, with better-predicting models giving more weight to the determination of harvest regulations. We tested the effectiveness of this strategy by examining convergence rates of 'predictor' models when the true model for population dynamics was known a priori. We generated time series for cases when the a priori model was 1 of the predictor models as well as for several cases when the a priori model was not in the model set. We further examined the addition of different levels of uncertainty into the variance structure of predictor models, reflecting different levels of confidence about estimated parameters. We showed that in certain situations, the model-selection process favors a predictor model that incorporates the hypotheses of additive harvest mortality and weakly density-dependent recruitment, even when the model is not used to generate data. Higher levels of predictor model variance led to decreased rates of convergence to the model that generated the data, but model weight trajectories were in general more stable. We suggest that predictive models should incorporate all sources of uncertainty about estimated parameters, that the variance structure should be similar for all predictor models, and that models with different functional forms for population dynamics should be considered for inclusion in predictor model! sets. All of these suggestions should help lower the probability of erroneous learning in mallard ABM and adaptive management in general.

Demand-supply dynamics in tourism systems: A spatio-temporal GIS analysis. The Alberta ski industry case study

NASA Astrophysics Data System (ADS)

Bertazzon, Stefania

The present research focuses on the interaction of supply and demand of down-hill ski tourism in the province of Alberta. The main hypothesis is that the demand for skiing depends on the socio-economic and demographic characteristics of the population living in the province and outside it. A second, consequent hypothesis is that the development of ski resorts (supply) is a response to the demand for skiing. From the latter derives the hypothesis of a dynamic interaction between supply (ski resorts) and demand (skiers). Such interaction occurs in space, within a range determined by physical distance and the means available to overcome it. The above hypotheses implicitly define interactions that take place in space and evolve over time. The hypotheses are tested by temporal, spatial, and spatio-temporal regression models, using the best available data and the latest commercially available software. The main purpose of this research is to explore analytical techniques to model spatial, temporal, and spatio-temporal dynamics in the context of regional science. The completion of the present research has produced more significant contributions than was originally expected. Many of the unexpected contributions resulted from theoretical and applied needs arising from the application of spatial regression models. Spatial regression models are a new and largely under-applied technique. The models are fairly complex and a considerable amount of preparatory work is needed, prior to their specification and estimation. Most of this work is specific to the field of application. The originality of the solutions devised is increased by the lack of applications in the field of tourism. The scarcity of applications in other fields adds to their value for other applications. The estimation of spatio-temporal models has been only partially attained in the present research. This apparent limitation is due to the novelty and complexity of the analytical methods applied. This opens new directions for further work in the field of spatial analysis, in conjunction with the development of specific software.

Darwinism, not mutationism, explains the design of organisms.

PubMed

Gardner, Andy

2013-04-01

Shapiro claims that advances in molecular genetics have undermined Darwinism, leading him to advocate mutationism. However, this extreme view is bourne out of conceptual error. He has misunderstood the distinction between gradualism and saltationism, which do not concern the rate of genetic change, but rather the emergence of complex design. And he has misunderstood the relationship between the dynamics of natural selection and the agency of individual organisms: these are not competing hypotheses, but rather alternative conceptualizations of the same phenomenon. Copyright © 2012 Elsevier Ltd. All rights reserved.

Hierarchically Structured Non-Intrusive Sign Language Recognition. Chapter 2

NASA Technical Reports Server (NTRS)

Zieren, Jorg; Zieren, Jorg; Kraiss, Karl-Friedrich

2007-01-01

This work presents a hierarchically structured approach at the nonintrusive recognition of sign language from a monocular frontal view. Robustness is achieved through sophisticated localization and tracking methods, including a combined EM/CAMSHIFT overlap resolution procedure and the parallel pursuit of multiple hypotheses about hands position and movement. This allows handling of ambiguities and automatically corrects tracking errors. A biomechanical skeleton model and dynamic motion prediction using Kalman filters represents high level knowledge. Classification is performed by Hidden Markov Models. 152 signs from German sign language were recognized with an accuracy of 97.6%.

A review of the consequences of fluid and electrolyte shifts in weightlessness

NASA Technical Reports Server (NTRS)

Leach, C. S.

1979-01-01

This review describes the renal-endocrine mechanisms related to the early losses of fluid-electrolytes from the body during weightlessness as well as their contribution to longer term adaptation of fluid-electrolyte balance. The hypotheses presented were generated by a systematic analysis of body fluid and renal dynamics observed under conditions of actual and simulated spaceflight. These have increased our understanding of the effects of acute headward fluid shifts on renal excretion, the factors promoting excess sodium excretion and the regulation of extracellular fluid composition.

A review of the consequences of fluid and electrolyte shifts in weightlessness

NASA Technical Reports Server (NTRS)

Leach, C. S.

1978-01-01

This review describes the renal-endocrine mechanisms related to the early losses of fluid-electrolytes from the body during weightlessness as well as their contribution to longer term adaptation of fluid-electrolyte balance. The hypotheses presented were generated by a systematic analysis of body fluid and renal dynamics observed under conditions of actual and simulated spaceflight. These have increased our understanding of the effects of acute headward fluid shifts on renal excretion, the factors promoting excess sodium excretion and the regulation of extracellular fluid composition.

Stochastic ontogenetic growth model

NASA Astrophysics Data System (ADS)

West, B. J.; West, D.

2012-02-01

An ontogenetic growth model (OGM) for a thermodynamically closed system is generalized to satisfy both the first and second law of thermodynamics. The hypothesized stochastic ontogenetic growth model (SOGM) is shown to entail the interspecies allometry relation by explicitly averaging the basal metabolic rate and the total body mass over the steady-state probability density for the total body mass (TBM). This is the first derivation of the interspecies metabolic allometric relation from a dynamical model and the asymptotic steady-state distribution of the TBM is fit to data and shown to be inverse power law.

Response of Submerged Macrophyte Communities to External and Internal Restoration Measures in North Temperate Shallow Lakes.

PubMed

Hilt, Sabine; Alirangues Nuñez, Marta M; Bakker, Elisabeth S; Blindow, Irmgard; Davidson, Thomas A; Gillefalk, Mikael; Hansson, Lars-Anders; Janse, Jan H; Janssen, Annette B G; Jeppesen, Erik; Kabus, Timm; Kelly, Andrea; Köhler, Jan; Lauridsen, Torben L; Mooij, Wolf M; Noordhuis, Ruurd; Phillips, Geoff; Rücker, Jacqueline; Schuster, Hans-Heinrich; Søndergaard, Martin; Teurlincx, Sven; van de Weyer, Klaus; van Donk, Ellen; Waterstraat, Arno; Willby, Nigel; Sayer, Carl D

2018-01-01

Submerged macrophytes play a key role in north temperate shallow lakes by stabilizing clear-water conditions. Eutrophication has resulted in macrophyte loss and shifts to turbid conditions in many lakes. Considerable efforts have been devoted to shallow lake restoration in many countries, but long-term success depends on a stable recovery of submerged macrophytes. However, recovery patterns vary widely and remain to be fully understood. We hypothesize that reduced external nutrient loading leads to an intermediate recovery state with clear spring and turbid summer conditions similar to the pattern described for eutrophication. In contrast, lake internal restoration measures can result in transient clear-water conditions both in spring and summer and reversals to turbid conditions. Furthermore, we hypothesize that these contrasting restoration measures result in different macrophyte species composition, with added implications for seasonal dynamics due to differences in plant traits. To test these hypotheses, we analyzed data on water quality and submerged macrophytes from 49 north temperate shallow lakes that were in a turbid state and subjected to restoration measures. To study the dynamics of macrophytes during nutrient load reduction, we adapted the ecosystem model PCLake. Our survey and model simulations revealed the existence of an intermediate recovery state upon reduced external nutrient loading, characterized by spring clear-water phases and turbid summers, whereas internal lake restoration measures often resulted in clear-water conditions in spring and summer with returns to turbid conditions after some years. External and internal lake restoration measures resulted in different macrophyte communities. The intermediate recovery state following reduced nutrient loading is characterized by a few macrophyte species (mainly pondweeds) that can resist wave action allowing survival in shallow areas, germinate early in spring, have energy-rich vegetative propagules facilitating rapid initial growth and that can complete their life cycle by early summer. Later in the growing season these plants are, according to our simulations, outcompeted by periphyton, leading to late-summer phytoplankton blooms. Internal lake restoration measures often coincide with a rapid but transient colonization by hornworts, waterweeds or charophytes. Stable clear-water conditions and a diverse macrophyte flora only occurred decades after external nutrient load reduction or when measures were combined.

What to do? The effects of discrepancies, incentives, and time on dynamic goal prioritization.

PubMed

Schmidt, Aaron M; DeShon, Richard P

2007-07-01

This study examined factors that influence the dynamic pursuit of multiple goals over time. As hypothesized, goal-performance discrepancies were significantly related to subsequent time allocation. Greater distance from a given goal resulted in greater time subsequently allocated to that goal. In addition, the incentives offered for goal attainment determined the relative influence of discrepancies for each goal. When the incentives for each goal were equivalent, progress toward each goal exhibited equal influence, with greater time allocated to whichever goal was furthest from completion at the time. However, with an incentive available for only 1 of the 2 goals, time allocation was largely determined by progress toward the rewarded goal. Likewise, when incentives for each task differed in their approach-avoidance framing, progress toward the avoidance-framed goal was a stronger predictor of subsequent allocation than was progress toward the approach-framed goal. Finally, the influence of goal-performance discrepancies differed as a function of the time remaining for goal pursuit. The implications for future work on dynamic goal prioritization and the provision of performance incentives are discussed.

The genomic and epidemiological dynamics of human influenza A virus.

PubMed

Rambaut, Andrew; Pybus, Oliver G; Nelson, Martha I; Viboud, Cecile; Taubenberger, Jeffery K; Holmes, Edward C

2008-05-29

The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions.

Amino acid substitutions affecting protein dynamics in eglin C do not affect heat capacity change upon unfolding.

PubMed

Gribenko, Alexey V; Keiffer, Timothy R; Makhatadze, George I

2006-08-01

The heat capacity change upon unfolding (deltaC(p)) is a thermodynamic parameter that defines the temperature dependence of the thermodynamic stability of proteins; however, physical basis of the heat capacity change is not completely understood. Although empirical surface area-based calculations can predict heat capacity changes reasonably well, accumulating evidence suggests that changes in hydration of those surfaces is not the only parameter contributing to the observed heat capacity changes upon unfolding. Because packing density in the protein interior is similar to that observed in organic crystals, we hypothesized that changes in protein dynamics resulting in increased rigidity of the protein structure might contribute to the observed heat capacity change upon unfolding. Using differential scanning calorimetry we characterized the thermodynamic behavior of a serine protease inhibitor eglin C and two eglin C variants with altered native state dynamics, as determined by NMR. We found no evidence of changes in deltaC(p) in either of the variants, suggesting that changes in rigidity do not contribute to the heat capacity change upon unfolding in this model system. Copyright 2006 Wiley-Liss, Inc.

Fractal patterns in Stock Intertrading Times

NASA Astrophysics Data System (ADS)

White, Ainslie; Lee, Youngki; Ivanov, Plamen Ch.

2003-03-01

We study intertrades times (ITT) of stock trades of a range of companies included in the New York Stock Exchange's Trades and Quotes (TAQ) database. The time between transactions is an indicator of the dynamics of the market, and in the field of econometrics, intertrade durations play a key role in the understanding of the market activity and microstructure. Previous work has mainly focused on the properties of price changes of individual company stocks as well as global financial indices (e.g. SP500, DJ etc.). We hypothesize that there is a relation between the dynamics of price change and the trading activity. To investigate this relation we first study the statistical features of ITT data. The TAQ database covers all transactions on the NSE, AMEX, NASDAQ and the US regional exchanges. We have performed a preliminary analysis of 100 company stocks from a range of industries of the US economy selecting predominantly those companies which have large market capitalisations (MC). We focus on companies with large MC, since the dynamics of the price change and trading activity of stocks of such companies has a considerable impact on the market behaviour.

Sex differences in in-group cooperation vary dynamically with competitive conditions and outcomes.

PubMed

Bailey, Drew H; Winegard, Benjamin; Oxford, Jon; Geary, David C

2012-03-18

Men's but not women's investment in a public goods game varied dynamically with the presence or absence of a perceived out-group. Three hundred fifty-four (167 male) young adults participated in multiple iterations of a public goods game under intergroup and individual competition conditions. Participants received feedback about whether their investments in the group were sufficient to earn a bonus to be shared among all in-group members. Results for the first trial confirm previous research in which men's but not women's investments were higher when there was a competing out-group. We extended these findings by showing that men's investment in the in-group varied dynamically by condition depending on the outcome of the previous trial: In the group condition, men, but not women, decreased spending following a win (i.e., earning an in-group bonus). In the individual condition, men, but not women, increased spending following a win. We hypothesize that these patterns reflect a male bias to calibrate their level of in-group investment such that they sacrifice only what is necessary for their group to successfully compete against a rival group.

Molecular-level dynamics of refractory dissolved organic matter

NASA Astrophysics Data System (ADS)

Niggemann, J.; Gerdts, G.; Dittmar, T.

2012-04-01

Refractory dissolved organic matter (DOM) accounts for most of the global oceanic organic carbon inventory. Processes leading to its formation and factors determining its stability are still largely unknown. We hypothesize that refractory DOM carries a universal molecular signature. Characterizing spatial and temporal variability in this universal signature is a key to understanding dynamics of refractory DOM. We present results from a long-term study of the DOM geo-metabolome in the open North Sea. Geo-metabolomics considers the entity of DOM as a population of compounds, each characterized by a specific function and reactivity in the cycling of energy and elements. Ten-thousands of molecular formulae were identified in DOM by ultrahigh resolution mass spectrometry analysis (FT-ICR-MS, Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry). The DOM pool in the North Sea was influenced by a complex interplay of processes that produced, transformed and degraded dissolved molecules. We identified a stable fraction in North Sea DOM with a molecular composition similar to deep ocean DOM. Molecular-level changes in this stable fraction provide novel information on dynamics and interactions of refractory DOM.

Automatic conversational scene analysis in children with Asperger syndrome/high-functioning autism and typically developing peers.

PubMed

Tavano, Alessandro; Pesarin, Anna; Murino, Vittorio; Cristani, Marco

2014-01-01

Individuals with Asperger syndrome/High Functioning Autism fail to spontaneously attribute mental states to the self and others, a life-long phenotypic characteristic known as mindblindness. We hypothesized that mindblindness would affect the dynamics of conversational interaction. Using generative models, in particular Gaussian mixture models and observed influence models, conversations were coded as interacting Markov processes, operating on novel speech/silence patterns, termed Steady Conversational Periods (SCPs). SCPs assume that whenever an agent's process changes state (e.g., from silence to speech), it causes a general transition of the entire conversational process, forcing inter-actant synchronization. SCPs fed into observed influence models, which captured the conversational dynamics of children and adolescents with Asperger syndrome/High Functioning Autism, and age-matched typically developing participants. Analyzing the parameters of the models by means of discriminative classifiers, the dialogs of patients were successfully distinguished from those of control participants. We conclude that meaning-free speech/silence sequences, reflecting inter-actant synchronization, at least partially encode typical and atypical conversational dynamics. This suggests a direct influence of theory of mind abilities onto basic speech initiative behavior.

Modelling social interaction as perceptual crossing: an investigation into the dynamics of the interaction process

NASA Astrophysics Data System (ADS)

Froese, Tom; Di Paolo, Ezequiel A.

2010-03-01

This paper continues efforts to establish a mutually informative dialogue between psychology and evolutionary robotics in order to investigate the dynamics of social interaction. We replicate a recent simulation model of a minimalist experiment in perceptual crossing and confirm the results with significantly simpler artificial agents. A series of psycho-physical tests of their behaviour informs a hypothetical circuit model of their internal operation. However, a detailed study of the actual internal dynamics reveals this circuit model to be unfounded, thereby offering a tale of caution for those hypothesising about sub-personal processes in terms of behavioural observations. In particular, it is shown that the behaviour of the agents largely emerges out of the interaction process itself rather than being an individual achievement alone. We also extend the original simulation model in two novel directions in order to test further the extent to which perceptual crossing between agents can self-organise in a robust manner. These modelling results suggest new hypotheses that can become the basis for further psychological experiments.

Static and dynamic bending has minor effects on xylem hydraulics of conifer branches (Picea abies, Pinus sylvestris)

PubMed Central

Mayr, Stefan; Bertel, Clara; Dämon, Birgit; Beikircher, Barbara

2014-01-01

The xylem hydraulic efficiency and safety is usually measured on mechanically unstressed samples, although trees may be exposed to combined hydraulic and mechanical stress in the field. We analysed changes in hydraulic conductivity and vulnerability to drought-induced embolism during static bending of Picea abies and Pinus sylvestris branches as well as the effect of dynamic bending on the vulnerability. We hypothesized this mechanical stress to substantially impair xylem hydraulics. Intense static bending caused an only small decrease in hydraulic conductance (−19.5 ± 2.4% in P. abies) but no shift in vulnerability thresholds. Dynamic bending caused a 0.4 and 0.8 MPa decrease of the water potential at 50 and 88% loss of conductivity in P. sylvestris, but did not affect vulnerability thresholds in P. abies. With respect to applied extreme bending radii, effects on plant hydraulics were surprisingly small and are thus probably of minor eco-physiological importance. More importantly, results indicate that available xylem hydraulic analyses (of conifers) sufficiently reflect plant hydraulics under field conditions. PMID:24697679

Dynamic Stabilization of Simple Fractures With Active Plates Delivers Stronger Healing Than Conventional Compression Plating

PubMed Central

Tsai, Stanley; Bliven, Emily K.; von Rechenberg, Brigitte; Kindt, Philipp; Augat, Peter; Henschel, Julia; Fitzpatrick, Daniel C.; Madey, Steven M.

2017-01-01

Objectives: Active plates dynamize a fracture by elastic suspension of screw holes within the plate. We hypothesized that dynamic stabilization with active plates delivers stronger healing relative to standard compression plating. Methods: Twelve sheep were randomized to receive either a standard compression plate (CP) or an active plate (ACTIVE) for stabilization of an anatomically reduced tibial osteotomy. In the CP group, absolute stabilization was pursued by interfragmentary compression with 6 cortical screws. In the ACTIVE group, dynamic stabilization after bony apposition was achieved with 6 elastically suspended locking screws. Fracture healing was analyzed weekly on radiographs. After sacrifice 9 weeks postsurgery, the torsional strength of healed tibiae and contralateral tibiae was measured. Finally, computed tomography was used to assess fracture patterns and healing modes. Results: Healing in both groups included periosteal callus formation. ACTIVE specimens had almost 6 times more callus area by week 9 (P < 0.001) than CP specimens. ACTIVE specimens recovered on average 64% of their native strength by week 9, and were over twice as strong as CP specimens, which recovered 24% of their native strength (P = 0.008). Microcomputed tomography demonstrated that compression plating induced a combination of primary bone healing and gap healing. Active plating consistently stimulated biological bone healing by periosteal callus formation. Conclusions: Compared with compression plating, dynamic stabilization of simple fractures with active plates delivers significantly stronger healing. PMID:27861456

Comparison of Three Ionic Liquid-Tolerant Cellulases by Molecular Dynamics

PubMed Central

Jaeger, Vance; Burney, Patrick; Pfaendtner, Jim

2015-01-01

We have employed molecular dynamics to investigate the differences in ionic liquid tolerance among three distinct family 5 cellulases from Trichoderma viride, Thermogata maritima, and Pyrococcus horikoshii. Simulations of the three cellulases were conducted at a range of temperatures in various binary mixtures of the ionic liquid 1-ethyl-3-methyl-imidazolium acetate with water. Our analysis demonstrates that the effects of ionic liquids on the enzymes vary in each individual case from local structural disturbances to loss of much of one of the enzyme’s secondary structure. Enzymes with more negatively charged surfaces tend to resist destabilization by ionic liquids. Specific and unique structural changes in the enzymes are induced by the presence of ionic liquids. Disruption of the secondary structure, changes in dynamical motion, and local changes in the binding pocket are observed in less tolerant enzymes. Ionic-liquid-induced denaturation of one of the enzymes is indicated over the 500 ns timescale. In contrast, the most tolerant cellulase behaves similarly in water and in ionic-liquid-containing mixtures. Unlike the heuristic approaches that attempt to predict enzyme stability using macroscopic properties, molecular dynamics allows us to predict specific atomic-level structural and dynamical changes in an enzyme’s behavior induced by ionic liquids and other mixed solvents. Using these insights, we propose specific experimentally testable hypotheses regarding the origin of activity loss for each of the systems investigated in this study. PMID:25692593

Examining Dynamic Stall for an Oscillating NACA 4412 Hydrofoil

NASA Astrophysics Data System (ADS)

McVay, Eric; Lang, Amy; Gamble, Lawren; Bradshaw, Michael

2013-11-01

Dynamic stall is unsteady separation that occurs when a hydrofoil pitches through the static stall angle while simultaneously experiencing a rapid change in angle of attack. The NACA 4412 hydrofoil was selected for this research because it has strong trailing edge turbulent boundary layer separation characteristics. General dynamic stall angle of attack for approximately symmetric airfoils has been recorded to occur at 24 degrees, with separation beginning at about 16 degrees. It is predicted that the boundary layer will stay attached at a higher angle of attack because of the cambered geometry of the hydrofoil. It is also hypothesized that the boundary layer separation occurs closer to the trailing edge and that the dynamic stall angle of attack occurs somewhere between 24 and 28 degrees for the oscillating NACA 4412 hydrofoil. This research was conducted in a water tunnel facility using Time Resolved Digital Particle Image Velocimetry (TR-DPIV). The hydrofoil was pitched up from 0 to 30 degrees at Reynolds numbers of 60,000, 80,000 and 100,000. Flow characteristics, dynamic stall angles of attack, and points of boundary layer separation were compared at each velocity with both tripped and un-tripped surfaces. Follow-on research will be conducted using flow control techniques from sharks and dolphins to examine the potential benefits of these natural designs for separation control. Support for this research by NSF REU Grant #1062611 and CBET Grant #0932352 is gratefully acknowledged.

Estimating rates of local extinction and colonization in colonial species and an extension to the metapopulation and community levels

USGS Publications Warehouse

Barbraud, C.; Nichols, J.D.; Hines, J.E.; Hafner, H.

2003-01-01

Coloniality has mainly been studied from an evolutionary perspective, but relatively few studies have developed methods for modelling colony dynamics. Changes in number of colonies over time provide a useful tool for predicting and evaluating the responses of colonial species to management and to environmental disturbance. Probabilistic Markov process models have been recently used to estimate colony site dynamics using presence-absence data when all colonies are detected in sampling efforts. Here, we define and develop two general approaches for the modelling and analysis of colony dynamics for sampling situations in which all colonies are, and are not, detected. For both approaches, we develop a general probabilistic model for the data and then constrain model parameters based on various hypotheses about colony dynamics. We use Akaike's Information Criterion (AIC) to assess the adequacy of the constrained models. The models are parameterised with conditional probabilities of local colony site extinction and colonization. Presence-absence data arising from Pollock's robust capture-recapture design provide the basis for obtaining unbiased estimates of extinction, colonization, and detection probabilities when not all colonies are detected. This second approach should be particularly useful in situations where detection probabilities are heterogeneous among colony sites. The general methodology is illustrated using presence-absence data on two species of herons (Purple Heron, Ardea purpurea and Grey Heron, Ardea cinerea). Estimates of the extinction and colonization rates showed interspecific differences and strong temporal and spatial variations. We were also able to test specific predictions about colony dynamics based on ideas about habitat change and metapopulation dynamics. We recommend estimators based on probabilistic modelling for future work on colony dynamics. We also believe that this methodological framework has wide application to problems in animal ecology concerning metapopulation and community dynamics.

The Fragility of Individual-Based Explanations of Social Hierarchies: A Test Using Animal Pecking Orders

PubMed Central

2016-01-01

The standard approach in accounting for hierarchical differentiation in biology and the social sciences considers a hierarchy as a static distribution of individuals possessing differing amounts of some valued commodity, assumes that the hierarchy is generated by micro-level processes involving individuals, and attempts to reverse engineer the processes that produced the hierarchy. However, sufficient experimental and analytical results are available to evaluate this standard approach in the case of animal dominance hierarchies (pecking orders). Our evaluation using evidence from hierarchy formation in small groups of both hens and cichlid fish reveals significant deficiencies in the three tenets of the standard approach in accounting for the organization of dominance hierarchies. In consequence, we suggest that a new approach is needed to explain the organization of pecking orders and, very possibly, by implication, for other kinds of social hierarchies. We develop an example of such an approach that considers dominance hierarchies to be dynamic networks, uses dynamic sequences of interaction (dynamic network motifs) to explain the organization of dominance hierarchies, and derives these dynamic sequences directly from observation of hierarchy formation. We test this dynamical explanation using computer simulation and find a good fit with actual dynamics of hierarchy formation in small groups of hens. We hypothesize that the same dynamic sequences are used in small groups of many other animal species forming pecking orders, and we discuss the data required to evaluate our hypothesis. Finally, we briefly consider how our dynamic approach may be generalized to other kinds of social hierarchies using the example of the distribution of empty gastropod (snail) shells occupied in populations of hermit crabs. PMID:27410230

Decreased steady-state cerebral blood flow velocity and altered dynamic cerebral autoregulation during 5-h sustained 15% O2 hypoxia.

PubMed

Nishimura, Naoko; Iwasaki, Ken-ichi; Ogawa, Yojiro; Aoki, Ken

2010-05-01

Effects of hypoxia on cerebral circulation are important for occupational, high-altitude, and aviation medicine. Increased risk of fainting might be attributable to altered cerebral circulation by hypoxia. Dynamic cerebral autoregulation is reportedly impaired immediately by mild hypoxia. However, continuous exposure to hypoxia causes hyperventilation, resulting in hypocapnia. This hypocapnia is hypothesized to restore impaired dynamic cerebral autoregulation with reduced steady-state cerebral blood flow (CBF). However, no studies have examined hourly changes in alterations of dynamic cerebral autoregulation and steady-state CBF during sustained hypoxia. We therefore examined cerebral circulation during 5-h exposure to 15% O2 hypoxia and 21% O2 in 13 healthy volunteers in a sitting position. Waveforms of blood pressure and CBF velocity in the middle cerebral artery were measured using finger plethysmography and transcranial Doppler ultrasonography. Dynamic cerebral autoregulation was assessed by spectral and transfer function analysis. As expected, steady-state CBF velocity decreased significantly from 2 to 5 h of hypoxia, accompanying 2- to 3-Torr decreases in end-tidal CO2 (ETCO2). Furthermore, transfer function gain and coherence in the very-low-frequency range increased significantly at the beginning of hypoxia, indicating impaired dynamic cerebral autoregulation. However, contrary to the proposed hypothesis, indexes of dynamic cerebral autoregulation showed no significant restoration despite ETCO2 reductions, resulting in persistent higher values of very-low-frequency power of CBF velocity variability during hypoxia (214+/-40% at 5 h of hypoxia vs. control) without significant increases in blood pressure variability. These results suggest that sustained mild hypoxia reduces steady-state CBF and continuously impairs dynamic cerebral autoregulation, implying an increased risk of shortage of oxygen supply to the brain.

Long residence times of rapidly decomposable soil organic matter: application of a multi-phase, multi-component, and vertically-resolved model (TOUGHREACTv1) to soil carbon dynamics

NASA Astrophysics Data System (ADS)

Riley, W. J.; Maggi, F. M.; Kleber, M.; Torn, M. S.; Tang, J. Y.; Dwivedi, D.; Guerry, N.

2014-01-01

Accurate representation of soil organic matter (SOM) dynamics in Earth System Models is critical for future climate prediction, yet large uncertainties exist regarding how, and to what extent, the suite of proposed relevant mechanisms should be included. To investigate how various mechanisms interact to influence SOM storage and dynamics, we developed a SOM reaction network integrated in a one-dimensional, multi-phase, and multi-component reactive transport solver. The model includes representations of bacterial and fungal activity, multiple archetypal polymeric and monomeric carbon substrate groups, aqueous chemistry, aqueous advection and diffusion, gaseous diffusion, and adsorption (and protection) and desorption from the soil mineral phase. The model predictions reasonably matched observed depth-resolved SOM and dissolved organic carbon (DOC) stocks in grassland ecosystems as well as lignin content and fungi to aerobic bacteria ratios. We performed a suite of sensitivity analyses under equilibrium and dynamic conditions to examine the role of dynamic sorption, microbial assimilation rates, and carbon inputs. To our knowledge, observations do not exist to fully test such a complicated model structure or to test the hypotheses used to explain observations of substantial storage of very old SOM below the rooting depth. Nevertheless, we demonstrated that a reasonable combination of sorption parameters, microbial biomass and necromass dynamics, and advective transport can match observations without resorting to an arbitrary depth-dependent decline in SOM turnover rates, as is often done. We conclude that, contrary to assertions derived from existing turnover time based model formulations, observed carbon content and δ14C vertical profiles are consistent with a representation of SOM dynamics consisting of (1) carbon compounds without designated intrinsic turnover times, (2) vertical aqueous transport, and (3) dynamic protection on mineral surfaces.

Investigations Into Internal and External Aspects of Dynamic Agent-Environment Couplings

NASA Astrophysics Data System (ADS)

Dautenhahn, Kerstin

This paper originates from my work on `social agents'. An issue which I consider important to this kind of research is the dynamic coupling of an agent with its social and non-social environment. I hypothesize `internal dynamics' inside an agent as a basic step towards understanding. The paper therefore focuses on the internal and external dynamics which couple an agent to its environment. The issue of embodiment in animals and artifacts and its relation to `social dynamics' is discussed first. I argue that embodiment is linked to a concept of a body and is not necessarily given when running a control program on robot hardware. I stress the individual characteristics of an embodied cognitive system, as well as its social embeddedness. I outline the framework of a physical-psychological state space which changes dynamically in a self-modifying way as a holistic approach towards embodied human and artificial cognition. This framework is meant to discuss internal and external dynamics of an embodied, natural or artificial agent. In order to stress the importance of a dynamic memory I introduce the concept of an `autobiographical agent'. The second part of the paper gives an example of the implementation of a physical agent, a robot, which is dynamically coupled to its environment by balancing on a seesaw. For the control of the robot a behavior-oriented approach using the dynamical systems metaphor is used. The problem is studied through building a complete and co-adapted robot-environment system. A seesaw which varies its orientation with one or two degrees of freedom is used as the artificial `habitat'. The problem of stabilizing the body axis by active motion on a seesaw is solved by using two inclination sensors and a parallel, behavior-oriented control architecture. Some experiments are described which demonstrate the exploitation of the dynamics of the robot-environment system.

Spatio-temporal Dynamics of Audiovisual Speech Processing

PubMed Central

Bernstein, Lynne E.; Auer, Edward T.; Wagner, Michael; Ponton, Curtis W.

2007-01-01

The cortical processing of auditory-alone, visual-alone, and audiovisual speech information is temporally and spatially distributed, and functional magnetic resonance imaging (fMRI) cannot adequately resolve its temporal dynamics. In order to investigate a hypothesized spatio-temporal organization for audiovisual speech processing circuits, event-related potentials (ERPs) were recorded using electroencephalography (EEG). Stimuli were congruent audiovisual /bα/, incongruent auditory /bα/ synchronized with visual /gα/, auditory-only /bα/, and visual-only /bα/ and /gα/. Current density reconstructions (CDRs) of the ERP data were computed across the latency interval of 50-250 milliseconds. The CDRs demonstrated complex spatio-temporal activation patterns that differed across stimulus conditions. The hypothesized circuit that was investigated here comprised initial integration of audiovisual speech by the middle superior temporal sulcus (STS), followed by recruitment of the intraparietal sulcus (IPS), followed by activation of Broca's area (Miller and d'Esposito, 2005). The importance of spatio-temporally sensitive measures in evaluating processing pathways was demonstrated. Results showed, strikingly, early (< 100 msec) and simultaneous activations in areas of the supramarginal and angular gyrus (SMG/AG), the IPS, the inferior frontal gyrus, and the dorsolateral prefrontal cortex. Also, emergent left hemisphere SMG/AG activation, not predicted based on the unisensory stimulus conditions was observed at approximately 160 to 220 msec. The STS was neither the earliest nor most prominent activation site, although it is frequently considered the sine qua non of audiovisual speech integration. As discussed here, the relatively late activity of the SMG/AG solely under audiovisual conditions is a possible candidate audiovisual speech integration response. PMID:17920933

Complexity, information loss, and model building: from neuro- to cognitive dynamics

NASA Astrophysics Data System (ADS)

Arecchi, F. Tito

2007-06-01

A scientific problem described within a given code is mapped by a corresponding computational problem, We call complexity (algorithmic) the bit length of the shortest instruction which solves the problem. Deterministic chaos in general affects a dynamical systems making the corresponding problem experimentally and computationally heavy, since one must reset the initial conditions at a rate higher than that of information loss (Kolmogorov entropy). One can control chaos by adding to the system new degrees of freedom (information swapping: information lost by chaos is replaced by that arising from the new degrees of freedom). This implies a change of code, or a new augmented model. Within a single code, changing hypotheses is equivalent to fixing different sets of control parameters, each with a different a-priori probability, to be then confirmed and transformed to an a-posteriori probability via Bayes theorem. Sequential application of Bayes rule is nothing else than the Darwinian strategy in evolutionary biology. The sequence is a steepest ascent algorithm, which stops once maximum probability has been reached. At this point the hypothesis exploration stops. By changing code (and hence the set of relevant variables) one can start again to formulate new classes of hypotheses . We call semantic complexity the number of accessible scientific codes, or models, that describe a situation. It is however a fuzzy concept, in so far as this number changes due to interaction of the operator with the system under investigation. These considerations are illustrated with reference to a cognitive task, starting from synchronization of neuron arrays in a perceptual area and tracing the putative path toward a model building.

Dynamic multistate site occupancy models to evaluate hypotheses relevant to conservation of Golden Eagles in Denali National Park, Alaska

USGS Publications Warehouse

Martin, Julien; McIntyre, Carol L.; Hines, James E.; Nichols, James D.; Schmutz, Joel A.; MacCluskie, Margaret C.

2009-01-01

The recent development of multistate site occupancy models offers great opportunities to frame and solve decision problems for conservation that can be viewed in terms of site occupancy. These models have several characteristics (e.g., they account for detectability) that make them particularly well suited for addressing management and conservation problems. We applied multistate site occupancy models to evaluate hypotheses related to the conservation and management of Golden Eagles (Aquila chrysaetos) in Denali National Park, Alaska, and provided estimates of transition probabilities among three occupancy states for nesting areas (occupied with successful reproduction, occupied with unsuccessful reproduction, and unoccupied). Our estimation models included the effect of potential recreational activities (hikers) and environmental covariates such as a snowshoe hare (Lepus americanus) index on transition probabilities among the three occupancy states. Based on the most parsimonious model, support for the hypothesis of an effect of potential human disturbance on site occupancy dynamics was equivocal. There was some evidence that potential human disturbance negatively affected local colonization of territories, but there was no evidence of an effect on reproductive performance parameters. In addition, models that assume a positive relationship between the hare index and successful reproduction were well supported by the data. The statistical approach that we used is particularly useful to parameterize management models that can then be used to make optimal decisions related to the management of Golden Eagles in Denali. Although in our case we were particularly interested in managing recreational activities, we believe that such models should be useful to for a broad class of management and conservation problems.

Microtubule-Targeting Agents Eribulin and Paclitaxel Differentially Affect Neuronal Cell Bodies in Chemotherapy-Induced Peripheral Neuropathy.

PubMed

Benbow, Sarah J; Wozniak, Krystyna M; Kulesh, Bridget; Savage, April; Slusher, Barbara S; Littlefield, Bruce A; Jordan, Mary Ann; Wilson, Leslie; Feinstein, Stuart C

2017-07-01

Chemotherapy-induced peripheral neuropathy (CIPN) is a common side effect of anticancer treatment with microtubule-targeted agents (MTAs). The frequency of severe CIPN, which can be dose limiting and even life threatening, varies widely among different MTAs. For example, paclitaxel induces a higher frequency of severe CIPN than does eribulin. Different MTAs also possess distinct mechanisms of microtubule-targeted action. Recently, we demonstrated that paclitaxel and eribulin differentially affect sciatic nerve axons, with paclitaxel inducing more pronounced neurodegenerative effects and eribulin inducing greater microtubule stabilizing biochemical effects. Here, we complement and extend these axonal studies by assessing the effects of paclitaxel and eribulin in the cell bodies of sciatic nerve axons, housed in the dorsal root ganglia (DRG). Importantly, the microtubule network in cell bodies is known to be significantly more dynamic than in axons. Paclitaxel induced activating transcription factor 3 expression, a marker of neuronal stress/injury. Paclitaxel also increased expression levels of acetylated tubulin and end binding protein 1, markers of microtubule stability and growth, respectively. These effects are hypothesized to be detrimental to the dynamic microtubule network within the cell bodies. In contrast, eribulin had no significant effect on any of these parameters in the cell bodies. Taken together, DRG cell bodies and their axons, two distinct neuronal cell compartments, contain functionally distinct microtubule networks that exhibit unique biochemical responses to different MTA treatments. We hypothesize that these distinct mechanistic actions may underlie the variability seen in the initiation, progression, persistence, and recovery from CIPN.

Cortical dynamics of figure-ground segmentation: shine-through.

PubMed

Francis, Gregory

2009-01-01

The shine-through effect occurs when a brief offset vernier target is followed by a grating of non-offset vernier elements. Rather than mask the target, this stimulus sequence produces a percept of the target vernier occluding the mask elements. We analyzed the dynamics of the 3D LAMINART model of depth perception and found that it explains the appearance of shine-through for these stimuli. The model explanation proposes that shine-through is due to a combination of false binocular disparity matches between the target and the central element of the mask, and a weakening of between disparity competition due to spatial competition and boundary grouping. Simulations of the model demonstrate that its behavior closely matches empirical data on the properties of shine-through. The model is contrasted with an alternative explanation of shine-through, and novel mask conditions are studied that allow for empirical tests of the model hypotheses.

Population dynamics of Lutzomyia shannoni (Diptera: Psychodidae) in relation to the epizootiology of vesicular stomatitis virus on Ossabaw Island, Georgia.

PubMed

Comer, J A; Kavanaugh, D M; Stallknecht, D E; Corn, J L

1994-11-01

Population dynamics of Lutzomyia shannoni Dyar were studied on Ossabaw Island, GA, to define further the role of this species in the epizootiology of the New Jersey serotype of vesicular stomatitis (VSNJ) virus. Bimonthly collections of sand flies egressing from hollow trees from April to November 1991 indicated that there were three generations of sand flies. Data from light trap collections from 1986 through 1989 indicated that similar seasonal cycles occurred during previous years. At this site, we hypothesize that L. shannoni undergoes facultative diapause. Two isolates of VSNJ virus were obtained from female sand flies collected in May and June of 1991. We believe that the virus overwinters in immature L. shannoni and that transovarially infected sand flies emerging each spring initiate a summer amplification cycle in swine on Ossabaw Island.

Stochastic inference with spiking neurons in the high-conductance state

NASA Astrophysics Data System (ADS)

Petrovici, Mihai A.; Bill, Johannes; Bytschok, Ilja; Schemmel, Johannes; Meier, Karlheinz

2016-10-01

The highly variable dynamics of neocortical circuits observed in vivo have been hypothesized to represent a signature of ongoing stochastic inference but stand in apparent contrast to the deterministic response of neurons measured in vitro. Based on a propagation of the membrane autocorrelation across spike bursts, we provide an analytical derivation of the neural activation function that holds for a large parameter space, including the high-conductance state. On this basis, we show how an ensemble of leaky integrate-and-fire neurons with conductance-based synapses embedded in a spiking environment can attain the correct firing statistics for sampling from a well-defined target distribution. For recurrent networks, we examine convergence toward stationarity in computer simulations and demonstrate sample-based Bayesian inference in a mixed graphical model. This points to a new computational role of high-conductance states and establishes a rigorous link between deterministic neuron models and functional stochastic dynamics on the network level.

Dynamic expression patterns of ECM molecules in the developing mouse olfactory pathway

PubMed Central

Shay, Elaine L.; Greer, Charles A.; Treloar, Helen B.

2009-01-01

Olfactory sensory neuron (OSN) axons follow stereotypic spatio-temporal paths in the establishment of the olfactory pathway. Extracellular matrix (ECM) molecules are expressed early in the developing pathway and are proposed to have a role in its initial establishment. During later embryonic development, OSNs sort out and target specific glomeruli to form precise, complex topographic projections. We hypothesized that ECM cues may help to establish this complex topography. The aim of this study was to characterize expression of ECM molecules during the period of glomerulogenesis, when synaptic contacts are forming. We examined expression of laminin-1, perlecan, tenascin-C and CSPGs and found a coordinated pattern of expression of these cues in the pathway. These appear to restrict axons to the pathway while promoting axon outgrowth within. Thus, ECM molecules are present in dynamic spatio-temporal positions to affect OSN axons as they navigate to the olfactory bulb and establish synapses. PMID:18570250

The biology and polymer physics underlying large-scale chromosome organization.

PubMed

Sazer, Shelley; Schiessel, Helmut

2018-02-01

Chromosome large-scale organization is a beautiful example of the interplay between physics and biology. DNA molecules are polymers and thus belong to the class of molecules for which physicists have developed models and formulated testable hypotheses to understand their arrangement and dynamic properties in solution, based on the principles of polymer physics. Biologists documented and discovered the biochemical basis for the structure, function and dynamic spatial organization of chromosomes in cells. The underlying principles of chromosome organization have recently been revealed in unprecedented detail using high-resolution chromosome capture technology that can simultaneously detect chromosome contact sites throughout the genome. These independent lines of investigation have now converged on a model in which DNA loops, generated by the loop extrusion mechanism, are the basic organizational and functional units of the chromosome. © 2017 The Authors. Traffic published by John Wiley & Sons Ltd.

The dynamic spillover of satisfaction between work and marriage: the role of time and mood.

PubMed

Heller, Daniel; Watson, David

2005-11-01

Previous research has indicated important linkages between work and family domains and roles. However, the nature of the dynamic spillover between job and marital satisfaction remains poorly understood. The current study tests both the concurrent and lagged associations between job and marital satisfaction at a within-individual level of analysis using a diary study of 76 fully employed, married adults. The authors further examine the mediating role of mood in this spillover process. Consistent with their hypotheses, findings indicate both a concurrent and a lagged (job to marital and marital to job) job satisfaction-marital satisfaction association at the within-subject level of analysis and lend some support for the mediating role of mood (most notably positive affect) in these associations. The authors hope these findings stimulate new research that uses more complex designs and comprehensive theoretical models to investigate work-family links. ((c) 2005 APA, all rights reserved).

The seasonal response of the Held-Suarez climate model to prescribed ocean temperature anomalies. II - Dynamical analysis

NASA Technical Reports Server (NTRS)

Phillips, T. J.

1984-01-01

The heating associated with equatorial, subtropical, and midlatitude ocean temperature anamolies in the Held-Suarez climate model is analyzed. The local and downstream response to the anomalies is analyzed, first by examining the seasonal variation in heating associated with each ocean temperature anomaly, and then by combining knowledge of the heating with linear dynamical theory in order to develop a more comprehensive explanation of the seasonal variation in local and downstream atmospheric response to each anomaly. The extent to which the linear theory of propagating waves can assist the interpretation of the remote cross-latitudinal response of the model to the ocean temperature anomalies is considered. Alternative hypotheses that attempt to avoid the contradictions inherent in a strict application of linear theory are investigated, and the impact of sampling errors on the assessment of statistical significance is also examined.

Social influence and bullying behavior: intervention-based network dynamics of the fairplayer.manual bullying prevention program.

PubMed

Wölfer, Ralf; Scheithauer, Herbert

2014-01-01

Bullying is a social phenomenon and although preventive interventions consequently address social mechanisms, evaluations hardly consider the complexity of peer processes. Therefore, the present study analyzes the efficacy of the fairplayer.manual bullying prevention program from a social network perspective. Within a pretest-posttest control group design, longitudinal data were available from 328 middle-school students (MAge  = 13.7 years; 51% girls), who provided information on bullying behavior and interaction patterns. The revealed network parameters were utilized to examine the network change (MANCOVA) and the network dynamics (SIENA). Across both forms of analyses, findings revealed the hypothesized intervention-based decrease of bullies' social influence. Hence the present bullying prevention program, as one example of programs that successfully addresses both individual skills and social mechanisms, demonstrates the desired effect of reducing contextual opportunities for the exhibition of bullying behavior. © 2014 Wiley Periodicals, Inc.

Entraining IDyOT: Timing in the Information Dynamics of Thinking

PubMed Central

Forth, Jamie; Agres, Kat; Purver, Matthew; Wiggins, Geraint A.

2016-01-01

We present a novel hypothetical account of entrainment in music and language, in context of the Information Dynamics of Thinking model, IDyOT. The extended model affords an alternative view of entrainment, and its companion term, pulse, from earlier accounts. The model is based on hierarchical, statistical prediction, modeling expectations of both what an event will be and when it will happen. As such, it constitutes a kind of predictive coding, with a particular novel hypothetical implementation. Here, we focus on the model's mechanism for predicting when a perceptual event will happen, given an existing sequence of past events, which may be musical or linguistic. We propose a range of tests to validate or falsify the model, at various different levels of abstraction, and argue that computational modeling in general, and this model in particular, can offer a means of providing limited but useful evidence for evolutionary hypotheses. PMID:27803682

Loss of 'complexity' and aging. Potential applications of fractals and chaos theory to senescence

NASA Technical Reports Server (NTRS)

Lipsitz, L. A.; Goldberger, A. L.

1992-01-01

The concept of "complexity," derived from the field of nonlinear dynamics, can be adapted to measure the output of physiologic processes that generate highly variable fluctuations resembling "chaos." We review data suggesting that physiologic aging is associated with a generalized loss of such complexity in the dynamics of healthy organ system function and hypothesize that such loss of complexity leads to an impaired ability to adapt to physiologic stress. This hypothesis is supported by observations showing an age-related loss of complex variability in multiple physiologic processes including cardiovascular control, pulsatile hormone release, and electroencephalographic potentials. If further research supports this hypothesis, measures of complexity based on chaos theory and the related geometric concept of fractals may provide new ways to monitor senescence and test the efficacy of specific interventions to modify the age-related decline in adaptive capacity.

Chimeras and clusters in networks of hyperbolic chaotic oscillators

NASA Astrophysics Data System (ADS)

Cano, A. V.; Cosenza, M. G.

2017-03-01

We show that chimera states, where differentiated subsets of synchronized and desynchronized dynamical elements coexist, can emerge in networks of hyperbolic chaotic oscillators subject to global interactions. As local dynamics we employ Lozi maps, which possess hyperbolic chaotic attractors. We consider a globally coupled system of these maps and use two statistical quantities to describe its collective behavior: the average fraction of elements belonging to clusters and the average standard deviation of state variables. Chimera states, clusters, complete synchronization, and incoherence are thus characterized on the space of parameters of the system. We find that chimera states are related to the formation of clusters in the system. In addition, we show that chimera states arise for a sufficiently long range of interactions in nonlocally coupled networks of these maps. Our results reveal that, under some circumstances, hyperbolicity does not impede the formation of chimera states in networks of coupled chaotic systems, as it had been previously hypothesized.

Global dynamics of selective attention and its lapses in primary auditory cortex.

PubMed

Lakatos, Peter; Barczak, Annamaria; Neymotin, Samuel A; McGinnis, Tammy; Ross, Deborah; Javitt, Daniel C; O'Connell, Monica Noelle

2016-12-01

Previous research demonstrated that while selectively attending to relevant aspects of the external world, the brain extracts pertinent information by aligning its neuronal oscillations to key time points of stimuli or their sampling by sensory organs. This alignment mechanism is termed oscillatory entrainment. We investigated the global, long-timescale dynamics of this mechanism in the primary auditory cortex of nonhuman primates, and hypothesized that lapses of entrainment would correspond to lapses of attention. By examining electrophysiological and behavioral measures, we observed that besides the lack of entrainment by external stimuli, attentional lapses were also characterized by high-amplitude alpha oscillations, with alpha frequency structuring of neuronal ensemble and single-unit operations. Entrainment and alpha-oscillation-dominated periods were strongly anticorrelated and fluctuated rhythmically at an ultra-slow rate. Our results indicate that these two distinct brain states represent externally versus internally oriented computational resources engaged by large-scale task-positive and task-negative functional networks.

Controls upon microbial accessibility to soil organic matter following woody plant encroachment into grasslands

NASA Astrophysics Data System (ADS)

Creamer, C. A.; Boutton, T. W.; Filley, T. R.

2009-12-01

Woody plant encroachment (WPE) into savannas and grasslands is a global phenomenon that alters soil organic matter (SOM) dynamics through changes in litter quality and quantity, soil structure, microbial ecology, and soil hydrology. To elucidate the controls upon microbial accessibility to SOM, bulk soils from a chronosequence of progressive WPE into native grasslands at the Texas A&M Agricultural Experimental Station La Copita Research Area were incubated for one year. The quantity and stable carbon isotope composition of respired CO2, plant biopolymer chemistry in SOM, and microbial community structure were tracked. Respiration rates declined steadily over the course of the experiment with 15-25% of the total CO2 respired released in the first month of incubation. Between 8 and 18% of the total carbon was mineralized to CO2 throughout the incubation. After day 84 a significantly (p < 0.05) greater portion of carbon was mineralized from soils of older woody clusters (34-86 years) than from soils of younger clusters (14-23 years) and the native grassland. Approximately 80% of patterns seen in cumulative CO2 loss could be explained by the proportions of macro- and micro-aggregates within each soil, suggesting soil structure is a major controlling factor of respiration rates. Despite documented carbon accrual within La Copita soils due to WPE, we observed no evidence of enhanced carbon stabilization in these respiration experiments. In fact, a greater proportion of total carbon was lost from the soil of mature woody stands than from young stands, suggesting carbon accumulation observed with WPE may be due to greater input rates or microbial dynamics not captured in the laboratory incubation. A cluster approximately 34 years in age represents a transition point in WPE where respiration dynamics become distinct between grassland and wooded elements. By day 84 of the incubation CO2 respired from all soils was depleted with respect to bulk SOM (1.5 to 5‰) and this pattern remained for the rest of the incubation. As the depletion of CO2 relative to bulk SOM was observed in grassland and cluster soils, we hypothesized the depleted signature resulted from the utilization of depleted biopolymers, specifically lignin, cutin and suberin, as hypothesized by others. Quantitative and isotopic comparisons of these monomers prior to and following the incubation will determine if selective compound utilization is a reason for this depletion. The results discussed herein provide important insights into the dynamics of SOM accrual with WPE as well as respiration dynamics during laboratory incubations.

Carbon Cycle Dynamics through the Early Eocene Climatic Optimum: Orbital Couplings to Lacustrine Cycling

NASA Astrophysics Data System (ADS)

Rosengard, S. Z.; Grogan, D. S.; Whiteside, J. H.; van Keuren, M.; Musher, D.

2010-12-01

The early Eocene represents the most recent hothouse climate state of Earth history, a period during which Earth’s surface temperatures warmed and reached a steady peak at the Early Eocene Climatic Optimum (EECO), 53.5-50 Ma. Interspersed through the primary warming interval were several hyperthermals, or rapid peaks in surface temperature and pulses of carbon dioxide into the atmosphere, followed by rapid declines, lasting 10^4 to 10^5 years. Various hypotheses have been offered to explain the climatic triggers during the hothouse interval, including changes in ocean circulation, methane release from hydrates, volcanism, and turnover of terrestrial organic matter, implicating various couplings and feedbacks in the global carbon cycle. The present study investigates the prevailing changes in carbon cycle dynamics that occurred during a specific subinterval of the Early Eocene Climatic Optimum. We sampled a carbon-rich 300-ft ( 1100 kyr) section of lacustrine Green River Formation sediments from the TOSCO core in the Uinta Basin at a one-foot resolution for organic carbon content and δ^{13}C. The compiled data comprise a high-resolution profile of total organic carbon and isotopic organic carbon composition through the section, showing cyclic patterns that we hypothesize reflect orbital signals. Bulk isotopic carbon and shale oil measurements from an earlier Fischer Assay across TOSCO’s entire 1030-ft core were then filtered using the expected frequency of a 23-kyr precession cycle. The overlaid cycles reveal δ^{13}C and oil content to be anti-phase through the 300-ft section, except for an interval of 50 feet (180 kyr) from the Mahogany Zone to the B-groove of the core, where the two measurements are in-phase. Given that shale oil, a proxy for lake primary productivity and carbon burial, and δ^{13}C typically correlate inversely, this short, 180-kyr interval of in-phase variation suggests a significant alteration in the local carbon cycle. These preliminary findings reveal a dynamic, inconstant coupling between precessional variations in solar insolation and the carbon cycle during the EECO. As the organic carbon profile fundamentally records ecosystem processes, this precession-carbon cycle coupling is likely modulated by ecological dynamics within the paleolake, such as changing trophic and community structure. Because precession-driven changes in solar insolation dominantly control hydrology and lake water balance, the lacustrine ecosystem response to such perturbations may have precipitated key shifts in the dynamics of carbon cycling through the most stable interval of Earth’s latest hothouse.

Towards a Computational Comparative Neuroprimatology: Framing the language-ready brain.

PubMed

Arbib, Michael A

2016-03-01

We make the case for developing a Computational Comparative Neuroprimatology to inform the analysis of the function and evolution of the human brain. First, we update the mirror system hypothesis on the evolution of the language-ready brain by (i) modeling action and action recognition and opportunistic scheduling of macaque brains to hypothesize the nature of the last common ancestor of macaque and human (LCA-m); and then we (ii) introduce dynamic brain modeling to show how apes could acquire gesture through ontogenetic ritualization, hypothesizing the nature of evolution from LCA-m to the last common ancestor of chimpanzee and human (LCA-c). We then (iii) hypothesize the role of imitation, pantomime, protosign and protospeech in biological and cultural evolution from LCA-c to Homo sapiens with a language-ready brain. Second, we suggest how cultural evolution in Homo sapiens led from protolanguages to full languages with grammar and compositional semantics. Third, we assess the similarities and differences between the dorsal and ventral streams in audition and vision as the basis for presenting and comparing two models of language processing in the human brain: A model of (i) the auditory dorsal and ventral streams in sentence comprehension; and (ii) the visual dorsal and ventral streams in defining "what language is about" in both production and perception of utterances related to visual scenes provide the basis for (iii) a first step towards a synthesis and a look at challenges for further research. Copyright © 2015 Elsevier B.V. All rights reserved.

Towards a Computational Comparative Neuroprimatology: Framing the language-ready brain

NASA Astrophysics Data System (ADS)

Arbib, Michael A.

2016-03-01

We make the case for developing a Computational Comparative Neuroprimatology to inform the analysis of the function and evolution of the human brain. First, we update the mirror system hypothesis on the evolution of the language-ready brain by (i) modeling action and action recognition and opportunistic scheduling of macaque brains to hypothesize the nature of the last common ancestor of macaque and human (LCA-m); and then we (ii) introduce dynamic brain modeling to show how apes could acquire gesture through ontogenetic ritualization, hypothesizing the nature of evolution from LCA-m to the last common ancestor of chimpanzee and human (LCA-c). We then (iii) hypothesize the role of imitation, pantomime, protosign and protospeech in biological and cultural evolution from LCA-c to Homo sapiens with a language-ready brain. Second, we suggest how cultural evolution in Homo sapiens led from protolanguages to full languages with grammar and compositional semantics. Third, we assess the similarities and differences between the dorsal and ventral streams in audition and vision as the basis for presenting and comparing two models of language processing in the human brain: A model of (i) the auditory dorsal and ventral streams in sentence comprehension; and (ii) the visual dorsal and ventral streams in defining ;what language is about; in both production and perception of utterances related to visual scenes provide the basis for (iii) a first step towards a synthesis and a look at challenges for further research.

Interacting Learning Processes during Skill Acquisition: Learning to control with gradually changing system dynamics.

PubMed

Ludolph, Nicolas; Giese, Martin A; Ilg, Winfried

2017-10-16

There is increasing evidence that sensorimotor learning under real-life conditions relies on a composition of several learning processes. Nevertheless, most studies examine learning behaviour in relation to one specific learning mechanism. In this study, we examined the interaction between reward-based skill acquisition and motor adaptation to changes of object dynamics. Thirty healthy subjects, split into two groups, acquired the skill of balancing a pole on a cart in virtual reality. In one group, we gradually increased the gravity, making the task easier in the beginning and more difficult towards the end. In the second group, subjects had to acquire the skill on the maximum, most difficult gravity level. We hypothesized that the gradual increase in gravity during skill acquisition supports learning despite the necessary adjustments to changes in cart-pole dynamics. We found that the gradual group benefits from the slow increment, although overall improvement was interrupted by the changes in gravity and resulting system dynamics, which caused short-term degradations in performance and timing of actions. In conclusion, our results deliver evidence for an interaction of reward-based skill acquisition and motor adaptation processes, which indicates the importance of both processes for the development of optimized skill acquisition schedules.

COPEWELL: A Conceptual Framework and System Dynamics Model for Predicting Community Functioning and Resilience After Disasters.

PubMed

Links, Jonathan M; Schwartz, Brian S; Lin, Sen; Kanarek, Norma; Mitrani-Reiser, Judith; Sell, Tara Kirk; Watson, Crystal R; Ward, Doug; Slemp, Cathy; Burhans, Robert; Gill, Kimberly; Igusa, Tak; Zhao, Xilei; Aguirre, Benigno; Trainor, Joseph; Nigg, Joanne; Inglesby, Thomas; Carbone, Eric; Kendra, James M

2018-02-01

Policy-makers and practitioners have a need to assess community resilience in disasters. Prior efforts conflated resilience with community functioning, combined resistance and recovery (the components of resilience), and relied on a static model for what is inherently a dynamic process. We sought to develop linked conceptual and computational models of community functioning and resilience after a disaster. We developed a system dynamics computational model that predicts community functioning after a disaster. The computational model outputted the time course of community functioning before, during, and after a disaster, which was used to calculate resistance, recovery, and resilience for all US counties. The conceptual model explicitly separated resilience from community functioning and identified all key components for each, which were translated into a system dynamics computational model with connections and feedbacks. The components were represented by publicly available measures at the county level. Baseline community functioning, resistance, recovery, and resilience evidenced a range of values and geographic clustering, consistent with hypotheses based on the disaster literature. The work is transparent, motivates ongoing refinements, and identifies areas for improved measurements. After validation, such a model can be used to identify effective investments to enhance community resilience. (Disaster Med Public Health Preparedness. 2018;12:127-137).

How to assess the impact of a physical parameterization in simulations of moist convection?

NASA Astrophysics Data System (ADS)

Grabowski, Wojciech

2017-04-01

A numerical model capable in simulating moist convection (e.g., cloud-resolving model or large-eddy simulation model) consists of a fluid flow solver combined with required representations (i.e., parameterizations) of physical processes. The later typically include cloud microphysics, radiative transfer, and unresolved turbulent transport. Traditional approaches to investigate impacts of such parameterizations on convective dynamics involve parallel simulations with different parameterization schemes or with different scheme parameters. Such methodologies are not reliable because of the natural variability of a cloud field that is affected by the feedback between the physics and dynamics. For instance, changing the cloud microphysics typically leads to a different realization of the cloud-scale flow, and separating dynamical and microphysical impacts is difficult. This presentation will present a novel modeling methodology, the piggybacking, that allows studying the impact of a physical parameterization on cloud dynamics with confidence. The focus will be on the impact of cloud microphysics parameterization. Specific examples of the piggybacking approach will include simulations concerning the hypothesized deep convection invigoration in polluted environments, the validity of the saturation adjustment in modeling condensation in moist convection, and separation of physical impacts from statistical uncertainty in simulations applying particle-based Lagrangian microphysics, the super-droplet method.

Collapse of resilience patterns in generalized Lotka-Volterra dynamics and beyond.

PubMed

Tu, Chengyi; Grilli, Jacopo; Schuessler, Friedrich; Suweis, Samir

2017-06-01

Recently, a theoretical framework aimed at separating the roles of dynamics and topology in multidimensional systems has been developed [Gao et al., Nature (London) 530, 307 (2016)10.1038/nature16948]. The validity of their method is assumed to hold depending on two main hypotheses: (i) The network determined by the the interaction between pairs of nodes has negligible degree correlations; (ii) the node activities are uniform across nodes on both the drift and the pairwise interaction functions. Moreover, the authors consider only positive (mutualistic) interactions. Here we show the conditions proposed by Gao and collaborators [Nature (London) 530, 307 (2016)10.1038/nature16948] are neither sufficient nor necessary to guarantee that their method works in general and validity of their results are not independent of the model chosen within the class of dynamics they considered. Indeed we find that a new condition poses effective limitations to their framework and we provide quantitative predictions of the quality of the one-dimensional collapse as a function of the properties of interaction networks and stable dynamics using results from random matrix theory. We also find that multidimensional reduction may work also for an interaction matrix with a mixture of positive and negative signs, opening up an application of the framework to food webs, neuronal networks, and social and economic interactions.

Free Flight Ground Testing of ADEPT in Advance of the Sounding Rocket One Flight Experiment

NASA Technical Reports Server (NTRS)

Smith, B. P.; Dutta, S.

2017-01-01

The Adaptable Deployable Entry and Placement Technology (ADEPT) project will be conducting the first flight test of ADEPT, titled Sounding Rocket One (SR-1), in just two months. The need for this flight test stems from the fact that ADEPT's supersonic dynamic stability has not yet been characterized. The SR-1 flight test will provide critical data describing the flight mechanics of ADEPT in ballistic flight. These data will feed decision making on future ADEPT mission designs. This presentation will describe the SR-1 scientific data products, possible flight test outcomes, and the implications of those outcomes on future ADEPT development. In addition, this presentation will describe free-flight ground testing performed in advance of the flight test. A subsonic flight dynamics test conducted at the Vertical Spin Tunnel located at NASA Langley Research Center provided subsonic flight dynamics data at high and low altitudes for multiple center of mass (CoM) locations. A ballistic range test at the Hypervelocity Free Flight Aerodynamics Facility (HFFAF) located at NASA Ames Research Center provided supersonic flight dynamics data at low supersonic Mach numbers. Execution and outcomes of these tests will be discussed. Finally, a hypothesized trajectory estimate for the SR-1 flight will be presented.

Dynamic mechanistic explanation: computational modeling of circadian rhythms as an exemplar for cognitive science.

PubMed

Bechtel, William; Abrahamsen, Adele

2010-09-01

We consider computational modeling in two fields: chronobiology and cognitive science. In circadian rhythm models, variables generally correspond to properties of parts and operations of the responsible mechanism. A computational model of this complex mechanism is grounded in empirical discoveries and contributes a more refined understanding of the dynamics of its behavior. In cognitive science, on the other hand, computational modelers typically advance de novo proposals for mechanisms to account for behavior. They offer indirect evidence that a proposed mechanism is adequate to produce particular behavioral data, but typically there is no direct empirical evidence for the hypothesized parts and operations. Models in these two fields differ in the extent of their empirical grounding, but they share the goal of achieving dynamic mechanistic explanation. That is, they augment a proposed mechanistic explanation with a computational model that enables exploration of the mechanism's dynamics. Using exemplars from circadian rhythm research, we extract six specific contributions provided by computational models. We then examine cognitive science models to determine how well they make the same types of contributions. We suggest that the modeling approach used in circadian research may prove useful in cognitive science as researchers develop procedures for experimentally decomposing cognitive mechanisms into parts and operations and begin to understand their nonlinear interactions.