Heterogeneous models place the root of the placental mammal phylogeny

Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size, and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and data set, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and data set heterogeneity have been applied to mammal data. Here, we show the impact of accurate model assignment and the importance of data sets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, data set power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root

Timing and Reconstruction of the Most Recent Common Ancestor of the Subtype C Clade of Human Immunodeficiency Virus Type 1

Human immunodeficiency virus type 1 (HIV-1) subtype C is responsible for more than 55% of HIV-1 infections worldwide. When this subtype first emerged is unknown. We have analyzed all available gag (p17 and p24) and env (C2-V3) subtype C sequences with known sampling dates, which ranged from 1983 to 2000. The majority of these sequences come from the Karonga District in Malawi and include some of the earliest known subtype C sequences. Linear regression analyses of sequence divergence estimates (with four different approaches)were plotted against sample year to estimate the year in which there was zero divergence from the reconstructed ancestral sequence. Here we suggest that the most recent common ancestor of subtype C appeared in the mid- to late 1960s. Sensitivity analyses, by which possible biases due to oversampling from one district were explored, gave very similar estimates

Dynamics of a semiconductor laser with optical feedback

We investigate both experimentally and theoretically the dynamics of a semiconductor laser with optical feedback in the low-frequency fluctuation regime. First we demonstrate that low-frequency fluctuations can be observed for both single and multimode operation of a semiconductor laser with optical feedback. The analysis of the fast dynamics associated with this low-frequency instability is well described by single-mode rate equations. In the multimode regime, fast pulsation is observed in every laser mode. In this case the fluctuations in total intensity are much smaller than those in the intensity of each individual mode, This indicates the presence of anticorrelations dynamics at high frequency between the different laser modes. (S1050-2947(99)08307-9)

Toward Open Science at the European Scale: Geospatial Semantic Array Programming for Integrated Environmental Modelling

[Excerpt] Interfacing science and policy raises challenging issues when large spatial-scale (regional, continental, global) environmental problems need transdisciplinary integration within a context of modelling complexity and multiple sources of uncertainty. This is characteristic of science-based support for environmental policy at European scale, and key aspects have also long been investigated by European Commission transnational research. Approaches (either of computational science or of policy-making) suitable at a given domain-specific scale may not be appropriate for wide-scale transdisciplinary modelling for environment (WSTMe) and corresponding policy-making. In WSTMe, the characteristic heterogeneity of available spatial information and complexity of the required data-transformation modelling (D-TM) appeal for a paradigm shift in how computational science supports such peculiarly extensive integration processes. In particular, emerging wide-scale integration requirements of typical currently available domain-specific modelling strategies may include increased robustness and scalability along with enhanced transparency and reproducibility. This challenging shift toward open data and reproducible research (open science) is also strongly suggested by the potential - sometimes neglected - huge impact of cascading effects of errors within the impressively growing interconnection among domain-specific computational models and frameworks. Concise array-based mathematical formulation and implementation (with array programming tools) have proved helpful in supporting and mitigating the complexity of WSTMe when complemented with generalized modularization and terse array-oriented semantic constraints. This defines the paradigm of Semantic Array Programming (SemAP) where semantic transparency also implies free software use (although black-boxes - e.g. legacy code - might easily be semantically interfaced). A new approach for WSTMe has emerged by formalizing unorganized best practices and experience-driven informal patterns. The approach introduces a lightweight (non-intrusive) integration of SemAP and geospatial tools - called Geospatial Semantic Array Programming (GeoSemAP). GeoSemAP exploits the joint semantics provided by SemAP and geospatial tools to split a complex D-TM into logical blocks which are easier to check by means of mathematical array-based and geospatial constraints. Those constraints take the form of precondition, invariant and postcondition semantic checks. This way, even complex WSTMe may be described as the composition of simpler GeoSemAP blocks. GeoSemAP allows intermediate data and information layers to be more easily and formally semantically described so as to increase fault-tolerance, transparency and reproducibility of WSTMe. This might also help to better communicate part of the policy-relevant knowledge, often diffcult to transfer from technical WSTMe to the science-policy interface. [...

Modal Codon Usage: Assessing the Typical Codon Usage of a Genome

Most genomes are heterogeneous in codon usage, so a codon usage study should start by defining the codon usage that is typical to the genome. Although this is commonly taken to be the genomewide average, we propose that the mode—the codon usage that matches the most genes—provides a more useful approximation of the typical codon usage of a genome. We provide a method for estimating the modal codon usage, which utilizes a continuous approximation to the number of matching genes and a simplex optimization. In a survey of bacterial and archaeal genomes, as many as 20% more of the genes in a given genome match the modal codon usage than the average codon usage. We use the mode to examine the evolution of the multireplicon genomes of Agrobacterium tumefaciens C58 and Borrelia burgdorferi B31. In A. tumefaciens, the circular and linear chromosomes are characterized by a common “chromosome-like” codon usage, whereas both plasmids share a distinct “plasmid-like” codon usage. In B. burgdorferi, in addition to different codon-usage biases on the leading and lagging strands of DNA replication found by McInerney (McInerney JO. 1998. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci USA. 95:10698–10703), we also detect a codon-usage similarity between linear plasmid lp38 and the leading strand of the chromosome and a high similarity among the cp32 family of plasmids

Probabilistic streamflow prediction and uncertainty estimation in ephemeral catchments

Conference theme 'Digital Water.'Probabilistic streamflow predictions at the daily scale are of major practical interest for environmental management and planning, including risk assessment as part of reservoir management operations. Ephemeral catchments, where streamflow is frequently zero or negligible, pose particularly stark challenges in this context, due to asymmetry of the error distribution and the discrete (rather than continuous) nature of zero flows. In this work, our focus is on two practical error modelling approaches where predictive uncertainty is approximated by a (transformed) Gaussian error model. The first approach, termed "pragmatic", does not distinguish between zero and positive flows during calibration, but sets negative flows to zero when making predictions. The second approach, termed "explicit", applies a "censored" Gaussian assumption in both calibration and prediction. We report a comparison of these two approaches over 74 Australian catchments with diverse hydroclimatology, using multiple performance metrics. The performance of the approaches depended on the catchment type as follows: (1) "mid-ephemeral" catchments, where 5-50% of days have zero flows, are best modelled using the "explicit" approach in combination with the Box-Cox streamflow transformation with a power parameter of 0.2; (2) "low-ephemeral" catchments, with fewer than 5% zero flow days, can be modelled using the pragmatic approach with (relatively) little loss of predictive performance; (3) "high-ephemeral" catchments, with more than 50% zero flow days, prove challenging to both approaches, and require more specialised techniques. The findings provide practical guidance towards improving probabilistic streamflow predictions in ephemeral catchments. Previous chapter Next chapterDmitri Kavetski, David McInerney, Mark Thyer, Julien Lerat and George Kuczer

A One Health Framework for the Evaluation of Rabies Control Programmes: A Case Study from Colombo City, Sri Lanka

<div><p>Background</p><p>One Health addresses complex challenges to promote the health of all species and the environment by integrating relevant sciences at systems level. Its application to zoonotic diseases is recommended, but few coherent frameworks exist that combine approaches from multiple disciplines. Rabies requires an interdisciplinary approach for effective and efficient management.</p><p>Methodology/Principal Findings</p><p>A framework is proposed to assess the value of rabies interventions holistically. The economic assessment compares additional monetary and non-monetary costs and benefits of an intervention taking into account epidemiological, animal welfare, societal impact and cost data. It is complemented by an ethical assessment. The framework is applied to Colombo City, Sri Lanka, where modified dog rabies intervention measures were implemented in 2007. The two options included for analysis were the control measures in place until 2006 (“baseline scenario”) and the new comprehensive intervention measures (“intervention”) for a four-year duration. Differences in control cost; monetary human health costs after exposure; Disability-Adjusted Life Years (DALYs) lost due to human rabies deaths and the psychological burden following a bite; negative impact on animal welfare; epidemiological indicators; social acceptance of dogs; and ethical considerations were estimated using a mixed method approach including primary and secondary data. Over the four years analysed, the intervention cost US $1.03 million more than the baseline scenario in 2011 prices (adjusted for inflation) and caused a reduction in dog rabies cases; 738 DALYs averted; an increase in acceptability among non-dog owners; a perception of positive changes in society including a decrease in the number of roaming dogs; and a net reduction in the impact on animal welfare from intermediate-high to low-intermediate.</p><p>Conclusions</p><p>The findings illustrate the multiple outcomes relevant to stakeholders and allow greater understanding of the value of the implemented rabies control measures, thereby providing a solid foundation for informed decision-making and sustainable control.</p></div

Levelset and B-spline deformable model techniques for image segmentation: a pragmatic comparative study

International audienceDeformable contours are now widely used in image segmentation, using different models, criteria and numerical schemes. Some theoretical comparisons between some deformable model methods have already been published. Yet, very few experimental comparative studies on real data have been reported. In this paper,we compare a levelset with a B-spline based deformable model approach in order to understand the mechanisms involved in these widely used methods and to compare both evolution and results on various kinds of image segmentation problems. In general, both methods yield similar results. However, specific differences appear when considering particular problems

Colloidal dispersion of poly ionic liquid Cu composite particles for protective surface coating against SAR CoV 2

Herein, we report a waterproof anti SARS CoV 2 protective film prepared by spray coating of an aqueous colloidal dispersion of poly ionic liquid copper PIL Cu composite nanoparticles onto a substrate. The PIL dispersion was prepared by suspension polymerization of 3 dodecyl 1 vinylimdiazolium bromide in water at 70 C. The copper acetate salt was added into the PIL nanoparticle dispersion and in situ reduced into copper nanoparticles anchoring onto the PIL nanoparticles. Despite being waterborne, the PIL in bulk is intrinsically insoluble in water and the formed coating is stable in water. The formed surface coating by PIL copper composite nanoparticles was able to deactivate SARS CoV 2 virions by 90.0 in 30 minutes and thus may effectively prevent the spread of SARS CoV 2 through surface contact. This method may provide waterborne dispersions for a broad range of antivirus protective surface coatings for both outdoor and indoor application

Why honey is effective as a medicine. 1. Its use in modern medicine

Honey has been used as a medicine for thousands of years and its curative properties are well documented. However, modern medicine turned its back on honey and it is only now, with the advent of multi-resistant bacteria, that the antibiotic properties of honey are being rediscovered