Protein quality as a complementary functional unit in life cycle assessment (LCA)

Goal and theoretical commentary A number of recent life cycle assessment (LCA) studies have concluded that animal-sourced foods should be restricted—or even avoided—within the human diet due to their relatively high environmental impacts (particularly those from ruminants) compared with other protein-rich foods (mainly protein-rich plant foods). From a nutritional point of view, however, issues such as broad nutrient bioavailability, amino acid balances, digestibility and even non-protein nutrient density (e.g., micronutrients) need to be accounted for before making such recommendations to the global population. This is especially important given the contribution of animal sourced foods to nutrient adequacy in the global South and vulnerable populations of high-income countries (e.g., children, women of reproductive age and elderly). Often, however, LCAs simplify this reality by using ‘protein’ as a functional unit in their models and basing their analyses on generic nutritional requirements. Even if a ‘nutritional functional unit’ (nFU) is utilised, it is unlikely to consider the complexities of amino acid composition and subsequent protein accretion. The discussion herein focuses on nutritional LCA (nLCA), particularly on the usefulness of nFUs such as ‘protein,’ and whether protein quality should be considered when adopting the nutrient as an (n)FU. Further, a novel and informative case study is provided to demonstrate the strengths and weaknesses of protein-quality adjustment. Case study methods To complement current discussions, we present an exploratory virtual experiment to determine how Digestible Indispensable Amino Acid Scores (DIAAS) might play a role in nLCA development by correcting for amino acid quality and digestibility. DIAAS is a scoring mechanism which considers the limiting indispensable amino acids (IAAs) within an IAA balance of a given food (or meal) and provides a percentage contribution relative to recommended daily intakes for IAA and subsequent protein anabolism; for clarity, we focus only on single food items (4 × animal-based products and 4 × plant-based products) in the current case exemplar. Further, we take beef as a sensitivity analysis example (which we particularly recommend when considering IAA complementarity at the meal-level) to elucidate how various cuts of the same intermediary product could affect the interpretation of nLCA results of the end-product(s). Recommendations First, we provide a list of suggestions which are intended to (a) assist with deciding whether protein-quality correction is necessary for a specific research question and (b) acknowledge additional uncertainties by providing mitigating opportunities to avoid misinterpretation (or worse, dis-interpretation) of protein-focused nLCA studies. We conclude that as relevant (primary) data availability from supply chain ‘gatekeepers’ (e.g., international agri-food distributors and processors) becomes more prevalent, detailed consideration of IAA provision of contrasting protein sources needs to be acknowledged—ideally quantitatively with DIAAS being one example—in nLCA studies utilising protein as a nFU. We also contend that future nLCA studies should discuss the complementarity of amino acid balances at the meal-level, as a minimum, rather than the product level when assessing protein metabolic responses of consumers. Additionally, a broader set of nutrients should ideally be included when evaluating “protein-rich foods” which provide nutrients that extend beyond amino acids, which is of particular importance when exploring dietary-level nLCA

Comparing families of dynamic causal models

Mathematical models of scientific data can be formally compared using Bayesian model evidence. Previous applications in the biological sciences have mainly focussed on model selection in which one first selects the model with the highest evidence and then makes inferences based on the parameters of that model. This “best model” approach is very useful but can become brittle if there are a large number of models to compare, and if different subjects use different models. To overcome this shortcoming we propose the combination of two further approaches: (i) family level inference and (ii) Bayesian model averaging within families. Family level inference removes uncertainty about aspects of model structure other than the characteristic of interest. For example: What are the inputs to the system? Is processing serial or parallel? Is it linear or nonlinear? Is it mediated by a single, crucial connection? We apply Bayesian model averaging within families to provide inferences about parameters that are independent of further assumptions about model structure. We illustrate the methods using Dynamic Causal Models of brain imaging data

Isotope effect in superconductors with coexisting interactions of phonon and nonphonon mechanisms

We examine the isotope effect of superconductivity in systems with coexisting interactions of phonon and nonphonon mechanisms in addition to the direct Coulomb interaction. The interaction mediated by the spin fluctuations is discussed as an example of the nonphonon interaction. Extended formulas for the transition temperature Tc and the isotope-effect coefficient alpha are derived for cases (a) omega_np omega_D, where omega_np is an effective cutoff frequency of the nonphonon interaction that corresponds to the Debye frequency omega_D in the phonon interaction. In case (a), it is found that the nonphonon interaction does not change the condition for the inverse isotope effect, i.e., mu^* > lambda_ph/2, but it modifies the magnitude of alpha markedly. In particular, it is found that a giant isotope shift occurs when the phonon and nonphonon interactions cancel each other largely. For instance, strong critical spin fluctuations may give rise to the giant isotope effect. In case (b), it is found that the inverse isotope effect occurs only when the nonphonon interaction and the repulsive Coulomb interaction, in total effect, work as repulsive interactions against the superconductivity. We discuss the relevance of the present result to some organic superconductors, such as kappa-(ET)2Cu(NCS)2 and Sr2RuO4 superconductors, in which inverse isotope effects have been observed, and briefly to high-Tc cuprates, in which giant isotope effects have been observed.Comment: 4 pages, 2 figures, (with jpsj2.cls, ver.1.2), v2:linguistic correction

Universality in Heavy Fermions Revisited

A previous scaling analysis of pressure experiments in heavy fermion is reviewed and enlarged. We show that the critical exponents obtained from this analysis indicate that a one-parameter scaling describes these experiments. We obtain explicitly the enhancemente factors showing that these systems are indeed near criticality and that the scaling approach is appropriate. The physics responsible for the one-parameter scaling and breakdown of hyperscaling is clarified. We discuss a microsocopic theory that is in agreement with the experiments. The scaling theory is generalized for the case the shift and crossover exponents are different. The exponents governing the physical behavior along the non-Fermi liquid trajectory are obtained for this case.Comment: 7 pages, Latex, 3 Postscript figures, to be published in Physical Review

Green turtles highlight connectivity across a regional marine protected area network in west Africa

Networks of marine protected areas (MPAs) are invaluable for the protection of species with high dispersal capacity, yet connectivity within networks is poorly understood. We demonstrate the connectivity within the regional MPA network in West Africa (RAMPAO), mediated by the largest green turtle population in the eastern Atlantic Ocean. We equipped with satellite tags 45 female green turtles nesting in the Bijagó s Archipelago, Guinea-Bissau, and tracked them during internesting, migration, and foraging to quantify the degree of coverage the RAMPAO network provides during each of these critical periods. During the internesting period, turtles were largely concentrated around the nesting islands, with a mean of 94.8% (SD 0.1%, range: 46% - 100%, n = 40 turtles) of tracking positions falling within MPA limits. Among the 35 turtles successfully tracked into the foraging period, we identified variable migratory strategies, with 12 turtles remaining near-resident at distances of 40-90 km from breeding sites, 10 turtles migrating 300-400 km to The Gambia and Senegal, and 13 turtles traveling >1000 km to northern Mauritania. Of the 35 foraging turtles, 26 used MPAs, with a mean of 78.0% (SD 34.8%, range: 3.7% - 100%) of their tracking positions falling within the limits of RAMPAO MPAs, across Guinea-Bissau, Senegal and Mauritania. Migration corridors with high concentrations of passing turtles were mostly located nearshore, and 21% of these high passage areas fell within the MPA network. Overall, we found that this population connects five RAMPAO MPAs, yet some foraging sites (e.g., in the Bijagó s) and important migration areas (e.g., Cap-Vert peninsula) described here are currently unprotected. These results are relevant to any considerations of MPA extension or establishment within the regional network, which would contribute towards meeting the Convention on Biological Diversity targets for national marine protected area estate coverage. By documenting biological connectivity across RAMPAO, this study represents an important example of the relevance of international protected area networks for green turtle conservation and for wider conservation action at a regional scale.Fundação para a Ciência e Tecnologia - FCTinfo:eu-repo/semantics/publishedVersio

Quantum key distribution and 1 Gbit/s data encryption over a single fibre

We perform quantum key distribution (QKD) in the presence of 4 classical channels in a C-band dense wavelength division multiplexing (DWDM) configuration using a commercial QKD system. The classical channels are used for key distillation and 1 Gbps encrypted communication, rendering the entire system independent from any other communication channel than a single dedicated fibre. We successfully distil secret keys over fibre spans of up to 50 km. The separation between quantum channel and nearest classical channel is only 200 GHz, while the classical channels are all separated by 100 GHz. In addition to that we discuss possible improvements and alternative configurations, for instance whether it is advantageous to choose the quantum channel at 1310 nm or to opt for a pure C-band configuration.Comment: 9 pages, 7 figure

Analysis of Gene Expression in an Inbred Line of Soft-Shell Clams ( Mya arenaria

Mya arenaria is a bivalve mollusk of commercial and economic importance, currently impacted by ocean warming, acidification, and invasive species. In order to inform studies on the growth of M. arenaria, we selected and inbred a population of soft-shell clams for a fast-growth phenotype. This population displayed significantly faster growth (p<0.0001), as measured by 35.4% greater shell size. To assess the biological basis of this growth heterosis, we characterized the complete transcriptomes of six individuals and identified differentially expressed genes by RNAseq. Pathways differentially expressed included structural gene pathways. Also differentially expressed was the nucleotide-binding oligomerization domain 2 (NOD2) receptor pathway that contributes to determination of growth, immunity, apoptosis, and proliferation. NOD2 pathway members that were upregulated included a subset of isoforms of RIPK2 (mean 3.3-fold increase in expression), ERK/MAPK14 (3.8-fold), JNK/MAPK8 (4.1-fold), and NFκB (4.08-fold). These transcriptomes will be useful resources for both the aquaculture community and researchers with an interest in mollusks and growth heterosis

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

Background The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. Methodology/Principal Findings To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes () and latency of the optimized engineered gene networks. Conclusions/Significance Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.National Institutes of Health (U.S.) (Grant # 7R01GM74712-5)United States. Defense Advanced Research Projects Agency (contract HR0011-10-C-0168)National Science Foundation (U.S.) (NSF CAREER award 0968682)BBN Technologie

Clinical pharmacodynamic factors in docetaxel toxicity

Neutropenia is the main dose-limiting toxicity occurring in docetaxel treatment. The objective of this study was to identify pharmacodynamic (PD) factors responsible for the neutropaenia caused by docetaxel. Data were obtained from 92 patients treated with docetaxel as a monochemotherapy in two different treatment centres. A semiphysiological population pharmacokinetic–pharmacodynamic (PK/PD) model was applied to describe the time course of neutrophils and the neutropaenic effect of docetaxel. The plasma docetaxel concentration was assumed to inhibit the proliferation of neutrophil precursors through a linear model: Drug effect=Slope × Conc. Slope corresponds to the patients' sensitivity to the neutropaenic effect of docetaxel. Covariate analysis was performed by testing the relationship between the patients' characteristics and Slope using the program NONMEM. The neutropaenic effect of docetaxel showed a high interindividual variability. Three significant PD covariates were identified: serum α1-acid glycoprotein levels (AAG), level of chemotherapy pretreatment, and treatment centre. Extensive pretreatment was associated with an increase in Slope values meaning a higher haematotoxicity. An increase in AAG was associated with a decrease of both Slope and docetaxel plasma clearance. Patients treated in one centre had both higher Slope and docetaxel clearance. The centre effect (most likely due to a bias in the PK part of the study between the two centres) reveals the robustness of the PK/PD model. Individual dosing of docetaxel should be based on previous chemotherapy but not on the AAG level since it has a similar influence on PD and PK docetaxel parameters. This methodology should be applied to further investigate elderly patients and to identify more precisely the characteristics of previous chemotherapy that contribute to the cumulative myelotoxicity

Transformation of animal agriculture should be evidence-driven and respectful of livestock’s benefits and contextual aspects

Response to a Letter to the Edito