Applying causal inference to understand emergent behavior

Emergent behaviors in simulations require explanation, so that valid behaviors can be separated from design or cod-ing errors. Validation of emergent behavior requires ac-cumulation of insight into the behavior and the conditions under which it arises. Previously, we have introduced an approach, Explanation Exploration (EE), to gather insight into emergent behaviors using semi-automatic model adap-tation. We improve our previous work by iteratively apply-ing causal inference procedures to samples gathered from the semi-automatic model adaptation. Iterative application of causal inference procedures reveals the interactions of identified abstractions within the model that cause the emergent behavior. Uncovering these interactions gives the subject matter expert new insight into the emergent be-havior and facilitates the validation process.

The Remarkably Featureless High Resolution X-ray Spectrum of Mrk 478

An observation of Mrk 478 using the Chandra Low Energy Transmission Grating Spectrometer is presented. The source exhibited 30-40% flux variations on timescales of order 10000 s together with a slow decline in the spectral softness over the full 80 ks observation. The 0.15--3.0 keV spectrum is well fitted by a single power law with photon index of Gamma = 2.91 +/- 0.03. Combined with high energy data from BeppoSAX, the spectrum from 0.15 to 10 keV is well fit as the sum of two power laws with Gamma = 3.03 +/- 0.04, which dominates below 2 keV and 1.4 +/- 0.2, which dominates above 2 keV (quoting 90% confidence uncertainties). No significant emission or absorption features are detected in the high resolution spectrum, supporting our previous findings using the Extreme Ultraviolet Explorer but contradicting the claims of emission lines by Hwang & Bowyer (1997). There is no evidence of a warm absorber, as found in the high resolution spectra of many Sy 1 galaxies including others classified as narrow line Sy 1 galaxies such as Mrk 478. We suggest that the X-ray continuum may result from Comptonization of disk thermal emission in a hot corona through a range of optical depths.Comment: 21 pages, 7 figures; accepted for publication in the Astronomical Journa

New Neanderthal remains associated with the ‘flower burial’ at Shanidar Cave

Shanidar Cave in Iraqi Kurdistan became an iconic Palaeolithic site following Ralph Solecki's mid twentieth-century discovery of Neanderthal remains. Solecki argued that some of these individuals had died in rockfalls and—controversially—that others were interred with formal burial rites, including one with flowers. Recent excavations have revealed the articulated upper body of an adult Neanderthal located close to the ‘flower burial’ location—the first articulated Neanderthal discovered in over 25 years. Stratigraphic evidence suggests that the individual was intentionally buried. This new find offers the rare opportunity to investigate Neanderthal mortuary practices utilising modern archaeological techniques.Leverhulme Trust (Research Grant RPG-2013-105), the Rust Family Foundation, the British Academy, the Wenner-Gren Foundation, the Society of Antiquaries, the McDonald Institute of Archaeological Research at the University of Cambridge and the Natural Environment Research Council’s Oxford Radiocarbon Dating Facility (grant NF/2016/2/14). The ongoing dating program is supported by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement number 324139 “PalaeoChron” awarded to Professor Tom Higham, University of Oxfor

Research agenda and priorities for Australian and New Zealand paramedicine : A Delphi consensus study

Introduction: The systematic development of a research agenda is essential for coordinated, collaborative, and efficient research endeavours in any discipline. The aim of this study was to create and prioritise a stakeholder-informed, consensus-derived paramedicine research agenda for Australia and New Zealand. Methods: The study utilised a modified Delphi consensus method consisting of three phases. Phase 1, the findings of which were previously published, consisted of a survey of Australian and New Zealand paramedicine stakeholders to inform the subsequent consensus process. Phase 2 contained three Delphi rounds involving key paramedicine profession stakeholders to generate a research agenda. Panellists were asked to rate their agreement with the inclusion of each item using a 5-point Likert scale. Consensus was defined as 80% agreement signalled by ‘Strongly Agree’ and ‘Agree’ responses. Phase 3 involved one additional round of voting to determine the importance and thus establish priorities amongst the final list of agenda items. Results: There were 341 responses to the survey in Phase 1 and thematic analysis produced a provisional agenda consisting of 109 perceived research priorities. Sixty-three key paramedicine profession stakeholders were invited to Phases 2 and 3, of which 56 (88.9%) completed all three rounds in Phase 2, and 43 (68.3%) completed the final Phase 3. Thirty-seven items achieved consensus and were subsequently prioritised constituting the final research agenda. Panellists gave the highest priority to ‘Paramedics role in broader healthcare system’, ‘New and emerging roles in for paramedics’, ‘Patient safety’, ‘System improvement’, and ‘Clinical reasoning processes and models’. Conclusion: Using a modified Delphi consensus method and drawing from a broad range of stakeholders, a 37-item Australian and New Zealand paramedicine research agenda with item prioritisation was developed. The agenda serves to inform industry and other key stakeholders to guide their research endeavours ultimately leading to meaningful and tangible impact within the paramedicine profession

Contrasting longitudinal and cross-sectional relationships between insulin resistance and percentage of body fat, fitness, and physical activity in children - the LOOK study

Telford RD, Cunningham RB, Shaw JE, Dunstan DW, Lafferty ARA, Reynolds GJ, Hickman PE, Southcott E, Potter JM, Waring P, Telford RM. Contrasting longitudinal and cross-sectional relationships between insulin resistance and percentage of body fat, fitnes

“What if There's Something Wrong with Her?”‐How Biomedical Technologies Contribute to Epistemic Injustice in Healthcare

While there is a steadily growing literature on epistemic injustice in healthcare, there are few discussions of the role that biomedical technologies play in harming patients in their capacity as knowers. Through an analysis of newborn and pediatric genetic and genomic sequencing technologies (GSTs), I argue that biomedical technologies can lead to epistemic injustice through two primary pathways: epistemic capture and value partitioning. I close by discussing the larger ethical and political context of critical analyses of GSTs and their broader implications for just and equitable healthcare delivery

Oral Delivery of Nisin in Resistant Starch Based Matrices Alters the Gut Microbiota in Mice

peer-reviewedThere is a growing recognition of the role the gastrointestinal microbiota plays in health and disease. Ingested antimicrobial proteins and peptides have the potential to alter the gastrointestinal microbiota; particularly if protected from digestion. Nisin is an antimicrobial peptide that is used as a food preservative. This study examined the ability of nisin to affect the murine microbiota when fed to mice in two different starch based matrices; a starch dough comprising raw starch granules and a starch gel comprising starch that was gelatinized and retrograded. The effects of the two starch matrices by themselves on the microbiota were also examined. Following 16S rRNA compositional sequencing, beta diversity analysis highlighted a significant difference (p = 0.001, n = 10) in the murine microbiota between the four diet groups. The differences between the two nisin containing diets were mainly attributable to differences in the nisin release from the starch matrices while the differences between the carriers were mainly attributable to the type of resistant starch they possessed. Indeed, the differences in the relative abundance of several genera in the mice consuming the starch dough and starch gel diets, in particular Akkermansia, the relative abundance of which was 0.5 and 11.9%, respectively (p = 0.0002, n = 10), points to the potential value of resistance starch as a modulator of beneficial gut microbes. Intact nisin and nisin digestion products (in particular nisin fragment 22–31) were detected in the feces and the nisin was biologically active. However, despite a three-fold greater consumption of nisin in the group fed the nisin in starch dough diet, twice as much nisin was detected in the feces of the group which consumed the nisin in starch gel diet. In addition, the relative abundance of three times as many genera from the lower gastrointestinal tract (GIT) were significantly different (p < 0.001, n = 10) to the control for the group fed the nisin in starch gel diet, implying that the starch gel afforded a degree of protection from digestion to the nisin entrapped within it

Measuring adherence to antiretroviral treatment in resource-poor settings: The feasibility of collecting routine data for key indicators

<p>Abstract</p> <p>Background</p> <p>An East African survey showed that among the few health facilities that measured adherence to antiretroviral therapy, practices and definitions varied widely. We evaluated the feasibility of collecting routine data to standardize adherence measurement using a draft set of indicators.</p> <p>Methods</p> <p>Targeting 20 facilities each in Ethiopia, Kenya, Rwanda, and Uganda, in each facility we interviewed up to 30 patients, examined 100 patient records, and interviewed staff.</p> <p>Results</p> <p>In 78 facilities, we interviewed a total of 1,631 patients and reviewed 8,282 records. Difficulties in retrieving records prevented data collection in two facilities. Overall, 94.2% of patients reported perfect adherence; dispensed medicine covered 91.1% of days in a six month retrospective period; 13.7% of patients had a gap of more than 30 days in their dispensed medication; 75.8% of patients attended clinic on or before the date of their next appointment; and 87.1% of patients attended within 3 days.</p> <p>In each of the four countries, the facility-specific median indicators ranged from: 97%-100% for perfect self-reported adherence, 90%-95% of days covered by dispensed medicines, 2%-19% of patients with treatment gaps of 30 days or more, and 72%-91% of appointments attended on time. Individual facilities varied considerably.</p> <p>The percentages of days covered by dispensed medicine, patients with more than 95% of days covered, and patients with a gap of 30 days or more were all significantly correlated with the percentages of patients who attended their appointments on time, within 3 days, or within 30 days of their appointment. Self reported recent adherence in exit interviews was significantly correlated only with the percentage of patients who attended within 3 days of their appointment.</p> <p>Conclusions</p> <p>Field tests showed that data to measure adherence can be collected systematically from health facilities in resource-poor settings. The clinical validity of these indicators is assessed in a companion article. Most patients and facilities showed high levels of adherence; however, poor levels of performance in some facilities provide a target for quality improvement efforts.</p

Confronting Uncertainty in Wildlife Management: Performance of Grizzly Bear Management

Scientific management of wildlife requires confronting the complexities of natural and social systems. Uncertainty poses a central problem. Whereas the importance of considering uncertainty has been widely discussed, studies of the effects of unaddressed uncertainty on real management systems have been rare. We examined the effects of outcome uncertainty and components of biological uncertainty on hunt management performance, illustrated with grizzly bears (Ursus arctos horribilis) in British Columbia, Canada. We found that both forms of uncertainty can have serious impacts on management performance. Outcome uncertainty alone – discrepancy between expected and realized mortality levels – led to excess mortality in 19% of cases (population-years) examined. Accounting for uncertainty around estimated biological parameters (i.e., biological uncertainty) revealed that excess mortality might have occurred in up to 70% of cases. We offer a general method for identifying targets for exploited species that incorporates uncertainty and maintains the probability of exceeding mortality limits below specified thresholds. Setting targets in our focal system using this method at thresholds of 25% and 5% probability of overmortality would require average target mortality reductions of 47% and 81%, respectively. Application of our transparent and generalizable framework to this or other systems could improve management performance in the presence of uncertainty. &nbsp

Roadmap on Li-ion battery manufacturing research

Growth in the Li-ion battery market continues to accelerate, driven primarily by the increasing need for economic energy storage for electric vehicles. Electrode manufacture by slurry casting is the first main step in cell production but much of the manufacturing optimisation is based on trial and error, know-how and individual expertise. Advancing manufacturing science that underpins Li-ion battery electrode production is critical to adding to the electrode manufacturing value chain. Overcoming the current barriers in electrode manufacturing requires advances in materials, manufacturing technology, in-line process metrology and data analytics, and can enable improvements in cell performance, quality, safety and process sustainability. In this roadmap we explore the research opportunities to improve each stage of the electrode manufacturing process, from materials synthesis through to electrode calendering. We highlight the role of new process technology, such as dry processing, and advanced electrode design supported through electrode level, physics-based modelling. Progress in data driven models of electrode manufacturing processes is also considered. We conclude there is a growing need for innovations in process metrology to aid fundamental understanding and to enable feedback control, an opportunity for electrode design to reduce trial and error, and an urgent imperative to improve the sustainability of manufacture