SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

BACKGROUND: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. RESULTS: We present the Systems Biology Markup Language (SBML) Qualitative Models Package ("qual"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models. CONCLUSIONS: SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.

Critical behavior of a system with orientational and positional degrees of freedom: A Monte Carlo simulation study

The critical behavior of a system constituted by molecules with a preferred symmetry axis is studied by means of a Monte Carlo simulation of a simplified two-dimensional model. The system exhibits two phase transitions, associated with the vanishing of the positional order of the center of mass of the molecules and with the orientational order of the symmetry axis. The evolution of the order parameters and the specific heat is also studied. The transition associated with the positional degrees of freedom is found to change from a second-order to a first-order behavior when the two phase transitions are close enough, due to the coupling with the orientational degrees of freedom. This fact is qualitatively compared with similar results found in pure liquid crystals and liquid-crystal mixtures.

Portable penetrometer for agricultural soil: sensitivity test to identify critical compaction depth

To express the negative effects of soil compaction, some researchers use critical values for soil mechanical strength that severely impair plant growth. The aim of this study was to identify this critical compaction depth, to test the functionality of a new, portable penetrometer developed from a spring dynamometer, and compare it to an electronic penetrometer traditionally used in compaction studies of agricultural soils. Three soils with distinct texture were conventionally tilled using a disk plow, and cultivated with different plant species. The critical soil resistance defined to establish critical compaction depth was equal to 1.5 MPa. The results of the new equipment were similar to the electronic penetrometer, indicating its viability as a tool for assessing the soil physical conditions for plant growth.

Critical evaluation of outcome scales assessment of lateral ankle ligament reconstruction.

BACKGROUND: Outcome following foot and ankle surgery can be assessed by disease- and region-specific scores. Many scoring systems exist, making comparison among studies difficult. The present study focused on outcome measures for a common foot and ankle abnormality and compared the results obtained by 2 disease-specific and 2 body region-specific scores. METHODS: We reviewed 41 patients who underwent lateral ankle ligament reconstruction. Four outcome scales were administered simultaneously: the Cumberland Ankle Instability Tool (CAIT) and the Chronic Ankle Instability Scale (CAIS), which are disease specific, and the American Orthopedic Foot & Ankle Society (AOFAS) hindfoot scale and the Foot and Ankle Ability Measure (FAAM), which are both body region-specific. The degree of correlation between scores was assessed by Pearson's correlation coefficient. Nonparametric tests, the Kruskal-Wallis and the Mann-Whitney test for pairwise comparison of the scores, were performed. RESULTS: A significant difference (P < .005) was observed between the CAIS and the AOFAS score (P = .0002), between the CAIS and the FAAM 1 (P = .0001), and between the CAIT and the AOFAS score (P = .0003). CONCLUSIONS: This study compared the performances of 4 disease- and body region-specific scoring systems. We demonstrated a correlation between the 4 administered scoring systems and notable differences between the results given by each of them. Disease-specific scores appeared more accurate than body region-specific scores. A strong correlation between the AOFAS score and the other scales was observed. The FAAM seemed a good compromise because it offered the possibility to evaluate the patient according to his or her own functional demand. CLINICAL RELEVANCE: The present study contributes to the development of more critical and accurate outcome assesment methods in foot and ankle surgery.

Disorder-induced critical phenomena in magnetically glassy Cu-Al-Mn alloys

Measurements of magnetic hysteresis loops in Cu-Al-Mn alloys of different Mn content at low temperatures are presented. The loops are smooth and continuous above a certain temperature, but exhibit a magnetization discontinuity below that temperature. Scaling analysis suggest that this system displays a disorder-induced phase transition line. Measurements allow one to determine the critical exponents ß=0.03±0.01 and ß¿=0.4±0.1, which coincide with those reported recently in a different system, thus supporting the existence of universality for disorder-induced critical points.

A Laboratory Investigation into the Effects of the Aggregated Related Facts of Critical VMA in Asphalt Paving Mixtures, June 2000

This report summarizes research conducted at Iowa State University on behalf of the Iowa Department of Transportation, focusing on the volumetric state of hot-mix asphalt (HMA) mixtures as they transition from stable to unstable configurations. This has raditionally been addressed during mix design by meeting a minimum voids in the mineral aggregate (VMA) requirement, based solely upon the nominal maximum aggregate size without regard to other significant aggregate-related properties. The goal was to expand the current specification to include additional aggregate properties, e.g., fineness modulus, percent crushed fine and coarse aggregate, and their interactions. The work was accomplished in three phases: a literature review, extensive laboratory testing, and statistical analysis of test results. The literature review focused on the history and development of the current specification, laboratory methods of identifying critical mixtures, and the effects of other aggregate-related factors on critical mixtures. The laboratory testing involved three maximum aggregate sizes (19.0, 12.5, and 9.5 millimeters), three gradations (coarse, fine, and dense), and combinations of natural and manufactured coarse and fine aggregates. Specimens were compacted using the Superpave Gyratory Compactor (SGC), conventionally tested for bulk and maximum theoretical specific gravities and physically tested using the Nottingham Asphalt Tester (NAT) under a repeated load confined configuration to identify the transition state from sound to unsound. The statistical analysis involved using ANOVA and linear regression to examine the effects of identified aggregate factors on critical state transitions in asphalt paving mixtures and to develop predictive equations. The results clearly demonstrate that the volumetric conditions of an HMA mixture at the stable unstable threshold are influenced by a composite measure of the maximum aggregate size and gradation and by aggregate shape and texture. The currently defined VMA criterion, while significant, is seen to be insufficient by itself to correctly differentiate sound from unsound mixtures. Under current specifications, many otherwise sound mixtures are subject to rejection solely on the basis of failing to meet the VMA requirement. Based on the laboratory data and statistical analysis, a new paradigm to volumetric mix design is proposed that explicitly accounts for aggregate factors (gradation, shape, and texture).

Chronic malnutrition favours smaller critical size for metamorphosis initiation in Drosophila melanogaster.

Critical size at which metamorphosis is initiated represents an important checkpoint in insect development. Here, we use experimental evolution in Drosophila melanogaster to test the long-standing hypothesis that larval malnutrition should favour a smaller critical size. We report that six fly populations subject to 112 generations of laboratory natural selection on an extremely poor larval food evolved an 18% smaller critical size (compared to six unselected control populations). Thus, even though critical size is not plastic with respect to nutrition, smaller critical size can evolve as an adaptation to nutritional stress. We also demonstrate that this reduction in critical size (rather than differences in growth rate) mediates a trade-off in body weight that the selected populations experience on standard food, on which they show a 15-17% smaller adult body weight. This illustrates how developmental mechanisms that control life history may shape constraints and trade-offs in life history evolution.

Critical review of K- ppn bound states

We make a thorough study of the process of three-body kaon absorption in nuclei, in connection with a recent FINUDA experiment which claims the existence of a deeply bound kaonic state from the observation of a peak in the Lambdad invariant mass distribution following K- absorption on 6Li. We show that the peak is naturally explained in terms of K- absorption from three nucleons leaving the rest as spectators. We can also reproduce all the other observables measured in the same experiment and used to support the hypothesis of the deeply bound kaon state. Our study also reveals interesting aspects of kaon absorption in nuclei, a process that must be understood in order to make progress in the search for K- deeply bound states in nuclei.

Report and Recommendations of the Iowa Vertical Infrastructure Advisory Committee, December 15, 2006

This report summaries the work of the committee over the last year and its vision for the future. The committee is followed with interest the work of the Department of Corrections and the Department of Veterans Affairs in evaluating the needs of their facilities and recommends similar evaluations of facilities around the state by other agencies. The committee members are ready to offer advice on the needs of the state's again infrastructure and steps that could be taken to evaluate vacant and underutilized buildings and reduce operational and maintenance costs.

Report and Recommendations of the Iowa Vertical Infrastructure Advisory Committee, December 15, 2009

This report summaries the work of the committee over the last year and its vision for the future. The committee is followed with interest the work of the Department of Corrections and the Department of Veterans Affairs in evaluating the needs of their facilities and recommends similar evaluations of facilities around the state by other agencies. The committee members are ready to offer advice on the needs of the state's again infrastructure and steps that could be taken to evaluate vacant and underutilized buildings and reduce operational and maintenance costs.

Report and Recommendations of the Iowa Vertical Infrastructure Advisory Committee, December 13, 2011

This report summaries the work of the committee over the last year and its vision for the future. The committee is followed with interest the work of the Department of Corrections and the Department of Veterans Affairs in evaluating the needs of their facilities and recommends similar evaluations of facilities around the state by other agencies. The committee members are ready to offer advice on the needs of the state's again infrastructure and steps that could be taken to evaluate vacant and underutilized buildings and reduce operational and maintenance costs.

Report and Recommendations of the Iowa Vertical Infrastructure Advisory Committee, December 15, 2010

This report summaries the work of the committee over the last year and its vision for the future. The committee is followed with interest the work of the Department of Corrections and the Department of Veterans Affairs in evaluating the needs of their facilities and recommends similar evaluations of facilities around the state by other agencies. The committee members are ready to offer advice on the needs of the state's again infrastructure and steps that could be taken to evaluate vacant and underutilized buildings and reduce operational and maintenance costs.