Peach: a simple Perl-based system for distributed computation and its application to cryo-EM data processing

A simple distributed processing system named "Peach" was developed to meet the rising computational demands of modern structural biology (and other) laboratories without additional expense by using existing hardware resources more efficiently. A central server distributes jobs to idle workstations in such a way that each computer is used maximally, but without disturbing intermittent interactive users. As compared to other distributed systems, Peach is simple, easy to install, easy to administer, easy to use, scalable, and robust. While it was designed to queue and distribute large numbers of small tasks to participating computers, it can also be used to send single jobs automatically to the fastest currently available computer and/or survey the activity of an entire laboratory's computers. Tests of robustness and scalability are reported, as are three specific electron cryomicroscopy applications where Peach enabled projects that would not otherwise have been feasible without an expensive, dedicated cluster.     

Optimal foraging, specialization, and a solution to Liem's paradox

Species that appear highly specialized on the basis of their phenotype (e.g., morphology, behavior, and physiology) also sometimes act as ecological generalists. This apparent paradox has been used to argue against the importance of competition as a diversifying evolutionary force. We provide an alternative explanation based on optimal foraging theory. Some resources are intrinsically easy to use and are widely preferred, while others require specialized phenotypic traits on the part of the consumer. This asymmetry allows optimally foraging consumers to evolve phenotypic specializations on nonpreferred resources without greatly compromising their ability to use preferred resources. The evolution of phenotypic specialization on nonpreferred resources can be driven by competition, but the specialists act as ecological generalists whenever their preferred resources are available. Our model identifies at least three different concepts of specialization that need to be distinguished, based on diet, prey utilization efficiencies, and phenotypic adaptations. The relationships among these concepts are complex and often counterintuitive. Specialists should often reject the very resources that they have evolved traits to use. The most extreme phenotypic specializations should occur in the absence of a trade-off between using preferred and nonpreferred resources. Our model may explain why extreme phenotypic-specializations evolve more often in fish communities than in terrestrial vertebrate communities and provides a mechanism whereby species can coexist in stable communities despite common preferences for some resources.     

Visuospatial Tasks Affect Locomotor Control More than Nonspatial Tasks in Older People

Background

Previous research has shown that visuospatial processing requiring working memory is particularly important for balance control during standing and stepping, and that limited spatial encoding contributes to increased interference in postural control dual tasks. However, visuospatial involvement during locomotion has not been directly determined. This study examined the effects of a visuospatial cognitive task versus a nonspatial cognitive task on gait speed, smoothness and variability in older people, while controlling for task difficulty.

Methods

Thirty-six people aged ≥75 years performed three walking trials along a 20 m walkway under the following conditions: (i) an easy nonspatial task; (ii) a difficult nonspatial task; (iii) an easy visuospatial task; and (iv) a difficult visuospatial task. Gait parameters were computed from a tri-axial accelerometer attached to the sacrum. The cognitive task response times and percentage of correct answers during walking and seated trials were also computed.

Results

No significant differences in either cognitive task type error rates or response times were evident in the seated conditions, indicating equivalent task difficulty. In the walking trials, participants responded faster to the visuospatial tasks than the nonspatial tasks but at the cost of making significantly more cognitive task errors. Participants also walked slower, took shorter steps, had greater step time variability and less smooth pelvis accelerations when concurrently performing the visuospatial tasks compared with the nonspatial tasks and when performing the difficult compared with the easy cognitive tasks.

Conclusions

Compared with nonspatial cognitive tasks, visuospatial cognitive tasks led to a slower, more variable and less smooth gait pattern. These findings suggest that visuospatial processing might share common networks with locomotor control, further supporting the hypothesis that gait changes during dual task paradigms are not simply due to limited attentional resources but to competition for common networks for spatial information encoding.     

Cognitive Ergonomics in Virtual Environments: Development of an Intuitive and Appropriate Input Device for Navigating in a Virtual Maze

For patients suffering from mild cognitive impairments, the navigation through a virtual maze should be as intuitive and efficient as possible in order to minimize cognitive and physical strain. This paper discusses the appropriateness of interaction devices for being used for easy navigation tasks. Information gained from human centered evaluation was used to develop an intuitive and ergonomic interaction device. Two experiments examined the usability of tracked interaction devices. Usability problems with the devices are discussed. The findings from the experiments were translated into general design guidance, in addition to specific recommendations. A new device was designed on the basis of these recommendations and its usability was evaluated in a second experiment. The results were used to develop a lightweight interaction device for navigation in the virtual maze.     

EMG biofeedback and discriminative muscle control

The awareness model of biofeedback suggests that training teaches new skills or enhances performance at old skills, while the cognitive or feed-forward models suggest that biofeedback brings attention to the response of interest but does not actually increase task skill. In a test of the predictions made by these models, subjects were tested on one or more cross-modal matching tasks, provided brief training, and retested on the task(s). Thirty subjects participated in integer-matching tasks in which they were instructed to produce various levels of frontalis activity corresponding to the levels of a ratio scale. Forty-five subjects participated in a tone-matching task in which they tried to match their frontalis tension to the pitch of a tone. The results indicated that the groups receiving biofeedback training improved at the more difficult integer task and at the tone task. Subjects performed better on the integer tasks than at the tone task. Our findings suggest that an awareness model accounts for changes occurring during biofeedback training. However, an awareness model may be applicable only for tasks of moderate difficulty; for relatively easy tasks, a feed-forward model may be more appropriate. The clinical utility of cross-modal matching tasks is also described.     

Performance of Humans vs. Exploration Algorithms on the Tower of London Test

The Tower of London Test (TOL) used to assess executive functions was inspired in Artificial Intelligence tasks used to test problem-solving algorithms. In this study, we compare the performance of humans and of exploration algorithms. Instead of absolute execution times, we focus on how the execution time varies with the tasks and/or the number of moves. This approach used in Algorithmic Complexity provides a fair comparison between humans and computers, although humans are several orders of magnitude slower. On easy tasks (1 to 5 moves), healthy elderly persons performed like exploration algorithms using bounded memory resources, i.e., the execution time grew exponentially with the number of moves. This result was replicated with a group of healthy young participants. However, for difficult tasks (5 to 8 moves) the execution time of young participants did not increase significantly, whereas for exploration algorithms, the execution time keeps on increasing exponentially. A pre-and post-test control task showed a 25% improvement of visuo-motor skills but this was insufficient to explain this result. The findings suggest that naive participants used systematic exploration to solve the problem but under the effect of practice, they developed markedly more efficient strategies using the information acquired during the test.     

EMG biofeedback and discriminative muscle control

The awareness model of biofeedback suggests that training teaches new skills or enhances performance at old skills, while the cognitive or feed-forward models suggest that biofeedback brings attention to the response of interest but does not actually increase task skill. In a test of the predictions made by these models, subjects were tested on one or more cross-modal matching tasks, provided brief training, and retested on the task(s). Thirty subjects participated in integer-matching tasks in which they were instructed to produce various levels of frontalis activity corresponding to the levels of a ratio scale. Forty-five subjects participated in a tone-matching task in which they tried to match their frontalis tension to the pitch of a tone. The results indicated that the groups receiving biofeedback training improved at the more difficult integer task and at the tone task. Subjects performed better on the integer tasks than at the tone task. Our findings suggest that an awareness model accounts for changes occurring during biofeedback training. However, an awareness model may be applicable only for tasks of moderate difficulty; for relatively easy tasks, a feed-forward model may be more appropriate. The clinical utility of cross-modal matching tasks is also described.This paper is based on a thesis conducted by the second author under the direction of the first author. Portions of this paper were presented at the annual meeting of the Association for Applied Psychophysiology and Biofeedback, March 1989, San Diego.     

Eradications and People: Lessons from the Plant Eradication Program in Galapagos

It is often argued that the benefit of eradication of an invasive species—a one-off injection of funds and the problem is solved—far outweighs the cost of a perennial control program. Furthermore, these are very attractive projects for funding agencies as outcomes are clear and easy to assess. Galapagos is in the early stage of the invasion process, with most alien species not yet naturalized and still restricted to gardens and farms. These species should be easy targets for early and cost-effective eradication projects, which would prevent many future problems. We review 30 plant eradication projects covering 23 potentially invasive species with limited distributions on four of the Galapagos Islands. Of the 30 projects, only four were successful: these were all less than 1 ha in net area, on land with a single owner and did not have persistent seed banks. Of the other 26 projects, most failed due to a lack of support from institutions that did not offer continuity of resources, from land owners who denied permission to carry out the work or from being too ambitious. As a result of these problems, 64.3% of the funding secured for the program was spent on discontinued projects. We highlight lessons learned to inform plant eradication programs in the future.     

A decision-making approach to the operation of flexible manufacturing systems

This paper introduces a generic decision-making framework for assigning resources of a manufacturing system to production tasks. Resources are broadly defined production units, such as machines, human operators, or material handling vehicles; and tasks are activities performed by resources. In the specific context of FMS, resources correspond to individual machines; tasks correspond to operations to be performed on parts. The framework assumes a hierarchical structure of the system and calls for the execution of four consecutive steps to make a decision for the assignment of a resource to a task. These steps are 1) establishment of decision-making criteria, 2) formation of alternative assignments, 3) estimation of the consequences of the assignments, and 4) selection of the best alternative assignment. This framework has been applied to an existing FMS as an operational policy that decides what task will be executed on which resource of this FMS. Simulation runs provide some initial results of the application of this policy. It is shown that the policy provides flexibility in terms of system performance and computational effort.     

The claim from adoption

In this article several justifications of what I call 'the claim from adoption' are examined. The claim from adoption is that, instead of expending resources on bringing new children into the world using reproductive technology and then caring for these children, we ought to devote these resources to the adoption and care of existing destitute children.
Arguments trading on the idea that resources should be directed to adoption instead of assisted reproduction because already existing people can benefit from such a use of resources whereas we cannot benefit individuals by bringing them into existence are rejected. It is then argued that a utilitarian argument proposed by Christian Munthe that supports the claim from adoption in some situations should be rejected because the support it offers does not extend to certain situations in which it seems morally obvious that resources should be expended on adoption rather than assisted reproduction. A version of the Priority View improves upon Munthe's utilitarianism by supporting the claim from adoption in the cases in which Munthe's argument failed. Some allegedly counterintuitive implications of the Priority View are then discussed, and it is concluded that the Priority View is more plausible than utilitarianism.
n a concluding section on policy issues it is argued that, even though the claim from adoption can be justified in a variety of situations, it does not follow that, in these situations, governments should direct resources away from assisted reproduction and towards adoption.     

磷元素扩散模型在水陆复合生态系统研究中的应用

以梅子垭村的一个小集水区及与之相邻的梅子垭水库为研究对象,根据降雨过程中集水区产生的径流输入及在水库库湾 不同取样点上所取水样的分析结果,初步建立了P元素在库湾 中的一维A.B.卡拉乌舍夫扩散模型。并对水库的水质状况与对应水流域的植被类型的特征之间的关系进行了分析。研究结果表明,水库水质与毗邻陆地生态系统的状况密切相关,以经济效益为主要目的的对陆地生态系统的过度开发将导致水库水质恶化;因此有必要将水陆生态系统综合考虑,以达到水陆复合生态系统的最大生态及经济效益。     

Exploring or Avoiding Novel Food Resources? The Novelty Conflict in an Invasive Bird

For an animal invading a novel region, the ability to develop new behaviors should facilitate the use of novel food resources and hence increase its survival in the new environment. However, the need to explore new resources may entail costs such as exposing the animal to unfamiliar predators. These two opposing forces result in an exploration-avoidance conflict, which can be expected to interfere with the acquisition of new resources. However, its consequences should be less dramatic in highly urbanized environments where new food opportunities are common and predation risk is low. We tested this hypothesis experimentally by presenting three foraging tasks to introduced common mynas (Acridotheres tristis) from environments with low and high urbanization levels from Australia. Individuals from the highly urbanized environments, where mynas are both more opportunistic when foraging and less fearful to predators, resolved a technical task faster than those from less urbanized environments. These differences did not reflect innovative 'personalities' and were not confounded by sex, morphology or motivational state. Rather, the principal factors underlying differences in mynas' problem-solving ability were neophobic-neophilic responses, which varied across habitats. Thus, mynas seem to modulate their problem-solving ability according to the benefits and costs of innovating in their particular habitat, which may help us understand the great success of the species in highly urbanized environments.     

Dimensions of rationing: who should do what?

Priority setting is a complex interaction of multiple decisions at various levels in the organisation and constrained by history. There is no self evident set of ethical principles or analytical tools to determine what decisions we should take at various levels, nor is there an obvious or easy way to resolve the clash of claims on resources. To make priority setting more "rational" we should concentrate on the processes and structure of decision making and the relation of macro and micro decisions. The debate should promote reasoned, informed, and open argument, draw on a variety of perspectives, and involve a plurality of interests. The aim must be to build up, over time, the capacity to engage in continuous, collective argument.     

Online analysis of development

The genomics revolution has altered the very nature of research in molecular biology, from how to find genes to how to find out what specific genes do. Given the availability of so many fully (or nearly) sequenced genomes, it is now relatively easy to track down dozens or even hundreds of genes relevant to a particular field of study. Unfortunately, up till now, the tools for determining what these genes actually do in embryos and cells have not kept pace, but the burgeoning field of bioinformatics should help correct this shortcoming and introduce the power of genomics to the study of developmental biology. In this review, some of the bioinformatics resources relevant to developmental biologists are described along with some simple approaches for applying these tools to analyzing early development.     

A subsequent movement alters lower extremity muscle activity and kinetics in drop jumps vs. drop landings

Drop landings and drop jumps are common training exercises and injury research model tasks. Drop landings have a single landing, whereas drop jumps include a subsequent jump after initial landing. With the expected ground impact, instant and landing surface suggested to modulate landing neuromechanics, muscle activity, and kinetics should be the same in both tasks when landing from the same height onto the same surface. Although previous researchers have noted some differences between these tasks across separate studies, little research has compared these tasks in the same study. Thus, we examined whether a subsequent movement after initial landing alters muscle activity and kinetics between drop landings and jumps. Fifteen women performed 10 drop landings and drop jumps each from 45 cm. Muscle onsets and integrated muscle activation amplitudes 150 milliseconds before (preactivity) and after landing (postactivity) in the medial and lateral quadriceps, hamstrings, and lateral gastrocnemius and peak and time-to-peak vertical ground reaction forces were examined across tasks (p ≤ 0.05). When performing drop jumps, subjects demonstrated later (p = 0.02) gastrocnemius and lesser lateral gastrocnemius (p = 0.002) and medial quadriceps (p = 0.02) preactivity followed by increased postactivity in all muscles (p = 0.006), with higher peak vertical ground reaction forces (p = 0.04) but no differences in times to these peaks (p = 0.60) than drop landings. The later gastrocnemius activation, higher gastrocnemius and quadriceps postlanding amplitudes, and higher ground reaction forces in drop jumps may allow subjects to propel the body vertically after the initial landing vs. simply absorbing impact in drop landings. Our results indicate that in addition to landing surface and height, anticipation of a subsequent task changes landing neuromechanics. Generalizations of results from landing-only studies should not be made with landing followed-by-subsequent-activity studies. Landing exercises should be incorporated based on sport-specific demands.     

The ‘Goldilocks Zone’: Getting the Measure of Manual Asymmetries

Some studies have shown that manual asymmetries decrease in older age. These results have often been explained with reference to models of reduced hemispheric specialisation. An alternative explanation, however, is that hand differences are subtle, and capturing them requires tasks that yield optimal performance with both hands. Whereas the hemispheric specialisation account implies that reduced manual asymmetries should be reliably observed in older adults, the ‘measurement difficulty’ account suggests that manual asymmetries will be hard to detect unless a task has just the right level of difficulty—i.e. within the ‘Goldilocks Zone’, where it is not too easy or too hard, but just right. Experiment One tested this hypothesis and found that manual asymmetries were only detected when participants performed in this zone; specifically, performance on a tracing task was only superior in the preferred hand when task constraints were high (i.e. fast speed tracing). Experiment Two used three different tasks to examine age differences in manual asymmetries; one task produced no asymmetries, whilst two tasks revealed asymmetries in both younger and older groups (with poorer overall performance in the old group across all tasks). Experiment Three revealed task-dependent asymmetries in both age groups, but highlighted further detection difficulties linked with the metric of performance and compensatory strategies used by participants. Results are discussed with reference to structural learning theory, whereby we suggest that the processes of inter-manual transfer lead to relatively small performance differences between the hands (despite a strong phenomenological sense of performance disparities).     

Dual Task Performance in Normal Aging: A Comparison of Choice Reaction Time Tasks

This study examined dual task performance in 28 younger (18–30 years) and 28 older (>60 years) adults using two sets of choice reaction time (RT) tasks paired with digit tasks. Set one paired simple choice RT with digit forward; set two paired complex choice RT with digit backward. Each task within each set had easy and hard conditions. For the simple choice RT, participants viewed single letters and pressed a specified keyboard key if the letter was X or Z or a different key for other letters (easy). For the hard condition, there were 4 target letters (X, Z, O, Y). Digit forward consisted of 4 (easy) or 5 (hard) digits. For the complex choice RT, participants viewed 4×4 matrices of Xs and Os, and indicated whether four Xs (easy) or four Xs or four Os (hard) appeared in a row. Digit backward consisted of 3 (easy) or 4 (hard) digits. Within each set, participants performed every possible combination of tasks. We found that in the simple choice RT tasks older adults were significantly slower than, but as accurate as younger adults. In the complex choice RT tasks, older adults were significantly less accurate, but as fast as younger adults. For both age groups and both dual task sets, RT decreased and error rates increased with greater task difficulty. Older adults had greater dual task costs for error rates in the simple choice RT, whereas in the complex choice RT, it was the younger group that had greater dual task costs. Findings suggest that younger and older adults may adopt differential behavioral strategies depending on complexity and difficulty of dual tasks.     

Informing about mammographic screening: Ethical challenges and suggested solutions

Providing high quality and user oriented information about mammographic screening is no easy task, as screening has been subject to heated professional and public debates. Although the information has to be developed and provided in context for each screening program, the basic challenges are very much the same for all programs. Accordingly, the objective of this article is to analyze key ethical challenges in informing about mammographic screening, and based on these, to suggest some guiding principles for practical solutions. A literature review identifies five crucial issues with respect to informing women about mammographic screening. By analyzing and addressing these issues, five guiding principles are suggested: the content and the form of information should be developed through open and transparent processes with strong stakeholder involvement. Facts should be presented in a balanced way and uncertainties should be acknowledged, e.g., by presenting outcomes in ranges. Information should be layered without attempts to frame information. Attending mammographic screening should be as easy as not attending. Although apparently trivial, the suggested principles can be useful for elaborating specific information material about mammographic screening in a field of great ethical controversy.     

Bioinformatics database infrastructure for biotechnology research

Many databases are available that provide valuable data resources for the biotechnological researcher. According to their core data, they can be divided into different types. Some databases provide primary data, like all published nucleotide sequences, others deal with protein sequences. In addition to these two basic types of databases, a huge number of more specialized resources are available, like databases about protein structures, protein identification, special features of genes and/or proteins, or certain organisms. Furthermore, some resources offer integrated views on different types of data, allowing the user to do easy customized queries over large datasets and to compare different types of data.     

Condor-COPASI: high-throughput computing for biochemical networks

ABSTRACT: BACKGROUND: Mathematical modelling has become a standard technique to improve our understanding of complex biological systems. As models become larger and more complex, simulations and analyses require increasing amounts of computational power. Clusters of computers in a high-throughput computing environment can help to provide the resources required for computationally expensive model analysis. However, exploiting such a system can be difficult for users without the necessary expertise. RESULTS: We present Condor-COPASI, a server-based software tool that integrates COPASI, a biological pathway simulation tool, with Condor, a high-throughput computing environment. Condor-COPASI provides a web-based interface, which makes it extremely easy for a user to run a number of model simulation and analysis tasks in parallel. Tasks are transparently split into smaller parts, and and submitted for execution on a Condor pool. Result output is presented to the user in a number of formats, including tables and interactive graphical displays. CONCLUSIONS: Condor-COPASI can effectively use a Condor high-throughput computing environment to provide significant gains in performance for a number of model simulation and analysis tasks. Condor-COPASI is free, open source software, released under the Artistic License 2.0, and is suitable for use by any institution with access to a Condor pool. Source code is freely available for download at http://code.google.com/p/condor-copasi/, along with full instructions on deployment and usage.