Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation

BACKGROUND: Experimental populations of Escherichia coli have evolved for 20,000 generations in a uniform environment. Their rate of improvement, as measured in competitions with the ancestor in that environment, has declined substantially over this period. This deceleration has been interpreted as the bacteria approaching a peak or plateau in a fitness landscape. Alternatively, this deceleration might be caused by non-transitive competitive interactions, in particular such that the measured advantage of later genotypes relative to earlier ones would be greater if they competed directly. RESULTS: To distinguish these two hypotheses, we performed a large set of competitions using one of the evolved lines. Twenty-one samples obtained at 1,000-generation intervals each competed against five genetically marked clones isolated at 5,000-generation intervals, with three-fold replication. The pattern of relative fitness values for these 315 pairwise competitions was compared with expectations under transitive and non-transitive models, the latter structured to produce the observed deceleration in fitness relative to the ancestor. In general, the relative fitness of later and earlier generations measured by direct competition agrees well with the fitness inferred from separately competing each against the ancestor. These data thus support the transitive model. CONCLUSION: Non-transitive competitive interactions were not a major feature of evolution in this population. Instead, the pronounced deceleration in its rate of fitness improvement indicates that the population early on incorporated most of those mutations that provided the greatest gains, and subsequently relied on beneficial mutations that were fewer in number, smaller in effect, or both

National medicines policies – a review of the evolution and development processes

OBJECTIVES: Continuous provision of appropriate medicines of assured quality, in adequate quantities, and at reasonable prices is a concern for all national governments. A national medicines policy (NMP) developed in a collaborative fashion identifies strategies needed to meet these objectives and provides a comprehensive framework to develop all components of a national pharmaceutical sector. To meet the health needs of the population, there is a general need for medicine policies based on universal principles, but nevertheless adapted to the national situation. This review aims to provide a quantitative and qualitative (describing the historical development) study of the development process and evolution of NMPs. METHODS: The number of NMPs and their current status has been obtained from the results of the assessment of WHO Level I indicators. The policy formulation process is examined in more detail with case studies from four countries: Sri Lanka, Australia, former Yugoslav Republic of Macedonia and South Africa. RESULTS: The number of NMPs worldwide has increased in the last 25 years with the highest proportional increase in the last 5–10 years in high-income countries. Higher income countries seem to have more NMP implementation plans available and have updated their NMP more recently. The four case studies show that the development of a NMP is a complex process that is country specific. In addition, it demonstrates that an appropriate political window is needed for the policy to be passed (for South Africa and the FYR Macedonia, a major political event acted as a trigger for initiating the policy development). Policy-making does not stop with the official adoption of a policy but should create mechanisms for implementation and monitoring. The NMPs of the FYR Macedonia and Australia provide indicators for monitoring. CONCLUSIONS: To date, not all countries have a NMP since political pressure by national experts or non-governmental organizations is generally needed to establish a NMP. Case studies in four countries showed that the policy process is just as important as the policy document since the process must create a mechanism by which all stakeholders are brought together and a sense of collective ownership of the final policy may be achieved

All functions are (locally) ss-harmonic (up to a small error) - and applications

The classical and the fractional Laplacians exhibit a number of similarities, but also some rather striking, and sometimes surprising, structural differences. A quite important example of these differences is that any function (regardless of its shape) can be locally approximated by functions with locally vanishing fractional Laplacian, as it was recently proved by Serena Dipierro, Ovidiu Savin and myself. This informal note is an exposition of this result and of some of its consequences

Transparent reporting of multivariable prediction models developed or validated using clustered data: TRIPOD-Cluster checklist

The increasing availability of large combined datasets (or big data), such as those from electronic health records and from individual participant data meta-analyses, provides new opportunities and challenges for researchers developing and validating (including updating) prediction models. These datasets typically include individuals from multiple clusters (such as multiple centres, geographical locations, or different studies). Accounting for clustering is important to avoid misleading conclusions and enables researchers to explore heterogeneity in prediction model performance across multiple centres, regions, or countries, to better tailor or match them to these different clusters, and thus to develop prediction models that are more generalisable. However, this requires prediction model researchers to adopt more specific design, analysis, and reporting methods than standard prediction model studies that do not have any inherent substantial clustering. Therefore, prediction model studies based on clustered data need to be reported differently so that readers can appraise the study methods and findings, further increasing the use and implementation of such prediction models developed or validated from clustered datasets

Transparent reporting of multivariable prediction models developed or validated using clustered data (TRIPOD-Cluster): explanation and elaboration

The TRIPOD-Cluster (transparent reporting of multivariable prediction models developed or validated using clustered data) statement comprises a 19 item checklist, which aims to improve the reporting of studies developing or validating a prediction model in clustered data, such as individual participant data meta-analyses (clustering by study) and electronic health records (clustering by practice or hospital). This explanation and elaboration document describes the rationale; clarifies the meaning of each item; and discusses why transparent reporting is important, with a view to assessing risk of bias and clinical usefulness of the prediction model. Each checklist item of the TRIPOD-Cluster statement is explained in detail and accompanied by published examples of good reporting. The document also serves as a reference of factors to consider when designing, conducting, and analysing prediction model development or validation studies in clustered data. To aid the editorial process and help peer reviewers and, ultimately, readers and systematic reviewers of prediction model studies, authors are recommended to include a completed checklist in their submission

The Poison Pen: Bedside Diagnosis of Urinary Diquat

Diquat is a bipyridyl herbicide with nephrotoxic effects. This in vitro study demonstrates a colorimetric test for detection of diquat in human urine. Urine specimens using ten concentrations of diquat herbicide solution and controls for urine and glyphosate were prepared. A two-step assay (addition of bicarbonate followed by sodium dithionite) was performed, with a resulting color change of the original solution for each specimen. Color change intensity was noted immediately and after 30 min, by gross visual inspection. A green color with concentration-dependent intensity was detected in all specimens, in which concentrations of diquat solution ranged from 0.73 to 730 mg/L. This colorimetric effect disappeared after 30 min. The sodium bicarbonate/dithionite test may be useful as a qualitative bedside technique for the detection of urinary diquat in the appropriate clinical setting

Detection of Lyman-alpha Emitting Galaxies at Redshift z=4.55

Studies of the formation and early history of galaxies have been hampered by the difficulties inherent in detecting faint galaxy populations at high redshift. As a consequence, observations at the highest redshifts (3.5 < z < 5) have been restricted to objects that are intrinsically bright. These include quasars, radio galaxies, and some Ly alpha-emitting objects that are very close to (within ~10 kpc) -- and appear to be physically associated with -- quasars. But the extremely energetic processes which make these objects easy to detect also make them unrepresentative of normal (field) galaxies. Here we report the discovery using Keck spectroscopic observations of two Ly alpha-emitting galaxies at redshift z = 4.55, which are sufficiently far from the nearest quasar (~700 kpc) that radiation from the quasar is unlikely to provide the excitation source of the Ly alpha emission. Instead, these galaxies appear to be undergoing their first burst of star formation, at a time when the Universe was less than one billion years old.Comment: 8 pages, 1 landscape table, and 3 PostScript figures. Uses aaspp4.sty, flushrt.sty, aj_pt4.sty, overcite.sty (style macros available from xxx.lanl.gov) Figure 1 is bitmapped to 100 dpi. The original PostScript version of Fig. 1 is available via anonymous ftp to ftp://hubble.ifa.hawaii.edu/pub/preprints To appear in Natur

Effect of the economic recession on pharmaceutical policy and medicine sales in eight European countries

Abstract Objective: To identify pharmaceutical policy changes during the economic recession in eight European countries and to determine whether policy measures resulted in lower sales of, and less expenditure on, pharmaceuticals. Methods: Information on pharmaceutical policy changes between 2008 and 2011 in eight European countries was obtained from publications and pharmaceutical policy databases. Data on the volume and value of the quarterly sales of products between 2006 and 2011 in the 10 highest-selling therapeutic classes in each country were obtained from a pharmaceutical market research database. We compared these indicators in economically stable countries; Austria, Estonia and Finland, to those in economically less stable countries, Greece, Ireland, Portugal, Slovakia and Spain. Findings: Economically stable countries implemented two to seven policy changes each, whereas less stable countries implemented 10 to 22 each. Of the 88 policy changes identified, 33 occurred in 2010 and 40 in 2011. They involved changing out-of-pocket payments for patients in 16 cases, price mark-up schemes in 13 and price cuts in 11. Sales volumes increased moderately in all countries except Greece and Portugal, which experienced slight declines after 2009. Sales values decreased in both groups of countries, but fell more in less stable countries. Conclusion: Less economically stable countries implemented more pharmaceutical policy changes during the recession than economically stable countries. Unexpectedly, pharmaceutical sales volumes increased in almost all countries, whereas sales values declined, especially in less stable countries