Plant conservation legislation and policy in Scotland

Summary

There is a range of legislation and policy relating to plant conservation in Scotland, including international, European and domestic measures (Scottish Office, 1998). There are, in addition, opportunities and challenges for plant conservation as a result of devolution. This paper reviews examples taken from the range of current policies and laws to illustrate both where these have been beneficial and where they have not been so successful for plant conservation, and offers some views on what lessons have been learnt from these actions.     

Organizational responses to new ocean science and technology developments

Abstract

Rapid developments in ocean science and technology, together with the emerging new ocean regime, present considerable challenges to the international organizational structure. After indicating some recent ocean science and technology developments, the author examines the capacity for organizational response, both within and outside the UN system. Next, the paper identifies aspects of national ocean interests that tend to dictate policies of individual nations toward the responses of these international organizations to new advances. Finally, the author looks to prospects for the 1980s.     

Indices of national interest in the oceans

Abstract

Each of the 148 independent States of the world has a particular set of interests in the oceans; these interests are reflected in policies regarding the international law of the sea. By analyzing the nature of national marine interests it is possible both to develop a generalized model which can be applied to any one of the world's countries, and to divide States into groupings, depending on their physical, economic, historic or other characteristics with respect to the marine environment. The four basic components of the national marine interest are accessibility, investment, dependence and control. These components are important to an understanding of the positions of the 30 land‐locked, 20 shelf‐locked and 98 other countries in current and upcoming law of the sea negotiations.     

Identifying important bird habitats in a sub-arctic area undergoing rapid land-use change

Capsule Habitats in lowland South Iceland sustain bird populations of international importance, with highest densities in wet habitats.

Aims In areas important for biodiversity there is an urgent need to assess large-scale variation in the biodiversity value of habitats to inform management. We carried out a large-scale survey to assess the conservation value of sub-arctic, Icelandic bird habitats.

Methods Bird counts were carried out on 200 transects in the five most common vegetated habitat types in South Iceland. Based on these counts, breeding bird density and diversity were compared between habitats and total population sizes of common species in these habitats were calculated.

Results Overall, eight species (seven waders and Meadow Pipit) composed over 95% of all birds counted. The combined density of those species exceeded 275 birds/km² in all habitats. The two wettest habitat types had the highest density of birds.

Conclusion Wet habitats in lowland South Iceland held particularly high densities of breeding birds, notably waders, which constitute populations of international importance. Wet habitat types are generally of higher value for more species, than dryer ones.     

Genomic duplication problems for unrooted gene trees

Background

Discovering the location of gene duplications and multiple gene duplication episodes is a fundamental issue in evolutionary molecular biology. The problem introduced by Guigó et al. in 1996 is to map gene duplication events from a collection of rooted, binary gene family trees onto theirs corresponding rooted binary species tree in such a way that the total number of multiple gene duplication episodes is minimized. There are several models in the literature that specify how gene duplications from gene families can be interpreted as one duplication episode. However, in all duplication episode problems gene trees are rooted. This restriction limits the applicability, since unrooted gene family trees are frequently inferred by phylogenetic methods.

Results

In this article we show the first solution to the open problem of episode clustering where the input gene family trees are unrooted. In particular, by using theoretical properties of unrooted reconciliation, we show an efficient algorithm that reduces this problem into the episode clustering problems defined for rooted trees. We show theoretical properties of the reduction algorithm and evaluation of empirical datasets.

Conclusions

We provided algorithms and tools that were successfully applied to several empirical datasets. In particular, our comparative study shows that we can improve known results on genomic duplication inference from real datasets.

     

The new system of review by multicentre research ethics committees: prospective study

ObjectiveTo assess the function of the new system of review by multicentre research ethics committees and to highlight areas where improvement is still needed.DesignProspectively collected data from a multicentre study was examined with respect to the ethics review process. Administrative, financial, and time elements of the review process were audited.SettingA single multicentre research ethics committee and 125 local ethics committees from six regions of England.ResultsOnly 40% of local ethics committees considered our study in the manner specified in the 1998 directive. Less than a third of committees replied within the 21 day period stipulated, although committees acting by executive subcommittee replied more quickly than those not acting by executive subcommittee. There was a tendency for executive subcommittees to approve studies in a shorter time. Local ethics committees asked for a large number of non-local changes to the application. The financial cost of applying to multiple ethics committees remains high, mainly because multiple copies of research applications are being requested.ConclusionsThe new system of approval by multicentre research ethics committee for multicentre studies was introduced to reduce administrative costs, speed up the process of reviews by multiple research ethics committees, and standardise the conclusions of the local research ethics committees. Since its introduction an improvement has been seen, but the system is not yet universally functioning as intended. Ethics review still remains a hindrance to the financial resources and commencement of national studies. We strongly support the structure of review by multicentre research ethics committees but suggest that the system has yet to achieve its aims.     

PREVENTION-ACHD: PRospEctiVE study on implaNTable cardioverter-defibrillator therapy and suddeN cardiac death in Adults with Congenital Heart Disease; Rationale and Design

Background

Many adult congenital heart disease (ACHD) patients are at risk of sudden cardiac death (SCD). An implantable cardioverter-defibrillator (ICD) may prevent SCD, but the evidence for primary prevention indications is still unsatisfactory.

Study Design

PREVENTION-ACHD is a prospective study with which we aim to prospectively validate a new risk score model for primary prevention of SCD in ACHD patients, as well as the currently existing guideline recommendations. Patients are screened using a novel risk score to predict SCD as well as current ICD indications according to an international Consensus Statement. Patients are followed up for two years. The primary endpoint is the occurrence of SCD and sustained ventricular arrhythmias. The Study was registered at ClinicalTrials.gov (NCT03957824).

Conclusion

PREVENTION-ACHD is the first prospective study on SCD in ACHD patients. In the light of a growing and aging population of patients with more severe congenital heart defects, more robust clinical evidence on primary prevention of SCD is urgently needed.

     

Scotlands threatened mires and mosses: Policies to protect the peatlands of caithness and sutherland

Summary

Scottish peatlands have suffered loss and damage for centuries through cutting for fuel and agricultural and forestry practices. The ombrogenous blanket mires of Caithness and Sutherland (the ‘Flow Country’) are of international importance for the range and quality of their peatland types and vegetation, and their breeding bird populations. Loss of this habitat in the last decade, due to rapid expansion of forestry, caused great concern which was expressed by voluntary and statutory nature conservation organizations and the national media. Government at both national and local levels responded with changes in forestry policies, protection of large areas of peatland and by a land-use strategy which divides the area into four forestry policy zones.     

Abstracts from the 2018 Respiratory Effectiveness Group Summit

Background

Genetic and environmental factors play a role in the development of COPD. The epigenome, and more specifically DNA methylation, is recognized as important link between these factors. We postulate that DNA methylation is one of the routes by which cigarette smoke influences the development of COPD. In this study, we aim to identify CpG-sites that are associated with cigarette smoke exposure and lung function levels in whole blood and validate these CpG-sites in lung tissue.

Methods

The association between pack years and DNA methylation was studied genome-wide in 658 current smokers with >5 pack years using robust linear regression analysis. Using mediation analysis, we subsequently selected the CpG-sites that were also associated with lung function levels. Significant CpG-sites were validated in lung tissue with pyrosequencing and expression quantitative trait methylation (eQTM) analysis was performed to investigate the association between DNA methylation and gene expression.

Results

15 CpG-sites were significantly associated with pack years and 10 of these were additionally associated with lung function levels. We validated 5 CpG-sites in lung tissue and found several associations between DNA methylation and gene expression.

Conclusion

This study is the first to validate a panel of CpG-sites that are associated with cigarette smoking and lung function levels in whole blood in the tissue of interest: lung tissue.

     

Immaculate conceptions in sub‐Saharan Africa: Exploratory analysis of inconsistencies in the timing of first sexual intercourse and first birth

Abstract

Survey data from a number of developing countries show that a considerable proportion of parous women report that they had their first birth one or more years before they first had sexual intercourse. In this paper, I use data from eight African Demographic and Health Surveys to explore factors that contribute to cross‐national differentials in the prevalence of these “immaculate conceptions.” The results suggest that this data problem results not only from recall errors, but also from the fact that some respondents misinterpret the question on first sexual intercourse and report their age at the onset of intercourse with either their first or current husband rather than their age at sexual initiation.     

An economic analysis of the international transfer of marine technology

Abstract

This paper develops a general economic framework for the analysis of international technology transfer, provides an analysis and categorization of countries, and concludes with a case study on the Peruvian fish‐meal industry.

The economic framework focuses upon the impact of technology transfer on the resource allocation choices of a country and the analytical techniques or models available to facilitate the making of these choices. The optimization of investment is first considered and then the discussion is broadened to include the concepts of an efficient technology frontier and a social‐welfare function. The paper also dwells upon cost‐benefit analysis and other measurement techniques relevant to technology transfer and social‐choice considerations. A categorization of countries, using several indicators, is then attempted with need, potential, and interest as the determining parameters.

Finally, the Peruvian fish‐meal industry is considered as a case study with the theoretical arguments developed earlier applied to it.     

Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty

Background

Biological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost importance since it uncovers how a network evolves and how it resists to external stimuli and internal variations. Two temporal networks have co-evolving subnetworks if the evolving topologies of these subnetworks remain similar to each other as the network topology evolves over a period of time. In this paper, we consider the problem of identifying co-evolving subnetworks given a pair of temporal networks, which aim to capture the evolution of molecules and their interactions over time. Although this problem shares some characteristics of the well-known network alignment problems, it differs from existing network alignment formulations as it seeks a mapping of the two network topologies that is invariant to temporal evolution of the given networks. This is a computationally challenging problem as it requires capturing not only similar topologies between two networks but also their similar evolution patterns.

Results

We present an efficient algorithm, Tempo, for solving identifying co-evolving subnetworks with two given temporal networks. We formally prove the correctness of our method. We experimentally demonstrate that Tempo scales efficiently with the size of network as well as the number of time points, and generates statistically significant alignments—even when evolution rates of given networks are high. Our results on a human aging dataset demonstrate that Tempo identifies novel genes contributing to the progression of Alzheimer’s, Huntington’s and Type II diabetes, while existing methods fail to do so.

Conclusions

Studying temporal networks in general and human aging specifically using Tempo enables us to identify age related genes from non age related genes successfully. More importantly, Tempo takes the network alignment problem one huge step forward by moving beyond the classical static network models.

     

The domestic context of Brazilian maritime policy

Abstract

The domestic context of Brazil's emerging maritime policy is discussed from three perspectives. Basic national policy guidelines are examined first, with particular attention given to their, influence in shaping maritime policy. Bureaucratic politics has shaped, and been shaped by, these guidelines, and is examined in a subsequent section. International politics, too, has played an important role in shaping Brazilian maritime policy, and its relationship to the domestic context is explored in a final section. The crucial decision to extend the territorial sea to 200 mi in 1970, including its historical background and aftermath, illustrates these forces shaping maritime policy. Other maritime issues are analyzed to illustrate these forces when relevant.

It is acknowledged that Brazil's prominent position in the South Atlantic has not led it to become a maritime‐oriented state. Increasing efforts have nevertheless been made during the past decade to utilize ocean space and the resources of the sea for national policy ends. As Brazilian maritime policy gained cohesiveness and dynamism in the late 1960s and 1970s, it became complementary to national economic progress and increasingly involved in international economic and political questions.     

The integration of long-term marginal electricity supply mixes in the ecoinvent consequential database version 3.4 and examination of modeling choices

Purpose

The long-term marginal electricity supply mixes of 40 countries were generated and integrated into version 3.4 of the ecoinvent consequential database. The total electricity production originating from these countries accounts for 77% of the current global electricity generation. The goal of this article is to provide an overview of the methodology used to calculate the marginal mixes and to evaluate the influence of key parameters and methodological choices on the results.

Methods

The marginal mixes are based on public energy projections from national and international authorities and reflect the accumulated effect of changes in demand for electricity on the installation and operation of new-generation capacities. These newly generated marginal mixes are first examined in terms of their compositions and environmental impacts. They are then compared to several sets of alternative electricity supply mixes calculated using different methodological choices or data sources.

Results and discussion

Renewable energy sources (RES) as well as natural gas power plants show the highest growth rates and usually dominate the marginal mixes. Nevertheless, important variations may exist between the marginal mixes of the different countries in terms of their technological compositions and environmental impacts. The examination of the modeling choices reveals substantial variations between the marginal mixes integrated into the ecoinvent consequential database version 3.4 and marginal mixes generated using alternative modeling options. These different modeling possibilities include changes in the methodology, temporal parameters, and the underlying energy scenarios. Furthermore, in most of the impact categories, average (i.e., attributional) mixes cause higher impact scores than marginal mixes due to higher shares of RES in marginal mixes.

Conclusions

Accurate and consistent data for electricity supply is integrated into a consequential database providing a strong basis for the development of consequential Life Cycle Assessments. The methodology adopted in this version of the database eliminates several shortcomings from the previous approach which led to unrealistic marginal mixes in several countries. The use of energy scenarios allows the evolution of the electricity system to be considered within the definition of the marginal mixes. The modeling choices behind the electricity marginal mix should be adjusted to the goal and scope of individual studies and their influence on the results evaluated.

     

Energy simulation and LCA for macro-scale analysis of eco-innovations in the housing stock

Purpose

Energy consumption of buildings is one of the major drivers of environmental impacts. Life cycle assessment (LCA) may support the assessment of burdens and benefits associated to eco-innovations aiming at reducing these environmental impacts. Energy efficiency policies however typically focus on the meso- or macro-scale, while interventions are typically taken at the micro-scale. This paper presents an approach that bridges this gap by using the results of energy simulations and LCA studies at the building level to estimate the effect of micro-scale eco-innovations on the macro-scale, i.e. the housing stock in Europe.

Methods

LCA and dynamic energy simulations are integrated to accurately assess the life cycle environmental burdens and benefits of eco-innovation measures at the building level. This allows quantitatively assessing the effectiveness of these measures to lower the energy use and environmental impact of buildings. The analysis at this micro-scale focuses on 24 representative residential buildings within the EU. For the upscaling to the EU housing stock, a hybrid approach is used. The results of the micro-scale analysis are upscaled to the EU housing stock scale by adopting the eco-innovation measures to (part of) the EU building stock (bottom–up approach) and extrapolating the relative impact reduction obtained for the reference buildings to the baseline stock model. The reference buildings in the baseline stock model have been developed by European Commission-Joint Research Centre based on a statistical analysis (top–down approach) of the European housing stock. The method is used to evaluate five scenarios covering various aspects: building components (building envelope insulation), technical installations (renewable energy), user behaviour (night setback of the setpoint temperature), and a combined scenario.

Results and discussion

Results show that the proposed combination of bottom–up and top–down approaches allow accurately assessing the impact of eco-innovation measures at the macro-scale. The results indicate that a combination of policy measures is necessary to lower the environmental impacts of the building stock to a significative extent.

Conclusions

Interventions addressing energy efficiency at building level may lead to the need of a trade-off between resource efficiency and environmental impacts. LCA integrated with dynamic energy simulation may help unveiling the potential improvements and burdens associated to eco-innovations.

     

Cost-benefit and cost-effectiveness analyses in pest management

Abstract

Economics is the study of how people allocate scarce resources among competing needs. It is applicable to pest control because managers must often make difficult choices about how to allocate a limited budget among many possible control programmes. Therefore, pest managers are required to make economic decisions, and pest management is not an exclusively biological problem. Economics offers a structured theoretical framework within which pest management issues can be critically examined, and offers quantitative tools to decision-makers faced with complex choices.

Economic theory suggests that individual selfinterested land owners are unlikely to provide pest management services at a level acceptable to the community. This line of analysis provides a justification for active Government involvement in the provision of pest management services. Quantitative tools developed by applied economists assist with the identification of socially desirable public policies, and suggest profitable areas of future research.     

Nominal Data And Factor Analysis: A Comment On Geier

Abstract

Use of nominally coded data in a factor analysis is incorrect. This paper first critiques a recent Plains Anthropologist article incorrectly using nominal data, and then provides a comparative example to illustrate the problem. Several alternatives are discussed briefly.     

Norway's law of the sea policy in the 1970s

Abstract

The Norwegian government has stated that creating a new international law of the sea is a foreign policy matter of the highest political priority in the period 1978–1981. A reasonable explanation might be the close correlation that normally exists between the political significance and the economic importance of issues and the area on which they impinge. As to Norway, it should suffice to point to the fact that the country ranks fifth among the merchant marine nations of the world, takes the fifth largest fish catch, and has sovereignty over the biggest continental shelf in Europe. Against this background, the author discusses the hypothesis that economic factors are the guiding hand in Norwegian ocean policy. However, the conclusion reached is that economic factors play a rather modest role in explaining this policy and that the reasons behind it are to be found at the intersection between economic interests, security policies, jurisdiction, the protection of resources and the environment as they are reflected in the rather peculiar situation of the North.     

A novel algorithm for alignment of multiple PPI networks based on simulated annealing

Background

To infer gene regulatory networks (GRNs) from gene-expression data is still a fundamental and challenging problem in systems biology. Several existing algorithms formulate GRNs inference as a regression problem and obtain the network with an ensemble strategy. Recent studies on data driven dynamic network construction provide us a new perspective to solve the regression problem.

Results

In this study, we propose a data driven dynamic network construction method to infer gene regulatory network (D3GRN), which transforms the regulatory relationship of each target gene into functional decomposition problem and solves each sub problem by using the Algorithm for Revealing Network Interactions (ARNI). To remedy the limitation of ARNI in constructing networks solely from the unit level, a bootstrapping and area based scoring method is taken to infer the final network. On DREAM4 and DREAM5 benchmark datasets, D3GRN performs competitively with the state-of-the-art algorithms in terms of AUPR.

Conclusions

We have proposed a novel data driven dynamic network construction method by combining ARNI with bootstrapping and area based scoring strategy. The proposed method performs well on the benchmark datasets, contributing as a competitive method to infer gene regulatory networks in a new perspective.

     

Selected Research Articles from the 2019 International Workshop on Computational Network Biology: Modeling,Analysis, and Control (CNB-MAC)

Background

Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual’s susceptibility to hereditary and complex diseases and affect how our bodies respond to therapeutic drugs. Reconstructing haplotypes of an individual from short sequencing reads is an NP-hard problem that becomes even more challenging in the case of polyploids. While increasing lengths of sequencing reads and insert sizes helps improve accuracy of reconstruction, it also exacerbates computational complexity of the haplotype assembly task. This has motivated the pursuit of algorithmic frameworks capable of accurate yet efficient assembly of haplotypes from high-throughput sequencing data.

Results

We propose a novel graphical representation of sequencing reads and pose the haplotype assembly problem as an instance of community detection on a spatial random graph. To this end, we construct a graph where each read is a node with an unknown community label associating the read with the haplotype it samples. Haplotype reconstruction can then be thought of as a two-step procedure: first, one recovers the community labels on the nodes (i.e., the reads), and then uses the estimated labels to assemble the haplotypes. Based on this observation, we propose ComHapDet – a novel assembly algorithm for diploid and ployploid haplotypes which allows both bialleleic and multi-allelic variants.

Conclusions

Performance of the proposed algorithm is benchmarked on simulated as well as experimental data obtained by sequencing Chromosome 5 of tetraploid biallelic Solanum-Tuberosum (Potato). The results demonstrate the efficacy of the proposed method and that it compares favorably with the existing techniques.