Addressing the sample size problem in behavioural operational research: simulating the newsvendor problem

Laboratory-based experimental studies with human participants are beneficial for testing hypotheses in behavioural operational research. However, such experiments are not without their problems. One specific problem is obtaining a sufficient sample size, not only in terms of the number of participants but also the time they are willing to devote to an experiment. In this paper, we explore how agent-based simulation (ABS) can be used to address the sample size problem and demonstrate the approach in the newsvendor setting. The decision-making strategies of a small sample of individual decision-makers are determined through laboratory experiments. The interactions of these suppliers and retailers are then simulated using an ABS to generate a large sample set of decisions. With only a small number of participants, we demonstrate that it is possible to produce similar results to previous experimental studies that involved much larger sample sizes. We conclude that ABS provides the potential to extend the scope of experimental research in behavioural operational research

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al

Millennial-scale sustainability of the Chesapeake Bay Native American oyster fishery

Estuaries around the world are in a state of decline following decades or more of overfishing, pollution, and climate change. Oysters (Ostreidae), ecosystem engineers in many estuaries, influence water quality, construct habitat, and provide food for humans and wildlife. In North America\u27s Chesapeake Bay, once-thriving eastern oyster (Crassostrea virginica) populations have declined dramatically, making their restoration and conservation extremely challenging. Here we present data on oyster size and human harvest from Chesapeake Bay archaeological sites spanning similar to 3,500 y of Native American, colonial, and historical occupation. We compare oysters from archaeological sites with Pleistocene oyster reefs that existed before human harvest, modern oyster reefs, and other records of human oyster harvest from around the world. Native American fisheries were focused on nearshore oysters and were likely harvested at a rate that was sustainable over centuries to millennia, despite changing Holocene climatic conditions and sea-level rise. These data document resilience in oyster populations under long-term Native American harvest, sea-level rise, and climate change; provide context for managing modern oyster fisheries in the Chesapeake Bay and elsewhere around the world; and demonstrate an interdisciplinary approach that can be applied broadly to other fisheries

Continuity, Deconfinement, and (Super) Yang-Mills Theory

We study the phase diagram of SU(2) Yang-Mills theory with one adjoint Weyl fermion on R^3xS^1 as a function of the fermion mass m and the compactification scale L. This theory reduces to thermal pure gauge theory as m->infinity and to circle-compactified (non-thermal) supersymmetric gluodynamics in the limit m->0. In the m-L plane, there is a line of center symmetry changing phase transitions. In the limit m->infinity, this transition takes place at L_c=1/T_c, where T_c is the critical temperature of the deconfinement transition in pure Yang-Mills theory. We show that near m=0, the critical compactification scale L_c can be computed using semi-classical methods and that the transition is of second order. This suggests that the deconfining phase transition in pure Yang-Mills theory is continuously connected to a transition that can be studied at weak coupling. The center symmetry changing phase transition arises from the competition of perturbative contributions and monopole-instantons that destabilize the center, and topological molecules (neutral bions) that stabilize the center. The contribution of molecules can be computed using supersymmetry in the limit m=0, and via the Bogomolnyi--Zinn-Justin (BZJ) prescription in the non-supersymmetric gauge theory. Finally, we also give a detailed discussion of an issue that has not received proper attention in the context of N=1 theories---the non-cancellation of nonzero-mode determinants around supersymmetric BPS and KK monopole-instanton backgrounds on R^3xS^1. We explain why the non-cancellation is required for consistency with holomorphy and supersymmetry and perform an explicit calculation of the one-loop determinant ratio.Comment: A discussion of the non-cancellation of the nonzero mode determinants around supersymmetric monopole-instantons in N=1 SYM on R^3xS^1 is added, including an explicit calculation. The non-cancellation is, in fact, required by supersymmetry and holomorphy in order for the affine-Toda superpotential to be reproduced. References have also been adde

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide

Consolidating emerging evidence surrounding HIVST and HIVSS: A rapid systematic mapping protocol

BACKGROUND: HIV self-testing (HIVST) is becoming popular with policy makers and commissioners globally, with a key aim of expanding access through reducing barriers to testing for individuals at risk of HIV infection. HIV self-sampling (HIVSS) was available previously to self-testing but was confined mainly to the USA and the UK. It remains to be seen whether the momentum behind HIVST will also energise efforts to expand HIVSS. Recent years have seen a rapid growth in the type of evidence related to these interventions as well as several systematic reviews. The vast majority of this evidence relates to acceptability as well as values and preferences, although new types of evidence are emerging. This systematic map aims to consolidate all emerging evidence related to HIVST and HIVSS to respond to this rapidly changing area. METHODS: We will systematically search databases and the abstracts of five conferences from 2006 to the present date, with monthly-automated database searches. Searches will combine key terms relating to HIV (e.g. HIV, AIDS, human immune-deficiency syndrome) with terms related to self-testing (e.g. home-test, self-test, mail-test, home dried blood spot test). Abstracts will be reviewed against inclusion criteria in duplicate. Data will be manually extracted through a standard form and then entered to an open access relational map (HIVST.org). When new and sufficient evidence emerges which addresses existing knowledge gaps, we will complete a review on a relevant topic. DISCUSSION: This innovative approach will allow rapid cataloguing, documenting and dissemination of new evidence and key findings as they emerge into the public domain. SYSTEMATIC REVIEW REGISTRATION: This protocol has not been registered with PROSPERO as they do not register systematic maps

Coring, profiling, and trenching: Archaeological field strategies for investigating the Pleistocene-Holocene-Anthropocene continuum

Archaeologists have long emphasized the importance of large-scale excavations and multi-year or even decades-long projects at a single site or site complex. Here, we highlight archaeological field strategies, termed coring, profiling, and trenching (CPT), that rely on relatively small-scale excavations or the collection of new samples from intact deposits in previously excavated trenches (aka test units or pits). Examples from multiple sites in Africa, Asia, and North America demonstrate that CPT is highly effective for obtaining high-resolution archaeobiological and geoarchaeological samples (e.g., faunal and botanical remains, sediments) and artefacts from areas that have seen limited or no archaeological research, little systematic application of archaeological science methods, or research only on a relatively narrow time period or geographic scale. Designed to complement large-scale excavations at single sites, CPT is ideal for multi-scalar research that works in tandem with remote sensing techniques, providing samples for detailed laboratory analyses and offering a bridge between surface surveys and large-scale excavation. Given the threats facing archaeological sites around the world from climate change and human development, as well as financial, training and infrastructure constraints, and concerns from many Indigenous communities about large excavations, we argue that CPT is an important method for addressing 21st century human-environmental research questions

Neuroinflammation, Mast Cells, and Glia: Dangerous Liaisons

The perspective of neuroinflammation as an epiphenomenon following neuron damage is being replaced by the awareness of glia and their importance in neural functions and disorders. Systemic inflammation generates signals that communicate with the brain and leads to changes in metabolism and behavior, with microglia assuming a pro-inflammatory phenotype. Identification of potential peripheral-to-central cellular links is thus a critical step in designing effective therapeutics. Mast cells may fulfill such a role. These resident immune cells are found close to and within peripheral nerves and in brain parenchyma/meninges, where they exercise a key role in orchestrating the inflammatory process from initiation through chronic activation. Mast cells and glia engage in crosstalk that contributes to accelerate disease progression; such interactions become exaggerated with aging and increased cell sensitivity to stress. Emerging evidence for oligodendrocytes, independent of myelin and support of axonal integrity, points to their having strong immune functions, innate immune receptor expression, and production/response to chemokines and cytokines that modulate immune responses in the central nervous system while engaging in crosstalk with microglia and astrocytes. In this review, we summarize the findings related to our understanding of the biology and cellular signaling mechanisms of neuroinflammation, with emphasis on mast cell-glia interactions

Submillimeter Studies of Prestellar Cores and Protostars: Probing the Initial Conditions for Protostellar Collapse

Improving our understanding of the initial conditions and earliest stages of protostellar collapse is crucial to gain insight into the origin of stellar masses, multiple systems, and protoplanetary disks. Observationally, there are two complementary approaches to this problem: (1) studying the structure and kinematics of prestellar cores observed prior to protostar formation, and (2) studying the structure of young (e.g. Class 0) accreting protostars observed soon after point mass formation. We discuss recent advances made in this area thanks to (sub)millimeter mapping observations with large single-dish telescopes and interferometers. In particular, we argue that the beginning of protostellar collapse is much more violent in cluster-forming clouds than in regions of distributed star formation. Major breakthroughs are expected in this field from future large submillimeter instruments such as Herschel and ALMA.Comment: 12 pages, 9 figures, to appear in the proceedings of the conference "Chemistry as a Diagnostic of Star Formation" (C.L. Curry & M. Fich eds.

Thermodynamics of Holographic Defects

Using the AdS/CFT correspondence, we study the thermodynamic properties and the phase diagram of matter fields on (2+1)-dimensional defects coupled to a (3+1)-dimensional N=4 SYM "heat bath". Considering a background magnetic field, (net) quark density, defect "magnitude" $\delta N_c$ and the mass of the matter, we study the defect contribution to the thermodynamic potentials and their first and second derivatives to map the phases and study their physical properties. We find some features that are qualitatively similar to other systems e.g. in (3+1) dimensions and a number of features that are particular to the defect nature, such as its magnetic properties, unexpected properties at T->0 and finite density; and the finite $\delta N_c$ effects, e.g. a diverging susceptibility and vanishing density of states at small temperatures, a physically consistent negative heat capacity and new types of consistent phases.Comment: 33 pages, 16 figures (jpg and pdf), typos fixed and references added, final version published in JHE