Interactive simulation and visualization

Journal ArticleMost of us perform data analysis and visualization only after everything else is finished, which often means that we don't discover errors invalidating the results of our simulation until postprocessing. A better approach would be to improve the integration of simulation and visualization into the entire process so that you can make adjustments along the way. We call this approach computational steering. Computational steering is the capacity to control all aspects of the computational science pipeline-the succession of steps required to solve computational science and engineering problems. When you interactively explore a simulation in time and space, you steer it. In this sense, you can rely on steering to assist in debugging and to modify the computational aspects of your application

Deception and Fraud in the Publication of Scientific Research: Are There Solutions?

A number of events in the U.S. and abroad have refocused the scientific community on historical issues of whether, and how, integrity of our technical literature can be assured. Solutions to this problem are neither simple nor certain. Professional societies have addressed scientific misconduct, and effective responses by the research community will require cooperation of scientific publications. While the incidence of scientific fraud is difficult to estimate with precision and certainly varies with discipline, identified and publicized recent cases beg attention from editorial boards. Several egregious cases are described. The peer review system serves the function of examination and critique by scientists in relevant disciplines to assess submitted papers prior to publication. There is even a developing literature and several specific journals dedicated to the subject of fraud, professional integrity and ways to monitor or correct existing conditions. Underlying the field of professional and scientific publication is a fundamental assumption that data are real and that research actually occurred. Typically, the process is “blind” in both directions, although some journals permit “author-directed” reviews. A reviewer’s responsibilities include ensuring that text properly reflects data, that tables and figures are necessary/appropriate, and that conclusions fairly and reasonably reflect results and the body of information. Thus, existing peer review systems probably cannot detect anything but the most obvious fraud. In addition to imposing or perpetuating stringent review protocols, journals also can amend author guidelines to speak explicitly about publishing requirements. Cases of properly documented fraud warrant immediate public announcement, followed by official withdrawal or retraction. Reflection on these issues led editors of one journal to institute changes in editorial policies and develop a code of ethics for authors, reviewers, and editors. Prevention of dishonest research is already difficult, and we should ensure that this remains the case. Editors should formally commit reviewers/authors to ethical conduct in technical publications prior to publication and review

Coexistence and competitive exclusion in mutualism

The competitive exclusion principle is fundamental to understanding coexistence. Well-established theories predict the conditions for coexistence in consumer-resource interactions. Given that species often compete for commodities offered by mutualists, competitive exclusion theory should also be critical to understanding how mutualisms function. We explicitly apply the competitive exclusion principle to mutualism and derive a rule analogous to Tilman's R* rule for exploitative competition. Coexistence is impossible when competitors compete solely for a shared partner-provided commodity because superior competitors deplete that commodity sufficiently to exclude inferior competitors. We then investigate how competition between two guild members for a partner-provided commodity and a resource external to the mutualism affects competitor coexistence. There are three key results. First, coexistence is possible via partitioning of a partner-provided commodity and another resource. Second, unlike in classic R* Theory, competitive outcomes are influenced both by species' abilities to obtain commodities and their mutualisms with the shared commodity-providing partner, which can indirectly alleviate competitors' commodity limitation. Third, the outcome of competition has important consequences for the commodity-providing partner, which depend on the type of mutualism and the competitive abilities of competing mutualists. This theory provides a novel framework for investigating how competitors for mutualistic commodities coexist in nature.Science Foundation Arizona Grant [BSP0528-13]; ETH Zurich Center for Adaptation to a Changing EnvironmentThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Micro-CT Image-Derived Metrics Quantify Arterial Wall Distensibility Reduction in a Rat Model of Pulmonary Hypertension

We developed methods to quantify arterial structural and mechanical properties in excised rat lungs and applied them to investigate the distensibility decrease accompanying chronic hypoxia-induced pulmonary hypertension. Lungs of control and hypertensive (three weeks 11% O2) animals were excised and a contrast agent introduced before micro-CT imaging with a special purpose scanner. For each lung, four 3D image data sets were obtained, each at a different intra-arterial contrast agent pressure. Vessel segment diameters and lengths were measured at all levels in the arterial tree hierarchy, and these data used to generate features sensitive to distensibility changes. Results indicate that measurements obtained from 3D micro-CT images can be used to quantify vessel biomechanical properties in this rat model of pulmonary hypertension and that distensibility is reduced by exposure to chronic hypoxia. Mechanical properties can be assessed in a localized fashion and quantified in a spatially-resolved way or as a single parameter describing the tree as a whole. Micro-CT is a nondestructive way to rapidly assess structural and mechanical properties of arteries in small animal organs maintained in a physiological state. Quantitative features measured by this method may provide valuable insights into the mechanisms causing the elevated pressures in pulmonary hypertension of differing etiologies and should become increasingly valuable tools in the study of complex phenotypes in small-animal models of important diseases such as hypertension

The road half traveled

This brief reviews the extensive evidence on agricultural market reforms in Sub-Saharan Africa and summarizes the impact reforms have had on market performance, agricultural production, use of modern inputs, and poverty. It offers eight recommendations for completing the reform process and developing a new agenda for agricultural markets in Sub-Saharan Africa.

The road half traveled

During the past two decades, most countries in Sub-Saharan Africa undertook extensive economic reforms to reduce the role of the government and increase the role of the market in their economies. Because of the importance of the agricultural sector in the region, agricultural market reforms occupied a central place in these liberalization efforts. Agricultural reforms included the removal of price controls, deregulation of agricultural marketing, closure of state-owned enterprises that monopolized agricultural trade, and changes in the foreign exchange market to provide greater incentives for exports. The expectation was that improving price incentives for farmers and reducing government intervention in the agricultural sector would be enough to generate a supply response and allow well-functioning markets to emerge quickly. Almost two decades later, the general consensus is that the reform programs in Sub-Saharan Africa have not met expectations. At the beginning of the 21st century, Sub-Saharan Africa confronts a number of daunting problems: extensive hunger, malnutrition, poverty, resource degradation, and the spread of AIDS. Because the majority of the region's population remains dependent on agriculture for its livelihood, well-functioning and efficient agricultural markets continue to be key to improving Sub-Saharan Africa's economic health. This report reviews the extensive evidence on agricultural market reforms in Sub-Saharan Africa and summarizes the impact reforms have had on market performance, agricultural production, use of modern inputs,and poverty. The report offers eight recommmendations for completing the reform process and developing a new agenda for agricultural markets in Sub-Saharan Africa.

Reforming agricultural markets in Africa

"Since the early 1980s, almost all African governments have embarked on economic reform programs to reduce state intervention in the economy and to allow markets to play a larger role. In the agricultural sector these programs were designed to eliminate price controls on agricultural commodities, disband or privatize state farms and state-owned enterprises, reduce the heavy taxation of agricultural exports, phase out subsidies on fertilizer and other inputs, and allow greater competition in agricultural markets. These measures have been highly controversial. Proponents argue that the reforms have improved market efficiency, reduced budget deficits, stimulated export production, and increased the share of the final price received by farmers. Opponents argue that the reforms have destabilized agricultural prices, widened the income distribution gap, and reduced access to low-cost inputs. Reforming Agricultural Markets in Africa by Mylène Kherallah, Christopher Delgado, Eleni Gabre-Madhin, Nicholas Minot, and Michael Johnson, published by The Johns Hopkins University Press for IFPRI, reviews the experience of the last 20 years. It evaluates the degree to which the reforms have actually been implemented, their impact on agricultural production and prices, and the net effect on the well-being of African households." Author's Introduction.

Diverging volumetric trajectories following pediatric traumatic brain injury.

Traumatic brain injury (TBI) is a significant public health concern, and can be especially disruptive in children, derailing on-going neuronal maturation in periods critical for cognitive development. There is considerable heterogeneity in post-injury outcomes, only partially explained by injury severity. Understanding the time course of recovery, and what factors may delay or promote recovery, will aid clinicians in decision-making and provide avenues for future mechanism-based therapeutics. We examined regional changes in brain volume in a pediatric/adolescent moderate-severe TBI (msTBI) cohort, assessed at two time points. Children were first assessed 2-5 months post-injury, and again 12 months later. We used tensor-based morphometry (TBM) to localize longitudinal volume expansion and reduction. We studied 21 msTBI patients (5 F, 8-18 years old) and 26 well-matched healthy control children, also assessed twice over the same interval. In a prior paper, we identified a subgroup of msTBI patients, based on interhemispheric transfer time (IHTT), with significant structural disruption of the white matter (WM) at 2-5 months post injury. We investigated how this subgroup (TBI-slow, N = 11) differed in longitudinal regional volume changes from msTBI patients (TBI-normal, N = 10) with normal WM structure and function. The TBI-slow group had longitudinal decreases in brain volume in several WM clusters, including the corpus callosum and hypothalamus, while the TBI-normal group showed increased volume in WM areas. Our results show prolonged atrophy of the WM over the first 18 months post-injury in the TBI-slow group. The TBI-normal group shows a different pattern that could indicate a return to a healthy trajectory

Inflatable nested toroid structure

An inflatable structure comprises at least two generally toroidal, inflatable modules. When in a deployed mode, the first, inner module has a major diameter less than that of a second, outer module and is positioned within the inner circumference of the outer module such that the first module is nested circumferentially alongside the second module. The inflatable structure, in a non-deployed, non-inflated mode, is of compact configuration and adapted to be transported to a site of deployment. When deployed, the inflatable structure is of substantially increased interior volume. In one embodiment, access between the interior of the first module and the second module is provided by at least one port or structural pass-through. In another embodiment, the inflatable structure includes at least one additional generally toroidal module external of and circumferentially surrounding the second module