BOOTSIE – ESTIMATION OF COEFFICIENT OF VARIATION OF AFLP DATA BY BOOTSTRAP ANALYSIS

Bootsie is an English-native replacement for ASG Coelho\u27s “DBOOT” utility for estimating coefficient of variation of a population of AFLP marker data using bootstrapping. Bootsie improves on DBOOT by supporting batch processing, time-to-completion estimation, builtin graphs, and a suite of export tools for creating data files for other population genetics software

Improvements in environmental performance of agriculture correlate with investments in agri-environment schemes (AES).

<p>Temporal trend in (<b>A</b>) farmland bird populations and (<b>B</b>) GHG emissions from synthetic fertiliser were calculated over time for each country using Kendall’s <i>τ</i> (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002242#pbio.1002242.s005" target="_blank">S1 Text</a> for full methods). Investments in AES were scaled by the ratio of investments in AES relative to financial transfers to agricultural producers for all other purposes so as to account for the fact that environmental improvements can be offset by policies that maximise production. Values were then summed across 5-y periods with a pre-emptive 2-y lag for land retirement. Habitat quality will take at least one growing season to improve following land retirement and any changes in bird populations from improved breeding success will thus largely be measurable the following year, i.e., two years later [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002242#pbio.1002242.ref087" target="_blank">87</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002242#pbio.1002242.ref088" target="_blank">88</a>]. Spearman’s rank correlation: <i>ρ</i> = 0.95, <i>p</i> = 0.005 and <i>ρ</i> = -0.93, <i>p</i> = 0.008 for (<b>A</b>) and (<b>B</b>), respectively. Points are responses in individual countries: AU = Australia [data available for (<b>B</b>) only], CA = Canada, EU (aggregated together), NO = Norway, CH = Switzerland, and US. Data used to make this figure are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002242#pbio.1002242.s001" target="_blank">S1 Data</a>.</p

Financial support to farmers from taxpayers and consumers associated with agricultural policies as a proportion of the total value of agricultural production (VoP) at the farm gate.

<p>We distinguished between policies aiming to achieve specific environmental objectives beyond those required by regulation (purple segments) and all other types of support irrespective of their influence on farm production or income (orange segments), e.g., market price support, monetary transfers based on output, input subsidies. Sizes of symbols were scaled to VoP in hundreds of millions of United States dollars. Data are from the most recent year available (2008–2013) and described in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002242#pbio.1002242.s005" target="_blank">S1 Text</a>. Green and brown shading in the background is the percent of cropland and pasture at 5’ resolution in the year 2000 [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002242#pbio.1002242.ref007" target="_blank">7</a>]. Financial support data were preferentially sourced from the Organisation for Economic Cooperation and Development (OECD) (<i>n</i> = 21 countries), supplemented from the World Trade Organization (WTO) where possible for additional countries (<i>n</i> = 12). Data used to make this figure are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002242#pbio.1002242.s001" target="_blank">S1 Data</a>.</p

Resolving Conflicts between Agriculture and the Natural Environment

<div><p>Agriculture dominates the planet. Yet it has many environmental costs that are unsustainable, especially as global food demand rises. Here, we evaluate ways in which different parts of the world are succeeding in their attempts to resolve conflict between agriculture and wild nature. We envision that coordinated global action in conserving land most sensitive to agricultural activities and policies that internalise the environmental costs of agriculture are needed to deliver a more sustainable future.</p></div

Additional file 3: of Standard and competing risk analysis of the effect of albuminuria on cardiovascular and cancer mortality in patients with type 2 diabetes mellitus

Figure S1. Proportional cause-specific hazards assessment cardiovascular mortality. (PDF 1874 kb

Successes associated with different policy approaches and the local¹ obstacles to their implementation.

<p>¹Globally, the major obstacle for all approaches is to avoid displacing production and causing environmental degradation elsewhere.</p><p>Successes associated with different policy approaches and the local<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002242#t001fn001" target="_blank">¹</a> obstacles to their implementation.</p

Additional file 1: of Standard and competing risk analysis of the effect of albuminuria on cardiovascular and cancer mortality in patients with type 2 diabetes mellitus

Table S1. Adjusted estimates for the effect of baseline risk factors on cardiovascular mortality from Cox-PH, Lunn-McNeil and Fine-Gray Models. (DOCX 15 kb

Additional file 4: of Standard and competing risk analysis of the effect of albuminuria on cardiovascular and cancer mortality in patients with type 2 diabetes mellitus

Figure S2. Proportional cause-specific hazards assessment for cancer mortality. (PDF 1233 kb

Estimated numbers of threatened species negatively impacted by agriculture.

<p>We counted the total number of species classified as either critically endangered, endangered, or vulnerable by the IUCN Red List in different taxonomic units and the number that were assessed to be threatened by at least one agricultural activity [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002242#pbio.1002242.ref011" target="_blank">11</a>]. Agricultural activities were annual and perennial nontimber crops, wood and pulp plantations, livestock farming and ranching, logging and wood harvesting, abstracting of surface water (agricultural use), abstraction of ground water (agricultural use), and agricultural and forestry effluents. Many other species may become threatened with agricultural expansion (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002242#pbio.1002242.s003" target="_blank">S2 Fig</a>).</p

Additional file 2: of Standard and competing risk analysis of the effect of albuminuria on cardiovascular and cancer mortality in patients with type 2 diabetes mellitus

Table S2. Adjusted estimates for the effect of baseline risk factors on cancer mortality from Cox-PH, Lunn-McNeil and Fine-Gray Models. (DOCX 15 kb