Key challenges in agent-based modelling for geo-spatial simulation

Agent-based modelling (ABM) is fast becoming the dominant paradigm in social simulation due primarily to a worldview that suggests that complex systems emerge from the bottom-up, are highly decentralised, and are composed of a multitude of heterogeneous objects called agents. These agents act with some purpose and their interaction, usually through time and space, generates emergent order, often at higher levels than those at which such agents operate. ABM however raises as many challenges as it seeks to resolve. It is the purpose of this paper to catalogue these challenges and to illustrate them using three somewhat different agent-based models applied to city systems. The seven challenges we pose involve: the purpose for which the model is built, the extent to which the model is rooted in independent theory, the extent to which the model can be replicated, the ways the model might be verified, calibrated and validated, the way model dynamics are represented in terms of agent interactions, the extent to which the model is operational, and the way the model can be communicated and shared with others. Once catalogued, we then illustrate these challenges with a pedestrian model for emergency evacuation in central London, a hypothetical model of residential segregation tuned to London data which elaborates the standard Schelling (1971) model, and an agent-based residential location built according to spatial interactions principles, calibrated to trip data for Greater London. The ambiguities posed by this new style of modelling are drawn out as conclusions

In-flight absolute radiometric calibration of the thematic mapper

The TM multispectral scanner system was calibrated in an absolute manner before launch. To determine the temporal changes of the absolute radiometric calibration of the entire system, spectroradiometric measurements of the ground and the atmosphere were made simultaneously with TM collections over White Sands, New Mexico. By entering the measured values in an atmospheric radiative transfer program, the radiance levels of the in four of the spectral bands of the TM were determined. Tables show values for the reflectance of snow at White Sands measured by a modular 8 channel radiometer, and values for exoatmospheric irradiance within the TM passbands, calculated for the Earth-Sun distance using a solar radiometer

In-flight absolute radiometric calibration of the thematic mapper

In order to determine temporal changes of the absolute radiometric calibration of the entire TM system in flight spectroradiometric measurements of the ground and the atmosphere were made simultaneously with TM image collections over the White Sands, New Mexico area. By entering the measured values in an atmospheric radiative transfer program, the radiance levels in four of the spectral bands of the TM were determined, band 1:0.45 to 0.52 micrometers, band 2:0.53 to 0.61 micrometers band 3:0.62 to 0.70 micrometers and 4:0.78 to 0.91 micrometers. These levels were compared to the output digital counts from the detectors that sampled the radiometrically measured ground area, thus providing an absolute radiometric calibration of the entire TM system utilizing those detectors

Modeling the power flow in normal conductor-insulator-superconductor junctions

Normal conductor-insulator-superconductor (NIS) junctions promise to be interesting for x-ray and phonon sensing applications, in particular due to the expected self-cooling of the N electrode by the tunneling current. Such cooling would enable the operation of the active element of the sensor below the cryostat temperature and at a correspondingly higher sensitivity. It would also allow the use of MS junctions as microcoolers. At present, this cooling has not been realized in large area junctions (suitable for a number of detector applications). In this article, we discuss a detailed modeling of the heat flow in such junctions; we show how the heat flow into the normal electrode by quasiparticle back-tunneling and phonon absorption from quasiparticle pair recombination can overcompensate the cooling power. This provides a microscopic explanation of the self-heating effects we observe in our large area NIS junctions. The model suggests a number of possible solutions

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles

To better decipher the functional impact of alternative splicing, we classified alternative splicing events in 10 818 pairs of human and mouse genes based on conservation at genome and transcript levels. Expression levels of conserved alternative splices in human and mouse expressed sequence tag databases show strong correlation, indicating that alternative splicing is similarly regulated in both species. A total of 43% (8921) of mouse alternative splices could be found in the human genome but not in human transcripts. Five of eleven tested mouse predictions were observed in human tissues, demonstrating that mouse transcripts provide a valuable resource for identifying alternative splicing events in human genes. Combining gene-specific measures of conserved and diverged alternative splicing with both gene classification based on Gene Ontology (GO) and microarray-determined gene expression in 52 diverse human tissues and cell lines, we found conserved alternative splicing most enriched in brain-expressed signaling pathways. Diverged alternative splicing is more prevalent in testis and cancerous cell line up-regulated processes, including protein biosynthesis, responses to stress and responses to endogenous stimuli. Using conservation as a surrogate for functional significance, these results suggest that alternative splicing plays an important role in enhancing the functional capacity of central nervous systems, while non-functional splicing more frequently occurs in testis and cell lines, possibly as a result of cellular stress and rapid proliferation

Types of patients in a psychiatric intensive care unit

Objective: This paper reports the findings of a descriptive study of a patient populationover a three-month period on an eight bed psychiatric intensive care unit (PICU) in Western Australia. The report provides a quantitative insight into the profile of patients in PICUs. It provides information on patients' diagnoses, presenting signs, symptoms and/or behaviours,legal codes assigned to patients, treatment interventions and management. Method: Data were collected prospectively from August to October 1999. A total of 122 patients were admitted to the PICU during the review period. Data were entered into an Access program then exported to SPSS (Version 9 for Windows) for analysis and frequency distributions were obtained. Results: The results confirmed that the majority of patients admitted to the PICU were assessed as a high level of risk or needed containment. This finding is in line with the admission criteria developed by staff working in the PICU. It also supports the view that staffworking in these units require expertise and confidence to communicate with and manage potentially aggressive and highly aroused patients. Conclusion: This study demonstrates the importance of ongoing evaluations of patient populations in promoting best practice initiatives in psychiatric care

Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines

partially because of the limited scale at which the expression of specific splicing events has been measured. We generated the first genome-scale expression compendium of human alternative splicing events using custom whole-transcript microarrays monitoring expression of 24,426 alternative splicing events in 48 diverse human samples. Over 11,700 genes and 9,500 splicing events were differentially expressed, providing a rich resource for studying splicing regulation. An unbiased, systematic screen of 21,760 4-mer to 7-mer words for cis-regulatory motifs identified 143 RNA 'words' enriched near regulated cassette exons, including six clusters of motifs represented by UCUCU, UGCAUG, UGCU, UGUGU, UUUU and AGGG, which map to trans-acting regulators PTB, Fox, Muscleblind, CELF/CUG-BP, TIA-1 and hnRNP F/H, respectively. Each cluster showed a distinct pattern of genomic location and tissue specificity. For example, UCUCU occurs 110 to 35 nucleotides preceding cassette exons upregulated in brain and striated muscle but depleted in other tissues. UCUCU and UGCAUG seem to have similar function but independent action, occurring 5' and 3', respectively, of 33% of the cassette exons upregulated in skeletal muscle but co-occurring for only 2%

A Question of Choice

Women's reproductive rights, reproductive health, and constitutional privacy rights in the United States are addressed in light of the contemporary onslaught of the Christian Right. The misuse of State power by fundamentalist social forces in America is critiqued. The article also briefly reviews the question of State control over women's bodies

Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways

BACKGROUND: Interpretation of lists of genes or proteins with altered expression is a critical and time-consuming part of microarray and proteomics research, but relatively little attention has been paid to methods for extracting biological meaning from these output lists. One powerful approach is to examine the expression of predefined biological pathways and gene sets, such as metabolic and signaling pathways and macromolecular complexes. Although many methods for measuring pathway expression have been proposed, a systematic analysis of the performance of multiple methods over multiple independent data sets has not previously been reported. RESULTS: Five different measures of pathway expression were compared in an analysis of nine publicly available mRNA expression data sets. The relative sensitivity of the metrics varied greatly across data sets, and the biological pathways identified for each data set are also dependent on the choice of pathway activation metric. In addition, we show that removing incoherent pathways prior to analysis improves specificity. Finally, we create and analyze a public map of pathway expression in human tissues by gene-set analysis of a large compendium of human expression data. CONCLUSION: We show that both the detection sensitivity and identity of pathways significantly perturbed in a microarray experiment are highly dependent on the analysis methods used and how incoherent pathways are treated. Analysts should thus consider using multiple approaches to test the robustness of their biological interpretations. We also provide a comprehensive picture of the tissue distribution of human gene pathways and a useful public archive of human pathway expression data