Modeling habits as self-sustaining patterns of sensorimotor behavior

In the recent history of psychology and cognitive neuroscience, the notion of habit has been reduced to a stimulus-triggered response probability correlation. In this paper we use a computational model to present an alternative theoretical view (with some philosophical implications), where habits are seen as self-maintaining patterns of behavior that share properties in common with self-maintaining biological processes, and that inhabit a complex ecological context, including the presence and influence of other habits. Far from mechanical automatisms, this organismic and self-organizing concept of habit can overcome the dominating atomistic and statistical conceptions, and the high temporal resolution effects of situatedness, embodiment and sensorimotor loops emerge as playing a more central, subtle and complex role in the organization of behavior. The model is based on a novel "iterant deformable sensorimotor medium (IDSM)," designed such that trajectories taken through sensorimotor-space increase the likelihood that in the future, similar trajectories will be taken. We couple the IDSM to sensors and motors of a simulated robot, and show that under certain conditions, the IDSM conditions, the IDSM forms self-maintaining patterns of activity that operate across the IDSM, the robot's body, and the environment. We present various environments and the resulting habits that form in them. The model acts as an abstraction of habits at a much needed sensorimotor "meso-scale" between microscopic neuron-based models and macroscopic descriptions of behavior. Finally, we discuss how this model and extensions of it can help us understand aspects of behavioral self-organization, historicity and autonomy that remain out of the scope of contemporary representationalist frameworks.

The water requirements of salmon in the River Lune

This report looks at the upstream movement in the River Lune of 9704 salmon which were monitored in the years 1960-1966. It explores the Broadraine Weir near Kirby Lonsdale with its fish monitoring station, the visual counting and trapping salmon, electronic monitoring of fish, and analysis of river flows.

River Ouse: fisheries drought report 1996

The basis for undertaking this study was to examine factors and potential impacts affecting fish and fishing in relation to low flow drought conditions and what other impacts may arise as a result of further reduced flows resulting from abstraction. The study formed the basis of a three year project to concentrate on effects relating to potable water abstractions at Moor Monkton by YWS. To fully evaluate the possible effects on fisheries the study set out to encompass fish population surveys from fry to adult stock, analysis of angler catch data, reports from anglers and river reports from Environment Agency Fisheries staff. In order to evaluate any effects of drought and abstraction a three year study was instigated to examine fish populations. Fish population surveys were conducted at six sites in which the triennial rolling programme formed the basis of site selection. Multi-method sampling techniques were carried out at several sites in order to evaluate capture efficiency. Roach were prolific above the weir at Linton-on-Ouse, with gudgeon, perch and small bream also well represented. Roach dominated catches on the R.Ouse below Linton, with perch and bleak also relatively abundant. Low flows were not thought to be directly correlated to successful recruitment of coarse fish, rather the associated high temperatures during drought conditions showing a strong positive effect with most species exhibiting growth rates above their long-term average. At this stage in the study there are no clear indications that the drought has caused any deleterious effects to coarse fish populations or marked changes in species composition, with evidence of good recruitment by several species, indicating that the higher temperatures have generally been beneficial to recruitment. However, the indication that dace did not benefit as well as other coarse fish under these conditions may suggest some species are affected more than others. The successful strong recruitment of most coarse fish suggests that, in future, fisheries will be supported by the 1995 year-class.

Ichthyoplankton community in the Columbia River plume off Oregon: effects of fluctuating oceanographic conditions

Ichthyoplankton samples were collected at approximately 2-week intervals, primarily during spring and summer 1999−2004, from two stations located 20 and 30 km from shore near the Columbia River, Oregon. Northern anchovy (Engraulis mordax) was the most abundant species collected, and was the primary species associated with summer upwelling conditions, but it showed significant interannual and seasonal fluctuations in abundance and occurrence. Other abundant taxa included sanddabs (Citharichthys spp.), English sole (Parophrys vetulus), and blacksmelts (Bathylagidae). Two-way cluster analysis revealed strong species associations based primarily on season (before or after the spring transition date). Ichthyoplankton abundances were compared to biological and environmental data, and egg and larvae abundances were found to be most correlated with sea surface temperature. The Pacific Decadal Oscillation changed sign (from negative to positive) in late 2002 and indicated overall warmer conditions in the North Pacific Ocean. Climate change is expected to alter ocean upwelling, temperatures, and Columbia River flows, and consequently fish eggs and larvae distributions and survival. Long-term research is needed to identify how ichthyoplankton and fish recruitment are affected by regional and largescale oceanographic proces

Argumentation of the River Derwent using Thirlmere

This is the Argumentation of the River Derwent using Thirlmere produced by the Cumberland River Authority in 1972. This report focuses on the augmentation of the River Derwent by a limited discharge from the Thirlmere Reservoir in short terms. A Working Party of officers from both the Authority and the Corporation was established and experimental releases of water from Thirlmere were made in dry periods in order to assess more clearly their effect upon river flows, and on the level of Bassenthwaite Lake. This report contains the Working Party's evaluations, conclusions and recommendations.

Forestry Impacts on Freshwater Habitat of Anadromous Salmonids in the Pacific Northwest and Alaska: requirements for protection and restoration

This synthesis presents a science overview of the major forest management Issues involved in the recovery of anadromous salmonids affected by timber harvest in the Pacific Northwest and Alaska. The issues involve the components of ecosystem-based watershed management and how best to implement them, including how to: Design buffer zones to protect fish habitat while enabling economic timber production; Implement effective Best Management Practices (BMPs) to prevent nonpoint-source pollution; Develop watershed-level procedures across property boundaries to prevent cumulative impacts; Develop restoration procedures to contribute to recovery of ecosystem processes; and Enlist support of private landowners in watershed planning, protection, and restoration. Buffer zones, BMPs, cumulative impact prevention, and restoration are essential elements of what must be a comprehensive approach to habitat protection and restoration applied at the watershed level within a larger context of resource concerns in the river basin, species status under the Endangered Species Act (ESA), and regional environmental and economic issues (Fig. ES. 1). This synthesis 1) reviews salmonid habitat requirements and potential effects of logging; 2) describes the technical foundation of forest practices and restoration; 3) analyzes current federal and non-federal forest practices; and 4) recommends required elements of comprehensive watershed management for recovery of anadromous salmonids.

National Centers for Coastal Ocean Science Coastal Ecosystem Assessment Program: a manual of methods

Environmental managers strive to preserve natural resources for future generations but have limited decision-making tools to define ecosystem health. Many programs offer relevant broad-scale, environmental policy information on regional ecosystem health. These programs provide evidence of environmental condition and change, but lack connections between local impacts and direct effects on living resources. To address this need, the National Oceanic and Atmospheric Administration/National Ocean Service (NOAA/NOS) Cooperative Oxford Laboratory (COL), in cooperation with federal, state, and academic partners, implemented an integrated biotic ecosystem assessment on a sub-watershed 14-digit Hydrologic Unit Code (HUD) scale in Chesapeake Bay. The goals of this effort were to 1) establish a suite of bioindicators that are sensitive to ecosystem change, 2) establish the effects of varying land-use patterns on water quality and the subsequent health of living resources, 3) communicate these findings to local decision-makers, and 4) evaluate the success of management decisions in these systems. To establish indicators, three sub-watersheds were chosen based on statistical analysis of land-use patterns to represent a gradient from developed to agricultural. The Magothy (developed), Corsica (agricultural), and Rhode (reference) Rivers were identified. A random stratified design was developed based on depth (2m contour) and river mile. Sampling approaches were coordinated within this structure to allow for robust system comparisons. The sampling approach was hierarchal, with metrics chosen to represent a range from community to cellular level responses across multiple organisms. This approach allowed for the identification of sub-lethal stressors, and assessment of their impact on the organism and subsequently the population. Fish, crabs, clams, oysters, benthic organisms, and bacteria were targeted, as each occupies a separate ecological niche and may respond dissimilarly to environmental stressors. Particular attention was focused on the use of pathobiology as a tool for assessing environmental condition. By integrating the biotic component with water quality, sediment indices, and land- use information, this holistic evaluation of ecosystem health will provide management entities with information needed to inform local decision-making processes and establish benchmarks for future restoration efforts.

An oceanographic characterizations of the Olympic Coast National Marine Sanctuary and Pacific Northwest: interpretive summary of ocean climate and regional processes through satellite remote sensing

This report presents the results of a two-year investigation and summary of oceanographic satellite data obtained from multiple operational data providers and sources, spanning years of operational data collection. Long-term summaries of Sea Surface Temperature (SST) and SST fronts, Sea Surface Height Anomalies (SSHA), surface currents, ocean color chlorophyll and turbidity, and winds are provided. Merged satellite oceanographic data revealed information on: (1) seasonal cycles and timing of transition periods; (2) linkages between seasonal effects (warming and cooling), upwelling processes and transport; and (3) nutrient/sediment sources, sinks, and physical limiting factors controlling surface response for Olympic Coast marine environments. These data and information can be used for building relevant hind cast models, ecological forecasts, and regional environmental indices (e.g. upwelling, climate, “hot spot”) on biological distribution and/or response in the PNW.

The zooplankton species composition and abundance in Ogun River, Abeokuta, Ogun State, southwestern Nigeria

Investigation on the species composition and abundance of zooplankton in Ogun River, Abeokuta, Ogun state, Southwestern Nigeria was carried out for a period of seven months (December, 2011-June, 2012), Using hand trawling method, 55 µm mesh size plankton net was trawled horizontally ten times to capture zooplankton. The zooplankton samples were put into properly labeled plastic containers and preserved in 4% formalin solution. A total of sixteen genera from five taxonomic groups were recorded from Ogun River. Cladocera predominated both in terms of species composition and abundance. Five species of Cladocera was recorded consisting of 31.25%. Protozoa and Rotifera recorded four species each consisting of 25%. Copepoda recorded two species consisting of 12.5%, and Ostracoda with one species consisting of 6.25%. The low nature of zooplankton abundance and species composition observed in this study must have been caused by the polluted nature of the water due to the anthropogenic activities carried out around its shores The dominance of Cladocera in this river is similar to findings from River Echara and River Imo, Southeastern Nigeria.

Selected trace metal concentration in bottom water and sediments of Kyoga basin lakes, and its potential to aquatic pollution

Although other research studies on areas such as the physical-chemical, nutrients and phytoplankton status of Lake Kyoga systems have been given a lot of attention (e.g. Mungoma 1988 and NaFIRRI 2006), efforts to determine the pollution status of this system, especially by heavy metals as one of the worldwide emerging environmental problems, is still limited. Many trace metals are regarded as serious pollutants of aquatic ecosystems because of their persistence, toxicity and ability to be incorporated into food chains (Mwamburi J., and Nathan O.F., 1997). Given the rapid human population growth and the associated economic activities both within the rural and urban areas in Uganda, such fish production systems are becoming very prone to various kinds of pollution including that by heavy metals. Anthropogenic factors such deforestation, use of chemicals and dumping of metallic products, spillages of fuels from outboard engines and many others and or natural processes involving atmospheric deposition by wind or rain, surface run-offs and streams flows from the catchment introduces heavy metals into the lake environment,.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Mobilization potential of heavy metals: A comparison between river and lake sediments

Toxic metals introduced into aquatic environments by human activities accumulation in sediments. A common notion is that the association of metals with acid volatile sulfides (AVS) affords a mechanism for partitioning metals from water to solid phase, thereby reducing biological availability. However, variation in environmental conditions can mobilize the sediment-bound metal and result in adverse environmental impacts. The AVS levels and the effect of AVS on the fate of Cu, Cd, Zn, Ni in sediments in the the Changjiang River, a suboxic river with sandy bottom sediment and the Donghu Lake, a anoxic lake with muddy sediment in China, were compared through aeration, static adsorption and release experiments in laboratory. Sips isotherm equation, kinetic equation and grade ion exchange theory were used to describe the heavy metal adsorb and release process. The results showed that AVS level in the lake sediment are higher than that of the river. Heavy metals in the overlying water can transfer to sediments incessantly as long as the sediment remains undisturbed. The metal release process is mainly related to AVS oxidation in lake sediment while also related to Org-C and Fe-Mn oxyhydroxide oxidation in river sediment. The effect of sulfides on Zn and Ni is high, followed by Cd, and Cu is easy bound to Org-C. AVS plays a major role in controlling metals activity in lake sediment and its presence increase the adsorption capacity both of the lake and river sediments.

Statistical analysis of microscale gas flows and stock price changes

First, recent studies on the information preservation (IP) method, a particle approach for low-speed micro-scale gas flows, are reviewed. The IP method was validated for benchmark issues such as Couette, Poiseuille and Rayleigh flows, compared well with measured data for typical internal flows through micro-channels and external flows past micro flat plates, and combined with the Navier-Stokes equations to be a hybrid scheme for subsonic, rarefied gas flows. Second, the focus is moved to the microscopic characteristic of China stock market, particularly the price correlation between stock deals. A very interesting phenomenon was found that showed a reverse transition behaviour between two neighbouring price changes. This behaviour significantly differs from the transition rules for atomic and molecular energy levels, and it is very helpful to understand the essential difference between stock markets and nature.

Modelling raindrop impact and splash erosion processes within a spatial cell: a stochastic approach

A new approach is proposed to simulate splash erosion on local soil surfaces. Without the effect of wind and other raindrops, the impact of free-falling raindrops was considered as an independent event from the stochastic viewpoint. The erosivity of a single raindrop depending on its kinetic energy was computed by an empirical relationship in which the kinetic energy was expressed as a power function of the equivalent diameter of the raindrop. An empirical linear function combining the kinetic energy and soil shear strength was used to estimate the impacted amount of soil particles by a single raindrop. Considering an ideal local soil surface with size of I m x I m, the expected number of received free-failing raindrops with different diameters per unit time was described by the combination of the raindrop size distribution function and the terminal velocity of raindrops. The total splash amount was seen as the sum of the impact amount by all raindrops in the rainfall event. The total splash amount per unit time was subdivided into three different components, including net splash amount, single impact amount and re-detachment amount. The re-detachment amount was obtained by a spatial geometric probability derived using the Poisson function in which overlapped impacted areas were considered. The net splash amount was defined as the mass of soil particles collected outside the splash dish. It was estimated by another spatial geometric probability in which the average splashed distance related to the median grain size of soil and effects of other impacted soil particles and other free-falling raindrops were considered. Splash experiments in artificial rainfall were carried out to validate the availability and accuracy of the model. Our simulated results suggested that the net splash amount and re-detachment amount were small parts of the total splash amount. Their proportions were 0.15% and 2.6%, respectively. The comparison of simulated data with measured data showed that this model could be applied to simulate the soil-splash process successfully and needed information of the rainfall intensity and original soil properties including initial bulk intensity, water content, median grain size and some empirical constants related to the soil surface shear strength, the raindrop size distribution function and the average splashed distance. Copyright (c) 2007 John Wiley & Sons, Ltd.