Conformational Spread in the Flagellar Motor Switch: A Model Study

The reliable response to weak biological signals requires that they be amplified with fidelity. In E. coli, the flagellar motors that control swimming can switch direction in response to very small changes in the concentration of the signaling protein CheY-P, but how this works is not well understood. A recently proposed allosteric model based on cooperative conformational spread in a ring of identical protomers seems promising as it is able to qualitatively reproduce switching, locked state behavior and Hill coefficient values measured for the rotary motor. In this paper we undertook a comprehensive simulation study to analyze the behavior of this model in detail and made predictions on three experimentally observable quantities: switch time distribution, locked state interval distribution, Hill coefficient of the switch response. We parameterized the model using experimental measurements, finding excellent agreement with published data on motor behavior. Analysis of the simulated switching dynamics revealed a mechanism for chemotactic ultrasensitivity, in which cooperativity is indispensable for realizing both coherent switching and effective amplification. These results showed how cells can combine elements of analog and digital control to produce switches that are simultaneously sensitive and reliable. © 2012 Ma et al.

Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 A˚, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced "leopard skin"-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions, can capture processes that are otherwise obscured to the amino acid-based formalism.

Using Bayesian Mixture Models That Combine Expert Knowledge and GIS Data to Define Ecoregions

Conservation planning and management programs typically assume relatively homogeneous ecological landscapes. Such “ecoregions” serve multiple purposes: they support assessments of competing environmental values, reveal priorities for allocating scarce resources, and guide effective on-ground actions such as the acquisition of a protected area and habitat restoration. Ecoregions have evolved from a history of organism–environment interactions, and are delineated at the scale or level of detail required to support planning. Depending on the delineation method, scale, or purpose, they have been described as provinces, zones, systems, land units, classes, facets, domains, subregions, and ecological, biological, biogeographical, or environmental regions. In each case, they are essential to the development of conservation strategies and are embedded in government policies at multiple scales.

Energy Efficiency Resources for Undergraduate Engineering Education: Final Report

This report presents the findings of an investigation of energy efficiency resources for undergraduate engineering education, undertaken by web-based research, conversations with educators, and a university survey. The investigation draws on the results of a number of previous investigations undertaken by the research team for NFEE related to energy efficiency education and presents the following findings and recommendations, as explained in greater detail in the body of the report. The findings suggest that even though certain EE concepts and principles have been identified by lecturers as being important there is little to no coverage of a number of these concepts in some programs/courses. Similarly, many topics relating to the most important EE workforce skills and significant shortages as identified in industry research, do not rate highly in terms of both perceived importance by lecturers, or coverage within existing courses. Overall, these findings suggest that despite growing awareness of the importance of EE in both industry and academia, the current depth and breadth of EE content in courses does not reflect this. It confirms that efforts in these areas can be better supported.

Ecological and Behavioral Methods for the Study of Bats [2nd. Ed.]

"First published in 1988, Ecological and Behavioral Methods for the Study of Bats is widely acknowledged as the primary reference for both amateur and professional bat researchers. Bats are the second most diverse group of mammals on the earth. They live on every continent except Antarctica, ranging from deserts to tropical forests to mountains, and their activities have a profound effect on the ecosystems in which they live. Despite their ubiquity and importance, bats are challenging to study. This volume provides researchers, conservationists, and consultants with the ecological background and specific information essential for studying bats in the wild and in captivity. Chapters detail many of the newest and most commonly used field and laboratory techniques needed to advance the study of bats, describe how these methods are applied to the study of the ecology and behavior of bats, and offer advice on how to interpret the results of research. The book includes forty-three chapters, fourteen of which are new to the second edition, with information on molecular ecology and evolution, bioacoustics, chemical communication, flight dynamics, population models, and methods for assessing postnatal growth and development. Fully illustrated and featuring contributions from the world’s leading experts in bat biology, this reference contains everything bat researchers and natural resource managers need to know for the study and conservation of this wide-ranging, ecologically vital, and diverse taxon."--Publisher website

NEU-MODEL : a multi-level object-oriented dynamic emulation laboratory

Computational neuroscience aims to elucidate the mechanisms of neural information processing and population dynamics, through a methodology of incorporating biological data into complex mathematical models. Existing simulation environments model at a particular level of detail; none allow a multi-level approach to neural modelling. Moreover, most are not engineered to produce compute-efficient solutions, an important issue because sufficient processing power is a major impediment in the field. This project aims to apply modern software engineering techniques to create a flexible high performance neural modelling environment, which will allow rigorous exploration of model parameter effects, and modelling at multiple levels of abstraction.

Staged homicides: An examination of common features of faked burglaries, suicides, accidents and car accidents

A staged crime scene involves deliberate alteration of evidence by the offender to simulate events that did not occur for the purpose of misleading authorities (Geberth, 2006; Turvey, 2000). This study examined 115 staged homicides from the USA to determine common elements; victim and perpetrator characteristics; and specific features of different types of staged scenes. General characteristics include: multiple victims and offenders; a previous relationship be- tween parties involved; and victims discovered in their own home, often by the offender. Staged scenes were separated by type with staged burglaries, suicides, accidents, and car accidents examined in more detail. Each type of scene displays differently with separate indicators and common features. Features of staged burglaries were: no points of entry/exit staged; non-valuables taken; scene ransacking; offender self- injury; and offenders bringing weapons to the scene. Features of staged suicides included: weapon arrangement and simulating self-injury to the victim; rearranging the body; and removing valuables. Examples of elements of staged accidents were arranging the implement/weapon and re- positioning the deceased; while staged car accidents involved: transporting the body to the vehicle and arranging both; mutilation after death; attempts to secure an alibi; and clean up at the primary crime scene. The results suggest few staging behaviors are used, despite the credibility they may have offered the façade. This is the first peer-reviewed, published study to examine the specific features of these scenes, and is the largest sample studied to date.

Education paths for documentary distribution: DAF, ATOM and the study guides that bind them

An expanding education market targeted through ‘bridging material’ enabling cineliteracies has the potential to offer Australian producers with increased distribution opportunities, educators with targeted teaching aids and students with enhanced learning outcomes. For Australian documentary producers, the key to unlocking the potential of the education sector is engaging with its curriculum-based requirements at the earliest stages of pre-production. Two key mechanisms can lead to effective educational engagement; the established area of study guides produced in association with the Australian Teachers of Media (ATOM) and the emerging area of philanthropic funding coordinated by the Documentary Australia Foundation (DAF). DAF has acted as a key financial and cultural philanthropic bridge between individuals, foundations, corporations and the Australian documentary sector for over 14 years. DAF does not make or commission films but through management and receipt of grants and donations provides ‘expertise, information, guidance and resources to help each sector work together to achieve their goals’. The DAF application process also requires film-makers to detail their ‘Education and Outreach Strategy’ for each film with 582 films registered and 39 completed as of June 2014. These education strategies that can range from detailed to cursory efforts offer valuable insights into the Australian documentary sector's historical and current expectations of education as a receptive and dynamic audience for quality factual content. A recurring film-maker education strategy found in the DAF data is an engagement with ATOM to create a study guide for their film. This study guide then acts as a ‘bridging material’ between content and education audience. The frequency of this effort suggests these study guides enable greater educator engagement with content and increased interest and distribution of the film to educators. The paper Education paths for documentary distribution: DAF, ATOM and the study guides that bind them will address issues arising out of the changing needs of the education sector and the impact targeting ‘cineliteracy’ outcomes may have for Australian documentary distribution.

Vision-based operations of a large industrial vehicle : autonomous hot metal carrier

Hot metal carriers (HMCs) are large forklift-type vehicles used to move molten metal in aluminum smelters. This paper reports on field experiments that demonstrate that HMCs can operate autonomously and in particular can use vision as a primary sensor to locate the load of aluminum. We present our complete system but focus on the vision system elements and also detail experiments demonstrating reliable operation of the materials handling task. Two key experiments are described, lasting 2 and 5 h, in which the HMC traveled 15 km in total and handled the load 80 times.

On the relevance of travel journalism : An introduction

Not many people will be instantly familiar with British woman Dale Sheppard-Floyd, but – at least symbolically – she represents a significant milestone in the development of travel and tourism. In fact, the milestone was so significant that the United Nations World Tourism Organization booked Madrid’s venerable Museo del Prado to announce to the world’s media her visit to Spain on 13 December 2012. For Ms Sheppard-Floyd’s arrival for a three-day trip meant that more than one billion times in that year, someone had crossed a border as a tourist. An astounding number, considering that, in 1950, there had been only 25 million tourist arrivals worldwide, and even only two decades previously – in 1990 – the number had been less than half at 435 million arrivals (World Tourism Organization, 2012a, 2012b). While people have traveled for pleasure for millennia (Towner, 1995), tourism really came into its own with the expansion of the middle classes in the 19th and 20th century, and today it is considered the world’s largest business sector, with unprecedented numbers of people venturing outside of their immediate environments to explore the world around them. In 2012, travel and tourism’s total contribution to the world economy amounted to a staggering $6.6 trillion, or 9 per cent of GDP (World Travel & Tourism Council, 2013). More than 260 million jobs were generated by it worldwide, which equates to one in every 11 jobs across the globe. While there were some hiccups during the Global Financial Crisis, growth in 2012 was stronger than in other industries, such as manufacturing, financial services and retail (World Travel & Tourism Council, 2013)...

Designing a digital experience for young children with developmental disabilities

This paper reports on the development of a playful digital experience, Anim-action, designed for young children with developmental disabilities. This experience was built using the Stomp platform, a technology designed specifically to meet the needs of people with intellectual disability through facilitating whole body interaction. We provide detail on how knowledge gained from key stakeholders informed the design of the application and describe the design guidelines used in the development process. A study involving 13 young children with developmental disabilities was conducted to evaluate the extent to which Anim-action facilitates cognitive, social and physical activity. Results demonstrated that Anim-action effectively supports cognitive and physical activity. In particular, it promoted autonomy and encouraged problem solving and motor planning. Conversely, there were limitations in the system’s ability to support social interaction, in particular, cooperation. Results have been analyzed to determine how design guidelines might be refined to address these limitations.

Dynamic agent composition for large-scale agent-based models

PURPOSE: This paper describes dynamic agent composition, used to support the development of flexible and extensible large-scale agent-based models (ABMs). This approach was motivated by a need to extend and modify, with ease, an ABM with an underlying networked structure as more information becomes available. Flexibility was also sought after so that simulations are set up with ease, without the need to program. METHODS: The dynamic agent composition approach consists in having agents, whose implementation has been broken into atomic units, come together at runtime to form the complex system representation on which simulations are run. These components capture information at a fine level of detail and provide a vast range of combinations and options for a modeller to create ABMs. RESULTS: A description of the dynamic agent composition is given in this paper, as well as details about its implementation within MODAM (MODular Agent-based Model), a software framework which is applied to the planning of the electricity distribution network. Illustrations of the implementation of the dynamic agent composition are consequently given for that domain throughout the paper. It is however expected that this approach will be beneficial to other problem domains, especially those with a networked structure, such as water or gas networks. CONCLUSIONS: Dynamic agent composition has many advantages over the way agent-based models are traditionally built for the users, the developers, as well as for agent-based modelling as a scientific approach. Developers can extend the model without the need to access or modify previously written code; they can develop groups of entities independently and add them to those already defined to extend the model. Users can mix-and-match already implemented components to form large-scales ABMs, allowing them to quickly setup simulations and easily compare scenarios without the need to program. The dynamic agent composition provides a natural simulation space over which ABMs of networked structures are represented, facilitating their implementation; and verification and validation of models is facilitated by quickly setting up alternative simulations.

Computational micromodel for epigenetic mechanisms

Characterization of the epigenetic profile of humans since the initial breakthrough on the human genome project has strongly established the key role of histone modifications and DNA methylation. These dynamic elements interact to determine the normal level of expression or methylation status of the constituent genes in the genome. Recently, considerable evidence has been put forward to demonstrate that environmental stress implicitly alters epigenetic patterns causing imbalance that can lead to cancer initiation. This chain of consequences has motivated attempts to computationally model the influence of histone modification and DNA methylation in gene expression and investigate their intrinsic interdependency. In this paper, we explore the relation between DNA methylation and transcription and characterize in detail the histone modifications for specific DNA methylation levels using a stochastic approach.