An introduction to the Cambridge advanced modeller

Complex products and their development processes may be viewed as systems, whose different aspects can be modelled as networks of interactions between elements in different domains. Many approaches have been proposed to explore, support or improve engineering processes by building such models. Developing these approaches, and applying them to problems of realistic complexity, often requires specialised computer software suitable for manipulating large data sets. However, creating suitable tools can be difficult–because software development is time-consuming and requires skills that many researchers and practitioners do not possess. We developed an approach which aims to address this problem by recognising the iterative nature of modelling research and its often tight coupling with prototype software development, and by reducing the effort of software prototyping and revision within this process. The approach is enabled by, and embodied in, the Cambridge Advanced Modeller (CAM)–a configurable software platform we have developed, refined and applied over several years and through a number of research projects

A tale of two gyres: Contrasting distributions of dissolved cobalt and iron in the Atlantic Ocean during an Atlantic Meridional Transect (AMT-19).

Cobalt (Co) and iron (Fe) are essential for phytoplankton nutrition, and as such constitute a vital link in the marine biological carbon pump. Atmospheric deposition is an important, and in some places the dominant, source of trace elements (TEs) to the global ocean. Dissolved cobalt (dCo) and iron (dFe) were determined along an Atlantic Meridional Transect (AMT-19; Oct/Nov 2009) between 50°N and 40°S in the upper 150 m in order to investigate the behaviour and distribution of these two essential, bioactive TEs. During AMT-19, large differences in the distributions of dCo and dFe were observed. In the North Atlantic gyre provinces, extremely low mixed layer dCo concentrations (23 ± 9 pM) were observed, which contrasts with the relatively high mixed layer dFe concentrations (up to 1.0 nM) coincident with the band of highest atmospheric deposition (∼5–30°N). In the South Atlantic gyre, the opposite trend was observed, with relatively high dCo (55 ± 18 pM) observed throughout the water column, but low dFe concentrations (0.29 ± 0.08 nM). Given that annual dust supply is an order of magnitude greater in the North than the South Atlantic, the dCo distribution was somewhat unexpected. However, the distribution of dCo shows similarities with the distribution of phosphate (PO43−) in the euphotic zone of the Atlantic Ocean, where the North Atlantic gyre is characterised by chronically low PO4, and higher concentrations are observed in the South Atlantic gyre (Mather et al., 2008), suggesting the potential for a similar biological control of dCo distributions. Inverse correlations between dCo and Prochlorococcus abundance in the North Atlantic gyre provinces, combined with extremely low dCo where nitrogen fixation rates were highest (∼20–28°N), suggests the dominance of biological controls on dCo distributions. The contrasting dCo and dFe distributions in the North and South Atlantic gyres provides insights into the differences between the dominant controls on the distribution of these two bioactive trace metals in the central Atlantic Ocean

Statistical Inference for Valued-Edge Networks: Generalized Exponential Random Graph Models

Across the sciences, the statistical analysis of networks is central to the production of knowledge on relational phenomena. Because of their ability to model the structural generation of networks, exponential random graph models are a ubiquitous means of analysis. However, they are limited by an inability to model networks with valued edges. We solve this problem by introducing a class of generalized exponential random graph models capable of modeling networks whose edges are valued, thus greatly expanding the scope of networks applied researchers can subject to statistical analysis

Circumstellar discs: What will be next?

This prospective chapter gives our view on the evolution of the study of circumstellar discs within the next 20 years from both observational and theoretical sides. We first present the expected improvements in our knowledge of protoplanetary discs as for their masses, sizes, chemistry, the presence of planets as well as the evolutionary processes shaping these discs. We then explore the older debris disc stage and explain what will be learnt concerning their birth, the intrinsic links between these discs and planets, the hot dust and the gas detected around main sequence stars as well as discs around white dwarfs.Comment: invited review; comments welcome (32 pages

DADOS-Survey: an open-source application for CHERRIES-compliant Web surveys

BACKGROUND: The Internet has been increasingly utilized in biomedical research. From online searching for literature to data sharing, the Internet has emerged as a primary means of research for many physicians and scientists. As a result, Web-based surveys have been employed as an alternative to traditional, paper-based surveys. We describe DADOS-Survey, an open-source Web-survey application developed at our institution that, to the best of our knowledge, is the first to be compliant with the Checklist for Reporting Results of Internet E-Surveys (CHERRIES). DADOS-Survey was designed with usability as a priority, allowing investigators to design and execute their own studies with minimal technical difficulties in doing so. RESULTS: To date, DADOS-Survey has been successfully implemented in five Institutional Review Board-approved studies conducted by various departments within our academic center. Each of these studies employed a Web-survey design as their primary methodology. Our initial experience indicates that DADOS-Survey has been used with relative ease by each of the investigators and survey recipients. This has been further demonstrated through formal and field usability testing, during which time suggestions for improvement were incorporated into the software design. CONCLUSION: DADOS-Survey has the potential to have an important role in the future direction of Web-survey administration in biomedical research. This CHERRIES-compliant application is tailored to the emerging requirements of quality data collection in medicine

Effect of the UK government's 2-week target on waiting times in women with breast cancer in southeast England

A government target of a maximum 2-week wait for women referred urgently with suspected breast cancer was introduced in April 1999. We have assessed changes in the distributions of waiting times and the proportions of cases meeting proposed targets before and after this date, using clinical audit data on 5750 women attending 19 hospitals in southeast England during the period July 1997-December 2000, who were subsequently found to have breast cancer. The proportion of cases being seen within 2 weeks of referral rose from 66.0 to 75.2%, and the median wait to first appointment fell from 13.6 to 12.3 days, following the introduction of the government target. The proportion of cases waiting 5 weeks or less between first hospital appointment and treatment fell from 83.8 to 80.3%, and median waits for treatment increased from 21.4 to 24.1 days. We also examined the effects on waiting times of various sociodemographic and care related factors. A total of 85.7% of screening cases vs 67.9% of symptomatic cases were seen within 2 weeks, and 95.0% of cases treated with tamoxifen received treatment within 5 weeks, as opposed to 77.6% of cases treated with surgery, 81.2% of chemotherapy cases and 52.8% of radiotherapy cases. While waiting times from GP referral to first hospital appointment have improved since the introduction of the government target, times from first appointment to treatment have increased, and consequently total waiting times have changed little

Does present use of cardiovascular medication reflect elevated cardiovascular risk scores estimated ten years ago? A population based longitudinal observational study

Background It is desirable that those at highest risk of cardiovascular disease should have priority for preventive measures, eg. treatment with prescription drugs to modify their risk. We wanted to investigate to what extent present use of cardiovascular medication (CVM) correlates with cardiovascular risk estimated by three different risk scores (Framingham, SCORE and NORRISK) ten years ago. Methods Prospective logitudinal observational study of 20 252 participants in The Hordaland Health Study born 1950-57, not using CVM in 1997-99. Prescription data obtained from The Norwegian Prescription Database in 2008. Results 26% of men and 22% of women aged 51-58 years had started to use some CVM during the previous decade. As a group, persons using CVM scored significantly higher on the risk algorithms Framingham, SCORE and NORRISK compared to those not treated. 16-20% of men and 20-22% of women with risk scores below the high-risk thresholds for the three risk scores were treated with CVM, while 60-65% of men and 25-45% of women with scores above the high-risk thresholds received no treatment. Among women using CVM, only 2.2% (NORRISK), 4.4% (SCORE) and 14.5% (Framingham) had risk scores above the high-risk values. Low education, poor self-reported general health, muscular pains, mental distress (in females only) and a family history of premature cardiovascular disease correlated with use of CVM. Elevated blood pressure was the single factor most strongly predictive of CVM treatment. Conclusion Prescription of CVM to middle-aged individuals by large seems to occur independently of estimated total cardiovascular risk, and this applies especially to females

Prevalence of chronic kidney disease among people living with HIV/AIDS in Burundi: a cross-sectional study

<p>Abstract</p> <p>Background</p> <p>Since little is known about chronic kidney disease (CKD) among people living with HIV/AIDS (PLWHA) in Sub-Saharan Africa, the prevalence and nature of CKD were assessed in Burundi through a multicenter cross-sectional study.</p> <p>Methods</p> <p>Patients underwent assessments at baseline and 3 months later. Glomerular Filtration Rate (GFR) was estimated using abbreviated 4-variable Modification of Diet in Renal Diseases (MDRD) and Cockroft-Gault estimation methods. Patients were classified at month 3 into various CKD stages using the National Kidney Foundation (NKF) definition, which combines GFR and urinary abnormalities. Risk factors for presence of proteinuria (PRO) and aseptic leukocyturia (LEU) were further analyzed using multiple logistic regression.</p> <p>Results</p> <p>Median age of the patients in the study (N = 300) was 40 years, 70.3% were female and 71.7% were on highly active antiretroviral therapy. Using the MDRD method, CKD prevalence in patients was 45.7%, 30.2% of whom being classified as stage 1 according to the NKF classification, 13.5% as stage 2 and 2% as stage 3. No patient was classified as stage 4 or 5. Among CKD patients with urinary abnormality, PRO accounted for 6.1% and LEU for 18.4%. Significant associations were found between LEU and non-steroidal anti-inflammatory drug (NSAID) use, previous history of tuberculosis, low body mass index and female gender and between PRO and high viral load.</p> <p>Conclusion</p> <p>Our study, using a very sensitive definition for CKD evaluation, suggests a potentially high prevalence of CKD among PLWHA in Burundi. Patients should be regularly monitored and preventative measures implemented, such as monitoring NSAID use and adjustment of drug dosages according to body weight. Urine dipsticks could be used as a screening tool to detect patients at risk of renal impairment.</p

Variability in Isotope Discrimination Factors in Coral Reef Fishes: Implications for Diet and Food Web Reconstruction

Interpretation of stable isotope ratios of carbon and nitrogen (δ13C and δ15N) is generally based on the assumption that with each trophic level there is a constant enrichment in the heavier isotope, leading to diet-tissue discrimination factors of 3.4‰ for 15N (ΔN) and ∼0.5‰ for 13C (ΔC). Diet-tissue discrimination factors determined from paired tissue and gut samples taken from 152 individuals from 26 fish species at Ningaloo Reef, Western Australia demonstrate a large amount of variability around constant values. While caution is necessary in using gut contents to represent diet due to the potential for high temporal variability, there were significant effects of trophic position and season that may also lead to variability in ΔN under natural conditions. Nitrogen enrichment increased significantly at higher trophic levels (higher tissue δ15N), with significantly higher ΔN in carnivorous species. Changes in diet led to significant changes in ΔN, but not tissue δ15N, between seasons for several species: Acanthurus triostegus, Chromis viridis, Parupeneus signatus and Pomacentrus moluccensis. These results confirm that the use of meta-analysis averages for ΔN is likely to be inappropriate for accurately determining diets and trophic relationships using tissue stable isotope ratios. Where feasible, discrimination factors should be directly quantified for each species and trophic link in question, acknowledging the potential for significant variation away from meta-analysis averages and, perhaps, controlled laboratory diets and conditions