How serious are they? The use of data linkage to explore different definitions of serious road crash injuries

Over recent years, the focus in road safety has shifted towards a greater understanding of road crash serious injuries in addition to fatalities. Police reported crash data are often the primary source of crash information; however, the definition of serious injury within these data is not consistent across jurisdictions and may not be accurately operationalised. This study examined the linkage of police-reported road crash data with hospital data to explore the potential for linked data to enhance the quantification of serious injury. Data from the Queensland Road Crash Database (QRCD), the Queensland Hospital Admitted Patients Data Collection (QHAPDC), Emergency Department Information System (EDIS), and the Queensland Injury Surveillance Unit (QISU) for the year 2009 were linked. Nine different estimates of serious road crash injury were produced. Results showed that there was a large amount of variation in the estimates of the number and profile of serious road crash injuries depending on the definition or measure used. The results also showed that as the definition of serious injury becomes more precise the vulnerable road users become more prominent. These results have major implications in terms of how serious injuries are identified for reporting purposes. Depending on the definitions used, the calculation of cost and understanding of the impact of serious injuries would vary greatly. This study has shown how data linkage can be used to investigate issues of data quality. It has also demonstrated the potential improvements to the understanding of the road safety problem, particularly serious injury, by conducting data linkage.

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data

Background: A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networks from transcript profiling data remains an important yet challenging endeavor. A transcript profile specifies the abundances of many genes in a biological sample of interest. Prevailing strategies for learning the structure of a genetic network from high-dimensional transcript profiling data assume sparsity and linearity. Many methods consider relatively small directed graphs, inferring graphs with up to a few hundred nodes. This work examines large undirected graphs representations of genetic networks, graphs with many thousands of nodes where an undirected edge between two nodes does not indicate the direction of influence, and the problem of estimating the structure of such a sparse linear genetic network (SLGN) from transcript profiling data. Results: The structure learning task is cast as a sparse linear regression problem which is then posed as a LASSO (l1-constrained fitting) problem and solved finally by formulating a Linear Program (LP). A bound on the Generalization Error of this approach is given in terms of the Leave-One-Out Error. The accuracy and utility of LP-SLGNs is assessed quantitatively and qualitatively using simulated and real data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM) initiative provides gold standard data sets and evaluation metrics that enable and facilitate the comparison of algorithms for deducing the structure of networks. The structures of LP-SLGNs estimated from the INSILICO1, INSILICO2 and INSILICO3 simulated DREAM2 data sets are comparable to those proposed by the first and/or second ranked teams in the DREAM2 competition. The structures of LP-SLGNs estimated from two published Saccharomyces cerevisae cell cycle transcript profiling data sets capture known regulatory associations. In each S. cerevisiae LP-SLGN, the number of nodes with a particular degree follows an approximate power law suggesting that its degree distributions is similar to that observed in real-world networks. Inspection of these LP-SLGNs suggests biological hypotheses amenable to experimental verification. Conclusion: A statistically robust and computationally efficient LP-based method for estimating the topology of a large sparse undirected graph from high-dimensional data yields representations of genetic networks that are biologically plausible and useful abstractions of the structures of real genetic networks. Analysis of the statistical and topological properties of learned LP-SLGNs may have practical value; for example, genes with high random walk betweenness, a measure of the centrality of a node in a graph, are good candidates for intervention studies and hence integrated computational – experimental investigations designed to infer more realistic and sophisticated probabilistic directed graphical model representations of genetic networks. The LP-based solutions of the sparse linear regression problem described here may provide a method for learning the structure of transcription factor networks from transcript profiling and transcription factor binding motif data.

Controversy on the Free Energy of Formation of CaO Additional Evidence in Support of Thermochemical Data

The standard free energies of formation of CaO derived from a variety of high-temperature equilibrium measurements made by seven groups of experimentalists are significantly different from those given in the standard compilations of thermodynamic data. Indirect support for the validity of the compiled data comes from new solid-state electrochemical measurements using single-crystal CaF2 and SrF2 as electrolytes. The change in free energy for the following reactions are obtained: CaO + MgF2 --> MgO + CaF2 Delta G degrees = -68,050 -2.47 T(+/-100) J mol(-1) SrO + CaF2 --> SrF2 + CaO Delta G degrees = -35,010 + 6.39 T (+/-80) J mol(-1) The standard free energy changes associated with cell reactions agree with data in standard compilations within +/- 4 kJ mol(-1). The results of this study do not support recent suggestions for a major revision in thermodynamic data for CaO.

Denoising neural data with state-space smoothing: Method and application

Neural data are inevitably contaminated by noise. When such noisy data are subjected to statistical analysis, misleading conclusions can be reached. Here we attempt to address this problem by applying a state-space smoothing method, based on the combined use of the Kalman filter theory and the Expectation–Maximization algorithm, to denoise two datasets of local field potentials recorded from monkeys performing a visuomotor task. For the first dataset, it was found that the analysis of the high gamma band (60–90 Hz) neural activity in the prefrontal cortex is highly susceptible to the effect of noise, and denoising leads to markedly improved results that were physiologically interpretable. For the second dataset, Granger causality between primary motor and primary somatosensory cortices was not consistent across two monkeys and the effect of noise was suspected. After denoising, the discrepancy between the two subjects was significantly reduced.

Refinement of defection strategies stabilizes cooperation

Cooperation among unrelated individuals is an enduring evolutionary riddle and a number of possible solutions have been suggested. Most of these suggestions attempt to refine cooperative strategies, while little attention is given to the fact that novel defection strategies can also evolve in the population. Especially in the presence of punishment to the defectors and public knowledge of strategies employed by the players, a defecting strategy that avoids getting punished by selectively cooperating only with the punishers can get a selective benefit over non-conditional defectors. Furthermore, if punishment ensures cooperation from such discriminating defectors, defectors who punish other defectors can evolve as well. We show that such discriminating and punishing defectors can evolve in the population by natural selection in a Prisoner’s Dilemma game scenario, even if discrimination is a costly act. These refined defection strategies destabilize unconditional defectors. They themselves are, however, unstable in the population. Discriminating defectors give selective benefit to the punishers in the presence of non-punishers by cooperating with them and defecting with others. However, since these players also defect with other discriminators they suffer fitness loss in the pure population. Among the punishers, punishing cooperators always benefit in contrast to the punishing defectors, as the latter not only defect with other punishing defectors but also punish them and get punished. As a consequence of both these scenarios, punishing cooperators get stabilized in the population. We thus show ironically that refined defection strategies stabilize cooperation. Furthermore, cooperation stabilized by such defectors can work under a wide range of initial conditions and is robust to mistakes.

The challenges of Weibo for data-driven digital media research

Data generated via user activity on social media platforms is routinely used for research across a wide range of social sciences and humanities disciplines. The availability of data through the Twitter APIs in particular has afforded new modes of research, including in media and communication studies; however, there are practical and political issues with gaining access to such data, and with the consequences of how that access is controlled. In their paper ‘Easy Data, Hard Data’, Burgess and Bruns (2015) discuss both the practical and political aspects of Twitter data as they relate to academic research, describing how communication research has been enabled, shaped and constrained by Twitter’s “regimes of access” to data, the politics of data use, and emerging economies of data exchange. This conceptual model, including the ‘easy data, hard data’ formulation, can also be applied to Sina Weibo. In this paper, we build on this model to explore the practical and political challenges and opportunities associated with the ‘regimes of access’ to Weibo data, and their consequences for digital media and communication studies. We argue that in the Chinese context, the politics of data access can be even more complicated than in the case of Twitter, which makes scientific research relying on large social data from this platform more challenging in some ways, but potentially richer and more rewarding in others.

Cardiovascular diseases and vulnerable plaques: data, modeling, predictions and clinical applications PREFACE

Introduction Two symposia on “cardiovascular diseases and vulnerable plaques” Cardiovascular disease (CVD) is the leading cause of death worldwide. Huge effort has been made in many disciplines including medical imaging, computational modeling, bio- mechanics, bioengineering, medical devices, animal and clinical studies, population studies as well as genomic, molecular, cellular and organ-level studies seeking improved methods for early detection, diagnosis, prevention and treatment of these diseases [1-14]. However, the mechanisms governing the initiation, progression and the occurrence of final acute clinical CVD events are still poorly understood. A large number of victims of these dis- eases who are apparently healthy die suddenly without prior symptoms. Available screening and diagnostic methods are insufficient to identify the victims before the event occurs [8,9]. Most cardiovascular diseases are associated with vulnerable plaques. A grand challenge here is to develop new imaging techniques, predictive methods and patient screening tools to identify vulnerable plaques and patients who are more vulnerable to plaque rupture and associated clinical events such as stroke and heart attack, and recommend proper treatment plans to prevent those clinical events from happening. Articles in this special issue came from two symposia held recently focusing on “Cardio-vascular Diseases and Vulnerable Plaques: Data, Modeling, Predictions and Clinical Applications.” One was held at Worcester Polytechnic Institute (WPI), Worcester, MA, USA, July 13-14, 2014, right after the 7th World Congress of Biomechanics. This symposium was endorsed by the World Council of Biomechanics, and partially supported by a grant from NIH-National Institute of Biomedical Image and Bioengineering. The other was held at Southeast University (SEU), Nanjing, China, April 18-20, 2014.

Determination of the enthalpies of sublimation and evaporation from thermogravimetric data: Application to metalorganic complexes of Al and Cr

A series of bimetallic acetylacetonate (acac) complexes, AlxCr1-x(acac)(3), 0 <= x <= 1, have been synthesized for application as precursors for the CVD Of Substituted oxides, such as (AlxCr1-x)(2)O-3. Detailed thermal analysis has been carried out on these complexes, which are solids that begin subliming at low temperatures, followed by melting, and evaporation from the melt. By applying the Langmuir equation to differential thermogravimetry data, the vapour pressure of these complexes is estimated. From these vapour pressure data, the distinctly different enthalpies of sublimation and evaporation are calculated, using the Clausius-Clapeyron equation. Such a determination of both the enthalpies of sublimation and evaporation of complexes, which sublime and melt congruently, does not appear to have been reported in the literature to date.

Comparison of Interproton Distances in DNA Models with Nuclear Overhauser Enhancement Data

The conformational flexibility inherent in the polynucleotide chain plays an important role in deciding its three-dimensonal structure and enables it to undergo structural transitions in order to fulfil all its functions. Following certain stereochemical guidelines, both right and left handed double-helical models have been built in our laboratory and they are in reasonably good agreement with the fibre patterns for various polymorphous forms of DNA. Recently, nuclear magnetic resonance spectroscopy has become an important technique for studying the solution conformation and polymorphism of nucleic acids. Several workers have used 1H nuclear magnetic resonance nuclear Overhauser enhancement measurements to estimate the interproton distances for the various DNA oligomers and compared them with the interproton distances for particular models of A and Β form DNA. In some cases the solution conformation does not seem to fit either of these models. We have been studying various models for DNA with a view to exploring the full conformational space allowed for nucleic acid polymers. In this paper, the interproton distances calculated for the different stereochemically feasible models of DNA are presented and they are compared and correlated against those obtained from 1Η nuclear magnetic resonance nuclear Overhauser enhancement measurements of various nucleic acid oligomers.

Secondary attribute retrieval using tree data structures

Several techniques are known for searching an ordered collection of data. The techniques and analyses of retrieval methods based on primary attributes are straightforward. Retrieval using secondary attributes depends on several factors. For secondary attribute retrieval, the linear structures—inverted lists, multilists, doubly linked lists—and the recently proposed nonlinear tree structures—multiple attribute tree (MAT), K-d tree (kdT)—have their individual merits. It is shown in this paper that, of the two tree structures, MAT possesses several features of a systematic data structure for external file organisation which make it superior to kdT. Analytic estimates for the complexity of node searchers, in MAT and kdT for several types of queries, are developed and compared.

Crystalline A-DNA: The X-Ray Analysis of the Fragment d(G-G-T-A-T-A-C-C)

An A-DNA type double helical conformation was observed in the single crystal X-ray structure of the octamer d(G-G-T-A-T-A-C-C), 1, and its 5-bromouracil-containing analogue, 2. The structure of the isomorphous crystals (space group P61) was solved by a search technique based on packing criteria and R-factor calculations, with use of only low order data. At the present stage of refinement the R factors are 31 % for 1 and 28 % for 2 at a resolution of 2.25 A (0.225 nm). The molecules interact through their minor grooves by hydrogen bonding and base to sugar van der Waals contacts. The stable A conformation observed in the crystal may have some structural relevance to promoter regions where the T-A-T-A sequence is frequently found.

Crystal data for high-temperature dicalcium lead propionate, Ca2Pb(CH3CH2COO)6

The high-temperature paraelectric phase of dicalcium lead propionate, DCLP, at 363 ± 5 K is tetragonal, with a = 12.574 (6), c = 17.403 (9) Å, V = 2751.4 Å3, Z = 4 and corresponds to the space group P41212 (or P43212). The thermal expansion curve shows the transition somewhere between 328 and 343 K.

Infant product-related injuries: comparing specialised injury surveillance and routine emergency department data

- Objective To explore the potential for using a basic text search of routine emergency department data to identify product-related injury in infants and to compare the patterns from routine ED data and specialised injury surveillance data. - Methods Data was sourced from the Emergency Department Information System (EDIS) and the Queensland Injury Surveillance Unit (QISU) for all injured infants between 2009 and 2011. A basic text search was developed to identify the top five infant products in QISU. Sensitivity, specificity, and positive predictive value were calculated and a refined search was used with EDIS. Results were manually reviewed to assess validity. Descriptive analysis was conducted to examine patterns between datasets. - Results The basic text search for all products showed high sensitivity and specificity, and most searches showed high positive predictive value. EDIS patterns were similar to QISU patterns with strikingly similar month-of-age injury peaks, admission proportions and types of injuries. - Conclusions This study demonstrated a capacity to identify a sample of valid cases of product-related injuries for specified products using simple text searching of routine ED data. - Implications As the capacity for large datasets grows and the capability to reliably mine text improves, opportunities for expanded sources of injury surveillance data increase. This will ultimately assist stakeholders such as consumer product safety regulators and child safety advocates to appropriately target prevention initiatives.

Deriving optimal fishing effort for managing Australia's Moreton Bay multispecies trawl fishery with aggregated effort data

Deriving an estimate of optimal fishing effort or even an approximate estimate is very valuable for managing fisheries with multiple target species. The most challenging task associated with this is allocating effort to individual species when only the total effort is recorded. Spatial information on the distribution of each species within a fishery can be used to justify the allocations, but often such information is not available. To determine the long-term overall effort required to achieve maximum sustainable yield (MSY) and maximum economic yield (MEY), we consider three methods for allocating effort: (i) optimal allocation, which optimally allocates effort among target species; (ii) fixed proportions, which chooses proportions based on past catch data; and (iii) economic allocation, which splits effort based on the expected catch value of each species. Determining the overall fishing effort required to achieve these management objectives is a maximizing problem subject to constraints due to economic and social considerations. We illustrated the approaches using a case study of the Moreton Bay Prawn Trawl Fishery in Queensland (Australia). The results were consistent across the three methods. Importantly, our analysis demonstrated the optimal total effort was very sensitive to daily fishing costs-the effort ranged from 9500-11 500 to 6000-7000, 4000 and 2500 boat-days, using daily cost estimates of $0, $500, $750, and $950, respectively. The zero daily cost corresponds to the MSY, while a daily cost of $750 most closely represents the actual present fishing cost. Given the recent debate on which costs should be factored into the analyses for deriving MEY, our findings highlight the importance of including an appropriate cost function for practical management advice. The approaches developed here could be applied to other multispecies fisheries where only aggregated fishing effort data are recorded, as the literature on this type of modelling is sparse.