Simple individual-based models effectively represent Afrotropical forest bird movement in complex landscapes

Reliable estimates of dispersal rates between habitat patches (i.e. functional connectivity) are critical for predicting long-term effects of habitat fragmentation on population persistence. Connectivity measures are frequently derived from least cost path or graph-based approaches, despite the fact that these methods make biologically unrealistic assumptions. Individual-based models (IBMs) have been proposed as an alternative as they allow modelling movement behaviour in response to landscape resistance. However, IBMs typically require excessive data to be useful for management. Here, we test the extent to which an IBM requiring only an uncomplicated set of movement rules [the 'stochastic movement simulator' (SMS)] can predict animal movement behaviour in real-world landscapes. Movement behaviour of two forest birds, the Cabanis's greenbul Phyllastrephus cabanisi (a forest specialist) and the white-starred robin Pogonocichla stellata (a habitat generalist), across an Afrotropical matrix was simulated using SMS. Predictions from SMS were evaluated against a set of detailed movement paths collected by radiotracking homing individuals. SMS was capable of generating credible predictions of bird movement, although simulations were sensitive to the cost values and the movement rules specified. Model performance was generally highest when movement was simulated across low-contrasting cost surfaces and when virtual individuals were assigned low directional persistence and limited perceptual range. SMS better predicted movements of the habitat specialist than the habitat generalist, which highlights its potential to model functional connectivity when species movements are affected by the matrix. Synthesis and applications. Modelling the dispersal process with greater biological realism is likely to be critical for improving our predictive capability regarding functional connectivity and population persistence. For more realistic models to be widely applied, it is vital that their application is not overly complicated or data demanding. Here, we show that given relatively basic understanding of a species' dispersal ecology, the stochastic movement simulator represents a promising tool for estimating connectivity, which can help improve the design of functional ecological networks aimed at successful species conservation

England SimSmoke: the impact of nicotine vaping on smoking prevalence and smoking‐attributable deaths in England

BACKGROUND AND AIMS: While the use of nicotine vaping products (NVPs) is widespread, their impact on smoking prevalence is controversial. This study considered the potential impact of NVPs on smoking prevalence in England. DESIGN: Indirect simulation model. The England SimSmoke model is validated through 2012, before NVP use became more widely used by smokers. Because information on NVP-related transitions is limited, an indirect method is used; the difference in observed smoking prevalence (reflecting NVPs) is compared with a 2012-2019 counterfactual No-NVP scenario (without NVPs) to estimate the impact of NVPs on smoking and smoking-attributable deaths. SETTING: England, 2000-2019. PARTICIPANTS: Nationally representative sample of population. MEASUREMENTS: England's population, mortality rates, and smoking prevalence estimates from three national surveys and tobacco control policies. FINDINGS: Between 2000 and 2012, SimSmoke projected a decline in age 18+ smoking prevalence of 23.5% in men and 27.0% in women. These projections, as well as those by specific age groups, were generally consistent with findings from the three national surveys. Comparing 2012-2019 relative reduction in age 18+ prevalence from the Annual Population Survey (males 27.5%) with the model-predicted No-NVP reduction (males 7.3%), the implied NVP-attributable relative reduction in adult smoking prevalence was 20.2% (95% CI, 18.8%-22.0%) for males and 20.4% (18.7%-22.2%) for females. The NVP-attributable reduction was 27.2% (22.8%-31.6%) for males and 31.7% (27.4%-36.5%) for females ages 18-24 and 18.6% (15.2%-21.8%) for males and 15.0% (11.1%-18.8%) for females ages 25-34, with similar reductions for ages 35 and above. The implied reduction in smoking prevalence between 2012 and 2019 equates to 165,660 (132,453-199,501) averted deaths by 2052. Other surveys yielded smaller, but relatively consistent results. CONCLUSIONS: An indirect method of simulation modeling indicates that substantial reductions in smoking prevalence occurred in England from 2012 to 2019 coinciding with the growth in nicotine vaping product use

Metabolic profiles of male meat eaters, fish eaters, vegetarians, and vegans from the EPIC-Oxford cohort

Background: Human metabolism is influenced by dietary factors and lifestyle, environmental, and genetic factors; thus, men who exclude some or all animal products from their diet might have different metabolic profiles than meat eaters. Objective: We aimed to investigate differences in concentrations of 118 circulating metabolites, including acylcarnitines, amino acids, biogenic amines, glycerophospholipids, hexose, and sphingolipids related to lipid, protein, and carbohydrate metabolism between male meat eaters, fish eaters, vegetarians, and vegans from the Oxford arm of the European Prospective Investigation into Cancer and Nutrition. Design: In this cross-sectional study, concentrations of metabolites were measured by mass spectrometry in plasma from 379 men categorized according to their diet group. Differences in mean metabolite concentrations across diet groups were tested by using ANOVA, and a false discovery rate–controlling procedure was used to account for multiple testing. Principal component analysis was used to investigate patterns in metabolic profiles. Results: Concentrations of 79% of metabolites differed significantly by diet group. In the vast majority of these cases, vegans had the lowest concentration, whereas meat eaters most often had the highest concentrations of the acylcarnitines, glycerophospholipids, and sphingolipids, and fish eaters or vegetarians most often had the highest concentrations of the amino acids and a biogenic amine. A clear separation between patterns in the metabolic profiles of the 4 diet groups was seen, with vegans being noticeably different from the other groups because of lower concentrations of some glycerophospholipids and sphingolipids. Conclusions: Metabolic profiles in plasma could effectively differentiate between men from different habitual diet groups, especially vegan men compared with men who consume animal products. The difference in metabolic profiles was mainly explained by the lower concentrations of glycerophospholipids and sphingolipids in vegans

Mortality and incidence of second cancers following treatment for testicular cancer

We studied 5555 seminoma patients and 3733 patients with nonseminomatous testicular cancers diagnosed in Southeast England between 1960 and 2004. For both groups survival improved over time: 10-year relative survival increased from 78% in 1960–1969 to 99% in 1990–2004 for seminomas, and from 55 to 95% for nonseminomas. In the early period mortality was still significantly increased more than 15 years after diagnosis in both groups, whereas in more recent periods the excess deaths mainly occurred in the first 5 years after diagnosis. For seminomas, there was a significant excess of cancers of the colon (standardised incidence ratio (SIR) 2.36; 95% confidence interval (CI) 1.13–4.35), soft tissue (SIR 13.64; CI 1.65–49.28) and bladder (SIR 4.28; CI 2.28–7.31) in the long term (20+ years after diagnosis), of pancreatic cancer in both the medium (10–19 years) (SIR 2.91; CI 1.26–5.73) and long term (SIR 5.48; CI 2.37–10.80), of leukaemia in both the short (0–9 years) (SIR 3.01; CI 1.44–5.54) and long term (SIR 4.48; CI 1.64–9.75), and of testis cancer in both the short (SIR 6.69; CI 4.28–9.95) and medium term (SIR 3.96; CI 1.08–10.14). For nonseminomas, significant excesses were found in the long term for cancers of the stomach (SIR 5.13; CI 1.40–13.13), rectum (SIR 4.49; CI 1.22–11.51) and pancreas (SIR 10.17: CI 3.73–22.13), and for testis cancer in the medium term (SIR 5.94; CI 2.18–12.93). Leukaemia was significantly increased in the short term (SIR 6.78; CI 2.93–13.36). The better survival observed is largely attributable to improved treatment, and the trend in reducing the toxicity of therapy should continue to reduce future health risks in testicular cancer survivors

An internal health systems research portfolio assessment of a low-income country research institution

<p>Abstract</p> <p>Background</p> <p>In order to determine the type and amount of health systems research being conducted within ICDDR,B (also known as the Centre), a leading research institution in Bangladesh, an internal review of all on-going research protocols was conducted in September 2007.</p> <p>Methods</p> <p>A review of all ongoing research protocols within the Centre was conducted. The names of the investigators and the institutional divisions of the protocols were removed in order to decrease the amount of reviewer bias. The building blocks of the World Health Organization's "Framework for Action" on health systems was used to categorize the protocols considered to be health systems research projects. Several additional items were collected, e.g. the highest level of education completed by the Principal Investigator. A total dollar value was placed on the health systems research portfolio of the institution based on the budgets of the selected protocols.</p> <p>Results</p> <p>As of September 2007 16 out of 118 (13.5%) reviewed protocols were considered to be health systems research projects. Results of the six building blocks of the health system categorization demonstrated that a majority of these protocols involved elements of health services delivery. There was very little engagement in more downstream systems and policy research that involved leadership and governance of the health system. Eleven of the HSR studies were local in scope, while there was only one study that has a multinational focus. The Centre's total dollar value for the health systems research project portfolio added up to US$ 3,723,331.</p> <p>Conclusions</p> <p>This internal review can serve as a snap shot of on-going activities, and as a baseline for future assessments against which to monitor progress in the area of health systems research. Further, it can serve as a model for other institutions striving to assess and develop health systems research programmes and capacity.</p

Weakened magnetic braking as the origin of anomalously rapid rotation in old field stars

A knowledge of stellar ages is crucial for our understanding of many astrophysical phenomena, and yet ages can be difficult to determine. As they become older, stars lose mass and angular momentum, resulting in an observed slowdown in surface rotation. The technique of 'gyrochronology' uses the rotation period of a star to calculate its age. However, stars of known age must be used for calibration, and, until recently, the approach was untested for old stars (older than 1 gigayear, Gyr). Rotation periods are now known for stars in an open cluster of intermediate age (NGC 6819; 2.5 Gyr old), and for old field stars whose ages have been determined with asteroseismology. The data for the cluster agree with previous period-age relations, but these relations fail to describe the asteroseismic sample. Here we report stellar evolutionary modelling, and confirm the presence of unexpectedly rapid rotation in stars that are more evolved than the Sun. We demonstrate that models that incorporate dramatically weakened magnetic braking for old stars can---unlike existing models---reproduce both the asteroseismic and the cluster data. Our findings might suggest a fundamental change in the nature of ageing stellar dynamos, with the Sun being close to the critical transition to much weaker magnetized winds. This weakened braking limits the diagnostic power of gyrochronology for those stars that are more than halfway through their main-sequence lifetimes.Comment: 25 pages, 3 figures in main paper, 6 extended data figures, 1 table. Published in Nature, January 2016. Please see https://youtu.be/O6HzYgP5uyc for a video description of the resul

Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata)

This is the final version. Available on open access from Wiley via the DOI in this recordData archiving: The data that support these findings are openly available at: European Nucleotide Archive (https://www.ebi.ac.uk/ena/ browser/home)—reference numbers: PRJEB42705 (all introduction populations) and PRJEB10680 (GHP). All scripts and associated data are available on Github repository: mapping and SNP calling (https://github.com/josieparis/gatk-snp-calling); population genomics and haplotype scans (https://github.com/ bfraser-commits/Rapid_genomic_adaptation_guppies); the software for multivariate AF analyses (AF-vapeR) (https://github. com/JimWhiting91/afvaper); and simulation analyses (https:// github.com/JimWhiting91/fibr_simulations).Although rapid phenotypic evolution has been documented often, the genomic basis of rapid adaptation to natural environments is largely unknown in multicellular organisms. Population genomic studies of experimental populations of Trinidadian guppies (Poecilia reticulata) provide a unique opportunity to study this phenomenon. Guppy populations that were transplanted from high-predation (HP) to low-predation (LP) environments have been shown to evolve toward the phenotypes of naturally colonized LP populations in as few as eight generations. These changes persist in common garden experiments, indicating that they have a genetic basis. Here, we report results of whole genome variation in four experimental populations colonizing LP sites along with the corresponding HP source population. We examined genome-wide patterns of genetic variation to estimate past demography and used a combination of genome scans, forward simulations, and a novel analysis of allele frequency change vectors to uncover the signature of selection. We detected clear signals of population growth and bottlenecks at the genome-wide level that matched the known history of population numbers. We found a region on chromosome 15 under strong selection in three of the four populations and with our multivariate approach revealing subtle parallel changes in allele frequency in all four populations across this region. Investigating patterns of genome-wide selection in this uniquely replicated experiment offers remarkable insight into the mechanisms underlying rapid adaptation, providing a basis for comparison with other species and populations experiencing rapidly changing environments.Max Planck SocietyEuropean Research Council (ERC)Natural Environment Research Council (NERC)University of SussexUniversity of ExeterNational Science Foundation (NSF

Integrating evolution into ecological modelling: accommodating phenotypic changes in agent based models.

PMCID: PMC3733718This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Evolutionary change is a characteristic of living organisms and forms one of the ways in which species adapt to changed conditions. However, most ecological models do not incorporate this ubiquitous phenomenon. We have developed a model that takes a 'phenotypic gambit' approach and focuses on changes in the frequency of phenotypes (which differ in timing of breeding and fecundity) within a population, using, as an example, seasonal breeding. Fitness per phenotype calculated as the individual's contribution to population growth on an annual basis coincide with the population dynamics per phenotype. Simplified model variants were explored to examine whether the complexity included in the model is justified. Outputs from the spatially implicit model underestimated the number of individuals across all phenotypes. When no phenotype transitions are included (i.e. offspring always inherit their parent's phenotype) numbers of all individuals are always underestimated. We conclude that by using a phenotypic gambit approach evolutionary dynamics can be incorporated into individual based models, and that all that is required is an understanding of the probability of offspring inheriting the parental phenotype

Survival from testicular cancer in England and Wales up to 2001

www.bjcancer.com For many years testicular cancer has been the prime example of the tumour that is chemocurable, even when metastatic. The disappointment in oncology is that these results have so far not been replicated in the more common solid tumours. Why this should be is not clear but germ-cell tumours retain sensitivity to chemotherapy in vitro and a number of mechanisms including reduced DNA repair capacity and proneness to apoptosis have been proposed (Mayer et al, 2003). Most patients with testicular cancer present after finding a lump in the testicle that may or may not be painful. A small proportion of patients present with symptoms of metastatic disease. With the exception of some patients with metastatic disease, initial treatment after first assessment is to remove the tumour by inguinal orchidectomy. Patients are staged by tumour marke