Finer Level Of Detail Research Articles

Comparing molecular dynamics force fields in the essential subspace.

The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their “unbalanced” counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements.

Dynamic agent composition for large-scale agent-based models

Abstract 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.

Micro-macro analysis of complex networks.

Complex systems have attracted considerable interest because of their wide range of applications, and are often studied via a “classic” approach: study a specific system, find a complex network behind it, and analyze the corresponding properties. This simple methodology has produced a great deal of interesting results, but relies on an often implicit underlying assumption: the level of detail on which the system is observed. However, in many situations, physical or abstract, the level of detail can be one out of many, and might also depend on intrinsic limitations in viewing the data with a different level of abstraction or precision. So, a fundamental question arises: do properties of a network depend on its level of observability, or are they invariant? If there is a dependence, then an apparently correct network modeling could in fact just be a bad approximation of the true behavior of a complex system. In order to answer this question, we propose a novel micro-macro analysis of complex systems that quantitatively describes how the structure of complex networks varies as a function of the detail level. To this extent, we have developed a new telescopic algorithm that abstracts from the local properties of a system and reconstructs the original structure according to a fuzziness level. This way we can study what happens when passing from a fine level of detail (“micro”) to a different scale level (“macro”), and analyze the corresponding behavior in this transition, obtaining a deeper spectrum analysis. The obtained results show that many important properties are not universally invariant with respect to the level of detail, but instead strongly depend on the specific level on which a network is observed. Therefore, caution should be taken in every situation where a complex network is considered, if its context allows for different levels of observability.

Derivation of soil-attribute estimations from legacy soil maps

It is increasingly necessary to apply quantitative techniques to legacy soil polygon maps given that legacy soil maps may be the only source of soil information over large areas. Spatial disaggregation provides a means of extracting information from legacy soil maps and enables us to downscale the original information to produce new soil class maps at finer levels of detail. This is a useful outcome in its own right; however, the disaggregated soil-class coverage can also be used to make digital maps of soil properties with associated estimates of uncertainty. In this work, we take the spatially disaggregated soil-class coverage for all of Western Australia and the agricultural region of South Australia and demonstrate its application in mapping clay content at six depth intervals in the soil profile. Estimates of uncertainty are provided in the form of the 90% prediction interval. The work can be considered an example of harmonisation to a common output specification. The validation results highlighted areas in the landscape and taxonomic spaces where more knowledge of soil properties is necessary.

Economic poverty and inequality at regional level in Malta: focus on the situation of children

1This paper performs an economic poverty and inequality mapping of three children age categories in Malta; it consists in the first attempt based on income from the EU-SILC survey and Census data. From a policy-making point of view, the availability of such key economic indicators at locality level certainly provides a valuable tool in assessing the effectiveness of national strategies and in identifying areas that need to be targeted by new policies; in fact sample surveys alone cannot provide reliable information at such a fine level of detail, while national censuses are not designed to and cannot be extended to cover specific topics such as economic poverty and inequality. Thus, the merging of the two sources provides policy-makers with a new insight into the differences between localities. There are also benefits of a technical nature, particularly in terms of sampling strategies, that can be derived from this study. Through such an exercise it is possible to identify economic homogeneity and/or heterogeneity among households with children in different localities: this is useful when defining strata for sampling design for surveys aiming at studying other economic phenomena relating to children.

On Multi-Layer Modeling and Analysis of Wireless Access Markets

Advances in networking and regulatory changes on access and competition rules enable new network architectures, service paradigms, and partnerships, opening new opportunities for business cases. Unlike traditional cellular-based markets, new spectrum and wireless access markets are formed that have larger sizes, are more diverse, and can offer an improved set of services. The analysis of such markets is challenging due to a plethora of phenomena that manifest in different spatio-temporal scales. The main objective of this work is the development of a modular multi-layer modeling framework and simulation platform for analyzing wireless access markets. This framework employs game theory and queueing-theoretical models to instantiate a market at multiple spatio-temporal scales. At a microscopic layer, it models each entity of the market in a fine level of detail. By applying various aggregations, it also models the average behavior of certain clusters of entities. In that way, it can analyze a certain phenomenon at the appropriate level of detail, addressing the tradeoff between the loss of accuracy and computational complexity. The analysis then focuses on the flex service, a novel paradigm which allows users to select their provider dynamically. The proposed framework is used to model and analyze the performance of markets that offer the flex service. It employs various metrics, such as blocking probability, percentage of disconnected users, social welfare, and profit, to assess whether this service is beneficial to users, regulators, and providers, respectively. Furthermore, it highlights various challenges in modeling such markets and demonstrates the advantages in using the proposed multi-layer framework.

How Surgical Mentors Teach: A Classification of In Vivo Teaching Behaviors Part 2: Physical Teaching Guidance

To study surgical teaching captured on film and analyze it at a fine level of detail to categorize physical teaching behaviors. We describe live, filmed, intraoperative nonverbal exchanges between surgical attending physicians and their trainees (residents and fellows). From the films, we chose key teaching moments and transcribed participants' utterances, actions, and gestures. In follow-up interviews, attending physicians and trainees watched videos of their teaching case and answered open-ended questions about their teaching methods. Using a grounded theory approach, we examined the videos and interviews for what might be construed as a teaching behavior and refined the physical teaching categories through constant comparison. We filmed 5 cases in the operating suite of a university teaching hospital that provides gynecologic surgical care. We included 5 attending gynecologic surgeons, 3 fellows, and 5 residents for this study. More than 6 hours of film and 3 hours of interviews were transcribed, and more than 250 physical teaching motions were captured. Attending surgeons relied on actions and gestures, sometimes wordlessly, to achieve pedagogical and surgical goals simultaneously. Physical teaching included attending physician-initiated actions that required immediate corollary actions from the trainee, gestures to illustrate a step or indicate which instrument to be used next, supporting or retracting tissues, repositioning the trainee's instruments, and placement of the attending physicians' hands on the trainees' hands to guide them. Attending physicians often voiced surprise at the range of their own teaching behaviors captured on film. Interrater reliability was high using the Cohen κ, which was 0.76 for the physical categories. Physical guidance is essential in educating a surgical trainee, may be tacit, and is not always accompanied by speech. Awareness of teaching behaviors may encourage deliberate teaching and reflection on how to innovate pedagogy for the teaching operating room.

How Surgical Mentors Teach: A Classification of In Vivo Teaching Behaviors Part 1: Verbal Teaching Guidance

To illuminate surgical teaching at a fine level of detail by filming intraoperative communication between surgical attending physicians and trainees and provide a naturalistic categorization and analysis of verbal teaching behaviors. Live, intraoperative verbal exchanges between surgical attending physicians and their trainees (residents and fellows) were filmed, and key verbal teaching moments were transcribed. In follow-up interviews, attending physicians and trainees watched video clips of their teaching case and answered open-ended questions about their surgical teaching methods. Using a grounded theory approach, we examined the videos and interviews for what might be construed as a teaching behavior and refined verbal teaching categories through constant comparison. We filmed 5 cases in the operating suite of a university teaching hospital that provides gynecologic surgical care. We included 5 attending gynecologic surgeons, 3 fellows, and 5 residents for this study. More than 6 hours of film, 3 hours of interviews, and more than 400 verbal teaching utterances from our participating attending surgeons were transcribed. We found that attending surgeons used unique types of verbal guidance to describe relevant anatomy, explain the rationale behind a specific surgical action, command the trainee to perform the next step, reference a specific aspect of the surgery, and provide an indirect verbal construct. Attending physicians prefixed speech with polite terms and used terse language, colorful verbal analogies, and sometimes humor. Our participants denied a significant Hawthorne effect. Interrater reliability was high using Cohen κ with 0.77 for the verbal categories. Our categorization of live intraoperative verbal teaching can provide a measurable, replicable basis for studying how spoken guidance can lead to the best intraoperative learning. Because surgical teaching occurs on a microscopic level, film review is important when analyzing intraoperative teaching behaviors.

PTU-022 A Novel Photometric Stereo Imaging Sensor For Endoscopy Imaging: Proof Of Concept Studies On A Porcine Model

IntroductionThe American Society of Gastroenterology Endoscopy led Preservation and Incorporation of Valuable Endoscopic Innovations initiative has identified real time polyp diagnosis as one of the next major technology-driven changes in...

Teams, wages and wage dispersion

Purpose – The purpose of this paper is to estimate the influence of workplace teams on wages and wage dispersion within UK establishments. Design/methodology/approach – Four types of workplace teams are analyzed using linked employer and employee data from the British Workplace Employee Relations Survey. Findings – Workplace teams are positively associated with wages but negatively associated with wage dispersion within establishments. The four team variables examined have the same directional influence on both wages and dispersion suggesting that it is the use of teams that is important not necessarily the particular characteristics of teams that are being used. The role of occupation is also examined as teams may be more likely to form in certain occupations. The team results for both wages and wage dispersion are robust to the inclusion of detailed occupational information. Originality/value – The influence of workplace teams is examined on both employee wages and wage dispersion within establishments. Additionally, the paper extends the previous empirical literature on teams by controlling for occupations at a fine level of detail not previously explored.

Performance Monitoring and Analysis of Task-Based OpenMP

OpenMP, a typical shared memory programming paradigm, has been extensively applied in high performance computing community due to the popularity of multicore architectures in recent years. The most significant feature of the OpenMP 3.0 specification is the introduction of the task constructs to express parallelism at a much finer level of detail. This feature, however, has posed new challenges for performance monitoring and analysis. In particular, task creation is separated from its execution, causing the traditional monitoring methods to be ineffective. This paper presents a mechanism to monitor task-based OpenMP programs with interposition and proposes two demonstration graphs for performance analysis as well. The results of two experiments are discussed to evaluate the overhead of monitoring mechanism and to verify the effects of demonstration graphs using the BOTS benchmarks.

Microscopic Eye Movements Compensate for Nonhomogeneous Vision within the Fovea

Humans rely on the fovea, the small region of the retina where receptors are most densely packed, for seeing fine spatial detail. Outside the fovea, it is well established that a variety of visual functions progressively decline with eccentricity. In contrast, little is known about how vision varies within the central fovea, as incessant microscopic eye movements prevent isolation of adjacent foveal locations. Using a new method for restricting visual stimulation to a selected retinal region, we examined the discrimination of fine patterns at different eccentricities within the foveola. We show that high-acuity judgments are impaired when stimuli are presented just a few arcminutes away from the preferred retinal locus of fixation. Furthermore, we show that this dependence on eccentricity is normally counterbalanced by the occurrence of precisely directed microsaccades, which bring the preferred fixation locus onto the stimulus. Thus, contrary to common assumptions, vision is not uniform within the foveola, but targeted microscopic eye movements compensate for this lack of homogeneity. Our results reveal that microsaccades, like larger saccades, enable examination of the stimulus at a finer level of detail and suggest that a reduced precision in oculomotor control may be responsible for the visual acuity impairments observed in various disorders.

The Spatial Distribution of Chacma Baboon (Papio ursinus) Habitat Based on an Environmental Envelope Model

Predictive spatial modeling has become a key research tool for species distribution modeling where actual data are limited. Although qualitative maps and distribution descriptions for chacma baboons (Papio ursinus) are freely available, quantitative data are limited and do not provide the empirical information required to make informed decisions about issues such as population assessment, conservation, and management. Here we present the first quantitative, repeatable, and detailed predicted spatial distribution of the chacma baboon across southern Africa. Our distribution is at a finer level of detail than has previously been available. We used an environmental envelope model implemented within a geographic information system to achieve this. The model used environmental layers representing water availability, temperature and altitude, and model parameters determined from georeferenced observational data. The data extracted from the environmental layers suggest chacma baboons inhabit areas with mean minimum temperatures of the coolest month as low as −6.1 °C, mean maximum temperatures of the warmest month as high as 38.2 °C, mean annual rainfall up to 1,555 mm, and altitude up to 3,286 m. Our model demonstrates that the distribution of chacma baboons may be limited by temperature and rainfall, with the predicted northern extent of its range being temperature dependent. The model also implies that some areas well known for chacma baboon occupation today may in fact be marginal habitat. The resulting map highlights areas of suitable habitat in southern Africa. In addition, a linear “patchy” corridor was identified following the East African Rift Valley connecting the southern habitat with northeast Africa. We find the greatest proportion of suitable habitat to be located in South Africa. This modeling approach is generic and would be suitable to analyze other primate species across similar geographic extents.

Spatial accessibility and the spread of HIV-1 subtypes and recombinants

The global spread of HIV-1 main group (group M) has resulted in differential distributions of subtypes and recombinants, with the greatest diversity being found in sub-Saharan Africa. The explanations for the current subtype distribution patterns are likely multifactorial, but the promotion of human migrations and movements through transportation link availability and quality, summarized through 'accessibility', have been consistently cited as strong drivers. We sought to address the question of whether accessibility has been a significant factor in HIV-1 spread across mainland Africa through spatial analyses of molecular epidemiology, transport network and land cover data. The distribution of HIV-1 subtypes and recombinants in sub-Saharan Africa for the period 1998-2008 was mapped using molecular epidemiology data at a finer level of detail than ever before. Moreover, hypotheses on the role of distance, road network structure and accessibility in explaining the patterns seen were tested using spatial datasets representing African transport infrastructure, land cover and an accessibility model of landscape travel speed. Coherent spatial patterns in HIV-1 subtype distributions across the continent exist, and a substantial proportion of the variance in the distribution and diversity pattern seen can be explained by variations in regional spatial accessibility. The study confirms quantitatively the influence of transport infrastructure on HIV-1 spread within Africa, presents an approach for examining potential future impacts of road development projects and, more generally, highlights the importance of accessibility in the spread of communicable diseases.

Social learning and spread of alternative means of opening an artificial fruit in four groups of vervet monkeys

Two-action experiments, in which observer individuals watch models use one of two alternative methods to achieve the same goal, have become recognized as a powerful method for studying social learning. We applied this approach to vervet monkeys, Chlorocebus aethiops, using an artificial fruit (‘vervetable’) which could be opened by either lifting a door panel on its front, or alternatively by sliding the panel to the left or right. In each of two groups a model was trained to lift the door and in two others the model slid it to either the left or right. Members of each group could then watch their model before the group was given access to multiple baited vervetables. Over the course of 100 openings we found a significant tendency for the lift and slide approaches to spread preferentially in the groups in which they were seeded. The same was true for slide left versus slide right, indicating these monkeys can attend to and learn from a fine level of detail in what others do. This effect cannot be explained by mere local enhancement since monkeys grasped a knob centred in the door to perform all techniques. Instead, imitation or emulation is implicated. No significant diminution of the tendency to adopt the seeded technique occurred among individuals learning later rather earlier in the study. Our results show that vervet monkeys have the capacity to learn from others by either emulation or imitation and what they learn has the potential to spread across their group.

The effect of species geographical distribution estimation methods on richness and phylogenetic diversity estimates

Diversity assessments are widely used in various fields of knowledge and rely on good estimates of species distribution. There are several methods available to estimate species distribution and the effect of using them is not clearly understood. In this research, we assess the effect of species distributions derived from four geographical distribution estimation methods on derived species richness and phylogenetic diversity (PD). We used the following four most common approaches to determine species geographical distributions: (1) range-wide occurrences are records of presence from databases and museum collections; (2) marginal occurrences are generally expert drawn distributional maps; (3) species distribution modeling (SDM) combines geographic records and environmental data to predict species occurrence; and (4) a combined approach that constrains the statistical modeling predictions by the marginal occurrence distributions. Using these approaches, we estimated richness and PD and their correspondent geographic hotspots for three different analysis resolutions using non-overlapping square windows of 2°, 4°, and 6° across Australia. We also assessed the differences of the resultant geographical distributions for three different spatial resolutions. We found markedly different hotspots when using range-wide occurrences and statistical modeling approaches. Range-wide occurrences resulted in low values of species richness and PD and statistical modeling resulted in high values. The combined and marginal occurrences approaches both had intermediate values, with the combined approach showing a finer level of detail than the marginal occurrences. There is a tendency for species range sizes between methods to converge with decreasing spatial resolution. Even for a relatively well-sampled group such as the Australian marsupials, the range-wide occurrences approach is likely to underestimate the presence of species. Conversely, because SDMs usually do not account for dispersal abilities or biotic interactions, it is likely that species geographical distributions using this approach are overestimated. Depending on the method used, the resultant estimates of diversity may be completely different. Caution is needed when choosing the method to estimate species distribution.

Liquid-flooded compression and expansion in scroll machines – Part I: Model development

A detailed mechanistic model has been developed for scroll compressors and scroll expanders with liquid flooding for application to the Liquid Flooded Ericsson Cycle. This model is based on the integration of a set of differential equations that arise from the conservation laws. The impact of the flooding liquid on the working process is also included through mixture properties as well as treatment of two-phase flow pressure drop. With the working process known, it is then possible to solve for the compressor power, total mass flow rate and other model outputs. The fine level of detail in the model allows for the investigation of the impact of design changes to the scroll machines. This model can also be readily extended to allow for the analysis of liquid flooded vapor compression refrigeration.

Fine‐scale quantification of floral and faunal breaks and their geographic correlates, with an example from south‐eastern Australia

AbstractAim We introduce a method to quantify shared breaks in aggregate biotic distributions and their relationships to geographic variables. The method is based on quantification of distributional taxic and abiotic data that can be applied over multiple spatial scales. We aim to show biogeographic breaks and varying transition zones at a fine level of detail (5‐km resolution) and develop an approach to assess existing bioregionalization schemes.Location Global applicability, using an example from New South Wales in south‐eastern Australia.Methods Moving window analyses, rotated in 15° increments through 360°, are used to assess the degree of anisotropic spatial turnover between sets of gridded cells containing georeferenced species observations. Patterns of biotic turnover are compared with equivalent analyses for elevation and lithology. Identified breaks are assessed against an existing bioregionalization scheme (Interim Biogeographic Regionalisation of Australia, IBRA).Results There was fine‐scale concordance between turnover patterns and several IBRA bioregions. Breaks in turnover of flora and fauna corresponded with the boundaries of the Hunter Valley and Sydney Basin regions, particularly the boundary between the Brigalow Belt South and Sydney Basin. Low‐turnover zones were quantified; prominent examples are the Sydney Cataract and Wyong bioregions. Turnover along many boundaries was gradational, confirming that mapped breaks are not abrupt. A previously unidentified break was identified in the South East Corner bioregion. Spatial turnover patterns were similar between biota and were reflected in mean correlation coefficients between turnover in each group: mammals–reptiles (r = 0.70, P << 0.01); mammals–flora (r = 0.56, P << 0.01); and reptiles–flora (r = 0.51, P << 0.01). Generally, patterns of abiotic turnover reflected biotic turnover, although mean turnover correlations were weaker than between biota.Main conclusions Using this method we were able to characterize taxic breaks and overlaps in detail and at a spatially fine resolution. For our study region, we confirm the overall integrity of the IBRA framework, but suggest that it may benefit from revision in some respects.

Keeping At-Risk Students in School

The wage premium for college graduates is substantial. Far fewer of these benefits accrue to students who complete some college (i.e., those who do not persist to graduation), and, partly for this reason, colleges often adopt programs aimed at helping to keep at-risk students in school. This article reports on a systematic review and meta-analysis of studies of such retention programs. The studies suggest small but potentially important effects on short-term retention rates and grades earned by program participants. Studies of more comprehensive interventions using relatively more appropriate comparison groups suggested more effective results than did studies that used weaker interventions, relatively less appropriate comparison groups, or both. Even the best studies included in this review are methodologically suspect and as such do not provide a very strong basis for making policy recommendations. From a public policy perspective, this review points to the need for more investment in rigorous studies that investigate, at a finer level of detail, the specific aspects of programs that are associated with program success. Rigorous studies are also needed that investigate the interaction between programs and student characteristics to determine what types of programs are most effective for which students.

The Languages of Black Africans in England

The achievement of integration and a reduction in the social exclusion of ethnic minority communities in England are policy matters of major concern. This paper argues that policy-makers and service providers pursuing these aims need to understand the language support needs of minority ethnic groups at a fine level of detail: groupings such as ‘Black’ or even ‘Black African’ are of limited utility. Although much ethnicity research has tended to view Black Africans as a homogenous group, appreciation of their diverse language use is important because people from different parts of sub-Saharan Africa face different language barriers on arrival in the UK. This paper examines evidence available from large-scale survey data on the association between language and indicators often used to assess integration and social exclusion. The paper provides empirical statistical evidence on Black Africans living in England and languages in the form of tables and maps using data-sets not previously analysed for this purpose. These are (1) the Labour Force Survey (LFS); and (2) the National Pupil Database (NPD). The results show that Black Africans speak a very wide range of languages at home. Somalis are by far the least integrated and most socially excluded of the major language groups, followed by Ghanaians. Zimbabweans and Nigerians, on the other hand, face only slight language barriers. The paper concludes with some implications of the findings for policy-makers and service providers.