Upgrading Marine Ecosystem Restoration Using Ecological-Social Concepts

Conservation and environmental management are principal countermeasures to the degradation of marine ecosystems and their services. However, in many cases, current practices are insufficient to reverse ecosystem declines. We suggest that restoration ecology, the science underlying the concepts and tools needed to restore ecosystems, must be recognized as an integral element for marine conservation and environmental management. Marine restoration ecology is a young scientific discipline, often with gaps between its application and the supporting science. Bridging these gaps is essential to using restoration as an effective management tool and reversing the decline of marine ecosystems and their services. Ecological restoration should address objectives that include improved ecosystem services, and it therefore should encompass social ecological elements rather than focusing solely on ecological parameters. We recommend using existing management frameworks to identify clear restoration targets, to apply quantitative tools for assessment, and to make the re-establishment of ecosystem services a criterion for success

Epistasis not needed to explain low dN/dS

An important question in molecular evolution is whether an amino acid that occurs at a given position makes an independent contribution to fitness, or whether its effect depends on the state of other loci in the organism's genome, a phenomenon known as epistasis. In a recent letter to Nature, Breen et al. (2012) argued that epistasis must be "pervasive throughout protein evolution" because the observed ratio between the per-site rates of non-synonymous and synonymous substitutions (dN/dS) is much lower than would be expected in the absence of epistasis. However, when calculating the expected dN/dS ratio in the absence of epistasis, Breen et al. assumed that all amino acids observed in a protein alignment at any particular position have equal fitness. Here, we relax this unrealistic assumption and show that any dN/dS value can in principle be achieved at a site, without epistasis. Furthermore, for all nuclear and chloroplast genes in the Breen et al. dataset, we show that the observed dN/dS values and the observed patterns of amino acid diversity at each site are jointly consistent with a non-epistatic model of protein evolution.Comment: This manuscript is in response to "Epistasis as the primary factor in molecular evolution" by Breen et al. Nature 490, 535-538 (2012

Effect of pulsed delivery and bouillon base on saltiness and bitterness perceptions of salt delivery profiles partially substituted with KCl

Reducing salt levels in processed food is an important target for a growing numbers of food manufacturers. The effects of pulsed delivery (Dynataste) and bouillon base on saltiness and bitterness perception of partially substituted solutions (KCl) were investigated. Pulsed delivery did not enhance salt perception and resulted in greater Overall Bitterness Scores for the same level of substitution with KCl. The presence of the bouillon base masked to a certain extent the loss of saltiness induced by the substitution and resulted in lower Overall Bitterness Scores of the substituted profiles

Preliminary study of the human activities and perception on the groundwater conservation in lowlands of Semarang

This paper aims at investigating the human activities and perception of the residents in lowland areas of Semarang city regarding the groundwater conservation. As the first step, classifying and rating land use in the study area is conducted as the interpretation of human activities. A map of human perception using the adapted Protocol Perception Monitoring is then configured to evaluate the deviation between the expected and observed behavior of the community in an integrated ecosystem. The result of preliminary study shows that about 68% areas in lowland have score 8 (built-up area, irrigated field crops), 25% has score 7 (industries and reservoirs), 1% has score 5 (plantation), 3% has score 2 (non-irrigated field crops) and about 3% has score 1 (forest, park and open areas). It means that more than 90% lowland areas in Semarang city have been intervened by the human activities. Based on the result of the perception mapping, it is found that there is a high deviation (about 40-90%) between expected and observed behavior in critical areas, including the understanding of area situation, utilization of groundwater and water resources (wells/PDAM) as well as the community comprehension of government regulation on groundwater conservation

Thinking About Causation : A Causal Language with Epistemic Operators

In this paper we propose a formal framework for modeling the interaction of causal and (qualitative) epistemic reasoning. To this purpose, we extend the notion of a causal model [11, 16, 17, 26] with a representation of the epistemic state of an agent. On the side of the object language, we add operators to express knowledge and the act of observing new information. We provide a sound and complete axiomatization of the logic, and discuss the relation of this framework to causal team semantics.Peer reviewe

Clinical applications of cardiac CT angiography

ECG-gated multislice CT provides a cost-effective, non-invasive technology for evaluation of the coronary arteries, as well as for additional clinical applications, which require morphological assessment of the heart and adjacent structures with simultaneous evaluation of the coronary circulation

Risk factor studies of age-at-onset in a sample ascertained for Parkinson disease affected sibling pairs: a cautionary tale

An association between exposure to a risk factor and age-at-onset of disease may reflect an effect on the rate of disease occurrence or an acceleration of the disease process. The difference in age-at-onset arising from case-only studies, however, may also reflect secular trends in the prevalence of exposure to the risk factor. Comparisons of age-at-onset associated with risk factors are commonly performed in case series enrolled for genetic linkage analysis of late onset diseases. We describe how the results of age-at-onset studies of environmental risk factors reflect the underlying structure of the source population, rather than an association with age-at-onset, by contrasting the effects of coffee drinking and cigarette smoking on Parkinson disease age-at-onset with the effects on age-at-enrollment in a population based study sample. Despite earlier evidence to suggest a protective association of coffee drinking and cigarette smoking with Parkinson disease risk, the age-at-onset results are comparable to the patterns observed in the population sample, and thus a causal inference from the age-at-onset effect may not be justified. Protective effects of multivitamin use on PD age-at-onset are also shown to be subject to a bias from the relationship between age and multivitamin initiation. Case-only studies of age-at-onset must be performed with an appreciation for the association between risk factors and age and ageing in the source population

Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices. Akaike information criterion (AIC) values indicate that a model allowing multiple nucleotide changes fits the empirical substitution matrices significantly better. Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated. The selective constraints are characteristic of proteins rather than species. However, their relative strengths among amino acid pairs can be approximated not to depend very much on protein families but amino acid pairs, because the present model, in which selective constraints are approximated to be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can provide a good fit to other empirical substitution matrices including cpREV for chloroplast proteins and mtREV for vertebrate mitochondrial proteins. The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences.Comment: Table 9 in this article includes corrections for errata in the Table 9 published in 10.1371/journal.pone.0017244. Supporting information is attached at the end of the article, and a computer-readable dataset of the ML estimates of selective constraints is available from 10.1371/journal.pone.001724

Increasing condom use in heterosexual men: development of a theory-based interactive digital intervention

Increasing condom use to prevent sexually transmitted infections is a key public health goal. Interventions are more likely to be effective if they are theory- and evidence-based. The Behaviour Change Wheel (BCW) provides a framework for intervention development. To provide an example of how the BCW was used to develop an intervention to increase condom use in heterosexual men (the MenSS website), the steps of the BCW intervention development process were followed, incorporating evidence from the research literature and views of experts and the target population. Capability (e.g. knowledge) and motivation (e.g. beliefs about pleasure) were identified as important targets of the intervention. We devised ways to address each intervention target, including selecting interactive features and behaviour change techniques. The BCW provides a useful framework for integrating sources of evidence to inform intervention content and deciding which influences on behaviour to target