Codon-based analysis of selection pressure and genetic structure in the Psammobates tentorius (Bell, 1828) species complex, and phylogeny inferred from both codons and amino acid sequences

This study used codon analysis (dN/dS and Tv/Ti) to investigate selection pressure and genetic structure in the highly polymorphic Psammobates tentorius species complex, and amino acid sequences to construct a phylogeny tree for it. Our results revealed a strong selection signal at node ‘C2 + C3’, possibly driven by aridity intensification resulting from the development of the Benguela Current. A similar signal was noticed at C3, possibly due to the same driving force. These findings suggest that environmental selection pressure favoured those groups and that further cladogenic events were possible. Selection pressure was also found to be high at C1, C4 and C7, which may indicate that they are also favoured by the current selection pressure. The codon-based phylogeny did not retrieve any potentially undescribed species, but nonetheless provided support for the validity of the seven distinct clades retrieved with the DNA sequence data. The amino acid sequence-based phylogeny generally supported the seven lineages as valid putative species. Investigation at the genomic scale could, however, help to solve the issue. In general, we found the codon, dN, dS, Tv, Ti and amino acid sequence-based phylogenetic inferences useful in species delimitation and recommend their use in species delimitation studies

Haulout site selection by southern elephant seals at Marion Island

Using data from an ongoing mark-resight programme at Marion Island, we tested empirically whether southern elephant seals prefer certain terrestrial sites to others during the breeding, moulting and winter haulouts, and whether the pattern of site use is the same for different age and sex groups. Southern elephant seals preferred some sites, while discriminating against other sites, with different age and sex classes using different sites for certain haulout events. Wintering young animals did not show strong site selection. Some popular sites were used for all haulouts by all age and sex groups, and apparently have all the requirements of a good site for terrestrial haulout by southern elephant seals. Site selection becomes more apparent with age, suggesting the role of haulout experience in site selection

Formative research to design an implementation strategy for a postpartum hemorrhage initial response treatment bundle (E-MOTIVE): study protocol

BACKGROUND: Postpartum hemorrhage (PPH) is the leading cause of maternal death worldwide. When PPH occurs, early identification of bleeding and prompt management using evidence-based guidelines, can avert most PPH-related severe morbidities and deaths. However, adherence to the World Health Organization recommended practices remains a critical challenge. A potential solution to inefficient and inconsistent implementation of evidence-based practices is the application of a ‘clinical care bundle’ for PPH management. A clinical care bundle is a set of discrete, evidence-based interventions, administered concurrently, or in rapid succession, to every eligible person, along with teamwork, communication, and cooperation. Once triggered, all bundle components must be delivered. The E-MOTIVE project aims to improve the detection and first response management of PPH through the implementation of the “E-MOTIVE” bundle, which consists of (1) Early PPH detection using a calibrated drape, (2) uterine Massage, (3) Oxytocic drugs, (4) Tranexamic acid, (5) Intra Venous fluids, and (6) genital tract Examination and escalation when necessary. The objective of this paper is to describe the protocol for the formative phase of the E-MOTIVE project, which aims to design an implementation strategy to support the uptake of this bundle into practice. METHODS: We will use behavior change and implementation science frameworks [e.g. capability, opportunity, motivation and behavior (COM-B) and theoretical domains framework (TDF)] to guide data collection and analysis, in Kenya, Nigeria, South Africa, Sri Lanka, and Tanzania. There are four methodological components: qualitative interviews; surveys; systematic reviews; and design workshops. We will triangulate findings across data sources, participant groups, and countries to explore factors influencing current PPH detection and management, and potentially influencing E-MOTIVE bundle implementation. We will use these findings to develop potential strategies to improve implementation, which will be discussed and agreed with key stakeholders from each country in intervention design workshops. DISCUSSION: This formative protocol outlines our strategy for the systematic development of the E-MOTIVE implementation strategy. This focus on implementation considers what it would take to support roll-out and implementation of the E-MOTIVE bundle. Our approach therefore aims to maximize internal validity in the trial alongside future scalability, and implementation of the E-MOTIVE bundle in routine practice, if proven to be effective. TRIAL REGISTRATION: ClinicalTrials.gov: NCT0434166

Alternative Strategies to Reduce Maternal Mortality in India: A Cost-Effectiveness Analysis

A cost-effectiveness study by Sue Goldie and colleagues finds that better family planning, provision of safe abortion, and improved intrapartum and emergency obstetrical care could reduce maternal mortality in India by 75% in 5 years

Living in Living Cities

This paper presents an overview of current and potential applications of living technology to some urban problems. Living technology can be described as technology that exhibits the core features of living systems. These features can be useful to solve dynamic problems. In particular, urban problems concerning mobility, logistics, telecommunications, governance, safety, sustainability, and society and culture are presented, while solutions involving living technology are reviewed. A methodology for developing living technology is mentioned, while supraoptimal public transportation systems are used as a case study to illustrate the benefits of urban living technology. Finally, the usefulness of describing cities as living systems is discussed.Comment: 40 pages, 4 figures, overview pape

Inferring the conservative causal core of gene regulatory networks

<p>Abstract</p> <p>Background</p> <p>Inferring gene regulatory networks from large-scale expression data is an important problem that received much attention in recent years. These networks have the potential to gain insights into causal molecular interactions of biological processes. Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically.</p> <p>Results</p> <p>In this paper, we introduce a novel gene regulatory network inference (GRNI) algorithm, called C3NET. We compare C3NET with four well known methods, ARACNE, CLR, MRNET and RN, conducting in-depth numerical ensemble simulations and demonstrate also for biological expression data from <it>E. coli </it>that C3NET performs consistently better than the best known GRNI methods in the literature. In addition, it has also a low computational complexity. Since C3NET is based on estimates of mutual information values in conjunction with a maximization step, our numerical investigations demonstrate that our inference algorithm exploits causal structural information in the data efficiently.</p> <p>Conclusions</p> <p>For systems biology to succeed in the long run, it is of crucial importance to establish methods that extract large-scale gene networks from high-throughput data that reflect the underlying causal interactions among genes or gene products. Our method can contribute to this endeavor by demonstrating that an inference algorithm with a neat design permits not only a more intuitive and possibly biological interpretation of its working mechanism but can also result in superior results.</p

Inferring the conservative causal core of gene regulatory networks

<p>Abstract</p> <p>Background</p> <p>Inferring gene regulatory networks from large-scale expression data is an important problem that received much attention in recent years. These networks have the potential to gain insights into causal molecular interactions of biological processes. Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically.</p> <p>Results</p> <p>In this paper, we introduce a novel gene regulatory network inference (GRNI) algorithm, called C3NET. We compare C3NET with four well known methods, ARACNE, CLR, MRNET and RN, conducting in-depth numerical ensemble simulations and demonstrate also for biological expression data from <it>E. coli </it>that C3NET performs consistently better than the best known GRNI methods in the literature. In addition, it has also a low computational complexity. Since C3NET is based on estimates of mutual information values in conjunction with a maximization step, our numerical investigations demonstrate that our inference algorithm exploits causal structural information in the data efficiently.</p> <p>Conclusions</p> <p>For systems biology to succeed in the long run, it is of crucial importance to establish methods that extract large-scale gene networks from high-throughput data that reflect the underlying causal interactions among genes or gene products. Our method can contribute to this endeavor by demonstrating that an inference algorithm with a neat design permits not only a more intuitive and possibly biological interpretation of its working mechanism but can also result in superior results.</p

Spatial variability in sustainable development trajectories in South Africa:provincial level safe and just operating spaces

The Sustainable Development Goals (SDGs) represents the first globally agreed framework to address human development and environmental stewardship in an integrated way. One approach to summarising national SDG status is our “barometer for inclusive sustainable development in South Africa”. The barometer downscales global social and planetary boundaries to provide status and trends for 20 critical indicators of environmental stress and social deprivation. In this paper, we explore the sub-national heterogeneity in sustainable development indicators by creating barometers defining the ‘safe and just operating space’ for South Africa’s nine provinces. Our results show that environmental stress varies significantly and provinces need to focus on quite different issues. Although generally environmental stress is increasing, there are areas where it is decreasing, most notably, marine harvesting. Social deprivation results show more of a pattern with high levels of deprivation in employment, income and safety across the provinces, and historically disadvantaged provinces showing the most deprivation overall. Although deprivation is generally decreasing, there are notable exceptions such as food security in six provinces. Our provincial barometers and trend plots are novel in that they present comparable environmental and social data on key indicators over time for all South Africa’s provinces. They are visual tools that communicate the range of key challenges and risks that provincial governments face, and are non-specialist and accessible to a range of audiences. In addition, the paper provides a critical case study of spatial disaggregation of national data that is required for the SDGs implementation

Impact of increasing capacity for generating and using research on maternal and perinatal health practices in South East Asia (SEA-ORCHID Project)

Writing committee: P. Lumbiganon, S. J. McDonald, M. Laopaiboon, T. Turner, S. Green, C. A. Crowther. The SEA-ORCHID Study Group consists of: Pisake Lumbiganon, Mario Festin, Jacqueline Ho, Hakimi Mohammad, David Henderson-Smart, Sally Green and Caroline Crowther. Educators and Fellows. AUSTRALIA: Jacki Short, Tari Turner, Ruth MartisBackground: Maternal and neonatal mortality and morbidity remain unacceptably high in many low and middle income countries. SEA-ORCHID was a five year international collaborative project in South East Asia which aimed to determine whether health care and health outcomes for mothers and babies could be improved by developing capacity for research generation, synthesis and use. Methods: Nine hospitals in Indonesia, Malaysia, the Philippines and Thailand participated in SEA-ORCHID. These hospitals were supported by researchers from three Australian centres. Health care practices and outcomes were assessed for 1000 women at each hospital both before and after the intervention. The capacity development intervention was tailored to the needs and context of each hospital and delivered over an 18 month period. Main outcomes included adherence to forms of care likely to be beneficial and avoidance of forms of care likely to be ineffective or harmful. Results: We observed substantial variation in clinical practice change between sites. The capacity development intervention had a positive impact on some care practices across all countries, including increased family support during labour and decreased perineal shaving before birth, but in some areas there was no significant change in practice and a few beneficial practices were followed less often. Conclusion: The results of SEA-ORCHID demonstrate that investing in developing capacity for research use, synthesis and generation can lead to improvements in maternal and neonatal health practice and highlight the difficulty of implementing evidence-based practice change.The SEA-ORCHID Study Group... [C. A. Crowther... Ruth Martis...